Index: palm/trunk/SCRIPTS/palmtest
===================================================================
--- palm/trunk/SCRIPTS/palmtest	(revision 4090)
+++ palm/trunk/SCRIPTS/palmtest	(revision 4091)
@@ -81,42 +81,52 @@
 
 
+def disable_color():
+    global disable_colored_output
+    disable_colored_output = True
+
+
 version = '1.0.1'
 
-scripts_dir = os.path.dirname(os.path.realpath(__file__))
-trunk_dir = os.path.realpath(os.path.join(scripts_dir, '..'))
-workspace_dir = os.path.realpath(os.path.join(trunk_dir, '..'))
-
-trunk_tests_dir = os.path.join(trunk_dir, 'TESTS')
-trunk_tests_cases_dir = os.path.join(trunk_tests_dir, 'cases')
-trunk_tests_builds_dir = os.path.join(trunk_tests_dir, 'builds')
-
-tests_dir = os.path.join(workspace_dir, 'tests')
-
-available_cores = multiprocessing.cpu_count()
-terminal_columns, terminal_lines = shutil.get_terminal_size()
-hline = '#' * min(terminal_columns, 300) + '\n'
-table_width_intro = 12
-table_width_builds = len(max([s for s in next(os.walk(trunk_tests_builds_dir))[1] if not s[0] == '.'], key=len)) + len('_debug')
-table_width_cases = len(max([s for s in next(os.walk(trunk_tests_cases_dir))[1] if not s[0] == '.'], key=len))
-table_width_cores = 7
-table_width_total = table_width_intro + table_width_builds + table_width_cases + table_width_cores + 3
-
-task_table_line_template = \
-    '{:' + str(table_width_intro) + '} ' + \
-    '{:' + str(table_width_cases) + '} ' + \
-    '{:' + str(table_width_builds) + '} ' + \
-    '{:' + str(table_width_cores) + '} '
-
-config_table_line_template = \
-    '{:' + str(table_width_intro) + '} ' + \
-    '{:' + str(max(table_width_builds, table_width_cases)) + '} ' + \
-    '{:8} '
-
-file_table_line_template = \
-    '{:' + str(table_width_intro) + '} ' + \
-    '{:' + str(table_width_cases + 13) + '} '
-
-# for debugging
-exist_ok = False
+
+class Environment:
+
+    scripts_dir = os.path.dirname(os.path.realpath(__file__))
+    trunk_dir = os.path.realpath(os.path.join(scripts_dir, '..'))
+    workspace_dir = os.path.realpath(os.path.join(trunk_dir, '..'))
+
+    trunk_tests_dir = os.path.join(trunk_dir, 'TESTS')
+    trunk_tests_cases_dir = os.path.join(trunk_tests_dir, 'cases')
+    trunk_tests_builds_dir = os.path.join(trunk_tests_dir, 'builds')
+
+    tests_dir = os.path.join(workspace_dir, 'tests')
+
+
+class LogFormatter:
+
+    terminal_columns, terminal_lines = shutil.get_terminal_size()
+    hline = '#' * min(terminal_columns, 300) + '\n'
+    table_width_intro = 12
+    table_width_builds = len(max([s for s in next(os.walk(Environment.trunk_tests_builds_dir))[1] if not s[0] == '.'], key=len)) + len('_debug')
+    table_width_cases = len(max([s for s in next(os.walk(Environment.trunk_tests_cases_dir))[1] if not s[0] == '.'], key=len))
+    table_width_cores = 7
+    table_width_total = table_width_intro + table_width_builds + table_width_cases + table_width_cores + 3
+
+    intro_table_line_template = \
+        '{:' + str(table_width_intro) + '} '
+
+    task_table_line_template = \
+        '{:' + str(table_width_intro) + '} ' + \
+        '{:' + str(table_width_cases) + '} ' + \
+        '{:' + str(table_width_builds) + '} ' + \
+        '{:' + str(table_width_cores) + '} '
+
+    config_table_line_template = \
+        '{:' + str(table_width_intro) + '} ' + \
+        '{:' + str(max(table_width_builds, table_width_cases)) + '} ' + \
+        '{:8} '
+
+    file_table_line_template = \
+        '{:' + str(table_width_intro) + '} ' + \
+        '{:' + str(table_width_cases + 13) + '} '
 
 
@@ -208,7 +218,7 @@
         with Logger(cwd, verbose=verbose) as logger:
             # read line without blocking
-            logger.to_log(hline)
+            logger.to_log(LogFormatter.hline)
             logger.to_log('CMD: ' + cmd_str + '\n')
-            logger.to_log(hline)
+            logger.to_log(LogFormatter.hline)
             while t.is_alive():
                 try:
@@ -226,5 +236,5 @@
                 else:  # got line
                     logger.to_log(line.decode("utf-8"))
-            logger.to_log(hline)
+            logger.to_log(LogFormatter.hline)
 
         rc = p.poll()
@@ -379,6 +389,6 @@
         self.job_name = self.setup_name + '__' + build_name + '__' + str(self.cores)
         self.job_dir = os.path.join(self.test_dir, 'JOBS', self.job_name)
-        self.ref_monitoring_dir = os.path.join(trunk_tests_cases_dir, self.setup_name, 'MONITORING')
-        self.ref_output_dir = os.path.join(trunk_tests_cases_dir, self.setup_name, 'OUTPUT')
+        self.ref_monitoring_dir = os.path.join(Environment.trunk_tests_cases_dir, self.setup_name, 'MONITORING')
+        self.ref_output_dir = os.path.join(Environment.trunk_tests_cases_dir, self.setup_name, 'OUTPUT')
         self.res_monitoring_dir = os.path.join(self.job_dir, 'MONITORING')
         self.res_output_dir = os.path.join(self.job_dir, 'OUTPUT')
@@ -449,5 +459,5 @@
                 ext_list = [file_dict['extension']] if file_dict['extension'] else []
                 file_specific_ending = '.'.join([file_dict['postfix']] + file_dict['cycle_info'] + ext_list )
-                logger.to_all(file_table_line_template.format('Checking:', self.setup_name + file_specific_ending))
+                logger.to_all(LogFormatter.file_table_line_template.format('Checking:', self.setup_name + file_specific_ending))
                 ref_file_path = os.path.join(file_dict['ref_path'], self.setup_name + file_specific_ending)
                 res_file_path = os.path.join(file_dict['res_path'], self.job_name + file_specific_ending)
@@ -530,5 +540,5 @@
         if os.path.isdir(source_data_dir_path) and re.match('.+_d3d.*', source_data_dir):
             job_restart_dir = os.path.join(self.test_dir, 'JOBS', name, 'RESTART')
-            os.makedirs(job_restart_dir, exist_ok=exist_ok)
+            os.makedirs(job_restart_dir, exist_ok=False)
             job_data_dir_path = os.path.join(job_restart_dir, name + '_d3d')
             os.symlink(source_data_dir_path, job_data_dir_path, target_is_directory=True)
@@ -593,5 +603,5 @@
         if not attempted:
             with Logger(self.test_dir, verbose=self.verbose) as logger:
-                status_prefix = task_table_line_template.format('Testing:', self.test_case.name, build_name, self.cores)
+                status_prefix = LogFormatter.task_table_line_template.format('Testing:', self.test_case.name, build_name, self.cores)
                 logger.to_all(status_prefix)
                 logger.to_log('[started]' + '\n')
@@ -601,5 +611,5 @@
 
                 input_dir = os.path.join(self.test_dir, 'JOBS', name, 'INPUT')
-                os.makedirs(input_dir, exist_ok=exist_ok)
+                os.makedirs(input_dir, exist_ok=False)
 
                 # copying needs to be done per file, because input files need to be renamed
@@ -672,5 +682,5 @@
     def configure(self):
         try:
-            with open(os.path.join(trunk_tests_builds_dir, self.build_name, 'build_config.yml'), 'r') as f:
+            with open(os.path.join(Environment.trunk_tests_builds_dir, self.build_name, 'build_config.yml'), 'r') as f:
                 build_config = yaml.load(f)
         except:
@@ -745,5 +755,5 @@
 
         try:
-            with open(os.path.join(workspace_dir, 'palmtest.yml'), 'r') as f:
+            with open(os.path.join(Environment.workspace_dir, 'palmtest.yml'), 'r') as f:
                 palmtest_config = yaml.load(f)
         except:
@@ -758,5 +768,5 @@
         except:
             try:
-                with open(os.path.join(scripts_dir, '.palm.config.default.in'), 'r') as palm_config_template_file:
+                with open(os.path.join(Environment.scripts_dir, '.palm.config.default.in'), 'r') as palm_config_template_file:
                     template = palm_config_template_file.read()
             except:
@@ -770,5 +780,5 @@
         cpp_options_str = ['-D' + s for s in self.compiler['definitions']]
         template = template.replace('@PALM_CPP_OPTIONS_STR@', ' '.join(cpp_options_str))
-        template = template.replace('@PALM_CORES@', str(available_cores))
+        template = template.replace('@PALM_CORES@', str(multiprocessing.cpu_count()))
         template = template.replace('@PALM_COMPILER_OPTIONS@', '{{palmtest.compiler.options}} ' + ' '.join(self.compiler['includes']))
         template = template.replace('@PALM_LINKER_OPTIONS@', ' '.join(self.linker['options']))
@@ -873,5 +883,5 @@
         if not attempted:
             with Logger(self.test_dir, verbose=self.verbose) as logger:
-                status_prefix = task_table_line_template.format('Building:', '', build_name, '')
+                status_prefix = LogFormatter.task_table_line_template.format('Building:', '', build_name, '')
                 logger.to_all(status_prefix)
                 logger.to_log('[started]' + '\n')
@@ -907,6 +917,6 @@
         self.verbose = verbose
         self.dry_run = dry_run
-        self.user_code_dir = os.path.join(trunk_tests_cases_dir, self.name, 'USER_CODE')
-        self.input_dir = os.path.join(trunk_tests_cases_dir, self.name, 'INPUT')
+        self.user_code_dir = os.path.join(Environment.trunk_tests_cases_dir, self.name, 'USER_CODE')
+        self.input_dir = os.path.join(Environment.trunk_tests_cases_dir, self.name, 'INPUT')
         self.number_of_cores = []
         self.build_names = []
@@ -915,5 +925,5 @@
 
     def configure(self, requested_build_names, requested_cores):
-        f_name = os.path.join(trunk_tests_cases_dir, self.name, 'case_config.yml')
+        f_name = os.path.join(Environment.trunk_tests_cases_dir, self.name, 'case_config.yml')
         try:
             with open(f_name, 'r') as f:
@@ -983,18 +993,18 @@
 
     def prepare(self):
-        global disable_colored_output
-        disable_colored_output = self.no_color
-        self.test_dir = os.path.join(tests_dir, self.test_id)
+        if self.no_color:
+            disable_color()
+        self.test_dir = os.path.join(Environment.tests_dir, self.test_id)
         try:
-            os.makedirs(self.test_dir, exist_ok=exist_ok)
+            os.makedirs(self.test_dir, exist_ok=False)
         except:
             print('ERROR: Found existing test directory: ' + self.test_dir)
             exit(1)
         with Logger(self.test_dir, verbose=self.verbose) as logger:
-            logger.to_all(hline)
+            logger.to_all(LogFormatter.hline)
             logger.to_all('This is the PALM tester  (version: ' + version + ')' + '\n')
-            logger.to_all(hline)
+            logger.to_all(LogFormatter.hline)
             try:
-                with open(os.path.join(workspace_dir, 'palmtest.yml'), 'r') as f:
+                with open(os.path.join(Environment.workspace_dir, 'palmtest.yml'), 'r') as f:
                     pass
             except:
@@ -1005,10 +1015,10 @@
 
             self.execution_trunk_dir = os.path.join(self.test_dir, 'trunk')
-            os.symlink(trunk_dir, self.execution_trunk_dir)
+            os.symlink(Environment.trunk_dir, self.execution_trunk_dir)
             self.execution_jobs_dir = os.path.join(self.test_dir, 'JOBS')
-            os.makedirs(self.execution_jobs_dir, exist_ok=exist_ok)
+            os.makedirs(self.execution_jobs_dir, exist_ok=False)
 
             try:
-                with open(os.path.join(scripts_dir, '.palm.iofiles'), 'r') as iofiles_template_file:
+                with open(os.path.join(Environment.scripts_dir, '.palm.iofiles'), 'r') as iofiles_template_file:
                     iofiles_template = iofiles_template_file.read()
                 with open(os.path.join(self.test_dir, '.palm.iofiles'), 'w') as iofiles_file:
@@ -1018,11 +1028,12 @@
                 exit(1)
 
+            available_cores = multiprocessing.cpu_count()
             final_cores_list = list(filter(lambda x: x <= available_cores, self.requested_cores))
 
-            logger.to_all(config_table_line_template.format('Object:', 'Name:', 'Action:') + 'Status:\n')
-            logger.to_all(hline)
+            logger.to_all(LogFormatter.config_table_line_template.format('Object:', 'Name:', 'Action:') + 'Status:\n')
+            logger.to_all(LogFormatter.hline)
 
             if 'all' in self.requested_build_names:
-                self.requested_build_names = [name for name in next(os.walk(trunk_tests_builds_dir))[1] if not name[0] == '.']
+                self.requested_build_names = [name for name in next(os.walk(Environment.trunk_tests_builds_dir))[1] if not name[0] == '.']
             found_build_names = []
             for build_name in self.requested_build_names:
@@ -1032,13 +1043,13 @@
                     self.build_database[build_name] = build
                     found_build_names.append(build_name)
-                    logger.to_all(config_table_line_template.format('Build', build_name, 'approved'))
+                    logger.to_all(LogFormatter.config_table_line_template.format('Build', build_name, 'approved'))
                     logger.to_all(message + '\n')
                 else:
-                    logger.to_all(config_table_line_template.format('Build', build_name, 'rejected'))
+                    logger.to_all(LogFormatter.config_table_line_template.format('Build', build_name, 'rejected'))
                     logger.to_all(message + '\n')
             final_build_list = found_build_names
 
             if 'all' in self.test_case_names:
-                self.test_case_names = sorted([name for name in next(os.walk(trunk_tests_cases_dir))[1] if not name[0] == '.'])
+                self.test_case_names = sorted([name for name in next(os.walk(Environment.trunk_tests_cases_dir))[1] if not name[0] == '.'])
 
             additional_initial_runs_2 = [self.test_case_names]
@@ -1079,5 +1090,5 @@
                         # removing as configuration failed should only apply to added dependencies
                         approved_test_case_order[i].remove(test_case_name)
-                        logger.to_all(config_table_line_template.format(info, test_case_name, 'rejected'))
+                        logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'rejected'))
                         logger.to_all(message + '\n')
                     elif test_case.requires_binary_files:
@@ -1085,11 +1096,11 @@
                             # removing as dependency is already removed
                             approved_test_case_order[i].remove(test_case_name)
-                            logger.to_all(config_table_line_template.format(info, test_case_name, 'disabled'))
+                            logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'disabled'))
                             logger.to_all(colored('[requires dependency \"' + test_case.use_binary_files_from + '\"]', 'red') + '\n')
                         else:
-                            logger.to_all(config_table_line_template.format(info, test_case_name, 'approved'))
+                            logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'approved'))
                             logger.to_all(message + '\n')
                     else:
-                        logger.to_all(config_table_line_template.format(info, test_case_name, 'approved'))
+                        logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'approved'))
                         logger.to_all(message + '\n')
 
@@ -1123,12 +1134,14 @@
                 if not test_case_configuration_failed:
                     self.test_case_queue.append(test_case)
-            logger.to_all(hline)
-
-            r = '{:' + str(table_width_intro) + '} '
-
-            logger.to_all(r.format('Test ID:') + self.test_id + '\n')
-            logger.to_all(r.format('Builds:') + str('\n' + r.format('')).join(sorted(self.build_database.keys())) + '\n')
-            logger.to_all(r.format('Cases:') + str('\n' + r.format('')).join([c.name for c in self.test_case_queue]) + '\n')
-            logger.to_all(r.format('Cores:') + ' '.join([str(i) for i in final_cores_list]) + '\n')
+            logger.to_all(LogFormatter.hline)
+
+            logger.to_all(LogFormatter.intro_table_line_template.format('Test ID:') +
+                          self.test_id + '\n')
+            logger.to_all(LogFormatter.intro_table_line_template.format('Builds:') +
+                          str('\n' + LogFormatter.intro_table_line_template.format('')).join(sorted(self.build_database.keys())) + '\n')
+            logger.to_all(LogFormatter.intro_table_line_template.format('Cases:') +
+                          str('\n' + LogFormatter.intro_table_line_template.format('')).join([c.name for c in self.test_case_queue]) + '\n')
+            logger.to_all(LogFormatter.intro_table_line_template.format('Cores:') +
+                          ' '.join([str(i) for i in final_cores_list]) + '\n')
 
     def _execute(self, test_case, build_name, cores):
@@ -1186,12 +1199,12 @@
     def execute(self):
         with Logger(self.test_dir, verbose=self.verbose) as logger:
-            logger.to_all(hline)
-            logger.to_all(task_table_line_template.format('Task:', 'Case:', 'Build:', 'Cores:') + 'Status:\n')
-            logger.to_all(hline)
+            logger.to_all(LogFormatter.hline)
+            logger.to_all(LogFormatter.task_table_line_template.format('Task:', 'Case:', 'Build:', 'Cores:') + 'Status:\n')
+            logger.to_all(LogFormatter.hline)
             self.test_report = dict()
             for test_case in self.test_case_queue:
-                logger.to_log(hline)
-                logger.to_file(hline)
-                logger.to_file(hline)
+                logger.to_log(LogFormatter.hline)
+                logger.to_file(LogFormatter.hline)
+                logger.to_file(LogFormatter.hline)
                 status_dict = dict()
                 for build_name in test_case.build_names:
@@ -1200,10 +1213,10 @@
                         status_dict[build_name][cores] = self._execute(test_case, build_name, cores)
                 self.test_report[test_case.name] = status_dict
-                logger.to_log(hline)
+                logger.to_log(LogFormatter.hline)
                 logger.to_file('\n' * 10)
 
     def report(self):
         with Logger(self.test_dir, verbose=self.verbose) as logger:
-            logger.to_all(hline)
+            logger.to_all(LogFormatter.hline)
             r = '{:10}' + '    total: ' + '{:<3d}' + \
                              '    ok: ' + colored('{:<3d}', 'green') + \
@@ -1274,5 +1287,5 @@
 
     def get_items(self):
-        case_names = [name for name in next(os.walk(trunk_tests_cases_dir))[1] if not name[0] == '.']
+        case_names = [name for name in next(os.walk(Environment.trunk_tests_cases_dir))[1] if not name[0] == '.']
         return case_names + ['all']
 
@@ -1281,5 +1294,5 @@
 
     def get_items(self):
-        build_names = [name for name in next(os.walk(trunk_tests_builds_dir))[1] if not name[0] == '.']
+        build_names = [name for name in next(os.walk(Environment.trunk_tests_builds_dir))[1] if not name[0] == '.']
         return build_names + ['all']
 
@@ -1367,6 +1380,6 @@
             action='store',
             dest='cores',
-            default=[i for i in range(1, available_cores+1)],
-            choices=[i for i in range(1, available_cores+1)],
+            default=[i for i in range(1, multiprocessing.cpu_count()+1)],
+            choices=[i for i in range(1, multiprocessing.cpu_count()+1)],
             help='The number of cores tests are supposed to be executed on. (default: %(default)s)',
             nargs='+',
Index: palm/trunk/SCRIPTS/palmtutorial
===================================================================
--- palm/trunk/SCRIPTS/palmtutorial	(revision 4091)
+++ palm/trunk/SCRIPTS/palmtutorial	(revision 4091)
@@ -0,0 +1,1411 @@
+#!/usr/bin/env python3
+# PYTHON_ARGCOMPLETE_OK
+
+import os
+import sys
+import shutil
+from datetime import datetime
+import subprocess
+import multiprocessing
+import socket
+import getpass
+import math
+import re
+import threading
+import queue
+from contextlib import ContextDecorator
+
+try:
+    from argparse import ArgumentParser
+    from argparse import RawTextHelpFormatter
+except ImportError:
+    sys.exit(
+        'ERROR: You need argparse!\n' +
+        '   install it from http://pypi.python.org/pypi/argparse\n' +
+        '   or run \"pip install argparse\".'
+    )
+
+try:
+    import numpy as np
+except ImportError:
+    sys.exit(
+        'ERROR: You need numpy!\n' +
+        '   install it from http://pypi.python.org/pypi/numpy\n' +
+        '   or run \"python3 -m pip install numpy\".'
+    )
+
+try:
+    import netCDF4
+except ImportError:
+    sys.exit(
+        'ERROR: You need netCDF4!\n' +
+        '   install it from http://pypi.python.org/pypi/netCDF4\n' +
+        '   or run \"python3 -m pip install netCDF4\".'
+    )
+
+try:
+    import yaml
+except ImportError:
+    sys.exit(
+        'ERROR: You need PyYAML!\n' +
+        '   install it from http://pypi.python.org/pypi/PyYAML\n' +
+        '   or run \"python3 -m pip install PyYAML\".'
+    )
+
+try:
+    import argcomplete
+except ImportError:
+    print(
+        'INFO: To use Tab-completion you need argcomplete!\n' +
+        '   install it from http://pypi.python.org/pypi/argcomplete\n' +
+        '   or run \"python3 -m pip install argcomplete\".'
+    )
+    has_argcomplete = False
+else:
+    has_argcomplete = True
+
+try:
+    from termcolor import colored as tcolored
+except ImportError:
+    def tcolored(string, color):
+        return string
+
+disable_colored_output = False
+
+
+def colored(string, color):
+    if not disable_colored_output:
+        return tcolored(string, color)
+    else:
+        return string
+
+
+def disable_color():
+    global disable_colored_output
+    disable_colored_output = True
+
+
+version = '1.0.1'
+
+
+class Environment:
+
+    scripts_dir = os.path.dirname(os.path.realpath(__file__))
+    trunk_dir = os.path.realpath(os.path.join(scripts_dir, '..'))
+    workspace_dir = os.path.realpath(os.path.join(trunk_dir, '..'))
+
+    trunk_tests_dir = os.path.join(trunk_dir, 'TUTORIALS')
+    trunk_tests_cases_dir = os.path.join(trunk_tests_dir, 'cases')
+    trunk_tests_builds_dir = os.path.join(trunk_tests_dir, 'builds')
+
+    tests_dir = os.path.join(workspace_dir, 'tutorials')
+
+
+class LogFormatter:
+
+    terminal_columns, terminal_lines = shutil.get_terminal_size()
+    hline = '#' * min(terminal_columns, 300) + '\n'
+    table_width_intro = 12
+    table_width_builds = len(max([s for s in next(os.walk(Environment.trunk_tests_builds_dir))[1] if not s[0] == '.'], key=len)) + len('_debug')
+    table_width_cases = len(max([s for s in next(os.walk(Environment.trunk_tests_cases_dir))[1] if not s[0] == '.'], key=len))
+    table_width_cores = 7
+    table_width_total = table_width_intro + table_width_builds + table_width_cases + table_width_cores + 3
+
+    intro_table_line_template = \
+        '{:' + str(table_width_intro) + '} '
+
+    task_table_line_template = \
+        '{:' + str(table_width_intro) + '} ' + \
+        '{:' + str(table_width_cases) + '} ' + \
+        '{:' + str(table_width_builds) + '} ' + \
+        '{:' + str(table_width_cores) + '} '
+
+    config_table_line_template = \
+        '{:' + str(table_width_intro) + '} ' + \
+        '{:' + str(max(table_width_builds, table_width_cases)) + '} ' + \
+        '{:8} '
+
+    file_table_line_template = \
+        '{:' + str(table_width_intro) + '} ' + \
+        '{:' + str(table_width_cases + 13) + '} '
+
+
+class SignificantDigitsRounder:
+
+    @staticmethod
+    def _round(value, digits=10):
+        if value == 0.0:
+            return value
+        negative = value < 0.0
+        value = -value if negative else value
+        rounded_value = round(value, -int(math.floor(math.log10(value))) + (digits - 1))
+        rounded_value = -rounded_value if negative else rounded_value
+        return rounded_value
+
+
+    vectorized_round = np.vectorize(_round)
+
+    _vectorized_round = np.vectorize(round)
+
+
+    @classmethod
+    def around(cls, array, digits=10):
+        # TODO: divide both arrays and check decimal point
+        sign_mask = np.ma.masked_where(array >= 0.0, array).mask
+        pos_array = np.where(sign_mask, array, -array)
+        non_zero_maks = np.ma.masked_where(pos_array == 0.0, pos_array).mask
+        non_zero_array = np.where(non_zero_maks, 1.0, pos_array)
+        i1 = -np.floor(np.log10(non_zero_array)).astype(int) + (digits - 1)
+        rounded_non_zero_array = cls._vectorized_round(non_zero_array, i1)
+        rounded_pos_array = np.where(non_zero_maks, 0.0, rounded_non_zero_array)
+        return np.where(sign_mask, rounded_pos_array, -rounded_pos_array)
+
+
+
+class Logger(ContextDecorator):
+
+    def __init__(self, logfile_dir, logfile_name='palmtest.log', logfile_mode='a', verbose=False):
+        self.logfile_path = os.path.join(logfile_dir, logfile_name)
+        self.logfile_mode = logfile_mode
+        self.verbose = verbose
+
+    def __enter__(self):
+        self._file = open(self.logfile_path, self.logfile_mode)
+        return self
+
+    def to_file(self, message):
+        self._file.write(message)
+        self._file.flush()
+
+    def to_log(self, message):
+        if self.verbose:
+            sys.stdout.write(message)
+            sys.stdout.flush()
+        self._file.write(message)
+        self._file.flush()
+
+    def to_all(self, message):
+        sys.stdout.write(message)
+        sys.stdout.flush()
+        self._file.write(message)
+        self._file.flush()
+
+    def __exit__(self, *exc):
+        self._file.close()
+        return False
+
+
+class Executor:
+
+    @staticmethod
+    def _enqueue_output(out, queue):
+        for line in iter(out.readline, b''):
+            queue.put(line)
+        out.close()
+
+    @staticmethod
+    def execute(cmd, cwd='.', verbose=True, dry_run=False):
+        assert isinstance(cmd, list)
+        if dry_run:
+            cmd = ['echo'] + cmd
+        cmd_str = ' '.join(cmd)
+        p = subprocess.Popen(cmd_str, cwd=cwd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True, bufsize=1)
+        q = queue.Queue()
+        t = threading.Thread(target=Executor._enqueue_output, args=(p.stdout, q))
+        t.daemon = True # thread dies with the program
+        t.start()
+
+        with Logger(cwd, verbose=verbose) as logger:
+            # read line without blocking
+            logger.to_log(LogFormatter.hline)
+            logger.to_log('CMD: ' + cmd_str + '\n')
+            logger.to_log(LogFormatter.hline)
+            while t.is_alive():
+                try:
+                    line = q.get_nowait()  # or q.get(timeout=.1)
+                except queue.Empty:
+                    pass  # print('no output yet')
+                else:  # got line
+                    logger.to_log(line.decode("utf-8"))
+            line = True
+            while line:
+                try:
+                    line = q.get_nowait()  # or q.get(timeout=.1)
+                except queue.Empty:
+                    line = False
+                else:  # got line
+                    logger.to_log(line.decode("utf-8"))
+            logger.to_log(LogFormatter.hline)
+
+        rc = p.poll()
+        failed = rc != 0
+        return failed
+
+
+class NetCDFInterface:
+
+    def __init__(self, filename):
+        self.filename = filename
+
+    def is_healthy(self):
+        try:
+            self.get_run_name()
+        except:
+            return False
+        else:
+            return True
+
+    def get_run_name(self):
+        with netCDF4.Dataset(self.filename, mode='r') as netcdf:
+            l = getattr(netcdf, 'title').split()
+            i = l.index('run:')
+            return l[i+1]
+
+    def get_var_list(self):
+        with netCDF4.Dataset(self.filename, mode='r') as netcdf:
+            var_list = list(netcdf.variables.keys())
+            var_list = filter(None, var_list)
+            return sorted(var_list)
+
+    def show_content(self):
+        with netCDF4.Dataset(self.filename, mode='r') as netcdf:
+            for name in netcdf.ncattrs():
+                print("Global attr", name, "=", getattr(netcdf, name))
+            print(netcdf)
+            for v in netcdf.variables:
+                print(v)
+
+    def get_times_list(self):
+        attributes, times = self.read_var('time')
+        times = [str(time) for time in times]
+        times = list(filter(None, times))
+        return times
+
+    def contains(self, variable):
+        return variable in self.get_var_list()
+
+    def read_var(self, variable):
+        with netCDF4.Dataset(self.filename, mode='r') as netcdf:
+            values = netcdf.variables[variable][:]  # extract values
+            attributes = dict()
+            try:
+                attributes['long_name'] = netcdf.variables[variable].name
+            except:
+                attributes['long_name'] = ''
+            try:
+                attributes['unit'] = netcdf.variables[variable].units
+            except:
+                attributes['unit'] = ''
+        return attributes, values
+
+
+class FileComparator:
+
+    @staticmethod
+    def compare_ascii(file_path1, file_path2, start_string=None):
+        try:
+            with open(file_path1, 'r') as file1:
+                content1 = file1.readlines()
+        except OSError:
+            return True, colored('[reference file not found]', 'red')
+        try:
+            with open(file_path2, 'r') as file2:
+                content2 = file2.readlines()
+        except OSError:
+            return True, colored('[output file not found]', 'red')
+        if start_string:
+            index1 = content1.index(start_string)
+            index2 = content2.index(start_string)
+            comparable_content1 = content1[index1:]
+            comparable_content2 = content2[index2:]
+            ln = index2 + 1
+        else:
+            comparable_content1 = content1
+            comparable_content2 = content2
+            ln = 1
+        if len(comparable_content1) != len(comparable_content2):
+            return True, colored('[mismatch in total number of lines]', 'red')
+        for line1, line2 in zip(comparable_content1, comparable_content2):
+                if not line1 == line2:
+                    return True, colored('[mismatch in content starting line ' + str(ln) + ']', 'red')
+                ln += 1
+        return False, colored('[file ok]', 'green')
+
+    @staticmethod
+    def compare_netcdf(file_path1, file_path2, digits=None):
+        nci1 = NetCDFInterface(file_path1)
+        nci2 = NetCDFInterface(file_path2)
+        if not nci1.is_healthy():
+            return True, colored('[reference file not found]', 'red')
+        if not nci2.is_healthy():
+            return True, colored('[output file not found]', 'red')
+        times_list1 = nci1.get_times_list()
+        times_list2 = nci2.get_times_list()
+        if not times_list1 == times_list2:
+            return True, colored('[wrong time dimension]', 'red')
+        else:
+            time_list = times_list1
+        var_list1 = nci1.get_var_list()
+        var_list2 = nci2.get_var_list()
+        if not var_list1 == var_list2:
+            return True, colored('[wrong set of variables]', 'red')
+        else:
+            var_list = var_list1
+        content1 = dict()
+        content2 = dict()
+        for var in var_list:
+            attributes1, values1 = nci1.read_var(var)
+            attributes2, values2 = nci2.read_var(var)
+            if sorted(attributes1.keys()) != sorted(attributes2.keys()):
+                return True, colored('[wrong set of attributes in variable \"'+var+'\"]', 'red')
+            if isinstance(digits, int):
+                values1 = SignificantDigitsRounder.around(values1, digits=digits)
+                values2 = SignificantDigitsRounder.around(values2, digits=digits)
+            content1[var] = values1
+            content2[var] = values2
+        #for decimals in
+        for i, time in enumerate(time_list):
+            for var in var_list:
+                t_content1 = content1[var][i]
+                t_content2 = content2[var][i]
+                if not (t_content1==t_content2).all():
+                    if isinstance(digits, int):
+                        return True, colored('[1st mismatch within ' + str(digits) + ' digits at time index ' + str(i) + ' in variable \"' + var + '\"]', 'red')
+                    else:
+                        return True, colored('[1st mismatch at time index ' + str(i) + ' in variable \"' + var + '\"]', 'red')
+        return False, colored('[file ok]', 'green')
+
+
+class OutputChecker:
+
+    def __init__(self, test_dir, setup_name, build_name, cores, significant_digits=None, verbose=True, dry_run=False):
+        self.test_dir = test_dir
+        self.setup_name = setup_name
+        self.build_name = build_name
+        self.cores = cores
+        self.significant_digits = significant_digits
+        self.verbose = verbose
+        self.dry_run = dry_run
+        self.job_name = self.setup_name + '__' + build_name + '__' + str(self.cores)
+        self.job_dir = os.path.join(self.test_dir, 'JOBS', self.job_name)
+        self.ref_monitoring_dir = os.path.join(Environment.trunk_tests_cases_dir, self.setup_name, 'MONITORING')
+        self.ref_output_dir = os.path.join(Environment.trunk_tests_cases_dir, self.setup_name, 'OUTPUT')
+        self.res_monitoring_dir = os.path.join(self.job_dir, 'MONITORING')
+        self.res_output_dir = os.path.join(self.job_dir, 'OUTPUT')
+        self.failed = None
+
+    def get_checkable_file_dicts(self):
+        if os.path.isdir(self.ref_monitoring_dir):
+            file_names_monitoring = [s for s in next(os.walk(self.ref_monitoring_dir))[2]]
+        else:
+            file_names_monitoring = []
+        file_paths_monitoring = []
+        for file_name in file_names_monitoring:
+            file_specific_ending = file_name[len(self.setup_name):]
+            file_specific_ending_split = file_specific_ending.split('.')
+            postfix = file_specific_ending_split[0]
+            if len(file_specific_ending_split) > 1:
+                extension = file_specific_ending_split[-1]
+            else:
+                extension = ''
+            if len(file_specific_ending_split) > 2:
+                cycle_info = file_specific_ending_split[1: -1]
+            else:
+                cycle_info = []
+            file_paths_monitoring.append(
+                dict(
+                    postfix=postfix,
+                    cycle_info=cycle_info,
+                    extension=extension,
+                    ref_path=self.ref_monitoring_dir,
+                    res_path=self.res_monitoring_dir,
+                )
+            )
+        if os.path.isdir(self.ref_output_dir):
+            file_names_output = [s for s in next(os.walk(self.ref_output_dir))[2]]
+        else:
+            file_names_output = []
+        file_paths_output = []
+        for file_name in file_names_output:
+            file_specific_ending = file_name[len(self.setup_name):]
+            file_specific_ending_split = file_specific_ending.split('.')
+            postfix = file_specific_ending_split[0]
+            if len(file_specific_ending_split) > 1:
+                extension = file_specific_ending_split[-1]
+            else:
+                extension = ''
+            if len(file_specific_ending_split) > 2:
+                cycle_info = file_specific_ending_split[1: -1]
+            else:
+                cycle_info = []
+            file_paths_output.append(
+                dict(
+                    postfix=postfix,
+                    cycle_info=cycle_info,
+                    extension=extension,
+                    ref_path=self.ref_output_dir,
+                    res_path=self.res_output_dir,
+                )
+            )
+        return file_paths_monitoring + file_paths_output
+
+    def check(self):
+        with Logger(self.test_dir, verbose=self.verbose) as logger:
+            logger.to_log('Checking output files:')
+            logger.to_all('\n')
+            failed = False
+            for file_dict in self.get_checkable_file_dicts():
+                file_failed = False
+                ext_list = [file_dict['extension']] if file_dict['extension'] else []
+                file_specific_ending = '.'.join([file_dict['postfix']] + file_dict['cycle_info'] + ext_list )
+                logger.to_all(LogFormatter.file_table_line_template.format('Checking:', self.setup_name + file_specific_ending))
+                ref_file_path = os.path.join(file_dict['ref_path'], self.setup_name + file_specific_ending)
+                res_file_path = os.path.join(file_dict['res_path'], self.job_name + file_specific_ending)
+                if re.match('_rc', file_dict['postfix']) and not file_dict['extension']:
+                    file_failed, message = FileComparator.compare_ascii(ref_file_path, res_file_path, start_string='Run-control output:\n')
+                elif re.match('nc', file_dict['extension']):
+                    if self.significant_digits is not None:
+                        if re.match('_ts', file_dict['postfix']) and 'timeseries' in self.significant_digits:
+                            file_failed, message = FileComparator.compare_netcdf(ref_file_path, res_file_path,
+                                                                                 digits=self.significant_digits['timeseries'])
+                        elif re.match('_pr', file_dict['postfix']) and 'profiles' in self.significant_digits:
+                            file_failed, message = FileComparator.compare_netcdf(ref_file_path, res_file_path,
+                                                                                 digits=self.significant_digits['profiles'])
+                        else:
+                            file_failed, message = FileComparator.compare_netcdf(ref_file_path, res_file_path,
+                                                                                 digits=self.significant_digits['other'])
+                    else:
+                        file_failed, message = FileComparator.compare_netcdf(ref_file_path, res_file_path)
+                else:
+                    message = colored('[ignored]', 'blue')
+                if file_failed:
+                    failed = True
+                logger.to_all(message + '\n')
+            if self.dry_run:
+                failed = False
+        return failed
+
+
+class PALMJob:
+    """The PALM job class deals with the execution of a single PALM job"""
+
+    @staticmethod
+    def get_job_name(setup_name, build_name, cores):
+        return setup_name + '__' + build_name + '__' + str(cores)
+
+    def __init__(self, test_dir, test_case, build_name, cores, verbose=False, dry_run=False):
+        self.test_dir = test_dir
+        self.test_case = test_case
+        self.build_name = build_name
+        self.cores = cores
+        self.verbose = verbose
+        self.dry_run = dry_run
+
+        self.attempted_debug = False
+        self.failed_debug = None
+        self.attempted_non_debug = False
+        self.failed_non_debug = None
+
+    def _link_restart_files(self, build_name):
+        if self.dry_run:
+            return True, colored('[restart data dry]', 'blue')
+        name = self.get_job_name(self.test_case.name, build_name, self.cores)
+        source_name = self.get_job_name(self.test_case.use_binary_files_from, build_name, self.cores)
+        source_restart_dir = os.path.join(self.test_dir, 'JOBS', source_name, 'RESTART')
+        try:
+            source_data_dirs_grp = [d for r, d, f in os.walk(source_restart_dir)]
+        except:
+            source_data_dirs_grp = []
+        if len(source_data_dirs_grp) == 0:
+            source_data_dirs = []
+        else:
+            source_data_dirs = source_data_dirs_grp[0]
+        if len(source_data_dirs) == 0 and re.match('.+_debug', build_name):
+            source_build_name = build_name[:-len('_debug')]
+            source_name = self.get_job_name(self.test_case.use_binary_files_from, source_build_name, self.cores)
+            source_restart_dir = os.path.join(self.test_dir, 'JOBS', source_name, 'RESTART')
+            try:
+                source_data_dirs_grp = [d for r, d, f in os.walk(source_restart_dir)]
+            except:
+                source_data_dirs_grp = []
+            if len(source_data_dirs_grp) == 0:
+                source_data_dirs = []
+            else:
+                source_data_dirs = source_data_dirs_grp[0]
+        if len(source_data_dirs) == 0:
+            source_data_dir = 'no_restart_data'
+        else:
+            source_data_dir = sorted(source_data_dirs)[-1]
+        source_data_dir_path = os.path.join(source_restart_dir, source_data_dir)
+        if os.path.isdir(source_data_dir_path) and re.match('.+_d3d.*', source_data_dir):
+            job_restart_dir = os.path.join(self.test_dir, 'JOBS', name, 'RESTART')
+            os.makedirs(job_restart_dir, exist_ok=False)
+            job_data_dir_path = os.path.join(job_restart_dir, name + '_d3d')
+            os.symlink(source_data_dir_path, job_data_dir_path, target_is_directory=True)
+            return False, colored('[linked restart data from: ' + source_data_dir_path + ']', 'green')
+        else:
+            return True, colored('[no restart data found]', 'red')
+
+    def _execute(self, name, build_name):
+        execution_failed = Executor.execute(
+            [
+                os.path.join(self.test_dir, 'trunk', 'SCRIPTS', 'palmrun'),
+                '-c', '\"' + build_name + '\"',
+                '-r', name,
+                '-a', '\"' + ' '.join(self.test_case.activation_strings) + '\"',
+                '-X', str(self.cores),
+                '-T', str(self.cores),
+                '-B',
+                '-v',
+                '-z',
+            ],
+            cwd=self.test_dir,
+            verbose=self.verbose,
+            dry_run=self.dry_run,
+        )
+
+        if self.dry_run:
+            return False, colored('[execution dry]', 'blue')
+        elif execution_failed:
+            return True, colored('[execution failed]', 'red')
+        else:
+            return False, colored('[execution ok]', 'green')
+
+    def _check(self, build_name):
+        checker = OutputChecker(
+            self.test_dir,
+            self.test_case.name,
+            build_name,
+            self.cores,
+            significant_digits=self.test_case.significant_digits,
+            verbose=self.verbose,
+            dry_run=self.dry_run,
+        )
+        check_failed = checker.check()
+
+        if self.dry_run:
+            return False, colored('[checks dry]', 'blue')
+        if check_failed:
+            return True, colored('[checks failed]', 'red')
+        else:
+            return False, colored('[checks ok]', 'green')
+
+    def execute(self, debug=False):
+        if debug:
+            attempted = self.attempted_debug
+            build_name = self.build_name + '_debug'
+            failed = self.failed_debug
+        else:
+            attempted = self.attempted_non_debug
+            build_name = self.build_name
+            failed = self.failed_non_debug
+
+        if not attempted:
+            with Logger(self.test_dir, verbose=self.verbose) as logger:
+                status_prefix = LogFormatter.task_table_line_template.format('Testing:', self.test_case.name, build_name, self.cores)
+                logger.to_all(status_prefix)
+                logger.to_log('[started]' + '\n')
+                attempted = True
+
+                name = self.get_job_name(self.test_case.name, build_name, self.cores)
+
+                input_dir = os.path.join(self.test_dir, 'JOBS', name, 'INPUT')
+                os.makedirs(input_dir, exist_ok=False)
+
+                # copying needs to be done per file, because input files need to be renamed
+                for input_file in self.test_case.input_file_names:
+                    postfix = input_file[len(self.test_case.name):]
+                    src = os.path.join(self.test_case.input_dir, input_file)
+                    dst = os.path.join(input_dir, name + postfix)
+                    shutil.copy(src, dst)
+
+                # copying the entire directory is ok, because source files do not need to be renamed
+                user_code_dir = os.path.join(self.test_dir, 'JOBS', name, 'USER_CODE')
+                if os.path.isdir(self.test_case.user_code_dir):
+                    shutil.copytree(self.test_case.user_code_dir, user_code_dir, copy_function=shutil.copy)
+
+                if self.test_case.requires_binary_files:
+                    link_restart_files_failed, message = self._link_restart_files(build_name)
+                    logger.to_log(status_prefix)
+                    logger.to_log(message + ' ')
+                    logger.to_log('\n')
+
+                failed, message = self._execute(name, build_name)
+                logger.to_log(status_prefix)
+                logger.to_all(message + ' ')
+                logger.to_log('\n')
+
+                failed, message = self._check(build_name)
+                logger.to_log(status_prefix)
+                logger.to_log(message + ' ')
+
+                logger.to_all('\n')
+
+        if debug:
+            self.attempted_debug = attempted
+            self.failed_debug = failed
+        else:
+            self.attempted_non_debug = attempted
+            self.failed_non_debug = failed
+
+        return failed
+
+    def status(self):
+        return dict(
+            attempted=self.attempted_non_debug or self.attempted_debug,
+            failed=self.failed_non_debug and self.failed_debug,
+            debugged=self.attempted_debug,
+            non_debug_failed=self.failed_non_debug,
+        )
+
+
+class PALMBuild:
+    """The PALM build class deals with configuration and execution of all required PALM builds"""
+
+    def __init__(self, test_dir, build_name, verbose=False, dry_run=False):
+        self.test_dir = test_dir
+        self.build_name = build_name
+        self.verbose = verbose
+        self.dry_run = dry_run
+        self.configured = False
+        self.executed = False
+        self.available = False
+        self.requires_mpi = False
+        self.requires_netcdf = False
+        self.requires_fftw = False
+        self.requires_rrtmg = False
+        self.attempted_non_debug = False
+        self.attempted_debug = False
+        self.failed_non_debug = None
+        self.failed_debug = None
+
+    def configure(self):
+        try:
+            with open(os.path.join(Environment.trunk_tests_builds_dir, self.build_name, 'build_config.yml'), 'r') as f:
+                build_config = yaml.load(f)
+        except:
+            return True, colored('[build not found]', 'red')
+
+        if 'compiler' in build_config:
+            self.compiler = build_config['compiler']
+        else:
+            return True, colored('[missing \"compiler\" keyword]', 'red')
+
+        if not isinstance(self.compiler, dict):
+            return True, colored('[\"compiler\" keyword must be dict]', 'red')
+
+        if 'linker' in build_config:
+            self.linker = build_config['linker']
+        else:
+            return True, colored('[missing \"linker\" keyword]', 'red')
+
+        if not isinstance(self.linker, dict):
+            return True, colored('[\"linker\" keyword must be dict]', 'red')
+
+        if 'mpi_wrapper' in self.compiler:
+            if 'mpi_wrapper}}' in self.compiler['mpi_wrapper']:
+                self.requires_mpi = True
+        else:
+            return True, colored('[missing \"mpi_wrapper\" keyword]', 'red')
+
+        if 'includes' in self.compiler:
+            for include in self.compiler['includes']:
+                if 'include.netcdf}}' in include:
+                    self.requires_netcdf = True
+                if 'include.fftw}}' in include:
+                    self.requires_fftw = True
+                if 'include.rrtmg}}' in include:
+                    self.requires_rrtmg = True
+        else:
+            return True, colored('[missing \"includes\" keyword in compiler]', 'red')
+
+        if 'options' in self.linker:
+            for lib in self.linker['options']:
+                if 'lib.netcdf}}' in lib:
+                    self.requires_netcdf = True
+                if 'lib.fftw}}' in lib:
+                    self.requires_fftw = True
+                if 'lib.rrtmg}}' in lib:
+                    self.requires_rrtmg = True
+        else:
+            return True, colored('[missing \"options\" keyword in linker]', 'red')
+
+        library_names = []
+        if self.requires_netcdf:
+            library_names.append('netcdf')
+        if self.requires_fftw:
+            library_names.append('fftw')
+        if self.requires_rrtmg:
+            library_names.append('rrtmg')
+
+        if not 'executable' in self.compiler:
+            return True, colored('[missing \"executable\" keyword in compiler]', 'red')
+
+        if not 'definitions' in self.compiler:
+            return True, colored('[missing \"definitions\" keyword in compiler]', 'red')
+
+        if not 'options' in self.compiler:
+            return True, colored('[missing \"options\" keyword in compiler]', 'red')
+
+        if not 'default' in self.compiler['options']:
+            return True, colored('[missing \"default\" keyword in compiler.options]', 'red')
+
+        if not 'debug' in self.compiler['options']:
+            return True, colored('[missing \"debug\" keyword in compiler.options]', 'red')
+
+        try:
+            with open(os.path.join(Environment.workspace_dir, 'palmtest.yml'), 'r') as f:
+                palmtest_config = yaml.load(f)
+        except:
+            return True, colored('[palmtest.yml not found]', 'red')
+
+        if 'palm_config_template' in palmtest_config:
+            if isinstance(palmtest_config['palm_config_template'], str):
+                custom_template = palmtest_config['palm_config_template']
+        try:
+            with open(os.path.join(custom_template), 'r') as palm_config_template_file:
+                template = palm_config_template_file.read()
+        except:
+            try:
+                with open(os.path.join(Environment.scripts_dir, '.palm.config.default.in'), 'r') as palm_config_template_file:
+                    template = palm_config_template_file.read()
+            except:
+                return True, colored('[trunk/SCRIPTS/.palm.config.default.in not found]', 'red')
+
+        template = template.replace('@CMAKE_INSTALL_PREFIX@', self.test_dir)
+        template = template.replace('@PALM_HOSTNAME@', socket.gethostname())
+        template = template.replace('@CMAKE_USERNAME@', getpass.getuser())
+        template = template.replace('@MPI_Fortran_COMPILER@', self.compiler['mpi_wrapper'])
+        template = template.replace('@CMAKE_Fortran_COMPILER@', self.compiler['executable'])
+        cpp_options_str = ['-D' + s for s in self.compiler['definitions']]
+        template = template.replace('@PALM_CPP_OPTIONS_STR@', ' '.join(cpp_options_str))
+        template = template.replace('@PALM_CORES@', str(multiprocessing.cpu_count()))
+        template = template.replace('@PALM_COMPILER_OPTIONS@', '{{palmtest.compiler.options}} ' + ' '.join(self.compiler['includes']))
+        template = template.replace('@PALM_LINKER_OPTIONS@', ' '.join(self.linker['options']))
+
+        if 'environments' in palmtest_config:
+            available_environments = palmtest_config['environments']
+        else:
+            return True, colored('[missing \"environments\" keyword in palmtest.yml]', 'red')
+
+        if 'id' in self.compiler:
+            c_id = self.compiler['id']
+        else:
+            return True, colored('[missing \"id\" keyword in compiler]', 'red')
+
+        if c_id in available_environments:
+            self.available = True
+
+            environment = available_environments[c_id]
+
+            if 'mpi_execution_command' in environment:
+                template = template.replace('@PALM_EXECUTE_COMMAND@', environment['mpi_execution_command'])
+            else:
+                template = template.replace('@PALM_EXECUTE_COMMAND@', 'mpirun -n {{mpi_tasks}}')
+
+            if 'executable' not in environment:
+                return True, colored('[palmtest.yml environment \"' + c_id + '\" has no \"executable\"]', 'red')
+            value = environment['executable']
+            if isinstance(value, str):
+                template = template.replace('{{' + '.'.join([c_id, 'executable']) + '}}', value)
+            if self.requires_mpi:
+                if 'mpi_wrapper' not in environment:
+                    return True, colored('[palmtest.yml environment \"' + c_id + '\" has no \"mpi_wrapper\"]', 'red')
+                value = environment['mpi_wrapper']
+                if isinstance(value, str):
+                    template = template.replace('{{' + '.'.join([c_id, 'mpi_wrapper']) + '}}', value)
+            if 'include' not in environment:
+                return True, colored('[palmtest.yml environment \"' + c_id + '\" has no \"include\"]', 'red')
+            if 'lib' not in environment:
+                return True, colored('[palmtest.yml environment \"' + c_id + '\" has no \"lib\"]', 'red')
+            for lib in library_names:
+                if lib not in environment['include']:
+                    return True, colored('[palmtest.yml environment \"' + c_id + '\" has no \"include.'+lib+'\"]', 'red')
+                value = environment['include'][lib]
+                if isinstance(value, str):
+                    template = template.replace('{{' + '.'.join([c_id, 'include', lib]) + '}}', value)
+                if lib not in environment['lib']:
+                    return True, colored('[palmtest.yml environment \"' + c_id + '\" has no \"lib.'+lib+'\"]', 'red')
+                value = environment['lib'][lib]
+                if isinstance(value, str):
+                    template = template.replace('{{' + '.'.join([c_id, 'lib', lib]) + '}}', value)
+
+            with open(os.path.join(self.test_dir, '.palm.config.' + self.build_name), 'w') as palm_config_file:
+                palm_config_file.write(
+                    template.replace(
+                        '{{palmtest.compiler.options}}',
+                        ' '.join(self.compiler['options']['default']),
+                    )
+                )
+            with open(os.path.join(self.test_dir, '.palm.config.' + self.build_name + '_debug'), 'w') as palm_config_file:
+                palm_config_file.write(
+                    template.replace(
+                        '{{palmtest.compiler.options}}',
+                        ' '.join(self.compiler['options']['debug']),
+                    )
+                )
+            self.configured = True
+            return False, colored('[configuration ok]', 'green')
+
+        else:
+            return True, colored('[palmtest.yml environment \"' + c_id + '\" not found]', 'red')
+
+    def _execute(self, build_name):
+        self.attempted = True
+        build_failed = Executor.execute(
+            [
+                os.path.join(self.test_dir, 'trunk', 'SCRIPTS', 'palmbuild'),
+                '-c', '\"' + build_name + '\"',
+                '-v',
+            ],
+            cwd=self.test_dir,
+            verbose=self.verbose,
+            dry_run=self.dry_run,
+        )
+
+        if self.dry_run:
+            return False, colored('[build dry]', 'blue')
+        if build_failed:
+            return True, colored('[build failed]', 'red')
+        else:
+            return False, colored('[build ok]', 'green')
+
+    def build(self, debug=False):
+        if debug:
+            attempted = self.attempted_debug
+            build_name = self.build_name + '_debug'
+            failed = self.failed_debug
+        else:
+            attempted = self.attempted_non_debug
+            build_name = self.build_name
+            failed = self.failed_non_debug
+
+        if not attempted:
+            with Logger(self.test_dir, verbose=self.verbose) as logger:
+                status_prefix = LogFormatter.task_table_line_template.format('Building:', '', build_name, '')
+                logger.to_all(status_prefix)
+                logger.to_log('[started]' + '\n')
+                attempted = True
+
+                failed, message = self._execute(build_name)
+                logger.to_log(status_prefix)
+                logger.to_all(message + ' ')
+                logger.to_all('\n')
+
+        if debug:
+            self.attempted_debug = attempted
+            self.failed_debug = failed
+        else:
+            self.attempted_non_debug = attempted
+            self.failed_non_debug = failed
+
+        return failed
+
+    def report(self):
+        return dict(
+            failed_debug=self.failed_debug,
+            failed_non_debug=self.failed_non_debug,
+        )
+
+
+class PALMTestCase:
+    """The PALM test case class deals with the configuration and execution of all PALM test cases"""
+
+    def __init__(self,test_dir,  name, verbose=False, dry_run=False):
+        self.test_dir = test_dir
+        self.name = name
+        self.verbose = verbose
+        self.dry_run = dry_run
+        self.user_code_dir = os.path.join(Environment.trunk_tests_cases_dir, self.name, 'USER_CODE')
+        self.input_dir = os.path.join(Environment.trunk_tests_cases_dir, self.name, 'INPUT')
+        self.number_of_cores = []
+        self.build_names = []
+        self.input_file_names = []
+        self.configured = False
+
+    def configure(self, requested_build_names, requested_cores):
+        f_name = os.path.join(Environment.trunk_tests_cases_dir, self.name, 'case_config.yml')
+        try:
+            with open(f_name, 'r') as f:
+                config = yaml.load(f)
+        except:
+            return True, colored('[Case \"' + self.name + '\" could not be found.]', 'red')
+        try:
+            self.use_binary_files_from = config['use_binary_files_from']
+        except:
+            self.use_binary_files_from = None
+        self.requires_binary_files = bool(self.use_binary_files_from)
+
+        if 'allowed_builds' not in config:
+            return True, colored('[missing \"allowed_builds\" keyword]', 'red')
+        self.allowed_build_names = config['allowed_builds']
+
+        if 'allowed_number_of_cores' not in config:
+            return True, colored('[missing \"allowed_number_of_cores\" keyword]', 'red')
+        self.allowed_number_of_cores = config['allowed_number_of_cores']
+
+        if 'activation_strings' not in config:
+            return True, colored('[missing \"activation_strings\" keyword]', 'red')
+        self.activation_strings = config['activation_strings']
+
+        if 'significant_digits_for_netcdf_checks' not in config:
+            return True, colored('[missing \"significant_digits_for_netcdf_checks\" keyword]', 'red')
+        self.significant_digits = config['significant_digits_for_netcdf_checks']
+
+        if 'timeseries' not in config['significant_digits_for_netcdf_checks']:
+            return True, colored('[missing \"timeseries\" keyword in significant_digits_for_netcdf_checks]', 'red')
+
+        if 'profiles' not in config['significant_digits_for_netcdf_checks']:
+            return True, colored('[missing \"profiles\" keyword in significant_digits_for_netcdf_checks]', 'red')
+
+        if 'other' not in config['significant_digits_for_netcdf_checks']:
+            return True, colored('[missing \"other\" keyword in significant_digits_for_netcdf_checks]', 'red')
+
+        self.number_of_cores = sorted(set(requested_cores).intersection(self.allowed_number_of_cores))
+        self.build_names = sorted(set(requested_build_names).intersection(self.allowed_build_names))
+        self.input_file_names = [s for s in next(os.walk(self.input_dir))[2]]
+        self.configured = True
+        if len(self.number_of_cores) == 0 :
+            return True, colored('[no allowed cores requested]', 'blue')
+        if len(self.build_names) == 0:
+            return True, colored('[no allowed builds requested]', 'blue')
+        if len(self.input_file_names) == 0:
+            return True, colored('[no input files found]', 'red')
+        return False, colored('[configuration ok]', 'green')
+
+
+
+class PALMTest:
+
+    def __init__(self, args):
+        self.verbose = args.verbose
+        self.no_auto_debug = args.no_auto_debug
+        self.force_debug = args.force_debug
+        self.fail_on_debug = args.fail_on_debug
+        self.dry_run = args.dry_run
+        self.no_color = args.no_color
+        self.test_id = args.test_id
+        self.test_case_names = args.cases
+        self.requested_build_names = args.builds
+        self.requested_cores = args.cores
+        self.test_case_queue = []
+        self.build_database = dict()
+
+    def prepare(self):
+        if self.no_color:
+            disable_color()
+        self.test_dir = os.path.join(Environment.tests_dir, self.test_id)
+        try:
+            os.makedirs(self.test_dir, exist_ok=False)
+        except:
+            print('ERROR: Found existing test directory: ' + self.test_dir)
+            exit(1)
+        with Logger(self.test_dir, verbose=self.verbose) as logger:
+            logger.to_all(LogFormatter.hline)
+            logger.to_all('This is the PALM tester  (version: ' + version + ')' + '\n')
+            logger.to_all(LogFormatter.hline)
+            try:
+                with open(os.path.join(Environment.workspace_dir, 'palmtest.yml'), 'r') as f:
+                    pass
+            except:
+                logger.to_all('ERROR: No palmtest.yml file was found in your working directory!\n')
+                logger.to_all('INFO:  A template for this file can be found at: trunk/TESTS/palmtest.yml\n')
+                logger.to_all('       Please copy the template to your working directory and adjust it to your system!\n')
+                exit(1)
+
+            self.execution_trunk_dir = os.path.join(self.test_dir, 'trunk')
+            os.symlink(Environment.trunk_dir, self.execution_trunk_dir)
+            self.execution_jobs_dir = os.path.join(self.test_dir, 'JOBS')
+            os.makedirs(self.execution_jobs_dir, exist_ok=False)
+
+            try:
+                with open(os.path.join(Environment.scripts_dir, '.palm.iofiles'), 'r') as iofiles_template_file:
+                    iofiles_template = iofiles_template_file.read()
+                with open(os.path.join(self.test_dir, '.palm.iofiles'), 'w') as iofiles_file:
+                    iofiles_file.write(iofiles_template.replace('$fast_io_catalog', '$base_data'))
+            except:
+                logger.to_all('ERROR: No .palm.iofiles file was found in trunk/SCRIPTS/')
+                exit(1)
+
+            available_cores = multiprocessing.cpu_count()
+            final_cores_list = list(filter(lambda x: x <= available_cores, self.requested_cores))
+
+            logger.to_all(LogFormatter.config_table_line_template.format('Object:', 'Name:', 'Action:') + 'Status:\n')
+            logger.to_all(LogFormatter.hline)
+
+            if 'all' in self.requested_build_names:
+                self.requested_build_names = [name for name in next(os.walk(Environment.trunk_tests_builds_dir))[1] if not name[0] == '.']
+            found_build_names = []
+            for build_name in self.requested_build_names:
+                build = PALMBuild(self.test_dir, build_name, verbose=self.verbose, dry_run=self.dry_run)
+                configuration_failed, message = build.configure()
+                if not configuration_failed:
+                    self.build_database[build_name] = build
+                    found_build_names.append(build_name)
+                    logger.to_all(LogFormatter.config_table_line_template.format('Build', build_name, 'approved'))
+                    logger.to_all(message + '\n')
+                else:
+                    logger.to_all(LogFormatter.config_table_line_template.format('Build', build_name, 'rejected'))
+                    logger.to_all(message + '\n')
+            final_build_list = found_build_names
+
+            if 'all' in self.test_case_names:
+                self.test_case_names = sorted([name for name in next(os.walk(Environment.trunk_tests_cases_dir))[1] if not name[0] == '.'])
+
+            additional_initial_runs_2 = [self.test_case_names]
+            while len(additional_initial_runs_2[-1]) > 0:
+                additional_initial_runs_1 = []
+                for test_case_name in additional_initial_runs_2[-1]:
+                    test_case = PALMTestCase(self.test_dir, test_case_name, verbose=self.verbose)
+                    test_case_configuration_failed, message = test_case.configure(final_build_list, final_cores_list)
+                    if not test_case_configuration_failed:
+                        if test_case.requires_binary_files:
+                            additional_initial_runs_1.append(test_case.use_binary_files_from)
+                additional_initial_runs_2.append(sorted(set(additional_initial_runs_1)))
+
+            test_case_order = []
+            for i in range(len(additional_initial_runs_2)-1):
+                # low and high refer to priority
+                low = additional_initial_runs_2[i]
+                high = additional_initial_runs_2[i+1]
+                for item in high:
+                    while item in low:
+                        low.remove(item)
+                test_case_order.append(low)
+
+            test_case_order_no_dublicates = []
+            for test_cases in test_case_order:
+                seen = set()
+                seen_add = seen.add
+                test_case_order_no_dublicates.append( [x for x in test_cases if not (x in seen or seen_add(x))] )
+
+            approved_test_case_order = [[]] + list(reversed(test_case_order_no_dublicates))
+            for i, test_cases in enumerate(list(approved_test_case_order)):
+                info = 'Case (dep)' if i < len(approved_test_case_order)-1 else 'Case'
+                for test_case_name in list(test_cases):
+                    sys.stdout.flush()
+                    test_case = PALMTestCase(self.test_dir, test_case_name, verbose=self.verbose)
+                    test_case_configuration_failed, message = test_case.configure(final_build_list, final_cores_list)
+                    if test_case_configuration_failed:
+                        # removing as configuration failed should only apply to added dependencies
+                        approved_test_case_order[i].remove(test_case_name)
+                        logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'rejected'))
+                        logger.to_all(message + '\n')
+                    elif test_case.requires_binary_files:
+                        if test_case.use_binary_files_from not in approved_test_case_order[i-1]:
+                            # removing as dependency is already removed
+                            approved_test_case_order[i].remove(test_case_name)
+                            logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'disabled'))
+                            logger.to_all(colored('[requires dependency \"' + test_case.use_binary_files_from + '\"]', 'red') + '\n')
+                        else:
+                            logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'approved'))
+                            logger.to_all(message + '\n')
+                    else:
+                        logger.to_all(LogFormatter.config_table_line_template.format(info, test_case_name, 'approved'))
+                        logger.to_all(message + '\n')
+
+            final_case_list = []
+            for cases in approved_test_case_order:
+                for case in cases:
+                    if case not in final_case_list:
+                        final_case_list.append(case)
+
+            for build_name in final_build_list:
+                build = PALMBuild(
+                    self.test_dir,
+                    build_name,
+                    verbose=self.verbose,
+                    dry_run=self.dry_run,
+                )
+                configuration_failed, message = build.configure()
+                if not configuration_failed:
+                    self.build_database[build_name] = build
+                else:
+                    logger.to_all(message + '\n')
+
+            for case_name in final_case_list:
+                test_case = PALMTestCase(
+                    self.test_dir,
+                    case_name,
+                    verbose=self.verbose,
+                    dry_run=self.dry_run,
+                )
+                test_case_configuration_failed, message = test_case.configure(final_build_list, final_cores_list)
+                if not test_case_configuration_failed:
+                    self.test_case_queue.append(test_case)
+            logger.to_all(LogFormatter.hline)
+
+            logger.to_all(LogFormatter.intro_table_line_template.format('Test ID:') +
+                          self.test_id + '\n')
+            logger.to_all(LogFormatter.intro_table_line_template.format('Builds:') +
+                          str('\n' + LogFormatter.intro_table_line_template.format('')).join(sorted(self.build_database.keys())) + '\n')
+            logger.to_all(LogFormatter.intro_table_line_template.format('Cases:') +
+                          str('\n' + LogFormatter.intro_table_line_template.format('')).join([c.name for c in self.test_case_queue]) + '\n')
+            logger.to_all(LogFormatter.intro_table_line_template.format('Cores:') +
+                          ' '.join([str(i) for i in final_cores_list]) + '\n')
+
+    def _execute(self, test_case, build_name, cores):
+        job = PALMJob(
+            self.test_dir,
+            test_case,
+            build_name,
+            cores,
+            verbose=self.verbose,
+            dry_run=self.dry_run
+        )
+        if self.force_debug:
+            build_failed_non_debug = True
+            job_failed_non_debug = True
+            build_failed_debug = self.build_database[build_name].build(debug=True)
+            if build_failed_debug:
+                job_failed_debug = True
+            else:
+                job_failed_debug = job.execute(debug=True)
+        elif self.no_auto_debug:
+            build_failed_non_debug = self.build_database[build_name].build(debug=False)
+            if build_failed_non_debug:
+                job_failed_non_debug = True
+            else:
+                job_failed_non_debug = job.execute(debug=False)
+            build_failed_debug = None
+            job_failed_debug = None
+        else:
+            build_failed_non_debug = self.build_database[build_name].build(debug=False)
+            if build_failed_non_debug:
+                job_failed_non_debug = True
+                build_failed_debug = self.build_database[build_name].build(debug=True)
+                if build_failed_debug:
+                    job_failed_debug = False
+                else:
+                    job_failed_debug = job.execute(debug=True)
+            else:
+                job_failed_non_debug = job.execute(debug=False)
+                if job_failed_non_debug:
+                    build_failed_debug = self.build_database[build_name].build(debug=True)
+                    if build_failed_debug:
+                        job_failed_debug = True
+                    else:
+                        job_failed_debug = job.execute(debug=True)
+                else:
+                    build_failed_debug = None
+                    job_failed_debug = None
+        return dict(
+            build_failed_non_debug=build_failed_non_debug,
+            job_failed_non_debug=job_failed_non_debug,
+            build_failed_debug=build_failed_debug,
+            job_failed_debug=job_failed_debug,
+        )
+
+    def execute(self):
+        with Logger(self.test_dir, verbose=self.verbose) as logger:
+            logger.to_all(LogFormatter.hline)
+            logger.to_all(LogFormatter.task_table_line_template.format('Task:', 'Case:', 'Build:', 'Cores:') + 'Status:\n')
+            logger.to_all(LogFormatter.hline)
+            self.test_report = dict()
+            for test_case in self.test_case_queue:
+                logger.to_log(LogFormatter.hline)
+                logger.to_file(LogFormatter.hline)
+                logger.to_file(LogFormatter.hline)
+                status_dict = dict()
+                for build_name in test_case.build_names:
+                    status_dict[build_name] = dict()
+                    for cores in test_case.number_of_cores:
+                        status_dict[build_name][cores] = self._execute(test_case, build_name, cores)
+                self.test_report[test_case.name] = status_dict
+                logger.to_log(LogFormatter.hline)
+                logger.to_file('\n' * 10)
+
+    def report(self):
+        with Logger(self.test_dir, verbose=self.verbose) as logger:
+            logger.to_all(LogFormatter.hline)
+            r = '{:10}' + '    total: ' + '{:<3d}' + \
+                             '    ok: ' + colored('{:<3d}', 'green') + \
+                       '    debugged: ' + colored('{:<3d}', 'yellow') + \
+                         '    failed: ' + colored('{:<3d}', 'red')
+            n_all = 0
+            n_ok = 0
+            n_debugged = 0
+            n_failed = 0
+            for build_name, build in self.build_database.items():
+                status = build.report()
+                b = status['failed_non_debug']
+                bd = status['failed_debug']
+                n_all += 1
+                if not b and b is not None:
+                    n_ok += 1
+                if bd is not None:
+                    n_debugged += 1
+                if b and (bd or bd is None):
+                    n_failed += 1
+            logger.to_all(r.format('Builds:', n_all, n_ok, n_debugged, n_failed) + '\n')
+            total_failed = n_failed
+            total_debugged = n_debugged
+            n_all = 0
+            n_ok = 0
+            n_debugged = 0
+            n_failed = 0
+            # {'case_name': {'build_name': {4: {'build_failed_debug': None,
+            #                                   'build_failed_non_debug': False,
+            #                                   'job_failed_debug': None,
+            #                                   'job_failed_non_debug': False}}},
+            for case_name, case in self.test_report.items():
+                for build_name, build in case.items():
+                    for cores, results in build.items():
+                        n_all += 1
+                        b = results['build_failed_non_debug']
+                        bd = results['build_failed_debug']
+                        j = results['job_failed_non_debug']
+                        jd = results['job_failed_debug']
+                        if not j:
+                            n_ok += 1
+                        if jd is not None:
+                            n_debugged += 1
+                        if j and (jd or jd is None):
+                            n_failed += 1
+            logger.to_all(r.format('Tests:', n_all, n_ok, n_debugged, n_failed) + '\n')
+            total_failed += n_failed
+            total_debugged += n_debugged
+        if self.fail_on_debug:
+            return (total_failed + total_debugged) > 0
+        else:
+            return total_failed > 0
+
+
+class CustomCompleter:
+
+    def __init__(self):
+        pass
+
+    def __call__(self, prefix, parsed_args, **kwargs):
+        return (i for i in self.get_items() if i.startswith(prefix))
+
+    def get_items(self):
+        return []
+
+
+class CaseCompleter(CustomCompleter):
+
+    def get_items(self):
+        case_names = [name for name in next(os.walk(Environment.trunk_tests_cases_dir))[1] if not name[0] == '.']
+        return case_names + ['all']
+
+
+class BuildCompleter(CustomCompleter):
+
+    def get_items(self):
+        build_names = [name for name in next(os.walk(Environment.trunk_tests_builds_dir))[1] if not name[0] == '.']
+        return build_names + ['all']
+
+
+class PALMTestArgumentParser(ArgumentParser):
+
+    def __init__(self):
+        super().__init__(
+            description='This is the PALM tester\n' +
+                        'Developer Support: knoop@muk.uni-hannover.de',
+            formatter_class=RawTextHelpFormatter,
+            add_help=True,
+        )
+        self.add_argument(
+            '--version',
+            action='version',
+            version=version,
+        )
+        self.add_argument(
+            '--verbose',
+            action='store_true',
+            dest='verbose',
+            help='Increase verbosity of terminal output.',
+            required=False,
+        )
+        self.add_argument(
+            '--no-auto-debug',
+            action='store_true',
+            dest='no_auto_debug',
+            help='Disable automatic debugging in case of test failure.',
+            required=False,
+        )
+        self.add_argument(
+            '--force-debug',
+            action='store_true',
+            dest='force_debug',
+            help='Force debugging regardless of test failure (ignores --no-auto-debug).',
+            required=False,
+        )
+        self.add_argument(
+            '--fail-on-debug',
+            action='store_true',
+            dest='fail_on_debug',
+            help='Return a non-zero exit status in case debugging was required.',
+            required=False,
+        )
+        self.add_argument(
+            '--dry-run',
+            action='store_true',
+            dest='dry_run',
+            help='Prepare and process all requested tests without actually building or executing PALM.',
+            required=False,
+        )
+        self.add_argument(
+            '--no-color',
+            action='store_true',
+            dest='no_color',
+            help='Disable colored terminal output.',
+            required=False,
+        )
+        self.add_argument(
+            '--cases',
+            action='store',
+            dest='cases',
+            default=['all'],
+            help='A list of test cases to be executed. (default: %(default)s)',
+            nargs='+',
+            required=False,
+            type=str,
+            metavar='STR',
+        ).completer = CaseCompleter()
+        self.add_argument(
+            '--builds',
+            action='store',
+            dest='builds',
+            default=['all'],
+            help='A list of builds to be executed. (default: %(default)s)',
+            nargs='+',
+            required=False,
+            type=str,
+            metavar='STR',
+        ).completer = BuildCompleter()
+        self.add_argument(
+            '--cores',
+            action='store',
+            dest='cores',
+            default=[i for i in range(1, multiprocessing.cpu_count()+1)],
+            choices=[i for i in range(1, multiprocessing.cpu_count()+1)],
+            help='The number of cores tests are supposed to be executed on. (default: %(default)s)',
+            nargs='+',
+            required=False,
+            type=int,
+            metavar='INT',
+        )
+        self.add_argument(
+            '--test-id',
+            action='store',
+            dest='test_id',
+            default=datetime.now().strftime('%Y-%m-%d_%H:%M:%S.%f'),
+            help='An individual test id. (default: current timestamp)',
+            required=False,
+            type=str,
+            metavar='STR',
+        )
+
+
+if __name__ == '__main__':
+    parser = PALMTestArgumentParser()
+    if has_argcomplete:
+        argcomplete.autocomplete(parser)
+    args = parser.parse_args()
+    palm_test = PALMTest(args)
+    palm_test.prepare()
+    palm_test.execute()
+    failed = palm_test.report()
+    exit(1 if failed else 0)
Index: palm/trunk/TUTORIALS/builds/gfortran_default/build_config.yml
===================================================================
--- palm/trunk/TUTORIALS/builds/gfortran_default/build_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/builds/gfortran_default/build_config.yml	(revision 4091)
@@ -0,0 +1,53 @@
+---
+# this is a palmtest build configuration file
+
+compiler:
+  id: GNU
+  executable: "{{GNU.executable}}"
+  mpi_wrapper: "{{GNU.mpi_wrapper}}"
+  definitions:
+    - "MPI_REAL=MPI_DOUBLE_PRECISION"
+    - "MPI_2REAL=MPI_2DOUBLE_PRECISION"
+    - "__parallel"
+    - "__netcdf"
+    - "__netcdf4"
+    - "__netcdf4_parallel"
+    - "__fftw"
+    - "__rrtmg"
+    - "__gfortran"
+  options:
+    default:
+      - "-cpp"
+      - "-Wall"
+      - "-Werror"
+      - "-Wextra"
+      - "-pedantic"
+      - "-Wno-uninitialized"
+      - "-Wno-maybe-uninitialized"
+      - "-Wno-conversion"
+      - "-Wno-compare-reals"
+      - "-Ofast"
+      - "-ffree-line-length-none"
+    debug:
+      - "-cpp"
+      - "-O0"
+      - "-Wall"
+      - "-Werror"
+      - "-Wextra"
+      - "-pedantic"
+      - "-fcheck=all"
+      - "-fbacktrace"
+      - "-Wno-conversion"
+      - "-Wno-compare-reals"
+      - "-finit-real=nan"
+      - "-ffree-line-length-none"
+  includes:
+    - "{{GNU.include.netcdf}}"
+    - "{{GNU.include.fftw}}"
+    - "{{GNU.include.rrtmg}}"
+
+linker:
+  options:
+    - "{{GNU.lib.netcdf}}"
+    - "{{GNU.lib.fftw}}"
+    - "{{GNU.lib.rrtmg}}"
Index: palm/trunk/TUTORIALS/builds/intel_default/build_config.yml
===================================================================
--- palm/trunk/TUTORIALS/builds/intel_default/build_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/builds/intel_default/build_config.yml	(revision 4091)
@@ -0,0 +1,59 @@
+---
+# this is a palmtest build configuration file
+
+compiler:
+  id: Intel
+  executable: "{{Intel.executable}}"
+  mpi_wrapper: "{{Intel.mpi_wrapper}}"
+  definitions:
+    - "MPI_REAL=MPI_DOUBLE_PRECISION"
+    - "MPI_2REAL=MPI_2DOUBLE_PRECISION"
+    - "__parallel"
+    - "__netcdf"
+    - "__netcdf4"
+    - "__netcdf4_parallel"
+    - "__fftw"
+    - "__rrtmg"
+    - "__intel_compiler"
+  options:
+    default:
+      - "-cpp"
+      - "-O3"
+      - "-fp-model source"
+      - "-fno-alias"
+      - "-fpe0"
+      - "-ftz"
+      - "-no-prec-div"
+      - "-no-prec-sqrt"
+      - "-ip"
+      - "-nbs"
+      - "-diag-disable 8290,8291"
+    debug:
+      - "-cpp"
+      - "-g"
+      - "-debug"
+      - "-traceback"
+      - "-fpe0"
+      - "-C"
+      - "-check nooutput_conversion"
+      - "-w"
+      - "-xT"
+      - "-O0"
+      - "-ftz"
+      - "-fno-alias"
+      - "-no-prec-div"
+      - "-no-prec-sqrt"
+      - "-ip"
+      - "-nbs"
+      - "-convert little_endian"
+      - "-diag-disable 8290,8291"
+  includes:
+    - "{{Intel.include.netcdf}}"
+    - "{{Intel.include.fftw}}"
+    - "{{Intel.include.rrtmg}}"
+
+linker:
+  options:
+    - "{{Intel.lib.netcdf}}"
+    - "{{Intel.lib.fftw}}"
+    - "{{Intel.lib.rrtmg}}"
Index: palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/INPUT/dispersion_eulerian_and_lpm_extended_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/INPUT/dispersion_eulerian_and_lpm_extended_p3d	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/INPUT/dispersion_eulerian_and_lpm_extended_p3d	(revision 4091)
@@ -0,0 +1,149 @@
+&initialization_parameters
+
+!-- grid setup
+    nx = 39,
+    ny = 39,
+    nz = 40,
+
+    dx = 2.0,
+    dy = 2.0,
+    dz = 2.0,
+
+!-- init-action
+    initializing_actions = 'set_constant_profiles',
+
+!-- advection schemes
+    momentum_advec = 'ws-scheme',           ! default advection scheme
+    scalar_advec   = 'ws-scheme',
+
+!-- wind speed setup
+    ug_surface = 1.0,
+    vg_surface = 0.0,
+
+!-- temperature setup
+    neutral = .T.,                          ! strictly neutral flow
+
+!-- tracer setup
+    passive_scalar     = .T.,
+    s_surface          = 0.0008,            !equivalent to 420ppm CO2 as background concentration
+    surface_scalarflux = 0.02,              !kg emission per square meter and second
+    bc_s_b             = 'neumann',
+
+!-- boundary conditions
+    bc_uv_t = 'neumann',                    ! free-slip boundary condition
+    roughness_length = 0.1,                 ! applies to all surfaces locally
+
+!-- special methods
+    dp_external = .T.,                      ! use horizontal pressure gradient
+    dpdxy = -0.0002, 0.0,                   ! for forcing
+
+!-- special setups
+    omega = 0.0,                            ! no Coriolis force
+
+    topography = 'read_from_file',
+    topography_grid_convention = 'cell_center',   ! default
+/
+
+
+&runtime_parameters
+
+!-- simulation time
+    end_time                = 1800.0,
+    termination_time_needed =  900.0,
+
+!-- others
+    create_disturbances = .T.,
+
+!-- global output settings
+    skip_time_data_output =    0.0,
+    dt_data_output        = 1800.0,
+
+    averaging_interval    = 1800.0,
+    dt_averaging_input    =    6.0,
+
+!-- time series / run control
+    dt_run_control        =  6.0,
+    dt_dots               =  6.0,
+
+!-- profiles
+    skip_time_dopr        =    0.0,
+    dt_dopr               = 1800.0,
+    averaging_interval_pr = 1800.0,
+    dt_averaging_input_pr =    6.0,
+
+    do3d_at_begin         = .TRUE.,
+    do2d_at_begin         = .TRUE.,
+
+    dt_do2d_xy            = 1800.0,
+    dt_do2d_xz            = 1800.0,
+
+    data_output_pr = '#u', 'u*2', 'wu', 'w*u*', 'w"u"',
+                     '#v', 'v*2', 'wv', 'w*v*', 'w"v"',
+                     'w*2',
+                     'e', 'e*',
+                     '#km',
+                     '#l',
+                     '#s', 'ws', 'w*s*', 'w"s"', 
+
+!-- output variables
+    data_output = 'u', 'u_av',
+                  'u_xy', 'u_xz', 'u_xz_av',
+                  'v', 'v_av',
+                  'w', 'w_av',
+                  's', 's_av',
+                  'ssws*_xy',
+                  'pc', 'pc_av', 'pc_xy', 'pc_xz', 'pc_xz_av',
+                  
+
+    section_xy = -1,21,22,23,
+    section_xz = -1,17,18,19,
+
+/
+
+&particle_parameters
+
+!-- Boundary conditions for particles
+    bc_par_lr = 'absorb',
+    bc_par_b  = 'reflect',
+    bc_par_t  = 'reflect', 
+
+!-- Define point source
+    psb = 45.0,  
+    pst = 45.0, 
+    pss = 40.0,
+    psn = 40.0,
+    psl = 25.0, 
+    psr = 25.0, 
+
+!-- Time after new particle set is released 
+    dt_prel = 1.0,
+
+!-- Time steps after array are deallocated
+    step_dealloc = 100,
+
+!-- Particles per point (default = 1)
+    particles_per_point = 100,
+
+!-- Maximum time for particles
+    particle_maximum_age = 200.0,
+
+!-- Add random fluctuations for initial particle position
+    random_start_position = .FALSE.,
+
+!-- SGS-velocities for particles 
+    use_sgs_for_particles = .TRUE., 
+
+!-- Particle time series interval
+    dt_dopts = 10.0, 
+
+/
+
+&user_parameters
+    emission_stripe_width_y = 6.0,  !in meters
+    emission_stripe_orig_y  = 12.0, 62.0,  !in meters
+    s_ts_pos_x = 17.0, 61.0, 75.0,
+    s_ts_pos_y = 25.0, 15.0, 41.0,
+           
+/
+
+
Index: palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/INPUT/dispersion_eulerian_and_lpm_extended_topo
===================================================================
--- palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/INPUT/dispersion_eulerian_and_lpm_extended_topo	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/INPUT/dispersion_eulerian_and_lpm_extended_topo	(revision 4091)
@@ -0,0 +1,40 @@
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
Index: palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/MONITORING/dispersion_eulerian_and_lpm_extended_rc
===================================================================
--- palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/MONITORING/dispersion_eulerian_and_lpm_extended_rc	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/MONITORING/dispersion_eulerian_and_lpm_extended_rc	(revision 4091)
@@ -0,0 +1,619 @@
+
+ ******************************    --------------------------------------------
+ * PALM 6.0  Rev: 3986        *    atmosphere - run without 1D - prerun
+ ******************************    --------------------------------------------
+
+ Date:               2019-05-24    Run:       e5_dispersion                     
+ Time:                 09:06:59    Run-No.:   00
+ Run on host:        imuk_defau
+ Number of PEs:               2    Processor grid (x,y): (   1,   2) calculated
+                                   A 1d-decomposition along y is used
+ ------------------------------------------------------------------------------
+
+ Numerical Schemes:
+ -----------------
+
+ --> Use the Moeng_Wyngaard turbulence closure (LES mode).
+ --> Use the boussinesq approximation for the model equations.
+ --> Solve perturbation pressure via FFT using temperton-algorithm routines
+     perturbation pressure is calculated at every Runge-Kutta step
+ --> Momentum advection via Wicker-Skamarock-Scheme 5th order
+ --> Scalar advection via Wicker-Skamarock-Scheme 5th order
+ --> Loop optimization method: cache
+ --> Time differencing scheme: runge-kutta-3       
+ --> No pt-equation solved. Neutral stratification with pt = 300.00 K assumed
+ --> Additional prognostic equation for a passive scalar
+ --> External pressure gradient directly prescribed by the user:
+      -0.20000E-03  0.00000E+00Pa/m in x/y direction
+     starting from dp_level_b =   0.000m.
+
+ ------------------------------------------------------------------------------
+
+
+ Run time and time step information:
+ ----------------------------------
+
+ Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
+ Start time:              0.000 s
+ End time:             1800.000 s
+
+
+ Computational grid and domain size:
+ ----------------------------------
+
+ Grid length:      dx =       2.000 m    dy =       2.000 m
+                dz(1) =       2.000 m
+
+ Domain size:       x =     80.000 m     y =     80.000 m  z(u) =     81.000 m
+
+
+
+ Number of gridpoints (x,y,z):  (0:  39, 0:  39, 0:  41)
+ Subdomain size (x,y,z):        (    40,     20,     42)
+
+
+    Characteristic levels of the geo. wind component ug:
+
+       Height:         0.0     0.0  m
+       ug:            1.00    1.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+    Characteristic levels of the geo. wind component vg:
+
+       Height:         0.0     0.0  m
+       vg:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+
+ Topography information:
+ ----------------------
+
+ Topography: read_from_file                          
+ Topography grid definition convention:
+ cell center (scalar grid points)
+
+
+
+ Boundary conditions:
+ -------------------
+
+                     p                    uv                                  pt
+
+ B. bound.: p(0)     = p(1)   | uv(0)     = -uv(1)                | pt(0)     = pt_surface       
+ T. bound.: p(nzt+1) = 0      | uv(nzt+1) = uv(nzt)               | pt(nzt+1) = pt(nzt) + dpt/dz_
+
+                     e
+
+ B. bound.: e(0)     = e(1)                                                                      
+ T. bound.: e(nzt+1) = e(nzt) = e(nzt-1)                                                         
+
+                     s
+
+ B. bound.: s(0)      = s(1)                                                                     
+ T. bound.: s(nzt+1) = s(nzt) + ds/dz                                                            
+
+ Bottom surface fluxes are used in diffusion terms at k=1
+       Predefined constant scalar flux:  0.200E-01 kg/(m**2 s)
+
+
+    Constant flux layer between bottom surface and first computational u,v-level:
+
+       z_mo =   1.00 m   z0 = 0.1000 m   z0h = 0.10000 m   kappa = 0.40
+       Rif value range:     -20.00 <= rif <= 20.00
+       Predefined surface temperature
+
+
+ Lateral boundaries:
+       left/right:  cyclic              
+       north/south: cyclic              
+
+
+ Initial profiles:
+ ----------------
+
+    Characteristic levels of the initial temperature profile:
+
+       Height:           0.0  m
+       Temperature:   300.00  K
+       Gradient:      ------  K/100m
+       Gridpoint:          0
+
+    Characteristic levels of the initial scalar profile:
+
+       Height:                       0.0       0.0  m
+       Scalar concentration:     0.8E-03   0.8E-03  kg/m**3
+       Gradient:                --------   0.0E+00  (kg/m**3)/100m
+       Gridpoint:                      0         0
+
+
+ List output:
+ -----------
+
+    1D-Profiles:
+       Output every             9999999.90 s
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+
+
+ Data output:
+ -----------
+
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+
+    1D-Profiles:
+       Output format: netCDF 64bit offset                     
+
+
+       Profile: u, u*2, wu, w*u*, w"u", v, v*2, wv, w*v*, w"v", w, w*2,      
+
+              : e, e*, km, l, s, ws, w*s*, w"s",                             
+       Output every              1800.00 s
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+
+    2D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       XY-cross-section  Arrays:  u, ssws*, pc,                                                        
+       Output every              1800.00 s  and at the start
+       Cross sections at k = /-1/21/22/23/
+       scalar-coordinates:   /-1.0/41.0/43.0/45.0/ m
+
+
+       Number of output time levels allowed: unlimited
+
+
+       XZ-cross-section  Arrays:  u, pc,                                                               
+       Output every              1800.00 s  and at the start
+       Cross sections at j = /-1/17/18/19/
+       scalar-coordinates:   /-2.0/34.0/36.0/38.0/ m
+
+
+       Number of output time levels allowed: unlimited
+
+
+    2D-Arrays(time-averaged):
+       Output format: netCDF 64bit offset                     
+
+
+       XZ-cross-section  Arrays:  u, pc,                                                               
+       Output every              1800.00 s  and at the start
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+       Cross sections at j = /-1/17/18/19/
+       scalar-coordinates:   /-2.0/34.0/36.0/38.0/ m
+
+
+       Number of output time levels allowed: unlimited
+
+
+    3D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w, s, pc,                                                      
+       Output every              1800.00 s  and at the start
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    3D-Arrays(time-averaged):
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w, s, pc,                                                      
+       Output every              1800.00 s  and at the start
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    Time series:
+       Output format: netCDF 64bit offset                     
+
+       Output every                 6.00 s
+
+ ------------------------------------------------------------------------------
+
+
+ Physical quantities:
+ -------------------
+
+    Geograph. latitude  :   latitude  = 55.0 degr
+    Geograph. longitude :   longitude =  0.0 degr
+    Angular velocity    :   omega  = 0.000E+00 rad/s
+    Coriolis parameter  :   f      =  0.000000 1/s
+                            f*     =  0.000000 1/s
+
+    Day of the year at model start :   day_init      =     172
+    UTC time at model start        :   time_utc_init = 43200.0 s
+
+    Gravity             :   g      =  9.8 m/s**2
+
+    Reference state used in buoyancy terms: initial_profile
+
+
+ Cloud physics quantities / methods:
+ ----------------------------------
+
+
+
+ LES / Turbulence quantities:
+ ---------------------------
+
+    Mixing length is limited to 1.80 * z
+
+
+ Actions during the simulation:
+ -----------------------------
+
+    Disturbance impulse (u,v) every :   ****** s
+    Disturbance amplitude           :     0.25 m/s
+    Lower disturbance level         :     5.00 m (GP    3)
+    Upper disturbance level         :    25.00 m (GP   13)
+    Disturbances cease as soon as the disturbance energy exceeds 0.010 m**2/s**2
+    Random number generator used    : random-parallel
+
+    Particles:
+    ---------
+
+       Particle advection is active (switched on at t =     0.0 s)
+       Start of new particle generations every     1.0 s
+       Boundary conditions: left/right: absorb          north/south: cyclic         
+                            bottom:     reflect         top:         reflect        
+       Maximum particle age:                     200.0 s
+       Advection stopped at t = 9999999.9 s
+
+       SGS velocity components are used for particle advection
+          minimum timestep for advection: 0.00020
+
+       Number of particles simultaneously released at each point:   100
+
+       Number of particles in total domain:        100
+
+       Output of particle time series in NetCDF format every    10.00 s
+
+       Number of particle groups:  1
+
+       Particle group  1:
+          Particle radius:  0.000E+00m
+          Particles are advected only passively (no inertia)
+
+          Boundaries of particle source: x:    25.0 -     25.0 m
+                                         y:    40.0 -     40.0 m
+                                         z:    45.0 -     45.0 m
+          Particle distances:  dx =      2.0 m  dy =      2.0 m  dz =      2.0 m
+
+
+
+ ##############################################################################
+
+ User-defined variables and actions:
+ -----------------------------------
+
+
+ Parameters for traffic emission:
+
+stripe origin(s) in y-direction (in m):  12.0,  62.0 , stripe width in y-direction (in m):   6.0
+ Parameters for timeseries of scalar concentration:
+
+x-pos of measurement (in m):  17.0,  61.0,  75.0 , y-pos of measurement (in m):  25.0,  15.0,  41.0
+ ------------------------------------------------------------------------------
+
+
+
+Run-control output:
+------------------
+
+RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  0      0 00:00:00.00   1.3200A   1.3650D -0.7720D -0.6273  0.000  0.00   0.000E+00      0.  0.389E+00  0.234E-01  0.203E-01  0.477E-02    9   9  23    8  30  30   21  20  30    0.000    0.000       0
+  0      6 00:00:06.92   1.2100A   1.4890   1.1283   1.1116  0.051  0.00   0.000E+00      0.  0.378E+00  0.370E-01  0.105E-02  0.291E-03    6  30  31   13  30   9   20  19   9    0.000    0.000       0
+  0     11 00:00:13.11   1.2400A   1.4473   1.0563   1.1138  0.054  0.00   0.000E+00      0.  0.375E+00  0.390E-01  0.111E-02  0.285E-03   10   7  13    9  30   9   20  19   9    0.000    0.000       0
+  0     15 00:00:18.14   1.3000A   1.3807   0.9939   1.1071  0.057  0.00   0.000E+00      0.  0.372E+00  0.408E-01  0.115E-02  0.275E-03   10   7  15   12  30   9   20  19   9    0.000    0.000       0
+  0     20 00:00:24.67   1.3300A   1.3579   0.9239   1.0906  0.060  0.00   0.000E+00      0.  0.370E+00  0.429E-01  0.118E-02  0.270E-03    8   6  16   12  30   9   20  19   9    0.000    0.000       0
+  0     24 00:00:30.05   1.3700A   1.3172   0.9042   1.0713  0.061  0.00   0.000E+00      0.  0.368E+00  0.445E-01  0.120E-02  0.274E-03   13  33  17    4  30   9   20  19   9    0.000    0.000       0
+  0     29 00:00:36.97   1.3800A   1.3057   0.8737   1.0429  0.062  0.00   0.000E+00      0.  0.366E+00  0.462E-01  0.116E-02  0.266E-03    7   6  15    9  30   9   20  18   9    0.000    0.000       0
+  0     33 00:00:42.49   1.3900A   1.2988   0.8136   1.0199  0.063  0.00   0.000E+00      0.  0.365E+00  0.474E-01  0.111E-02  0.251E-03    7   6  17    9  30   9   20  17   9    0.000    0.000       0
+  0     37 00:00:48.08   1.4200A   1.2710   0.7732   0.9973  0.065  0.00   0.000E+00      0.  0.363E+00  0.485E-01  0.107E-02  0.240E-03    7   6  20   17  30   9   20  17   9    0.000    0.000       0
+  0     42 00:00:55.22   1.4200A   1.2637   0.7625   0.9704  0.067  0.00   0.000E+00      0.  0.362E+00  0.499E-01  0.101E-02  0.220E-03    9   5  19   17  30   9   20  17   9    0.000    0.000       0
+  0     46 00:01:00.88   1.4100A   1.2745   0.7341   0.9442  0.069  0.00   0.000E+00      0.  0.361E+00  0.511E-01  0.957E-03  0.204E-03    9   5  21   16  30   9   20  17   9    0.000    0.000       0
+  0     50 00:01:06.56   1.4300A   1.2551   0.6922   0.9033  0.070  0.00   0.000E+00      0.  0.360E+00  0.521E-01  0.935E-03  0.192E-03    8   5  22   16  30   9   20  17   9    0.000    0.000       0
+  0     54 00:01:12.28   1.4400A   1.2541   0.6393   0.8456  0.071  0.00   0.000E+00      0.  0.359E+00  0.530E-01  0.892E-03  0.173E-03    8   5  24   17  30   9   20  17   9    0.000    0.000       0
+  0     58 00:01:18.01   1.4300A   1.2585   0.5951   0.7714  0.072  0.00   0.000E+00      0.  0.358E+00  0.537E-01  0.846E-03  0.151E-03    9   4  26   17  30   9   20  17   9    0.000    0.000       0
+  0     63 00:01:25.20   1.4700A   1.2267  -0.6258   0.6649  0.073  0.00   0.000E+00      0.  0.357E+00  0.543E-01  0.816E-03  0.125E-03    9   4  28    5  10  38   20  12   9    0.000    0.000       0
+  0     67 00:01:31.04   1.4400A   1.2536   0.6474  -0.6420  0.074  0.00   0.000E+00      0.  0.357E+00  0.546E-01  0.804E-03  0.105E-03    8   6   2   15  13   1   10  27   8    0.000    0.000       0
+  0     71 00:01:36.79   1.4200A   1.2675   0.6710  -0.7287  0.075  0.00   0.000E+00      0.  0.356E+00  0.548E-01  0.796E-03  0.874E-04    9   6   3   15  13   1   10  28   9    0.000    0.000       0
+  0     75 00:01:42.41   1.3700A   1.3098   0.6852  -0.7498  0.074  0.00   0.000E+00      0.  0.356E+00  0.548E-01  0.794E-03  0.740E-04    8   5   5   16  13   0    9  26   8    0.000    0.000       0
+  0     80 00:01:49.28   1.3800A   1.3045   0.7412  -0.7444  0.074  0.00   0.000E+00      0.  0.355E+00  0.545E-01  0.821E-03  0.663E-04    9   5   7   16  13   1    9  25   8    0.000    0.000       0
+  0     84 00:01:54.78   1.3700A   1.3108  -0.7748  -0.7834  0.073  0.00   0.000E+00      0.  0.354E+00  0.540E-01  0.837E-03  0.642E-04    9  34   9   13  29   6   12  15   5    0.000    0.000       0
+  0     88 00:02:00.25   1.3800A   1.3077  -0.8434  -0.9061  0.072  0.00   0.000E+00      0.  0.354E+00  0.533E-01  0.846E-03  0.646E-04    8   4  10   13  28   7    9  28   9    0.000    0.000       0
+  0     93 00:02:07.11   1.3700A   1.3136  -0.9182  -0.9126  0.070  0.00   0.000E+00      0.  0.353E+00  0.522E-01  0.846E-03  0.684E-04    8   6   1   12  27   8    9  27   9    0.000    0.000       0
+  0     97 00:02:12.42   1.3100A   1.3785  -0.9304   0.8759  0.069  0.00   0.000E+00      0.  0.352E+00  0.513E-01  0.801E-03  0.681E-04    8   6   3   12  26   8   11   9  38    0.000    0.000       0
+  0    102 00:02:18.80   1.2600A   1.4270  -0.8817  -0.8300  0.067  0.00   0.000E+00      0.  0.351E+00  0.502E-01  0.775E-03  0.678E-04   10   7   5   11  25   8   11  17   4    0.000    0.000       0
+  0    107 00:02:25.17   1.2800A   1.4037  -0.7974  -0.9058  0.065  0.00   0.000E+00      0.  0.350E+00  0.492E-01  0.787E-03  0.679E-04   10   6   7   11  25   8   10  17   5    0.000    0.000       0
+  0    111 00:02:30.42   1.3500A   1.3356   0.7718  -0.9060  0.064  0.00   0.000E+00      0.  0.350E+00  0.484E-01  0.818E-03  0.701E-04   10   5   9    9  14   9    9  17   5    0.000    0.000       0
+  0    116 00:02:37.27   1.4000A   1.2840  -0.6888  -0.8775  0.062  0.00   0.000E+00      0.  0.349E+00  0.475E-01  0.832E-03  0.775E-04   10   5  12   14  26   6    8  18   5    0.000    0.000       0
+  0    120 00:02:42.91   1.4200A   1.2716   0.6961  -0.8126  0.062  0.00   0.000E+00      0.  0.348E+00  0.470E-01  0.833E-03  0.837E-04    9  35  14   14  13   5    8  24   2    0.000    0.000       0
+  0    124 00:02:48.60   1.4200A   1.2653   0.7244  -0.8011  0.061  0.00   0.000E+00      0.  0.347E+00  0.467E-01  0.828E-03  0.839E-04    9  35  16   13  14   6    9  17   7    0.000    0.000       0
+  0    128 00:02:54.35   1.4700A   1.2261   0.7089  -0.7734  0.061  0.00   0.000E+00      0.  0.347E+00  0.464E-01  0.831E-03  0.839E-04    9  35  18   13  15   7    8  17   8    0.000    0.000       0
+  0    132 00:03:00.24   1.4800A   1.2187   0.6960  -0.7555  0.061  0.00   0.000E+00      0.  0.346E+00  0.462E-01  0.841E-03  0.849E-04   10  35  20   12  15   7    7  18   8    0.000    0.000       0
+  0    136 00:03:06.15   1.4800A   1.2174  -0.6675   0.7564  0.061  0.00   0.000E+00      0.  0.346E+00  0.461E-01  0.847E-03  0.826E-04   10  35  22   11  26   9   21  20   9    0.000    0.000       0
+  0    140 00:03:12.11   1.5000A   1.2015   0.7294  -0.7639  0.062  0.00   0.000E+00      0.  0.345E+00  0.460E-01  0.861E-03  0.805E-04   10  35  24   10  13   9    7  21   8    0.000    0.000       0
+  0    144 00:03:18.12   1.5100A   1.1907   0.8129  -0.8121  0.063  0.00   0.000E+00      0.  0.345E+00  0.458E-01  0.879E-03  0.783E-04    9   7  37   10  14   9    6  21   8    0.000    0.000       0
+  0    148 00:03:24.13   1.5100A   1.1893   0.8573  -0.8446  0.064  0.00   0.000E+00      0.  0.344E+00  0.457E-01  0.896E-03  0.750E-04    9   7   0    9  14   9    5  21   8    0.000    0.000       0
+  0    152 00:03:30.22   1.5200A   1.1819   0.8575  -0.8516  0.065  0.00   0.000E+00      0.  0.343E+00  0.456E-01  0.910E-03  0.738E-04   12  34  31    9  15   9    4  21   8    0.000    0.000       0
+  0    156 00:03:36.31   1.5100A   1.1919   0.8148  -0.8355  0.066  0.00   0.000E+00      0.  0.343E+00  0.454E-01  0.892E-03  0.712E-04   12  31  34    8  16   9    4  21   8    0.000    0.000       0
+  0    160 00:03:42.32   1.5100A   1.1953  -0.7492  -0.8303  0.066  0.00   0.000E+00      0.  0.342E+00  0.452E-01  0.880E-03  0.698E-04   13  31  36    8  24   8    3  21   8    0.000    0.000       0
+  0    164 00:03:48.40   1.5300A   1.1772  -0.6966  -0.8189  0.066  0.00   0.000E+00      0.  0.341E+00  0.449E-01  0.891E-03  0.742E-04   11   3  32   11  26   9    3  20   8    0.000    0.000       0
+  0    168 00:03:54.51   1.5100A   1.1899   0.7022   0.7744  0.066  0.00   0.000E+00      0.  0.340E+00  0.447E-01  0.870E-03  0.741E-04   11  31  30    8  14   9    7  19  30    0.000    0.000       0
+  0    172 00:04:00.46   1.4500A   1.2416   0.7303   0.7444  0.065  0.00   0.000E+00      0.  0.340E+00  0.445E-01  0.819E-03  0.675E-04   11  31  33    8  15   9    7  18  30    0.000    0.000       0
+  0    176 00:04:06.21   1.4200A   1.2674   0.7296   0.7059  0.065  0.00   0.000E+00      0.  0.339E+00  0.442E-01  0.792E-03  0.609E-04   11  31  35    7  15   9    7  16  30    0.000    0.000       0
+  0    181 00:04:13.35   1.4500A   1.2448   0.6885   0.6773  0.064  0.00   0.000E+00      0.  0.338E+00  0.438E-01  0.814E-03  0.584E-04   11  30  38    7  16   9    8  15  30    0.000    0.000       0
+  0    185 00:04:19.09   1.4400A   1.2503   0.6635   0.6655  0.063  0.00   0.000E+00      0.  0.338E+00  0.436E-01  0.840E-03  0.592E-04   11  30   0    6  15   9    8  11  31    0.000    0.000       0
+  0    189 00:04:24.95   1.4900A   1.2112   0.6471   0.6842  0.062  0.00   0.000E+00      0.  0.337E+00  0.435E-01  0.899E-03  0.627E-04    9  37   2    6  15   9    8  11  31    0.000    0.000       0
+  0    193 00:04:30.91   1.4700A   1.2218  -0.6884   0.6836  0.060  0.00   0.000E+00      0.  0.337E+00  0.434E-01  0.939E-03  0.674E-04    9  36   4   12  25   9    9  11  31    0.000    0.000       0
+  0    197 00:04:36.82   1.4900A   1.2078  -0.6806   0.6524  0.059  0.00   0.000E+00      0.  0.336E+00  0.435E-01  0.980E-03  0.760E-04    9  35   6   11  26   8    9  11  31    0.000    0.000       0
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+  0   1110 00:26:00.55   1.3400A   1.3403   0.4464  -0.5077  0.047  0.00   0.000E+00      0.  0.303E+00  0.272E-01  0.566E-03  0.314E-04   36  32  27    7  15   9   11  27   9    0.000    0.000       0
+  0   1115 00:26:07.26   1.3500A   1.3348   0.4378  -0.4949  0.047  0.00   0.000E+00      0.  0.304E+00  0.271E-01  0.571E-03  0.324E-04   36  32  31    7  15   9   12  20   8    0.000    0.000       0
+  0   1119 00:26:12.66   1.3500A   1.3343   0.4634  -0.5031  0.047  0.00   0.000E+00      0.  0.304E+00  0.269E-01  0.580E-03  0.335E-04   38  34   0   15  14   9   11  20   8    0.000    0.000       0
+  0   1123 00:26:18.06   1.3500A   1.3353   0.4603  -0.5157  0.047  0.00   0.000E+00      0.  0.304E+00  0.268E-01  0.581E-03  0.331E-04   39  33   2   15  15   9   11  20   8    0.000    0.000       0
+  0   1128 00:26:24.81   1.3500A   1.3375  -0.4647  -0.5178  0.048  0.00   0.000E+00      0.  0.304E+00  0.266E-01  0.576E-03  0.305E-04   39  33   7   20  18   5   10  21   8    0.000    0.000       0
+  0   1132 00:26:30.19   1.3400A   1.3401  -0.5051  -0.5115  0.048  0.00   0.000E+00      0.  0.304E+00  0.265E-01  0.570E-03  0.295E-04   39  33  10   20  17   6   10  21   7    0.000    0.000       0
+  0   1137 00:26:36.89   1.3400A   1.3424  -0.5877  -0.5214  0.048  0.00   0.000E+00      0.  0.304E+00  0.263E-01  0.569E-03  0.292E-04   39  33  15   20  17   8    9  21   7    0.000    0.000       0
+  0   1141 00:26:42.25   1.3400A   1.3456  -0.5444  -0.5017  0.048  0.00   0.000E+00      0.  0.304E+00  0.263E-01  0.570E-03  0.302E-04   39  33  18   20  16   8    8  21   7    0.000    0.000       0
+  0   1146 00:26:48.95   1.3400A   1.3477  -0.5116  -0.4645  0.048  0.00   0.000E+00      0.  0.304E+00  0.262E-01  0.576E-03  0.338E-04   39  33  23   20  16   9    8  21   7    0.000    0.000       0
+  0   1150 00:26:54.28   1.3300A   1.3510  -0.4994  -0.4812  0.048  0.00   0.000E+00      0.  0.304E+00  0.261E-01  0.573E-03  0.348E-04   39  33  26   19  16   9   17  19   9    0.000    0.000       0
+  0   1155 00:27:00.93   1.3300A   1.3526  -0.4459  -0.5341  0.048  0.00   0.000E+00      0.  0.304E+00  0.262E-01  0.571E-03  0.343E-04   39  33  30   18  17   9   17  20   9    0.000    0.000       0
+  0   1159 00:27:06.25   1.3300A   1.3542  -0.4040  -0.5865  0.049  0.00   0.000E+00      0.  0.304E+00  0.262E-01  0.568E-03  0.339E-04   39  33  34   18  16   9   16  20   9    0.000    0.000       0
+  0   1164 00:27:12.90   1.3300A   1.3550  -0.3740  -0.5820  0.049  0.00   0.000E+00      0.  0.304E+00  0.262E-01  0.565E-03  0.347E-04   39  33  38    5  38  34   15  20   9    0.000    0.000       0
+  0   1168 00:27:18.22   1.3300A   1.3544  -0.3646  -0.5478  0.049  0.00   0.000E+00      0.  0.304E+00  0.263E-01  0.562E-03  0.351E-04   39  33   2    5  38  35   14  21   9    0.000    0.000       0
+  0   1173 00:27:24.87   1.3300A   1.3549  -0.4069  -0.5289  0.049  0.00   0.000E+00      0.  0.304E+00  0.263E-01  0.561E-03  0.358E-04   39  33   6   13  28   6   13  20   8    0.000    0.000       0
+  0   1177 00:27:30.19   1.3300A   1.3538   0.4410  -0.5205  0.049  0.00   0.000E+00      0.  0.304E+00  0.263E-01  0.559E-03  0.355E-04   39  33   9   10  14   9   15  23   9    0.000    0.000       0
+  0   1182 00:27:36.84   1.3300A   1.3537   0.5104  -0.4994  0.050  0.00   0.000E+00      0.  0.304E+00  0.263E-01  0.553E-03  0.319E-04   39  33  14    9  14   9   15  23   9    0.000    0.000       0
+  0   1186 00:27:42.16   1.3300A   1.3537   0.5515  -0.4892  0.050  0.00   0.000E+00      0.  0.304E+00  0.263E-01  0.547E-03  0.282E-04   39  33  17    8  14   9   17  16   9    0.000    0.000       0
+  0   1191 00:27:48.81   1.3300A   1.3523   0.5723  -0.4610  0.050  0.00   0.000E+00      0.  0.304E+00  0.262E-01  0.542E-03  0.269E-04   39  33  21    8  15   9   11  21   8    0.000    0.000       0
+  0   1195 00:27:54.13   1.3300A   1.3523   0.5681  -0.4753  0.050  0.00   0.000E+00      0.  0.304E+00  0.261E-01  0.537E-03  0.270E-04   39  33  25    7  15   9   10  24   8    0.000    0.000       0
+  0   1200 00:28:00.78   1.3300A   1.3520   0.5670  -0.4614  0.050  0.00   0.000E+00      0.  0.304E+00  0.259E-01  0.530E-03  0.278E-04   39  33  29    8  15   9    9  24   8    0.000    0.000       0
+  0   1204 00:28:06.10   1.3300A   1.3506   0.5652  -0.4639  0.049  0.00   0.000E+00      0.  0.304E+00  0.258E-01  0.526E-03  0.294E-04   39  33  32    8  15   9    9  23   8    0.000    0.000       0
+  0   1209 00:28:12.75   1.3300A   1.3492   0.5592  -0.4491  0.048  0.00   0.000E+00      0.  0.304E+00  0.257E-01  0.524E-03  0.316E-04   39  33  36    8  16   9    7  20   6    0.000    0.000       0
+  0   1213 00:28:18.07   1.3300A   1.3506   0.5412  -0.4506  0.047  0.00   0.000E+00      0.  0.304E+00  0.257E-01  0.525E-03  0.337E-04   39  33   0    7  17   9    9  19   5    0.000    0.000       0
+  0   1218 00:28:24.72   1.3300A   1.3509   0.5064  -0.4481  0.047  0.00   0.000E+00      0.  0.304E+00  0.257E-01  0.525E-03  0.344E-04   39  33   4    8  17   9    8  20   6    0.000    0.000       0
+  0   1222 00:28:30.04   1.3300A   1.3505   0.4727  -0.4398  0.046  0.00   0.000E+00      0.  0.304E+00  0.257E-01  0.528E-03  0.352E-04   39  33   7   10  15   9    6  20   5    0.000    0.000       0
+  0   1227 00:28:36.69   1.3300A   1.3501   0.4626  -0.4334  0.046  0.00   0.000E+00      0.  0.304E+00  0.257E-01  0.530E-03  0.370E-04   39  33  11   11  15   9    6  20   5    0.000    0.000       0
+  0   1231 00:28:42.01   1.3300A   1.3505  -0.4791   0.4327  0.046  0.00   0.000E+00      0.  0.304E+00  0.258E-01  0.530E-03  0.373E-04   39  33  15   23  20   6   20  21   9    0.000    0.000       0
+  0   1236 00:28:48.66   1.3300A   1.3548  -0.5030   0.4165  0.046  0.00   0.000E+00      0.  0.304E+00  0.258E-01  0.532E-03  0.380E-04   40  28  14   23  19   8   20  20   9    0.000    0.000       0
+  0   1241 00:28:55.29   1.3200A   1.3593   0.5324   0.4218  0.047  0.00   0.000E+00      0.  0.305E+00  0.259E-01  0.531E-03  0.383E-04   40  28  18    9  15   9   20  18   9    0.000    0.000       0
+  0   1245 00:29:00.57   1.3200A   1.3633   0.5390   0.4500  0.047  0.00   0.000E+00      0.  0.305E+00  0.260E-01  0.533E-03  0.385E-04   40  28  22    9  15   9   20  18   9    0.000    0.000       0
+  0   1250 00:29:07.17   1.3200A   1.3669   0.5372   0.4260  0.048  0.00   0.000E+00      0.  0.305E+00  0.262E-01  0.538E-03  0.387E-04   40  28  26    9  16   9   20  18   9    0.000    0.000       0
+  0   1254 00:29:12.44   1.3100A   1.3696   0.5175   0.4413  0.048  0.00   0.000E+00      0.  0.305E+00  0.264E-01  0.539E-03  0.388E-04   40  28  29    9  17   9   20  26   9    0.000    0.000       0
+  0   1259 00:29:18.99   1.3100A   1.3718   0.4937   0.4903  0.049  0.00   0.000E+00      0.  0.305E+00  0.265E-01  0.544E-03  0.375E-04   40  28  33    1  30   8   20  26   9    0.000    0.000       0
+  0   1263 00:29:24.23   1.3100A   1.3727   0.4834   0.4844  0.049  0.00   0.000E+00      0.  0.305E+00  0.267E-01  0.542E-03  0.350E-04   40  28  36    1  31   8   20  27   9    0.000    0.000       0
+  0   1268 00:29:30.78   1.3100A   1.3733   0.4580  -0.4357  0.050  0.00   0.000E+00      0.  0.305E+00  0.268E-01  0.540E-03  0.323E-04   40  28   0    1  32   8    4  29   9    0.000    0.000       0
+  0   1272 00:29:36.02   1.3100A   1.3721  -0.4464  -0.4623  0.050  0.00   0.000E+00      0.  0.305E+00  0.269E-01  0.541E-03  0.312E-04   41  28   4   11  25   9    4  29   9    0.000    0.000       0
+  0   1277 00:29:42.57   1.3100A   1.3716  -0.4717  -0.4663  0.050  0.00   0.000E+00      0.  0.305E+00  0.270E-01  0.542E-03  0.310E-04   41  28   8   10  25   9   10  13   3    0.000    0.000       0
+  0   1282 00:29:49.12   1.3100A   1.3706  -0.4893  -0.4734  0.051  0.00   0.000E+00      0.  0.305E+00  0.270E-01  0.543E-03  0.302E-04   41  28  12   10  25   9   10  12   2    0.000    0.000       0
+  0   1286 00:29:54.36   1.3100A   1.3702  -0.4948  -0.4869  0.050  0.00   0.000E+00      0.  0.305E+00  0.270E-01  0.542E-03  0.277E-04   41  28  15    9  25   9   10  12   3    0.000    0.000       0
+  0   1291 00:30:00.94   1.3200A   1.3686  -0.5021  -0.4951  0.050  0.00   0.000E+00      0.  0.305E+00  0.269E-01  0.545E-03  0.248E-04   41  28  19   10  25   8    9  12   3    0.000    0.000       0
Index: palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/USER_CODE/user_module.f90
===================================================================
--- palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/USER_CODE/user_module.f90	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/USER_CODE/user_module.f90	(revision 4091)
@@ -0,0 +1,1380 @@
+!> @file user_module.f90
+!------------------------------------------------------------------------------!
+! This file is part of the PALM model system.
+!
+! PALM is free software: you can redistribute it and/or modify it under the
+! terms of the GNU General Public License as published by the Free Software
+! Foundation, either version 3 of the License, or (at your option) any later
+! version.
+!
+! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
+! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+! A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+!
+! You should have received a copy of the GNU General Public License along with
+! PALM. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 1997-2019 Leibniz Universitaet Hannover
+!------------------------------------------------------------------------------!
+!
+! Current revisions:
+! -----------------
+! 
+! 
+! Former revisions:
+! -----------------
+! $Id: user_module.f90 3986 2019-05-20 14:08:14Z Giersch $
+! Redundant integration of control parameters in user_rrd_global removed
+! 
+! 3911 2019-04-17 12:26:19Z knoop
+! Bugfix: added before_prognostic_equations case in user_actions
+! 
+! 3768 2019-02-27 14:35:58Z raasch
+! variables commented + statements added to avoid compiler warnings about unused variables
+!
+! 3767 2019-02-27 08:18:02Z raasch
+! unused variable for file index removed from rrd-subroutines parameter list
+! 
+! 3747 2019-02-16 15:15:23Z gronemeier
+! Add routine user_init_arrays
+! 
+! 3703 2019-01-29 16:43:53Z knoop
+! An example for a user defined global variable has been added (Giersch)
+! 
+! 2718 2018-01-02 08:49:38Z suehring
+! Corrected "Former revisions" section
+! 
+! 2696 2017-12-14 17:12:51Z kanani
+! Change in file header (GPL part)
+!
+! 2101 2017-01-05 16:42:31Z suehring
+!
+! 2000 2016-08-20 18:09:15Z knoop
+! Forced header and separation lines into 80 columns
+! 
+! 1873 2016-04-18 14:50:06Z maronga
+! Module renamed (removed _mod)
+! 
+! 
+! 1850 2016-04-08 13:29:27Z maronga
+! Module renamed
+! 
+! 
+! 1682 2015-10-07 23:56:08Z knoop
+! Code annotations made doxygen readable 
+!
+! 1320 2014-03-20 08:40:49Z raasch
+! kind-parameters added to all INTEGER and REAL declaration statements, 
+! kinds are defined in new module kinds, 
+! old module precision_kind is removed,
+! revision history before 2012 removed,
+! comment fields (!:) to be used for variable explanations added to
+! all variable declaration statements 
+!
+! 1036 2012-10-22 13:43:42Z raasch
+! code put under GPL (PALM 3.9)
+!
+! Revision 1.1  1998/03/24 15:29:04  raasch
+! Initial revision
+!
+!
+! Description:
+! ------------
+!> Declaration of user-defined variables. This module may only be used
+!> in the user-defined routines (contained in user_interface.f90).
+!------------------------------------------------------------------------------!
+ MODULE user
+
+
+    USE arrays_3d
+
+    USE control_parameters
+
+    USE cpulog
+
+    USE indices
+
+    USE kinds
+
+    USE pegrid
+
+    USE statistics
+
+    USE surface_mod
+
+    IMPLICIT NONE
+
+    INTEGER(iwp) ::  dots_num_palm   !< 
+    INTEGER(iwp) ::  dots_num_user = 0  !< 
+    INTEGER(iwp) ::  user_idummy     !< 
+    
+    LOGICAL ::  user_module_enabled = .FALSE.   !< 
+    
+    REAL(wp) ::  user_rdummy   !< 
+
+!
+!-- Sample for user-defined output
+!    REAL(wp) :: global_parameter !< user defined global parameter 
+!
+!    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE ::  u2       !< user defined array
+!    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE ::  u2_av    !< user defined array
+!    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE ::  ustvst   !< user defined array
+
+!-- User-defined parameters
+    INTEGER(iwp), DIMENSION(1:3) ::  s_ts_pos_x_ind = 0
+    INTEGER(iwp), DIMENSION(1:3) ::  s_ts_pos_y_ind = 0
+    INTEGER(iwp)                 ::  size_of_pos_array
+
+    REAL(wp)                 ::  emission_stripe_width_y = 0.0_wp
+    REAL(wp), DIMENSION(1:2) ::  emission_stripe_orig_y = 0.0_wp
+    REAL(wp), DIMENSION(1:3) ::  s_ts_pos_x = 0.0
+    REAL(wp), DIMENSION(1:3) ::  s_ts_pos_y = 0.0
+
+    SAVE
+
+    PRIVATE
+
+!
+!- Public functions
+    PUBLIC &
+       user_parin, &
+       user_check_parameters, &
+       user_check_data_output_ts, &
+       user_check_data_output_pr, &
+       user_check_data_output, &
+       user_define_netcdf_grid, &
+       user_init, &
+       user_init_arrays, &
+       user_header, &
+       user_actions, &
+       user_3d_data_averaging, &
+       user_data_output_2d, &
+       user_data_output_3d, &
+       user_statistics, &
+       user_rrd_global, &
+       user_rrd_local, &
+       user_wrd_global, &
+       user_wrd_local, &
+       user_last_actions
+
+!
+!- Public parameters, constants and initial values
+   PUBLIC &
+      user_module_enabled
+
+    INTERFACE user_parin
+       MODULE PROCEDURE user_parin
+    END INTERFACE user_parin
+
+    INTERFACE user_check_parameters
+       MODULE PROCEDURE user_check_parameters
+    END INTERFACE user_check_parameters
+
+    INTERFACE user_check_data_output_ts
+       MODULE PROCEDURE user_check_data_output_ts
+    END INTERFACE user_check_data_output_ts
+
+    INTERFACE user_check_data_output_pr
+       MODULE PROCEDURE user_check_data_output_pr
+    END INTERFACE user_check_data_output_pr
+
+    INTERFACE user_check_data_output
+       MODULE PROCEDURE user_check_data_output
+    END INTERFACE user_check_data_output
+
+    INTERFACE user_define_netcdf_grid
+       MODULE PROCEDURE user_define_netcdf_grid
+    END INTERFACE user_define_netcdf_grid
+
+    INTERFACE user_init
+       MODULE PROCEDURE user_init
+    END INTERFACE user_init
+
+    INTERFACE user_init_arrays
+       MODULE PROCEDURE user_init_arrays
+    END INTERFACE user_init_arrays
+
+    INTERFACE user_header
+       MODULE PROCEDURE user_header
+    END INTERFACE user_header
+
+    INTERFACE user_actions
+       MODULE PROCEDURE user_actions
+       MODULE PROCEDURE user_actions_ij
+    END INTERFACE user_actions
+
+    INTERFACE user_3d_data_averaging
+       MODULE PROCEDURE user_3d_data_averaging
+    END INTERFACE user_3d_data_averaging
+
+    INTERFACE user_data_output_2d
+       MODULE PROCEDURE user_data_output_2d
+    END INTERFACE user_data_output_2d
+
+    INTERFACE user_data_output_3d
+       MODULE PROCEDURE user_data_output_3d
+    END INTERFACE user_data_output_3d
+
+    INTERFACE user_statistics
+       MODULE PROCEDURE user_statistics
+    END INTERFACE user_statistics
+
+    INTERFACE user_rrd_global
+       MODULE PROCEDURE user_rrd_global
+    END INTERFACE user_rrd_global
+
+    INTERFACE user_rrd_local
+       MODULE PROCEDURE user_rrd_local
+    END INTERFACE user_rrd_local
+
+    INTERFACE user_wrd_global
+       MODULE PROCEDURE user_wrd_global
+    END INTERFACE user_wrd_global
+
+    INTERFACE user_wrd_local
+       MODULE PROCEDURE user_wrd_local
+    END INTERFACE user_wrd_local
+
+    INTERFACE user_last_actions
+       MODULE PROCEDURE user_last_actions
+    END INTERFACE user_last_actions
+
+
+ CONTAINS
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Parin for &user_parameters for user module
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_parin
+
+
+    CHARACTER (LEN=80) ::  line   !< 
+
+    INTEGER(iwp) ::  i                 !< 
+    INTEGER(iwp) ::  j                 !< 
+
+
+    NAMELIST /user_parameters/  &
+       user_module_enabled, &
+       data_output_pr_user, &
+       data_output_user, &
+       region, &
+       data_output_masks_user, &
+       emission_stripe_orig_y, emission_stripe_width_y,       &
+       s_ts_pos_x, s_ts_pos_y
+
+!
+!-- Next statement is to avoid compiler warnings about unused variables. Please remove in case
+!-- that you are using them.
+    IF ( dots_num_palm == 0  .OR.  dots_num_user == 0  .OR.  user_idummy == 0  .OR.                &
+         user_rdummy == 0.0_wp )  CONTINUE
+
+!
+!-- Set revision number of this default interface version. It will be checked within
+!-- the main program (palm). Please change the revision number in case that the
+!-- current revision does not match with previous revisions (e.g. if routines
+!-- have been added/deleted or if parameter lists in subroutines have been changed).
+    user_interface_current_revision = 'r3703'
+
+!
+!-- Position the namelist-file at the beginning (it was already opened in
+!-- parin), search for user-defined namelist-group ("userpar", but any other
+!-- name can be choosed) and position the file at this line.
+    REWIND ( 11 )
+
+    line = ' '
+    DO WHILE ( INDEX( line, '&user_parameters' ) == 0 )
+       READ ( 11, '(A)', END=12 )  line
+    ENDDO
+    BACKSPACE ( 11 )
+
+!-- Set default module switch to true
+    user_module_enabled = .TRUE.
+
+!-- Read user-defined namelist
+    READ ( 11, user_parameters, ERR = 10 )
+
+    GOTO 12
+
+10  BACKSPACE( 11 )
+    READ( 11 , '(A)') line
+    CALL parin_fail_message( 'user_parameters', line )
+
+12  CONTINUE
+
+!
+!-- Determine the number of user-defined profiles and append them to the
+!-- standard data output (data_output_pr)
+    IF ( user_module_enabled )  THEN
+       IF ( data_output_pr_user(1) /= ' ' )  THEN
+          i = 1
+          DO WHILE ( data_output_pr(i) /= ' '  .AND.  i <= 100 )
+             i = i + 1
+          ENDDO
+          j = 1
+          DO WHILE ( data_output_pr_user(j) /= ' '  .AND.  j <= 100 )
+             data_output_pr(i) = data_output_pr_user(j)
+             max_pr_user_tmp   = max_pr_user_tmp + 1
+             i = i + 1
+             j = j + 1
+          ENDDO
+       ENDIF
+    ENDIF
+
+
+ END SUBROUTINE user_parin
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Check &userpar control parameters and deduce further quantities.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_parameters
+
+
+!-- Here the user may add code to check the validity of further &userpar 
+!-- control parameters or deduce further quantities.
+
+
+ END SUBROUTINE user_check_parameters
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set module-specific timeseries units and labels
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_data_output_ts( dots_max, dots_num, dots_label, dots_unit )
+
+
+    INTEGER(iwp)  ::  i
+ 
+    INTEGER(iwp),      INTENT(IN)     ::  dots_max
+    INTEGER(iwp),      INTENT(INOUT)  ::  dots_num
+    
+    CHARACTER(LEN=7)   ::  i_char = ''
+    CHARACTER (LEN=*), DIMENSION(dots_max), INTENT(INOUT)  :: dots_label
+    CHARACTER (LEN=*), DIMENSION(dots_max), INTENT(INOUT)  :: dots_unit
+
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( dots_num == 0  .OR.  dots_label(1)(1:1) == ' '  .OR.  dots_unit(1)(1:1) == ' ' )  CONTINUE
+
+!
+!-- Sample for user-defined time series
+!-- For each time series quantity you have to give a label and a unit,
+!-- which will be used for the NetCDF file. They must not contain more than
+!-- seven characters. The value of dots_num has to be increased by the
+!-- number of new time series quantities. Its old value has to be store in
+!-- dots_num_palm. See routine user_statistics on how to output calculate
+!-- and output these quantities.
+
+!    dots_num_palm = dots_num
+
+!    dots_num = dots_num + 1
+!    dots_num_user = dots_num_user + 1
+!    dots_label(dots_num) = 'abs_umx'
+!    dots_unit(dots_num)  = 'm/s'
+
+!    dots_num = dots_num + 1
+!    dots_num_user = dots_num_user + 1
+!    dots_label(dots_num) = 'abs_vmx'
+!    dots_unit(dots_num)  = 'm/s'
+
+!-- Additional timeseries output
+    size_of_pos_array = SIZE(s_ts_pos_x)
+    
+    DO  i = 1, size_of_pos_array
+       WRITE (i_char,'(''_'',I3.3)')  i
+       dots_label(dots_num+i) = 's_pos' // TRIM(i_char)
+       dots_unit(dots_num+i)  = 'kg'
+    ENDDO
+
+    dots_num_palm = dots_num
+    dots_num = dots_num + size_of_pos_array
+
+
+ END SUBROUTINE user_check_data_output_ts
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set the unit of user defined profile output quantities. For those variables
+!> not recognized by the user, the parameter unit is set to "illegal", which
+!> tells the calling routine that the output variable is not defined and leads
+!> to a program abort.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_data_output_pr( variable, var_count, unit, dopr_unit )
+
+
+    USE profil_parameter
+
+
+    CHARACTER (LEN=*) ::  unit     !< 
+    CHARACTER (LEN=*) ::  variable !< 
+    CHARACTER (LEN=*) ::  dopr_unit !< local value of dopr_unit
+
+!    INTEGER(iwp) ::  user_pr_index !<
+    INTEGER(iwp) ::  var_count     !<
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( unit(1:1) == ' '  .OR.  dopr_unit(1:1) == ' '  .OR.  var_count == 0 )  CONTINUE
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary.
+!--    Add additional CASE statements depending on the number of quantities
+!--    for which profiles are to be calculated. The respective calculations
+!--    to be performed have to be added in routine user_statistics.
+!--    The quantities are (internally) identified by a user-profile-number
+!--    (see variable "user_pr_index" below). The first user-profile must be assigned
+!--    the number "pr_palm+1", the second one "pr_palm+2", etc. The respective
+!--    user-profile-numbers have also to be used in routine user_statistics!
+!       CASE ( 'u*v*' )                      ! quantity string as given in
+!                                            ! data_output_pr_user
+!          user_pr_index = pr_palm + 1
+!          dopr_index(var_count)  = user_pr_index    ! quantities' user-profile-number
+!          dopr_unit = 'm2/s2'  ! quantity unit
+!          unit = dopr_unit
+!          hom(:,2,user_pr_index,:)       = SPREAD( zu, 2, statistic_regions+1 )
+!                                            ! grid on which the quantity is
+!                                            ! defined (use zu or zw)
+
+       CASE DEFAULT
+          unit = 'illegal'
+
+    END SELECT
+
+
+ END SUBROUTINE user_check_data_output_pr
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set the unit of user defined output quantities. For those variables
+!> not recognized by the user, the parameter unit is set to "illegal", which
+!> tells the calling routine that the output variable is not defined and leads
+!> to a program abort.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_data_output( variable, unit )
+
+
+    CHARACTER (LEN=*) ::  unit     !< 
+    CHARACTER (LEN=*) ::  variable !<
+
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary
+!       CASE ( 'u2' )
+!          unit = 'm2/s2'
+!
+!       CASE ( 'u*v*' )
+!          unit = 'm2/s2'
+!
+       CASE DEFAULT
+          unit = 'illegal'
+
+    END SELECT
+
+
+ END SUBROUTINE user_check_data_output
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Initialize user-defined arrays
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_init_arrays
+
+
+!    INTEGER(iwp) :: i       !< loop index
+!    INTEGER(iwp) :: j       !< loop index
+!    INTEGER(iwp) :: region  !< index for loop over statistic regions
+
+!
+!-- Allocate user-defined arrays and set flags for statistic regions.
+!-- Sample for user-defined output
+!    ALLOCATE( u2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!    ALLOCATE( ustvst(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+
+!
+!-- Example for defining a statistic region:
+!     IF ( statistic_regions >= 1 )  THEN
+!        region = 1
+! 
+!        rmask(:,:,region) = 0.0_wp
+!        DO  i = nxl, nxr
+!           IF ( i >= INT( 0.25 * nx ) .AND. i <= INT( 0.75 * nx ) )  THEN
+!              DO  j = nys, nyn
+!                 IF ( i >= INT( 0.25 * ny ) .AND. i <= INT( 0.75 * ny ) )  THEN
+!                    rmask(j,i,region) = 1.0_wp
+!                 ENDIF
+!              ENDDO
+!           ENDIF
+!        ENDDO
+! 
+!     ENDIF
+
+ END SUBROUTINE user_init_arrays
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Execution of user-defined initializing actions
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_init
+
+ 
+    USE grid_variables
+
+!    CHARACTER (LEN=20) :: field_char   !<
+
+    INTEGER(iwp), DIMENSION(1:2) ::  eso_ind      !< index values of emission_stripe_orig
+    INTEGER(iwp)                 ::  esw_ind      !< index value of emission_stripe_width
+    INTEGER(iwp)                 ::  i, j, m      !< running index
+
+!
+!-- Here the user-defined initializing actions follow:
+!-- Sample for user-defined output
+!    ustvst = 0.0_wp
+
+!
+!-- Calculate indices for locations of additional timeseries output, used in
+!-- user_statistics
+    s_ts_pos_x_ind = NINT( s_ts_pos_x * ddx )
+    s_ts_pos_y_ind = NINT( s_ts_pos_y * ddy )
+    
+!
+!-- Passive scalar shall only be released from a line source of width 
+!-- emission_stripe_width, stripe origin is precribed by parameter 
+!-- emission_stripe_orig under &userpar
+    eso_ind = NINT( emission_stripe_orig_y * ddy )
+    esw_ind = NINT( emission_stripe_width_y * ddy )
+    WRITE(9,*) 'd', esw_ind
+    FLUSH(9)
+
+    DO i = nxl, nxr
+       DO  j = nys, nyn
+          DO m = surf_def_h(0)%start_index(j,i), surf_def_h(0)%end_index(j,i)
+             IF ( ( eso_ind(1) <= j  .AND.  j < (eso_ind(1)+esw_ind) )  .OR.  ( eso_ind(2) <= j  .AND.  j < (eso_ind(2)+esw_ind) ) )  THEN
+                surf_def_h(0)%ssws(m) = surface_scalarflux
+             ELSE
+                surf_def_h(0)%ssws(m) = 0.0_wp
+            ENDIF
+          ENDDO
+       ENDDO
+    ENDDO   
+    
+
+ END SUBROUTINE user_init
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set the grids on which user-defined output quantities are defined.
+!> Allowed values for grid_x are "x" and "xu", for grid_y "y" and "yv", and
+!> for grid_z "zu" and "zw".
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_define_netcdf_grid( variable, found, grid_x, grid_y, grid_z )
+
+
+    CHARACTER (LEN=*) ::  grid_x     !<
+    CHARACTER (LEN=*) ::  grid_y     !<
+    CHARACTER (LEN=*) ::  grid_z     !<
+    CHARACTER (LEN=*) ::  variable   !<
+
+    LOGICAL ::  found   !<
+
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary
+!       CASE ( 'u2', 'u2_xy', 'u2_xz', 'u2_yz' )
+!          found  = .TRUE.
+!          grid_x = 'xu'
+!          grid_y = 'y'
+!          grid_z = 'zu'
+
+!       CASE ( 'u*v*', 'u*v*_xy', 'u*v*_xz', 'u*v*_yz' )
+!          found  = .TRUE.
+!          grid_x = 'x'
+!          grid_y = 'y'
+!          grid_z = 'zu'
+
+       CASE DEFAULT
+          found  = .FALSE.
+          grid_x = 'none'
+          grid_y = 'none'
+          grid_z = 'none'
+
+    END SELECT
+
+
+ END SUBROUTINE user_define_netcdf_grid
+
+
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Print a header with user-defined information.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_header( io )
+
+
+    INTEGER(iwp) ::  i    !< 
+    INTEGER(iwp) ::  io   !< 
+
+!
+!-- If no user-defined variables are read from the namelist-file, no
+!-- information will be printed.
+    IF ( .NOT. user_module_enabled )  THEN
+       WRITE ( io, 100 )
+       RETURN
+    ENDIF
+
+!
+!-- Printing the information.
+    WRITE ( io, 110 )
+
+!
+!-- Parameters for traffic emission
+    WRITE ( io, 120 )
+    WRITE ( io, 121 ) emission_stripe_orig_y, emission_stripe_width_y
+    
+!
+!-- Parameters for timeseries of scalar concentration
+    WRITE ( io, 122 )
+    WRITE ( io, 123 ) s_ts_pos_x, s_ts_pos_y
+    
+    
+    IF ( statistic_regions /= 0 )  THEN
+       WRITE ( io, 200 )
+       DO  i = 0, statistic_regions
+          WRITE ( io, 201 )  i, region(i)
+       ENDDO
+    ENDIF
+
+!
+!-- Format-descriptors
+100 FORMAT (//' *** no user-defined variables found'/)
+110 FORMAT (//1X,78('#')                                                       &
+            //' User-defined variables and actions:'/                          &
+              ' -----------------------------------'//)
+120 FORMAT (' Parameters for traffic emission:' /)
+121 FORMAT ('stripe origin(s) in y-direction (in m): ',F5.1,', ',F5.1,' , stripe width in y-direction (in m): ',F5.1)
+122 FORMAT (' Parameters for timeseries of scalar concentration:' /)
+123 FORMAT ('x-pos of measurement (in m): ',F5.1,', ',F5.1,', ',F5.1,' , y-pos of measurement (in m): ',F5.1,', ',F5.1,', ',F5.1)
+200 FORMAT (' Output of profiles and time series for following regions:' /)
+201 FORMAT (4X,'Region ',I1,':   ',A)
+
+
+ END SUBROUTINE user_header
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Call for all grid points
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_actions( location )
+
+
+    CHARACTER (LEN=*) ::  location !< 
+
+!    INTEGER(iwp) ::  i !<
+!    INTEGER(iwp) ::  j !<
+!    INTEGER(iwp) ::  k !<
+
+    CALL cpu_log( log_point(24), 'user_actions', 'start' )
+
+!
+!-- Here the user-defined actions follow
+!-- No calls for single grid points are allowed at locations before and
+!-- after the timestep, since these calls are not within an i,j-loop
+    SELECT CASE ( location )
+
+       CASE ( 'before_timestep' )
+!
+!--       Enter actions to be done before every timestep here
+
+       CASE ( 'before_prognostic_equations' )
+!
+!--       Enter actions to be done before all prognostic equations here
+
+       CASE ( 'after_integration' )
+!
+!--       Enter actions to be done after every time integration (before
+!--       data output)
+!--       Sample for user-defined output:
+!          DO  i = nxlg, nxrg
+!             DO  j = nysg, nyng
+!                DO  k = nzb, nzt
+!                   u2(k,j,i) = u(k,j,i)**2
+!                ENDDO
+!             ENDDO
+!          ENDDO
+!          DO  i = nxlg, nxr
+!             DO  j = nysg, nyn
+!                DO  k = nzb, nzt+1
+!                   ustvst(k,j,i) =  &
+!                      ( 0.5_wp * ( u(k,j,i) + u(k,j,i+1) ) - hom(k,1,1,0) ) * &
+!                      ( 0.5_wp * ( v(k,j,i) + v(k,j+1,i) ) - hom(k,1,2,0) )
+!                ENDDO
+!             ENDDO
+!          ENDDO
+
+
+       CASE ( 'after_timestep' )
+!
+!--       Enter actions to be done after every timestep here
+
+
+       CASE ( 'u-tendency' )
+!
+!--       Enter actions to be done in the u-tendency term here
+
+
+       CASE ( 'v-tendency' )
+
+
+       CASE ( 'w-tendency' )
+
+
+       CASE ( 'pt-tendency' )
+
+
+       CASE ( 'sa-tendency' )
+
+
+       CASE ( 'e-tendency' )
+
+
+       CASE ( 'q-tendency' )
+
+
+       CASE ( 's-tendency' )
+
+
+       CASE DEFAULT
+          CONTINUE
+
+    END SELECT
+
+    CALL cpu_log( log_point(24), 'user_actions', 'stop' )
+
+ END SUBROUTINE user_actions
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Call for grid point i,j
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_actions_ij( i, j, location )
+
+
+    CHARACTER (LEN=*) ::  location
+
+    INTEGER(iwp) ::  i
+    INTEGER(iwp) ::  j
+
+!
+!-- Here the user-defined actions follow
+    SELECT CASE ( location )
+
+       CASE ( 'u-tendency' )
+
+!
+!--       Next line is to avoid compiler warning about unused variables. Please remove.
+          IF ( i == 0  .OR.  j == 0 )  CONTINUE
+
+!
+!--       Enter actions to be done in the u-tendency term here
+
+
+       CASE ( 'v-tendency' )
+
+
+       CASE ( 'w-tendency' )
+
+
+       CASE ( 'pt-tendency' )
+
+
+       CASE ( 'sa-tendency' )
+
+
+       CASE ( 'e-tendency' )
+
+
+       CASE ( 'q-tendency' )
+
+
+       CASE ( 's-tendency' )
+
+
+       CASE DEFAULT
+          CONTINUE
+
+    END SELECT
+
+ END SUBROUTINE user_actions_ij
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Sum up and time-average user-defined output quantities as well as allocate
+!> the array necessary for storing the average.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_3d_data_averaging( mode, variable )
+
+
+    CHARACTER (LEN=*) ::  mode    !< 
+    CHARACTER (LEN=*) :: variable !< 
+
+!    INTEGER(iwp) ::  i !<
+!    INTEGER(iwp) ::  j !<
+!    INTEGER(iwp) ::  k !<
+
+    IF ( mode == 'allocate' )  THEN
+
+       SELECT CASE ( TRIM( variable ) )
+
+!
+!--       Uncomment and extend the following lines, if necessary.
+!--       The arrays for storing the user defined quantities (here u2_av) have
+!--       to be declared and defined by the user!
+!--       Sample for user-defined output:
+!          CASE ( 'u2' )
+!             IF ( .NOT. ALLOCATED( u2_av ) )  THEN
+!                ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!             ENDIF
+!             u2_av = 0.0_wp
+
+          CASE DEFAULT
+             CONTINUE
+
+       END SELECT
+
+    ELSEIF ( mode == 'sum' )  THEN
+
+       SELECT CASE ( TRIM( variable ) )
+
+!
+!--       Uncomment and extend the following lines, if necessary.
+!--       The arrays for storing the user defined quantities (here u2 and
+!--       u2_av) have to be declared and defined by the user!
+!--       Sample for user-defined output:
+!          CASE ( 'u2' )
+!             IF ( ALLOCATED( u2_av ) ) THEN
+!                DO  i = nxlg, nxrg
+!                   DO  j = nysg, nyng
+!                      DO  k = nzb, nzt+1
+!                         u2_av(k,j,i) = u2_av(k,j,i) + u2(k,j,i)
+!                      ENDDO
+!                   ENDDO
+!                ENDDO
+!             ENDIF
+
+          CASE DEFAULT
+             CONTINUE
+
+       END SELECT
+
+    ELSEIF ( mode == 'average' )  THEN
+
+       SELECT CASE ( TRIM( variable ) )
+
+!
+!--       Uncomment and extend the following lines, if necessary.
+!--       The arrays for storing the user defined quantities (here u2_av) have
+!--       to be declared and defined by the user!
+!--       Sample for user-defined output:
+!          CASE ( 'u2' )
+!             IF ( ALLOCATED( u2_av ) ) THEN
+!                DO  i = nxlg, nxrg
+!                   DO  j = nysg, nyng
+!                      DO  k = nzb, nzt+1
+!                         u2_av(k,j,i) = u2_av(k,j,i) / REAL( average_count_3d, KIND=wp )
+!                      ENDDO
+!                   ENDDO
+!                ENDDO
+!             ENDIF
+
+       END SELECT
+
+    ENDIF
+
+
+ END SUBROUTINE user_3d_data_averaging
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Resorts the user-defined output quantity with indices (k,j,i) to a
+!> temporary array with indices (i,j,k) and sets the grid on which it is defined.
+!> Allowed values for grid are "zu" and "zw".
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_data_output_2d( av, variable, found, grid, local_pf, two_d, nzb_do, nzt_do )
+
+
+    CHARACTER (LEN=*) ::  grid     !< 
+    CHARACTER (LEN=*) ::  variable !< 
+
+    INTEGER(iwp) ::  av     !< flag to control data output of instantaneous or time-averaged data
+!    INTEGER(iwp) ::  i      !< grid index along x-direction
+!    INTEGER(iwp) ::  j      !< grid index along y-direction
+!    INTEGER(iwp) ::  k      !< grid index along z-direction
+!    INTEGER(iwp) ::  m      !< running index surface elements
+    INTEGER(iwp) ::  nzb_do !< lower limit of the domain (usually nzb)
+    INTEGER(iwp) ::  nzt_do !< upper limit of the domain (usually nzt+1)
+
+    LOGICAL      ::  found !< 
+    LOGICAL      ::  two_d !< flag parameter that indicates 2D variables (horizontal cross sections)
+
+!    REAL(wp) ::  fill_value = -999.0_wp    !< value for the _FillValue attribute
+
+    REAL(wp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) ::  local_pf !< 
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( av == 0  .OR.  local_pf(nxl,nys,nzb_do) == 0.0_wp  .OR.  two_d )  CONTINUE
+
+
+    found = .TRUE.
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary.
+!--    The arrays for storing the user defined quantities (here u2 and u2_av)
+!--    have to be declared and defined by the user!
+!--    Sample for user-defined output:
+!       CASE ( 'u2_xy', 'u2_xz', 'u2_yz' )
+!          IF ( av == 0 )  THEN
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ELSE
+!             IF ( .NOT. ALLOCATED( u2_av ) ) THEN
+!                ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!                u2_av = REAL( fill_value, KIND = wp )
+!             ENDIF
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2_av(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ENDIF
+!
+!          grid = 'zu'
+!
+!--    In case two-dimensional surface variables are output, the user
+!--    has to access related surface-type. Uncomment and extend following lines
+!--    appropriately (example output of vertical surface momentum flux of u-
+!--    component). Please note, surface elements can be distributed over 
+!--    several data type, depending on their respective surface properties.
+!       CASE ( 'usws_xy' )
+!          IF ( av == 0 )  THEN
+!
+!--           Horizontal default-type surfaces
+!             DO  m = 1, surf_def_h(0)%ns
+!                i = surf_def_h(0)%i(m)
+!                j = surf_def_h(0)%j(m)
+!                local_pf(i,j,1) = surf_def_h(0)%usws(m)
+!             ENDDO
+!
+!--           Horizontal natural-type surfaces
+!             DO  m = 1, surf_lsm_h%ns
+!                i = surf_lsm_h%i(m)
+!                j = surf_lsm_h%j(m)
+!                local_pf(i,j,1) = surf_lsm_h%usws(m)
+!             ENDDO
+!
+!--           Horizontal urban-type surfaces
+!             DO  m = 1, surf_usm_h%ns
+!                i = surf_usm_h%i(m)
+!                j = surf_usm_h%j(m)
+!                local_pf(i,j,1) = surf_usm_h%usws(m)
+!             ENDDO
+!          ENDIF
+!
+!          grid = 'zu'
+!--       
+
+
+       CASE DEFAULT
+          found = .FALSE.
+          grid  = 'none'
+
+    END SELECT
+
+
+ END SUBROUTINE user_data_output_2d
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Resorts the user-defined output quantity with indices (k,j,i) to a
+!> temporary array with indices (i,j,k).
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_data_output_3d( av, variable, found, local_pf, nzb_do, nzt_do )
+
+
+    CHARACTER (LEN=*) ::  variable !< 
+
+    INTEGER(iwp) ::  av    !< 
+!    INTEGER(iwp) ::  i     !<
+!    INTEGER(iwp) ::  j     !<
+!    INTEGER(iwp) ::  k     !<
+    INTEGER(iwp) ::  nzb_do !< lower limit of the data output (usually 0)
+    INTEGER(iwp) ::  nzt_do !< vertical upper limit of the data output (usually nz_do3d)
+
+    LOGICAL      ::  found !< 
+
+!    REAL(wp) ::  fill_value = -999.0_wp    !< value for the _FillValue attribute
+
+    REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) ::  local_pf !< 
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( av == 0  .OR.  local_pf(nxl,nys,nzb_do) == 0.0_wp )  CONTINUE
+
+
+    found = .TRUE.
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary.
+!--    The arrays for storing the user defined quantities (here u2 and u2_av)
+!--    have to be declared and defined by the user!
+!--    Sample for user-defined output:
+!       CASE ( 'u2' )
+!          IF ( av == 0 )  THEN
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ELSE
+!             IF ( .NOT. ALLOCATED( u2_av ) ) THEN
+!                ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!                u2_av = REAL( fill_value, KIND = wp )
+!             ENDIF
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2_av(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ENDIF
+!
+
+       CASE DEFAULT
+          found = .FALSE.
+
+    END SELECT
+
+
+ END SUBROUTINE user_data_output_3d
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Calculation of user-defined statistics, i.e. horizontally averaged profiles
+!> and time series.
+!> This routine is called for every statistic region sr defined by the user,
+!> but at least for the region "total domain" (sr=0).
+!> See section 3.5.4 on how to define, calculate, and output user defined
+!> quantities.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_statistics( mode, sr, tn )
+
+
+    USE netcdf_interface,                                                      &
+       ONLY:  dots_max
+       
+    CHARACTER (LEN=*) ::  mode   !< 
+    INTEGER(iwp) ::  i    !<
+!    INTEGER(iwp) ::  j    !<
+!    INTEGER(iwp) ::  k    !<
+    INTEGER(iwp) ::  sr   !< 
+    INTEGER(iwp) ::  tn   !< 
+
+!    REAL(wp), DIMENSION(:), ALLOCATABLE ::  ts_value_l   !<
+    REAL(wp), DIMENSION(dots_num_palm+1:dots_max) ::  ts_value_l   !< 
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( sr == 0  .OR.  tn == 0 )  CONTINUE
+
+    IF ( mode == 'profiles' )  THEN
+
+!
+!--    Sample on how to calculate horizontally averaged profiles of user-
+!--    defined quantities. Each quantity is identified by the index
+!--    "pr_palm+#" where "#" is an integer starting from 1. These
+!--    user-profile-numbers must also be assigned to the respective strings
+!--    given by data_output_pr_user in routine user_check_data_output_pr.
+!       !$OMP DO
+!       DO  i = nxl, nxr
+!          DO  j = nys, nyn
+!             DO  k = nzb+1, nzt
+!!
+!!--             Sample on how to calculate the profile of the resolved-scale
+!!--             horizontal momentum flux u*v*
+!                sums_l(k,pr_palm+1,tn) = sums_l(k,pr_palm+1,tn) +             &
+!                      ( 0.5_wp * ( u(k,j,i) + u(k,j,i+1) ) - hom(k,1,1,sr) ) *&
+!                      ( 0.5_wp * ( v(k,j,i) + v(k,j+1,i) ) - hom(k,1,2,sr) )  &
+!                                     * rmask(j,i,sr)                          &
+!                                     * MERGE( 1.0_wp, 0.0_wp,                 &
+!                                              BTEST( wall_flags_0(k,j,i), 0 ) )
+!!
+!!--             Further profiles can be defined and calculated by increasing
+!!--             the second index of array sums_l (replace ... appropriately)
+!                sums_l(k,pr_palm+2,tn) = sums_l(k,pr_palm+2,tn) + ...           &
+!                                         * rmask(j,i,sr)
+!             ENDDO
+!          ENDDO
+!       ENDDO
+
+    ELSEIF ( mode == 'time_series' )  THEN
+
+
+!       ALLOCATE ( ts_value_l(dots_num_user) )
+!
+!--    Sample on how to add values for the user-defined time series quantities.
+!--    These have to be defined before in routine user_init. This sample
+!--    creates two time series for the absolut values of the horizontal
+!--    velocities u and v.
+!       ts_value_l = 0.0_wp
+!       ts_value_l(1) = ABS( u_max )
+!       ts_value_l(2) = ABS( v_max )
+!
+!--     Collect / send values to PE0, because only PE0 outputs the time series.
+!--     CAUTION: Collection is done by taking the sum over all processors.
+!--              You may have to normalize this sum, depending on the quantity
+!--              that you like to calculate. For serial runs, nothing has to be
+!--              done.
+!--     HINT: If the time series value that you are calculating has the same
+!--           value on all PEs, you can omit the MPI_ALLREDUCE call and
+!--           assign ts_value(dots_num_palm+1:,sr) = ts_value_l directly.
+!#if defined( __parallel )
+!       IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
+!       CALL MPI_ALLREDUCE( ts_value_l(1),                         &
+!                           ts_value(dots_num_palm+1,sr),                        &
+!                           dots_num_user, MPI_REAL, MPI_MAX, comm2d,   &
+!                           ierr )
+!#else
+!       ts_value(dots_num_palm+1:dots_num_palm+dots_num_user,sr) = ts_value_l
+!#endif
+
+
+       ts_value_l = 0.0_wp
+
+       DO  i = 1, size_of_pos_array
+
+          IF ( nxl <= s_ts_pos_x_ind(i)  .AND.  nxr >= s_ts_pos_x_ind(i) )  THEN
+             IF ( nys <= s_ts_pos_y_ind(i)  .AND.  nyn >= s_ts_pos_y_ind(i) )  THEN
+
+                ts_value_l(dots_num_palm+i) = s(2,s_ts_pos_y_ind(i),s_ts_pos_x_ind(i))
+
+             ENDIF
+          ENDIF
+       ENDDO
+       
+!
+!--     Collect / send values to PE0, because only PE0 outputs the time series.
+!--     CAUTION: Collection is done by taking the sum over all processors.
+!--              You may have to normalize this sum, depending on the quantity
+!--              that you like to calculate. For serial runs, nothing has to be
+!--              done.
+!--     HINT: If the time series value that you are calculating has the same
+!--           value on all PEs, you can omit the MPI_ALLREDUCE call and
+!--           assign ts_value(dots_num_palm+1:,sr) = ts_value_l directly.
+#if defined( __parallel )
+       IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
+       CALL MPI_ALLREDUCE( ts_value_l(dots_num_palm+1),                         &
+                           ts_value(dots_num_palm+1,sr),                        &
+                           dots_max-dots_num_palm, MPI_REAL, MPI_SUM, comm2d,   &
+                           ierr )
+#else
+       ts_value(dots_num_palm+1:,sr) = ts_value_l
+#endif
+
+    ENDIF
+
+ END SUBROUTINE user_statistics
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Reading global restart data that has been defined by the user.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_rrd_global( found )
+
+
+    LOGICAL, INTENT(OUT)  ::  found
+
+
+    found = .TRUE.
+
+
+    SELECT CASE ( restart_string(1:length) )
+
+       CASE ( 'global_paramter' )
+!          READ ( 13 )  global_parameter
+
+       CASE DEFAULT
+ 
+          found = .FALSE.
+
+    END SELECT
+
+
+ END SUBROUTINE user_rrd_global
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Reading processor specific restart data from file(s) that has been defined 
+!> by the user.
+!> Subdomain index limits on file are given by nxl_on_file, etc.
+!> Indices nxlc, etc. indicate the range of gridpoints to be mapped from the
+!> subdomain on file (f) to the subdomain of the current PE (c). They have been
+!> calculated in routine rrd_local.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_rrd_local( k, nxlf, nxlc, nxl_on_file, nxrf, nxrc,         &
+                            nxr_on_file, nynf, nync, nyn_on_file, nysf,     &
+                            nysc, nys_on_file, tmp_3d, found )
+
+
+    INTEGER(iwp) ::  idum            !<
+    INTEGER(iwp) ::  k               !<
+    INTEGER(iwp) ::  nxlc            !<
+    INTEGER(iwp) ::  nxlf            !<
+    INTEGER(iwp) ::  nxl_on_file     !<
+    INTEGER(iwp) ::  nxrc            !<
+    INTEGER(iwp) ::  nxrf            !<
+    INTEGER(iwp) ::  nxr_on_file     !<
+    INTEGER(iwp) ::  nync            !<
+    INTEGER(iwp) ::  nynf            !<
+    INTEGER(iwp) ::  nyn_on_file     !<
+    INTEGER(iwp) ::  nysc            !<
+    INTEGER(iwp) ::  nysf            !<
+    INTEGER(iwp) ::  nys_on_file     !<
+
+    LOGICAL, INTENT(OUT)  ::  found
+
+    REAL(wp), DIMENSION(nzb:nzt+1,nys_on_file-nbgp:nyn_on_file+nbgp,nxl_on_file-nbgp:nxr_on_file+nbgp) :: tmp_3d   !<
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    idum = k + nxlc + nxlf + nxrc + nxrf + nync + nynf + nysc + nysf +                             &
+           INT( tmp_3d(nzb,nys_on_file,nxl_on_file) )
+
+!
+!-- Here the reading of user-defined restart data follows:
+!-- Sample for user-defined output
+
+    found = .TRUE.
+
+    SELECT CASE ( restart_string(1:length) )
+
+       CASE ( 'u2_av' )
+!          IF ( .NOT. ALLOCATED( u2_av ) ) THEN
+!               ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!          ENDIF
+!          IF ( k == 1 )  READ ( 13 )  tmp_3d
+!             u2_av(:,nysc-nbgp:nync+nbgp,nxlc-nbgp:nxrc+nbgp) =         &
+!                tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
+!
+       CASE DEFAULT
+
+          found = .FALSE.
+
+    END SELECT
+
+ END SUBROUTINE user_rrd_local
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Writes global and user-defined restart data into binary file(s) for restart
+!> runs.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_wrd_global
+
+!    CALL wrd_write_string( 'global_parameter' )
+!    WRITE ( 14 )  global_parameter
+
+ END SUBROUTINE user_wrd_global
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Writes processor specific and user-defined restart data into binary file(s) 
+!> for restart runs.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_wrd_local
+
+!
+!-- Here the user-defined actions at the end of a job follow.
+!-- Sample for user-defined output:
+!    IF ( ALLOCATED( u2_av ) )  THEN
+!       CALL wrd_write_string( 'u2_av' )
+!       WRITE ( 14 )  u2_av
+!    ENDIF
+
+ END SUBROUTINE user_wrd_local
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Execution of user-defined actions at the end of a job.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_last_actions
+
+!
+!-- Here the user-defined actions at the end of a job might follow.
+
+
+ END SUBROUTINE user_last_actions
+
+ END MODULE user
Index: palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/case_config.yml
===================================================================
--- palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/case_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/dispersion_eulerian_and_lpm_extended/case_config.yml	(revision 4091)
@@ -0,0 +1,16 @@
+---
+# this is a palmtest job configuration file
+
+allowed_builds:
+  - gfortran_default
+  - intel_default
+
+allowed_number_of_cores: []
+
+activation_strings:
+  - "d3#"
+
+significant_digits_for_netcdf_checks:
+  timeseries: 4
+  profiles: 6
+  other: 8
Index: palm/trunk/TUTORIALS/cases/example_cbl/INPUT/example_cbl_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/example_cbl/INPUT/example_cbl_p3d	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/example_cbl/INPUT/example_cbl_p3d	(revision 4091)
@@ -0,0 +1,94 @@
+!-------------------------------------------------------------------------------
+!-- INITIALIZATION PARAMETER NAMELIST
+!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/inipar
+!-------------------------------------------------------------------------------
+&initialization_parameters
+!
+!-- grid parameters
+!-------------------------------------------------------------------------------
+    nx                         = 39, ! Number of gridboxes in x-direction (nx+1)
+    ny                         = 39, ! Number of gridboxes in y-direction (ny+1)
+    nz                         = 40, ! Number of gridboxes in z-direction (nz)
+
+    dx                         = 50.0, ! Size of single gridbox in x-direction
+    dy                         = 50.0, ! Size of single gridbox in y-direction
+    dz                         = 50.0, ! Size of single gridbox in z-direction
+
+    dz_stretch_level           = 1225.0, ! Height (in m) where stretching starts
+    dz_stretch_factor          = 1.08,   ! dz(k+1) = dz(k) * dz_stretch_factor
+!
+!-- initialization
+!-------------------------------------------------------------------------------
+    initializing_actions       = 'set_constant_profiles', ! initial conditions
+
+    ug_surface                 = 0.0, ! u-comp of geostrophic wind at surface
+    vg_surface                 = 0.0, ! v-comp of geostrophic wind at surface
+
+    pt_surface                 = 300.0, ! initial surface potential temp
+
+    pt_vertical_gradient       =    0.0,
+                                    1.0, ! piecewise temp gradients
+    pt_vertical_gradient_level =    0.0,
+                                  800.0, ! height level of temp gradients
+
+
+!
+!-- boundary conditions
+!-------------------------------------------------------------------------------
+    surface_heatflux           = 0.1, ! sensible heat flux at the bottom surface
+    bc_pt_b                    = 'neumann', ! required with surface_heatflux
+!
+!-- numerics
+!-------------------------------------------------------------------------------
+    fft_method                 = 'temperton-algorithm',   ! build-in fft method
+
+/ ! end of initialization parameter namelist
+
+!-------------------------------------------------------------------------------
+!-- RUNTIME PARAMETER NAMELIST
+!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/d3par
+!-------------------------------------------------------------------------------
+&runtime_parameters
+!
+!-- run steering
+!-------------------------------------------------------------------------------
+    end_time                   = 1800.0, ! simulation time of the 3D model
+
+    create_disturbances        = .TRUE., ! randomly perturbate horiz. velocity
+    dt_disturb                 = 150.0,  ! interval for random perturbations
+    disturbance_energy_limit   = 0.01,   ! upper limit for perturbation energy
+
+    data_output_2d_on_each_pe  = .FALSE., ! don't do 2D output on each MPI rank
+
+!
+!-- data output
+!-------------------------------------------------------------------------------
+    netcdf_data_format         = 2, ! use NetCDF3
+
+    dt_run_control             = 0.0,    ! output interval for run control
+    dt_data_output             = 900.0,  ! output interval for general data
+    dt_data_output_av          = 1800.0, ! output interval for averaged data
+    dt_dopr                    = 900.0,  ! output interval for profile data
+
+    data_output                = 'w_xy',
+                                 'w_xz',
+                                 'w_xz_av',
+                                 'theta_xy',
+                                 'theta_xz',
+
+    data_output_pr             = 'wtheta', 'w"theta"', 'w*theta*',
+                                 'w*2',
+                                 '#theta', 'theta*2',
+
+    section_xy                 = 2,
+                                 10, ! grid index for 2D XY cross sections
+    section_xz                 = 20, ! grid index for 2D XZ cross sections
+
+    averaging_interval         = 900.0, ! averaging interval general data
+    dt_averaging_input         = 10.0,  ! averaging general data sampling rate
+
+    averaging_interval_pr      = 600.0, ! averaging interval profile data
+    dt_averaging_input_pr      = 10.0,  ! averaging profile data sampling rate
+
+/ ! end of runtime parameter namelist
+
Index: palm/trunk/TUTORIALS/cases/example_cbl/MONITORING/example_cbl_rc
===================================================================
--- palm/trunk/TUTORIALS/cases/example_cbl/MONITORING/example_cbl_rc	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/example_cbl/MONITORING/example_cbl_rc	(revision 4091)
@@ -0,0 +1,352 @@
+
+ ******************************    --------------------------------------------
+ * PALM 6.0  Rev: 3527M       *    atmosphere - run without 1D - prerun
+ ******************************    --------------------------------------------
+
+ Date:               2018-11-15    Run:       example_cbl_short__intel_default__
+ Time:                 21:35:00    Run-No.:   00
+ Run on host:        intel_defa
+ Number of PEs:               4    Processor grid (x,y): (   2,   2) calculated
+ ------------------------------------------------------------------------------
+
+ Numerical Schemes:
+ -----------------
+
+ --> Use the Moeng_Wyngaard turbulence closure (LES mode).
+ --> Use the boussinesq approximation for the model equations.
+ --> Solve perturbation pressure via FFT using temperton-algorithm routines
+     perturbation pressure is calculated at every Runge-Kutta step
+ --> Momentum advection via Wicker-Skamarock-Scheme 5th order
+ --> Scalar advection via Wicker-Skamarock-Scheme 5th order
+ --> Loop optimization method: cache
+ --> Time differencing scheme: runge-kutta-3       
+ ------------------------------------------------------------------------------
+
+
+ Run time and time step information:
+ ----------------------------------
+
+ Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
+ Start time:              0.000 s
+ End time:             1800.000 s
+
+
+ Computational grid and domain size:
+ ----------------------------------
+
+ Grid length:      dx =      50.000 m    dy =      50.000 m
+                dz(1) =      50.000 m
+                dz(2) =     999.000 m
+
+ Domain size:       x =   2000.000 m     y =   2000.000 m  z(u) =   2862.511 m
+
+ Vertical stretching starts at height:    1225.0 m,
+ Vertical stretching starts at index:           25,
+ Vertical stretching ends at height:   9999999.9 m,
+ Vertical stretching ends at index:             41,
+ Factor used for stretching:                 1.080,
+
+ Number of gridpoints (x,y,z):  (0:  39, 0:  39, 0:  41)
+ Subdomain size (x,y,z):        (    20,     20,     42)
+
+
+    Characteristic levels of the geo. wind component ug:
+
+       Height:         0.0     0.0  m
+       ug:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+    Characteristic levels of the geo. wind component vg:
+
+       Height:         0.0     0.0  m
+       vg:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+
+ Topography information:
+ ----------------------
+
+ Topography: flat                                    
+
+
+ Boundary conditions:
+ -------------------
+
+                     p                    uv                                  pt
+
+ B. bound.: p(0)     = p(1)   | uv(0)     = -uv(1)                | pt(0)     = pt(1)            
+ T. bound.: p(nzt+1) = 0      | uv(nzt+1) = ug(nzt+1), vg(nzt+1)  | pt(nzt+1) = pt(nzt) + dpt/dz_
+
+                     e
+
+ B. bound.: e(0)     = e(1)                                                                      
+ T. bound.: e(nzt+1) = e(nzt) = e(nzt-1)                                                         
+
+ Bottom surface fluxes are used in diffusion terms at k=1
+       Predefined constant heatflux:    0.100000 K m/s
+
+
+    Constant flux layer between bottom surface and first computational u,v-level:
+
+       z_mo =  25.00 m   z0 = 0.1000 m   z0h = 0.10000 m   kappa = 0.40
+       Rif value range:     -20.00 <= rif <= 20.00
+
+
+ Lateral boundaries:
+       left/right:  cyclic              
+       north/south: cyclic              
+
+
+ Initial profiles:
+ ----------------
+
+    Characteristic levels of the initial temperature profile:
+
+       Height:           0.0     0.0   800.0  m
+       Temperature:   300.00  300.00  300.00  K
+       Gradient:      ------    0.00    1.00  K/100m
+       Gridpoint:          0       0      16
+
+
+ List output:
+ -----------
+
+    1D-Profiles:
+       Output every             9999999.90 s
+       Time averaged over         600.00 s
+       Averaging input every       10.00 s
+
+
+ Data output:
+ -----------
+
+       Time averaged over         600.00 s
+       Averaging input every       10.00 s
+
+    1D-Profiles:
+       Output format: netCDF 64bit offset                     
+
+
+       Profile: wtheta, w"theta", w*theta*, w*2, theta, theta*2,             
+       Output every               900.00 s
+       Time averaged over         600.00 s
+       Averaging input every       10.00 s
+
+    2D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       XY-cross-section  Arrays:  w, theta,                                                            
+       Output every               900.00 s  
+       Cross sections at k = /2/10/
+       scalar-coordinates:   /75.0/475.0/ m
+
+
+       Number of output time levels allowed: unlimited
+
+
+       XZ-cross-section  Arrays:  w, theta,                                                            
+       Output every               900.00 s  
+       Cross sections at j = /20/
+       scalar-coordinates:   /1000.0/ m
+
+
+       Number of output time levels allowed: unlimited
+
+
+    2D-Arrays(time-averaged):
+       Output format: netCDF 64bit offset                     
+
+
+       XZ-cross-section  Arrays:  w,                                                                   
+       Output every              1800.00 s  
+       Time averaged over         900.00 s
+       Averaging input every       10.00 s
+       Cross sections at j = /20/
+       scalar-coordinates:   /1000.0/ m
+
+
+       Number of output time levels allowed: unlimited
+
+
+    Time series:
+       Output format: netCDF 64bit offset                     
+
+       Output every                 0.00 s
+
+ ------------------------------------------------------------------------------
+
+
+ Physical quantities:
+ -------------------
+
+    Geograph. latitude  :   latitude  = 55.0 degr
+    Geograph. longitude :   longitude =  0.0 degr
+    Angular velocity    :   omega  = 0.729E-04 rad/s
+    Coriolis parameter  :   f      =  0.000119 1/s
+                            f*     =  0.000084 1/s
+
+    Day of the year at model start :   day_init      =     172
+    UTC time at model start        :   time_utc_init = 43200.0 s
+
+    Gravity             :   g      =  9.8 m/s**2
+
+    Reference state used in buoyancy terms: initial_profile
+
+
+ Cloud physics quantities / methods:
+ ----------------------------------
+
+
+
+ LES / Turbulence quantities:
+ ---------------------------
+
+    Mixing length is limited to 1.80 * z
+
+
+ Actions during the simulation:
+ -----------------------------
+
+    Disturbance impulse (u,v) every :   150.00 s
+    Disturbance amplitude           :     0.25 m/s
+    Lower disturbance level         :   125.00 m (GP    3)
+    Upper disturbance level         :   625.00 m (GP   13)
+    Disturbances cease as soon as the disturbance energy exceeds 0.010 m**2/s**2
+    Random number generator used    : random-parallel
+
+
+
+ *** no user-defined variables found
+
+ ------------------------------------------------------------------------------
+
+
+
+Run-control output:
+------------------
+
+RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  0      0 00:00:00.00  20.0000A  -0.2131D -0.2288D  0.1182  0.000  1.38   0.000E+00    800.  0.104E-02  0.103E-02  0.597E-03  0.867E-13    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      1 00:00:20.00  20.0000D  -0.2125  -0.2273   0.1172  0.009  0.69  -0.132E+02    100.  0.103E-02  0.102E-02  0.570E-05  0.411E-15    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      2 00:00:40.00  20.0000D  -0.2117  -0.2252   0.1162  0.009  0.69  -0.133E+02    100.  0.102E-02  0.102E-02  0.935E-05  0.416E-15    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      3 00:01:00.00  20.0000D  -0.2106  -0.2227   0.1152  0.009  0.69  -0.134E+02    100.  0.101E-02  0.101E-02  0.130E-04  0.421E-15    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      4 00:01:20.00  20.0000D  -0.2093  -0.2197   0.1141  0.009  0.69  -0.134E+02    100.  0.100E-02  0.997E-03  0.166E-04  0.424E-15    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      5 00:01:40.00  20.0000D  -0.2077  -0.2164   0.1129  0.009  0.93  -0.134E+02    250.  0.992E-03  0.988E-03  0.203E-04  0.427E-15    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      6 00:02:00.00  20.0000D  -0.2058  -0.2126   0.1117  0.009  0.93  -0.133E+02    250.  0.983E-03  0.979E-03  0.239E-04  0.429E-15    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      7 00:02:20.00  20.0000D  -0.2037  -0.2086   0.1103  0.009  1.22  -0.131E+02    550.  0.974E-03  0.970E-03  0.275E-04  0.431E-15    7   7  11   11   7  19    5  26   7    0.000    0.000       0
+  0      8 00:02:40.00  20.0000D   0.3348D  0.3126D  0.1636  0.011  1.22  -0.105E+02    550.  0.202E-02  0.201E-02  0.601E-03  0.856E-13   10   3  39   10   8  27    5  36  28    0.000    0.000       0
+  0      9 00:03:00.00  20.0000D   0.3330   0.3039   0.1619  0.011  1.22  -0.105E+02    550.  0.199E-02  0.198E-02  0.374E-04  0.830E-15   10   3  39   10   8  27    5  36  28    0.000    0.000       0
+  0     10 00:03:20.00  20.0000D   0.3296  -0.2989   0.1601  0.011  1.22  -0.103E+02    550.  0.196E-02  0.195E-02  0.409E-04  0.827E-15   10   3  39    8   4   6    5  36  28    0.000    0.000       0
+  0     11 00:03:40.00  20.0000D   0.3249  -0.2986   0.1580  0.011  1.22  -0.101E+02    550.  0.194E-02  0.193E-02  0.444E-04  0.828E-15   10   3  39    8   4   6    5  36  28    0.000    0.000       0
+  0     12 00:04:00.00  20.0000D   0.3189  -0.2989   0.1558  0.012  1.22  -0.975E+01    550.  0.191E-02  0.190E-02  0.478E-04  0.831E-15   10   3  39    8   0   7    5  36  28    0.000    0.000       0
+  0     13 00:04:20.00  20.0000D   0.3119  -0.3005   0.1535  0.012  1.22  -0.940E+01    550.  0.189E-02  0.188E-02  0.513E-04  0.835E-15   10   3  39    8   0   7    5  36  28    0.000    0.000       0
+  0     14 00:04:40.00  20.0000D   0.3056  -0.3012   0.1512  0.013  1.22  -0.905E+01    550.  0.187E-02  0.185E-02  0.546E-04  0.842E-15   10   3   0    8   0   7    5  36  28    0.000    0.000       0
+  0     15 00:05:00.00  20.0000D   0.4151D -0.3964D -0.1812  0.013  1.22  -0.851E+01    550.  0.292E-02  0.289E-02  0.625E-03  0.860E-13    8  17   5    8   3   6    8  19   3    0.000    0.000       0
+  0     16 00:05:20.00  20.0000D   0.4183  -0.4076  -0.1810  0.014  1.22  -0.811E+01    550.  0.287E-02  0.285E-02  0.640E-04  0.129E-14    8  17   5    8   3   6    8  19   3    0.000    0.000       0
+  0     17 00:05:40.00  20.0000D   0.4163  -0.4151  -0.1796  0.015  1.22  -0.773E+01    550.  0.283E-02  0.280E-02  0.672E-04  0.129E-14    8  17   5    8   3   6    8  19   3    0.000    0.000       0
+  0     18 00:06:00.00  20.0000D   0.4097  -0.4189  -0.1772  0.015  1.22  -0.735E+01    550.  0.279E-02  0.276E-02  0.703E-04  0.130E-14    8  17   5    8   3   6    8  19   3    0.000    0.000       0
+  0     19 00:06:20.00  20.0000D   0.3992  -0.4192   0.1802  0.016  1.22  -0.698E+01    550.  0.275E-02  0.273E-02  0.734E-04  0.131E-14    8  17   5    8   3   6    2  36   2    0.000    0.000       0
+  0     20 00:06:40.00  20.0000D   0.3855  -0.4165   0.1983  0.017  1.22  -0.656E+01    550.  0.272E-02  0.269E-02  0.765E-04  0.133E-14    8  17   5    8   3   6    2  36   2    0.000    0.000       0
+  0     21 00:07:00.00  20.0000D   0.3695  -0.4109   0.2198  0.018  1.22  -0.616E+01    550.  0.269E-02  0.267E-02  0.795E-04  0.136E-14    8  17   5    8   3   6    2  36   2    0.000    0.000       0
+  0     22 00:07:20.00  20.0000D  -0.3706  -0.4030   0.2474  0.020  1.22  -0.577E+01    550.  0.267E-02  0.265E-02  0.824E-04  0.140E-14    8  13   9    8   3   6    2   6  12    0.000    0.000       0
+  0     23 00:07:40.00  20.0000D  -0.4267D -0.4554D  0.2850  0.021  1.22  -0.539E+01    550.  0.371E-02  0.369E-02  0.653E-03  0.886E-13    4   4   4    8   1   8    2   6  12    0.000    0.000       0
+  0     24 00:08:00.00  20.0000D  -0.4241  -0.4568   0.3233  0.023  1.22  -0.506E+01    550.  0.368E-02  0.366E-02  0.905E-04  0.190E-14    4   4   4    8   1   8    2   6  12    0.000    0.000       0
+  0     25 00:08:20.00  20.0000D  -0.4208  -0.4522   0.3672  0.024  1.22  -0.471E+01    550.  0.367E-02  0.365E-02  0.931E-04  0.196E-14    4   4   4    8   1   8    2   6  12    0.000    0.000       0
+  0     26 00:08:40.00  20.0000D  -0.4174  -0.4421   0.4169  0.026  1.22  -0.440E+01    550.  0.368E-02  0.366E-02  0.957E-04  0.204E-14    4   4   4    8   1   8    2   6  12    0.000    0.000       0
+  0     27 00:09:00.00  20.0000D  -0.4142  -0.4279   0.4727  0.028  1.22  -0.410E+01    550.  0.372E-02  0.370E-02  0.981E-04  0.214E-14    4   4   4    8   1   8    2   6  12    0.000    0.000       0
+  0     28 00:09:20.00  20.0000D  -0.4116  -0.4106   0.5348  0.030  1.18  -0.381E+01    500.  0.380E-02  0.378E-02  0.100E-03  0.227E-14    4   4   4    8   1   8    2   6  12    0.000    0.000       0
+  0     29 00:09:40.00  20.0000D  -0.4107  -0.4087   0.6032  0.032  1.18  -0.355E+01    500.  0.393E-02  0.391E-02  0.103E-03  0.242E-14    5   4   4    5   3  36    2   6  12    0.000    0.000       0
+  0     30 00:10:00.00  20.0000D   0.4798D  0.4695D  0.7094  0.035  1.18  -0.330E+01    500.  0.519E-02  0.516E-02  0.656E-03  0.867E-13    5  14  20    9   7  14    2   6  12    0.000    0.000       0
+  0     31 00:10:20.00  20.0000D   0.4589  -0.4757   0.8018  0.037  1.18  -0.308E+01    500.  0.543E-02  0.540E-02  0.108E-03  0.318E-14    5  14  20    8   2   6    3   6  12    0.000    0.000       0
+  0     32 00:10:40.00  20.0000D   0.4450  -0.4782   0.9236  0.040  1.18  -0.288E+01    500.  0.579E-02  0.576E-02  0.110E-03  0.344E-14    6  39  30    8   2   6    3   6  12    0.000    0.000       0
+  0     33 00:11:00.00  20.0000A   0.4349  -0.4767   1.0530  0.043  1.18  -0.266E+01    500.  0.629E-02  0.626E-02  0.111E-03  0.377E-14    6  39  30    8   2   6    3   6  12    0.000    0.000       0
+  0     34 00:11:20.00  20.0000A  -0.4684  -0.5184   1.1853  0.046  1.18  -0.249E+01    500.  0.699E-02  0.696E-02  0.111E-03  0.416E-14    1   3  23    1  29  17    3   6  12    0.000    0.000       0
+  0     35 00:11:40.00  20.0000A  -0.5110  -0.5803   1.3146  0.049  1.18  -0.233E+01    500.  0.793E-02  0.791E-02  0.112E-03  0.464E-14    1   3  23    1  29  17    3   6  12    0.000    0.000       0
+  0     36 00:12:00.00  20.0000A  -0.5522  -0.6460   1.4351  0.052  1.18  -0.218E+01    500.  0.920E-02  0.917E-02  0.112E-03  0.522E-14    1   3  23    1  29  17    3   6  12    0.000    0.000       0
+  0     37 00:12:20.00  20.0000A   0.6173  -0.7139   1.6132  0.055  1.18  -0.205E+01    500.  0.109E-01  0.108E-01  0.112E-03  0.591E-14    1  35  11    1  29  17    4   6  12    0.000    0.000       0
+  0     38 00:12:40.00  20.0000A   0.6867  -0.7795   1.7863  0.059  1.18  -0.193E+01    500.  0.130E-01  0.130E-01  0.112E-03  0.673E-14    1  35  11    1  29  17    4   6  12    0.000    0.000       0
+  0     39 00:13:00.00  20.0000A   0.7575  -0.8399   1.9135  0.062  1.18  -0.183E+01    500.  0.158E-01  0.158E-01  0.112E-03  0.767E-14    1  35  11    1  29  17    4   6  12    0.000    0.000       0
+  0     40 00:13:20.00  20.0000A   0.8277  -0.8934   2.1012  0.066  1.18  -0.173E+01    500.  0.193E-01  0.193E-01  0.114E-03  0.877E-14    1  35  11    1  29  17    5   6  12    0.000    0.000       0
+  0     41 00:13:40.00  20.0000A   0.8945  -0.9393   2.2220  0.069  1.18  -0.165E+01    500.  0.237E-01  0.236E-01  0.116E-03  0.100E-13    1  35  11    1  29  17    5   6  12    0.000    0.000       0
+  0     42 00:14:00.00  18.9000A   0.9549  -0.9777   2.3774  0.072  1.28  -0.157E+01    650.  0.290E-01  0.290E-01  0.120E-03  0.115E-13    1  35  11    1  29  17    6   6  12    0.000    0.000       0
+  0     43 00:14:18.89  18.4000A   1.0030  -1.0299   2.4491  0.075  1.28  -0.151E+01    650.  0.352E-01  0.351E-01  0.119E-03  0.123E-13    1  35  11    1  28  17    6   6  12    0.000    0.000       0
+  0     44 00:14:37.29  17.7000A   1.0386  -1.1114   2.5494  0.078  1.28  -0.147E+01    650.  0.421E-01  0.421E-01  0.122E-03  0.135E-13    1  35  11    1  28  17    7   6  12    0.000    0.000       0
+  0     45 00:14:55.00  16.2000A   1.0601  -1.1794   2.7727  0.081  1.28  -0.141E+01    650.  0.499E-01  0.498E-01  0.125E-03  0.146E-13    1  35  11    1  28  17    5  24   2    0.000    0.000       0
+  0     46 00:15:11.20  15.4000A   1.0661  -1.2312   2.9236  0.083  1.18  -0.138E+01    500.  0.578E-01  0.578E-01  0.122E-03  0.148E-13    1  35  11    1  28  17    6  24   2    0.000    0.000       0
+  0     47 00:15:26.60  14.3000A  -1.0749  -1.2699   3.1406  0.084  1.28  -0.135E+01    650.  0.662E-01  0.661E-01  0.124E-03  0.155E-13    1  24  19    1  28  17    6  24   2    0.000    0.000       0
+  0     48 00:15:40.89  13.8000A   1.1037  -1.2967   3.2568  0.086  1.28  -0.132E+01    650.  0.746E-01  0.745E-01  0.122E-03  0.156E-13    1  17  38    1  28  17    6  24   2    0.000    0.000       0
+  0     49 00:15:54.69  13.1000A   1.1514  -1.3146   3.4225  0.087  1.28  -0.131E+01    650.  0.832E-01  0.832E-01  0.125E-03  0.163E-13    1  17  38    1  28  17    7  24   2    0.000    0.000       0
+  0     50 00:16:07.79  12.9000A   1.1883  -1.3252   3.4997  0.088  1.29  -0.130E+01    650.  0.919E-01  0.919E-01  0.125E-03  0.167E-13    1  17  38    1  28  17    7  24   2    0.000    0.000       0
+  0     51 00:16:20.69  12.4000A   1.2162  -1.3305   3.6233  0.089  1.29  -0.129E+01    650.  0.101E+00  0.101E+00  0.130E-03  0.175E-13    1  17  38    1  28  17    8  24   2    0.000    0.000       0
+  0     52 00:16:33.09  12.3000A   1.2350  -1.3452   3.6676  0.090  1.29  -0.128E+01    650.  0.110E+00  0.110E+00  0.131E-03  0.179E-13    1  17  38    1  28  18    8  24   2    0.000    0.000       0
+  0     53 00:16:45.39  11.9000A   1.2464  -1.3669   3.7669  0.091  1.29  -0.126E+01    650.  0.119E+00  0.119E+00  0.136E-03  0.188E-13    1  17  38    1  28  18    9  34  13    0.000    0.000       0
+  0     54 00:16:57.29  11.4000A   1.2897  -1.3821   3.9424  0.092  1.29  -0.126E+01    650.  0.128E+00  0.128E+00  0.138E-03  0.191E-13    5  31  10    1  28  18    9  34  13    0.000    0.000       0
+  0     55 00:17:08.69  11.2000A   1.3175  -1.3912   4.0217  0.092  1.29  -0.124E+01    650.  0.136E+00  0.136E+00  0.138E-03  0.192E-13    5  31  10    1  28  18    9  34  13    0.000    0.000       0
+  0     56 00:17:19.89  10.8000A  -1.3130  -1.3950   4.1809  0.093  1.38  -0.123E+01    800.  0.145E+00  0.145E+00  0.141E-03  0.198E-13    5  29  17    1  28  18   10  34  13    0.000    0.000       0
+  0     57 00:17:30.69  10.6000A  -1.3858  -1.3942   4.2493  0.093  1.38  -0.123E+01    800.  0.153E+00  0.153E+00  0.141E-03  0.199E-13    5  29  17    1  28  18   10  34  13    0.000    0.000       0
+  0     58 00:17:41.29  10.4000A  -1.4208  -1.3896   4.3438  0.094  1.38  -0.122E+01    800.  0.162E+00  0.162E+00  0.144E-03  0.204E-13    5  29  17    1  28  18   11  34  13    0.000    0.000       0
+  0     59 00:17:51.69  10.2000A  -1.4345   1.3902   4.4002  0.095  1.38  -0.121E+01    800.  0.170E+00  0.170E+00  0.146E-03  0.208E-13    5  29  17    7  37  19   11  34  13    0.000    0.000       0
+  0     60 00:18:01.89  10.1000A  -1.4414   1.4901   4.4539  0.095  1.38  -0.120E+01    800.  0.177E+00  0.177E+00  0.148E-03  0.212E-13    4  32  19    7  37  19   12  34  13    0.000    0.000       0
+  0     61 00:18:11.99  10.0000A  -1.4695  -1.5076   4.4829  0.096  1.38  -0.120E+01    800.  0.185E+00  0.185E+00  0.151E-03  0.217E-13    4  32  19    8   7  16   12  34  13    0.000    0.000       0
+  0     62 00:18:21.99  10.0000A  -1.4856  -1.6263   4.4854  0.096  1.38  -0.119E+01    800.  0.193E+00  0.192E+00  0.154E-03  0.222E-13    4  32  19    8   7  16   13  34  13    0.000    0.000       0
+  0     63 00:18:31.99  10.0000A  -1.4918  -1.7187   4.4802  0.097  1.38  -0.118E+01    800.  0.200E+00  0.200E+00  0.158E-03  0.229E-13    4  32  19    8   7  16   12  34  13    0.000    0.000       0
+  0     64 00:18:41.99  10.1000A  -1.5052  -1.7636   4.4361  0.097  1.38  -0.116E+01    800.  0.207E+00  0.207E+00  0.163E-03  0.235E-13    4  32  18    8   7  16   14  34  13    0.000    0.000       0
+  0     65 00:18:52.09  10.2000A  -1.5591  -1.7463   4.4065  0.098  1.41  -0.116E+01    850.  0.214E+00  0.214E+00  0.169E-03  0.245E-13    4  32  18    8   7  16   13  34  13    0.000    0.000       0
+  0     66 00:19:02.29  10.3000A  -1.5903  -1.6646   4.3493  0.099  1.41  -0.115E+01    850.  0.221E+00  0.221E+00  0.175E-03  0.253E-13    4  32  18    8   7  16   13  34  13    0.000    0.000       0
+  0     67 00:19:12.59  10.5000A  -1.5979  -1.6322   4.2954  0.099  1.41  -0.115E+01    850.  0.228E+00  0.228E+00  0.180E-03  0.262E-13    4  32  18    9   7  16   15  35  12    0.000    0.000       0
+  0     68 00:19:23.09  10.5000A  -1.5832   1.6962   4.2656  0.100  1.41  -0.114E+01    850.  0.235E+00  0.234E+00  0.188E-03  0.273E-13    4  32  18   12  17  28   15  35  12    0.000    0.000       0
+  0     69 00:19:33.59  10.8000A  -1.5952  -1.7195   4.1677  0.101  1.41  -0.113E+01    850.  0.241E+00  0.241E+00  0.192E-03  0.279E-13    7  12   6    9   7  16   16  35  13    0.000    0.000       0
+  0     70 00:19:44.39  10.7000A  -1.5975  -1.7885   4.1887  0.101  1.41  -0.113E+01    850.  0.247E+00  0.247E+00  0.202E-03  0.293E-13    7  12   6   10   7  17   16  35  13    0.000    0.000       0
+  0     71 00:19:55.09  11.0000A   1.6027  -1.8310   4.1010  0.102  1.41  -0.112E+01    850.  0.253E+00  0.252E+00  0.204E-03  0.295E-13    7   1  37   10   7  17   12  23  18    0.000    0.000       0
+  0     72 00:20:06.09  10.9000A   1.7032  -1.8108   4.1396  0.103  1.41  -0.111E+01    850.  0.258E+00  0.258E+00  0.214E-03  0.308E-13    7  24  30   10   7  17   12  23  18    0.000    0.000       0
+  0     73 00:20:16.99  10.9000A   1.8376   1.7452   4.1413  0.104  1.41  -0.109E+01    850.  0.262E+00  0.262E+00  0.215E-03  0.309E-13    7  24  30   14  18  28   13  23  18    0.000    0.000       0
+  0     74 00:20:27.89  10.7000A   1.9136   1.8271   4.1969  0.105  1.41  -0.107E+01    850.  0.267E+00  0.266E+00  0.219E-03  0.313E-13    7  24  30   14  18  28   13  23  18    0.000    0.000       0
+  0     75 00:20:38.59  10.7000A   1.9332  -1.8931   4.1941  0.106  1.41  -0.106E+01    850.  0.270E+00  0.270E+00  0.218E-03  0.311E-13    7  24  30    9   4   0   13  23  17    0.000    0.000       0
+  0     76 00:20:49.29  10.7000A   1.9366  -1.9949   4.2226  0.107  1.41  -0.105E+01    850.  0.273E+00  0.273E+00  0.220E-03  0.314E-13    7  24  31    9   4   0   13  23  17    0.000    0.000       0
+  0     77 00:21:00.00  10.5000A   2.0189  -2.0694   4.2693  0.108  1.41  -0.104E+01    850.  0.276E+00  0.275E+00  0.223E-03  0.317E-13    7  24  31    9   4   0   14  23  17    0.000    0.000       0
+  0     78 00:21:10.50  10.5000A   2.0530  -2.1078   4.3031  0.109  1.41  -0.103E+01    850.  0.278E+00  0.277E+00  0.221E-03  0.314E-13    7  24  31    9   4   0   14  23  17    0.000    0.000       0
+  0     79 00:21:21.00  10.4000A   2.0502  -2.1052   4.3253  0.110  1.41  -0.102E+01    850.  0.279E+00  0.279E+00  0.223E-03  0.316E-13    7  24  31    9   4   0   14  23  17    0.000    0.000       0
+  0     80 00:21:31.40  10.4000A   2.0227  -2.0595   4.3225  0.111  1.41  -0.101E+01    850.  0.281E+00  0.280E+00  0.222E-03  0.315E-13    7  24  31    9   4   0   14  23  17    0.000    0.000       0
+  0     81 00:21:41.80  10.5000A   1.9814  -1.9732   4.2991  0.112  1.41  -0.100E+01    850.  0.282E+00  0.281E+00  0.224E-03  0.316E-13    7  24  31    9   4   0   15  23  17    0.000    0.000       0
+  0     82 00:21:52.30  10.4000A   1.9340  -1.9475   4.3286  0.113  1.41  -0.982E+00    850.  0.283E+00  0.282E+00  0.227E-03  0.321E-13    7  24  31   10   4   0   15  23  17    0.000    0.000       0
+  0     83 00:22:02.70  10.5000A   1.8924  -2.0069   4.3038  0.114  1.41  -0.972E+00    850.  0.283E+00  0.283E+00  0.226E-03  0.320E-13   14   4   0   10   4   0   15  23  17    0.000    0.000       0
+  0     84 00:22:13.20  10.7000A   1.9415  -2.0355   4.2040  0.115  1.41  -0.961E+00    850.  0.283E+00  0.283E+00  0.229E-03  0.324E-13   14   4   0   10   4   0   15  23  17    0.000    0.000       0
+  0     85 00:22:23.90  10.8000A   1.9325  -2.0217   4.1559  0.116  1.41  -0.952E+00    850.  0.284E+00  0.283E+00  0.234E-03  0.332E-13   14   4   0   10   4   0   16  23  17    0.000    0.000       0
+  0     86 00:22:34.70  11.0000A   1.8907  -1.9607   4.0835  0.117  1.38  -0.945E+00    800.  0.284E+00  0.283E+00  0.237E-03  0.336E-13   14   4   0   10   4   0   16  23  17    0.000    0.000       0
+  0     87 00:22:45.70  11.4000A   1.8309  -1.8652   3.9358  0.118  1.38  -0.942E+00    800.  0.283E+00  0.283E+00  0.242E-03  0.344E-13   14   4   0   10   3   0   16  23  17    0.000    0.000       0
+  0     88 00:22:57.10  12.0000A   1.8977  -1.8027   3.7438  0.119  1.38  -0.929E+00    800.  0.283E+00  0.283E+00  0.252E-03  0.357E-13   15   4   1    7  24   4   16  23  17    0.000    0.000       0
+  0     89 00:23:09.10  12.6000A   1.9544  -1.8206   3.5844  0.119  1.38  -0.923E+00    800.  0.283E+00  0.282E+00  0.265E-03  0.376E-13   15   4   1    8  23   4   17  23  17    0.000    0.000       0
+  0     90 00:23:21.70  12.9000A   1.9261  -1.9283   3.4830  0.120  1.38  -0.920E+00    800.  0.282E+00  0.282E+00  0.278E-03  0.395E-13   15   4   1    8  23   4   16  12  29    0.000    0.000       0
+  0     91 00:23:34.60  13.2000A   1.8512  -2.0241   3.4202  0.121  1.38  -0.928E+00    800.  0.282E+00  0.281E+00  0.284E-03  0.404E-13   15   4   1    8  23   4   11  22  39    0.000    0.000       0
+  0     92 00:23:47.80  13.4000A   1.7632  -2.1053   3.3553  0.121  1.38  -0.909E+00    800.  0.281E+00  0.281E+00  0.290E-03  0.412E-13   15   4   1    8  23   4   12  22  39    0.000    0.000       0
+  0     93 00:24:01.20  13.6000A   1.7138  -2.1674   3.2986  0.122  1.35  -0.903E+00    750.  0.281E+00  0.280E+00  0.293E-03  0.418E-13    3  22  38    8  23   4   12  22  39    0.000    0.000       0
+  0     94 00:24:14.80  13.9000A   1.7170  -2.2027   3.2411  0.122  1.35  -0.901E+00    750.  0.280E+00  0.279E+00  0.296E-03  0.423E-13    3  22  38    8  23   4   12  22  39    0.000    0.000       0
+  0     95 00:24:28.70  14.1000A   1.7197  -2.1983   3.1899  0.123  1.35  -0.896E+00    750.  0.279E+00  0.279E+00  0.301E-03  0.431E-13    3  22  38    8  23   4   12  22  39    0.000    0.000       0
+  0     96 00:24:42.80  14.1000A   1.7153  -2.1719   3.1976  0.123  1.35  -0.891E+00    750.  0.279E+00  0.278E+00  0.303E-03  0.435E-13    3  22  38    7  23   5   10  23   1    0.000    0.000       0
+  0     97 00:24:56.90  13.8000A   1.6963  -2.1325   3.2561  0.123  1.35  -0.890E+00    750.  0.279E+00  0.278E+00  0.302E-03  0.432E-13    3  22  38    7  23   5   10  23   1    0.000    0.000       0
+  0     98 00:25:10.70  13.8000A  -1.7049  -2.1009   3.2710  0.123  1.35  -0.891E+00    750.  0.279E+00  0.278E+00  0.295E-03  0.420E-13    8  25   1    8  23   5   11  23   1    0.000    0.000       0
+  0     99 00:25:24.50  13.8000A   1.7204  -2.1783   3.2616  0.123  1.35  -0.892E+00    750.  0.278E+00  0.278E+00  0.295E-03  0.417E-13   10  26  31    8  23   5   11  23   1    0.000    0.000       0
+  0    100 00:25:38.30  13.8000A   1.7625  -2.1980   3.2579  0.124  1.41  -0.893E+00    850.  0.278E+00  0.278E+00  0.294E-03  0.413E-13   10  26  31    8  23   5   12  23   1    0.000    0.000       0
+  0    101 00:25:52.10  14.0000A   1.7838  -2.1524   3.2052  0.124  1.38  -0.899E+00    800.  0.278E+00  0.277E+00  0.293E-03  0.409E-13   10  26  31    8  23   5   12  23   1    0.000    0.000       0
+  0    102 00:26:06.10  14.1000A   1.7815  -2.0874   3.1853  0.124  1.38  -0.896E+00    800.  0.278E+00  0.277E+00  0.297E-03  0.411E-13   10  26  31    8  22   5   13  23   1    0.000    0.000       0
+  0    103 00:26:20.20  14.4000A  -1.8038  -2.1448   3.1345  0.124  1.38  -0.895E+00    800.  0.277E+00  0.277E+00  0.298E-03  0.410E-13   16  22  38    8  22   5   12  23  19    0.000    0.000       0
+  0    104 00:26:34.60  14.4000A   1.7966  -2.1120   3.1256  0.124  1.38  -0.894E+00    800.  0.277E+00  0.276E+00  0.303E-03  0.414E-13    1  36  26    8  22   5   12  23  19    0.000    0.000       0
+  0    105 00:26:49.00  14.4000A   1.8540  -1.9957   3.1203  0.124  1.38  -0.894E+00    800.  0.276E+00  0.276E+00  0.301E-03  0.410E-13    1  37  26    8  22   5    9  38  26    0.000    0.000       0
+  0    106 00:27:03.40  14.1000A   1.8694   1.8628   3.1953  0.125  1.38  -0.898E+00    800.  0.276E+00  0.275E+00  0.299E-03  0.407E-13    1  37  26    8  35  24   10  38  26    0.000    0.000       0
+  0    107 00:27:17.50  13.8000A   1.8312   1.8697   3.2551  0.125  1.38  -0.900E+00    800.  0.275E+00  0.274E+00  0.292E-03  0.396E-13    1  37  26    8  35  24   10  38  26    0.000    0.000       0
+  0    108 00:27:31.30  13.8000A   1.8481   1.8974   3.2672  0.125  1.38  -0.900E+00    800.  0.274E+00  0.274E+00  0.285E-03  0.386E-13    1  16  38    8  35  23   10  38  26    0.000    0.000       0
+  0    109 00:27:45.10  13.9000A   1.9162   1.9278   3.2486  0.125  1.38  -0.900E+00    800.  0.274E+00  0.273E+00  0.284E-03  0.385E-13    1  16  39    8  35  23   10  38  26    0.000    0.000       0
+  0    110 00:27:59.00  13.9000A   1.9932   1.9444   3.2453  0.126  1.38  -0.902E+00    800.  0.273E+00  0.272E+00  0.285E-03  0.387E-13    1  16  39    8  36  23   11  38  26    0.000    0.000       0
+  0    111 00:28:12.90  13.9000A   2.0637   2.0411   3.2331  0.126  1.38  -0.897E+00    800.  0.272E+00  0.271E+00  0.285E-03  0.386E-13    1  16  39    9  36  24   13  37  36    0.000    0.000       0
+  0    112 00:28:26.80  14.0000A   2.1140   2.0927   3.2228  0.126  1.38  -0.895E+00    800.  0.271E+00  0.271E+00  0.285E-03  0.386E-13    1  16  39    9  36  24   13  37  36    0.000    0.000       0
+  0    113 00:28:40.80  14.0000A   2.1252   2.1098   3.2064  0.126  1.41  -0.895E+00    850.  0.270E+00  0.270E+00  0.287E-03  0.388E-13    1  16  39    9  36  23   13  37  37    0.000    0.000       0
+  0    114 00:28:54.80  14.0000A   2.1629   2.1114   3.2196  0.127  1.41  -0.893E+00    850.  0.269E+00  0.268E+00  0.287E-03  0.388E-13    1  16   0    9  36  23   13  37  37    0.000    0.000       0
+  0    115 00:29:08.80  13.9000A   2.1941   2.1436   3.2459  0.127  1.41  -0.889E+00    850.  0.268E+00  0.267E+00  0.286E-03  0.387E-13    1  16   0    9  37  23   14  37  37    0.000    0.000       0
+  0    116 00:29:22.70  13.9000A   2.1660   2.1317   3.2349  0.127  1.41  -0.888E+00    850.  0.266E+00  0.266E+00  0.284E-03  0.384E-13    1  16   0    9  37  23   14  37  37    0.000    0.000       0
+  0    117 00:29:36.60  14.2000A   2.1114   2.0437   3.1772  0.127  1.38  -0.891E+00    800.  0.265E+00  0.264E+00  0.285E-03  0.383E-13    1  16   1    9  37  23   14  37  37    0.000    0.000       0
+  0    118 00:29:50.80  14.3000A   2.1168   1.8997   3.1409  0.128  1.38  -0.905E+00    800.  0.263E+00  0.262E+00  0.291E-03  0.390E-13    1  16   1    9  37  23   14   9  10    0.000    0.000       0
+  0    119 00:30:05.10  14.4000A   2.0639  -1.9024   3.1211  0.128  1.38  -0.889E+00    800.  0.261E+00  0.260E+00  0.293E-03  0.391E-13    1  16   1   10   6  21   13   6  16    0.000    0.000       0
Index: palm/trunk/TUTORIALS/cases/example_cbl/case_config.yml
===================================================================
--- palm/trunk/TUTORIALS/cases/example_cbl/case_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/example_cbl/case_config.yml	(revision 4091)
@@ -0,0 +1,23 @@
+---
+# this is a palmtest job configuration file
+
+allowed_builds:
+  - gfortran_default
+  - intel_default
+  - cray_default
+
+allowed_number_of_cores:
+  - 1
+  - 2
+  - 4
+  - 8
+  - 16
+
+activation_strings:
+  - "d3#"
+  - "restart"
+
+significant_digits_for_netcdf_checks:
+  timeseries: 3
+  profiles: 5
+  other: 8
Index: palm/trunk/TUTORIALS/cases/example_neutral/INPUT/example_neutral_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/example_neutral/INPUT/example_neutral_p3d	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/example_neutral/INPUT/example_neutral_p3d	(revision 4091)
@@ -0,0 +1,89 @@
+ &initialization_parameters 
+
+     !-- Numerical grid   
+         nx = 49, 
+         ny = 49, 
+         nz = 100,
+
+         dx = 20.0, 
+         dy = 20.0, 
+         dz = 20.0,
+
+     !-- Pressure solver  
+         fft_method = 'temperton-algorithm',
+
+     !-- Initialization
+!         initializing_actions = 'set_constant_profiles',
+
+         initializing_actions = 'set_1d-model_profiles',
+         end_time_1d = 864000.0,
+         damp_level_1d = 1250.0,
+         mixing_length_1d = 'blackadar',
+         dissipation_1d = 'detering',
+
+         dt_run_control_1d = 3600.0,
+         dt_pr_1d = 86400.0,
+
+     !-- Rayleigh damping
+         rayleigh_damping_height = 1250.0,
+         rayleigh_damping_factor = 0.01,
+         galilei_transformation = .T.,
+
+     !-- Roughness length         
+         roughness_length = 0.1, 
+
+     !-- Geostrophic wind (large-scale pressure gradient)
+         ug_surface = 5.0, 
+         vg_surface = 0.0,
+
+     !-- Neutral stratification
+         pt_surface = 300.0,
+         pt_vertical_gradient = 0.0,
+         pt_vertical_gradient_level = 0.0,
+         neutral = .T.,
+
+     !-- Boundary conditions
+         bc_uv_b =  'dirichlet', 
+         bc_uv_t = 'neumann',
+
+         bc_p_b = 'neumann', 
+         bc_p_t = 'dirichlet',
+
+         constant_flux_layer = .T.,
+         /
+
+ &runtime_parameters  
+
+     !-- Simulation time 1.5h
+         end_time = 5400.0,
+
+     !-- Disturbances
+         create_disturbances = .T.,
+         dt_disturb = 150.0, 
+         disturbance_energy_limit = 0.01,
+ 
+     !-- Run control
+         dt_run_control = 60.0,
+
+     !-- Time series
+         dt_dopr = 5400.0,
+         
+     !-- Vertical profiles
+         averaging_interval_pr = 5400.0, 
+         dt_averaging_input_pr = 50.0,
+         data_output_pr = '#u', '#v', '#theta', 
+                          'w"u"', 'w*u*', 'wu', 'w"v"', 'w*v*', 'wv','w*2', 'theta*2',
+                          
+         /
+         
+ &spectra_parameters
+ 
+     !-- Output settings for spectra
+         data_output_sp =  'u', 'v', 'w',
+         dt_dosp = 5400.0,
+         comp_spectra_level =  2, 5, 10, 15, 20,
+         spectra_direction =  'x' , 'y' , 'x',
+         averaging_interval_sp = 5400.0,
+         
+         /
+ 
Index: palm/trunk/TUTORIALS/cases/example_neutral/MONITORING/example_neutral_rc
===================================================================
--- palm/trunk/TUTORIALS/cases/example_neutral/MONITORING/example_neutral_rc	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/example_neutral/MONITORING/example_neutral_rc	(revision 4091)
@@ -0,0 +1,571 @@
+
+
+
+1D run control output:
+------------------------------
+
+ITER.   HH:MM:SS    DT      UMAX   VMAX    U*   ALPHA   ENERG.
+-------------------------------------------------------------
+      0 00:00:00    0.01    5.00   0.10  0.100   45.0    12.38
+    236 01:00:13   17.16    5.00   0.40  0.182    9.4    12.06
+    436 02:00:11   18.46    5.00   0.79  0.169   18.3    11.93
+    631 03:00:07   18.29    5.00   1.11  0.171   24.6    11.90
+    831 04:00:03   17.65    5.00   1.37  0.177   28.2    11.94
+   1039 05:00:04   17.00    5.02   1.53  0.184   29.7    12.03
+   1255 06:00:15   16.47    5.12   1.63  0.190   29.9    12.14
+   1476 07:00:10   16.10    5.27   1.65  0.194   29.4    12.26
+   1701 08:00:05   15.88    5.40   1.62  0.197   28.4    12.37
+   1929 09:00:12   15.78    5.51   1.57  0.198   27.4    12.45
+   2157 10:00:08   15.78    5.56   1.50  0.198   26.5    12.49
+   2385 11:00:13   15.85    5.57   1.44  0.197   25.7    12.49
+   2611 12:00:09   15.97    5.54   1.39  0.196   25.2    12.45
+   2835 13:00:02   16.11    5.49   1.36  0.194   25.0    12.40
+   3058 14:00:09   16.24    5.41   1.34  0.192   25.0    12.32
+   3279 15:00:09   16.34    5.34   1.34  0.191   25.3    12.25
+   3499 16:00:12   16.40    5.28   1.36  0.190   25.7    12.19
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+  51883 234:00:04  16.22    5.35   1.42  0.193   26.2    12.28
+  52105 235:00:05  16.22    5.35   1.42  0.193   26.2    12.28
+  52327 236:00:05  16.22    5.35   1.42  0.193   26.2    12.27
+  52549 237:00:06  16.22    5.35   1.42  0.193   26.3    12.27
+  52771 238:00:07  16.22    5.35   1.42  0.193   26.3    12.27
+  52993 239:00:08  16.22    5.35   1.42  0.193   26.3    12.27
+  53215 240:00:08  16.22    5.35   1.42  0.193   26.3    12.28
+
+ ******************************    --------------------------------------------
+ * PALM 6.0  Rev: 3986        *    atmosphere - run with 1D - prerun
+ ******************************    --------------------------------------------
+
+ Date:               2019-05-22    Run:       e2_neutral                        
+ Time:                 08:38:02    Run-No.:   00
+ Run on host:        imuk_defau
+ Number of PEs:               4    Processor grid (x,y): (   2,   2) calculated
+ ------------------------------------------------------------------------------
+
+ Numerical Schemes:
+ -----------------
+
+ --> Use the Moeng_Wyngaard turbulence closure (LES mode).
+ --> Use the boussinesq approximation for the model equations.
+ --> Solve perturbation pressure via FFT using temperton-algorithm routines
+     perturbation pressure is calculated at every Runge-Kutta step
+ --> Momentum advection via Wicker-Skamarock-Scheme 5th order
+ --> Scalar advection via Wicker-Skamarock-Scheme 5th order
+ --> Loop optimization method: cache
+ --> Galilei-Transform applied to horizontal advection:
+     translation velocity = 0.6 * geostrophic wind
+     distance advected at the start of the run:     0.000 km(x)     0.000 km(y)
+ --> Time differencing scheme: runge-kutta-3       
+ --> Rayleigh-Damping active, starts above z =  1250.00 m
+     maximum damping coefficient: 0.010 1/s
+ --> No pt-equation solved. Neutral stratification with pt = 300.00 K assumed
+ ------------------------------------------------------------------------------
+
+
+ Run time and time step information:
+ ----------------------------------
+
+ Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
+ Start time:              0.000 s
+ End time:             5400.000 s
+
+
+ Computational grid and domain size:
+ ----------------------------------
+
+ Grid length:      dx =      20.000 m    dy =      20.000 m
+                dz(1) =      20.000 m
+
+ Domain size:       x =   1000.000 m     y =   1000.000 m  z(u) =   2010.000 m
+
+
+
+ Number of gridpoints (x,y,z):  (0:  49, 0:  49, 0: 101)
+ Subdomain size (x,y,z):        (    25,     25,    102)
+
+
+    Characteristic levels of the geo. wind component ug:
+
+       Height:         0.0     0.0  m
+       ug:            5.00    5.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+    Characteristic levels of the geo. wind component vg:
+
+       Height:         0.0     0.0  m
+       vg:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+
+ Topography information:
+ ----------------------
+
+ Topography: flat                                    
+
+
+ Boundary conditions:
+ -------------------
+
+                     p                    uv                                  pt
+
+ B. bound.: p(0)     = p(1)   | uv(0)     = -uv(1)                | pt(0)     = pt_surface       
+ T. bound.: p(nzt+1) = 0      | uv(nzt+1) = uv(nzt)               | pt(nzt+1) = pt(nzt) + dpt/dz_
+
+                     e
+
+ B. bound.: e(0)     = e(1)                                                                      
+ T. bound.: e(nzt+1) = e(nzt) = e(nzt-1)                                                         
+
+ Bottom surface fluxes are used in diffusion terms at k=1
+
+
+    Constant flux layer between bottom surface and first computational u,v-level:
+
+       z_mo =  10.00 m   z0 = 0.1000 m   z0h = 0.10000 m   kappa = 0.40
+       Rif value range:     -20.00 <= rif <= 20.00
+       Predefined surface temperature
+
+
+ Lateral boundaries:
+       left/right:  cyclic              
+       north/south: cyclic              
+
+
+ Initial profiles:
+ ----------------
+
+    Characteristic levels of the initial temperature profile:
+
+       Height:           0.0  m
+       Temperature:   300.00  K
+       Gradient:      ------  K/100m
+       Gridpoint:          0
+
+
+ List output:
+ -----------
+
+    1D-Profiles:
+       Output every             9999999.90 s
+       Time averaged over        5400.00 s
+       Averaging input every       50.00 s
+
+
+ Data output:
+ -----------
+
+       Time averaged over        5400.00 s
+       Averaging input every       50.00 s
+
+    1D-Profiles:
+       Output format: netCDF 64bit offset                     
+
+
+       Profile: u, v, theta, w"u", w*u*, wu, w"v", w*v*, wv, w*2, theta*2,   
+
+              :                                                              
+       Output every              5400.00 s
+       Time averaged over        5400.00 s
+       Averaging input every       50.00 s
+
+    Time series:
+       Output format: netCDF 64bit offset                     
+
+       Output every                50.00 s
+
+ ------------------------------------------------------------------------------
+
+
+ Physical quantities:
+ -------------------
+
+    Geograph. latitude  :   latitude  = 55.0 degr
+    Geograph. longitude :   longitude =  0.0 degr
+    Angular velocity    :   omega  = 0.729E-04 rad/s
+    Coriolis parameter  :   f      =  0.000119 1/s
+                            f*     =  0.000084 1/s
+
+    Day of the year at model start :   day_init      =     172
+    UTC time at model start        :   time_utc_init = 43200.0 s
+
+    Gravity             :   g      =  9.8 m/s**2
+
+    Reference state used in buoyancy terms: initial_profile
+
+
+ Cloud physics quantities / methods:
+ ----------------------------------
+
+
+
+ LES / Turbulence quantities:
+ ---------------------------
+
+    Mixing length is limited to 1.80 * z
+
+
+ Actions during the simulation:
+ -----------------------------
+
+    Disturbance impulse (u,v) every :   150.00 s
+    Disturbance amplitude           :     0.25 m/s
+    Lower disturbance level         :    50.00 m (GP    3)
+    Upper disturbance level         :   650.00 m (GP   33)
+    Disturbances cease as soon as the disturbance energy exceeds 0.010 m**2/s**2
+    Random number generator used    : random-parallel
+
+
+
+ 1D-Model parameters:
+ -------------------
+
+    Simulation time:                   864000.0 s
+    Run-controll output every:           3600.0 s
+    Vertical profile output every:      86400.0 s
+    Mixing length calculation:         blackadar           
+    Dissipation calculation:           detering            
+
+    Damping layer starts from  1250.0 m (GP   63)
+
+    Spectra:
+       Output format: see profiles or other quantities
+
+       Output every  5400.0 s
+
+       Arrays:     u    ,v    ,w    ,     ,     ,     ,     ,     ,     ,     ,
+       Directions:    x ,   y ,   x ,   x ,   x ,   x ,   x ,   x ,   x ,   x ,
+       height levels  k =   2,  5, 10, 15, 20,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,
+                          ***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,
+                          ***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,
+                          ***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,
+                          ***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***,***.
+       Time averaged over  5400.0 s,
+       Profiles for the time averaging are taken every   50.0 s
+ ------------------------------------------------------------------------------
+
+
+
+Run-control output:
+------------------
+
+RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  0      0 00:00:00.00   7.1000A   5.5341D  1.6240D  0.1325  0.193  0.00   0.000E+00      0.  0.122E+02  0.121E-02  0.167E-02  0.238E-12   15   5  15    5  35  45   29  41  35    0.000    0.000       0
+  0      9 00:01:04.63   7.2400A   5.4873   1.5482   0.0972  0.192  0.00   0.000E+00      0.  0.122E+02  0.618E-03  0.607E-05  0.100E-14   14  46  36    4  41  47   29  41  41    0.194    0.000       0
+  0     17 00:02:02.85   7.3100A   5.4632   1.5368   0.0893  0.190  0.00   0.000E+00      0.  0.122E+02  0.506E-03  0.526E-05  0.882E-15   14  36  34    4  47  25   26   9  10    0.369    0.000       0
+  0     21 00:02:32.13   6.9700A   5.5811D  1.6585D  0.1572  0.189  0.00   0.000E+00      0.  0.122E+02  0.171E-02  0.167E-02  0.238E-12   15   1  14    4  27  28   24  28  29    0.456    0.000       0
+  0     25 00:03:00.21   7.0500A   5.5535   1.6243   0.1343  0.188  0.00   0.000E+00      0.  0.122E+02  0.125E-02  0.928E-05  0.146E-14   15  40  14    4   1  27   24  28  32    0.541    0.000       0
+  0     34 00:04:04.04   7.1700A   5.5116   1.5863  -0.1239  0.186  0.00   0.000E+00      0.  0.122E+02  0.101E-02  0.785E-05  0.134E-14   15  40  21    4   6  29   24  10   5    0.732    0.000       0
+  0     42 00:05:01.32   6.9100A   5.6041D  1.7281D -0.1909  0.184  0.00   0.000E+00      0.  0.122E+02  0.215E-02  0.166E-02  0.236E-12   17  31  27    4  17   9   31  28  39    0.904    0.000       0
+  0     51 00:06:03.46   6.9200A   5.6016   1.6787  -0.1579  0.182  0.00   0.000E+00      0.  0.122E+02  0.153E-02  0.989E-05  0.167E-14   15  41  35    4  22  11   31  28  45    1.090    0.000       0
+  0     60 00:07:06.08   6.9800A   5.5792   1.6734   0.1504  0.180  0.00   0.000E+00      0.  0.122E+02  0.137E-02  0.880E-05  0.151E-14   15  42  43    4  31  19    4  11  25    1.278    0.000       0
+  0     64 00:07:34.03   6.6700A   5.6972D  1.7472D  0.2070  0.180  0.00   0.000E+00      0.  0.122E+02  0.256E-02  0.167E-02  0.239E-12   15  42  47    6  27  13    4  13  26    1.362    0.000       0
+  0     68 00:08:00.72   6.7000A   5.6885   1.7324  -0.1812  0.179  0.00   0.000E+00      0.  0.122E+02  0.213E-02  0.118E-04  0.192E-14   15  42   0    5  27  16    7  25  11    1.442    0.000       0
+  0     77 00:09:01.70   6.8500A   5.6287   1.7170  -0.1713  0.178  0.00   0.000E+00      0.  0.122E+02  0.187E-02  0.103E-04  0.175E-14   15  43   8    4  37  37   10  26  14    1.625    0.000       0
+  0     86 00:10:03.37   6.7300A   5.6741D  1.8181D  0.2449  0.177  0.00   0.000E+00      0.  0.122E+02  0.298E-02  0.167E-02  0.238E-12   15  33  19    4  42  38    7  22  35    1.810    0.000       0
+  0     95 00:11:03.88   6.7600A   5.6630   1.7875  -0.1798  0.176  0.00   0.000E+00      0.  0.122E+02  0.235E-02  0.118E-04  0.197E-14   15  33  27    4  47  40    7  37  28    1.992    0.000       0
+  0    104 00:12:05.35   6.9100A   5.6061   1.7676  -0.1636  0.175  0.00   0.000E+00      0.  0.122E+02  0.215E-02  0.107E-04  0.185E-14   14  39  27    4  38  14    9  34  32    2.176    0.000       0
+  0    108 00:12:32.96   6.4900A   5.7732D  1.8916D -0.2252  0.175  0.00   0.000E+00      0.  0.122E+02  0.331E-02  0.168E-02  0.239E-12   14  36  21    4   4  43    5  11  10    2.259    0.000       0
+  0    113 00:13:05.83   6.7200A   5.6805   1.8343  -0.2046  0.175  0.00   0.000E+00      0.  0.122E+02  0.280E-02  0.134E-04  0.221E-14   14  36  24    4   7  44    5  13  12    2.357    0.000       0
+  0    122 00:14:06.73   6.7800A   5.6561   1.7711   0.1785  0.174  0.00   0.000E+00      0.  0.122E+02  0.252E-02  0.119E-04  0.203E-14   15  37  32    4  21  16   16   4  12    2.540    0.000       0
+  0    130 00:15:01.44   6.7200A   5.6782D  1.8823D -0.2251  0.174  0.00   0.000E+00      0.  0.122E+02  0.357E-02  0.167E-02  0.237E-12   14  21   1    5  40   7   17  30  36    2.704    0.000       0
+  0    139 00:16:02.51   6.8200A   5.6376   1.8188   0.2050  0.173  0.00   0.000E+00      0.  0.122E+02  0.292E-02  0.133E-04  0.226E-14   14  22  10    5   6  24   16   4  24    2.888    0.000       0
+  0    148 00:17:04.25   6.8800A   5.6168   1.8121  -0.1967  0.173  0.00   0.000E+00      0.  0.122E+02  0.274E-02  0.121E-04  0.210E-14   14  23  18    5  30  19   11  23  26    3.073    0.000       0
+  0    152 00:17:31.80   6.6700A   5.7002D  1.9104D  0.2267  0.173  0.00   0.000E+00      0.  0.122E+02  0.392E-02  0.166E-02  0.238E-12   14  23  22    4  21  48   16   5  34    3.155    0.000       0
+  0    157 00:18:05.17   6.6800A   5.6958   1.8587   0.2145  0.173  0.00   0.000E+00      0.  0.122E+02  0.342E-02  0.145E-04  0.240E-14   14  24  26    4  25  48   16   5  38    3.256    0.000       0
+  0    166 00:19:05.63   6.7500A   5.6670   1.8479  -0.2109  0.173  0.00   0.000E+00      0.  0.122E+02  0.319E-02  0.132E-04  0.228E-14   14  42   1    5  40  25   16  49  42    3.437    0.000       0
+  0    175 00:20:06.57   6.6500A   5.7055D  1.9168D -0.3083  0.172  0.00   0.000E+00      0.  0.122E+02  0.435E-02  0.167E-02  0.237E-12   14  26  43    4  29  30    7   3  35    3.620    0.000       0
+  0    183 00:21:00.16   6.7200A   5.6774   1.8909  -0.2681  0.172  0.00   0.000E+00      0.  0.122E+02  0.379E-02  0.150E-04  0.257E-14   14  46  15    4  35  32    7   6  39    3.780    0.000       0
+  0    192 00:22:00.80   6.7400A   5.6693   1.8641  -0.2550  0.172  0.00   0.000E+00      0.  0.122E+02  0.365E-02  0.136E-04  0.237E-14   13   3   6    4  40  34    5   5   6    3.962    0.000       0
+  0    197 00:22:34.52   6.4600A   5.7880D  1.8960D -0.2770  0.172  0.00   0.000E+00      0.  0.122E+02  0.488E-02  0.167E-02  0.238E-12   13   5  10    4  35   5   15   0  15    4.064    0.000       0
+  0    201 00:23:00.53   6.5200A   5.7628   1.8995  -0.2673  0.172  0.00   0.000E+00      0.  0.122E+02  0.444E-02  0.166E-04  0.278E-14   13   6  14    6  16  43   15   0  18    4.142    0.000       0
+  0    211 00:24:05.98   6.5800A   5.7343   1.9142   0.2531  0.173  0.00   0.000E+00      0.  0.122E+02  0.417E-02  0.148E-04  0.259E-14   13  10  18    6  21  48    6  22  10    4.338    0.000       0
+  0    220 00:25:05.25   6.4300A   5.7991D  2.0079D  0.2837  0.173  0.00   0.000E+00      0.  0.122E+02  0.525E-02  0.167E-02  0.238E-12   14   7  25    4  26  45    6  25  15    4.516    0.000       0
+  0    229 00:26:03.67   6.5300A   5.7561   2.0097  -0.2471  0.173  0.00   0.000E+00      0.  0.122E+02  0.459E-02  0.160E-04  0.275E-14   14   8  33    4  30  46    9  34  37    4.691    0.000       0
+  0    238 00:27:02.73   6.6100A   5.7230   1.9647   0.2377  0.173  0.00   0.000E+00      0.  0.122E+02  0.436E-02  0.149E-04  0.260E-14   14   8  40    4  41   9    7   3  15    4.868    0.000       0
+  0    243 00:27:35.79   6.5300A   5.7556D  2.0387D  0.2905  0.173  0.00   0.000E+00      0.  0.122E+02  0.550E-02  0.167E-02  0.238E-12   11  19  44    4  36  22    4  40  11    4.967    0.000       0
+  0    247 00:28:02.04   6.6200A   5.7191   2.0384   0.2726  0.173  0.00   0.000E+00      0.  0.122E+02  0.503E-02  0.178E-04  0.298E-14   14  39  47    4  38  23    4  42  12    5.046    0.000       0
+  0    256 00:29:02.01   6.7000A   5.6867   1.9994   0.2764  0.173  0.00   0.000E+00      0.  0.122E+02  0.474E-02  0.162E-04  0.283E-14   12  20  29    4  22  20   16  43  43    5.226    0.000       0
+  0    265 00:30:01.98   6.5000A   5.7675D  2.1354D -0.3131  0.174  0.00   0.000E+00      0.  0.122E+02  0.589E-02  0.168E-02  0.239E-12   13  20  35    4  28  21    9   0   8    5.406    0.000       0
+  0    274 00:31:00.96   6.5500A   5.7468   2.0611   0.3310  0.174  0.00   0.000E+00      0.  0.122E+02  0.531E-02  0.178E-04  0.309E-14   12  25  42    4  32  23   10  38  39    5.583    0.000       0
+  0    283 00:32:00.01   6.6000A   5.7282   1.9744   0.3301  0.174  0.00   0.000E+00      0.  0.122E+02  0.520E-02  0.169E-04  0.303E-14   12  27  49    4  38  26   10  41  45    5.760    0.000       0
+  0    288 00:32:33.07   6.4700A   5.7826D  2.0511D  0.3494  0.174  0.00   0.000E+00      0.  0.122E+02  0.644E-02  0.167E-02  0.239E-12   12  19  30    3  16   9    9  47  14    5.859    0.000       0
+  0    293 00:33:05.65   6.5200A   5.7625   2.0372   0.3517  0.175  0.00   0.000E+00      0.  0.122E+02  0.595E-02  0.193E-04  0.331E-14   11  20  18    3  18  10    9  48  18    5.957    0.000       0
+  0    302 00:34:04.17   6.4900A   5.7754   2.0103  -0.3419  0.175  0.00   0.000E+00      0.  0.122E+02  0.576E-02  0.177E-04  0.314E-14   11  22  25    4  11   3   11   0  39    6.133    0.000       0
+  0    311 00:35:02.67   6.4600A   5.7862D  2.0723D -0.4333  0.176  0.00   0.000E+00      0.  0.122E+02  0.696E-02  0.168E-02  0.238E-12   12  25  47    4  46  23   10   2  45    6.308    0.000       0
+  0    320 00:36:01.70   6.6100A   5.7223   2.0269  -0.4070  0.176  0.00   0.000E+00      0.  0.122E+02  0.642E-02  0.196E-04  0.346E-14   11  15  49    4  11  47   10   4   1    6.485    0.000       0
+  0    329 00:37:01.26   6.6100A   5.7212   2.0273  -0.3639  0.177  0.00   0.000E+00      0.  0.122E+02  0.638E-02  0.183E-04  0.328E-14   12  25  48    5  15   1   10   6   8    6.664    0.000       0
+  0    334 00:37:34.32   6.4000A   5.8138D  2.0568D -0.3777  0.177  0.00   0.000E+00      0.  0.122E+02  0.771E-02  0.167E-02  0.238E-12   11  28   2    4  33  49   10   8  11    6.763    0.000       0
+  0    338 00:38:00.11   6.5100A   5.7650   2.0866  -0.3547  0.177  0.00   0.000E+00      0.  0.122E+02  0.734E-02  0.210E-04  0.362E-14   12  31  16    3  36  24    6  17   8    6.840    0.000       0
+  0    348 00:39:05.58   6.6100A   5.7213   2.0299  -0.3713  0.177  0.00   0.000E+00      0.  0.122E+02  0.726E-02  0.197E-04  0.347E-14   11  30  13    3  41  24   14  32  10    7.037    0.000       0
+  0    357 00:40:05.28   6.4000A   5.8125D  2.1157D -0.3479  0.178  0.00   0.000E+00      0.  0.122E+02  0.849E-02  0.167E-02  0.238E-12   12   4  40    3  29  26   13  33  17    7.216    0.000       0
+  0    366 00:41:03.22   6.5100A   5.7663   2.0435   0.3528  0.179  0.00   0.000E+00      0.  0.122E+02  0.803E-02  0.212E-04  0.370E-14   13  25  18    3  43  39    6  17  43    7.390    0.000       0
+  0    375 00:42:01.80   6.5200A   5.7589   2.0209  -0.3646  0.180  0.00   0.000E+00      0.  0.122E+02  0.801E-02  0.202E-04  0.352E-14   13  26  25    4  10  48    6  40  44    7.565    0.000       0
+  0    380 00:42:34.48   6.3200A   5.8475D  2.0952D  0.4152  0.180  0.00   0.000E+00      0.  0.122E+02  0.930E-02  0.166E-02  0.235E-12   14  27  29    3  36  25   10  17  12    7.663    0.000       0
+  0    385 00:43:06.19   6.3900A   5.8168   2.1067  -0.4372  0.180  0.00   0.000E+00      0.  0.122E+02  0.890E-02  0.232E-04  0.397E-14   13  29  32    3  39  25    5  44  48    7.759    0.000       0
+  0    394 00:44:03.48   6.3700A   5.8273   2.1167   0.4442  0.181  0.00   0.000E+00      0.  0.122E+02  0.883E-02  0.218E-04  0.380E-14   13  32  39    3  45  25    5  14  18    7.930    0.000       0
+  0    403 00:45:00.71   6.1500A   5.9269D  2.2306D  0.4913  0.182  0.00   0.000E+00      0.  0.122E+02  0.102E-01  0.167E-02  0.237E-12   14  32  46    5   2  29    5  17  20    8.102    0.000       0
+  0    413 00:46:03.33   6.2900A   5.8621   2.2858   0.4235  0.183  0.00   0.000E+00      0.  0.122E+02  0.978E-02  0.234E-04  0.411E-14   13  36   4    4   6  30    5  21  23    8.290    0.000       0
+  0    422 00:47:00.40   6.3300A   5.8419   2.3473   0.4612  0.184  0.00   0.000E+00      0.  0.122E+02  0.989E-02  0.231E-04  0.411E-14   13  40  10    3  33   6    7   4   7    8.461    0.000       0
+  0    427 00:47:32.01   6.1500A   5.9253D  2.3946D  0.5082  0.185  0.00   0.000E+00      0.  0.122E+02  0.114E-01  0.166E-02  0.236E-12   12  42  13    4  13  33    7   5  10    8.556    0.000       0
+  0    432 00:48:02.83   6.1400A   5.9311   2.3647   0.4958  0.186  0.00   0.000E+00      0.  0.122E+02  0.111E-01  0.253E-04  0.438E-14   12  43  18    4  15  34    8   8  12    8.648    0.000       0
+  0    442 00:49:04.80   6.2700A   5.8729   2.2905   0.4626  0.188  0.00   0.000E+00      0.  0.122E+02  0.112E-01  0.251E-04  0.448E-14   12  45  26    3  45   7    8  13  17    8.834    0.000       0
+  0    451 00:50:01.46   6.2800A   5.8648   2.3104   0.4734  0.190  0.00   0.000E+00      0.  0.122E+02  0.115E-01  0.247E-04  0.440E-14   10  45  45    4   8  44    7  17  24    9.004    0.000       0
+  0    461 00:51:04.38   6.3400A   5.8408   2.3822   0.5172  0.192  0.00   0.000E+00      0.  0.122E+02  0.119E-01  0.252E-04  0.455E-14   10  48   2    4  29   1    7  22  29    9.193    0.000       0
+  0    470 00:52:02.19   6.4800A   5.7759   2.4304   0.5241  0.194  0.00   0.000E+00      0.  0.122E+02  0.124E-01  0.261E-04  0.473E-14   13  16  43    4  19  44    6  48   7    9.367    0.000       0
+  0    479 00:53:00.56   6.5500A   5.7492   2.4268   0.4949  0.196  0.00   0.000E+00      0.  0.122E+02  0.128E-01  0.257E-04  0.461E-14    9   4  17    4  24  47    6  39   9    9.542    0.000       0
+  0    489 00:54:05.72   6.4600A   5.7875   2.3768   0.5158  0.199  0.00   0.000E+00      0.  0.122E+02  0.133E-01  0.256E-04  0.462E-14   11  17  32    3  30  47    9  20   2    9.737    0.000       0
+  0    498 00:55:03.48   6.3800A   5.8232   2.5198   0.5702  0.201  0.00   0.000E+00      0.  0.122E+02  0.139E-01  0.255E-04  0.452E-14   11  19  39    4  47  19    5  44  21    9.910    0.000       0
+  0    507 00:56:00.70   6.3700A   5.8276   2.5606   0.6513  0.203  0.00   0.000E+00      0.  0.122E+02  0.147E-01  0.259E-04  0.458E-14   11  21  46    3  31  34    6   1  23   10.082    0.000       0
+  0    517 00:57:04.63   6.3900A   5.8158   2.4356   0.7323  0.205  0.00   0.000E+00      0.  0.122E+02  0.157E-01  0.259E-04  0.457E-14   10  24   4    5   7  24    6   5  26   10.274    0.000       0
+  0    526 00:58:02.60   6.5000A   5.7703   2.3564   0.6519  0.207  0.00   0.000E+00      0.  0.122E+02  0.166E-01  0.266E-04  0.476E-14   10  25  11    5  13  25    6   8  29   10.448    0.000       0
+  0    535 00:59:01.18   6.4800A   5.7766   2.3260   0.5898  0.209  0.00   0.000E+00      0.  0.122E+02  0.176E-01  0.274E-04  0.497E-14   10  23  40    4  17  27    9  47  25   10.624    0.000       0
+  0    545 01:00:05.51   6.4300A   5.8008   2.3291   0.6336  0.212  0.00   0.000E+00      0.  0.122E+02  0.184E-01  0.277E-04  0.499E-14   10  25  47    4  16  24    7  11  11   10.817    0.000       0
+  0    554 01:01:03.28   6.3500A   5.8359   2.3239   0.6566  0.214  0.00   0.000E+00      0.  0.122E+02  0.190E-01  0.286E-04  0.520E-14    9  32  37    4  19  26    7  20  39   10.990    0.000       0
+  0    564 01:02:05.05   5.9900A   6.0061   2.3825   0.7823  0.216  0.00   0.000E+00      0.  0.122E+02  0.194E-01  0.288E-04  0.521E-14    9  35  44    3   0  41    7  24  41   11.175    0.000       0
+  0    574 01:03:04.40   5.9400A   6.0307   2.4539   0.8238  0.217  0.00   0.000E+00      0.  0.122E+02  0.196E-01  0.290E-04  0.522E-14    9  37   1    3   5  42    8  28  44   11.353    0.000       0
+  0    584 01:04:03.39   5.9300A   6.0371   2.4406  -0.8704  0.218  0.00   0.000E+00      0.  0.122E+02  0.198E-01  0.297E-04  0.537E-14   10  37   5    3  10  43    9  33   6   11.530    0.000       0
+  0    594 01:05:02.90   6.0300A   5.9827   2.4208   0.8608  0.219  0.00   0.000E+00      0.  0.122E+02  0.201E-01  0.302E-04  0.547E-14   11  38  10    3  15  44    5  29  33   11.709    0.000       0
+  0    604 01:06:03.73   6.1800A   5.9107   2.6135  -0.7488  0.219  0.00   0.000E+00      0.  0.122E+02  0.206E-01  0.305E-04  0.552E-14   11  40  17    4  38  32    4  27  19   11.891    0.000       0
+  0    614 01:07:05.52   6.1300A   5.9359   2.4763   0.8449  0.219  0.00   0.000E+00      0.  0.122E+02  0.211E-01  0.299E-04  0.531E-14    7   4  13    4  44  33   10  43   1   12.077    0.000       0
+  0    623 01:08:01.13   6.2300A   5.8874   2.2912   0.8845  0.219  0.00   0.000E+00      0.  0.122E+02  0.218E-01  0.308E-04  0.542E-14    8   7  43    4  48  34   11  45   6   12.243    0.000       0
+  0    633 01:09:03.01   6.1900A   5.9056   2.3335   0.9523  0.220  0.00   0.000E+00      0.  0.122E+02  0.227E-01  0.319E-04  0.573E-14    8  12   1    5  21  47    6  44  39   12.429    0.000       0
+  0    643 01:10:05.22   6.2300A   5.8897   2.3234   0.9165  0.220  0.00   0.000E+00      0.  0.122E+02  0.236E-01  0.333E-04  0.601E-14   14   0  20    4  24  17    7  47  42   12.616    0.000       0
+  0    652 01:11:00.48   6.1300A   5.9376   2.3321   1.1240  0.220  0.00   0.000E+00      0.  0.122E+02  0.246E-01  0.336E-04  0.600E-14   14   2  26    4  29  20    5  49  42   12.781    0.000       0
+  0    662 01:12:01.79   6.1500A   5.9277   2.4206   1.1537  0.222  0.00   0.000E+00      0.  0.122E+02  0.261E-01  0.337E-04  0.608E-14    8  14   9    3  19   2    6   2  43   12.965    0.000       0
+  0    672 01:13:03.64   6.2100A   5.8965   2.5242   0.9159  0.223  0.00   0.000E+00      0.  0.122E+02  0.275E-01  0.342E-04  0.616E-14   13   9  17    3  24   7    9   4   2   13.151    0.000       0
+  0    682 01:14:04.98   6.0200A   5.9909   2.5767   0.9425  0.224  0.00   0.000E+00      0.  0.122E+02  0.286E-01  0.356E-04  0.652E-14   10  19  17    3  30  12   10  15  11   13.335    0.000       0
+  0    692 01:15:05.38   6.0000A   5.9995   2.6448   0.9469  0.226  0.00   0.000E+00      0.  0.122E+02  0.293E-01  0.366E-04  0.662E-14    9  25  24    3  34  16   12  17  17   13.516    0.000       0
+  0    702 01:16:05.44   6.0400A   5.9816   2.7451   0.9431  0.228  0.00   0.000E+00      0.  0.122E+02  0.298E-01  0.378E-04  0.680E-14    9  29  30    3  40  20    6  15   4   13.696    0.000       0
+  0    712 01:17:05.33   5.8500A   6.0748   2.6259   1.0662  0.230  0.00   0.000E+00      0.  0.122E+02  0.302E-01  0.384E-04  0.678E-14   11  31  34    2  42  16    6  18   5   13.876    0.000       0
+  0    722 01:18:02.60   5.5500A   6.2427   2.5915   1.1587  0.232  0.00   0.000E+00      0.  0.122E+02  0.305E-01  0.383E-04  0.685E-14   11  35  40    3   3  26    7  22   5   14.048    0.000       0
+  0    733 01:19:03.19   5.5500A   6.2439   2.5737   1.3111  0.233  0.00   0.000E+00      0.  0.122E+02  0.307E-01  0.397E-04  0.708E-14   11  38  47    5  34  45    8  24   8   14.230    0.000       0
+  0    744 01:20:05.79   5.8000A   6.1010   2.4834   1.4113  0.234  0.00   0.000E+00      0.  0.122E+02  0.308E-01  0.434E-04  0.773E-14    9  49   3    3  26  35    9  27  12   14.417    0.000       0
+  0    754 01:21:04.77   5.9000A   6.0483   2.4762   1.4678  0.235  0.00   0.000E+00      0.  0.122E+02  0.308E-01  0.463E-04  0.822E-14   10   2   8    3  30  36   10  29  17   14.594    0.000       0
+  0    764 01:22:03.24   5.8400A   6.0847   2.3906   1.4754  0.237  0.00   0.000E+00      0.  0.122E+02  0.311E-01  0.470E-04  0.828E-14    9   5  15    3  34  44   13  32  22   14.770    0.000       0
+  0    774 01:23:01.29   5.8500A   6.0745   2.4260   1.3763  0.240  0.00   0.000E+00      0.  0.122E+02  0.315E-01  0.480E-04  0.845E-14   10   6  21    3  39  46   15  35  26   14.944    0.000       0
+  0    784 01:24:00.43   6.0800A   5.9598   2.4522   1.2245  0.243  0.00   0.000E+00      0.  0.122E+02  0.321E-01  0.518E-04  0.912E-14   10   8  27    5  49  16   16  37  31   15.121    0.000       0
+  0    794 01:25:02.48   6.3000A   5.8549   2.5481   1.2132  0.246  0.00   0.000E+00      0.  0.122E+02  0.326E-01  0.544E-04  0.956E-14   15  17  28    6   7  18    7  43  27   15.307    0.000       0
+  0    804 01:26:05.34   6.1900A   5.9099   2.5832   1.2948  0.248  0.00   0.000E+00      0.  0.121E+02  0.331E-01  0.528E-04  0.932E-14   17  45  48    6  11  23    8  47  29   15.496    0.000       0
+  0    813 01:27:00.30   5.9900A   6.0030   2.5195  -1.3523  0.250  0.00   0.000E+00      0.  0.121E+02  0.336E-01  0.507E-04  0.902E-14   14  37  43    2   0  12    9  43  36   15.661    0.000       0
+  0    824 01:28:05.12   5.7700A   6.1174   2.4504  -1.3802  0.250  0.00   0.000E+00      0.  0.121E+02  0.338E-01  0.490E-04  0.871E-14   13  40  49    5   9  24    8  45  42   15.855    0.000       0
+  0    834 01:29:03.06   5.8800A   6.0628   2.2952   1.3345  0.250  0.00   0.000E+00      0.  0.121E+02  0.338E-01  0.497E-04  0.893E-14   13  42   5    5  22  36   10   5  40   16.029    0.000       0
+  0    844 01:30:02.82   6.1500A   5.9278   2.2391   1.1944  0.249  0.00   0.000E+00      0.  0.121E+02  0.335E-01  0.516E-04  0.920E-14   15   6  23    5  26  40   11  49  11   16.208    0.000       0
Index: palm/trunk/TUTORIALS/cases/example_neutral/case_config.yml
===================================================================
--- palm/trunk/TUTORIALS/cases/example_neutral/case_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/example_neutral/case_config.yml	(revision 4091)
@@ -0,0 +1,16 @@
+---
+# this is a palmtest job configuration file
+
+allowed_builds:
+  - gfortran_default
+  - intel_default
+
+allowed_number_of_cores: []
+
+activation_strings:
+  - "d3#"
+
+significant_digits_for_netcdf_checks:
+  timeseries: 3
+  profiles: 2
+  other: 8
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/INPUT/flow_around_cube_cyclic_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/INPUT/flow_around_cube_cyclic_p3d	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/INPUT/flow_around_cube_cyclic_p3d	(revision 4091)
@@ -0,0 +1,80 @@
+&initialization_parameters
+   !-- grid setup
+      nx = 39,
+      ny = 39,
+      nz = 40,
+
+      dx = 2.0,
+      dy = 2.0,
+      dz = 2.0,
+
+   !-- pressure solver
+      fft_method = 'temperton-algorithm',     ! fast, but restrictions apply
+
+   !-- init-action
+      initializing_actions = 'set_constant_profiles',
+
+   !-- advection schemes
+      momentum_advec = 'ws-scheme',           ! default advection scheme
+      scalar_advec   = 'ws-scheme',
+
+   !-- wind speed setup
+      ug_surface = 1.0,
+      vg_surface = 0.0,
+
+   !-- temperature setup
+      neutral = .T.,                          ! strictly neutral flow
+
+   !-- boundary conditions
+      bc_uv_t = 'neumann',                    ! free-slip boundary condition
+
+      roughness_length = 0.1,                 ! applies to all surfaces locally
+
+   !-- special methods
+      dp_external = .T.,                      ! use horizontal pressure gradient
+      dpdxy = -0.0002, 0.0,                   ! for forcing
+
+   !-- special setups
+      omega = 0.0,                            ! no Coriolis force
+
+      topography = 'read_from_file',
+   /
+
+
+&runtime_parameters
+   !-- simulation time
+      end_time                = 2700.0,
+      termination_time_needed =  900.0,
+
+   !-- others
+      create_disturbances = .T.,
+
+   !-- global output settings
+      skip_time_data_output =    0.0,
+      dt_data_output        = 1800.0,
+
+      averaging_interval    = 1800.0,
+      dt_averaging_input    =    6.0,
+
+   !-- time series / run control
+      dt_run_control        =  60.0,
+      dt_dots               =  60.0,
+
+   !-- profiles
+      skip_time_dopr        =    0.0,
+      dt_dopr               = 1800.0,
+      averaging_interval_pr = 1800.0,
+      dt_averaging_input_pr =    6.0,
+
+      data_output_pr = '#u', 'u*2', 'wu', 'w*u*', 'w"u"',
+                       '#v', 'v*2', 'wv', 'w*v*', 'w"v"',
+                       'w*2',
+                       'e', 'e*',
+                       '#km',
+                       '#l',
+
+   !-- output variables
+      data_output = 'u', 'u_av',
+                    'v', 'v_av',
+                    'w', 'w_av',
+   /
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/INPUT/flow_around_cube_cyclic_topo
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/INPUT/flow_around_cube_cyclic_topo	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/INPUT/flow_around_cube_cyclic_topo	(revision 4091)
@@ -0,0 +1,40 @@
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
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+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/MONITORING/flow_around_cube_cyclic_rc
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/MONITORING/flow_around_cube_cyclic_rc	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/MONITORING/flow_around_cube_cyclic_rc	(revision 4091)
@@ -0,0 +1,269 @@
+
+ ******************************    --------------------------------------------
+ * PALM 6.0  Rev: 3986        *    atmosphere - run without 1D - prerun
+ ******************************    --------------------------------------------
+
+ Date:               2019-05-22    Run:       e3_cube_cyc                       
+ Time:                 09:22:07    Run-No.:   00
+ Run on host:        imuk_defau
+ Number of PEs:               2    Processor grid (x,y): (   1,   2) calculated
+                                   A 1d-decomposition along y is used
+ ------------------------------------------------------------------------------
+
+ Numerical Schemes:
+ -----------------
+
+ --> Use the Moeng_Wyngaard turbulence closure (LES mode).
+ --> Use the boussinesq approximation for the model equations.
+ --> Solve perturbation pressure via FFT using temperton-algorithm routines
+     perturbation pressure is calculated at every Runge-Kutta step
+ --> Momentum advection via Wicker-Skamarock-Scheme 5th order
+ --> Scalar advection via Wicker-Skamarock-Scheme 5th order
+ --> Loop optimization method: cache
+ --> Time differencing scheme: runge-kutta-3       
+ --> No pt-equation solved. Neutral stratification with pt = 300.00 K assumed
+ --> External pressure gradient directly prescribed by the user:
+      -0.20000E-03  0.00000E+00Pa/m in x/y direction
+     starting from dp_level_b =   0.000m.
+
+ ------------------------------------------------------------------------------
+
+
+ Run time and time step information:
+ ----------------------------------
+
+ Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
+ Start time:              0.000 s
+ End time:             2700.000 s
+
+
+ Computational grid and domain size:
+ ----------------------------------
+
+ Grid length:      dx =       2.000 m    dy =       2.000 m
+                dz(1) =       2.000 m
+
+ Domain size:       x =     80.000 m     y =     80.000 m  z(u) =     81.000 m
+
+
+
+ Number of gridpoints (x,y,z):  (0:  39, 0:  39, 0:  41)
+ Subdomain size (x,y,z):        (    40,     20,     42)
+
+
+    Characteristic levels of the geo. wind component ug:
+
+       Height:         0.0     0.0  m
+       ug:            1.00    1.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+    Characteristic levels of the geo. wind component vg:
+
+       Height:         0.0     0.0  m
+       vg:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+
+ Topography information:
+ ----------------------
+
+ Topography: read_from_file                          
+ Topography grid definition convention:
+ cell center (scalar grid points)
+
+
+
+ Boundary conditions:
+ -------------------
+
+                     p                    uv                                  pt
+
+ B. bound.: p(0)     = p(1)   | uv(0)     = -uv(1)                | pt(0)     = pt_surface       
+ T. bound.: p(nzt+1) = 0      | uv(nzt+1) = uv(nzt)               | pt(nzt+1) = pt(nzt) + dpt/dz_
+
+                     e
+
+ B. bound.: e(0)     = e(1)                                                                      
+ T. bound.: e(nzt+1) = e(nzt) = e(nzt-1)                                                         
+
+ Bottom surface fluxes are used in diffusion terms at k=1
+
+
+    Constant flux layer between bottom surface and first computational u,v-level:
+
+       z_mo =   1.00 m   z0 = 0.1000 m   z0h = 0.10000 m   kappa = 0.40
+       Rif value range:     -20.00 <= rif <= 20.00
+       Predefined surface temperature
+
+
+ Lateral boundaries:
+       left/right:  cyclic              
+       north/south: cyclic              
+
+
+ Initial profiles:
+ ----------------
+
+    Characteristic levels of the initial temperature profile:
+
+       Height:           0.0  m
+       Temperature:   300.00  K
+       Gradient:      ------  K/100m
+       Gridpoint:          0
+
+
+ List output:
+ -----------
+
+    1D-Profiles:
+       Output every             9999999.90 s
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+
+
+ Data output:
+ -----------
+
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+
+    1D-Profiles:
+       Output format: netCDF 64bit offset                     
+
+
+       Profile: u, u*2, wu, w*u*, w"u", v, v*2, wv, w*v*, w"v", w, w*2,      
+
+              : e, e*, km, l,                                                
+       Output every              1800.00 s
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+
+    3D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w,                                                             
+       Output every              1800.00 s  
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    3D-Arrays(time-averaged):
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w,                                                             
+       Output every              1800.00 s  
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    Time series:
+       Output format: netCDF 64bit offset                     
+
+       Output every                60.00 s
+
+ ------------------------------------------------------------------------------
+
+
+ Physical quantities:
+ -------------------
+
+    Geograph. latitude  :   latitude  = 55.0 degr
+    Geograph. longitude :   longitude =  0.0 degr
+    Angular velocity    :   omega  = 0.000E+00 rad/s
+    Coriolis parameter  :   f      =  0.000000 1/s
+                            f*     =  0.000000 1/s
+
+    Day of the year at model start :   day_init      =     172
+    UTC time at model start        :   time_utc_init = 43200.0 s
+
+    Gravity             :   g      =  9.8 m/s**2
+
+    Reference state used in buoyancy terms: initial_profile
+
+
+ Cloud physics quantities / methods:
+ ----------------------------------
+
+
+
+ LES / Turbulence quantities:
+ ---------------------------
+
+    Mixing length is limited to 1.80 * z
+
+
+ Actions during the simulation:
+ -----------------------------
+
+    Disturbance impulse (u,v) every :   ****** s
+    Disturbance amplitude           :     0.25 m/s
+    Lower disturbance level         :     5.00 m (GP    3)
+    Upper disturbance level         :    25.00 m (GP   13)
+    Disturbances cease as soon as the disturbance energy exceeds 0.010 m**2/s**2
+    Random number generator used    : random-parallel
+
+ ------------------------------------------------------------------------------
+
+
+
+Run-control output:
+------------------
+
+RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  0      0 00:00:00.00   1.3200A   1.3650D -0.7720D -0.6273  0.000  0.00   0.000E+00      0.  0.389E+00  0.234E-01  0.203E-01  0.477E-02    9   9  23    8  30  30   21  20  30    0.000    0.000       0
+  0     46 00:01:00.88   1.4100A   1.2745   0.7341   0.9442  0.069  0.00   0.000E+00      0.  0.361E+00  0.511E-01  0.957E-03  0.204E-03    9   5  21   16  30   9   20  17   9    0.000    0.000       0
+  0     88 00:02:00.25   1.3800A   1.3077  -0.8434  -0.9061  0.072  0.00   0.000E+00      0.  0.354E+00  0.533E-01  0.846E-03  0.646E-04    8   4  10   13  28   7    9  28   9    0.000    0.000       0
+  0    132 00:03:00.24   1.4800A   1.2187   0.6960  -0.7555  0.061  0.00   0.000E+00      0.  0.346E+00  0.462E-01  0.841E-03  0.849E-04   10  35  20   12  15   7    7  18   8    0.000    0.000       0
+  0    172 00:04:00.46   1.4500A   1.2416   0.7303   0.7444  0.065  0.00   0.000E+00      0.  0.340E+00  0.445E-01  0.819E-03  0.675E-04   11  31  33    8  15   9    7  18  30    0.000    0.000       0
+  0    213 00:05:00.56   1.4800A   1.2162  -0.7397   0.6731  0.055  0.00   0.000E+00      0.  0.333E+00  0.440E-01  0.110E-02  0.939E-04   28  16  20   13  23   9   20  19   8    0.000    0.000       0
+  0    253 00:06:00.20   1.4800A   1.2180  -0.5743  -0.7430  0.063  0.00   0.000E+00      0.  0.325E+00  0.438E-01  0.109E-02  0.559E-04   18  39  35   10  23   9    4  27   9    0.000    0.000       0
+  0    294 00:07:00.84   1.5000A   1.2019   0.6712   0.5836  0.053  0.00   0.000E+00      0.  0.319E+00  0.380E-01  0.100E-02  0.632E-04   30   9  31   15  14   9   19  10   9    0.000    0.000       0
+  0    334 00:08:00.10   1.4600A   1.2330   0.5700   0.6068  0.051  0.00   0.000E+00      0.  0.313E+00  0.363E-01  0.906E-03  0.584E-04   26  10   0   18  13   9   20  11   9    0.000    0.000       0
+  0    376 00:09:01.27   1.4400A   1.2529  -0.5782  -0.6260  0.054  0.00   0.000E+00      0.  0.309E+00  0.337E-01  0.788E-03  0.402E-04   41  13  30   17  26   9   16  25   8    0.000    0.000       0
+  0    417 00:10:00.87   1.4500A   1.2378  -0.6271  -0.5692  0.054  0.00   0.000E+00      0.  0.307E+00  0.324E-01  0.734E-03  0.352E-04   32  14   3   16  26   9    7  22   6    0.000    0.000       0
+  0    458 00:11:00.12   1.4300A   1.2561  -0.4355  -0.5508  0.053  0.00   0.000E+00      0.  0.306E+00  0.319E-01  0.684E-03  0.406E-04   30  29  38   10  25   9   16  21   9    0.000    0.000       0
+  0    501 00:12:01.43   1.4300A   1.2587   0.7102  -0.5519  0.049  0.00   0.000E+00      0.  0.304E+00  0.328E-01  0.688E-03  0.440E-04   28   0  14   11  17   9    4  11   9    0.000    0.000       0
+  0    542 00:13:00.30   1.4500A   1.2450  -0.5292  -0.4274  0.049  0.00   0.000E+00      0.  0.304E+00  0.322E-01  0.682E-03  0.374E-04   28  35   3    6  27   9   16  16   9    0.000    0.000       0
+  0    584 00:14:01.01   1.4400A   1.2478  -0.5565   0.6836  0.047  0.00   0.000E+00      0.  0.303E+00  0.321E-01  0.717E-03  0.503E-04   37  35  18   13  24   9   20  24   9    0.000    0.000       0
+  0    626 00:15:00.77   1.3800A   1.3077  -0.6396  -0.5159  0.051  0.00   0.000E+00      0.  0.302E+00  0.326E-01  0.673E-03  0.351E-04   30  37   6    4  25   8    2  28   9    0.000    0.000       0
+  0    669 00:16:00.17   1.3800A   1.3076  -0.4875  -0.4605  0.053  0.00   0.000E+00      0.  0.302E+00  0.316E-01  0.641E-03  0.331E-04   31  36  39   13  25   9   11  24   3    0.000    0.000       0
+  0    713 00:17:00.24   1.3600A   1.3229  -0.6296   0.4714  0.051  0.00   0.000E+00      0.  0.302E+00  0.307E-01  0.602E-03  0.317E-04   34  35  32   12  25   9   19  28   9    0.000    0.000       0
+  0    757 00:18:00.86   1.3800A   1.3009  -0.4377  -0.4774  0.051  0.00   0.000E+00      0.  0.302E+00  0.294E-01  0.548E-03  0.303E-04   37  30  25   10  21   9   16  20   8    0.000    0.000       0
+  0    800 00:19:00.76   1.3800A   1.3057  -0.5445   0.4946  0.052  0.00   0.000E+00      0.  0.302E+00  0.295E-01  0.556E-03  0.322E-04   35   6  35   13  24   9   20  12   9    0.000    0.000       0
+  0    844 00:20:01.17   1.3700A   1.3120  -0.4737  -0.4226  0.048  0.00   0.000E+00      0.  0.302E+00  0.293E-01  0.523E-03  0.281E-04   38   3  28   13  23   9   13  22   8    0.000    0.000       0
+  0    887 00:21:00.32   1.3500A   1.3345   0.6354   0.5531  0.049  0.00   0.000E+00      0.  0.303E+00  0.305E-01  0.568E-03  0.348E-04   36   0  13   11  16   9   20  12   9    0.000    0.000       0
+  0    932 00:22:00.44   1.3500A   1.3356  -0.4277  -0.4778  0.048  0.00   0.000E+00      0.  0.304E+00  0.298E-01  0.538E-03  0.303E-04   35  38   7   24   4  23    7  20   4    0.000    0.000       0
+  0    976 00:23:00.42   1.3600A   1.3220   0.4857  -0.5644  0.048  0.00   0.000E+00      0.  0.304E+00  0.302E-01  0.598E-03  0.398E-04   41   2   1   10  19   9   17  22   9    0.000    0.000       0
+  0   1020 00:24:00.48   1.3700A   1.3141   0.4438  -0.5511  0.049  0.00   0.000E+00      0.  0.304E+00  0.298E-01  0.584E-03  0.239E-04   41   0  37   11  16   9   17  17   9    0.000    0.000       0
+  0   1065 00:25:01.02   1.3200A   1.3686   0.4364  -0.5210  0.049  0.00   0.000E+00      0.  0.304E+00  0.279E-01  0.596E-03  0.420E-04   36  34  34   24  13  15   14  19   9    0.000    0.000       0
+  0   1110 00:26:00.55   1.3400A   1.3403   0.4464  -0.5077  0.047  0.00   0.000E+00      0.  0.303E+00  0.272E-01  0.566E-03  0.314E-04   36  32  27    7  15   9   11  27   9    0.000    0.000       0
+  0   1155 00:27:00.93   1.3300A   1.3526  -0.4459  -0.5341  0.048  0.00   0.000E+00      0.  0.304E+00  0.262E-01  0.571E-03  0.343E-04   39  33  30   18  17   9   17  20   9    0.000    0.000       0
+  0   1200 00:28:00.78   1.3300A   1.3520   0.5670  -0.4614  0.050  0.00   0.000E+00      0.  0.304E+00  0.259E-01  0.530E-03  0.278E-04   39  33  29    8  15   9    9  24   8    0.000    0.000       0
+  0   1245 00:29:00.57   1.3200A   1.3633   0.5390   0.4500  0.047  0.00   0.000E+00      0.  0.305E+00  0.260E-01  0.533E-03  0.385E-04   40  28  22    9  15   9   20  18   9    0.000    0.000       0
+  0   1291 00:30:00.94   1.3200A   1.3686  -0.5021  -0.4951  0.050  0.00   0.000E+00      0.  0.305E+00  0.269E-01  0.545E-03  0.248E-04   41  28  19   10  25   8    9  12   3    0.000    0.000       0
+  0   1336 00:31:00.54   1.3300A   1.3509   0.4976  -0.4628  0.049  0.00   0.000E+00      0.  0.305E+00  0.261E-01  0.605E-03  0.360E-04   41  28  16   11  14   9   16   5  13    0.000    0.000       0
+  0   1381 00:32:01.22   1.3400A   1.3410   0.5311  -0.4174  0.049  0.00   0.000E+00      0.  0.304E+00  0.262E-01  0.597E-03  0.351E-04   32  31  26    9  17   9    4  13   9    0.000    0.000       0
+  0   1426 00:33:01.14   1.3300A   1.3538   0.5617  -0.3814  0.051  0.00   0.000E+00      0.  0.304E+00  0.256E-01  0.580E-03  0.307E-04   31  31  26   10  18   9   17  16   8    0.000    0.000       0
+  0   1470 00:34:00.31   1.3500A   1.3368  -0.4133  -0.6027  0.056  0.00   0.000E+00      0.  0.304E+00  0.258E-01  0.587E-03  0.286E-04   33  28  10   17   9   9   17  20   9    0.000    0.000       0
+  0   1515 00:35:01.07   1.3700A   1.3156  -0.4154  -0.5481  0.052  0.00   0.000E+00      0.  0.305E+00  0.250E-01  0.577E-03  0.304E-04   41  19  26   17  27   9   14  22   9    0.000    0.000       0
+  0   1558 00:36:00.27   1.3800A   1.3078   0.4234  -0.6261  0.052  0.00   0.000E+00      0.  0.305E+00  0.261E-01  0.579E-03  0.329E-04   37  22  27   16  31   9   15  21   9    0.000    0.000       0
+  0   1602 00:37:00.48   1.3300A   1.3489  -0.4528  -0.4659  0.050  0.00   0.000E+00      0.  0.306E+00  0.254E-01  0.528E-03  0.291E-04   28  25  28    4  18   8   12  19   8    0.000    0.000       0
+  0   1647 00:38:00.68   1.3300A   1.3495  -0.4300  -0.5780  0.053  0.00   0.000E+00      0.  0.307E+00  0.254E-01  0.514E-03  0.310E-04   32  28  18    2  11   5   15  21   9    0.000    0.000       0
+  0   1692 00:39:00.73   1.3300A   1.3514  -0.4506   0.5417  0.049  0.00   0.000E+00      0.  0.307E+00  0.268E-01  0.540E-03  0.340E-04   31  13   5   12  26   9   20  11   9    0.000    0.000       0
+  0   1737 00:40:01.13   1.3500A   1.3370  -0.6432   0.3822  0.047  0.00   0.000E+00      0.  0.307E+00  0.275E-01  0.598E-03  0.377E-04   33  14  33    7  24   9   21   8   7    0.000    0.000       0
+  0   1782 00:41:00.63   1.3400A   1.3423  -0.4732   0.4168  0.047  0.00   0.000E+00      0.  0.308E+00  0.274E-01  0.572E-03  0.328E-04   35  10  24   14  25   9   20  27   9    0.000    0.000       0
+  0   1826 00:42:00.38   1.3700A   1.3125   0.4957  -0.4151  0.046  0.00   0.000E+00      0.  0.308E+00  0.271E-01  0.571E-03  0.302E-04   30  18  18   15  15   9    4  13   9    0.000    0.000       0
+  0   1871 00:43:00.76   1.3400A   1.3392  -0.4889  -0.5244  0.045  0.00   0.000E+00      0.  0.308E+00  0.274E-01  0.538E-03  0.318E-04   27  21  11   20  13   9   17  18   9    0.000    0.000       0
+  0   1915 00:44:00.31   1.3600A   1.3242  -0.4663  -0.5750  0.047  0.00   0.000E+00      0.  0.308E+00  0.274E-01  0.574E-03  0.324E-04   24  20  27   17  25   6   15  21   9    0.000    0.000       0
+  0   1960 00:45:00.87   1.3300A   1.3554   0.4779  -0.4899  0.044  0.00   0.000E+00      0.  0.308E+00  0.265E-01  0.611E-03  0.394E-04   35  22  18   20  24   8    9  21   8    0.000    0.000       0
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/case_config.yml
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/case_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_cyclic/case_config.yml	(revision 4091)
@@ -0,0 +1,16 @@
+---
+# this is a palmtest job configuration file
+
+allowed_builds:
+  - gfortran_default
+  - intel_default
+
+allowed_number_of_cores: []
+
+activation_strings:
+  - "d3#"
+
+significant_digits_for_netcdf_checks:
+  timeseries: 4
+  profiles: 6
+  other: 8
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/INPUT/flow_around_cube_noncyclic_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/INPUT/flow_around_cube_noncyclic_p3d	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/INPUT/flow_around_cube_noncyclic_p3d	(revision 4091)
@@ -0,0 +1,83 @@
+&initialization_parameters
+   !-- grid setup
+      nx = 79,
+      ny = 39,
+      nz = 40,
+
+      dx = 2.0,
+      dy = 2.0,
+      dz = 2.0,
+
+   !-- pressure solver
+      psolver   = 'multigrid',                ! required for non-cyclic bc
+      mg_cycles = 2,                          ! needs to be checked
+
+   !-- init-action
+      initializing_actions = 'cyclic_fill',
+
+   !-- advection schemes
+      momentum_advec = 'ws-scheme',           ! default advection scheme
+      scalar_advec   = 'ws-scheme',
+
+   !-- wind speed setup
+      ug_surface = 1.0,
+      vg_surface = 0.0,
+
+   !-- temperature setup
+      neutral = .T.,                          ! strictly neutral flow
+
+   !-- boundary conditions
+      bc_uv_t = 'neumann',                    ! free-slip boundary condition
+      bc_lr   = 'dirichlet/radiation',        ! non-cyclic left/right boundary
+
+      roughness_length = 0.1,                 ! applies to all surfaces locally
+
+   !-- special methods
+      turbulent_inflow      = .TRUE.,
+      recycling_width       = 80.0,
+      inflow_damping_height = 80.0, 
+
+   !-- special setups
+      omega = 0.0,                            ! no Coriolis force
+
+      topography = 'read_from_file',
+      topography_grid_convention = 'cell_center',   ! default
+   /
+
+
+&runtime_parameters
+   !-- simulation time
+      end_time                = 600.0,
+      termination_time_needed = 600.0,
+
+   !-- others
+
+   !-- global output settings
+      skip_time_data_output =    0.0,
+      dt_data_output        =  600.0,
+
+      averaging_interval    =  600.0,
+      dt_averaging_input    =    6.0,
+
+   !-- time series / run control
+      dt_run_control        =  60.0,
+      dt_dots               =  60.0,
+
+   !-- profiles
+      skip_time_dopr        =    0.0,
+      dt_dopr               =  600.0,
+      averaging_interval_pr =  600.0,
+      dt_averaging_input_pr =    6.0,
+
+      data_output_pr = '#u', 'u*2', 'wu', 'w*u*', 'w"u"',
+                       '#v', 'v*2', 'wv', 'w*v*', 'w"v"',
+                       'w*2',
+                       'e', 'e*',
+                       '#km',
+                       '#l',
+
+   !-- output variables
+      data_output = 'u', 'u_av',
+                    'v', 'v_av',
+                    'w', 'w_av',
+   /
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/INPUT/flow_around_cube_noncyclic_topo
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/INPUT/flow_around_cube_noncyclic_topo	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/INPUT/flow_around_cube_noncyclic_topo	(revision 4091)
@@ -0,0 +1,40 @@
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Index: palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/MONITORING/flow_around_cube_noncyclic_rc
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/MONITORING/flow_around_cube_noncyclic_rc	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/MONITORING/flow_around_cube_noncyclic_rc	(revision 4091)
@@ -0,0 +1,239 @@
+
+ ******************************    --------------------------------------------
+ * PALM 6.0  Rev: 3986        *    atmosphere - run with cyclic fill of 3D - prerun data
+ ******************************    --------------------------------------------
+
+ Date:               2019-05-22    Run:       e3_cube_noncyc                    
+ Time:                 11:49:29    Run-No.:   00
+ Run on host:        imuk_defau
+ Number of PEs:               2    Processor grid (x,y): (   1,   2) calculated
+                                   A 1d-decomposition along y is used
+ ------------------------------------------------------------------------------
+
+ Numerical Schemes:
+ -----------------
+
+ --> Use the Moeng_Wyngaard turbulence closure (LES mode).
+ --> Use the boussinesq approximation for the model equations.
+ --> Solve perturbation pressure via multigrid method (w-cycle)
+     number of grid levels:                    3
+     Gauss-Seidel red/black iterations:        2
+     fixed number of multigrid cycles:           2
+     perturbation pressure is calculated at every Runge-Kutta step
+ --> Momentum advection via Wicker-Skamarock-Scheme 5th order
+ --> Scalar advection via Wicker-Skamarock-Scheme 5th order
+ --> Loop optimization method: cache
+ --> Time differencing scheme: runge-kutta-3       
+ --> No pt-equation solved. Neutral stratification with pt = 300.00 K assumed
+ ------------------------------------------------------------------------------
+
+
+ Run time and time step information:
+ ----------------------------------
+
+ Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
+ Start time:              0.000 s
+ End time:              600.000 s
+
+
+ Computational grid and domain size:
+ ----------------------------------
+
+ Grid length:      dx =       2.000 m    dy =       2.000 m
+                dz(1) =       2.000 m
+
+ Domain size:       x =    160.000 m     y =     80.000 m  z(u) =     81.000 m
+
+
+
+ Number of gridpoints (x,y,z):  (0:  79, 0:  39, 0:  41)
+ Subdomain size (x,y,z):        (    80,     20,     42)
+
+
+    Characteristic levels of the geo. wind component ug:
+
+       Height:         0.0     0.0  m
+       ug:            1.00    1.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+    Characteristic levels of the geo. wind component vg:
+
+       Height:         0.0     0.0  m
+       vg:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+
+ Topography information:
+ ----------------------
+
+ Topography: read_from_file                          
+ Topography grid definition convention:
+ cell center (scalar grid points)
+
+
+
+ Boundary conditions:
+ -------------------
+
+                     p                    uv                                  pt
+
+ B. bound.: p(0)     = p(1)   | uv(0)     = -uv(1)                | pt(0)     = pt_surface       
+ T. bound.: p(nzt+1) = 0      | uv(nzt+1) = uv(nzt)               | pt(nzt+1) = pt(nzt) + dpt/dz_
+
+                     e
+
+ B. bound.: e(0)     = e(1)                                                                      
+ T. bound.: e(nzt+1) = e(nzt) = e(nzt-1)                                                         
+
+ Bottom surface fluxes are used in diffusion terms at k=1
+
+
+    Constant flux layer between bottom surface and first computational u,v-level:
+
+       z_mo =   1.00 m   z0 = 0.1000 m   z0h = 0.10000 m   kappa = 0.40
+       Rif value range:     -20.00 <= rif <= 20.00
+       Predefined surface temperature
+
+
+ Lateral boundaries:
+       left/right:  dirichlet/radiation 
+       north/south: cyclic              
+
+       use_cmax: T
+       pt damping layer width =     0.00 m, pt damping factor = 0.0000
+       turbulence recycling at inflow switched on
+       width of recycling domain:    80.0 m   grid index:   40
+       inflow damping height:   80.0 m   width:    8.0 m
+
+
+ Initial profiles:
+ ----------------
+
+    Characteristic levels of the initial temperature profile:
+
+       Height:           0.0  m
+       Temperature:   300.00  K
+       Gradient:      ------  K/100m
+       Gridpoint:          0
+
+
+ List output:
+ -----------
+
+    1D-Profiles:
+       Output every             9999999.90 s
+       Time averaged over         600.00 s
+       Averaging input every        6.00 s
+
+
+ Data output:
+ -----------
+
+       Time averaged over         600.00 s
+       Averaging input every        6.00 s
+
+    1D-Profiles:
+       Output format: netCDF 64bit offset                     
+
+
+       Profile: u, u*2, wu, w*u*, w"u", v, v*2, wv, w*v*, w"v", w*2,         
+
+              : e, e*, km, l,                                                
+       Output every               600.00 s
+       Time averaged over         600.00 s
+       Averaging input every        6.00 s
+
+    3D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w,                                                             
+       Output every               600.00 s  
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    3D-Arrays(time-averaged):
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w,                                                             
+       Output every               600.00 s  
+       Time averaged over         600.00 s
+       Averaging input every        6.00 s
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    Time series:
+       Output format: netCDF 64bit offset                     
+
+       Output every                60.00 s
+
+ ------------------------------------------------------------------------------
+
+
+ Physical quantities:
+ -------------------
+
+    Geograph. latitude  :   latitude  = 55.0 degr
+    Geograph. longitude :   longitude =  0.0 degr
+    Angular velocity    :   omega  = 0.000E+00 rad/s
+    Coriolis parameter  :   f      =  0.000000 1/s
+                            f*     =  0.000000 1/s
+
+    Day of the year at model start :   day_init      =     172
+    UTC time at model start        :   time_utc_init = 43200.0 s
+
+    Gravity             :   g      =  9.8 m/s**2
+
+    Reference state used in buoyancy terms: initial_profile
+
+
+ Cloud physics quantities / methods:
+ ----------------------------------
+
+
+
+ LES / Turbulence quantities:
+ ---------------------------
+
+    Mixing length is limited to 1.80 * z
+
+
+ Actions during the simulation:
+ -----------------------------
+
+    Disturbance impulse (u,v) every :   ****** s
+    Disturbance amplitude           :     0.25 m/s
+    Lower disturbance level         :     5.00 m (GP    3)
+    Upper disturbance level         :    25.00 m (GP   13)
+    Disturbances continued during the run from i/j =  10 to i/j =  59
+    Random number generator used    : random-parallel
+
+ ------------------------------------------------------------------------------
+
+
+
+Run-control output:
+------------------
+
+RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  0      0 00:00:00.00   1.7500A   1.0258   0.1887   0.1568  0.000  0.00   0.000E+00      0.  0.319E+00  0.433E-02  0.000E+00  0.000E+00   40  39  32   10   5  16    7  30  24    0.000    0.000       0
+  0     44 00:01:00.03   1.3800A   1.3023  -0.9059   1.1410  0.056  0.00   0.000E+00      0.  0.350E+00  0.257E-01  0.959E-03  0.115E-03   21  22  50    2   9  49   20  21  49    0.000    0.000       2
+  0     88 00:02:00.90   1.4100A   1.2728   0.7803   1.0866  0.054  0.00   0.000E+00      0.  0.353E+00  0.283E-01  0.870E-03  0.974E-04   16  34  62    1  31  49   20  23  49    0.000    0.000       2
+  0    132 00:03:01.09   1.3100A   1.3756  -0.6602   0.9525  0.054  0.00   0.000E+00      0.  0.360E+00  0.355E-01  0.804E-03  0.732E-04   15  39   0    1   9  49   20  24  49    0.000    0.000       2
+  0    177 00:04:00.32   1.2900A   1.3998   0.7440   1.0563  0.052  0.00   0.000E+00      0.  0.369E+00  0.433E-01  0.750E-03  0.740E-04   15  38  73    9  31  49   20  13  49    0.000    0.000       2
+  0    226 00:05:00.11   1.2100A   1.4904   0.6525   1.0411  0.052  0.00   0.000E+00      0.  0.378E+00  0.518E-01  0.765E-03  0.671E-04   14  37  73    2  31  49   20  24  49    0.000    0.000       2
+  0    276 00:06:00.87   1.1900A   1.5158   0.6775   1.0760  0.052  0.00   0.000E+00      0.  0.389E+00  0.623E-01  0.850E-03  0.750E-04   17   3  58   17  30  49   20  25  49    0.000    0.000       2
+  0    328 00:07:00.09   1.1000A   1.6348   0.6900   1.0862  0.059  0.00   0.000E+00      0.  0.398E+00  0.704E-01  0.901E-03  0.659E-04   21   8  73   11  18  49   20  12  49    0.000    0.000       2
+  0    382 00:08:00.89   1.0900A   1.6450  -0.8238   1.3869  0.061  0.00   0.000E+00      0.  0.404E+00  0.773E-01  0.110E-02  0.874E-04   21  12  50    9  10  49   20  13  49    0.000    0.000       2
+  0    437 00:09:00.12   1.0400A   1.7316   0.9994   1.3816  0.062  0.00   0.000E+00      0.  0.411E+00  0.826E-01  0.123E-02  0.863E-04   19   3  71   20  18  49   20  26  49    0.000    0.000       2
+  0    495 00:10:00.41   1.0200A   1.7623  -0.8743   1.4594  0.066  0.00   0.000E+00      0.  0.413E+00  0.853E-01  0.141E-02  0.860E-04   18   1  62   12  16  43   20  26  49    0.000    0.000       2
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/case_config.yml
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/case_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_noncyclic/case_config.yml	(revision 4091)
@@ -0,0 +1,19 @@
+---
+# this is a palmtest job configuration file
+
+allowed_builds:
+  - gfortran_default
+  - intel_default
+
+allowed_number_of_cores: []
+
+activation_strings:
+  - "d3#"
+  - "rec"
+
+use_binary_files_from: flow_around_cube_precursor
+
+significant_digits_for_netcdf_checks:
+  timeseries: 3
+  profiles: 0
+  other: 8
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/INPUT/flow_around_cube_precursor_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/INPUT/flow_around_cube_precursor_p3d	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/INPUT/flow_around_cube_precursor_p3d	(revision 4091)
@@ -0,0 +1,84 @@
+&initialization_parameters
+   !-- grid setup
+      nx = 39,
+      ny = 39,
+      nz = 40,
+
+      dx = 2.0,
+      dy = 2.0,
+      dz = 2.0,
+
+   !-- pressure solver
+      fft_method = 'temperton-algorithm',     ! fast, but restrictions apply
+
+   !-- init-action
+      initializing_actions = 'set_1d-model_profiles',
+
+   !-- advection schemes
+      momentum_advec = 'ws-scheme',           ! default advection scheme
+      scalar_advec   = 'ws-scheme',
+
+   !-- wind speed setup
+      ug_surface = 1.0,
+      vg_surface = 0.0,
+
+   !-- temperature setup
+      neutral = .T.,                          ! strictly neutral flow
+
+   !-- boundary conditions
+      bc_uv_t = 'neumann',                    ! free-slip boundary condition
+
+      roughness_length = 0.1,                 ! applies to all surfaces locally
+
+   !-- special methods
+      dp_external = .T.,                      ! use horizontal pressure gradient
+      dpdxy = -0.00003, 0.0,                  ! for forcing
+
+   !-- special setups
+      omega = 0.0,                            ! no Coriolis force
+
+      !1d-model setup
+      mixing_length_1d  = 'blackadar',        ! default
+      dissipation_1d    = 'detering',         ! default
+      end_time_1d       =  86400.0,           ! default
+      dt_run_control_1d =   3600.0,
+   /
+
+
+&runtime_parameters
+   !-- simulation time
+      end_time                = 1800.0,
+      termination_time_needed =  900.0,
+
+   !-- others
+      create_disturbances = .T.,
+
+   !-- global output settings
+      skip_time_data_output =    0.0,
+      dt_data_output        = 1800.0,
+
+      averaging_interval    = 1800.0,
+      dt_averaging_input    =    6.0,
+
+   !-- time series / run control
+      dt_run_control        =  60.0,
+      dt_dots               =  60.0,
+
+   !-- profiles
+      skip_time_dopr        =    0.0,
+      dt_dopr               = 1800.0,
+      averaging_interval_pr =    0.0,
+      dt_averaging_input_pr =    0.0,
+
+      data_output_pr = '#u', 'u*2', 'wu', 'w*u*', 'w"u"',
+                       '#v', 'v*2', 'wv', 'w*v*', 'w"v"',
+                       'w*2',
+                       'e', 'e*',
+                       '#km',
+                       '#l',
+
+   !-- output variables
+      data_output = 'u', 'u_av',
+                    'v', 'v_av',
+                    'w', 'w_av',
+   /
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/MONITORING/flow_around_cube_precursor_rc
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/MONITORING/flow_around_cube_precursor_rc	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/MONITORING/flow_around_cube_precursor_rc	(revision 4091)
@@ -0,0 +1,291 @@
+
+
+
+1D run control output:
+------------------------------
+
+ITER.   HH:MM:SS    DT      UMAX   VMAX    U*   ALPHA   ENERG.
+-------------------------------------------------------------
+      0 00:00:00    0.01    1.00   0.10  0.100   45.0     0.49
+   2398 01:00:00    1.13    1.00   0.00  0.055    0.0     0.34
+   6365 02:00:00    0.81    1.00   0.00  0.051    0.0     0.31
+  10896 03:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  15458 04:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  20019 05:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  24580 06:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  29141 07:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  33702 08:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  38262 09:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  42823 10:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  47384 11:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  51945 12:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  56506 13:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  61067 14:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  65628 15:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  70189 16:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  74750 17:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  79311 18:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  83872 19:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  88432 20:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  92993 21:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+  97554 22:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+ 102115 23:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+ 106676 24:00:00    0.79    1.00   0.00  0.051    0.0     0.31
+
+ ******************************    --------------------------------------------
+ * PALM 6.0  Rev: 3986        *    atmosphere - run with 1D - prerun
+ ******************************    --------------------------------------------
+
+ Date:               2019-05-22    Run:       e3_cube_pcr                       
+ Time:                 11:28:53    Run-No.:   00
+ Run on host:        imuk_defau
+ Number of PEs:               2    Processor grid (x,y): (   1,   2) calculated
+                                   A 1d-decomposition along y is used
+ ------------------------------------------------------------------------------
+
+ Numerical Schemes:
+ -----------------
+
+ --> Use the Moeng_Wyngaard turbulence closure (LES mode).
+ --> Use the boussinesq approximation for the model equations.
+ --> Solve perturbation pressure via FFT using temperton-algorithm routines
+     perturbation pressure is calculated at every Runge-Kutta step
+ --> Momentum advection via Wicker-Skamarock-Scheme 5th order
+ --> Scalar advection via Wicker-Skamarock-Scheme 5th order
+ --> Loop optimization method: cache
+ --> Time differencing scheme: runge-kutta-3       
+ --> No pt-equation solved. Neutral stratification with pt = 300.00 K assumed
+ --> External pressure gradient directly prescribed by the user:
+      -0.30000E-04  0.00000E+00Pa/m in x/y direction
+     starting from dp_level_b =   0.000m.
+
+ ------------------------------------------------------------------------------
+
+
+ Run time and time step information:
+ ----------------------------------
+
+ Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
+ Start time:              0.000 s
+ End time:             1800.000 s
+
+
+ Computational grid and domain size:
+ ----------------------------------
+
+ Grid length:      dx =       2.000 m    dy =       2.000 m
+                dz(1) =       2.000 m
+
+ Domain size:       x =     80.000 m     y =     80.000 m  z(u) =     81.000 m
+
+
+
+ Number of gridpoints (x,y,z):  (0:  39, 0:  39, 0:  41)
+ Subdomain size (x,y,z):        (    40,     20,     42)
+
+
+    Characteristic levels of the geo. wind component ug:
+
+       Height:         0.0     0.0  m
+       ug:            1.00    1.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+    Characteristic levels of the geo. wind component vg:
+
+       Height:         0.0     0.0  m
+       vg:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+
+ Topography information:
+ ----------------------
+
+ Topography: flat                                    
+
+
+ Boundary conditions:
+ -------------------
+
+                     p                    uv                                  pt
+
+ B. bound.: p(0)     = p(1)   | uv(0)     = -uv(1)                | pt(0)     = pt_surface       
+ T. bound.: p(nzt+1) = 0      | uv(nzt+1) = uv(nzt)               | pt(nzt+1) = pt(nzt) + dpt/dz_
+
+                     e
+
+ B. bound.: e(0)     = e(1)                                                                      
+ T. bound.: e(nzt+1) = e(nzt) = e(nzt-1)                                                         
+
+ Bottom surface fluxes are used in diffusion terms at k=1
+
+
+    Constant flux layer between bottom surface and first computational u,v-level:
+
+       z_mo =   1.00 m   z0 = 0.1000 m   z0h = 0.10000 m   kappa = 0.40
+       Rif value range:     -20.00 <= rif <= 20.00
+       Predefined surface temperature
+
+
+ Lateral boundaries:
+       left/right:  cyclic              
+       north/south: cyclic              
+
+
+ Initial profiles:
+ ----------------
+
+    Characteristic levels of the initial temperature profile:
+
+       Height:           0.0  m
+       Temperature:   300.00  K
+       Gradient:      ------  K/100m
+       Gridpoint:          0
+
+
+ List output:
+ -----------
+
+    1D-Profiles:
+       Output every             9999999.90 s
+
+
+ Data output:
+ -----------
+
+
+    1D-Profiles:
+       Output format: netCDF 64bit offset                     
+
+
+       Profile: u, u*2, wu, w*u*, w"u", v, v*2, wv, w*v*, w"v", w*2,         
+
+              : e, e*, km, l,                                                
+       Output every              1800.00 s
+       Time averaged over           0.00 s
+       Averaging input every        0.00 s
+
+    3D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w,                                                             
+       Output every              1800.00 s  
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    3D-Arrays(time-averaged):
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  u, v, w,                                                             
+       Output every              1800.00 s  
+       Time averaged over        1800.00 s
+       Averaging input every        6.00 s
+       Upper output limit at       81.00 m  (GP   41)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    Time series:
+       Output format: netCDF 64bit offset                     
+
+       Output every                60.00 s
+
+ ------------------------------------------------------------------------------
+
+
+ Physical quantities:
+ -------------------
+
+    Geograph. latitude  :   latitude  = 55.0 degr
+    Geograph. longitude :   longitude =  0.0 degr
+    Angular velocity    :   omega  = 0.000E+00 rad/s
+    Coriolis parameter  :   f      =  0.000000 1/s
+                            f*     =  0.000000 1/s
+
+    Day of the year at model start :   day_init      =     172
+    UTC time at model start        :   time_utc_init = 43200.0 s
+
+    Gravity             :   g      =  9.8 m/s**2
+
+    Reference state used in buoyancy terms: initial_profile
+
+
+ Cloud physics quantities / methods:
+ ----------------------------------
+
+
+
+ LES / Turbulence quantities:
+ ---------------------------
+
+    Mixing length is limited to 1.80 * z
+
+
+ Actions during the simulation:
+ -----------------------------
+
+    Disturbance impulse (u,v) every :   ****** s
+    Disturbance amplitude           :     0.25 m/s
+    Lower disturbance level         :     5.00 m (GP    3)
+    Upper disturbance level         :    25.00 m (GP   13)
+    Disturbances cease as soon as the disturbance energy exceeds 0.010 m**2/s**2
+    Random number generator used    : random-parallel
+
+
+
+ 1D-Model parameters:
+ -------------------
+
+    Simulation time:                    86400.0 s
+    Run-controll output every:           3600.0 s
+    Vertical profile output every:     ******** s
+    Mixing length calculation:         blackadar           
+    Dissipation calculation:           detering            
+
+ ------------------------------------------------------------------------------
+
+
+
+Run-control output:
+------------------
+
+RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  0      0 00:00:00.00   0.7100D   1.0000D -0.2288D  0.1182  0.051  0.00   0.000E+00      0.  0.308E+00  0.103E-02  0.149E-01  0.217E-11   41  37  37   11   7  19    5  26   7    0.000    0.000       0
+  0     34 00:01:01.43   1.8400A   0.9778  -0.0971   0.0632  0.046  0.00   0.000E+00      0.  0.307E+00  0.208E-03  0.246E-04  0.438E-14   41  25  22    9  32  31    6  25  26    0.000    0.000       0
+  0     66 00:02:00.31   1.8400A   0.9788  -0.0841  -0.0554  0.042  0.00   0.000E+00      0.  0.308E+00  0.156E-03  0.166E-04  0.306E-14   40  24   3    8  31   9    7  37  29    0.000    0.000       0
+  0     99 00:03:01.03   1.8400A   0.9801  -0.0744  -0.0529  0.039  0.00   0.000E+00      0.  0.309E+00  0.149E-03  0.143E-04  0.272E-14   41  24  25    8  30  30    7  38   9    0.000    0.000       0
+  0    132 00:04:01.63   1.8300A   0.9815  -0.0658  -0.0488  0.036  0.00   0.000E+00      0.  0.310E+00  0.154E-03  0.131E-04  0.249E-14   41  25   7    6  28   0    6  14  13    0.000    0.000       0
+  0    164 00:05:00.19   1.8300A   0.9829  -0.0672  -0.0507  0.035  0.00   0.000E+00      0.  0.311E+00  0.162E-03  0.131E-04  0.249E-14   40  37  34    6  27  16    8  35   9    0.000    0.000       0
+  0    197 00:06:00.57   1.8300A   0.9845  -0.0660   0.0459  0.034  0.00   0.000E+00      0.  0.312E+00  0.175E-03  0.130E-04  0.249E-14   40  37  17    6  27  36    6  26  32    0.000    0.000       0
+  0    230 00:07:00.96   1.8300A   0.9862  -0.0695  -0.0479  0.033  0.00   0.000E+00      0.  0.313E+00  0.193E-03  0.131E-04  0.251E-14   40  36  39    9  16  28    7  34   7    0.000    0.000       0
+  0    263 00:08:01.05   1.8200A   0.9878  -0.0769   0.0487  0.032  0.00   0.000E+00      0.  0.314E+00  0.213E-03  0.136E-04  0.256E-14   40  36  21    9  15   7    6  26  27    0.000    0.000       0
+  0    296 00:09:01.11   1.8200A   0.9895  -0.0763   0.0478  0.032  0.00   0.000E+00      0.  0.315E+00  0.233E-03  0.144E-04  0.273E-14   40  35   2    9  15  26    6  26   4    0.000    0.000       0
+  0    329 00:10:01.18   1.8200A   0.9911   0.0733   0.0498  0.031  0.00   0.000E+00      0.  0.316E+00  0.256E-03  0.155E-04  0.287E-14   40  34  24    7  31  17    8  16  32    0.000    0.000       0
+  0    362 00:11:01.03   1.8100A   0.9928  -0.0779   0.0522  0.031  0.00   0.000E+00      0.  0.317E+00  0.284E-03  0.167E-04  0.307E-14   41  33   6    9  13   6    8  16  10    0.000    0.000       0
+  0    395 00:12:00.75   1.8100A   0.9945  -0.0771   0.0487  0.031  0.00   0.000E+00      0.  0.318E+00  0.316E-03  0.176E-04  0.326E-14   41  31  27    9  12  25    9  16  29    0.000    0.000       0
+  0    428 00:13:00.48   1.8100A   0.9961   0.0808  -0.0559  0.031  0.00   0.000E+00      0.  0.319E+00  0.354E-03  0.169E-04  0.307E-14   41  30   8    7  14   9    4  33   3    0.000    0.000       0
+  0    461 00:14:00.11   1.8000A   0.9978   0.0774  -0.0583  0.031  0.00   0.000E+00      0.  0.320E+00  0.404E-03  0.182E-04  0.333E-14   41  28  29    7  14  29    3  34  19    0.000    0.000       0
+  0    495 00:15:01.31   1.8000A   0.9995   0.0932  -0.0580  0.031  0.00   0.000E+00      0.  0.321E+00  0.467E-03  0.192E-04  0.350E-14   41  26   8    7  15   8    3  33  32    0.000    0.000       0
+  0    528 00:16:00.71   1.8000A   1.0013  -0.0988   0.0619  0.031  0.00   0.000E+00      0.  0.322E+00  0.536E-03  0.204E-04  0.379E-14   40  19  23    3  31  18    7  15  22    0.000    0.000       0
+  0    561 00:17:00.07   1.7900A   1.0030  -0.0917  -0.0631  0.032  0.00   0.000E+00      0.  0.323E+00  0.610E-03  0.215E-04  0.395E-14   40  17   1    4  30  34    7  30   4    0.000    0.000       0
+  0    595 00:18:00.93   1.7900A   1.0048  -0.1076   0.0726  0.032  0.00   0.000E+00      0.  0.324E+00  0.695E-03  0.235E-04  0.420E-14   40  17  23    4  32  10    7  15  19    0.000    0.000       0
+  0    628 00:19:00.00   1.7900A   1.0065  -0.1159   0.0813  0.033  0.00   0.000E+00      0.  0.325E+00  0.782E-03  0.254E-04  0.450E-14   40  18   5    5  31  25    8  16  38    0.000    0.000       0
+  0    662 00:20:00.86   1.7900A   1.0083  -0.1148   0.0770  0.034  0.00   0.000E+00      0.  0.326E+00  0.883E-03  0.282E-04  0.515E-14   40  23  28    5  27  13    7  14  15    0.000    0.000       0
+  0    696 00:21:01.41   1.7800A   1.0101  -0.1335   0.1027  0.035  0.00   0.000E+00      0.  0.327E+00  0.996E-03  0.317E-04  0.574E-14   41  31  10    5  26  28    4  30  39    0.000    0.000       0
+  0    729 00:22:00.15   1.7800A   1.0118  -0.1459   0.1166  0.036  0.00   0.000E+00      0.  0.328E+00  0.110E-02  0.346E-04  0.615E-14   41  31  31    6  26   4    8  12   8    0.000    0.000       0
+  0    763 00:23:00.67   1.7800A   1.0135  -0.1589   0.1174  0.037  0.00   0.000E+00      0.  0.329E+00  0.120E-02  0.379E-04  0.681E-14   41  34  16    9  10  17   10  12  27    0.000    0.000       0
+  0    797 00:24:00.98   1.7700A   1.0152  -0.1596  -0.1127  0.038  0.00   0.000E+00      0.  0.329E+00  0.129E-02  0.419E-04  0.752E-14   41  36   1    6  27  32    9   8   1    0.000    0.000       0
+  0    831 00:25:01.16   1.7700A   1.0170   0.1825   0.1338  0.040  0.00   0.000E+00      0.  0.330E+00  0.136E-02  0.486E-04  0.901E-14   40   4  28    7  28  36    8  23   0    0.000    0.000       0
+  0    865 00:26:01.34   1.7700A   1.0188   0.1985  -0.1499  0.041  0.00   0.000E+00      0.  0.331E+00  0.142E-02  0.544E-04  0.993E-14   41   3  12    7  29  12    7   7  38    0.000    0.000       0
+  0    899 00:27:01.40   1.7600A   1.0205  -0.1776   0.1332  0.043  0.00   0.000E+00      0.  0.331E+00  0.148E-02  0.595E-04  0.107E-13   40   5  37    7  26  35    7  30   0    0.000    0.000       0
+  0    933 00:28:01.24   1.7600A   1.0223  -0.1837   0.1510  0.044  0.00   0.000E+00      0.  0.332E+00  0.154E-02  0.654E-04  0.117E-13   40   6  22    6  10   8    7  30  16    0.000    0.000       0
+  0    967 00:29:01.08   1.7600A   1.0240  -0.2025   0.1669  0.044  0.00   0.000E+00      0.  0.332E+00  0.162E-02  0.687E-04  0.124E-13   41   4   6    7  26   1    7  30   7    0.000    0.000       0
+  0   1001 00:30:00.89   1.7500A   1.0258   0.1887   0.1568  0.045  0.00   0.000E+00      0.  0.332E+00  0.174E-02  0.709E-04  0.128E-13   40  39  32   10   5  16    7  30  24    0.000    0.000       0
Index: palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/case_config.yml
===================================================================
--- palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/case_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/flow_around_cube_precursor/case_config.yml	(revision 4091)
@@ -0,0 +1,17 @@
+---
+# this is a palmtest job configuration file
+
+allowed_builds:
+  - gfortran_default
+  - intel_default
+
+allowed_number_of_cores: []
+
+activation_strings:
+  - "d3#"
+  - "restart"
+
+significant_digits_for_netcdf_checks:
+  timeseries: 3
+  profiles: 8
+  other: 8
Index: palm/trunk/TUTORIALS/cases/lsm_short/INPUT/lsm_short_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/lsm_short/INPUT/lsm_short_p3d	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/lsm_short/INPUT/lsm_short_p3d	(revision 4091)
@@ -0,0 +1,115 @@
+&initialization_parameters
+!
+!-- grid parameters
+!------------------------------------------------------------------------------
+   nx                         = 39,
+   ny                         = 39,
+   nz                         = 80,
+
+   dx                         = 50.0,
+   dy                         = 50.0,
+   dz                         = 25.0,
+
+!
+!-- initialization
+!------------------------------------------------------------------------------
+   initializing_actions       = 'set_constant_profiles',
+
+   ug_surface                 = 0.0, ! free convection
+   vg_surface                 = 0.0,
+
+   pt_surface                 = 293.0,
+   pt_vertical_gradient       =    0.0,  2.0,
+   pt_vertical_gradient_level = 0.0,  800,
+
+   day_of_year_init           = 232, ! Aug 20
+   time_utc_init              = 39600.0, ! 11:00 UTC
+   
+!
+!-- boundary conditions
+!------------------------------------------------------------------------------
+   constant_flux_layer        = .TRUE.,
+
+
+   bc_pt_b                    = 'dirichlet', ! required when using LSM
+!
+!-- numerics
+!------------------------------------------------------------------------------
+   fft_method                 = 'temperton-algorithm', ! 'fftw' if available
+/
+
+&runtime_parameters
+!
+!-- run steering
+!------------------------------------------------------------------------------
+   end_time                   = 600.0, ! 10 min
+
+   create_disturbances        = .T.,
+   dt_disturb                 = 150.0,
+   disturbance_energy_limit   = 0.01,
+!
+!-- general output settings
+!------------------------------------------------------------------------------
+   netcdf_data_format         = 2, ! NetCDF3
+   dt_dots                    = 0.0,
+   dt_run_control             = 30.0,
+!
+!-- profile output settings
+!------------------------------------------------------------------------------
+   dt_dopr                    = 600.0,
+   averaging_interval_pr      = 600.0,
+
+   data_output_pr             = '#u', '#v', '#theta',
+                                '#km', '#kh', '#l',
+                                'w', 'e', 'e*', 'p',
+                                'w"theta"', 'w*theta*', 'wtheta', 'w*e*', 
+                                'theta*2','u*2', 'v*2', 'w*2', 
+                                '#t_soil',
+!
+!-- 2D and 3D output settings
+!------------------------------------------------------------------------------
+   dt_do3d                    = 60.0,
+   dt_do2d_xy                 = 60.0,
+
+   section_xy                 = 0, ! surface variables only 
+
+   data_output                = 'theta', 'w', 'u', 'v',
+                                'us*_xy', 
+                                'ghf*_xy', 'shf*_xy', 
+                                'tsurf*_xy',
+                                't_soil',
+/
+
+&land_surface_parameters
+!
+!-- soil setup
+!------------------------------------------------------------------------------
+   soil_type                  = 3,
+   soil_moisture              = 0.0,   0.0,   0.0,   0.0,
+                                0.0,   0.0,   0.0,   0.0,
+   soil_temperature           = 293,   293,   293,   293,
+                                293,   293,   293,   293,  
+   deep_soil_temperature      = 293, 
+!
+!-- boundary conditions
+!------------------------------------------------------------------------------
+   surface_type               = 'vegetation',
+   vegetation_type            = 1,
+/
+
+&radiation_parameters
+!
+!-- general setup
+!------------------------------------------------------------------------------
+   radiation_scheme           = 'clear-sky',
+   dt_radiation               = 20.0,
+/
+
+&user_parameters
+!
+!-- User-defined setup
+!------------------------------------------------------------------------------
+
+  data_output_user           = 'v_h', 'v_h_xy',
+  
+/
Index: palm/trunk/TUTORIALS/cases/lsm_short/MONITORING/lsm_short_rc
===================================================================
--- palm/trunk/TUTORIALS/cases/lsm_short/MONITORING/lsm_short_rc	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/lsm_short/MONITORING/lsm_short_rc	(revision 4091)
@@ -0,0 +1,268 @@
+
+ ******************************    --------------------------------------------
+ * PALM 6.0  Rev: 3986        *    atmosphere - run without 1D - prerun
+ ******************************    --------------------------------------------
+
+ Date:               2019-05-23    Run:       e4_LSM1                           
+ Time:                 08:15:26    Run-No.:   00
+ Run on host:        imuk_defau
+ Number of PEs:               2    Processor grid (x,y): (   1,   2) calculated
+                                   A 1d-decomposition along y is used
+ ------------------------------------------------------------------------------
+
+ Numerical Schemes:
+ -----------------
+
+ --> Use the Moeng_Wyngaard turbulence closure (LES mode).
+ --> Use the boussinesq approximation for the model equations.
+ --> Solve perturbation pressure via FFT using temperton-algorithm routines
+     perturbation pressure is calculated at every Runge-Kutta step
+ --> Momentum advection via Wicker-Skamarock-Scheme 5th order
+ --> Scalar advection via Wicker-Skamarock-Scheme 5th order
+ --> Loop optimization method: cache
+ --> Time differencing scheme: runge-kutta-3       
+ ------------------------------------------------------------------------------
+
+
+ Run time and time step information:
+ ----------------------------------
+
+ Timestep:             variable     maximum value: 20.000 s    CFL-factor: 0.90
+ Start time:              0.000 s
+ End time:              600.000 s
+
+
+ Computational grid and domain size:
+ ----------------------------------
+
+ Grid length:      dx =      50.000 m    dy =      50.000 m
+                dz(1) =      25.000 m
+
+ Domain size:       x =   2000.000 m     y =   2000.000 m  z(u) =   2012.500 m
+
+
+
+ Number of gridpoints (x,y,z):  (0:  39, 0:  39, 0:  81)
+ Subdomain size (x,y,z):        (    40,     20,     82)
+
+
+    Characteristic levels of the geo. wind component ug:
+
+       Height:         0.0     0.0  m
+       ug:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+    Characteristic levels of the geo. wind component vg:
+
+       Height:         0.0     0.0  m
+       vg:            0.00    0.00  m/s
+       Gradient:    ------    0.00  1/100s
+       Gridpoint:        0       0
+
+
+ Topography information:
+ ----------------------
+
+ Topography: flat                                    
+
+
+ Boundary conditions:
+ -------------------
+
+                     p                    uv                                  pt
+
+ B. bound.: p(0)     = p(1)   | uv(0)     = -uv(1)                | pt(0)     = from soil model  
+ T. bound.: p(nzt+1) = 0      | uv(nzt+1) = ug(nzt+1), vg(nzt+1)  | pt(nzt+1) = pt(nzt) + dpt/dz_
+
+                     e
+
+ B. bound.: e(0)     = e(1)                                                                      
+ T. bound.: e(nzt+1) = e(nzt) = e(nzt-1)                                                         
+
+ Bottom surface fluxes are used in diffusion terms at k=1
+
+
+    Constant flux layer between bottom surface and first computational u,v-level:
+
+       z_mo =  12.50 m   z0 = 0.1000 m   z0h = 0.10000 m   kappa = 0.40
+       Rif value range:     -20.00 <= rif <= 20.00
+       Predefined surface temperature
+
+
+ Lateral boundaries:
+       left/right:  cyclic              
+       north/south: cyclic              
+
+
+ Initial profiles:
+ ----------------
+
+    Characteristic levels of the initial temperature profile:
+
+       Height:           0.0     0.0   800.0  m
+       Temperature:   293.00  293.00  293.00  K
+       Gradient:      ------    0.00    2.00  K/100m
+       Gridpoint:          0       0      32
+
+
+ List output:
+ -----------
+
+    1D-Profiles:
+       Output every             9999999.90 s
+       Time averaged over         600.00 s
+       Averaging input every        0.00 s
+
+
+ Data output:
+ -----------
+
+       Time averaged over         600.00 s
+       Averaging input every        0.00 s
+
+    1D-Profiles:
+       Output format: netCDF 64bit offset                     
+
+
+       Profile: u, v, theta, km, kh, l, w, e, e*, p, w"theta", w*theta*,     
+
+              : wtheta, w*e*, theta*2, u*2, v*2, w*2, t_soil,                
+       Output every               600.00 s
+       Time averaged over         600.00 s
+       Averaging input every        0.00 s
+
+    2D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       XY-cross-section  Arrays:  us*, ghf*, shf*, tsurf*, v_h,                                        
+       Output every                60.00 s  
+       Cross sections at k = /0/
+       scalar-coordinates:   /0.0/ m
+
+
+       Number of output time levels allowed: unlimited
+
+
+    3D-Arrays:
+       Output format: netCDF 64bit offset                     
+
+
+       Arrays:  theta, w, u, v, t_soil, v_h,                                         
+       Output every                60.00 s  
+       Upper output limit at     2012.50 m  (GP   81)
+
+
+       Number of output time levels allowed: unlimited
+
+
+    Time series:
+       Output format: netCDF 64bit offset                     
+
+       Output every                 0.00 s
+
+ ------------------------------------------------------------------------------
+
+
+ Physical quantities:
+ -------------------
+
+    Geograph. latitude  :   latitude  = 55.0 degr
+    Geograph. longitude :   longitude =  0.0 degr
+    Angular velocity    :   omega  = 0.729E-04 rad/s
+    Coriolis parameter  :   f      =  0.000119 1/s
+                            f*     =  0.000084 1/s
+
+    Day of the year at model start :   day_init      =     232
+    UTC time at model start        :   time_utc_init = 39600.0 s
+
+    Gravity             :   g      =  9.8 m/s**2
+
+    Reference state used in buoyancy terms: initial_profile
+
+
+ Cloud physics quantities / methods:
+ ----------------------------------
+
+
+
+ LES / Turbulence quantities:
+ ---------------------------
+
+    Mixing length is limited to 1.80 * z
+
+
+ Actions during the simulation:
+ -----------------------------
+
+    Disturbance impulse (u,v) every :   150.00 s
+    Disturbance amplitude           :     0.25 m/s
+    Lower disturbance level         :    62.50 m (GP    3)
+    Upper disturbance level         :   637.50 m (GP   26)
+    Disturbances cease as soon as the disturbance energy exceeds 0.010 m**2/s**2
+    Random number generator used    : random-parallel
+
+
+
+ Land surface model information:
+ ------------------------------
+
+    --> Soil bottom is closed (water content is conserved, default)
+    --> Land surface type  : bare soil
+    --> Soil porosity type : medium-fine
+
+    Initial soil temperature and moisture profile:
+
+       Height:              -0.01      -0.02      -0.05      -0.10      -0.20      -0.40      -0.80      -2.  m
+       Temperature:        293.00     293.00     293.00     293.00     293.00     293.00     293.00     293.  K
+       Moisture:             0.00       0.00       0.00       0.00       0.00       0.00       0.00       0.  m**3/m**3
+       Root fraction:        0.14       0.29       0.57       0.00       0.00       0.00       0.00       0.  
+       Grid point:              0          1          2          3          4          5          6
+
+
+ Radiation model information:
+ ----------------------------
+
+    --> Simple radiation scheme for clear sky is used (no clouds, default)
+
+    Albedo is set for land surface type: bare soil
+    Timestep: dt_radiation =  20.00  s
+
+
+ ##############################################################################
+
+ User-defined variables and actions:
+ -----------------------------------
+
+
+ ------------------------------------------------------------------------------
+
+
+
+Run-control output:
+------------------
+
+RUN  ITER. HH:MM:SS.SS    DT(E)     UMAX     VMAX     WMAX     U*    W*      THETA*     Z_I     ENERG.   DISTENERG    DIVOLD     DIVNEW     UMAX(KJI)    VMAX(KJI)    WMAX(KJI)   ADVECX   ADVECY   MGCYC
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  0      0 00:00:00.00  20.0000A   0.2156D  0.2450D -0.1312  0.100  0.00   0.220E-01      0.  0.135E-02  0.134E-02  0.658E-03  0.766E-13   25  17   0   16  28   0    7  18  26    0.000    0.000       0
+  0      2 00:00:40.00  20.0000A   0.2111   0.2466  -0.1285  0.003  0.23  -0.268E+00     50.  0.131E-02  0.131E-02  0.560E-05  0.497E-15   25  17   0   16  28   0    7  18  26    0.000    0.000       0
+  0      3 00:01:00.00  20.0000D   0.2081   0.2465  -0.1266  0.004  0.27  -0.599E+00     50.  0.130E-02  0.129E-02  0.624E-05  0.498E-15   25  17   0   16  28   0    7  18  26    0.000    0.000       0
+  0      5 00:01:40.00  20.0000D  -0.2094   0.2446  -0.1217  0.004  0.31  -0.131E+01     50.  0.127E-02  0.126E-02  0.837E-05  0.493E-15    7  33  11   16  28   0    7  18  26    0.000    0.000       0
+  0      6 00:02:00.00  20.0000D  -0.2111   0.2427  -0.1188  0.004  0.33  -0.166E+01     50.  0.125E-02  0.125E-02  0.980E-05  0.487E-15    7  33  11   16  28   0    7  18  26    0.000    0.000       0
+  0      8 00:02:40.00  20.0000D   0.3776D  0.3587D -0.1625  0.005  0.48  -0.196E+01    125.  0.261E-02  0.260E-02  0.668E-03  0.771E-13   24  33  26   16  28   0    8  14  16    0.000    0.000       0
+  0      9 00:03:00.00  20.0000D   0.3722   0.3556  -0.1610  0.005  0.83  -0.226E+01    575.  0.256E-02  0.255E-02  0.207E-04  0.988E-15   24  33  26   16  28   0    8  14  16    0.000    0.000       0
+  0     11 00:03:40.00  20.0000D   0.3550   0.3432  -0.1579  0.005  0.55  -0.272E+01    150.  0.247E-02  0.246E-02  0.251E-04  0.971E-15   24  33  26   16  28   0    8  14  16    0.000    0.000       0
+  0     12 00:04:00.00  20.0000D  -0.3449   0.3401  -0.1562  0.006  0.56  -0.293E+01    150.  0.243E-02  0.242E-02  0.276E-04  0.962E-15   23  21  14   20   7  10    8  14  16    0.000    0.000       0
+  0     14 00:04:40.00  20.0000D   0.3420   0.3323  -0.1523  0.006  0.91  -0.327E+01    575.  0.234E-02  0.233E-02  0.328E-04  0.942E-15   24  33  27   20   7  10    8  14  16    0.000    0.000       0
+  0     15 00:05:00.00  20.0000D  -0.4293D -0.4291D  0.2041  0.007  0.92  -0.284E+01    575.  0.367E-02  0.366E-02  0.685E-03  0.775E-13    9   1  26   20  18  30   21  35  21    0.000    0.000       0
+  0     17 00:05:40.00  20.0000D  -0.4055  -0.4078   0.2040  0.007  0.94  -0.297E+01    575.  0.350E-02  0.349E-02  0.459E-04  0.140E-14    9   1  26   20  18  30   21  35  21    0.000    0.000       0
+  0     18 00:06:00.00  20.0000D   0.4023  -0.3928   0.2016  0.007  0.72  -0.312E+01    250.  0.342E-02  0.341E-02  0.486E-04  0.139E-14    8  13  19   20  18  30   21  35  21    0.000    0.000       0
+  0     20 00:06:40.00  20.0000D   0.3954  -0.3782   0.2092  0.008  0.97  -0.302E+01    575.  0.327E-02  0.325E-02  0.541E-04  0.138E-14    8  13  19   20  17  30   22  35  21    0.000    0.000       0
+  0     21 00:07:00.00  20.0000D  -0.3920  -0.3839   0.2124  0.009  0.98  -0.296E+01    575.  0.319E-02  0.318E-02  0.569E-04  0.138E-14    9   1  25   20  17  30   22  35  21    0.000    0.000       0
+  0     23 00:07:39.69  19.2000D   0.5054D -0.4595D  0.2317  0.010  1.04  -0.262E+01    650.  0.440E-02  0.439E-02  0.697E-03  0.767E-13    7  27  37    5  30   4   22   6  36    0.000    0.000       0
+  0     25 00:08:17.69  18.5000D   0.5064  -0.4477   0.2469  0.011  1.01  -0.248E+01    575.  0.419E-02  0.417E-02  0.682E-04  0.178E-14    7  27  38    5  30   4    2   3  38    0.000    0.000       0
+  0     26 00:08:36.20  18.3000D   0.5183  -0.4375   0.2668  0.012  1.00  -0.239E+01    550.  0.410E-02  0.408E-02  0.692E-04  0.177E-14    7  27  38    5  30   4    2   3  38    0.000    0.000       0
+  0     28 00:09:12.50  17.8000D   0.5191  -0.4108   0.3157  0.013  1.01  -0.229E+01    550.  0.395E-02  0.394E-02  0.713E-04  0.178E-14    7  27  38    5  30   4    3  26  12    0.000    0.000       0
+  0     29 00:09:30.29  17.6000D   0.5104  -0.3948   0.3571  0.014  1.02  -0.228E+01    550.  0.390E-02  0.388E-02  0.724E-04  0.180E-14    7  27  38    5  30   4    3  26  12    0.000    0.000       0
+  0     31 00:10:05.29  17.2000D   0.5707D -0.5114D  0.4911  0.016  1.03  -0.211E+01    550.  0.525E-02  0.523E-02  0.703E-03  0.775E-13    7  27  38   15  33   9    3  26  12    0.000    0.000       0
Index: palm/trunk/TUTORIALS/cases/lsm_short/USER_CODE/user_module.f90
===================================================================
--- palm/trunk/TUTORIALS/cases/lsm_short/USER_CODE/user_module.f90	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/lsm_short/USER_CODE/user_module.f90	(revision 4091)
@@ -0,0 +1,1362 @@
+!> @file user_module.f90
+!------------------------------------------------------------------------------!
+! This file is part of the PALM model system.
+!
+! PALM is free software: you can redistribute it and/or modify it under the
+! terms of the GNU General Public License as published by the Free Software
+! Foundation, either version 3 of the License, or (at your option) any later
+! version.
+!
+! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
+! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+! A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+!
+! You should have received a copy of the GNU General Public License along with
+! PALM. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 1997-2019 Leibniz Universitaet Hannover
+!------------------------------------------------------------------------------!
+!
+! Current revisions:
+! -----------------
+! 
+! 
+! Former revisions:
+! -----------------
+! $Id: user_module.f90 3986 2019-05-20 14:08:14Z Giersch $
+! Redundant integration of control parameters in user_rrd_global removed
+! 
+! 3911 2019-04-17 12:26:19Z knoop
+! Bugfix: added before_prognostic_equations case in user_actions
+! 
+! 3768 2019-02-27 14:35:58Z raasch
+! variables commented + statements added to avoid compiler warnings about unused variables
+!
+! 3767 2019-02-27 08:18:02Z raasch
+! unused variable for file index removed from rrd-subroutines parameter list
+! 
+! 3747 2019-02-16 15:15:23Z gronemeier
+! Add routine user_init_arrays
+! 
+! 3703 2019-01-29 16:43:53Z knoop
+! An example for a user defined global variable has been added (Giersch)
+! 
+! 2718 2018-01-02 08:49:38Z suehring
+! Corrected "Former revisions" section
+! 
+! 2696 2017-12-14 17:12:51Z kanani
+! Change in file header (GPL part)
+!
+! 2101 2017-01-05 16:42:31Z suehring
+!
+! 2000 2016-08-20 18:09:15Z knoop
+! Forced header and separation lines into 80 columns
+! 
+! 1873 2016-04-18 14:50:06Z maronga
+! Module renamed (removed _mod)
+! 
+! 
+! 1850 2016-04-08 13:29:27Z maronga
+! Module renamed
+! 
+! 
+! 1682 2015-10-07 23:56:08Z knoop
+! Code annotations made doxygen readable 
+!
+! 1320 2014-03-20 08:40:49Z raasch
+! kind-parameters added to all INTEGER and REAL declaration statements, 
+! kinds are defined in new module kinds, 
+! old module precision_kind is removed,
+! revision history before 2012 removed,
+! comment fields (!:) to be used for variable explanations added to
+! all variable declaration statements 
+!
+! 1036 2012-10-22 13:43:42Z raasch
+! code put under GPL (PALM 3.9)
+!
+! Revision 1.1  1998/03/24 15:29:04  raasch
+! Initial revision
+!
+!
+! Description:
+! ------------
+!> Declaration of user-defined variables. This module may only be used
+!> in the user-defined routines (contained in user_interface.f90).
+!------------------------------------------------------------------------------!
+ MODULE user
+
+
+    USE arrays_3d
+
+    USE control_parameters
+
+    USE cpulog
+
+    USE indices
+
+    USE kinds
+
+    USE pegrid
+
+    USE statistics
+
+    USE surface_mod
+
+    IMPLICIT NONE
+
+    INTEGER(iwp) ::  dots_num_palm   !< 
+    INTEGER(iwp) ::  dots_num_user = 0  !< 
+    INTEGER(iwp) ::  user_idummy     !< 
+    
+    LOGICAL ::  user_module_enabled = .FALSE.   !< 
+    
+    REAL(wp) ::  user_rdummy   !< 
+
+!
+!-- Sample for user-defined output
+!    REAL(wp) :: global_parameter !< user defined global parameter 
+!
+!    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE ::  u2       !< user defined array
+!    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE ::  u2_av    !< user defined array
+!    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE ::  ustvst   !< user defined array
+    REAL(wp), DIMENSION(:,:,:), ALLOCATABLE ::  v_h, v_h_av  !< user defined arra
+     
+    SAVE
+
+    PRIVATE
+
+!
+!- Public functions
+    PUBLIC &
+       user_parin, &
+       user_check_parameters, &
+       user_check_data_output_ts, &
+       user_check_data_output_pr, &
+       user_check_data_output, &
+       user_define_netcdf_grid, &
+       user_init, &
+       user_init_arrays, &
+       user_header, &
+       user_actions, &
+       user_3d_data_averaging, &
+       user_data_output_2d, &
+       user_data_output_3d, &
+       user_statistics, &
+       user_rrd_global, &
+       user_rrd_local, &
+       user_wrd_global, &
+       user_wrd_local, &
+       user_last_actions
+
+!
+!- Public parameters, constants and initial values
+   PUBLIC &
+      user_module_enabled
+
+    INTERFACE user_parin
+       MODULE PROCEDURE user_parin
+    END INTERFACE user_parin
+
+    INTERFACE user_check_parameters
+       MODULE PROCEDURE user_check_parameters
+    END INTERFACE user_check_parameters
+
+    INTERFACE user_check_data_output_ts
+       MODULE PROCEDURE user_check_data_output_ts
+    END INTERFACE user_check_data_output_ts
+
+    INTERFACE user_check_data_output_pr
+       MODULE PROCEDURE user_check_data_output_pr
+    END INTERFACE user_check_data_output_pr
+
+    INTERFACE user_check_data_output
+       MODULE PROCEDURE user_check_data_output
+    END INTERFACE user_check_data_output
+
+    INTERFACE user_define_netcdf_grid
+       MODULE PROCEDURE user_define_netcdf_grid
+    END INTERFACE user_define_netcdf_grid
+
+    INTERFACE user_init
+       MODULE PROCEDURE user_init
+    END INTERFACE user_init
+
+    INTERFACE user_init_arrays
+       MODULE PROCEDURE user_init_arrays
+    END INTERFACE user_init_arrays
+
+    INTERFACE user_header
+       MODULE PROCEDURE user_header
+    END INTERFACE user_header
+
+    INTERFACE user_actions
+       MODULE PROCEDURE user_actions
+       MODULE PROCEDURE user_actions_ij
+    END INTERFACE user_actions
+
+    INTERFACE user_3d_data_averaging
+       MODULE PROCEDURE user_3d_data_averaging
+    END INTERFACE user_3d_data_averaging
+
+    INTERFACE user_data_output_2d
+       MODULE PROCEDURE user_data_output_2d
+    END INTERFACE user_data_output_2d
+
+    INTERFACE user_data_output_3d
+       MODULE PROCEDURE user_data_output_3d
+    END INTERFACE user_data_output_3d
+
+    INTERFACE user_statistics
+       MODULE PROCEDURE user_statistics
+    END INTERFACE user_statistics
+
+    INTERFACE user_rrd_global
+       MODULE PROCEDURE user_rrd_global
+    END INTERFACE user_rrd_global
+
+    INTERFACE user_rrd_local
+       MODULE PROCEDURE user_rrd_local
+    END INTERFACE user_rrd_local
+
+    INTERFACE user_wrd_global
+       MODULE PROCEDURE user_wrd_global
+    END INTERFACE user_wrd_global
+
+    INTERFACE user_wrd_local
+       MODULE PROCEDURE user_wrd_local
+    END INTERFACE user_wrd_local
+
+    INTERFACE user_last_actions
+       MODULE PROCEDURE user_last_actions
+    END INTERFACE user_last_actions
+
+
+ CONTAINS
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Parin for &user_parameters for user module
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_parin
+
+
+    CHARACTER (LEN=80) ::  line   !< 
+
+    INTEGER(iwp) ::  i                 !< 
+    INTEGER(iwp) ::  j                 !< 
+
+
+    NAMELIST /user_parameters/  &
+       user_module_enabled, &
+       data_output_pr_user, &
+       data_output_user, &
+       region, &
+       data_output_masks_user
+
+!
+!-- Next statement is to avoid compiler warnings about unused variables. Please remove in case
+!-- that you are using them.
+    IF ( dots_num_palm == 0  .OR.  dots_num_user == 0  .OR.  user_idummy == 0  .OR.                &
+         user_rdummy == 0.0_wp )  CONTINUE
+
+!
+!-- Set revision number of this default interface version. It will be checked within
+!-- the main program (palm). Please change the revision number in case that the
+!-- current revision does not match with previous revisions (e.g. if routines
+!-- have been added/deleted or if parameter lists in subroutines have been changed).
+    user_interface_current_revision = 'r3703'
+
+!
+!-- Position the namelist-file at the beginning (it was already opened in
+!-- parin), search for user-defined namelist-group ("userpar", but any other
+!-- name can be choosed) and position the file at this line.
+    REWIND ( 11 )
+
+    line = ' '
+    DO WHILE ( INDEX( line, '&user_parameters' ) == 0 )
+       READ ( 11, '(A)', END=12 )  line
+    ENDDO
+    BACKSPACE ( 11 )
+
+!-- Set default module switch to true
+    user_module_enabled = .TRUE.
+
+!-- Read user-defined namelist
+    READ ( 11, user_parameters, ERR = 10 )
+
+    GOTO 12
+
+10  BACKSPACE( 11 )
+    READ( 11 , '(A)') line
+    CALL parin_fail_message( 'user_parameters', line )
+
+12  CONTINUE
+
+!
+!-- Determine the number of user-defined profiles and append them to the
+!-- standard data output (data_output_pr)
+    IF ( user_module_enabled )  THEN
+       IF ( data_output_pr_user(1) /= ' ' )  THEN
+          i = 1
+          DO WHILE ( data_output_pr(i) /= ' '  .AND.  i <= 100 )
+             i = i + 1
+          ENDDO
+          j = 1
+          DO WHILE ( data_output_pr_user(j) /= ' '  .AND.  j <= 100 )
+             data_output_pr(i) = data_output_pr_user(j)
+             max_pr_user_tmp   = max_pr_user_tmp + 1
+             i = i + 1
+             j = j + 1
+          ENDDO
+       ENDIF
+    ENDIF
+
+
+ END SUBROUTINE user_parin
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Check &userpar control parameters and deduce further quantities.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_parameters
+
+
+!-- Here the user may add code to check the validity of further &userpar 
+!-- control parameters or deduce further quantities.
+
+
+ END SUBROUTINE user_check_parameters
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set module-specific timeseries units and labels
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_data_output_ts( dots_max, dots_num, dots_label, dots_unit )
+
+
+    INTEGER(iwp),      INTENT(IN)     ::  dots_max
+    INTEGER(iwp),      INTENT(INOUT)  ::  dots_num
+    CHARACTER (LEN=*), DIMENSION(dots_max), INTENT(INOUT)  :: dots_label
+    CHARACTER (LEN=*), DIMENSION(dots_max), INTENT(INOUT)  :: dots_unit
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( dots_num == 0  .OR.  dots_label(1)(1:1) == ' '  .OR.  dots_unit(1)(1:1) == ' ' )  CONTINUE
+
+!
+!-- Sample for user-defined time series
+!-- For each time series quantity you have to give a label and a unit,
+!-- which will be used for the NetCDF file. They must not contain more than
+!-- seven characters. The value of dots_num has to be increased by the
+!-- number of new time series quantities. Its old value has to be store in
+!-- dots_num_palm. See routine user_statistics on how to output calculate
+!-- and output these quantities.
+
+!    dots_num_palm = dots_num
+
+!    dots_num = dots_num + 1
+!    dots_num_user = dots_num_user + 1
+!    dots_label(dots_num) = 'abs_umx'
+!    dots_unit(dots_num)  = 'm/s'
+
+!    dots_num = dots_num + 1
+!    dots_num_user = dots_num_user + 1
+!    dots_label(dots_num) = 'abs_vmx'
+!    dots_unit(dots_num)  = 'm/s'
+
+
+ END SUBROUTINE user_check_data_output_ts
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set the unit of user defined profile output quantities. For those variables
+!> not recognized by the user, the parameter unit is set to "illegal", which
+!> tells the calling routine that the output variable is not defined and leads
+!> to a program abort.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_data_output_pr( variable, var_count, unit, dopr_unit )
+
+
+    USE profil_parameter
+
+
+    CHARACTER (LEN=*) ::  unit     !< 
+    CHARACTER (LEN=*) ::  variable !< 
+    CHARACTER (LEN=*) ::  dopr_unit !< local value of dopr_unit
+
+!    INTEGER(iwp) ::  user_pr_index !<
+    INTEGER(iwp) ::  var_count     !<
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( unit(1:1) == ' '  .OR.  dopr_unit(1:1) == ' '  .OR.  var_count == 0 )  CONTINUE
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary.
+!--    Add additional CASE statements depending on the number of quantities
+!--    for which profiles are to be calculated. The respective calculations
+!--    to be performed have to be added in routine user_statistics.
+!--    The quantities are (internally) identified by a user-profile-number
+!--    (see variable "user_pr_index" below). The first user-profile must be assigned
+!--    the number "pr_palm+1", the second one "pr_palm+2", etc. The respective
+!--    user-profile-numbers have also to be used in routine user_statistics!
+!       CASE ( 'u*v*' )                      ! quantity string as given in
+!                                            ! data_output_pr_user
+!          user_pr_index = pr_palm + 1
+!          dopr_index(var_count)  = user_pr_index    ! quantities' user-profile-number
+!          dopr_unit = 'm2/s2'  ! quantity unit
+!          unit = dopr_unit
+!          hom(:,2,user_pr_index,:)       = SPREAD( zu, 2, statistic_regions+1 )
+!                                            ! grid on which the quantity is
+!                                            ! defined (use zu or zw)
+
+       CASE DEFAULT
+          unit = 'illegal'
+
+    END SELECT
+
+
+ END SUBROUTINE user_check_data_output_pr
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set the unit of user defined output quantities. For those variables
+!> not recognized by the user, the parameter unit is set to "illegal", which
+!> tells the calling routine that the output variable is not defined and leads
+!> to a program abort.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_check_data_output( variable, unit )
+
+
+    CHARACTER (LEN=*) ::  unit     !< 
+    CHARACTER (LEN=*) ::  variable !<
+
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary
+!       CASE ( 'u2' )
+!          unit = 'm2/s2'
+
+       CASE ( 'v_h' )
+          unit = 'm/s'
+         
+!
+!       CASE ( 'u*v*' )
+!          unit = 'm2/s2'
+!
+       CASE DEFAULT
+          unit = 'illegal'
+
+    END SELECT
+
+
+ END SUBROUTINE user_check_data_output
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Initialize user-defined arrays
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_init_arrays
+
+
+!    INTEGER(iwp) :: i       !< loop index
+!    INTEGER(iwp) :: j       !< loop index
+!    INTEGER(iwp) :: region  !< index for loop over statistic regions
+
+!
+!-- Allocate user-defined arrays and set flags for statistic regions.
+!-- Sample for user-defined output
+!    ALLOCATE( u2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!    ALLOCATE( ustvst(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+     ALLOCATE( v_h(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+
+!
+!-- Example for defining a statistic region:
+!     IF ( statistic_regions >= 1 )  THEN
+!        region = 1
+! 
+!        rmask(:,:,region) = 0.0_wp
+!        DO  i = nxl, nxr
+!           IF ( i >= INT( 0.25 * nx ) .AND. i <= INT( 0.75 * nx ) )  THEN
+!              DO  j = nys, nyn
+!                 IF ( i >= INT( 0.25 * ny ) .AND. i <= INT( 0.75 * ny ) )  THEN
+!                    rmask(j,i,region) = 1.0_wp
+!                 ENDIF
+!              ENDDO
+!           ENDIF
+!        ENDDO
+! 
+!     ENDIF
+
+ END SUBROUTINE user_init_arrays
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Execution of user-defined initializing actions
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_init
+
+
+!    CHARACTER (LEN=20) :: field_char   !<
+!
+!-- Here the user-defined initializing actions follow:
+!-- Sample for user-defined output
+!    ustvst = 0.0_wp
+
+
+ END SUBROUTINE user_init
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Set the grids on which user-defined output quantities are defined.
+!> Allowed values for grid_x are "x" and "xu", for grid_y "y" and "yv", and
+!> for grid_z "zu" and "zw".
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_define_netcdf_grid( variable, found, grid_x, grid_y, grid_z )
+
+
+    CHARACTER (LEN=*) ::  grid_x     !<
+    CHARACTER (LEN=*) ::  grid_y     !<
+    CHARACTER (LEN=*) ::  grid_z     !<
+    CHARACTER (LEN=*) ::  variable   !<
+
+    LOGICAL ::  found   !<
+
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary
+!       CASE ( 'u2', 'u2_xy', 'u2_xz', 'u2_yz' )
+!          found  = .TRUE.
+!          grid_x = 'xu'
+!          grid_y = 'y'
+!          grid_z = 'zu'
+
+!       CASE ( 'u*v*', 'u*v*_xy', 'u*v*_xz', 'u*v*_yz' )
+!          found  = .TRUE.
+!          grid_x = 'x'
+!          grid_y = 'y'
+!          grid_z = 'zu'
+
+       CASE ( 'v_h', 'v_h_xy', 'v_h_xz', 'v_h_yz', 'v_h_av' )
+          found  = .TRUE.
+          grid_x = 'xu'
+          grid_y = 'y'
+          grid_z = 'zu'
+         
+       CASE DEFAULT
+          found  = .FALSE.
+          grid_x = 'none'
+          grid_y = 'none'
+          grid_z = 'none'
+
+    END SELECT
+
+
+ END SUBROUTINE user_define_netcdf_grid
+
+
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Print a header with user-defined information.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_header( io )
+
+
+    INTEGER(iwp) ::  i    !< 
+    INTEGER(iwp) ::  io   !< 
+
+!
+!-- If no user-defined variables are read from the namelist-file, no
+!-- information will be printed.
+    IF ( .NOT. user_module_enabled )  THEN
+       WRITE ( io, 100 )
+       RETURN
+    ENDIF
+
+!
+!-- Printing the information.
+    WRITE ( io, 110 )
+
+    IF ( statistic_regions /= 0 )  THEN
+       WRITE ( io, 200 )
+       DO  i = 0, statistic_regions
+          WRITE ( io, 201 )  i, region(i)
+       ENDDO
+    ENDIF
+
+!
+!-- Format-descriptors
+100 FORMAT (//' *** no user-defined variables found'/)
+110 FORMAT (//1X,78('#')                                                       &
+            //' User-defined variables and actions:'/                          &
+              ' -----------------------------------'//)
+200 FORMAT (' Output of profiles and time series for following regions:' /)
+201 FORMAT (4X,'Region ',I1,':   ',A)
+
+
+ END SUBROUTINE user_header
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Call for all grid points
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_actions( location )
+
+
+    CHARACTER (LEN=*) ::  location !< 
+
+    INTEGER(iwp) ::  i !<
+    INTEGER(iwp) ::  j !<
+    INTEGER(iwp) ::  k !<
+
+    CALL cpu_log( log_point(24), 'user_actions', 'start' )
+
+!
+!-- Here the user-defined actions follow
+!-- No calls for single grid points are allowed at locations before and
+!-- after the timestep, since these calls are not within an i,j-loop
+    SELECT CASE ( location )
+
+       CASE ( 'before_timestep' )
+!
+!--       Enter actions to be done before every timestep here
+
+       CASE ( 'before_prognostic_equations' )
+!
+!--       Enter actions to be done before all prognostic equations here
+
+       CASE ( 'after_integration' )
+!
+!--       Enter actions to be done after every time integration (before
+!--       data output)
+!--       Sample for user-defined output:
+!          DO  i = nxlg, nxrg
+!             DO  j = nysg, nyng
+!                DO  k = nzb, nzt
+!                   u2(k,j,i) = u(k,j,i)**2
+!                ENDDO
+!             ENDDO
+!          ENDDO
+!          DO  i = nxlg, nxr
+!             DO  j = nysg, nyn
+!                DO  k = nzb, nzt+1
+!                   ustvst(k,j,i) =  &
+!                      ( 0.5_wp * ( u(k,j,i) + u(k,j,i+1) ) - hom(k,1,1,0) ) * &
+!                      ( 0.5_wp * ( v(k,j,i) + v(k,j+1,i) ) - hom(k,1,2,0) )
+!                ENDDO
+!             ENDDO
+!          ENDDO
+
+          DO  i = nxlg, nxrg
+             DO  j = nysg, nyng
+                DO  k = nzb, nzt
+                   v_h(k,j,i) = SQRT(u(k,j,i)**2.+v(k,j,i)**2.)
+                ENDDO
+             ENDDO
+          ENDDO
+
+
+       CASE ( 'after_timestep' )
+!
+!--       Enter actions to be done after every timestep here
+
+
+       CASE ( 'u-tendency' )
+!
+!--       Enter actions to be done in the u-tendency term here
+
+
+       CASE ( 'v-tendency' )
+
+
+       CASE ( 'w-tendency' )
+
+
+       CASE ( 'pt-tendency' )
+
+
+       CASE ( 'sa-tendency' )
+
+
+       CASE ( 'e-tendency' )
+
+
+       CASE ( 'q-tendency' )
+
+
+       CASE ( 's-tendency' )
+
+
+       CASE DEFAULT
+          CONTINUE
+
+    END SELECT
+
+    CALL cpu_log( log_point(24), 'user_actions', 'stop' )
+
+ END SUBROUTINE user_actions
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Call for grid point i,j
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_actions_ij( i, j, location )
+
+
+    CHARACTER (LEN=*) ::  location
+
+    INTEGER(iwp) ::  i
+    INTEGER(iwp) ::  j
+
+!
+!-- Here the user-defined actions follow
+    SELECT CASE ( location )
+
+       CASE ( 'u-tendency' )
+
+!
+!--       Next line is to avoid compiler warning about unused variables. Please remove.
+          IF ( i == 0  .OR.  j == 0 )  CONTINUE
+
+!
+!--       Enter actions to be done in the u-tendency term here
+
+
+       CASE ( 'v-tendency' )
+
+
+       CASE ( 'w-tendency' )
+
+
+       CASE ( 'pt-tendency' )
+
+
+       CASE ( 'sa-tendency' )
+
+
+       CASE ( 'e-tendency' )
+
+
+       CASE ( 'q-tendency' )
+
+
+       CASE ( 's-tendency' )
+
+
+       CASE DEFAULT
+          CONTINUE
+
+    END SELECT
+
+ END SUBROUTINE user_actions_ij
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Sum up and time-average user-defined output quantities as well as allocate
+!> the array necessary for storing the average.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_3d_data_averaging( mode, variable )
+
+
+    CHARACTER (LEN=*) ::  mode    !< 
+    CHARACTER (LEN=*) :: variable !< 
+
+    INTEGER(iwp) ::  i !<
+    INTEGER(iwp) ::  j !<
+    INTEGER(iwp) ::  k !<
+
+    IF ( mode == 'allocate' )  THEN
+
+       SELECT CASE ( TRIM( variable ) )
+
+!
+!--       Uncomment and extend the following lines, if necessary.
+!--       The arrays for storing the user defined quantities (here u2_av) have
+!--       to be declared and defined by the user!
+!--       Sample for user-defined output:
+!          CASE ( 'u2' )
+!             IF ( .NOT. ALLOCATED( u2_av ) )  THEN
+!                ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!             ENDIF
+!             u2_av = 0.0_wp
+
+          CASE ( 'v_h' )
+             IF ( .NOT. ALLOCATED( v_h_av ) )  THEN
+                ALLOCATE( v_h_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+             ENDIF
+             v_h_av = 0.0_wp
+
+          CASE DEFAULT
+             CONTINUE
+
+       END SELECT
+
+    ELSEIF ( mode == 'sum' )  THEN
+
+       SELECT CASE ( TRIM( variable ) )
+
+!
+!--       Uncomment and extend the following lines, if necessary.
+!--       The arrays for storing the user defined quantities (here u2 and
+!--       u2_av) have to be declared and defined by the user!
+!--       Sample for user-defined output:
+!          CASE ( 'u2' )
+!             IF ( ALLOCATED( u2_av ) ) THEN
+!                DO  i = nxlg, nxrg
+!                   DO  j = nysg, nyng
+!                      DO  k = nzb, nzt+1
+!                         u2_av(k,j,i) = u2_av(k,j,i) + u2(k,j,i)
+!                      ENDDO
+!                   ENDDO
+!                ENDDO
+!             ENDIF
+
+          CASE ( 'v_h' )
+             IF ( ALLOCATED( v_h_av ) ) THEN
+                DO  i = nxlg, nxrg
+                   DO  j = nysg, nyng
+                      DO  k = nzb, nzt+1
+                         v_h_av(k,j,i) = v_h_av(k,j,i) + v_h(k,j,i)
+                      ENDDO
+                   ENDDO
+                ENDDO
+             ENDIF
+
+          CASE DEFAULT
+             CONTINUE
+
+       END SELECT
+
+    ELSEIF ( mode == 'average' )  THEN
+
+       SELECT CASE ( TRIM( variable ) )
+
+!
+!--       Uncomment and extend the following lines, if necessary.
+!--       The arrays for storing the user defined quantities (here u2_av) have
+!--       to be declared and defined by the user!
+!--       Sample for user-defined output:
+!          CASE ( 'u2' )
+!             IF ( ALLOCATED( u2_av ) ) THEN
+!                DO  i = nxlg, nxrg
+!                   DO  j = nysg, nyng
+!                      DO  k = nzb, nzt+1
+!                         u2_av(k,j,i) = u2_av(k,j,i) / REAL( average_count_3d, KIND=wp )
+!                      ENDDO
+!                   ENDDO
+!                ENDDO
+!             ENDIF
+
+        CASE ( 'v_h' )
+           IF ( ALLOCATED( v_h_av ) ) THEN
+              DO  i = nxlg, nxrg
+                 DO  j = nysg, nyng
+                    DO  k = nzb, nzt+1
+                       v_h_av(k,j,i) = v_h_av(k,j,i) / REAL( average_count_3d, KIND=wp )
+                    ENDDO
+                 ENDDO
+              ENDDO
+           ENDIF
+
+       END SELECT
+
+    ENDIF
+
+
+ END SUBROUTINE user_3d_data_averaging
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Resorts the user-defined output quantity with indices (k,j,i) to a
+!> temporary array with indices (i,j,k) and sets the grid on which it is defined.
+!> Allowed values for grid are "zu" and "zw".
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_data_output_2d( av, variable, found, grid, local_pf, two_d, nzb_do, nzt_do )
+
+
+    CHARACTER (LEN=*) ::  grid     !< 
+    CHARACTER (LEN=*) ::  variable !< 
+
+    INTEGER(iwp) ::  av     !< flag to control data output of instantaneous or time-averaged data
+    INTEGER(iwp) ::  i      !< grid index along x-direction
+    INTEGER(iwp) ::  j      !< grid index along y-direction
+    INTEGER(iwp) ::  k      !< grid index along z-direction
+!    INTEGER(iwp) ::  m      !< running index surface elements
+    INTEGER(iwp) ::  nzb_do !< lower limit of the domain (usually nzb)
+    INTEGER(iwp) ::  nzt_do !< upper limit of the domain (usually nzt+1)
+
+    LOGICAL      ::  found !< 
+    LOGICAL      ::  two_d !< flag parameter that indicates 2D variables (horizontal cross sections)
+
+    REAL(wp) ::  fill_value = -999.0_wp    !< value for the _FillValue attribute
+
+    REAL(wp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) ::  local_pf !< 
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( av == 0  .OR.  local_pf(nxl,nys,nzb_do) == 0.0_wp  .OR.  two_d )  CONTINUE
+
+
+    found = .TRUE.
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary.
+!--    The arrays for storing the user defined quantities (here u2 and u2_av)
+!--    have to be declared and defined by the user!
+!--    Sample for user-defined output:
+!       CASE ( 'u2_xy', 'u2_xz', 'u2_yz' )
+!          IF ( av == 0 )  THEN
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ELSE
+!             IF ( .NOT. ALLOCATED( u2_av ) ) THEN
+!                ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!                u2_av = REAL( fill_value, KIND = wp )
+!             ENDIF
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2_av(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ENDIF
+!
+!          grid = 'zu'
+
+      CASE ( 'v_h_xy', 'v_h_xz', 'v_h_yz' )
+         IF ( av == 0 )  THEN
+            DO  i = nxl, nxr
+               DO  j = nys, nyn
+                  DO  k = nzb_do, nzt_do
+                     local_pf(i,j,k) = v_h(k,j,i)
+                  ENDDO
+               ENDDO
+            ENDDO
+         ELSE
+            IF ( .NOT. ALLOCATED( v_h_av ) ) THEN
+               ALLOCATE( v_h_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+               v_h_av = REAL( fill_value, KIND = wp )
+            ENDIF
+            DO  i = nxl, nxr
+               DO  j = nys, nyn
+                  DO  k = nzb_do, nzt_do
+                     local_pf(i,j,k) = v_h_av(k,j,i)
+                  ENDDO
+               ENDDO
+            ENDDO
+         ENDIF
+
+         grid = 'zu'
+!
+!--    In case two-dimensional surface variables are output, the user
+!--    has to access related surface-type. Uncomment and extend following lines
+!--    appropriately (example output of vertical surface momentum flux of u-
+!--    component). Please note, surface elements can be distributed over 
+!--    several data type, depending on their respective surface properties.
+!       CASE ( 'usws_xy' )
+!          IF ( av == 0 )  THEN
+!
+!--           Horizontal default-type surfaces
+!             DO  m = 1, surf_def_h(0)%ns
+!                i = surf_def_h(0)%i(m)
+!                j = surf_def_h(0)%j(m)
+!                local_pf(i,j,1) = surf_def_h(0)%usws(m)
+!             ENDDO
+!
+!--           Horizontal natural-type surfaces
+!             DO  m = 1, surf_lsm_h%ns
+!                i = surf_lsm_h%i(m)
+!                j = surf_lsm_h%j(m)
+!                local_pf(i,j,1) = surf_lsm_h%usws(m)
+!             ENDDO
+!
+!--           Horizontal urban-type surfaces
+!             DO  m = 1, surf_usm_h%ns
+!                i = surf_usm_h%i(m)
+!                j = surf_usm_h%j(m)
+!                local_pf(i,j,1) = surf_usm_h%usws(m)
+!             ENDDO
+!          ENDIF
+!
+!          grid = 'zu'
+!--       
+
+
+       CASE DEFAULT
+          found = .FALSE.
+          grid  = 'none'
+
+    END SELECT
+
+
+ END SUBROUTINE user_data_output_2d
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Resorts the user-defined output quantity with indices (k,j,i) to a
+!> temporary array with indices (i,j,k).
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_data_output_3d( av, variable, found, local_pf, nzb_do, nzt_do )
+
+
+    CHARACTER (LEN=*) ::  variable !< 
+
+    INTEGER(iwp) ::  av    !< 
+    INTEGER(iwp) ::  i     !<
+    INTEGER(iwp) ::  j     !<
+    INTEGER(iwp) ::  k     !<
+    INTEGER(iwp) ::  nzb_do !< lower limit of the data output (usually 0)
+    INTEGER(iwp) ::  nzt_do !< vertical upper limit of the data output (usually nz_do3d)
+
+    LOGICAL      ::  found !< 
+
+    REAL(wp) ::  fill_value = -999.0_wp    !< value for the _FillValue attribute
+
+    REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) ::  local_pf !< 
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( av == 0  .OR.  local_pf(nxl,nys,nzb_do) == 0.0_wp )  CONTINUE
+
+
+    found = .TRUE.
+
+    SELECT CASE ( TRIM( variable ) )
+
+!
+!--    Uncomment and extend the following lines, if necessary.
+!--    The arrays for storing the user defined quantities (here u2 and u2_av)
+!--    have to be declared and defined by the user!
+!--    Sample for user-defined output:
+!       CASE ( 'u2' )
+!          IF ( av == 0 )  THEN
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ELSE
+!             IF ( .NOT. ALLOCATED( u2_av ) ) THEN
+!                ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!                u2_av = REAL( fill_value, KIND = wp )
+!             ENDIF
+!             DO  i = nxl, nxr
+!                DO  j = nys, nyn
+!                   DO  k = nzb_do, nzt_do
+!                      local_pf(i,j,k) = u2_av(k,j,i)
+!                   ENDDO
+!                ENDDO
+!             ENDDO
+!          ENDIF
+!
+
+      CASE ( 'v_h' )
+         IF ( av == 0 )  THEN
+            DO  i = nxl, nxr
+               DO  j = nys, nyn
+                  DO  k = nzb_do, nzt_do
+                     local_pf(i,j,k) = v_h(k,j,i)
+                  ENDDO
+               ENDDO
+            ENDDO
+         ELSE
+            IF ( .NOT. ALLOCATED( v_h_av ) ) THEN
+               ALLOCATE( v_h_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+               v_h_av = REAL( fill_value, KIND = wp )
+            ENDIF
+            DO  i = nxl, nxr
+               DO  j = nys, nyn
+                  DO  k = nzb_do, nzt_do
+                     local_pf(i,j,k) = v_h_av(k,j,i)
+                  ENDDO
+               ENDDO
+            ENDDO
+         ENDIF
+         
+         
+       CASE DEFAULT
+          found = .FALSE.
+
+    END SELECT
+
+
+ END SUBROUTINE user_data_output_3d
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Calculation of user-defined statistics, i.e. horizontally averaged profiles
+!> and time series.
+!> This routine is called for every statistic region sr defined by the user,
+!> but at least for the region "total domain" (sr=0).
+!> See section 3.5.4 on how to define, calculate, and output user defined
+!> quantities.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_statistics( mode, sr, tn )
+
+
+    CHARACTER (LEN=*) ::  mode   !< 
+!    INTEGER(iwp) ::  i    !<
+!    INTEGER(iwp) ::  j    !<
+!    INTEGER(iwp) ::  k    !<
+    INTEGER(iwp) ::  sr   !< 
+    INTEGER(iwp) ::  tn   !< 
+
+!    REAL(wp), DIMENSION(:), ALLOCATABLE ::  ts_value_l   !<
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    IF ( sr == 0  .OR.  tn == 0 )  CONTINUE
+
+    IF ( mode == 'profiles' )  THEN
+
+!
+!--    Sample on how to calculate horizontally averaged profiles of user-
+!--    defined quantities. Each quantity is identified by the index
+!--    "pr_palm+#" where "#" is an integer starting from 1. These
+!--    user-profile-numbers must also be assigned to the respective strings
+!--    given by data_output_pr_user in routine user_check_data_output_pr.
+!       !$OMP DO
+!       DO  i = nxl, nxr
+!          DO  j = nys, nyn
+!             DO  k = nzb+1, nzt
+!!
+!!--             Sample on how to calculate the profile of the resolved-scale
+!!--             horizontal momentum flux u*v*
+!                sums_l(k,pr_palm+1,tn) = sums_l(k,pr_palm+1,tn) +             &
+!                      ( 0.5_wp * ( u(k,j,i) + u(k,j,i+1) ) - hom(k,1,1,sr) ) *&
+!                      ( 0.5_wp * ( v(k,j,i) + v(k,j+1,i) ) - hom(k,1,2,sr) )  &
+!                                     * rmask(j,i,sr)                          &
+!                                     * MERGE( 1.0_wp, 0.0_wp,                 &
+!                                              BTEST( wall_flags_0(k,j,i), 0 ) )
+!!
+!!--             Further profiles can be defined and calculated by increasing
+!!--             the second index of array sums_l (replace ... appropriately)
+!                sums_l(k,pr_palm+2,tn) = sums_l(k,pr_palm+2,tn) + ...           &
+!                                         * rmask(j,i,sr)
+!             ENDDO
+!          ENDDO
+!       ENDDO
+
+    ELSEIF ( mode == 'time_series' )  THEN
+
+
+!       ALLOCATE ( ts_value_l(dots_num_user) )
+!
+!--    Sample on how to add values for the user-defined time series quantities.
+!--    These have to be defined before in routine user_init. This sample
+!--    creates two time series for the absolut values of the horizontal
+!--    velocities u and v.
+!       ts_value_l = 0.0_wp
+!       ts_value_l(1) = ABS( u_max )
+!       ts_value_l(2) = ABS( v_max )
+!
+!--     Collect / send values to PE0, because only PE0 outputs the time series.
+!--     CAUTION: Collection is done by taking the sum over all processors.
+!--              You may have to normalize this sum, depending on the quantity
+!--              that you like to calculate. For serial runs, nothing has to be
+!--              done.
+!--     HINT: If the time series value that you are calculating has the same
+!--           value on all PEs, you can omit the MPI_ALLREDUCE call and
+!--           assign ts_value(dots_num_palm+1:,sr) = ts_value_l directly.
+!#if defined( __parallel )
+!       IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
+!       CALL MPI_ALLREDUCE( ts_value_l(1),                         &
+!                           ts_value(dots_num_palm+1,sr),                        &
+!                           dots_num_user, MPI_REAL, MPI_MAX, comm2d,   &
+!                           ierr )
+!#else
+!       ts_value(dots_num_palm+1:dots_num_palm+dots_num_user,sr) = ts_value_l
+!#endif
+
+    ENDIF
+
+ END SUBROUTINE user_statistics
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Reading global restart data that has been defined by the user.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_rrd_global( found )
+
+
+    LOGICAL, INTENT(OUT)  ::  found
+
+
+    found = .TRUE.
+
+
+    SELECT CASE ( restart_string(1:length) )
+
+       CASE ( 'global_paramter' )
+!          READ ( 13 )  global_parameter
+
+       CASE DEFAULT
+ 
+          found = .FALSE.
+
+    END SELECT
+
+
+ END SUBROUTINE user_rrd_global
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Reading processor specific restart data from file(s) that has been defined 
+!> by the user.
+!> Subdomain index limits on file are given by nxl_on_file, etc.
+!> Indices nxlc, etc. indicate the range of gridpoints to be mapped from the
+!> subdomain on file (f) to the subdomain of the current PE (c). They have been
+!> calculated in routine rrd_local.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_rrd_local( k, nxlf, nxlc, nxl_on_file, nxrf, nxrc,         &
+                            nxr_on_file, nynf, nync, nyn_on_file, nysf,     &
+                            nysc, nys_on_file, tmp_3d, found )
+
+
+    INTEGER(iwp) ::  idum            !<
+    INTEGER(iwp) ::  k               !<
+    INTEGER(iwp) ::  nxlc            !<
+    INTEGER(iwp) ::  nxlf            !<
+    INTEGER(iwp) ::  nxl_on_file     !<
+    INTEGER(iwp) ::  nxrc            !<
+    INTEGER(iwp) ::  nxrf            !<
+    INTEGER(iwp) ::  nxr_on_file     !<
+    INTEGER(iwp) ::  nync            !<
+    INTEGER(iwp) ::  nynf            !<
+    INTEGER(iwp) ::  nyn_on_file     !<
+    INTEGER(iwp) ::  nysc            !<
+    INTEGER(iwp) ::  nysf            !<
+    INTEGER(iwp) ::  nys_on_file     !<
+
+    LOGICAL, INTENT(OUT)  ::  found
+
+    REAL(wp), DIMENSION(nzb:nzt+1,nys_on_file-nbgp:nyn_on_file+nbgp,nxl_on_file-nbgp:nxr_on_file+nbgp) :: tmp_3d   !<
+
+!
+!-- Next line is to avoid compiler warning about unused variables. Please remove.
+    idum = k + nxlc + nxlf + nxrc + nxrf + nync + nynf + nysc + nysf +                             &
+           INT( tmp_3d(nzb,nys_on_file,nxl_on_file) )
+
+!
+!-- Here the reading of user-defined restart data follows:
+!-- Sample for user-defined output
+
+    found = .TRUE.
+
+    SELECT CASE ( restart_string(1:length) )
+
+       CASE ( 'u2_av' )
+!          IF ( .NOT. ALLOCATED( u2_av ) ) THEN
+!               ALLOCATE( u2_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
+!          ENDIF
+!          IF ( k == 1 )  READ ( 13 )  tmp_3d
+!             u2_av(:,nysc-nbgp:nync+nbgp,nxlc-nbgp:nxrc+nbgp) =         &
+!                tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
+!
+       CASE DEFAULT
+
+          found = .FALSE.
+
+    END SELECT
+
+ END SUBROUTINE user_rrd_local
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Writes global and user-defined restart data into binary file(s) for restart
+!> runs.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_wrd_global
+
+!    CALL wrd_write_string( 'global_parameter' )
+!    WRITE ( 14 )  global_parameter
+
+ END SUBROUTINE user_wrd_global
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Writes processor specific and user-defined restart data into binary file(s) 
+!> for restart runs.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_wrd_local
+
+!
+!-- Here the user-defined actions at the end of a job follow.
+!-- Sample for user-defined output:
+!    IF ( ALLOCATED( u2_av ) )  THEN
+!       CALL wrd_write_string( 'u2_av' )
+!       WRITE ( 14 )  u2_av
+!    ENDIF
+
+ END SUBROUTINE user_wrd_local
+
+
+!------------------------------------------------------------------------------!
+! Description:
+! ------------
+!> Execution of user-defined actions at the end of a job.
+!------------------------------------------------------------------------------!
+ SUBROUTINE user_last_actions
+
+!
+!-- Here the user-defined actions at the end of a job might follow.
+
+
+ END SUBROUTINE user_last_actions
+
+ END MODULE user
Index: palm/trunk/TUTORIALS/cases/lsm_short/case_config.yml
===================================================================
--- palm/trunk/TUTORIALS/cases/lsm_short/case_config.yml	(revision 4091)
+++ palm/trunk/TUTORIALS/cases/lsm_short/case_config.yml	(revision 4091)
@@ -0,0 +1,16 @@
+---
+# this is a palmtest job configuration file
+
+allowed_builds:
+  - gfortran_default
+  - intel_default
+
+allowed_number_of_cores: []
+
+activation_strings:
+  - "d3#"
+
+significant_digits_for_netcdf_checks:
+  timeseries: 1
+  profiles: 0
+  other: 8
