[3494] | 1 | !> @file surface_output_merge.f90 |
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| 2 | !------------------------------------------------------------------------------! |
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| 3 | ! This file is part of the PALM model system. |
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| 4 | ! |
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| 5 | ! PALM is free software: you can redistribute it and/or modify it under the |
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| 6 | ! terms of the GNU General Public License as published by the Free Software |
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| 7 | ! Foundation, either version 3 of the License, or (at your option) any later |
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| 8 | ! version. |
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| 9 | ! |
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| 10 | ! PALM is distributed in the hope that it will be useful, but WITHOUT ANY |
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| 11 | ! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR |
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| 12 | ! A PARTICULAR PURPOSE. See the GNU General Public License for more details. |
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| 13 | ! |
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| 14 | ! You should have received a copy of the GNU General Public License along with |
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| 15 | ! PALM. If not, see <http://www.gnu.org/licenses/>. |
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| 16 | ! |
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| 17 | ! Copyright 1997-2018 Leibniz Universitaet Hannover |
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| 18 | !------------------------------------------------------------------------------! |
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| 19 | ! |
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| 20 | ! Current revisions: |
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| 21 | ! ----------------- |
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| 22 | ! |
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| 23 | ! |
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| 24 | ! Former revisions: |
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| 25 | ! ----------------- |
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| 26 | ! $Id: surface_output_to_vtk.f90 3494 2018-11-06 14:51:27Z suehring $ |
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| 27 | ! Initial version |
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| 28 | ! |
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| 29 | ! 3241 2018-09-12 15:02:00Z raasch |
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| 30 | ! |
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| 31 | ! |
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| 32 | ! Authors: |
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| 33 | ! -------- |
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| 34 | ! @author Matthias Suehring and Klaus Ketelsen |
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| 35 | ! |
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| 36 | !------------------------------------------------------------------------------! |
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| 37 | ! Description: |
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| 38 | ! ------------ |
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| 39 | !> This routine combines surface output from PALM-subdomains into one file. |
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| 40 | !> Output from every processor element is opened and read and output |
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| 41 | !> from all processor elements are written into one file for each timestep |
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| 42 | !> according to Paraview's VTK standard. |
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| 43 | !> Output is distinguished between instantaneous and time-averaged data. |
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| 44 | !------------------------------------------------------------------------------! |
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| 45 | PROGRAM surface_output_merge |
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| 46 | |
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| 47 | IMPLICIT NONE |
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| 48 | |
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| 49 | CHARACTER(LEN=4) :: char_time !< string indicating simulated time |
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| 50 | CHARACTER(LEN=4) :: file_suffix = '.bin' !< string which contain the suffix indicating surface data |
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| 51 | |
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| 52 | CHARACTER(LEN=10) :: char_dum !< dummy string |
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| 53 | |
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| 54 | CHARACTER(LEN=30) :: myid_char !< combined string indicating binary file |
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| 55 | |
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| 56 | CHARACTER(LEN=100) :: path !< path to the binary data |
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| 57 | CHARACTER(LEN=100) :: run !< name of the run |
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| 58 | CHARACTER(LEN=100) :: variable_name !< name of the processed output variable |
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| 59 | |
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| 60 | INTEGER(4) :: ftell !< intrinsic function, get current position in file |
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| 61 | INTEGER(4) :: fseek !< intrinsic function, go to given position in file |
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| 62 | INTEGER(4) :: ndum !< return parameter of intrinsic function fseek |
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| 63 | |
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| 64 | INTEGER, PARAMETER :: iwp = 4 !< integer precision |
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| 65 | INTEGER, PARAMETER :: wp = 8 !< float precision |
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| 66 | |
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| 67 | INTEGER(iwp) :: cycle_number !< cycle number |
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| 68 | INTEGER(iwp) :: f !< running index over all binary files |
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| 69 | INTEGER(iwp) :: file_id_in = 110 !< file unit for input binaray file |
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| 70 | INTEGER(iwp) :: file_id_out = 20 !< file unit for output VTK file |
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| 71 | INTEGER(iwp) :: file_id_out_header = 19 !< file unit for temporary header file |
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| 72 | INTEGER(iwp) :: length !< length of string on file |
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| 73 | INTEGER(iwp) :: n !< running index over all points and polygons |
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| 74 | INTEGER(iwp) :: npoints_total !< total number of points |
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| 75 | INTEGER(iwp) :: ns_total !< total number of polygons |
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| 76 | INTEGER(iwp) :: num_pe !< number of processors of the run |
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| 77 | |
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| 78 | INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: filepos !< current fileposition in binary file |
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| 79 | INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: npoints !< number of points/vertices in a binaray file |
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| 80 | INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ns !< number of surface elements in a binaray file |
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| 81 | |
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| 82 | LOGICAL :: convert_average_data = .FALSE. !< namelist parameter to decide whether average or instantaneous data should be converted |
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| 83 | LOGICAL, DIMENSION(:), ALLOCATABLE :: eof !< flag indicating that end of binary file is reached |
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| 84 | |
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| 85 | REAL(wp) :: simulated_time !< output time |
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| 86 | |
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| 87 | REAL(wp), DIMENSION(:), ALLOCATABLE :: var !< actual surface data |
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| 88 | |
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| 89 | REAL(wp), DIMENSION(:,:), ALLOCATABLE :: points !< point / vertex data |
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| 90 | REAL(wp), DIMENSION(:,:), ALLOCATABLE :: polygons !< polygon data |
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| 91 | |
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| 92 | ! |
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| 93 | !-- Read namelist. |
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| 94 | CALL surface_output_merge_parin |
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| 95 | ! |
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| 96 | !-- Allocate array which contains the file position in each output file, |
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| 97 | !-- in order to skip some reading. |
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| 98 | ALLOCATE( eof( 0:num_pe-1 ) ) |
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| 99 | ALLOCATE( filepos( 0:num_pe-1 ) ) |
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| 100 | ALLOCATE( npoints( 0:num_pe-1 ) ) |
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| 101 | ALLOCATE( ns( 0:num_pe-1 ) ) |
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| 102 | ! |
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| 103 | !-- Initialize file position. |
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| 104 | filepos = 0 |
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| 105 | ! |
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| 106 | !-- Open a temporary file which contains all necessary header information for the |
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| 107 | !-- VTK format. |
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| 108 | OPEN ( file_id_out_header, FILE = 'HEADER', STATUS = 'REPLACE', & |
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| 109 | FORM = 'FORMATTED' ) |
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| 110 | ! |
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| 111 | !-- READ grid setup, i.e. the number and position of vertices and surface elements |
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| 112 | !-- and merge all this information into one file. Further, create all the required |
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| 113 | !-- header information of the VTK file. |
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| 114 | !-- Note, PARAVIEW expects one VTK file for each variable and each timestep. |
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| 115 | !-- Hence, header information needs to be duplicated multiple times, which will be |
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| 116 | !-- be done later in a bash script. |
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| 117 | !-- Moreover, Paraview expects consecutive vertex and polygon data, which are |
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| 118 | !-- all distributed over the binaray files. Hence, first read vertex data from |
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| 119 | !-- binary file, write this to the HEADER file, close the binary file and read |
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| 120 | !-- data from the next binary file and so on. This requires several openenings |
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| 121 | !-- and closings of the binary files and temporarily storage of the |
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| 122 | !-- file-positions. |
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| 123 | DO f = 0, num_pe - 1 |
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| 124 | ! |
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| 125 | !-- Create filename of the treated binary file. |
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| 126 | CALL surface_output_merge_create_file_string |
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| 127 | ! |
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| 128 | !-- Open file with surface output for processor f. |
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| 129 | OPEN ( file_id_in + f, FILE = TRIM( path ) // TRIM( run ) // & |
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| 130 | TRIM( myid_char ), FORM='UNFORMATTED' ) |
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| 131 | ! |
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| 132 | !-- Read number of vertices / points and surface elements |
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| 133 | READ ( file_id_in + f ) npoints(f) |
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| 134 | READ ( file_id_in + f ) npoints_total |
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| 135 | READ ( file_id_in + f ) ns(f) |
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| 136 | READ ( file_id_in + f ) ns_total |
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| 137 | |
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| 138 | ! |
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| 139 | !-- Allocate arrays where all the surfaces and vertices will be stored. |
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| 140 | ALLOCATE( points(3,1:npoints(f)) ) |
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| 141 | |
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| 142 | ! |
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| 143 | !-- Read polygon data and store them in a temporary file. |
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| 144 | READ ( file_id_in + f ) points |
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| 145 | ! |
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| 146 | !-- Obtain current file position. Will be stored for next file opening. |
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| 147 | filepos(f) = ftell( file_id_in + f ) |
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| 148 | ! |
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| 149 | !-- Write header information. Only one time required. |
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| 150 | IF ( f == 0 ) THEN |
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| 151 | WRITE( file_id_out_header,'(A)' ) "# vtk DataFile Version 3.0" |
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| 152 | WRITE( file_id_out_header,'(A,F8.2,A)' ) "legacy vtk File generated by PALM, simulation time = xxx sec" |
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| 153 | WRITE( file_id_out_header,'(A)') "ASCII" |
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| 154 | |
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| 155 | WRITE( file_id_out_header,'(A)') "DATASET POLYDATA" |
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| 156 | WRITE( file_id_out_header,'(A,I5,A)') "POINTS ", npoints_total, " float" |
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| 157 | ENDIF |
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| 158 | ! |
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| 159 | !-- Write the vertex data into header file. |
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| 160 | DO n = 1, npoints(f) |
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| 161 | WRITE( file_id_out_header, '(8F10.1)' ) points(1:3,n) |
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| 162 | ENDDO |
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| 163 | ! |
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| 164 | !-- Deallocate vertex data and close binary file. |
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| 165 | DEALLOCATE( points ) |
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| 166 | |
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| 167 | CLOSE ( file_id_in + f ) |
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| 168 | ENDDO |
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| 169 | ! |
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| 170 | !-- Now, treat polygon data. |
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| 171 | DO f = 0, num_pe - 1 |
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| 172 | ! |
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| 173 | !-- Create filename of the treated binary file . |
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| 174 | CALL surface_output_merge_create_file_string |
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| 175 | ! |
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| 176 | !-- Open file with surface output for processor f. |
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| 177 | OPEN ( file_id_in + f, FILE = TRIM( path ) // TRIM( run ) // & |
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| 178 | TRIM( myid_char ), FORM='UNFORMATTED' ) |
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| 179 | ! |
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| 180 | !-- Move to last postion. |
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| 181 | ndum = fseek( file_id_in + f, filepos(f), 0 ) |
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| 182 | ! |
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| 183 | !-- Allocate array for polygon data |
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| 184 | ALLOCATE( polygons(5,1:ns(f)) ) |
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| 185 | ! |
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| 186 | !-- Read polygon data and store them in a temporary file. |
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| 187 | READ ( file_id_in + f ) polygons |
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| 188 | ! |
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| 189 | !-- Obtain current file position after reading the local polygon data. |
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| 190 | !-- Will be used for next file opening. |
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| 191 | filepos(f) = ftell( file_id_in + f ) |
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| 192 | ! |
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| 193 | !-- Write further header information. Only one time required. |
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| 194 | IF ( f == 0 ) & |
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| 195 | WRITE ( file_id_out_header, '(A,8I10)') "POLYGONS ", & |
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| 196 | ns_total, 5 * ns_total |
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| 197 | ! |
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| 198 | !-- Write the polygons into the header file. Note, polygon data is of type |
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| 199 | !-- integer, as it just connects the point-indices which describe the given |
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| 200 | !-- surface element. |
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| 201 | DO n = 1, ns(f) |
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| 202 | WRITE ( file_id_out_header, '(8I10)' ) INT (polygons(1:5,n) ) |
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| 203 | ENDDO |
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| 204 | ! |
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| 205 | !-- Deallocate array for polygon data and close the file. |
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| 206 | DEALLOCATE( polygons ) |
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| 207 | |
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| 208 | CLOSE ( file_id_in + f ) |
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| 209 | |
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| 210 | ENDDO |
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| 211 | |
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| 212 | f = 0 |
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| 213 | CALL surface_output_merge_create_file_string |
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| 214 | ! |
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| 215 | !-- Write further header information. Only once required. |
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| 216 | WRITE ( file_id_out_header, '(A,I10)') "CELL_DATA ", ns_total |
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| 217 | WRITE ( file_id_out_header, '(A,I10)') "SCALARS cell_scalars float 1 " |
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| 218 | WRITE ( file_id_out_header, '(A,I10)') "LOOKUP_TABLE default " |
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| 219 | ! |
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| 220 | !-- Header creation has now been completed. File can be closed. |
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| 221 | CLOSE( file_id_out_header ) |
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| 222 | ! |
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| 223 | !-- Now, read all the actual data from the surface output. Please note, Paraview |
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| 224 | !-- VTK format expects 1 file per variable and time step. |
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| 225 | !-- The output file is only created once and includes the variable and the |
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| 226 | !-- simulated time. |
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| 227 | !-- In the binaray files, several variables and timesteps are stored, data for a |
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| 228 | !-- given variable, however, is distributed over all binary files. Hence, read |
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| 229 | !-- variable data for a given timestep from the binary file, write this data into |
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| 230 | !-- the target output file, remember file position in binary file and close it, |
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| 231 | !-- open nex binary file and read the variable, and so on, until all variables |
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| 232 | !-- for all timesteps are processed. |
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| 233 | eof = .FALSE. |
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| 234 | DO |
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| 235 | DO f = 0, num_pe - 1 |
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| 236 | ! |
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| 237 | !-- Clean up strings- |
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| 238 | char_time = '' |
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| 239 | variable_name = '' |
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| 240 | ! |
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| 241 | !-- Create filename of the treated binary file. |
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| 242 | CALL surface_output_merge_create_file_string |
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| 243 | ! |
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| 244 | !-- Open binary file with surface output for processor f. |
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| 245 | OPEN ( file_id_in + f, FILE = TRIM( path ) // TRIM( run ) // & |
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| 246 | TRIM( myid_char ), FORM='UNFORMATTED' ) |
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| 247 | ! |
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| 248 | !-- Move to last postion. |
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| 249 | ndum = fseek( file_id_in + f, filepos(f), 0 ) |
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| 250 | ! |
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| 251 | !-- Read string length and string indicating the output time step. |
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| 252 | READ ( file_id_in + f ) length |
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| 253 | READ ( file_id_in + f ) char_time(1:length) |
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| 254 | ! |
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| 255 | !-- If string for the output time indicates the end-of-file, set the eof |
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| 256 | !-- flag and skip the read of the loop. |
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| 257 | IF ( char_time(1:length) == 'END' ) THEN |
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| 258 | eof(f) = .TRUE. |
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| 259 | CLOSE ( file_id_in + f ) |
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| 260 | CYCLE |
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| 261 | ENDIF |
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| 262 | ! |
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| 263 | !-- Read output time, and variable name. |
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| 264 | READ ( file_id_in + f ) simulated_time |
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| 265 | READ ( file_id_in + f ) length |
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| 266 | READ ( file_id_in + f ) variable_name(1:length) |
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| 267 | ! |
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| 268 | !-- For first loop index, open the target output file. First create the |
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| 269 | !-- filename string. Further, copy HEADER file with the given filename |
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| 270 | !-- string. The header information must be given in each VTK file! |
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| 271 | IF ( f == 0 ) THEN |
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| 272 | IF ( simulated_time < 10.0_wp ) THEN |
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| 273 | WRITE( char_dum, '(I1)' ) INT( simulated_time ) |
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| 274 | ELSEIF ( simulated_time < 100.0_wp ) THEN |
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| 275 | WRITE( char_dum, '(I2)' ) INT( simulated_time ) |
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| 276 | ELSEIF ( simulated_time < 1000.0_wp ) THEN |
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| 277 | WRITE( char_dum, '(I3)' ) INT( simulated_time ) |
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| 278 | ELSEIF ( simulated_time < 10000.0_wp ) THEN |
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| 279 | WRITE( char_dum, '(I4)' ) INT( simulated_time ) |
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| 280 | ELSEIF ( simulated_time < 100000.0_wp ) THEN |
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| 281 | WRITE( char_dum, '(I5)' ) INT( simulated_time ) |
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| 282 | ELSEIF ( simulated_time < 1000000.0_wp ) THEN |
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| 283 | WRITE( char_dum, '(I6)' ) INT( simulated_time ) |
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| 284 | ELSEIF ( simulated_time < 10000000.0_wp ) THEN |
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| 285 | WRITE( char_dum, '(I7)' ) INT( simulated_time ) |
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| 286 | ELSEIF ( simulated_time < 100000000.0_wp ) THEN |
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| 287 | WRITE( char_dum, '(I8)' ) INT( simulated_time ) |
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| 288 | ELSEIF ( simulated_time < 1000000000.0_wp ) THEN |
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| 289 | WRITE( char_dum, '(I9)' ) INT( simulated_time ) |
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| 290 | ENDIF |
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| 291 | ! |
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| 292 | !-- Copy HEADER file |
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| 293 | CALL system('cp HEADER ' // TRIM( path ) // TRIM( char_dum ) // & |
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| 294 | 's_' // TRIM( variable_name ) // '.vtk') |
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| 295 | !-- Open VTK file. |
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| 296 | OPEN ( file_id_out, FILE = TRIM( path ) // TRIM( char_dum ) // & |
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| 297 | 's_' // TRIM( variable_name ) // '.vtk', FORM='FORMATTED', & |
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| 298 | POSITION='APPEND' ) |
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| 299 | ENDIF |
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| 300 | ! |
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| 301 | !-- Allocate and read array for variable data. |
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| 302 | ALLOCATE( var(1:ns(f)) ) |
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| 303 | |
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| 304 | READ( file_id_in + f ) var |
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| 305 | ! |
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| 306 | !-- Write variable data into output VTK file. |
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| 307 | DO n = 1, ns(f) |
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| 308 | WRITE( file_id_out, * ) var(n) |
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| 309 | ENDDO |
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| 310 | ! |
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| 311 | !-- Remember file position in binary file and close it. |
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| 312 | filepos(f) = ftell( file_id_in + f ) |
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| 313 | |
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| 314 | CLOSE ( file_id_in + f ) |
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| 315 | ! |
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| 316 | !-- Deallocate temporary array for variable data. |
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| 317 | DEALLOCATE( var ) |
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| 318 | |
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| 319 | ENDDO |
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| 320 | ! |
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| 321 | !-- After data for a variable for one time step is read, close the output |
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| 322 | !-- VTK file and go to next variable or timestep. |
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| 323 | CLOSE ( file_id_out ) |
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| 324 | ! |
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| 325 | !-- If all files reached the end-of-file, exit the loop. |
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| 326 | IF ( ALL( eof ) ) EXIT |
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| 327 | |
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| 328 | ENDDO |
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| 329 | ! |
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| 330 | !-- Finally, remove HEADER file |
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| 331 | CALL system( 'rm HEADER' ) |
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| 332 | |
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| 333 | CONTAINS |
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| 334 | |
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| 335 | !------------------------------------------------------------------------------! |
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| 336 | ! Description: |
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| 337 | ! ------------ |
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| 338 | !> This subroutine read the namelist file. |
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| 339 | !------------------------------------------------------------------------------! |
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| 340 | SUBROUTINE surface_output_merge_parin |
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| 341 | |
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| 342 | IMPLICIT NONE |
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| 343 | |
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| 344 | INTEGER(iwp) :: file_id_parin = 90 |
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| 345 | |
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| 346 | NAMELIST /surface_output/ convert_average_data, cycle_number, num_pe, & |
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| 347 | path, run |
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| 348 | |
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| 349 | ! |
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| 350 | !-- Open namelist file. |
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| 351 | OPEN( file_id_parin, FILE='surface_output_parin', & |
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| 352 | STATUS='OLD', FORM='FORMATTED') |
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| 353 | ! |
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| 354 | !-- Read namelist. |
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| 355 | READ ( file_id_parin, surface_output ) |
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| 356 | ! |
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| 357 | !-- Close namelist file. |
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| 358 | CLOSE( file_id_parin ) |
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| 359 | |
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| 360 | END SUBROUTINE surface_output_merge_parin |
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| 361 | |
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| 362 | !------------------------------------------------------------------------------! |
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| 363 | ! Description: |
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| 364 | ! ------------ |
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| 365 | !> This subroutine creates the filename string of the treated binary file. |
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| 366 | !------------------------------------------------------------------------------! |
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| 367 | SUBROUTINE surface_output_merge_create_file_string |
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| 368 | |
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| 369 | IMPLICIT NONE |
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| 370 | |
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| 371 | CHARACTER(LEN=3) :: char_av = '' |
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| 372 | CHARACTER(LEN=4) :: char_cycle = '' |
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| 373 | |
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| 374 | ! |
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| 375 | !-- Create substring for the cycle number. |
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| 376 | IF ( cycle_number /= 0 ) THEN |
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| 377 | IF ( cycle_number < 10 ) THEN |
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| 378 | WRITE( char_cycle, '(I1)') cycle_number |
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| 379 | char_cycle = '.00' // TRIM( char_cycle ) |
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| 380 | ELSEIF ( cycle_number < 100 ) THEN |
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| 381 | WRITE( char_cycle, '(I2)') cycle_number |
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| 382 | char_cycle = '.0' // TRIM( char_cycle ) |
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| 383 | ELSEIF ( cycle_number < 1000 ) THEN |
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| 384 | WRITE( char_cycle, '(I3)') cycle_number |
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| 385 | char_cycle = '.' // TRIM( char_cycle ) |
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| 386 | ENDIF |
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| 387 | ENDIF |
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| 388 | ! |
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| 389 | !-- Create substring for averaged data. |
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| 390 | IF ( convert_average_data ) char_av = '_av' |
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| 391 | ! |
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| 392 | !-- Create substring for the processor id and combine all substrings. |
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| 393 | IF ( f < 10 ) THEN |
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| 394 | WRITE( char_dum, '(I1)') f |
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| 395 | myid_char = TRIM( char_av ) // '_surf_00000' // TRIM( char_dum ) // & |
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| 396 | TRIM( char_cycle ) // file_suffix |
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| 397 | ELSEIF ( f < 100 ) THEN |
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| 398 | WRITE( char_dum, '(I2)') f |
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| 399 | myid_char = TRIM( char_av ) // '_surf_0000' // TRIM( char_dum ) // & |
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| 400 | TRIM( char_cycle ) // file_suffix |
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| 401 | ELSEIF ( f < 1000 ) THEN |
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| 402 | WRITE( char_dum, '(I3)') f |
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| 403 | myid_char = TRIM( char_av ) // '_surf_000' // TRIM( char_dum ) // & |
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| 404 | TRIM( char_cycle ) // file_suffix |
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| 405 | ELSEIF ( f < 10000 ) THEN |
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| 406 | WRITE( char_dum, '(I4)') f |
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| 407 | myid_char = TRIM( char_av ) // '_surf_00' // TRIM( char_dum ) // & |
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| 408 | TRIM( char_cycle ) // file_suffix |
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| 409 | ELSEIF ( f < 100000 ) THEN |
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| 410 | WRITE( char_dum, '(I5)') f |
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| 411 | myid_char = TRIM( char_av ) // '_surf_0' // TRIM( char_dum ) // & |
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| 412 | TRIM( char_cycle ) // file_suffix |
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| 413 | ELSEIF ( f < 1000000 ) THEN |
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| 414 | WRITE( char_dum, '(I6)') f |
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| 415 | myid_char = TRIM( char_av ) // '_surf_' // TRIM( char_dum ) // & |
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| 416 | TRIM( char_cycle ) // file_suffix |
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| 417 | ENDIF |
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| 418 | |
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| 419 | END SUBROUTINE surface_output_merge_create_file_string |
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| 420 | |
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| 421 | END PROGRAM surface_output_merge |
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| 422 | |
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| 423 | |
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| 424 | |
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