Changes between Version 79 and Version 80 of doc/app/chemistry_parameters

Timestamp:

Dec 17, 2018 3:31:57 PM (6 years ago)

Author:

forkel

Comment:

--

doc/app/chemistry_parameters

@@ -24 +24 @@
   * smog: Photochemical smog mechanism (13 compounds, 12 reactions)\\
   * simple: Simplified version of SMOG (9 compounds, 7 reactions)\\
-  * simplep: SIMPLE plus one tracer named PM10 (10 compounds, 7 real reactions plus one dummy 'reaction')\\
+  * simplep: 'simple' plus one tracer named PM10 (10 compounds, 7 real reactions plus one dummy 'reaction')\\
   * phstat: Photo-stationary state (3 compounds, 2 reactions)\\
+  * phstatp: Photo-stationary state plus one passive tracer named PM10 (4 compounds, 2 real reactions plus one dummy 'reaction')\\
 
 Additional 'mechanisms' are available that describe the transport of one or two passive tracers, i.e. no chemical reactions are necessary:\\
@@ -32 +33 @@
 This list will be extended further in the future. 
 
-In order to select and apply a certain mechanism from this sample, please copy the repctive ready-to-use `chem_gasephase_mod.f90` from `UTIL/chemistry/gasphase_preproc/mechanisms/def_MECH` (where `MECH` stands for any of the available mechanisms) into the USER_CODE directory of the respective simulation Setup, i.e. .../JOBS/<run_identifier>/USER_CODE/chem_gasphase_mod.f90.
-
-Alternatively, the chemistry preprocessor can be executed also for the available machanism in order to create chem_gasphase_mod.f90 (although for the available mechanisms this is not necessary because the chem_gasphase_mod.f90 files are already existing) instead of copying chem_gasphase_mod.f90: Enter the directory UTIL/chemistry/gasphase_preproc and apply the run script, i.e. {{{run_kpp4palm.ksh -m MECH}}}, where MECH stands for any of the mechanisms listed above. The resulting chem_gasphase_mod.f90 will be copied directly into the SOURCE directory. 
+The standard mechanism which is in the SOURCE directory is 'phstatp'.
+
+In order to select and apply a certain mechanism from this sample, please copy the respective ready-to-use `chem_gasephase_mod.f90` from `UTIL/chemistry/gasphase_preproc/mechanisms/def_MECH` (where `MECH` stands for any of the available mechanisms) into the USER_CODE directory of the respective simulation Setup, i.e. .../JOBS/<run_identifier>/USER_CODE/chem_gasphase_mod.f90.
+
+Alternatively, the chemistry preprocessor can be executed also for the available machanism in order to create chem_gasphase_mod.f90 (although for the available mechanisms this is not necessary because the chem_gasphase_mod.f90 files are already existing) instead of copying chem_gasphase_mod.f90: Enter the directory UTIL/chemistry/gasphase_preproc and apply the run script, i.e. {{{run_kpp4palm.ksh -m MECH}}}, where MECH stands for any of the mechanisms listed above. The resulting chem_gasphase_mod.f90 will be copied by the script directly into the SOURCE directory. 
 
 In order to find out which reactions and compounds are included in the different mechanisms, please have a look into the files MECH.eqn and MECH.spc in `UTIL/chemistry/gasphase_preproc/mechanisms/def_MECH`.
 
-How to implement a new chemical mechanism or add further passive Tracers see the [wiki:chempar#no1 Readme-File]. If more than two passive tracers or different names of the passive tracers are desired, a new 'mechanism' must be created as described in the Readme file. The Readme file is also available in the PALM-4U subdirectory UTIL/chemistry/gasphase_preproc. 
+How to implement a new chemical mechanism or add further passive tracers see the [wiki:chempar#no1 Readme-File]. If more than two passive tracers or different names of the passive tracers are desired, a new 'mechanism' must be created as described in the Readme file. The Readme file is also available in the PALM-4U subdirectory UTIL/chemistry/gasphase_preproc. 
 
 Currently, areosol compounds can be considered either as passive compounds or the sectional aerosol module SALSA [wiki:wiki/doc/app/salsa] (Kokkola et al., 2008 Atmos. Chem. Phys., 8, 2469–2483, 2008) can be used to simulate the aerosol particle concentrations, and size distributions. 
@@ -569 +572 @@
 [=#testsetups '''Test setups:]\\
 
-Test setups are attached here for the small test_urban setup with two passive compounds and a 1km x 1km model domain with 10 m grid width, which is centered around the Ernst-Reuter-Platz in Berlin. For this domain, example input files are supplied for two chemsitry settings:
+Test setups are attached here for the small test_urban setup with two passive compounds and a 1km x 1km model domain with 10 m grid width, which is centered around the Ernst-Reuter-Platz in Berlin. For this domain, example input files are supplied for two chemistry settings:
  two passive compounds ('passive')\\ 
  the 'smog' mechanism\\
 
-Please note that PALM-4U comes by default with the code for two passive tracers, i.e. {{{chem_gashase_mod.f90}}} is prepared for 'passive'. In order to run PALM-4U with the 'smog' mechanism, copy the {{{chem_gashase_mod.f90}}}, which is supplied in {{{UTIL/chemistry/gasphase_preproc/mechanisms/def_smog}}} into {{{SOURCE}}} (or execute {{{run_kpp4palm.ksh -m smog}}}. 
+Please note that PALM-4U comes by default with the code for the photostationay equilibrium between NO, NO2 and O3 plus one passive tracer, i.e. {{{chem_gashase_mod.f90}}} is prepared for 'phstatp'. In order to run PALM-4U e.g. with the 'smog' mechanism, copy the {{{chem_gashase_mod.f90}}}, which is supplied in {{{UTIL/chemistry/gasphase_preproc/mechanisms/def_smog}}} into {{{SOURCE}}} (or execute {{{run_kpp4palm.ksh -m smog}}}. 
 
 So far, all example setups are supplied for 'PARAMETERIZED' emissions. Example emissions files for 'PREPROCESSED' and 'DEFAULT' emissions will be supplied here at a later time.