Changes between Version 75 and Version 76 of doc/app/chemistry_parameters

Timestamp:

Nov 30, 2018 12:03:10 PM (7 years ago)

Author:

kanani

Comment:

--

doc/app/chemistry_parameters

@@ -14 +14 @@
 
 All parts of code that are related to chemistry start with `chem_`.
-The main routines and the driver of the chemistry module is included in chemistry_model_mod.f90, subroutines are in chem_gasphase_mod.f90, chem_photolysis_mod.f90, and chem_emissions.f90.
+The main routines and the driver of the chemistry module is included in [[source:palm/trunk/SOURCE/chemistry_model_mod.f90|chemistry_model_mod.f90]], subroutines are in chem_gasphase_mod.f90, chem_photolysis_mod.f90, and chem_emissions.f90.
 
 The module chem_gasphase_mod.f90, where the gas phase chemistry rate equations are solved within PALM-4U depends on the chosen chemical mechanism. chem_gasphase_mod.f90 is generated by a preprocessor that is based on the Kinetic Pre-Processor KPP (Damian et al., 2002, Sandu et al., 2006), Release 2.2.3 from November 2012 (http://people.cs.vt.edu/asandu/Software/Kpp/, kpp-2.2.3.tar.gz) and an adapted version of the KPP postprocessor KP4 (Jöckel et al, 2010, https://www.geosci-model-dev.net/3/717/2010/). This adapted Version of KP4 which converts the KPP-generated code to a PALM-4U module is named kpp4palm.
@@ -32 +32 @@
 The list will be extended further. 
 
-Currently, areosol compounds can be considered as passive compounds. Implementation of the sectional aerosol module [wiki:doc/tec/salsa SALSA (Kokkola et al., 2008 Atmos. Chem. Phys., 8, 2469–2483, 2008) is under way at the University of Helsinki. 
+Currently, areosol compounds can be considered as passive compounds. Implementation of the sectional aerosol module [wiki:doc/tec/aerosol SALSA] (Kokkola et al., 2008 Atmos. Chem. Phys., 8, 2469–2483, 2008) is under way at the University of Helsinki. 
 
 Ready-to-use chem_gasphase_mod.f90 files for each of the mechanisms are supplied in the subdirectories `UTIL/chemistry/gasphase_preproc/mechanisms/def_MECH`, where 'MECH' stands for any of the available mechanisms. 
 For using a different chemical mechanism than the one that comes with checkout of PALM-4U (currently 'passive'), copy your preferred mechanism into the USER_CODE directory of the respective simulation setup (.../JOBS/<run_identifier>/USER_CODE/chem_gasphase_mod.f90).
-{{{!#comment
+{{{#!comment
 --> An alternative is to produce own mechanisms, but for the available mechanisms this step is unnecessary because the chem_gasphase_mod.f90 files are already available.
  Alternatively, the chemistry preprocessor can be executed: 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.