| 13 | | Since Version 5.0 a chemistry model is available in PALM which computes chemical conversion and tranport of reactive trace gases. In addition |
| 14 | | |
| 15 | | All parts of code that are related to chemistry start with `chem |
| 16 | | The main routines and the driver of the chemistry module is included in chemistry_model_mod.f90. 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. |
| 17 | | |
| 18 | | The module chem_gasphase_mod.f90, where the gas phase chemistry rate equations are solved within PALM4U 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 PALM4U module is named kpp4palm. |
| | 13 | Since Version 5.0 a chemistry model is available in PALM which computes chemical conversion and tranport of reactive trace gases. In addition, this module permits also the simulation of passive compounds in the gas phase and particulate matter. |
| | 14 | |
| | 15 | All parts of code that are related to chemistry start with `chem_`. |
| | 16 | 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. |
| | 17 | |
| | 18 | 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. |
| 29 | | Additionally 'mechanisms' are available that describes only the transport of one and two passive Tracers, respectively:\\ |
| 30 | | * passive1: Passive tracers (1 compound, 0 reactions)\\ |
| 31 | | * passive: Passive tracers (2 compounds, 0 reactions)\\ |
| | 29 | Additional 'mechanisms' are available that describe the transport of one or two passive tracers, i.e. no chemical reactions are necessary:\\ |
| | 30 | * passive1: Passive tracers (1 compound, 0 reactions)\\ |
| | 31 | * passive: Passive tracers (2 compounds, 0 reactions)\\ |
| 34 | | Currently, areosol compounds can be considered as passive compounds. Implementation of the sectional aerosol module SALSA (Kokkola et al., 2008 Atmos. Chem. Phys., 8, 2469–2483, 2008) is under way at the University of Helsinki. |
| 35 | | |
| 36 | | 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. |
| 37 | | For using a different chemical mechanism than the one that comes with checkout of PALM4U (currently 'passive'), copy your preferred mechanism into the SOURCE directory. Alteratively, the chemsitry 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 the mechanisms listed above. |
| 38 | | |
| 39 | | Further details about the use of the preprocessor and how to implement a new chemical mechanism see the [wiki:chempar#no1 Readme-File], This file is also available in the PALM4U subdirectory UTIL/chemistry/gasphase_preproc. (Note that the vector mode, which is mentioned in this document is not yet available in the trunk as there were different opinions about where to put one of the additional files.) |
| | 34 | 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. |
| | 35 | |
| | 36 | 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. |
| | 37 | 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). |
| | 38 | {{{!#comment |
| | 39 | --> 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. |
| | 40 | 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. |
| | 41 | }}} |
| | 42 | |
| | 43 | Further details about the use of the preprocessor and how to implement a new chemical mechanism see the [wiki:chempar#no1 Readme-File], This file is also available in the PALM-4U subdirectory UTIL/chemistry/gasphase_preproc. (Note that the vector mode, which is mentioned in this document is not yet available in the trunk - work-in-progress.) |
| 43 | | A main factor influencing atmospheric chemistry are the emissions of reactive compounds. In PALM |
| 44 | | * PARAMETERIZED: Traffic emissions are parameterized depending on the the values of street_type in the static file. Emission values for each street type and chemical compound must be supplied in the namelist as described below. No other emissions are considered. street_type can be obtained from `Openstreetmap`.\\ |
| 45 | | * DEFAULT: Gridded yearly emissions must be supplied by the user as specified in the PIDS document (see sample emissions file). Typical temporal variations are apllied by PALM4U.\\ |
| 46 | | * PRE-PROCESSED: Preprocessed hourly (other temporal intervals will be possible in later versions) 3-d emission fields must be supplied by the user. |
| | 47 | A main factor influencing atmospheric chemistry are the emissions of reactive compounds. In PALM-4U emissions can be applied in three different ways:\\ |
| | 48 | * PARAMETERIZED: Traffic emissions are parameterized depending on the the values of street_type in the static file. Emission values for each street type and chemical compound must be supplied in the namelist as described below. No other emissions are considered. street_type can be obtained from `Openstreetmap`.\\ |
| | 49 | * DEFAULT: Gridded yearly emissions must be supplied by the user as specified in the PIDS document (see sample emissions file). Typical temporal variations are apllied by PALM4U.\\ |
| | 50 | * PRE-PROCESSED: Preprocessed hourly (other temporal intervals will be possible in later versions) 3-d emission fields must be supplied by the user. |
| 50 | | IMPORTANT: In the PRE-PROCESSED mode the initial date of the simulation has to coincide with the first day for which emission values are available |
| 51 | | |
| 52 | | Find a more detailled description of the PALM4U emission input in the corresponding attached document [wiki:chempar#no1 here]. |
| 53 | | |
| 54 | | Chemistry is automatically activated when a {{{chemistry_parameters}}} namelist is set in the parameter file ({{{_p3d}}}). |
| | 54 | IMPORTANT: In the PRE-PROCESSED mode the initial date of the simulation has to coincide with the first day for which emission values are available. |
| | 55 | |
| | 56 | Find a more detailed description of the PALM-4U emission input in the corresponding attached document [wiki:chempar#no1 here]. |
| | 57 | |
| | 58 | The chemistry model is automatically activated when a {{{chemistry_parameters}}} namelist is included in the parameter file ({{{<run_identifier>_p3d}}}). |
