Simplified Chemistry - Revision history

Editor 2: fixed math display

2023-10-26T11:15:48Z

fixed math display

← Older revision		Revision as of 13:15, 26 October 2023
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	Now the OH concentrations are calculated with the respective kinetic and photolysis constants, based on chemical kinetic laws:		Now the OH concentrations are calculated with the respective kinetic and photolysis constants, based on chemical kinetic laws:
			<chem>
	<math>[\ce{OH}]=\frac{\mathrm{2[\ce{O(^1D)}]}k_{\ce{H2O}}[\ce{H2O}]}{k_{\ce{CH4}}[\ce{CH4}]+(k_{\ce{CO,1}}+k_{\ce{CO,2}})[\ce{CO}]}</math>
	~~with <math>~~[\ce{O(^1D)}]~~=\frac~~{~~J_{\ce{O3}~~}[~~\ce{O3}~~]}{k_{~~\ce{O2}~~}[~~\ce{O2}~~]+k_{~~\ce{N2}~~}[~~\ce{N2}~~]+k_{~~\ce{H2O}~~}[~~\ce{H2O}~~]}~~</math>.~~		[OH] =\frac{ 2 [O(^1D)] k_{H2O} [H2O] } { k_{CH4} [CH4] + k_{CO,1} [CO] + k_{CO,2} [CO]},
			</chem>

			with
			<math>
			[O(^1D)] = \frac{ J_{O3} [O3]}{k_{O2}[O2]+k_{N2}[N2]+k_{H2O}[H2O]}
			</math>.

	Additionally emission data of the main sinks of OH are implemented. Since the simulation is performed on a R2B05-grid the following emission data are the most suitable ones for the respective trace gases:		Additionally emission data of the main sinks of OH are implemented. Since the simulation is performed on a R2B05-grid the following emission data are the most suitable ones for the respective trace gases:

Luca R: Syntaxhighlighting

2023-09-07T08:31:19Z

Syntaxhighlighting

← Older revision		Revision as of 10:31, 7 September 2023
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	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Part 1: Runscript Directory Settings (Example configuration)		Part 1: Runscript Directory Settings (Example configuration)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight line lang=bash class="mw-collapsible-content">
	#!/bin/bash		#!/bin/bash
	CENTER=IMK		CENTER=IMK
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	#		#
	#-----------------------------------------------------------------------------		#-----------------------------------------------------------------------------
			</syntaxhighlight>
	</pre>
	</div>		</div>

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	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Part 2: Runscript Timing Settings (Example configuration)		Part 2: Runscript Timing Settings (Example configuration)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight line lang=bash class="mw-collapsible-content">
	! run_nml: general switches ----------		! run_nml: general switches ----------
	&# model timing		&# model timing
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	leadtime="P10D"		leadtime="P10D"
	checkpoint_interval="P30D"		checkpoint_interval="P30D"
			</syntaxhighlight>
	</pre>
	</div>		</div>

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	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Part 3: Runscript ICON-Parameter and -Namelist Settings (Example configuration)		Part 3: Runscript ICON-Parameter and -Namelist Settings (Example configuration)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight line lang=bash class="mw-collapsible-content">
	# model parameters		# model parameters
	model_equations=3 # equation system		model_equations=3 # equation system
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	reg_lat_def = -90.,1,90.		reg_lat_def = -90.,1,90.
	/		/
			</syntaxhighlight>
	</pre>
	</div>		</div>
	Please note in the last namelist section "output_nml" that you can set all output variables that you need to postprocess your data later. All assigned variables here will be written in the output netCDF-files as well. To learn more about post processing your data, check out a later chapter of this article or the [[Postprocessing]] article.		Please note in the last namelist section "output_nml" that you can set all output variables that you need to postprocess your data later. All assigned variables here will be written in the output netCDF-files as well. To learn more about post processing your data, check out a later chapter of this article or the [[Postprocessing]] article.
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	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Part 4: Runscript ICON-ART Settings (Example configuration)		Part 4: Runscript ICON-ART Settings (Example configuration)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight line lang=bash class="mw-collapsible-content">
	&art_nml		&art_nml
	lart_chem = .TRUE.		lart_chem = .TRUE.
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	/		/
	EOF		EOF
			</syntaxhighlight>
	</pre>
	</div>		</div>
	Please note that there are also several other namelist parameter you can select from (see [[Namelist]] article) but to perform our we're done for this part.		Please note that there are also several other namelist parameter you can select from (see [[Namelist]] article) but to perform our we're done for this part.
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	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Part 5: Runscript job Settings (Example configuration)		Part 5: Runscript job Settings (Example configuration)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight line lang=bash class="mw-collapsible-content">
	cp ${ICONFOLDER}/bin/icon ./icon.exe		cp ${ICONFOLDER}/bin/icon ./icon.exe

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	chmod +x job_ICON		chmod +x job_ICON
	sbatch job_ICON		sbatch job_ICON
			</syntaxhighlight>
	</pre>
	</div>		</div>

Line 460:		Line 460:
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Complete example configuration of the runscript		Complete example configuration of the runscript
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight line lang=bash class="mw-collapsible-content">
	#!/bin/bash		#!/bin/bash
	CENTER=IMK		CENTER=IMK
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	chmod +x job_ICON		chmod +x job_ICON
	sbatch job_ICON		sbatch job_ICON
			</syntaxhighlight>
	</pre>
	</div>		</div>

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	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Chemtracer-xml-file for OH chemistry (Example configuration)		Chemtracer-xml-file for OH chemistry (Example configuration)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight line lang=xml class="mw-collapsible-content">
	<?xml version="1.0" encoding="UTF-8"?>		<?xml version="1.0" encoding="UTF-8"?>
	<!DOCTYPE tracers SYSTEM "tracers.dtd">		<!DOCTYPE tracers SYSTEM "tracers.dtd">
Line 1,028:		Line 1,028:
	</chemtracer>		</chemtracer>
	</tracers>		</tracers>
			</syntaxhighlight>
	</pre>
	</div>		</div>

Tim R: Small improvements and corrections

2023-07-26T13:06:20Z

Small improvements and corrections

← Older revision		Revision as of 15:06, 26 July 2023
Line 36:		Line 36:

	== Setting up the Runscript ==		== Setting up the Runscript ==
	Let's start with the runscript that has to be prepared. Please note that the in the following explained parts have to be printed in one runscript-file with the naming designation "xyz.run". Here it is named <code>exp.testsuite.ohsim_simple_icon.run</code> but of course you can call it differently as well.		Let's start with the runscript that has to be prepared. Please note that the in the following explained parts have to be printed in one runscript-file with the naming designation "xyz.run". Here it is named <code>exp.testsuite.ohsim_simple_icon.run</code> but of course you can call it differently as well. The runscript can be stored under the following path in your icon directory: <code>/icon-kit/run</code>

	Inside of that, first check that all your directories are correct, probably they have to be adjusted. Abbreviations used here are the following:		Inside of that, first check in part 1 that all your paths to your directories are correct, probably they have to be adjusted. Note that "hp8526" is a name of a specific account here, make sure to double check especially these lines. Abbreviations used here are the following:
	*CENTER: Your organization		*CENTER: Your organization
	*EXPNAME: name of your ICON-Simulation		*EXPNAME: name of your ICON-Simulation
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	</div>		</div>

	Further, all the namelist parameters (from the regular ICON model without ART-extension) have to be set. For a regular ICON-ART-Simulation the following settings are recommended - if not stated differently.		Further, all the namelist parameters (from the regular ICON model without ART-extension) have to be set. For a regular ICON-ART-Simulation the following settings are recommended - if not stated differently. For a detailed description, check out the ICON Documentation ([https://code.mpimet.mpg.de/attachments/download/19568/ICON_tutorial_2019.pdf Drill et. al. (2019)]).

			Since we make use of LINOZ, in the radiation namelist section <code>&radiation_nml</code> the namelist parameter <code>irad_o3</code> has to be set to 10:

	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">

Tim R: /* Setting up the Runscript */

2023-07-26T12:39:32Z

Setting up the Runscript

← Older revision		Revision as of 14:39, 26 July 2023
Line 45:		Line 45:
	*INDIR: Directory where the necessary Input data are stored		*INDIR: Directory where the necessary Input data are stored
	*EXP:		*EXP:
	*lart: For ICON-ART Simulation that has to be switched to <code>~~Oheim_simple_icon~~.~~run~~</code>.		*lart: For ICON-ART Simulation that has to be switched to <code>.True.</code>.

	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">

Tim R: Changing transport namelist from "stdchem" to "hadv52aero"

2023-07-20T14:36:55Z

Changing transport namelist from "stdchem" to "hadv52aero"

Tim R at 14:17, 20 July 2023

2023-07-20T14:17:14Z

← Older revision		Revision as of 16:17, 20 July 2023
Line 1,034:		Line 1,034:
	== Running the simulation ==		== Running the simulation ==
	Double check all filled in paths and namelist - especially the ART-namelists. If every namelist parameter in the runscript is filled in correctly, the runscript has to be saved. Afterwards by typing		Double check all filled in paths and namelist - especially the ART-namelists. If every namelist parameter in the runscript is filled in correctly, the runscript has to be saved. Afterwards by typing
	./exp.testsuite~~.ohsim_simple_icon.run~~.ohsim_simple_icon.run		./exp.testsuite.ohsim_simple_icon.run
	a job can be submitted to the respective HPC-System. Type the terminal command		a job can be submitted to the respective HPC-System. Type the terminal command
	squeue		squeue

Tim R: typos

2023-07-20T14:16:05Z

typos

← Older revision		Revision as of 16:16, 20 July 2023
Line 36:		Line 36:

	== Setting up the Runscript ==		== Setting up the Runscript ==
	Let's start with the runscript that has to be prepared. Please note that the in the following explained parts have to be printed in one runscript-file with the naming designation "xyz.run". Here it is named <code>ohsim_simple_icon.run</code> but of course you can call it differently as well.		Let's start with the runscript that has to be prepared. Please note that the in the following explained parts have to be printed in one runscript-file with the naming designation "xyz.run". Here it is named <code>exp.testsuite.ohsim_simple_icon.run</code> but of course you can call it differently as well.

	Inside of that, first check that all your directories are correct, probably they have to be adjusted. Abbreviations used here are the following:		Inside of that, first check that all your directories are correct, probably they have to be adjusted. Abbreviations used here are the following:
Line 1,034:		Line 1,034:
	== Running the simulation ==		== Running the simulation ==
	Double check all filled in paths and namelist - especially the ART-namelists. If every namelist parameter in the runscript is filled in correctly, the runscript has to be saved. Afterwards by typing		Double check all filled in paths and namelist - especially the ART-namelists. If every namelist parameter in the runscript is filled in correctly, the runscript has to be saved. Afterwards by typing
	/.ohsim_simple_icon.run		./exp.testsuite.ohsim_simple_icon.run.ohsim_simple_icon.run
	a job can be submitted to the respective HPC-System. Type the terminal command		a job can be submitted to the respective HPC-System. Type the terminal command
	squeue		squeue

Tim R: /* Chemtracer-xml-file */

2023-07-20T12:47:44Z

Chemtracer-xml-file

← Older revision		Revision as of 14:47, 20 July 2023
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	* partly information about included emission data (ANT=anthropogenic emission, BIO=biogenic emission, BBE=biomass burning emission, more information about available emission data, see [[Emission Data]])		* partly information about included emission data (ANT=anthropogenic emission, BIO=biogenic emission, BBE=biomass burning emission, more information about available emission data, see [[Emission Data]])
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	~~Part 4:~~ Chemtracer-xml-file for OH chemistry (Example configuration)		Chemtracer-xml-file for OH chemistry (Example configuration)
	<pre class="mw-collapsible-content">		<pre class="mw-collapsible-content">
	<?xml version="1.0" encoding="UTF-8"?>		<?xml version="1.0" encoding="UTF-8"?>

Tim R: Update on Runscript settings

2023-07-14T11:10:23Z

Update on Runscript settings

Show changes

Tim R: Xml-files and running the simulation and model output

2023-07-14T10:42:41Z

Xml-files and running the simulation and model output

← Older revision		Revision as of 12:42, 14 July 2023
Line 620:		Line 620:

	=== Emission-xml-file ===		=== Emission-xml-file ===
	To link the information from the chemtracer-xml-file that we want to include emission data of a specific chemical species with the specific information about the respective emission, ICON-ART is working with, we need a second xml-file: The emission-xml-file. It is normally a standard grid-dependant xml-file you can use where nothing has to be changed. Since this Simulation is performed on a R2B05 grid, we use the <code>emissions_R2B05_0014_cs.xml</code>. Have a look at the article about [[Emission Data]] to check out all the available emission-xml-files.		To link the information from the chemtracer-xml-file that we want to include emission data of a specific chemical species with the specific information about the respective emission, ICON-ART is working with, we need a second xml-file: The emission-xml-file. It is normally a standard grid-dependant xml-file you can use where nothing has to be changed. Since this Simulation is performed on a R2B05 grid, we use the <code>emissions_R2B05_0014_cs.xml</code>. Have a look at the article about [[Emission Data]] to check out all the available emission-xml-files for different resolutions.

			== Running the simulation ==
			Double check all filled in paths and namelist - especially the ART-namelists. If every namelist parameter in the runscript is filled in correctly, the runscript has to be saved. Afterwards by typing
			/.ohsim_simple_icon.run
			a job can be submitted to the respective HPC-System. Type the terminal command
			squeue
			to view a list of your submitted and currently running and jobs.
			By changing in the output directory (which is according to our runscript <code>/hkfs/work/workspace/scratch/hp8526-ws_icon_oh/output/ohsim_icon_simple_atom1</code> you can check the slurm file for possible errors and run times after your job has been run through.

			In the output directory you can also find all output data for postprocessing in netCDF format.

← Older revision		Revision as of 16:36, 20 July 2023
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	<?source_lifetime Hayman et al., ACP, 2017 ?>		<?source_lifetime Hayman et al., ACP, 2017 ?>
	<lifetime type="real">286977600</lifetime>		<lifetime type="real">286977600</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<c_solve type="char">OH</c_solve>		<c_solve type="char">OH</c_solve>
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	<?source_lifetime Hodnebrog et al, Atmos. Sci. Lett., 2018 ?>		<?source_lifetime Hodnebrog et al, Atmos. Sci. Lett., 2018 ?>
	<lifetime type="real">5011200</lifetime>		<lifetime type="real">5011200</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<c_solve type="char">OH</c_solve>		<c_solve type="char">OH</c_solve>
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	<?source_lifetime Hodnebrog et al, Atmos. Sci. Lett., 2018 ?>		<?source_lifetime Hodnebrog et al, Atmos. Sci. Lett., 2018 ?>
	<lifetime type="real">1123200</lifetime>		<lifetime type="real">1123200</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<c_solve type="char">OH</c_solve>		<c_solve type="char">OH</c_solve>
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	<?source_lifetime Weimer (2015), p. 16 ?>		<?source_lifetime Weimer (2015), p. 16 ?>
	<lifetime type="real">8640</lifetime>		<lifetime type="real">8640</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Weimer (2015), p. 9 ?>		<?source_lifetime Weimer (2015), p. 9 ?>
	<lifetime type="real">1728000</lifetime>		<lifetime type="real">1728000</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Ehhalt et al., IPCC, 2001, Chapter 4 ?>		<?source_lifetime Ehhalt et al., IPCC, 2001, Chapter 4 ?>
	<lifetime type="real">5184000</lifetime>		<lifetime type="real">5184000</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<c_solve type="char">OH</c_solve>		<c_solve type="char">OH</c_solve>
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	<?source_lifetime Houghton et al., IPCC, Cambridge University Press, 2001 ?>		<?source_lifetime Houghton et al., IPCC, Cambridge University Press, 2001 ?>
	<lifetime type="real">3153600000</lifetime>		<lifetime type="real">3153600000</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Pinder et al., GRL, 2008?>		<?source_lifetime Pinder et al., GRL, 2008?>
	<lifetime type="real">86400</lifetime>		<lifetime type="real">86400</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Wypych, 2017, Atlas of Material Damage?>		<?source_lifetime Wypych, 2017, Atlas of Material Damage?>
	<lifetime type="real">4730400000</lifetime>		<lifetime type="real">4730400000</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Von Glasow, Chemical Geology, 2009 ?>		<?source_lifetime Von Glasow, Chemical Geology, 2009 ?>
	<lifetime type="real">1209600</lifetime>		<lifetime type="real">1209600</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Ullwer (2017) ?>		<?source_lifetime Ullwer (2017) ?>
	<lifetime type="real">504576000</lifetime>		<lifetime type="real">504576000</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Ullwer (2017) ?>		<?source_lifetime Ullwer (2017) ?>
	<lifetime type="real">216000</lifetime>		<lifetime type="real">216000</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
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	<?source_lifetime Day et al., ACP, 2008?>		<?source_lifetime Day et al., ACP, 2008?>
	<lifetime type="real">21600</lifetime>		<lifetime type="real">21600</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<init_name type="char"> HNO3 </init_name>		<init_name type="char"> HNO3 </init_name>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
Line 1,009:		Line 1,009:
	<?source_lifetime Fiedler et al., ACP, 2005?>		<?source_lifetime Fiedler et al., ACP, 2005?>
	<lifetime type="real">1800</lifetime>		<lifetime type="real">1800</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<unit type="char">mol mol-1</unit>		<unit type="char">mol mol-1</unit>
	<init_mode type="int">0</init_mode>		<init_mode type="int">0</init_mode>
Line 1,019:		Line 1,019:
	<?source_lifetime Ehhalt et al., IPCC, 2001, Chapter 4 ?>		<?source_lifetime Ehhalt et al., IPCC, 2001, Chapter 4 ?>
	<lifetime type="real">1555200</lifetime>		<lifetime type="real">1555200</lifetime>
	<transport type="char"> ~~stdchem~~ </transport>		<transport type="char"> hadv52aero </transport>
	<init_mode type="int"> 0 </init_mode>		<init_mode type="int"> 0 </init_mode>
	<init_name type="char">O3</init_name>		<init_name type="char">O3</init_name>