Lifetime Tracer Simulation - Revision history

Editor 2: fixed math display

2023-10-26T10:45:43Z

fixed math display

← Older revision		Revision as of 12:45, 26 October 2023
Line 12:		Line 12:

	The simulation is modeling the 01 October 2012 and is initialized with data from the ECMWF Integrated Forecast System (IFS) and includes boundary conditions and chemical lifetimes from the WMO Ozone assessment 2010. The boundary conditions and the chemical lifetimes are recalculated in a sort of rate at which the substances are depleted from the atmosphere with help of the implicit solution of the balance equation:		The simulation is modeling the 01 October 2012 and is initialized with data from the ECMWF Integrated Forecast System (IFS) and includes boundary conditions and chemical lifetimes from the WMO Ozone assessment 2010. The boundary conditions and the chemical lifetimes are recalculated in a sort of rate at which the substances are depleted from the atmosphere with help of the implicit solution of the balance equation:
⚫	~~<math>~~\frac{\partial(\bar{\rho)\hat{\~~Psi_{l~~}}/{\partial t} = -\nabla\cdot (\hat{v}\~~bar~~{\rho}\hat{\~~Psi_~~{l}})- \nabla\cdot\~~bar~~{(\rho v''\Psi_{g,l}''}+P_l-L_l+E_l~~</math>~~

			<math>
⚫	Here <math>\rho</math> is the density of air, <math>\hat{\Psi_{l}}</math> the barycentric-averaged mass mixing ratio, <math>\nabla\cdot (\hat{v}\bar{\rho}\hat{\Psi_{l}})</math> indicates the flux divergence that includes the horizontal and vertical advection of the gaseous compound l and <math>\nabla\cdot\~~bar~~{(\rho v''\Psi_{l}'')}</math> indicates the change due to turbulent fluxes. Further <math>P_l</math> describes the production rate due to chemical reactions, <math>L_l</math> the respective loss rate and emissions are noted with <math>E_l</math>. Everything is related to the respective compound l.
		⚫	\frac{\partial \bar{\rho} \hat{\Psi}_l }{ \partial t} = -\nabla \cdot (\hat{v} \overline{\rho} \hat{\Psi}_{l})- \nabla \cdot (\overline{\rho v'' \Psi_{g,l}'' })+P_l-L_l+E_l
			</math>

		⚫	Here <math>\rho</math> is the density of air, <math>\hat{\Psi_{l}}</math> the barycentric-averaged mass mixing ratio, <math>\nabla\cdot (\hat{v}\bar{\rho}\hat{\Psi_{l}})</math> indicates the flux divergence that includes the horizontal and vertical advection of the gaseous compound l and <math>\nabla\cdot\overline{(\rho v''\Psi_{l}'')}</math> indicates the change due to turbulent fluxes. Further <math>P_l</math> describes the production rate due to chemical reactions, <math>L_l</math> the respective loss rate and emissions are noted with <math>E_l</math>. Everything is related to the respective compound l.

	In this example no emission data is used.		In this example no emission data is used.

Luca R: set up syntaxhiglight

2023-09-07T08:07:02Z

set up syntaxhiglight

← Older revision		Revision as of 10:07, 7 September 2023
Line 36:		Line 36:
	<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 lang=bash line class="mw-collapsible-content">
	#!/bin/bash		#!/bin/bash
	CENTER=IMK		CENTER=IMK
Line 110:		Line 110:
	#		#
	#-----------------------------------------------------------------------------		#-----------------------------------------------------------------------------
			</syntaxhighlight>
	</pre>
	</div>		</div>

Line 116:		Line 116:
	<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 lang=bash line class="mw-collapsible-content">
	! run_nml: general switches ----------		! run_nml: general switches ----------
	&# model timing		&# model timing
Line 128:		Line 128:
	leadtime="P8H"		leadtime="P8H"
	checkpoint_interval="P30D"		checkpoint_interval="P30D"
			</syntaxhihlight>
	</pre>
	</div>		</div>

Line 135:		Line 135:
	<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 lang=bash line class="mw-collapsible-content">
	# model parameters		# model parameters
	model_equations=3 # equation system		model_equations=3 # equation system
Line 390:		Line 390:
	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.
Line 398:		Line 398:
	<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 lang=bash line class="mw-collapsible-content">
	&art_nml		&art_nml
	lart_chem = .TRUE.		lart_chem = .TRUE.
Line 411:		Line 411:
	/		/
	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 case study we're done for the ART setting at this point.		Please note that there are also several other namelist parameter you can select from (see [[Namelist]] article) but to perform our case study we're done for the ART setting at this point.
Line 418:		Line 418:
	<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 lang=bash line class="mw-collapsible-content">
	cp ${ICONFOLDER}/bin/icon ./icon.exe		cp ${ICONFOLDER}/bin/icon ./icon.exe

Line 438:		Line 438:
	chmod +x job_ICON		chmod +x job_ICON
	sbatch job_ICON		sbatch job_ICON
			</syntaxhighlight>
	</pre>
	</div>		</div>

Line 445:		Line 445:
	<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 lang=bash line class="mw-collapsible-content">
	#!/bin/bash		#!/bin/bash
	CENTER=IMK		CENTER=IMK
Line 818:		Line 818:
	chmod +x job_ICON		chmod +x job_ICON
	sbatch job_ICON		sbatch job_ICON
			</syntaxhighlight>
	</pre>
	</div>		</div>

Line 828:		Line 828:
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Standard Chemtracer-xml-file for simulations without emission data		Standard Chemtracer-xml-file for simulations without emission data
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight lang=xml line 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 1,139:		Line 1,139:
	</chemtracer>		</chemtracer>
	</tracers>		</tracers>
			</syntaxhighlight>
	</pre>
	</div>		</div>

Line 1,145:		Line 1,145:
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Chemtracer-xml-file for lifetime tracer simulation (Example configuration)		Chemtracer-xml-file for lifetime tracer simulation (Example configuration)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight lang=xml line 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 1,175:		Line 1,175:
	</chemtracer>		</chemtracer>
	</tracers>		</tracers>
			</syntaxhighlight>
	</pre>
	</div>		</div>

Tim R: /* Setting up the Runscript */

2023-07-26T13:18:42Z

Setting up the Runscript

← Older revision		Revision as of 15:18, 26 July 2023
Line 394:		Line 394:
	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.

	Now, we're getting to the ICON-ART settings. To enable chemistry in an ICON-ART Simulation in general, the switch <code>lart_chem</code> has to be set to <code>.TRUE.</code>. With <code>lart_diag_out</code> output of the diagnostic fields can be enabled. Due to setting <code>lart_chem=.TRUE.</code> either <code>lart_chemtracer</code> or <code>lart_mecca</code> ~~have~~ to be set to <code>.TRUE.</code>. Because we want to perform a simulation with simplified chemistry, we have to switch on <code>lart_chemtracer</code>. If this namelist parameter is set to <code>.TRUE.</code>, also <code>cart_chemtracer_xml</code> has to be fulfilled. Here you enter the path of your xml-file which describes the tracers occurring and their properties in the simulation. How to create this xml-file is explained in the next chapter.		Now, we're getting to the ICON-ART settings. To enable chemistry in an ICON-ART Simulation in general, the switch <code>lart_chem</code> has to be set to <code>.TRUE.</code>. With <code>lart_diag_out</code> output of the diagnostic fields can be enabled. Due to setting <code>lart_chem=.TRUE.</code> either <code>lart_chemtracer</code> or <code>lart_mecca</code> has to be set to <code>.TRUE.</code>. Because we want to perform a simulation with simplified chemistry, we have to switch on <code>lart_chemtracer</code>. If this namelist parameter is set to <code>.TRUE.</code>, also <code>cart_chemtracer_xml</code> has to be fulfilled. Here you enter the path of your xml-file which describes the tracers occurring and their properties in the simulation. How to create this xml-file is explained in the next chapter.
	An example configuration for this part is shown in the following:		An example configuration for this part is shown in the following:
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">

Tim R: Small improvements in and corrections in several parts

2023-07-26T13:10:40Z

Small improvements in and corrections in several parts

Tim R at 11:20, 26 July 2023

2023-07-26T11:20:43Z

← Older revision		Revision as of 13:20, 26 July 2023
Line 6:		Line 6:
	* the structure of lifetime tracers in xml-files		* the structure of lifetime tracers in xml-files
	* editing output variables		* editing output variables
			No emission data will be included in this simulation.

	== Configuration case ==		== Configuration case ==

Tim R at 11:20, 26 July 2023

2023-07-26T11:20:01Z

← Older revision		Revision as of 13:20, 26 July 2023
Line 6:		Line 6:
	* the structure of lifetime tracers in xml-files		* the structure of lifetime tracers in xml-files
	* editing output variables		* editing output variables


	== Configuration case ==		== Configuration case ==

Tim R: Chapter xml-files and running the simulation created

2023-07-20T14:20:15Z

Chapter xml-files and running the simulation created

Show changes

Tim R: Adding Description "Setting up the Runscript"

2023-07-20T13:11:57Z

Adding Description "Setting up the Runscript"

Show changes

Tim R at 09:37, 20 July 2023

2023-07-20T09:37:38Z

← Older revision		Revision as of 11:37, 20 July 2023
Line 1:		Line 1:
	- under construction -		- under construction -

			In this example it is shown how to simulate a lifetime driven tracer with simplified chemistry in ICON-ART. This tutorial teaches you...
			* the correct setup of the xml-file for such tracers.
			* the structure of lifetime tracers in xml-files
			* editing output variables

Tim R: Creation of Configuration example of "Lifetime tracer"

2023-07-20T09:03:57Z

Creation of Configuration example of "Lifetime tracer"

New page

- under construction -

← Older revision		Revision as of 15:10, 26 July 2023
Line 21:		Line 21:
	== 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.lifetime_tracer_test.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.lifetime_tracer_test.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>

	If you've ~~also~~ ~~worked~~ through the example of the [[Simplified Chemistry]], you can use nearly the same runscript. Note that you have to change the paths from Part 1, the timing settings from Part 2, the output variables from Part 3, the emission settings as well as the path of the chemtracer-xml-file in the ART-settings from Part 4 and finally the timing in the job settings from Part 5. Details can be found below.		If you've already walked through the example of the [[Simplified Chemistry]], you can use nearly the same runscript. Note that you have to change the paths from Part 1, the timing settings from Part 2, the output variables from Part 3, the emission settings as well as the path of the chemtracer-xml-file in the ART-settings from Part 4 and finally the timing in the job settings from Part 5. Details can be found below.

	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
Line 32:		Line 32:
	*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">
Line 113:		Line 113:
	</div>		</div>

	Additionally in the next lines of code you set the timing. In this simulation we only simulate one day (01 October 2012). To ~~really catch all day times and so the time dependent solar radiation, the output interval is set to 1 hours to~~ calculate <chem>CHBr3</chem> and <chem>CH2Br2</chem> to every time of the day~~. Because of~~ the ~~Photolysis~~ ~~dependency~~ of ~~<chem>CHBr3</chem>~~ ~~this~~ ~~is particularly~~ ~~important~~.		Additionally in the next lines of code you set the timing. In this simulation we only simulate one day (01 October 2012). To calculate <chem>CHBr3</chem> and <chem>CH2Br2</chem> to every time of the day the output interval is set to 1 hour.
	<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)
Line 394:		Line 394:
	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.

	Now, we're getting to the ICON-ART settings. To enable chemistry in an ICON-ART Simulation ~~inn~~ general, the switch <code>lart_chem</code> has to be set to <code>.TRUE.</code>. With <code>lart_diag_out</code> output of the diagnostic fields can be enabled. Due to setting <code>lart_chem=.TRUE.</code> either <code>lart_chemtracer</code> or <code>lart_mecca</code> have to be set to <code>.TRUE.</code>. Because we want to perform a simulation with simplified chemistry, we have to switch on <code>lart_chemtracer</code>. If this namelist parameter is set to <code>.TRUE.</code>, also <code>cart_chemtracer_xml</code> has to be fulfilled. Here you enter the path of your xml-file which describes the tracers occurring and their properties in the simulation. How to create this xml-file is explained in the next chapter.		Now, we're getting to the ICON-ART settings. To enable chemistry in an ICON-ART Simulation in general, the switch <code>lart_chem</code> has to be set to <code>.TRUE.</code>. With <code>lart_diag_out</code> output of the diagnostic fields can be enabled. Due to setting <code>lart_chem=.TRUE.</code> either <code>lart_chemtracer</code> or <code>lart_mecca</code> have to be set to <code>.TRUE.</code>. Because we want to perform a simulation with simplified chemistry, we have to switch on <code>lart_chemtracer</code>. If this namelist parameter is set to <code>.TRUE.</code>, also <code>cart_chemtracer_xml</code> has to be fulfilled. Here you enter the path of your xml-file which describes the tracers occurring and their properties in the simulation. How to create this xml-file is explained in the next chapter.
	An example configuration for this part is shown in the following:		An example configuration for this part is shown in the following:
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">