Atmospheric Chemistry - Revision history

Editor 2: fixed math display

2023-10-26T08:51:22Z

fixed math display

← Older revision		Revision as of 10:51, 26 October 2023
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	When we talk about simplified calculated chemistry in ICON-ART, we mean that the concentration of the gases we want to simulate is calculated with a parametrization. Here production and depletion rates are used to solve the differential equation		When we talk about simplified calculated chemistry in ICON-ART, we mean that the concentration of the gases we want to simulate is calculated with a parametrization. Here production and depletion rates are used to solve the differential equation

	<math>\frac~~{\mathrm~~{dc_i}~~}/{\mathrm~~{dt}} = P_i - \frac{c_i}/{\~~tau _i~~}</math>		<math>\frac{dc_i}{dt} = P_i - \frac{c_i}{\tau_i}</math>

	{{math\|1=''E'' = ''mc''{{sup\|2}}}}

	numerically and two calculate the concentration distribution. Here, <math>c_i</math> describes the number concentration of a certain tracer, <math>c_i</math> describes the chemical production and <math>\tau_i</math>is the belonging life time of tracer <math>i</math>.		numerically and two calculate the concentration distribution. Here, <math>c_i</math> describes the number concentration of a certain tracer, <math>c_i</math> describes the chemical production and <math>\tau_i</math>is the belonging life time of tracer <math>i</math>.

Tim R: /* Including MECCA-based Chemistry in a ICON-ART Simulation */

2023-08-10T12:39:14Z

Including MECCA-based Chemistry in a ICON-ART Simulation

← Older revision		Revision as of 14:39, 10 August 2023
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	Now, in the respective runscript the namelist parameter <code>lart_mecca</code> has be set to <code>.TRUE</code> and for <code>cart_mecca_xml</code> the path to the Mecca file can be provided.		Now, in the respective runscript the namelist parameter <code>lart_mecca</code> has be set to <code>.TRUE</code> and for <code>cart_mecca_xml</code> the path to the Mecca file can be provided.
	'''Important:''' As a final step, the ICON code has to be recompiled with the command <code>./config/dkrz/levante.intel --enable-art --enable-ecrad</code> and ~~after~~ executed <code>make -j 8</code>.		'''Important:''' As a final step, the ICON code has to be recompiled with the command <code>./config/dkrz/levante.intel --enable-art --enable-ecrad</code> and executed afterwards with <code>make -j 8</code>.

Tim R: /* Including MECCA-based Chemistry in a ICON-ART Simulation */

2023-08-10T10:36:05Z

Including MECCA-based Chemistry in a ICON-ART Simulation

← Older revision		Revision as of 12:36, 10 August 2023
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	After that the following steps have to be fulfilled to create the code of your specific mechanism and to be able to execute an ICON-ART simulation with MECCA-based chemistry:		After that the following steps have to be fulfilled to create the code of your specific mechanism and to be able to execute an ICON-ART simulation with MECCA-based chemistry:
	* set up a batch file: all previously set information about the mechanism can be selected and stated here (an example can be found below or also inside the supplement in <code>/caaba3.0/mecca/batch/example.bat</code>).		* set up a batch file: all previously set information about the mechanism can be selected and stated here (an example can be found below or also inside the supplement in <code>/caaba3.0/mecca/batch/example.bat</code>).
	* execute <code>./~~mecca~~</code> inside the folder <code>/caaba3.0/mecca</code>. Here the previously created batch file has to be selected and the Fortran files with the mechanism are created.		* execute <code>./xmecca</code> inside the folder <code>/caaba3.0/mecca</code>. Here the previously created batch file has to be selected and the Fortran files with the mechanism are created.
	* since the created Fortran code is only located inside Mecca and not in ICON-ART so far, a transfer has to be carried out. A script that performs this transfer can be obtained via <code>git clone https://gitlab.dkrz.de/art/mecca preproc.git</code>.		* since the created Fortran code is only located inside Mecca and not in ICON-ART so far, a transfer has to be carried out. A script that performs this transfer can be obtained via <code>git clone https://gitlab.dkrz.de/art/mecca preproc.git</code>.
	* in a new directory <code>Mecca_preproc</code> has been generated and the script <code>create_icon_code4.sh</code> can be found inside of it. By executing <code>./create_icon_code4.sh -h</code> paths to the Mecca- and ICON home directories can be provided as well as a name for the XML-file that is going to be linked in the unscript later.		* in a new directory <code>Mecca_preproc</code> has been generated and the script <code>create_icon_code4.sh</code> can be found inside of it. By executing <code>./create_icon_code4.sh -h</code> paths to the Mecca- and ICON home directories can be provided as well as a name for the XML-file that is going to be linked in the unscript later.

Tim R: improvements on explaining simplifying chemistry

2023-07-20T14:44:25Z

improvements on explaining simplifying chemistry

← Older revision		Revision as of 16:44, 20 July 2023
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	== Simplified Chemistry ==		== Simplified Chemistry ==
	When we talk about simplified calculated chemistry in ICON-ART, we mean that the concentration of the gases we want to simulate is calculated with a parametrization. Here production and depletion rates are ~~calculated~~ to solve the differential equation		When we talk about simplified calculated chemistry in ICON-ART, we mean that the concentration of the gases we want to simulate is calculated with a parametrization. Here production and depletion rates are used to solve the differential equation

	<math>\frac{\mathrm{dc_i}}/{\mathrm{dt}} = P_i - \frac{c_i}/{\tau _i}</math>		<math>\frac{\mathrm{dc_i}}/{\mathrm{dt}} = P_i - \frac{c_i}/{\tau _i}</math>
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	{{math\|1=''E'' = ''mc''{{sup\|2}}}}		{{math\|1=''E'' = ''mc''{{sup\|2}}}}

	numerically. Here, <math>c_i</math> describes the number concentration of a certain tracer, <math>c_i</math> describes the chemical production and <math>\tau_i</math>is the belonging life time of tracer <math>i</math>.		numerically and two calculate the concentration distribution. Here, <math>c_i</math> describes the number concentration of a certain tracer, <math>c_i</math> describes the chemical production and <math>\tau_i</math>is the belonging life time of tracer <math>i</math>.
	For the namelist settings you are able to use for atmospheric chemistry, check out the ART-namelist parameters (see [[Namelist\|ART namelists]]). The procedure of creating an ICON-ART simulation in Atmospheric Chemistry always comes back to switching on a namelist parameter and providing the path of the respective XML-file. How to create these for several cases, please check the examples below in the [[Atmospheric Chemistry\|Configurations]] part.		For the namelist settings you are able to use for atmospheric chemistry, check out the ART-namelist parameters (see [[Namelist\|ART namelists]]). The procedure of creating an ICON-ART simulation in Atmospheric Chemistry always comes back to switching on a namelist parameter and providing the path of the respective XML-file. How to create these for several cases, please check the examples below in the [[Atmospheric Chemistry\|Configurations]] part.

Tim R: /* Including MECCA-based Chemistry in a ICON-ART Simulation */

2023-07-20T14:41:44Z

Including MECCA-based Chemistry in a ICON-ART Simulation

← Older revision		Revision as of 16:41, 20 July 2023
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	* execute <code>./mecca</code> inside the folder <code>/caaba3.0/mecca</code>. Here the previously created batch file has to be selected and the Fortran files with the mechanism are created.		* execute <code>./mecca</code> inside the folder <code>/caaba3.0/mecca</code>. Here the previously created batch file has to be selected and the Fortran files with the mechanism are created.
	* since the created Fortran code is only located inside Mecca and not in ICON-ART so far, a transfer has to be carried out. A script that performs this transfer can be obtained via <code>git clone https://gitlab.dkrz.de/art/mecca preproc.git</code>.		* since the created Fortran code is only located inside Mecca and not in ICON-ART so far, a transfer has to be carried out. A script that performs this transfer can be obtained via <code>git clone https://gitlab.dkrz.de/art/mecca preproc.git</code>.
	* in a new directory <code>Mecca_preproc</code> has been generated and the script <code>create_icon_code4.sh</code> can be found inside of it. By executing <code>/.create_icon_code4.sh -h</code> paths to the Mecca- and ICON home directories can be provided as well as a name for the XML-file that is going to be linked in the unscript later.		* in a new directory <code>Mecca_preproc</code> has been generated and the script <code>create_icon_code4.sh</code> can be found inside of it. By executing <code>./create_icon_code4.sh -h</code> paths to the Mecca- and ICON home directories can be provided as well as a name for the XML-file that is going to be linked in the unscript later.
	* the Mecca-XML-file is now generated and can be found in ICON in <code>/icon home>/runctrl examples/xml ctrl</code>.		* the Mecca-XML-file is now generated and can be found in ICON in <code>/icon home>/runctrl examples/xml ctrl</code>.

Tim R: /* Simplified Chemistry */

2023-07-20T12:38:36Z

Simplified Chemistry

← Older revision		Revision as of 14:38, 20 July 2023
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	For the namelist settings you are able to use for atmospheric chemistry, check out the ART-namelist parameters (see [[Namelist\|ART namelists]]). The procedure of creating an ICON-ART simulation in Atmospheric Chemistry always comes back to switching on a namelist parameter and providing the path of the respective XML-file. How to create these for several cases, please check the examples below in the [[Atmospheric Chemistry\|Configurations]] part.		For the namelist settings you are able to use for atmospheric chemistry, check out the ART-namelist parameters (see [[Namelist\|ART namelists]]). The procedure of creating an ICON-ART simulation in Atmospheric Chemistry always comes back to switching on a namelist parameter and providing the path of the respective XML-file. How to create these for several cases, please check the examples below in the [[Atmospheric Chemistry\|Configurations]] part.

	To learn more about technical details of simplified chemistry, see also [https://gmd.copernicus.org/articles/10/2471/2017/ Weimer et. al. (2017)]		To learn more about technical details of simplified chemistry, see also [https://gmd.copernicus.org/articles/10/2471/2017/ Weimer et. al. (2017)].

	Note: When enabling simplified chemistry with the switch <code>lart_chemtracer = .TRUE.</code>, you can improve your runtime but the simulated concentration values are less exact compared to MECCA-based chemistry.		Note: When enabling simplified chemistry with the switch <code>lart_chemtracer = .TRUE.</code>, you can improve your runtime but the simulated concentration values are less exact compared to MECCA-based chemistry.


	== MECCA-based Chemistry ==		== MECCA-based Chemistry ==

Tim R: removed examples here, now in Chapter "Tutorial examples"

2023-07-20T08:59:40Z

removed examples here, now in Chapter "Tutorial examples"

Show changes

Tim R: /* Example: How to create a simulation with simplified chemistry? */

2023-07-04T15:05:49Z

Example: How to create a simulation with simplified chemistry?

← Older revision		Revision as of 17:05, 4 July 2023
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	</pre>		</pre>

	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 wee 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> ~~have~~ to be fulfilled.		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 wee 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.
	<pre>		<pre>
	&art_nml		&art_nml

Tim R: /* Configurations */

2023-07-04T15:05:26Z

Configurations

Show changes

Editor 1: /* Configurations */

2023-06-29T15:06:56Z

Configurations

← Older revision		Revision as of 17:06, 29 June 2023
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	In this first example it is shown how to perform a simulation with simplified chemistry in ICON-ART. Emission data will be applied on the simulation as well.		In this first example it is shown how to perform a simulation with simplified chemistry in ICON-ART. Emission data will be applied on the simulation as well.
	The depicted case is about simulating the tropospheric hydroxyl radical (OH), one of the most important oxidants of the atmosphere. It's main source in the lower ~~Troposphere~~ is the photolysis of ozone and its consequent reaction of an excited oxygen atom with the surrounding water vapor:		The depicted case is about simulating the tropospheric hydroxyl radical (OH), one of the most important oxidants of the atmosphere. It's main source in the lower troposphere is the photolysis of ozone and its consequent reaction of an excited oxygen atom with the surrounding water vapor:

	<chem>O3 + hv -> O2 + O(^1D)</chem>		<chem>O3 + hv -> O2 + O(^1D)</chem>