MECCA-based (full) Chemistry - Revision history

Admin 1: /* Step4: Transfer MECCA mechanism to ICON */ fixed broken link

2024-04-12T12:01:48Z

Step4: Transfer MECCA mechanism to ICON: fixed broken link

← Older revision		Revision as of 14:01, 12 April 2024
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	=== Step4: Transfer MECCA mechanism to ICON ===		=== Step4: Transfer MECCA mechanism to ICON ===
	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		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
	git clone https://gitlab.dkrz.de/art/~~mecca preproc~~.git		git clone https://gitlab.dkrz.de/art/mecca_preproc.git
	Now a new directory <code>Mecca_preproc</code> has been generated where the script <code>create_icon_code4.sh</code> can be found. By executing		Now a new directory <code>Mecca_preproc</code> has been generated where the script <code>create_icon_code4.sh</code> can be found. By executing
	./create_icon_code4.sh -h		./create_icon_code4.sh -h

Luca R: Syntaxhighlighting

2023-09-07T08:11:01Z

Syntaxhighlighting

← Older revision		Revision as of 10:11, 7 September 2023
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	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	Example batch file (<code>example.bat</code>)		Example batch file (<code>example.bat</code>)
	<~~pre~~ class="mw-collapsible-content">		<syntaxhighlight lang=bash line class="mw-collapsible-content">
	# -- Shell-script --		# -- Shell-script --

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	set graphviz = n # graphviz plots?		set graphviz = n # graphviz plots?
	set deltmp = n # delete temporary xmecca files?		set deltmp = n # delete temporary xmecca files?
			</syntaxhighlight>
	</pre>
	</div>		</div>
	The most parameters can be left as they are. Important is to rename the gas-equation-file and the replacement-file (if you have created one?).		The most parameters can be left as they are. Important is to rename the gas-equation-file and the replacement-file (if you have created one?).

Tim R: /* Preparing the MECCA-xml-file */

2023-08-10T13:09:48Z

Preparing the MECCA-xml-file

@@ Line 31: / Line 31: @@
 ==== What to do if not all reactions are wanted ====
-First, never edit the <code>gas.eqn</code> itself! Better copy and rename it for your respective chemical mechanism that you want to create, e.g. <code>gas_Mechanism1.eqn</code>. Afterwards you can open it and delete all reactions that are not wanted.
+First, never edit the <code>gas.eqn</code> itself! Better copy and rename it for your respective chemical mechanism that you want to create, e.g. <code>gas_Mechanism1.eqn</code>. Afterwards you can open it and delete all reactions that are not wanted (for Terminal users: to activate writing inside vi, use command  <code>:w</code>, for closing and saving: <code>:wq</code>).
 ==== What to do if you want to edit existing reactions of the gas.eqn or add new reactions to your mechanism ====
@@ Line 61: / Line 61: @@
 * The added reaction only works for your specific project, it is not implemented in MECCA then and it can't be applied from the <code>gas.eqn</code> afterwards.
 * if you try to edit a reaction with a not existing reaction number, an error message will be given

Tim R: Replacement files

2023-08-10T12:10:31Z

Replacement files

← Older revision		Revision as of 14:10, 10 August 2023
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	in the terminal. Once you have opened it, you can see all available reactions implemented in MECCA with their respective reaction codes which represents the full MECCA mechanism. In this configuration case we will implement a MECCA chemistry with all available reactions. That's why the <code>gas.eqn</code> can be left as it is.		in the terminal. Once you have opened it, you can see all available reactions implemented in MECCA with their respective reaction codes which represents the full MECCA mechanism. In this configuration case we will implement a MECCA chemistry with all available reactions. That's why the <code>gas.eqn</code> can be left as it is.

	==== What to do if not all reactions are wanted: ====		==== What to do if not all reactions are wanted ====
	First, never edit the <code>gas.eqn</code> itself! Better copy and rename it for your respective chemical mechanism that you want to create, e.g. <code>gas_Mechanism1.eqn</code>. Afterwards you can open it and delete all reactions that are not wanted.		First, never edit the <code>gas.eqn</code> itself! Better copy and rename it for your respective chemical mechanism that you want to create, e.g. <code>gas_Mechanism1.eqn</code>. Afterwards you can open it and delete all reactions that are not wanted.

	==== What to do if you want to edit existing reactions of the gas.eqn or add new reactions to your mechanism: ====		==== What to do if you want to edit existing reactions of the gas.eqn or add new reactions to your mechanism ====
	If a reaction of the <code>gas.eqn</code> is only similar to that one that you want to implement or a specific reaction is not implemented in the <code>gas.eqn</code>, you can make use of replacement-files. Inside the <code>mecca</code> directory, select the <code>rpl</code> directory in which you can copy and rename the <code>example.rpl</code> first of all. If you open it (again with the text editor or with the <code>vi</code>-command you can edit and add your reactions, depending on your scientific goal.		If a reaction of the <code>gas.eqn</code> is only similar to that one that you want to implement or a specific reaction is not implemented in the <code>gas.eqn</code>, you can make use of replacement-files. Inside the <code>mecca</code> directory, select the <code>rpl</code> directory in which you can copy and rename the <code>example.rpl</code> first of all. If you open it (again with the text editor or with the <code>vi</code>-command you can edit and add your reactions, depending on your scientific goal.
	If you want to edit a reaction, use the <code>#REPLACE</code> command as well as the number of the respective reaction (e.g. <G4110>) in the first line, then write <code><a></code> (<code><<b>></code>, <code><c></code>,...) for your first (second, third,...) reaction which belongs to the same reaction number. ~~For~~ ~~example,~~ ~~reaction~~ ~~<code>G4110</code>~~ ~~originally looks like this in the <code>gas~~.~~eqn</code>:~~		If you want to edit a reaction, use the <code>#REPLACE</code> command as well as the number of the respective reaction (e.g. <G4110>) in the first line, then write <code><a></code> (<code><nowiki><b></nowiki></code>, <code><c></code>,...) for your first (second, third,...) reaction which belongs to the same reaction number. Below some examples are shown.
			* <u>Editing one reaction:</u> Reaction <code>G4110</code> originally looks like this inside the <code>gas.eqn</code>:
⚫	<G4110> CO + OH = H + CO2 : {%StTrG} (1.57E-13+cair*3.54E-33){§1.15}; {&1628}
			<pre>
		⚫	<G4110> CO + OH = H + CO2 : {%StTrG} (1.57E-13+cair*3.54E-33){§1.15}; {&1628}
			</pre>

	Inside the replacement file you can change it for example like this:		Inside the replacement file you can change it for example like this:
			<pre>
	#REPLACE <G4110>		#REPLACE <G4110>
	<a> CO + OH = HO2 + CO2 : {%StTrG} 1.57E-13 + cair*3.54E-33 {&1628}		<a> CO + OH = HO2 + CO2 : {%StTrG} 1.57E-13 + cair*3.54E-33 {&1628}
	#ENDREPLACE		#ENDREPLACE
			</pre>
			* <u>Split one reaction into two (or more):</u> If you want to split a reaction into several subreactions (e.g. reaction <code>G4101</code>). Originally <code>G4110</code> looks like this inside the <code>gas.eqn</code>:
			<G4101> CH4 + OH {+O2}= CH3O2 + H2O : {%StTrG} 1.85E-20{§1.2}EXP(2.82log(temp)-987./temp); {&1627}
			The splitting can then be written as:
			#REPLACE <G4101>
			<a> CH4 + OH = CH3 + H2O : {%StTrG} 1.85E-20EXP(2.82log(temp)-987./temp); {&&1627}
			<nowiki><b></nowiki> CH3 + O2 = CH3O2 : {%StTrG} 1E-999; {&&}
			#ENDREPLACE
			* <u>Adding new reaction:</u> If you want to add a new reaction, define a not yet existing reaction number and write your new reaction:
			#REPLACE <>
			<G9876JD> XYZ + OH = RO2 + H2O : {%StG} 1.57E-13; {&&}
			#ENDREPLACE
			Note:
			* The added reaction only works for your specific project, it is not implemented in MECCA then and it can't be applied from the <code>gas.eqn</code> afterwards.
			* if you try to edit a reaction with a not existing reaction number, an error message will be given

Tim R at 11:39, 10 August 2023

2023-08-10T11:39:36Z

← Older revision		Revision as of 13:39, 10 August 2023
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	(Note: Adding MECCA-chemistry to ICON-ART also means that some namelist parameters will be overwritten in the runscript which means that some extra options (e.g. LINOZ-chemistry) are only available by setting them manually in the ICON-ART code.)		(Note: Adding MECCA-chemistry to ICON-ART also means that some namelist parameters will be overwritten in the runscript which means that some extra options (e.g. LINOZ-chemistry) are only available by setting them manually in the ICON-ART code.)

	In this configuration case a regular simulation with a MECCA chemistry implementation that will be applied in most cases is explained. To get an overview about the upcoming steps you can also check out the MECCA chemistry part in the [[Atmospheric Chemistry]] article.		[In this configuration case a regular simulation with a MECCA chemistry implementation that will be applied in most cases is explained. The implementation and link to ICON-ART works with an xml-file that has to created with help of the [http://www.geosci-model-dev.net/4/373/2011/gmd-4-373-2011-supplement.zip caaba3.0-supplement]. The created xml-file has to be included in the runscript as well. To get a better overview about the upcoming steps you can also check out the MECCA chemistry part in the [[Atmospheric Chemistry]] article.

			== Preparing the MECCA-xml-file ==

			=== Step 0: Download and open the caaba3.0-supplement ===
			Once you have downloaded the [http://www.geosci-model-dev.net/4/373/2011/gmd-4-373-2011-supplement.zip caaba3.0-supplement], you can open it in your preferred directory browser or terminal.

			=== Step 1: Setting up the chemical mechanism ===
			If you browse the <code>mecca</code> directory you can check out the <code>gas.eqn</code> file. Just use the text editor if you use the directory browser or use the command
			vi gas.eqn
			in the terminal. Once you have opened it, you can see all available reactions implemented in MECCA with their respective reaction codes which represents the full MECCA mechanism. In this configuration case we will implement a MECCA chemistry with all available reactions. That's why the <code>gas.eqn</code> can be left as it is.

			==== What to do if not all reactions are wanted: ====
			First, never edit the <code>gas.eqn</code> itself! Better copy and rename it for your respective chemical mechanism that you want to create, e.g. <code>gas_Mechanism1.eqn</code>. Afterwards you can open it and delete all reactions that are not wanted.

			==== What to do if you want to edit existing reactions of the gas.eqn or add new reactions to your mechanism: ====
			If a reaction of the <code>gas.eqn</code> is only similar to that one that you want to implement or a specific reaction is not implemented in the <code>gas.eqn</code>, you can make use of replacement-files. Inside the <code>mecca</code> directory, select the <code>rpl</code> directory in which you can copy and rename the <code>example.rpl</code> first of all. If you open it (again with the text editor or with the <code>vi</code>-command you can edit and add your reactions, depending on your scientific goal.
			If you want to edit a reaction, use the <code>#REPLACE</code> command as well as the number of the respective reaction (e.g. <G4110>) in the first line, then write <code><a></code> (<code><<b>></code>, <code><c></code>,...) for your first (second, third,...) reaction which belongs to the same reaction number. For example, reaction <code>G4110</code> originally looks like this in the <code>gas.eqn</code>:
			<G4110> CO + OH = H + CO2 : {%StTrG} (1.57E-13+cair*3.54E-33){§1.15}; {&1628}
			Inside the replacement file you can change it for example like this:
			#REPLACE <G4110>
			<a> CO + OH = HO2 + CO2 : {%StTrG} 1.57E-13 + cair*3.54E-33 {&1628}
			#ENDREPLACE

Tim R: adding the introduction

2023-08-10T10:34:15Z

adding the introduction

← Older revision		Revision as of 12:34, 10 August 2023
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	*the implementation of not yet in MECCA implemented reactions in your mechanism		*the implementation of not yet in MECCA implemented reactions in your mechanism
	*the creation of the to your mechanism belonging Mecca-xml data to link MECCA calculations with ICON-ART		*the creation of the to your mechanism belonging Mecca-xml data to link MECCA calculations with ICON-ART

			== Introductioin ==
			The MECCA(=Module Efficiently Calculating the Chemistry of the Atmosphere) based chemistry describes a full gas phase chemistry that can be applied as an extension to the parametrized [[Atmospheric Chemistry\|Simplified Chemistry]] (see above). MECCA based chemistry is generally more exact in the concentration values but the overall runtime is longer compared to purely simplified chemistry simulations. MECCA itself is originally a submodule of the CAABA box model where an air parcel is described as a box and outgoing from this model all exchange processes in- and outward of the box are calculated. As MECCA is part of this model, it contains a wide collection of the most important reactions, including Ozone-, Methane-, HOx-, NOx-, Carbonhydrogen-, Halogene- and Sulfur chemistry. MECCA is available in a [http://www.geosci-model-dev.net/4/373/2011/gmd-4-373-2011-supplement.zip supplement], available to download for free and containing all auxiliaries to perform MECCA-simulations.

			In this case we are going to have a look at the implementation of the fully available chemistry, meaning all in default mode available reactions will be implemented. This could also be adjusted easily if necessary and will be showed later. If we talk about "adding" MECCA chemistry to ICON-ART, it means that it is additionally calculated to the in any way calculated parametrized simplified chemistry in ICON-ART.

			(Note: Adding MECCA-chemistry to ICON-ART also means that some namelist parameters will be overwritten in the runscript which means that some extra options (e.g. LINOZ-chemistry) are only available by setting them manually in the ICON-ART code.)

			In this configuration case a regular simulation with a MECCA chemistry implementation that will be applied in most cases is explained. To get an overview about the upcoming steps you can also check out the MECCA chemistry part in the [[Atmospheric Chemistry]] article.

Tim R at 13:22, 14 July 2023

2023-07-14T13:22:22Z

← Older revision		Revision as of 15:22, 14 July 2023
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	In this configuration example a simulation with (full) MECCA-based chemistry is performed. If we talk about MECCA-based chemistry we mean a full gas phase chemistry that can be applied additionally to the existing standard parametrized chemistry from ICON-ART (explained in the article [[Atmospheric Chemistry]], example: [[Simplified Chemistry\|click here]]). MECCA uses the Kinetic PreProcessor (KPP) to convert the chemical equations into differential equations that can be used then e.g., in ICON-ART. MECCA already contains a comprehensive chemical mech-		In this configuration example a simulation with (full) MECCA-based chemistry is performed. If we talk about MECCA-based chemistry we mean a full gas phase chemistry that can be applied additionally to the existing standard parametrized chemistry from ICON-ART (explained in the article [[Atmospheric Chemistry]], example: [[Simplified Chemistry\|click here]]). MECCA uses the Kinetic PreProcessor (KPP) to convert the chemical equations into differential equations that can be used then e.g., in ICON-ART. MECCA already contains a comprehensive chemical mech-
	anism, but it also allows to create an own mechanism by changing equations or only picking a subset of equations.		anism, but it also allows to create an own mechanism by changing equations or only picking a subset of equations.
	To perform this example, a complete reaction mechanism is created and transferred to ICON-ART. ~~This article teaches you...~~		To perform this example, a complete reaction mechanism is created and transferred to ICON-ART.

			This article teaches you...
	*the implementation of (full) MECCA-based chemistry in ICON-ART		*the implementation of (full) MECCA-based chemistry in ICON-ART
	*the creation of a chemical mechanism and the selection of the respective desired chemical species and their reactions in MECCA		*the creation of a chemical mechanism and the selection of the respective desired chemical species and their reactions in MECCA

Tim R at 13:22, 14 July 2023

2023-07-14T13:22:04Z

← Older revision		Revision as of 15:22, 14 July 2023
Line 1:		Line 1:
	- work in progress -		- work in progress -

	In this configuration example a simulation with (full) MECCA-based chemistry is performed. If we talk about MECCA-based chemistry we mean a full gas phase chemistry that can be applied additionally to the existing standard parametrized chemistry from ICON-ART (explained in the article [[Atmospheric Chemistry]], example: [[Simplified Chemistry\|click here]]). To ~~perform~~ ~~this~~ ~~example~~ a ~~complete~~ ~~reaction~~ ~~mechanism~~ is ~~created~~ ~~and~~ ~~transferred~~ to ICON-ART. ~~This~~ ~~article~~ ~~teaches~~ ~~you...~~		In this configuration example a simulation with (full) MECCA-based chemistry is performed. If we talk about MECCA-based chemistry we mean a full gas phase chemistry that can be applied additionally to the existing standard parametrized chemistry from ICON-ART (explained in the article [[Atmospheric Chemistry]], example: [[Simplified Chemistry\|click here]]). MECCA uses the Kinetic PreProcessor (KPP) to convert the chemical equations into differential equations that can be used then e.g., in ICON-ART. MECCA already contains a comprehensive chemical mech-
			anism, but it also allows to create an own mechanism by changing equations or only picking a subset of equations.
			To perform this example, a complete reaction mechanism is created and transferred to ICON-ART. This article teaches you...
	*the implementation of (full) MECCA-based chemistry in ICON-ART		*the implementation of (full) MECCA-based chemistry in ICON-ART
	*the creation of a chemical mechanism and the selection of the respective desired chemical species and their reactions in MECCA		*the creation of a chemical mechanism and the selection of the respective desired chemical species and their reactions in MECCA

Tim R at 12:59, 14 July 2023

2023-07-14T12:59:46Z

← Older revision		Revision as of 14:59, 14 July 2023
Line 1:		Line 1:
	- work in progress -		- work in progress -

	In this configuration example a simulation with (full) MECCA-based chemistry is performed. If we talk about MECCA-based chemistry we mean a full gas phase chemistry that can be applied additionally to the existing standard parametrized chemistry from ICON-ART (explained in the article [[Atmospheric Chemistry]], example: [[Simplified Chemistry\|click here]]). To perform this example a complete reaction mechanism is created and transferred to ICON-ART. This article teaches you...		In this configuration example a simulation with (full) MECCA-based chemistry is performed. If we talk about MECCA-based chemistry we mean a full gas phase chemistry that can be applied additionally to the existing standard parametrized chemistry from ICON-ART (explained in the article [[Atmospheric Chemistry]], example: [[Simplified Chemistry\|click here]]). To perform this example a complete reaction mechanism is created and transferred to ICON-ART. This article teaches you...
	*the implementation of (full) MECCA-based chemistry in ICON-ART		*the implementation of (full) MECCA-based chemistry in ICON-ART

Tim R: Creating the article to MECCA-example

2023-07-14T12:55:29Z

Creating the article to MECCA-example

New page

- work in progress -
In this configuration example a simulation with (full) MECCA-based chemistry is performed. If we talk about MECCA-based chemistry we mean a full gas phase chemistry that can be applied additionally to the existing standard parametrized chemistry from ICON-ART (explained in the article [[Atmospheric Chemistry]], example: [[Simplified Chemistry|click here]]). To perform this example a complete reaction mechanism is created and transferred to ICON-ART. This article teaches you...
*the implementation of (full) MECCA-based chemistry in ICON-ART
*the creation of a chemical mechanism and the selection of the respective desired chemical species and their reactions in MECCA
*the implementation of not yet in MECCA implemented reactions in your mechanism
*the creation of the to your mechanism belonging Mecca-xml data to link MECCA calculations with ICON-ART