Nuclephile Substitution CH3Cl - SG - Revision history

Karsai: /* Free energy profile */

2022-04-15T15:06:54Z

Free energy profile

@@ Line 138: / Line 138: @@
 The free energy profile along the collective variable is plotted using the script ''integrateForward.py'':
 <div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>
-<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:integrateForwar_CH3Cl_SG}}</div>
+<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">
 This script obtains the free energy vs. the collective variable via a simple integration by trapezoid rule. The output is written to standard out so it has to be redirected to a file (we will arbitrarily choose the name ''free_energy.dat''). To execute the script type the following command:

2019-11-14T09:46:09Z

Download

← Older revision		Revision as of 09:46, 14 November 2019
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	== Download ==		== Download ==

	[~~http~~:~~//www.vasp.at/vasp-workshop/examples/~~CH3Cl_SG.tgz CH3Cl_SG.tgz]		[[Media:CH3Cl_SG.tgz\| CH3Cl_SG.tgz]]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]

2019-10-03T08:50:30Z

Running the calculation

← Older revision		Revision as of 08:50, 3 October 2019
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	=== Running the calculation ===		=== Running the calculation ===
	The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD.		The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD (note that the free energy is independent of the masses of atoms).

	For practical reasons, we split our (presumably long) meta dynamics calculation into shorter runs of length of 1000 fs (NSW=1000; POTIM=1). This is done automatically in the script ''run'' which looks as follows:		For practical reasons, we split our (presumably long) meta dynamics calculation into shorter runs of length of 1000 fs (NSW=1000; POTIM=1). This is done automatically in the script ''run'' which looks as follows:

2019-10-03T08:36:48Z

Download

← Older revision		Revision as of 08:36, 3 October 2019
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	<noinclude>		<noinclude>
	== Download ==		== Download ==

			[http://www.vasp.at/vasp-workshop/examples/CH3Cl_SG.tgz CH3Cl_SG.tgz]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]

2019-10-03T08:32:18Z

2019-10-03T08:31:59Z

Free energy profile

← Older revision		Revision as of 08:31, 3 October 2019
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	To plot that script via Gnuplot please use the following:		To plot that script via Gnuplot please use the following:
	gnuplot -e "set terminal jpeg; set xlabel 'Collective variable (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'free_energy.dat'" > free_energy.jpg		gnuplot -e "set terminal jpeg; set xlabel 'Collective variable (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'free_energy.dat'" > free_energy.jpg
			The free energy profile should look like the following:

			[[File:Free energy CH3Cl SG.jpg\|500px]]

			Again this method is only supposed to give a rough estimate for the free energy profile of a material.

	== References ==		== References ==

2019-10-03T08:27:56Z

Free energy profile

← Older revision		Revision as of 08:27, 3 October 2019
Line 139:		Line 139:
	<div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:integrateForwar_CH3Cl_SG}}</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:integrateForwar_CH3Cl_SG}}</div>

			This script obtains the free energy vs. the collective variable via a simple integration by trapezoid rule. The output is written to standard out so it has to be redirected to a file (we will arbitrarily choose the name ''free_energy.dat''). To execute the script type the following command:
			python integrateForward.py grad.dat > free_energy.dat
			To plot that script via Gnuplot please use the following:
			gnuplot -e "set terminal jpeg; set xlabel 'Collective variable (Ang)'; set ylabel 'Free energy (eV)'; set style data lines; plot 'free_energy.dat'" > free_energy.jpg

	== References ==		== References ==

2019-10-03T08:04:47Z

Free energy profile

@@ Line 139: / Line 139: @@
 <div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>
 <div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:integrateForwar_CH3Cl_SG}}</div>
 == References ==

2019-10-03T08:04:28Z

Free energy profile

← Older revision		Revision as of 08:04, 3 October 2019
Line 138:		Line 138:
	The free energy profile along the collective variable is plotted using the script ''integrateForward.py'':		The free energy profile along the collective variable is plotted using the script ''integrateForward.py'':
	<div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{[[integrateForwar_CH3Cl_SG]]}}</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:integrateForwar_CH3Cl_SG}}</div>



	#!/usr/bin/python		#!/usr/bin/python

2019-10-03T08:02:36Z

Free energy profile

← Older revision		Revision as of 08:02, 3 October 2019
Line 138:		Line 138:
	The free energy profile along the collective variable is plotted using the script ''integrateForward.py'':		The free energy profile along the collective variable is plotted using the script ''integrateForward.py'':
	<div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/integrateForward.py'''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{[[integrateForwar_CH3Cl_SG}}</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{[[integrateForwar_CH3Cl_SG]]}}</div>

	#!/usr/bin/python		#!/usr/bin/python