Nucleophile Substitution CH3Cl - Standard MD - Revision history

Karsai: /* Download */

2019-11-14T09:44:40Z

Download

← Older revision		Revision as of 09:44, 14 November 2019
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	== Download ==		== Download ==
	[~~http~~:~~//www.vasp.at/vasp-workshop/examples/~~CH3Cl_standard_Molecular_Dynamics.tgz CH3Cl_standard_Molecular_Dynamics.tgz]		[[Media:CH3Cl_standard_Molecular_Dynamics.tgz\| CH3Cl_standard_Molecular_Dynamics.tgz]]

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

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

Karsai: /* Calculation */

2019-09-27T09:48:34Z

Calculation

← Older revision		Revision as of 09:48, 27 September 2019
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	A parameter that approximates the reaction coordinate, the difference between two C-Cl distances, will be monitored. Expected values for reactant: <math>\approx 1 \AA</math>, for product: <math>~-1 \AA</math>, for transition state: <math> 0 \AA </math>.		A parameter that approximates the reaction coordinate, the difference between two C-Cl distances, will be monitored. Expected values for reactant: <math>\approx 1 \AA</math>, for product: <math>~-1 \AA</math>, for transition state: <math> 0 \AA </math>.

	~~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.~~
	=== 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.
	For practical reasons, we split our (pressumably long) molecular dynamics calculation into shorter runs of lengths of 1000 fs ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run the {{TAG\|CONTCAR}} file is copied to the {{TAG\|POSCAR}} so that the simulation continues in a seamless manner. All of this is done by the script ''run'' provided with this example:		For practical reasons, we split our (pressumably long) molecular dynamics calculation into shorter runs of lengths of 1000 fs ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run the {{TAG\|CONTCAR}} file is copied to the {{TAG\|POSCAR}} so that the simulation continues in a seamless manner. All of this is done by the script ''run'' provided with this example:
	#!/bin/bash		#!/bin/bash

Karsai at 09:47, 27 September 2019

2019-09-27T09:47:12Z

← Older revision		Revision as of 09:47, 27 September 2019
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	done		done

	The ~~only thing the~~ user has to ~~provide is~~ the ~~path of~~ the executable ~~under "executable_path"~~. ~~To execute~~ this script ~~type~~:		*The user has to adjust the ''runvasp'' variable, which holds the command for the executable command.
			*Please run this script by typing:
	bash ./run		bash ./run
	After the execution we should obtain 50 output files. Each contains a 1000 fs run totalling to a trajectory of 50 ps. It should be mentioned that this can take several hours on 8 cores so if the user has only limited time and resources available or is only interested to learn the execution of this example the number of runs (line "[ $i -le 50 ]") can be changed from 50 to a smaller value. Also the number of timesteps per run can be lowered ({{TAG\|NSW}}).		After the execution we should obtain 50 output files. Each contains a 1000 fs run totalling to a trajectory of 50 ps. It should be mentioned that this can take several hours on 8 cores so if the user has only limited time and resources available or is only interested to learn the execution of this example the number of runs (line "[ $i -le 50 ]") can be changed from 50 to a smaller value. Also the number of timesteps per run can be lowered ({{TAG\|NSW}}).

Karsai: /* Calculation */

2019-09-27T09:24:59Z

Calculation

← Older revision		Revision as of 09:24, 27 September 2019
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	== Calculation ==		== Calculation ==
			A parameter that approximates the reaction coordinate, the difference between two C-Cl distances, will be monitored. Expected values for reactant: <math>\approx 1 \AA</math>, for product: <math>~-1 \AA</math>, for transition state: <math> 0 \AA </math>.

			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.
	=== 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.~~		For practical reasons, we split our (pressumably long) molecular dynamics calculation into shorter runs of lengths of 1000 fs ({{TAG\|NSW}}=1000 and {{TAG\|POTIM}}=1). At the end of each run the {{TAG\|CONTCAR}} file is copied to the {{TAG\|POSCAR}} so that the simulation continues in a seamless manner. All of this is done by the script ''run'' provided with this example:
	~~We are chopping the "relatively"~~ long calculation into ~~smaller peaces~~. ~~So after~~ each ~~step we have to save the output and copy~~ the {{TAG\|CONTCAR}} file to {{TAG\|POSCAR}} ~~file to restart~~ the ~~calculation~~. All of this is done by the script ''run'' provided with this example:
	#!/bin/bash		#!/bin/bash

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	done		done

	The only thing the user has to provide is the path of the executable under "executable_path". To execute this script type		The only thing the user has to provide is the path of the executable under "executable_path". To execute this script type:
	bash ./run		bash ./run
	After the execution we should obtain 50 output files. Each contains a 1000 fs run totalling to a trajectory of 50 ps. It should be mentioned that this can take several hours on 8 cores so if the user has only limited time and resources available or is only interested to learn the execution of this example the number of runs (line "[ $i -le 50 ]") can be changed from 50 to a smaller value. Also the number of timesteps per run can be lowered ({{TAG\|NSW}}).		After the execution we should obtain 50 output files. Each contains a 1000 fs run totalling to a trajectory of 50 ps. It should be mentioned that this can take several hours on 8 cores so if the user has only limited time and resources available or is only interested to learn the execution of this example the number of runs (line "[ $i -le 50 ]") can be changed from 50 to a smaller value. Also the number of timesteps per run can be lowered ({{TAG\|NSW}}).

Karsai: /* {{TAG|ICONST}} */

2019-09-27T09:21:57Z

← Older revision		Revision as of 09:21, 27 September 2019
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	=== {{TAG\|ICONST}} ===		=== {{TAG\|ICONST}} ===
	A parameter that approximates the reaction coordinate, the difference between two C-Cl distances, will be monitored. Expected values for reactant: <math>\approx 1 \AA</math>, for product: <math>~-1 \AA</math>, for transition state: <math> 0 \AA </math>.

	For this example an {{TAG\|ICONST}} file is used which looks like:		For this example an {{TAG\|ICONST}} file is used which looks like:
	R 1 5 0		R 1 5 0

Karsai: /* {{TAG|ICONST}} */

2019-09-27T09:21:10Z

← Older revision		Revision as of 09:21, 27 September 2019
Line 60:		Line 60:

	=== {{TAG\|ICONST}} ===		=== {{TAG\|ICONST}} ===
			A parameter that approximates the reaction coordinate, the difference between two C-Cl distances, will be monitored. Expected values for reactant: <math>\approx 1 \AA</math>, for product: <math>~-1 \AA</math>, for transition state: <math> 0 \AA </math>.

	For this example an {{TAG\|ICONST}} file is used which looks like:		For this example an {{TAG\|ICONST}} file is used which looks like:
	R 1 5 0		R 1 5 0
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	*Second line: Same as the first line but interatomic distance between the first (C) and the sixth atom (Cl) in the {{TAG\|POSCAR}} file is selected.		*Second line: Same as the first line but interatomic distance between the first (C) and the sixth atom (Cl) in the {{TAG\|POSCAR}} file is selected.
	*Third line: This line selects a linear combination (option S) of the first two coordinates where the second and fourth column specify the coefficients of the coordinates. The setting of 1 and -1 corresponds to the difference between both. The 7 at the fourth entry specifies that difference between these two distances is monitored but no constraints are applied.		*Third line: This line selects a linear combination (option S) of the first two coordinates where the second and fourth column specify the coefficients of the coordinates. The setting of 1 and -1 corresponds to the difference between both. The 7 at the fourth entry specifies that difference between these two distances is monitored but no constraints are applied.


	== Calculation ==		== Calculation ==

Karsai: /* Download */

2019-09-26T11:41:07Z

Download

← Older revision		Revision as of 11:41, 26 September 2019
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	== Download ==		== Download ==
	[http://www.vasp.at/vasp-workshop/examples/~~CH3Cl_standard_MOL_DYN~~.tgz ~~CH3Cl_standard_MOL_DYN~~.tgz]		[http://www.vasp.at/vasp-workshop/examples/CH3Cl_standard_Molecular_Dynamics.tgz CH3Cl_standard_Molecular_Dynamics.tgz]

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

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

Karsai: /* Time evolution of distance */

2019-09-26T11:39:38Z

Time evolution of distance

← Older revision		Revision as of 11:39, 26 September 2019
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	*After that the task is to get a histogram (or probability distribution) of the data. The user should try to write a script for itself. Otherwise the ~~following~~ script can be used:		*After that the task is to get a histogram (or probability distribution) of the data. The user should try to write a script for itself. Otherwise the script ''probability_distribution_function.py'' can be used:
	#!/usr/bin/python		#!/usr/bin/python

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	[[File:Histogram 600K.jpg\|300px]]		[[File:Histogram 600K.jpg\|300px]]

	*The user should also calculate the mean value and variance of the Cl<sup>-</sup>-Cl<sup>-</sup> distance. It is recommended to the user to try to write an own script/program doing that. Otherwise the ~~user~~ can ~~use the following script~~:		*The user should also calculate the mean value and variance of the Cl<sup>-</sup>-Cl<sup>-</sup> distance. It is recommended to the user to try to write an own script/program doing that. Otherwise the script ''average_and_standard_deviation.py'' can be used:
	#!/usr/bin/python		#!/usr/bin/python

Karsai: /* Running the calculation */

2019-09-26T11:37:00Z

Running the calculation

← Older revision		Revision as of 11:37, 26 September 2019
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	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.
	We are chopping the "relatively" long calculation into smaller peaces. So after each step we have to save the output and copy the {{TAG\|CONTCAR}} file to {{TAG\|POSCAR}} file to restart the calculation. All of this is done by the script ''run'' provided with this example:		We are chopping the "relatively" long calculation into smaller peaces. So after each step we have to save the output and copy the {{TAG\|CONTCAR}} file to {{TAG\|POSCAR}} file to restart the calculation. All of this is done by the script ''run'' provided with this example:
	#~~run~~		#!/bin/bash

	runvasp="mpirun -np 8 executable_path/vasp_gam"		runvasp="mpirun -np 8 executable_path/vasp_gam"

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	let i=i+1		let i=i+1
	done		done

	The only thing the user has to provide is the path of the executable under "executable_path". To execute this script type		The only thing the user has to provide is the path of the executable under "executable_path". To execute this script type
	bash ./run		bash ./run

Karsai: /* Time evolution of distance */

2019-09-26T11:30:21Z

Time evolution of distance

← Older revision		Revision as of 11:30, 26 September 2019
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	let i=i+1		let i=i+1
	done		done
			To execute this script type:
			bash timeEv.sh
	It creates a file "timeEvol.dat" holding the value for the collective variable at every molecular dynamics step.		It creates a file "timeEvol.dat" holding the value for the collective variable at every molecular dynamics step.


	*After that the task is to get a histogram (or probability distribution) of the data. The user should try to write a script for itself. Otherwise the following script can be used ~~by typing "python probability_distribution_function.py > histogram_600K.dat" on the command line~~:		*After that the task is to get a histogram (or probability distribution) of the data. The user should try to write a script for itself. Otherwise the following script can be used:
	#!/usr/bin/python		#!/usr/bin/python

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	pair_cor=histogram[ix]/norm		pair_cor=histogram[ix]/norm
	print x, pair_cor		print x, pair_cor
			To execute this script type:
			python probability_distribution_function.py > histogram_600K.dat

	To plot the histogram the user should use his favourite program. Alternatively the histogram is plotted using gnuplot:		To plot the histogram the user should use his favourite program. Alternatively the histogram is plotted using gnuplot:
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	[[File:Histogram 600K.jpg\|300px]]		[[File:Histogram 600K.jpg\|300px]]

	*The user should also calculate the mean value and variance of the Cl<sup>-</sup>-Cl<sup>-</sup> distance. It is recommended to the user to try to write an own script/program doing that. Otherwise the user can ~~calculate the mean by typing "python average_and_standard_deviation.py" on the command line which calls~~ the following ~~python~~ script:		*The user should also calculate the mean value and variance of the Cl<sup>-</sup>-Cl<sup>-</sup> distance. It is recommended to the user to try to write an own script/program doing that. Otherwise the user can use the following script:
	#!/usr/bin/python		#!/usr/bin/python

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	print "Mean :",mean		print "Mean :",mean
	print "Standard devation :",standard_deviation		print "Standard devation :",standard_deviation
			To execute this script type:
			python average_and_standard_deviation.py
	The calculated mean value and standard deviation should be around 1.5986 <math>\AA</math> and 0.3403 <math>\AA</math>.		The calculated mean value and standard deviation should be around 1.5986 <math>\AA</math> and 0.3403 <math>\AA</math>.