Category:Molecular Dynamics - Revision history

Karsai at 16:51, 20 March 2020

2020-03-20T16:51:51Z

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	*Slow-growth approach: {{TAG\|Slow-growth approach}}.		*Slow-growth approach: {{TAG\|Slow-growth approach}}.
	*Monitoring of geometric parameters: [[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]].		*Monitoring of geometric parameters: [[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]].
	*Thermodynamic integration: [[Thermodynamic integration\|Thermodynamic integration]]		*Thermodynamic integration: [[:Category:Thermodynamic integration\|Thermodynamic integration]]

	== Compilation ==		== Compilation ==

Karsai: /* How to */

2020-03-12T15:41:42Z

How to

← Older revision		Revision as of 15:41, 12 March 2020
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	*Slow-growth approach: {{TAG\|Slow-growth approach}}.		*Slow-growth approach: {{TAG\|Slow-growth approach}}.
	*Monitoring of geometric parameters: [[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]].		*Monitoring of geometric parameters: [[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]].
			*Thermodynamic integration: [[Thermodynamic integration\|Thermodynamic integration]]

	== Compilation ==		== Compilation ==

Karsai at 17:39, 5 June 2019

2019-06-05T17:39:51Z

← Older revision		Revision as of 17:39, 5 June 2019
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	Besides the main output files, {{TAG\|OUTCAR}} and {{TAG\|OSZICAR}}, the {{TAG\|XDATCAR}} is an important output file. It contains the trajectory of the MD. ~~The~~ {{TAG\|REPORT}} file is important for ~~molecular dynamics runs~~ where the {{TAG\|ICONST}} file was used.		Besides the main output files, {{TAG\|OUTCAR}} and {{TAG\|OSZICAR}}, the {{TAG\|XDATCAR}} is an important output file. It contains the trajectory of the MD. Another important output file for molecular dynamics calculations is the {{TAG\|REPORT}} file. It contains various important information and is especially important for calculations where the {{TAG\|ICONST}} file was used.

	== Theory ==		== Theory ==

Karsai at 17:35, 5 June 2019

2019-06-05T17:35:18Z

← Older revision		Revision as of 17:35, 5 June 2019
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	-Dtbdyn		-Dtbdyn

			== References ==
			<references/>

			<noinclude>
	----		----

	[[Category:VASP\|Molecular Dynamics]]		[[Category:VASP\|Molecular Dynamics]]

Karsai at 17:34, 5 June 2019

2019-06-05T17:34:07Z

← Older revision		Revision as of 17:34, 5 June 2019
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	The input files for standard molecular dynamics runs are the same as for other calculational methods. However additionally to the structural data the {{TAG\|POSCAR}} file can contain the initial velocities as a separate block. It can also contain the input on which atomic positions should be constrained or not.		The input files for standard molecular dynamics runs are the same as for other calculational methods. However additionally to the structural data the {{TAG\|POSCAR}} file can contain the initial velocities as a separate block. It can also contain the input on which atomic positions should be constrained or not.

	Constrained and bias molecular dynamics also require an additional input file, the {{TAG\|ICONST}} file. This file specifies the collective variables. The ({{TAG\|ICONST}}) file is also required for the monitoring of geometric parameters.		Constrained and bias molecular dynamics ({{TAG\|Constrained molecular dynamics}}, {{TAG\|Metadynamics}} and {{TAG\|Biased molecular dynamics}}) also require an additional input file, the {{TAG\|ICONST}} file. This file specifies the collective variables. The ({{TAG\|ICONST}}) file is also required for the monitoring of geometric parameters ([[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]]).


	Besides the main output files {{TAG\|OUTCAR}} and {{TAG\|OSZICAR}}		Besides the main output files, {{TAG\|OUTCAR}} and {{TAG\|OSZICAR}}, the {{TAG\|XDATCAR}} is an important output file. It contains the trajectory of the MD. The {{TAG\|REPORT}} file is important for molecular dynamics runs where the {{TAG\|ICONST}} file was used.

	== Theory ==		== Theory ==
	*Ensembles: [[:Category:Ensembles\|Ensembles]].		*Ensembles: [[:Category:Ensembles\|Ensembles]].

Karsai at 17:30, 5 June 2019

2019-06-05T17:30:30Z

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	To get an idea about what basically molecular dynamics is and what the main contents are we refer the reader to references {{cite\|frenkel:book:1996}} and {{cite\|allen:book:1991}}. After understanding the theory behind molecular dynamics we refer the reader to {{TAG\|Molecular dynamics calculations}}, which describes how to run standard molecular dynamics simulations. Every advanced molecular dynamics method builds on the knowledge in that tutorial and should be ideally only viewed after understanding the basics.		To get an idea about what basically molecular dynamics is and what the main contents are we refer the reader to references {{cite\|frenkel:book:1996}} and {{cite\|allen:book:1991}}. After understanding the theory behind molecular dynamics we refer the reader to {{TAG\|Molecular dynamics calculations}}, which describes how to run standard molecular dynamics simulations. Every advanced molecular dynamics method builds on the knowledge in that tutorial and should be ideally only viewed after understanding the basics.

			== Important files ==

			The input files for standard molecular dynamics runs are the same as for other calculational methods. However additionally to the structural data the {{TAG\|POSCAR}} file can contain the initial velocities as a separate block. It can also contain the input on which atomic positions should be constrained or not.

			Constrained and bias molecular dynamics also require an additional input file, the {{TAG\|ICONST}} file. This file specifies the collective variables. The ({{TAG\|ICONST}}) file is also required for the monitoring of geometric parameters.


			Besides the main output files {{TAG\|OUTCAR}} and {{TAG\|OSZICAR}}
	== Theory ==		== Theory ==
	*Ensembles: [[:Category:Ensembles\|Ensembles]].		*Ensembles: [[:Category:Ensembles\|Ensembles]].

Karsai at 17:36, 4 June 2019

2019-06-04T17:36:23Z

← Older revision		Revision as of 17:36, 4 June 2019
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	== Theory ==		== Theory ==
			*Ensembles: [[:Category:Ensembles\|Ensembles]].
	*Thermostats: [[:Category:Thermostats\|Thermostats]].		*Thermostats: [[:Category:Thermostats\|Thermostats]].
	*Interface pinning: {{TAG\|Interface pinning calculations}}.		*Interface pinning: {{TAG\|Interface pinning calculations}}.

Karsai at 17:34, 4 June 2019

2019-06-04T17:34:50Z

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	== How to ==		== How to ==
	*Basic molecular dynamics calculations: {{TAG\|Molecular dynamics calculations}}.		*Basic molecular dynamics calculations: {{TAG\|Molecular dynamics calculations}}.
			*Ensembles: [[:Category:Ensembles\|Ensembles]].
	*Thermostats: [[:Category:Thermostats\|Thermostats]].		*Thermostats: [[:Category:Thermostats\|Thermostats]].
	*Interface pinning: {{TAG\|Interface pinning calculations}}.		*Interface pinning: {{TAG\|Interface pinning calculations}}.

Karsai at 17:33, 4 June 2019

2019-06-04T17:33:46Z

← Older revision		Revision as of 17:33, 4 June 2019
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			To get an idea about what basically molecular dynamics is and what the main contents are we refer the reader to references {{cite\|frenkel:book:1996}} and {{cite\|allen:book:1991}}. After understanding the theory behind molecular dynamics we refer the reader to {{TAG\|Molecular dynamics calculations}}, which describes how to run standard molecular dynamics simulations. Every advanced molecular dynamics method builds on the knowledge in that tutorial and should be ideally only viewed after understanding the basics.

	== Theory ==		== Theory ==

Karsai at 17:27, 4 June 2019

2019-06-04T17:27:24Z

← Older revision		Revision as of 17:27, 4 June 2019
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	'''IMPORTANT NOTE''': The simulation methods described in this section are included in VASP as of version 5.2.12, and require VASP to be compiled with the cpp flag [[Precompiler_flags\|-Dtbdyn]] that should be included in the corresponding line of makefile, as for instance in the following example:
	~~CPP = $(CPP_) -DHOST=\"IFC9_fftw\" \~~
	~~-Dkind8 -DNGXhalf -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc \~~
	~~-Dtbdyn~~

	== Theory ==		== Theory ==
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	*Slow-growth approach: {{TAG\|Slow-growth approach}}.		*Slow-growth approach: {{TAG\|Slow-growth approach}}.
	*Monitoring of geometric parameters: [[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]].		*Monitoring of geometric parameters: [[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]].

			== Compilation ==
			'''IMPORTANT NOTE''': The simulation methods described in this section are included in VASP as of version 5.2.12, and require VASP to be compiled with the cpp flag [[Precompiler_flags\|-Dtbdyn]] that should be included in the corresponding line of makefile, as for instance in the following example:
			CPP = $(CPP_) -DHOST=\"IFC9_fftw\" \
			-Dkind8 -DNGXhalf -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc \
			-Dtbdyn

	----		----

	[[Category:VASP\|Molecular Dynamics]]		[[Category:VASP\|Molecular Dynamics]]

← Older revision		Revision as of 17:34, 5 June 2019
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	The input files for standard molecular dynamics runs are the same as for other calculational methods. However additionally to the structural data the {{TAG\|POSCAR}} file can contain the initial velocities as a separate block. It can also contain the input on which atomic positions should be constrained or not.		The input files for standard molecular dynamics runs are the same as for other calculational methods. However additionally to the structural data the {{TAG\|POSCAR}} file can contain the initial velocities as a separate block. It can also contain the input on which atomic positions should be constrained or not.

	Constrained and bias molecular dynamics also require an additional input file, the {{TAG\|ICONST}} file. This file specifies the collective variables. The ({{TAG\|ICONST}}) file is also required for the monitoring of geometric parameters.		Constrained and bias molecular dynamics ({{TAG\|Constrained molecular dynamics}}, {{TAG\|Metadynamics}} and {{TAG\|Biased molecular dynamics}}) also require an additional input file, the {{TAG\|ICONST}} file. This file specifies the collective variables. The ({{TAG\|ICONST}}) file is also required for the monitoring of geometric parameters ([[MDALGO#Monitoring geometric parameters\|Monitoring geometric parameters]]).


	Besides the main output files {{TAG\|OUTCAR}} and {{TAG\|OSZICAR}}		Besides the main output files, {{TAG\|OUTCAR}} and {{TAG\|OSZICAR}}, the {{TAG\|XDATCAR}} is an important output file. It contains the trajectory of the MD. The {{TAG\|REPORT}} file is important for molecular dynamics runs where the {{TAG\|ICONST}} file was used.

	== Theory ==		== Theory ==
	*Ensembles: [[:Category:Ensembles\|Ensembles]].		*Ensembles: [[:Category:Ensembles\|Ensembles]].

← Older revision		Revision as of 17:34, 4 June 2019
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	== How to ==		== How to ==
	*Basic molecular dynamics calculations: {{TAG\|Molecular dynamics calculations}}.		*Basic molecular dynamics calculations: {{TAG\|Molecular dynamics calculations}}.
			*Ensembles: [[:Category:Ensembles\|Ensembles]].
	*Thermostats: [[:Category:Thermostats\|Thermostats]].		*Thermostats: [[:Category:Thermostats\|Thermostats]].
	*Interface pinning: {{TAG\|Interface pinning calculations}}.		*Interface pinning: {{TAG\|Interface pinning calculations}}.