Molecular-dynamics calculations - Revision history

Singraber at 12:48, 5 February 2026

2026-02-05T12:48:06Z

Huebsch: Huebsch moved page Molecular dynamics calculations to Molecular-dynamics calculations

2025-10-21T09:32:17Z

Huebsch moved page Molecular dynamics calculations to Molecular-dynamics calculations

← Older revision	Revision as of 09:32, 21 October 2025
(No difference)

Singraber at 21:27, 17 October 2025

2025-10-17T21:27:03Z

← Older revision		Revision as of 21:27, 17 October 2025
Line 8:		Line 8:
	**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.		**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.
	**{{TAG\|ISIF}} (optional).		**{{TAG\|ISIF}} (optional).
	**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for ~~Nose~~-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with ~~Nose~~-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).		**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nosé-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nosé-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).
	**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.		**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.
	*Decide which [[:Category:Ensembles\|ensemble]] to use:		*Decide which [[:Category:Ensembles\|ensemble]] to use:
	**~~{{TAG\|~~NVT ensemble}}: Set {{TAG\|ISIF}}=2.		**[[NVT ensemble]]: Set {{TAG\|ISIF}}=2.
	**~~{{TAG\|~~NpT ensemble}}: Set {{TAG\|ISIF}}=3.		**[[NpT ensemble]]: Set {{TAG\|ISIF}}=3.
	**~~{{TAG\|~~NVE ensemble}}: Set {{TAG\|MDALGO}}=1 and {{TAG\|ANDERSEN_PROB}}=0.0.		**[[NVE ensemble]]: Set {{TAG\|MDALGO}}=1 and {{TAG\|ANDERSEN_PROB}}=0.0.
	*Decide which thermostat to use (the combination of thermostats and ensembles is given in table):		*Decide which thermostat to use (the combination of thermostats and ensembles is given in table):
	**~~{{TAG\|~~Andersen thermostat}}: Set {{TAG\|MDALGO}}=1. Also set {{TAG\|ANDERSEN_PROB}}>0.0 to control the stochastic update frequency of the thermostat.		**[[Andersen thermostat]]: Set {{TAG\|MDALGO}}=1. Also set {{TAG\|ANDERSEN_PROB}}>0.0 to control the stochastic update frequency of the thermostat.
	**~~{{TAG\|Nose~~-Hoover thermostat}}: Set {{TAG\|MDALGO}}=2. Also set {{TAG\|SMASS}}>0.0 to control the coupling to the heat bath.		**[[Nosé-Hoover thermostat]]: Set {{TAG\|MDALGO}}=2. Also set {{TAG\|SMASS}}>0.0 to control the coupling to the heat bath.
	**~~{{TAG\|~~Langevin thermostat}}: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.		**[[Langevin thermostat]]: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.
	**~~{{TAG\|Nose~~-Hoover-chain thermostat}}: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the ~~Nose~~-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the ~~Nose~~-Hoover chains thermostat is set.		**[[Nosé-Hoover chain thermostat]]: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the Nosé-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the Nosé-Hoover chains thermostat is set.
	**~~{{TAG\|~~CSVR thermostat}}: Set {{TAG\|MDALGO}}=5 and additionally adjust {{TAG\|CSVR_PERIOD}}>0.		**[[CSVR thermostat]]: Set {{TAG\|MDALGO}}=5 and additionally adjust {{TAG\|CSVR_PERIOD}}>0.

	The following combinations of thermostats and barostats is possible:		The following combinations of thermostats and barostats is possible:
Line 25:		Line 25:

	== Compilation ==		== Compilation ==
	~~To run molecular dynamics calculation~~ VASP ~~has~~ to be compiled ~~using~~ the [[Precompiler_flags\|-Dtbdyn]] ~~precompiler flag in~~ the makefile.include ~~file~~. ~~A sample input using~~ this ~~tag would look like this:~~		Many of 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 [[Precompiler_flags\|preprocessor flag <code>-Dtbdyn</code>]]. This is usually the case because all [[makefile.include]] templates shipped with {{VASP}} since version 5.4.4 contain this flag by default.
	~~CPP = $(CPP_) -DHOST=\"IFC9_fftw\" \~~
	~~-Dkind8 -DNGXhalf -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc \~~
	~~-Dtbdyn~~

	----		----

	[[Category:Molecular dynamics]][[Category:Howto]]		[[Category:Molecular dynamics]][[Category:Howto]]

Jona: /* Initial velocities */

2024-10-22T15:52:10Z

Initial velocities

← Older revision		Revision as of 15:52, 22 October 2024
Line 23:		Line 23:
	The following combinations of thermostats and barostats is possible:		The following combinations of thermostats and barostats is possible:
	{{Template:MDCOMBINATIONS}}		{{Template:MDCOMBINATIONS}}

	~~== Initial velocities ==~~
	In VASP, velocities are initialized randomly following the Maxwell-Boltzmann distribution, adjusted to the initial temperature set by {{TAG\|TEBEG}} in the {{FILE\|INCAR}} file. Alternatively, starting velocities can be provided in the {{FILE\|POSCAR}} file, either manually or from a previous VASP run. Manually entered velocities must follow the format and units specified on the {{FILE\|POSCAR}} page.

	== Compilation ==		== Compilation ==

Huebsch at 11:44, 18 October 2024

2024-10-18T11:44:16Z

← Older revision		Revision as of 11:44, 18 October 2024
Line 24:		Line 24:
	{{Template:MDCOMBINATIONS}}		{{Template:MDCOMBINATIONS}}

	== Initial ~~Velocities~~ ==		== Initial velocities ==
	In VASP, velocities are initialized randomly following the Maxwell-Boltzmann distribution, adjusted to the initial temperature set by {{TAG\|TEBEG}} in the {{FILE\|INCAR}} file. Alternatively, starting velocities can be provided in the {{FILE\|POSCAR}} file, either manually or from a previous VASP run. Manually entered velocities must follow the format and units specified on the {{FILE\|POSCAR}} page.		In VASP, velocities are initialized randomly following the Maxwell-Boltzmann distribution, adjusted to the initial temperature set by {{TAG\|TEBEG}} in the {{FILE\|INCAR}} file. Alternatively, starting velocities can be provided in the {{FILE\|POSCAR}} file, either manually or from a previous VASP run. Manually entered velocities must follow the format and units specified on the {{FILE\|POSCAR}} page.

Jona at 17:23, 16 October 2024

2024-10-16T17:23:03Z

← Older revision		Revision as of 17:23, 16 October 2024
Line 19:		Line 19:
	**{{TAG\|Langevin thermostat}}: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.		**{{TAG\|Langevin thermostat}}: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.
	**{{TAG\|Nose-Hoover-chain thermostat}}: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the Nose-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the Nose-Hoover chains thermostat is set.		**{{TAG\|Nose-Hoover-chain thermostat}}: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the Nose-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the Nose-Hoover chains thermostat is set.
			**{{TAG\|CSVR thermostat}}: Set {{TAG\|MDALGO}}=5 and additionally adjust {{TAG\|CSVR_PERIOD}}>0.

	The following combinations of thermostats and barostats is possible:		The following combinations of thermostats and barostats is possible:

Jona at 17:20, 16 October 2024

2024-10-16T17:20:35Z

← Older revision		Revision as of 17:20, 16 October 2024
Line 18:		Line 18:
	**{{TAG\|Nose-Hoover thermostat}}: Set {{TAG\|MDALGO}}=2. Also set {{TAG\|SMASS}}>0.0 to control the coupling to the heat bath.		**{{TAG\|Nose-Hoover thermostat}}: Set {{TAG\|MDALGO}}=2. Also set {{TAG\|SMASS}}>0.0 to control the coupling to the heat bath.
	**{{TAG\|Langevin thermostat}}: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.		**{{TAG\|Langevin thermostat}}: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.
			**{{TAG\|Nose-Hoover-chain thermostat}}: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the Nose-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the Nose-Hoover chains thermostat is set.

	The following combinations of thermostats and barostats is possible:		The following combinations of thermostats and barostats is possible:

Jona at 17:13, 16 October 2024

2024-10-16T17:13:59Z

← Older revision		Revision as of 17:13, 16 October 2024
Line 21:		Line 21:
	The following combinations of thermostats and barostats is possible:		The following combinations of thermostats and barostats is possible:
	{{Template:MDCOMBINATIONS}}		{{Template:MDCOMBINATIONS}}

			== Initial Velocities ==
			In VASP, velocities are initialized randomly following the Maxwell-Boltzmann distribution, adjusted to the initial temperature set by {{TAG\|TEBEG}} in the {{FILE\|INCAR}} file. Alternatively, starting velocities can be provided in the {{FILE\|POSCAR}} file, either manually or from a previous VASP run. Manually entered velocities must follow the format and units specified on the {{FILE\|POSCAR}} page.

	== Compilation ==		== Compilation ==

Huebsch at 14:06, 7 April 2022

2022-04-07T14:06:20Z

← Older revision		Revision as of 14:06, 7 April 2022
Line 30:		Line 30:
	----		----

	[[Category:Molecular ~~Dynamics~~]][[Category:Howto]]		[[Category:Molecular dynamics]][[Category:Howto]]

Karsai at 17:55, 30 January 2020

2020-01-30T17:55:16Z

← Older revision		Revision as of 17:55, 30 January 2020
Line 8:		Line 8:
	**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.		**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.
	**{{TAG\|ISIF}} (optional).		**{{TAG\|ISIF}} (optional).
	**{{TAG\|MDALGO}}: This tag decides ~~whether~~ the molecular dynamics ~~run~~ is executed ~~using without a thermostat ({{TAG\|MDALGO}}=0 which is default) or with a thermostat ({{TAG\|MDALGO}}>0)~~. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nose-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nose-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).		**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nose-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nose-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).
	**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.		**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.
	*Decide which [[:Category:Ensembles\|ensemble]] to use:		*Decide which [[:Category:Ensembles\|ensemble]] to use:

← Older revision		Revision as of 21:27, 17 October 2025
Line 8:		Line 8:
	**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.		**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.
	**{{TAG\|ISIF}} (optional).		**{{TAG\|ISIF}} (optional).
	**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for ~~Nose~~-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with ~~Nose~~-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).		**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nosé-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nosé-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).
	**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.		**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.
	*Decide which [[:Category:Ensembles\|ensemble]] to use:		*Decide which [[:Category:Ensembles\|ensemble]] to use:
	**~~{{TAG\|~~NVT ensemble}}: Set {{TAG\|ISIF}}=2.		**[[NVT ensemble]]: Set {{TAG\|ISIF}}=2.
	**~~{{TAG\|~~NpT ensemble}}: Set {{TAG\|ISIF}}=3.		**[[NpT ensemble]]: Set {{TAG\|ISIF}}=3.
	**~~{{TAG\|~~NVE ensemble}}: Set {{TAG\|MDALGO}}=1 and {{TAG\|ANDERSEN_PROB}}=0.0.		**[[NVE ensemble]]: Set {{TAG\|MDALGO}}=1 and {{TAG\|ANDERSEN_PROB}}=0.0.
	*Decide which thermostat to use (the combination of thermostats and ensembles is given in table):		*Decide which thermostat to use (the combination of thermostats and ensembles is given in table):
	**~~{{TAG\|~~Andersen thermostat}}: Set {{TAG\|MDALGO}}=1. Also set {{TAG\|ANDERSEN_PROB}}>0.0 to control the stochastic update frequency of the thermostat.		**[[Andersen thermostat]]: Set {{TAG\|MDALGO}}=1. Also set {{TAG\|ANDERSEN_PROB}}>0.0 to control the stochastic update frequency of the thermostat.
	**~~{{TAG\|Nose~~-Hoover thermostat}}: Set {{TAG\|MDALGO}}=2. Also set {{TAG\|SMASS}}>0.0 to control the coupling to the heat bath.		**[[Nosé-Hoover thermostat]]: Set {{TAG\|MDALGO}}=2. Also set {{TAG\|SMASS}}>0.0 to control the coupling to the heat bath.
	**~~{{TAG\|~~Langevin thermostat}}: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.		**[[Langevin thermostat]]: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA}}>0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.
	**~~{{TAG\|Nose~~-Hoover-chain thermostat}}: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the ~~Nose~~-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the ~~Nose~~-Hoover chains thermostat is set.		**[[Nosé-Hoover chain thermostat]]: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the Nosé-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the Nosé-Hoover chains thermostat is set.
	**~~{{TAG\|~~CSVR thermostat}}: Set {{TAG\|MDALGO}}=5 and additionally adjust {{TAG\|CSVR_PERIOD}}>0.		**[[CSVR thermostat]]: Set {{TAG\|MDALGO}}=5 and additionally adjust {{TAG\|CSVR_PERIOD}}>0.

	The following combinations of thermostats and barostats is possible:		The following combinations of thermostats and barostats is possible:
Line 25:		Line 25:

	== Compilation ==		== Compilation ==
	~~To run molecular dynamics calculation~~ VASP ~~has~~ to be compiled ~~using~~ the [[Precompiler_flags\|-Dtbdyn]] ~~precompiler flag in~~ the makefile.include ~~file~~. ~~A sample input using~~ this ~~tag would look like this:~~		Many of 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 [[Precompiler_flags\|preprocessor flag <code>-Dtbdyn</code>]]. This is usually the case because all [[makefile.include]] templates shipped with {{VASP}} since version 5.4.4 contain this flag by default.
	~~CPP = $(CPP_) -DHOST=\"IFC9_fftw\" \~~
	~~-Dkind8 -DNGXhalf -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc \~~
	~~-Dtbdyn~~

	----		----

	[[Category:Molecular dynamics]][[Category:Howto]]		[[Category:Molecular dynamics]][[Category:Howto]]

← Older revision		Revision as of 17:55, 30 January 2020
Line 8:		Line 8:
	**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.		**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.
	**{{TAG\|ISIF}} (optional).		**{{TAG\|ISIF}} (optional).
	**{{TAG\|MDALGO}}: This tag decides ~~whether~~ the molecular dynamics ~~run~~ is executed ~~using without a thermostat ({{TAG\|MDALGO}}=0 which is default) or with a thermostat ({{TAG\|MDALGO}}>0)~~. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nose-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nose-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).		**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nose-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nose-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).
	**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.		**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.
	*Decide which [[:Category:Ensembles\|ensemble]] to use:		*Decide which [[:Category:Ensembles\|ensemble]] to use:

← Older revision		Revision as of 12:48, 5 February 2026
Line 3:		Line 3:
	*If a continuation run is performed copy {{TAG\|CONTCAR}} to {{TAG\|POSCAR}} or possibly deliver initial velocities in the {{TAG\|POSCAR}} file. They are written after the Wycoff positions in an own paragraph. If no initial velocities are provided random velocities are assumed at the beginning of the calculation. This is fully ok but the user should be aware that due to the initial random velocities the trajectories obtained from different calculations are difficult to compare.		*If a continuation run is performed copy {{TAG\|CONTCAR}} to {{TAG\|POSCAR}} or possibly deliver initial velocities in the {{TAG\|POSCAR}} file. They are written after the Wycoff positions in an own paragraph. If no initial velocities are provided random velocities are assumed at the beginning of the calculation. This is fully ok but the user should be aware that due to the initial random velocities the trajectories obtained from different calculations are difficult to compare.
	*Set main {{TAG\|INCAR}} tags:		*Set main {{TAG\|INCAR}} tags:
	**{{TAG\|IBRION}}=0: Molecular dynamics calculations are enabled by setting the {{TAG\|IBRION}} tag to 0.		**{{TAG\|IBRION\|0}}: Molecular dynamics calculations are enabled by setting the {{TAG\|IBRION}} tag to 0.
	**{{TAG\|POTIM}}: This tag sets the time step in fs for the molecular dynamics run.		**{{TAG\|POTIM}}: This tag sets the time step in fs for the molecular dynamics run.
	**{{TAG\|NSW}}: This tag sets the number of steps performed in the molecular dynamics run.		**{{TAG\|NSW}}: This tag sets the number of steps performed in the molecular dynamics run.
	**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.		**{{TAG\|TEBEG}}: If a thermostat is used define the desired temperature at which the molecular dynamics calculations should run.
	**{{TAG\|ISIF}} (optional).		**{{TAG\|ISIF}} (optional).
	**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nosé-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nosé-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB}}=0).		**{{TAG\|MDALGO}}: This tag decides with which thermostat the molecular dynamics calculation is executed. For regular molecular dynamics calculations the thermostat is selected by a one digit number (e.g. 1 for Andersen, 2 for Nosé-Hoover etc.). For biased molecular dynamics, metadynamics etc. the thermostat is selected the same way from VASP 6 or higher. In VASP 5.x it is selected by a two digit number where the first digit corresponds to the thermostat analogously to regular molecular dynamics and the second digit corresponds to the molecular dynamics type (e.g. 11 metadynamics with Andersen thermostat, 21 metadynamics with Nosé-Hoover thermostat etc.). The {{TAG\|NVE ensemble}} is a special case. It is available by selecting the Andersen thermostat and setting no collisions with the heat bath ({{TAG\|ANDERSEN_PROB\|0}}).
	**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF}}=2 the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF}}=3 the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.		**{{TAG\|ISIF}}: In molecular dynamics calculations this tag is used to choose the {{TAG\|NVT ensemble}} or {{TAG\|NpT ensemble}} (the {{TAG\|NVE ensemble}} is a special case!). For {{TAG\|ISIF\|2}} the volume is kept constant and the {{TAG\|NVT ensemble}} is used. Using this tag the stress tensor is calculated and hence the pressure can be monitored. For {{TAG\|ISIF\|3}} the stress tensor (pressure) is kept constant and the {{TAG\|NpT ensemble}} is used. Using this tag the volume is calculated and can be monitored.
	*Decide which [[:Category:Ensembles\|ensemble]] to use:		*Decide which [[:Category:Ensembles\|ensemble]] to use:
	**[[NVT ensemble]]: Set {{TAG\|ISIF}}=2.		**[[NVT ensemble]]: Set {{TAG\|ISIF\|2}}.
	**[[NpT ensemble]]: Set {{TAG\|ISIF}}=3.		**[[NpT ensemble]]: Set {{TAG\|ISIF\|3}}.
	**[[NVE ensemble]]: Set {{TAG\|MDALGO}}=1 and {{TAG\|ANDERSEN_PROB~~}}=~~0.0.		**[[NVE ensemble]]: Set {{TAG\|MDALGO\|1}} and {{TAG\|ANDERSEN_PROB\|0.0}}.
	*Decide which thermostat to use (the combination of thermostats and ensembles is given in table):		*Decide which thermostat to use (the combination of thermostats and ensembles is given in table):
	**[[Andersen thermostat]]: Set {{TAG\|MDALGO}}=1. Also set {{TAG\|ANDERSEN_PROB~~}}>~~0.0 to control the stochastic update frequency of the thermostat.		**[[Andersen thermostat]]: Set {{TAG\|MDALGO\|1}}. Also set {{TAG\|ANDERSEN_PROB\|0.0\|op=>}} to control the stochastic update frequency of the thermostat.
	**[[Nosé-Hoover thermostat]]: Set {{TAG\|MDALGO}}=2. Also set {{TAG\|SMASS}}~~>0.0~~ to control the coupling to the heat bath.		**[[Nosé-Hoover thermostat]]: Set {{TAG\|MDALGO\|2}}. Also set {{TAG\|SMASS\|0\|op=>=}} to control the coupling to the heat bath.
	**[[Langevin thermostat]]: Set {{TAG\|MDALGO}}=3. Also set {{TAG\|LANGEVIN_GAMMA~~}}>~~0.0 to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF}}=3) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.		**[[Langevin thermostat]]: Set {{TAG\|MDALGO\|3}}. Also set {{TAG\|LANGEVIN_GAMMA\|0.0\|op=>}} to control the friction parameter. If the {{TAG\|NpT ensemble}} is used (by setting {{TAG\|ISIF\|3}}) additionally the friction coefficient of the lattice {{TAG\|LANGEVIN_GAMMA_L}} has to be provided too.
	**[[Nosé-Hoover chain thermostat]]: Set {{TAG\|MDALGO}}=4. Also set the {{TAG\|NHC_NCHAINS}}>0 to adjust the length of the Nosé-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the Nosé-Hoover chains thermostat is set.		**[[Nosé-Hoover chain thermostat]]: Set {{TAG\|MDALGO\|4}}. Also set the {{TAG\|NHC_NCHAINS\|0\|op=>}} to adjust the length of the Nosé-Hoover chain. With {{TAG\|NHC_PERIOD}} the period (coupling strength to the heat bath) of the Nosé-Hoover chains thermostat is set.
	**[[CSVR thermostat]]: Set {{TAG\|MDALGO}}=5 and additionally adjust {{TAG\|CSVR_PERIOD}}>0.		**[[CSVR thermostat]]: Set {{TAG\|MDALGO\|5}} and additionally adjust {{TAG\|CSVR_PERIOD\|0\|op=>}}.

	The following combinations of thermostats and barostats is possible:		The following combinations of thermostats and barostats is possible: