MDALGO - Revision history

Singraber at 07:47, 24 October 2025

2025-10-24T07:47:49Z

← Older revision		Revision as of 07:47, 24 October 2025
Line 37:		Line 37:
	=== {{TAG\|MDALGO\|13}}: Multiple [[Andersen thermostat\|Andersen thermostats]] ===		=== {{TAG\|MDALGO\|13}}: Multiple [[Andersen thermostat\|Andersen thermostats]] ===
	<div id="multiAnderson"></div>		<div id="multiAnderson"></div>
	:Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]{{cite\|andersen:jcp:1980}} ({{TAG\|MDALGO}}=1). The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following tags must be set: {{TAG\|NSUBSYS}}, {{TAG\|TSUBSYS}}, and {{TAG\|PSUBSYS}}.		:Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]{{cite\|andersen:jcp:1980}} ({{TAG\|MDALGO\|1}}). The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following tags must be set: {{TAG\|NSUBSYS}}, {{TAG\|TSUBSYS}}, and {{TAG\|PSUBSYS}}.

	=== {{TAG\|MDALGO\|0}} (deprecated) ===		=== {{TAG\|MDALGO\|0}} (deprecated) ===

Singraber at 07:47, 24 October 2025

2025-10-24T07:47:18Z

Huebsch at 09:09, 22 October 2025

2025-10-22T09:09:19Z

Huebsch at 09:05, 22 October 2025

2025-10-22T09:05:09Z

Show changes

Huebsch: /* {{TAG|MDALGO}}=13: Multiple Andersen thermostats */

2025-10-22T07:29:23Z

{{TAG|MDALGO}}=13: Multiple Andersen thermostats

← Older revision		Revision as of 07:29, 22 October 2025
Line 51:		Line 51:
	== {{TAG\|MDALGO}}=13: Multiple Andersen thermostats ==		== {{TAG\|MDALGO}}=13: Multiple Andersen thermostats ==
	<div id="multiAnderson"></div>		<div id="multiAnderson"></div>
	Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]<ref name="Andersen80"/> (~~see remarks under~~ {{TAG\|MDALGO}}=1 ~~as well~~).		Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]<ref name="Andersen80"/> ({{TAG\|MDALGO}}=1).
	The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following ~~flags~~ must be set ~~by the user~~:		The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following tags must be set: {{TAG\|NSUBSYS}}, {{TAG\|TSUBSYS}}, and {{TAG\|PSUBSYS}}.
	*{{TAG\|NSUBSYS}}~~=[int array]~~
	~~:Define the last atom for each subsystem (two or three values must be supplied). For instance~~, ~~if total of 20 atoms is defined in the~~ {{~~FILE~~\|~~POSCAR~~}} ~~file~~, and ~~the initial 10 atoms belong to the subsystem 1, the next 7 atoms to the subsystem 2, and the last 3 atoms to the subsystem 3, {{TAG\|NSUBSYS}} should be defined as follows:~~

	~~:{{TAG\|NSUBSYS}}= 10 17 20~~

	~~:Note that the last number in the previous example is actually redundant (clearly the last three atoms belong to the last subsystem) and does not have to be user-supplied.~~

	*{{TAG\|TSUBSYS}}=[real array]
	~~:Simulation temperature for each subsystem~~
	*{{TAG\|PSUBSYS}}=[real array]
	~~:Collision probability for atoms in each subsystem. Only the values 0≤~~{{TAG\|PSUBSYS}}~~≤1 are allowed~~.

	== Related tags and articles ==		== Related tags and articles ==

Huebsch at 13:46, 21 October 2025

2025-10-21T13:46:32Z

Show changes

Singraber at 21:46, 17 October 2025

2025-10-17T21:46:08Z

← Older revision		Revision as of 21:46, 17 October 2025
Line 215:		Line 215:

	== {{TAG\|MDALGO}}=4: Nosé-Hoover chain thermostat ==		== {{TAG\|MDALGO}}=4: Nosé-Hoover chain thermostat ==
	For a description of Nosé-Hoover chain ~~theromastat~~, see [[~~NHC~~ thermostat]].		For a description of Nosé-Hoover chain thermostat, see [[Nosé-Hoover chain thermostat]].
	*To run an ''NVT''-simulation with a Nosé-Hoover chain thermostat, one has to:		*To run an ''NVT''-simulation with a Nosé-Hoover chain thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}

Singraber at 21:22, 17 October 2025

2025-10-17T21:22:33Z

← Older revision		Revision as of 21:22, 17 October 2025
Line 98:		Line 98:
	== {{TAG\|MDALGO}}=2: Nosé-Hoover thermostat ==		== {{TAG\|MDALGO}}=2: Nosé-Hoover thermostat ==

	For the description of the ~~Nose~~-Hoover thermostat see: [[Nosé-Hoover thermostat]].		For the description of the Nosé-Hoover thermostat see: [[Nosé-Hoover thermostat]].

	The Nosé-Hoover thermostat is currently only available for the NVT ensemble.		The Nosé-Hoover thermostat is currently only available for the NVT ensemble.

Singraber at 21:02, 17 October 2025

2025-10-17T21:02:40Z

Singraber: /* {{TAG|MDALGO}}=0: Standard molecular dynamics */

2025-10-17T20:57:27Z

{{TAG|MDALGO}}=0: Standard molecular dynamics

← Older revision		Revision as of 20:57, 17 October 2025
Line 5:		Line 5:

	== {{TAG\|MDALGO}}=0: Standard molecular dynamics ==		== {{TAG\|MDALGO}}=0: Standard molecular dynamics ==
	Selects a [[~~Nosé–Hoover~~ thermostat]] which allows to sample the [[NVT ensemble]]. {{NB\|deprecated\|If possible, we recommend to use one of the newer Nosé–Hoover thermostat implementations {{VASP}} provides ({{TAGO\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).}}		Selects a [[Nosé-Hoover thermostat]] which allows to sample the [[NVT ensemble]]. {{NB\|deprecated\|If possible, we recommend to use one of the newer Nosé–Hoover thermostat implementations {{VASP}} provides ({{TAGO\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).}}

	=== Standard molecular dynamics ===		=== Standard molecular dynamics ===

← Older revision		Revision as of 07:29, 22 October 2025
Line 51:		Line 51:
	== {{TAG\|MDALGO}}=13: Multiple Andersen thermostats ==		== {{TAG\|MDALGO}}=13: Multiple Andersen thermostats ==
	<div id="multiAnderson"></div>		<div id="multiAnderson"></div>
	Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]<ref name="Andersen80"/> (~~see remarks under~~ {{TAG\|MDALGO}}=1 ~~as well~~).		Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]<ref name="Andersen80"/> ({{TAG\|MDALGO}}=1).
	The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following ~~flags~~ must be set ~~by the user~~:		The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following tags must be set: {{TAG\|NSUBSYS}}, {{TAG\|TSUBSYS}}, and {{TAG\|PSUBSYS}}.
	*{{TAG\|NSUBSYS}}~~=[int array]~~
	~~:Define the last atom for each subsystem (two or three values must be supplied). For instance~~, ~~if total of 20 atoms is defined in the~~ {{~~FILE~~\|~~POSCAR~~}} ~~file~~, and ~~the initial 10 atoms belong to the subsystem 1, the next 7 atoms to the subsystem 2, and the last 3 atoms to the subsystem 3, {{TAG\|NSUBSYS}} should be defined as follows:~~

	~~:{{TAG\|NSUBSYS}}= 10 17 20~~

	~~:Note that the last number in the previous example is actually redundant (clearly the last three atoms belong to the last subsystem) and does not have to be user-supplied.~~

	*{{TAG\|TSUBSYS}}=[real array]
	~~:Simulation temperature for each subsystem~~
	*{{TAG\|PSUBSYS}}=[real array]
	~~:Collision probability for atoms in each subsystem. Only the values 0≤~~{{TAG\|PSUBSYS}}~~≤1 are allowed~~.

	== Related tags and articles ==		== Related tags and articles ==

← Older revision		Revision as of 07:47, 24 October 2025
Line 1:		Line 1:
	{{TAGDEF\|MDALGO\|0 {{!}} 1 {{!}} 2 {{!}} 3 {{!}} 4 {{!}} 5 {{!}} 11 {{!}} 21 {{!}} 13 \|0}}		{{TAGDEF\|MDALGO\|0 {{!}} 1 {{!}} 2 {{!}} 3 {{!}} 4 {{!}} 5 {{!}} 11 {{!}} 21 {{!}} 13 \|0}}

	Description: Specifies the [[thermostat]] and lattice dynamics for [[molecular-dynamics calculations]] (in case {{~~TAGO~~\|IBRION\|0}}).		Description: Specifies the [[thermostat]] and lattice dynamics for [[molecular-dynamics calculations]] (in case {{TAG\|IBRION\|0}}).
	----		----

	The algorithm for the [[thermostat]] and lattice dynamics is a crucial choise for any [[molecular-dynamics calculations\|molecular-dynamics (MD) calculations]] ({{~~TAGO~~\|IBRION\|0}}). In combination with the selected lattice degrees of freedom ({{TAG\|ISIF}}), {{TAG\|MDALGO}} determines the [[ensemble]] that is sampled during the [[molecular-dynamics calculations\|MD run]]. The main output file is the {{FILE\|REPORT}} file.		The algorithm for the [[thermostat]] and lattice dynamics is a crucial choise for any [[molecular-dynamics calculations\|molecular-dynamics (MD) calculations]] ({{TAG\|IBRION\|0}}). In combination with the selected lattice degrees of freedom ({{TAG\|ISIF}}), {{TAG\|MDALGO}} determines the [[ensemble]] that is sampled during the [[molecular-dynamics calculations\|MD run]]. The main output file is the {{FILE\|REPORT}} file.

	{{~~TAGO~~\|MDALGO\|op=>=1}} can be applied in the context of standard [[molecular-dynamics calculations]], [[constrained molecular dynamics]], [[metadynamics calculations]], the [[slow-growth approach]], monitoring geometric parameters using the {{FILE\|ICONST}} file, [[biased molecular dynamics]], and more.		{{TAG\|MDALGO\|op=>=1}} can be applied in the context of standard [[molecular-dynamics calculations]], [[constrained molecular dynamics]], [[metadynamics calculations]], the [[slow-growth approach]], monitoring geometric parameters using the {{FILE\|ICONST}} file, [[biased molecular dynamics]], and more.
	{{NB\|mind\|{{~~TAGO~~\|MDALGO\|0\|op=>=}} requires compilation with the precompiler option [[Precompiler options#-Dtbdyn\|<code>-Dtbdyn</code>]]. This option is present by default in all [[makefile.include]] templates since {{VASP}} 5.4.4.}}		{{NB\|mind\|{{TAG\|MDALGO\|0\|op=>=}} requires compilation with the precompiler option [[Precompiler options#-Dtbdyn\|<code>-Dtbdyn</code>]]. This option is present by default in all [[makefile.include]] templates since {{VASP}} 5.4.4.}}

	== Options ==		== Options ==

	=== {{~~TAGO~~\|MDALGO\|1}}: [[Andersen thermostat]] ===		=== {{TAG\|MDALGO\|1}}: [[Andersen thermostat]] ===

	:The [[Andersen thermostat]] can be used to sample an [[NVT ensemble]] or [[NVE ensemble]]. It requires setting an appropriate value for {{TAG\|ANDERSEN_PROB}}. For an [[NVE ensemble]], set {{~~TAGO~~\|ANDERSEN_PROB\|0.0}}. This is usually done after thermalization to a certain target temperature. {{NB\|tip\|Leave the value for {{TAG\|TEBEG}} that was set in the thermalization. For {{~~TAGO~~\|TEBEG\|0.1\|op=<}}, some part of the code assumes it is used for [[structure optimization]] and not an [[molecular-dynamics calculations\|MD run]].\|:}}		:The [[Andersen thermostat]] can be used to sample an [[NVT ensemble]] or [[NVE ensemble]]. It requires setting an appropriate value for {{TAG\|ANDERSEN_PROB}}. For an [[NVE ensemble]], set {{TAG\|ANDERSEN_PROB\|0.0}}. This is usually done after thermalization to a certain target temperature. {{NB\|tip\|Leave the value for {{TAG\|TEBEG}} that was set in the thermalization. For {{TAG\|TEBEG\|0.1\|op=<}}, some part of the code assumes it is used for [[structure optimization]] and not an [[molecular-dynamics calculations\|MD run]].\|:}}

	=== {{~~TAGO~~\|MDALGO\|2}}: [[Nosé-Hoover thermostat]] ===		=== {{TAG\|MDALGO\|2}}: [[Nosé-Hoover thermostat]] ===

	:The [[Nosé-Hoover thermostat]] is currently only available for the [[NVT ensemble]]. It requires setting an appropriate value for {{TAG\|SMASS}}.		:The [[Nosé-Hoover thermostat]] is currently only available for the [[NVT ensemble]]. It requires setting an appropriate value for {{TAG\|SMASS}}.
	{{NB\|tip\|The [[Nosé-Hoover thermostat]] is a special case of the [[Nosé-Hoover chain thermostat]] ({{~~TAGO~~\|MDALGO\|4}} with {{TAGDEF\|NHC_NCHAINS\|1}}). The control tags for {{~~TAGO~~\|MDALGO\|4}} may be more convenient to use than the older implementation ({{~~TAGO~~\|MDALGO\|2}}).\|:}}		{{NB\|tip\|The [[Nosé-Hoover thermostat]] is a special case of the [[Nosé-Hoover chain thermostat]] ({{TAG\|MDALGO\|4}} with {{TAGDEF\|NHC_NCHAINS\|1}}). The control tags for {{TAG\|MDALGO\|4}} may be more convenient to use than the older implementation ({{TAG\|MDALGO\|2}}).\|:}}

	=== {{~~TAGO~~\|MDALGO\|3}}: [[Langevin thermostat]] ===		=== {{TAG\|MDALGO\|3}}: [[Langevin thermostat]] ===

	:The [[Langevin thermostat]] is available for sampling the [[NVT ensemble]], [[NpT ensemble]] and [[NpH ensemble]]. The Langevin dynamics in the [[NpT ensemble]] is calculated by the method of Parrinello and Rahman{{cite\|parrinello:prl:1980}}{{cite\|parrinello:jap:1981}} combined with a [[Langevin thermostat]].		:The [[Langevin thermostat]] is available for sampling the [[NVT ensemble]], [[NpT ensemble]] and [[NpH ensemble]]. The Langevin dynamics in the [[NpT ensemble]] is calculated by the method of Parrinello and Rahman{{cite\|parrinello:prl:1980}}{{cite\|parrinello:jap:1981}} combined with a [[Langevin thermostat]].
	:* [[NVT ensemble]]: Set an appropriate value for the friction coefficients ({{TAG\|LANGEVIN_GAMMA}}) for all species in the {{FILE\|POSCAR}} file to enables the [[Langevin thermostat]]. Fix the cell shape and volume with {{~~TAGO~~\|ISIF\|2\|op=<=}}.		:* [[NVT ensemble]]: Set an appropriate value for the friction coefficients ({{TAG\|LANGEVIN_GAMMA}}) for all species in the {{FILE\|POSCAR}} file to enables the [[Langevin thermostat]]. Fix the cell shape and volume with {{TAG\|ISIF\|2\|op=<=}}.
	:* [[NpT ensemble]]: To enable lattice dynamics set {{~~TAGO~~\|ISIF\|3}} and specify a separate set of friction coefficient for the lattice degrees-of-freedom ({{TAG\|LANGEVIN_GAMMA_L}}) as well as a ficticious mass for the lattice degrees-of-freedom ({{TAG\|PMASS}}). At the moment, dynamics with ''fixed volume+variable shape'' ({{~~TAGO~~\|ISIF\|4}}) or ''fixed shape+variable volume'' ({{~~TAGO~~\|ISIF\|7}}) are not available. Optionally, one may define an external pressure ({{TAG\|PSTRESS}}). Like for the NVT ensemble, set an appropriate value for the friction coefficients ({{TAG\|LANGEVIN_GAMMA}}) for all species in the {{FILE\|POSCAR}} file to enables the [[Langevin thermostat]].		:* [[NpT ensemble]]: To enable lattice dynamics set {{TAG\|ISIF\|3}} and specify a separate set of friction coefficient for the lattice degrees-of-freedom ({{TAG\|LANGEVIN_GAMMA_L}}) as well as a ficticious mass for the lattice degrees-of-freedom ({{TAG\|PMASS}}). At the moment, dynamics with ''fixed volume+variable shape'' ({{TAG\|ISIF\|4}}) or ''fixed shape+variable volume'' ({{TAG\|ISIF\|7}}) are not available. Optionally, one may define an external pressure ({{TAG\|PSTRESS}}). Like for the NVT ensemble, set an appropriate value for the friction coefficients ({{TAG\|LANGEVIN_GAMMA}}) for all species in the {{FILE\|POSCAR}} file to enables the [[Langevin thermostat]].

	:Also see [[stochastic boundary conditions]].		:Also see [[stochastic boundary conditions]].

	=== {{~~TAGO~~\|MDALGO\|4}}: [[Nosé-Hoover chain thermostat]] ===		=== {{TAG\|MDALGO\|4}}: [[Nosé-Hoover chain thermostat]] ===
	:The [[Nosé-Hoover chain thermostat]] can be only used to sample an [[NVT ensemble]] and requires selecting the number of thermostats in the chain via {{TAG\|NHC_NCHAINS}} as well as choosing an appropriate setting for the thermostat parameter {{TAG\|NHC_PERIOD}}.		:The [[Nosé-Hoover chain thermostat]] can be only used to sample an [[NVT ensemble]] and requires selecting the number of thermostats in the chain via {{TAG\|NHC_NCHAINS}} as well as choosing an appropriate setting for the thermostat parameter {{TAG\|NHC_PERIOD}}.

	=== {{~~TAGO~~\|MDALGO\|5}}: [[CSVR thermostat\|Canonical sampling through velocity-rescaling (CSVR thermostat)]] ===		=== {{TAG\|MDALGO\|5}}: [[CSVR thermostat\|Canonical sampling through velocity-rescaling (CSVR thermostat)]] ===
	{{NB\|mind\|This option is available as of VASP 6.4.3.\|:}}		{{NB\|mind\|This option is available as of VASP 6.4.3.\|:}}
	:The [[CSVR thermostat]] can be used to sample an [[NVT ensemble]]. It requires setting {{TAG\|CSVR_PERIOD}}.		:The [[CSVR thermostat]] can be used to sample an [[NVT ensemble]]. It requires setting {{TAG\|CSVR_PERIOD}}.

	=== {{~~TAGO~~\|MDALGO\|13}}: Multiple [[Andersen thermostat\|Andersen thermostats]] ===		=== {{TAG\|MDALGO\|13}}: Multiple [[Andersen thermostat\|Andersen thermostats]] ===
	<div id="multiAnderson"></div>		<div id="multiAnderson"></div>
	:Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]{{cite\|andersen:jcp:1980}} ({{TAG\|MDALGO}}=1). The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following tags must be set: {{TAG\|NSUBSYS}}, {{TAG\|TSUBSYS}}, and {{TAG\|PSUBSYS}}.		:Up to three user-defined atomic subsystems may be coupled with independent [[Andersen thermostat\|Andersen thermostats]]{{cite\|andersen:jcp:1980}} ({{TAG\|MDALGO}}=1). The {{FILE\|POSCAR}} file must be organized such that the positions of atoms of subsystem ''i+1'' are defined after those for the subsystem ''i'', and the following tags must be set: {{TAG\|NSUBSYS}}, {{TAG\|TSUBSYS}}, and {{TAG\|PSUBSYS}}.

	=== {{~~TAGO~~\|MDALGO\|0}} (deprecated) ===		=== {{TAG\|MDALGO\|0}} (deprecated) ===
	:Selects a [[Nosé-Hoover thermostat]] which allows sampling the [[NVT ensemble]] at temperature {{TAG\|TEBEG}}. The [[Nosé-Hoover thermostat]] requires an appropriate setting for {{TAG\|SMASS}}. To sample an [[NVE ensemble]] set {{~~TAGO~~\|SMASS\|-3}}. {{NB\|deprecated\|If possible, we recommend using one of the newer Nosé-Hoover thermostat implementations {{VASP}} provides ({{~~TAGO~~\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical ,this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).\|:}}		:Selects a [[Nosé-Hoover thermostat]] which allows sampling the [[NVT ensemble]] at temperature {{TAG\|TEBEG}}. The [[Nosé-Hoover thermostat]] requires an appropriate setting for {{TAG\|SMASS}}. To sample an [[NVE ensemble]] set {{TAG\|SMASS\|-3}}. {{NB\|deprecated\|If possible, we recommend using one of the newer Nosé-Hoover thermostat implementations {{VASP}} provides ({{TAG\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical ,this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).\|:}}

	=== {{~~TAGO~~\|MDALGO\|11}} (deprecated) ===		=== {{TAG\|MDALGO\|11}} (deprecated) ===
	:For VASP 5.x {{TAGDEF\|MDALGO\|11}} selects the [[Andersen thermostat]]. This is replaced by {{~~TAGO~~\|MDALGO\|1}}.		:For VASP 5.x {{TAGDEF\|MDALGO\|11}} selects the [[Andersen thermostat]]. This is replaced by {{TAG\|MDALGO\|1}}.

	=== {{~~TAGO~~\|MDALGO\|21}} (deprecated) ===		=== {{TAG\|MDALGO\|21}} (deprecated) ===
	:For VASP 5.x it selects the [[Nosé-Hoover thermostat]]. This is replaced by {{~~TAGO~~\|MDALGO\|2}}.		:For VASP 5.x it selects the [[Nosé-Hoover thermostat]]. This is replaced by {{TAG\|MDALGO\|2}}.

	== Related tags and articles ==		== Related tags and articles ==

← Older revision		Revision as of 09:09, 22 October 2025
Line 1:		Line 1:
	{{TAGDEF\|MDALGO\|0 {{!}} 1 {{!}} 2 {{!}} 3 {{!}} 4 {{!}} 5 {{!}} 11 {{!}} 21 {{!}} 13 \|0}}		{{TAGDEF\|MDALGO\|0 {{!}} 1 {{!}} 2 {{!}} 3 {{!}} 4 {{!}} 5 {{!}} 11 {{!}} 21 {{!}} 13 \|0}}

	Description: Specifies the [[thermostat]] and lattice dynamics for [[molecular-dynamics calculations]] (in case {{~~TAGDEF~~\|IBRION\|0}}).		Description: Specifies the [[thermostat]] and lattice dynamics for [[molecular-dynamics calculations]] (in case {{TAGO\|IBRION\|0}}).
	----		----

	The algorithm for the [[thermostat]] and lattice dynamics is a crucial choise for any [[molecular-dynamics calculations\|molecular-dynamics (MD) calculations]] ({{~~TAGDEF~~\|IBRION\|0}}). In combination with the selected lattice degrees of freedom ({{TAG\|ISIF}}), {{TAG\|MDALGO}} determines the [[ensemble]] that is sampled during the [[molecular-dynamics calculations\|MD run]]. The main output file is the {{FILE\|REPORT}} file.		The algorithm for the [[thermostat]] and lattice dynamics is a crucial choise for any [[molecular-dynamics calculations\|molecular-dynamics (MD) calculations]] ({{TAGO\|IBRION\|0}}). In combination with the selected lattice degrees of freedom ({{TAG\|ISIF}}), {{TAG\|MDALGO}} determines the [[ensemble]] that is sampled during the [[molecular-dynamics calculations\|MD run]]. The main output file is the {{FILE\|REPORT}} file.

	{{TAGO\|MDALGO\|op=>=1}} can be applied in the context of standard [[molecular-dynamics calculations]], [[constrained molecular dynamics]], [[metadynamics calculations]], the [[slow-growth approach]], monitoring geometric parameters using the {{FILE\|ICONST}} file, [[biased molecular dynamics]], and more.		{{TAGO\|MDALGO\|op=>=1}} can be applied in the context of standard [[molecular-dynamics calculations]], [[constrained molecular dynamics]], [[metadynamics calculations]], the [[slow-growth approach]], monitoring geometric parameters using the {{FILE\|ICONST}} file, [[biased molecular dynamics]], and more.
Line 13:		Line 13:
	=== {{TAGO\|MDALGO\|1}}: [[Andersen thermostat]] ===		=== {{TAGO\|MDALGO\|1}}: [[Andersen thermostat]] ===

	:The [[Andersen thermostat]] can be used to sample an [[NVT ensemble]] or [[NVE ensemble]]. It requires setting an appropriate value for {{TAG\|ANDERSEN_PROB}}. For an [[NVE ensemble]], set {{~~TAGDEF~~\|ANDERSEN_PROB\|0.0}}. This is usually done after thermalization to a certain target temperature. {{NB\|tip\|Leave the value for {{TAG\|TEBEG}} that was set in the thermalization. For {{~~TAG~~\|TEBEG~~}}$<~~0.1$, some part of the code assumes it is used for [[structure optimization]] and not an [[molecular-dynamics calculations\|MD run]].\|:}}		:The [[Andersen thermostat]] can be used to sample an [[NVT ensemble]] or [[NVE ensemble]]. It requires setting an appropriate value for {{TAG\|ANDERSEN_PROB}}. For an [[NVE ensemble]], set {{TAGO\|ANDERSEN_PROB\|0.0}}. This is usually done after thermalization to a certain target temperature. {{NB\|tip\|Leave the value for {{TAG\|TEBEG}} that was set in the thermalization. For {{TAGO\|TEBEG\|0.1\|op=<}}, some part of the code assumes it is used for [[structure optimization]] and not an [[molecular-dynamics calculations\|MD run]].\|:}}

	=== {{TAGO\|MDALGO\|2}}: [[Nosé-Hoover thermostat]] ===		=== {{TAGO\|MDALGO\|2}}: [[Nosé-Hoover thermostat]] ===

	:The [[Nosé-Hoover thermostat]] is currently only available for the [[NVT ensemble]]. It requires setting an appropriate value for {{TAG\|SMASS}}.		:The [[Nosé-Hoover thermostat]] is currently only available for the [[NVT ensemble]]. It requires setting an appropriate value for {{TAG\|SMASS}}.
	{{NB\|tip\|The [[Nosé-Hoover thermostat]] is a special case of the [[Nosé-Hoover chain thermostat]] ({{~~TAGDEF~~\|MDALGO\|4}} with {{TAGDEF\|NHC_NCHAINS\|1}}). The control tags for {{~~TAGDEF~~\|MDALGO\|4}} may be more convenient to use than the older implementation ({{~~TAGDEF~~\|MDALGO\|2}}).\|:}}		{{NB\|tip\|The [[Nosé-Hoover thermostat]] is a special case of the [[Nosé-Hoover chain thermostat]] ({{TAGO\|MDALGO\|4}} with {{TAGDEF\|NHC_NCHAINS\|1}}). The control tags for {{TAGO\|MDALGO\|4}} may be more convenient to use than the older implementation ({{TAGO\|MDALGO\|2}}).\|:}}

	=== {{TAGO\|MDALGO\|3}}: [[Langevin thermostat]] ===		=== {{TAGO\|MDALGO\|3}}: [[Langevin thermostat]] ===
Line 40:		Line 40:

	=== {{TAGO\|MDALGO\|0}} (deprecated) ===		=== {{TAGO\|MDALGO\|0}} (deprecated) ===
	:Selects a [[Nosé-Hoover thermostat]] which allows sampling the [[NVT ensemble]] at temperature {{TAG\|TEBEG}}. The [[Nosé-Hoover thermostat]] requires an appropriate setting for {{TAG\|SMASS}}. To sample an [[NVE ensemble]] set {{~~TAGDEF~~\|SMASS\|-3}}. {{NB\|deprecated\|If possible, we recommend using one of the newer Nosé-Hoover thermostat implementations {{VASP}} provides ({{TAGO\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical ,this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).\|:}}		:Selects a [[Nosé-Hoover thermostat]] which allows sampling the [[NVT ensemble]] at temperature {{TAG\|TEBEG}}. The [[Nosé-Hoover thermostat]] requires an appropriate setting for {{TAG\|SMASS}}. To sample an [[NVE ensemble]] set {{TAGO\|SMASS\|-3}}. {{NB\|deprecated\|If possible, we recommend using one of the newer Nosé-Hoover thermostat implementations {{VASP}} provides ({{TAGO\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical ,this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).\|:}}

	=== {{TAGO\|MDALGO\|11}} (deprecated) ===		=== {{TAGO\|MDALGO\|11}} (deprecated) ===
	:For VASP 5.x {{TAGDEF\|MDALGO\|11}} selects the [[Andersen thermostat]]. This is replaced by {{~~TAGDEF~~\|MDALGO\|1}}.		:For VASP 5.x {{TAGDEF\|MDALGO\|11}} selects the [[Andersen thermostat]]. This is replaced by {{TAGO\|MDALGO\|1}}.

	=== {{TAGO\|MDALGO\|21}} (deprecated) ===		=== {{TAGO\|MDALGO\|21}} (deprecated) ===
	:For VASP 5.x it selects the [[Nosé-Hoover thermostat]]. This is replaced by {{~~TAGDEF~~\|MDALGO\|2}}.		:For VASP 5.x it selects the [[Nosé-Hoover thermostat]]. This is replaced by {{TAGO\|MDALGO\|2}}.

	== Related tags and articles ==		== Related tags and articles ==

← Older revision		Revision as of 21:02, 17 October 2025
Line 5:		Line 5:

	== {{TAG\|MDALGO}}=0: Standard molecular dynamics ==		== {{TAG\|MDALGO}}=0: Standard molecular dynamics ==
	Selects a [[Nosé-Hoover thermostat]] which allows to sample the [[NVT ensemble]]. {{NB\|deprecated\|If possible, we recommend to use one of the newer ~~Nosé–Hoover~~ thermostat implementations {{VASP}} provides ({{TAGO\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).}}		Selects a [[Nosé-Hoover thermostat]] which allows to sample the [[NVT ensemble]]. {{NB\|deprecated\|If possible, we recommend to use one of the newer Nosé-Hoover thermostat implementations {{VASP}} provides ({{TAGO\|MDALGO\|2 or 4}}). While the results (ensemble averages) should be identical this variant comes with some drawbacks regarding post-processing: the atom coordinates in output files will always be wrapped back into the box if atoms cross the periodic boundaries. This makes it impossible to carry out certain analysis, e.g., computing the mean squared displacement (MSD).}}

	=== Standard molecular dynamics ===		=== Standard molecular dynamics ===

	* For a standard molecular dynamics run with ~~Nose~~-Hoover thermostat, one has to:		* For a standard molecular dynamics run with [[Nosé-Hoover thermostat]], one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
	#Set {{TAG\|MDALGO}}=0, and choose an appropriate setting for {{TAG\|SMASS}}.		#Set {{TAG\|MDALGO}}=0, and choose an appropriate setting for {{TAG\|SMASS}}.
Line 96:		Line 96:
	#Set {{TAG\|MDALGO}}=1 and {{TAG\|ANDERSEN_PROB}}=0.0.		#Set {{TAG\|MDALGO}}=1 and {{TAG\|ANDERSEN_PROB}}=0.0.

	== {{TAG\|MDALGO}}=2: ~~Nose~~-Hoover thermostat==		== {{TAG\|MDALGO}}=2: Nosé-Hoover thermostat ==

	For the description of the Nose-Hoover thermostat see: ~~{{TAG\|Nose~~-Hoover thermostat}}.		For the description of the Nose-Hoover thermostat see: [[Nosé-Hoover thermostat]].

	The ~~Nose~~-Hoover thermostat is currently only available for the NVT ensemble.		The Nosé-Hoover thermostat is currently only available for the NVT ensemble.

	=== Standard molecular dynamics ===		=== Standard molecular dynamics ===

	* For a standard molecular dynamics run with ~~Nose~~-Hoover thermostat, one has to:		* For a standard molecular dynamics run with Nosé-Hoover thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
	#Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}.		#Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}.
Line 111:		Line 111:
	For a description of constrained molecular dynamics see {{TAG\|Constrained molecular dynamics}}.		For a description of constrained molecular dynamics see {{TAG\|Constrained molecular dynamics}}.

	* For a constrained molecular dynamics run with ~~Nose~~-Hoover thermostat, one has to:		* For a constrained molecular dynamics run with Nosé-Hoover thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
	#Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}.		#Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}.
Line 121:		Line 121:
	For a description of slow-growth approach see {{TAG\|Slow-growth approach}}.		For a description of slow-growth approach see {{TAG\|Slow-growth approach}}.

	* For a slow-growth approach run with ~~Nose~~-Hoover thermostat, one has to:		* For a slow-growth approach run with Nosé-Hoover thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
	#Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}		#Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}
Line 146:		Line 146:
	For a description of metadynamics see {{TAG\|Metadynamics}}.		For a description of metadynamics see {{TAG\|Metadynamics}}.

	* For a metadynamics run with ~~Nose~~-Hoover thermostat, one has to:		* For a metadynamics run with Nosé-Hoover thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
	#Set {{TAG\|MDALGO}}=2 (or {{TAG\|MDALGO}}=21 in VASP 5.x), and choose an appropriate setting for {{TAG\|SMASS}}.		#Set {{TAG\|MDALGO}}=2 (or {{TAG\|MDALGO}}=21 in VASP 5.x), and choose an appropriate setting for {{TAG\|SMASS}}.
Line 159:		Line 159:
	For a description of biased molecular dynamics see {{TAG\|Biased molecular dynamics}}.		For a description of biased molecular dynamics see {{TAG\|Biased molecular dynamics}}.

	* For a biased molecular dynamics run with ~~Nose~~-Hoover thermostat, one has to:		* For a biased molecular dynamics run with Nosé-Hoover thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}.
	#Set {{TAG\|MDALGO}}=2 (or {{TAG\|MDALGO}}=21 in VASP 5.x), and choose an appropriate setting for {{TAG\|SMASS}}.		#Set {{TAG\|MDALGO}}=2 (or {{TAG\|MDALGO}}=21 in VASP 5.x), and choose an appropriate setting for {{TAG\|SMASS}}.
Line 214:		Line 214:
	<div id="multiAnderson"></div>		<div id="multiAnderson"></div>

	== {{TAG\|MDALGO}}=4: ~~Nose~~ Hoover ~~chains~~ thermostat ==		== {{TAG\|MDALGO}}=4: Nosé-Hoover chain thermostat ==
	For a description of ~~Nose~~ Hoover ~~chains~~ theromastat, see ~~{{TAG\|~~NHC thermostat}}.		For a description of Nosé-Hoover chain theromastat, see [[NHC thermostat]].
	*To run an ''NVT''-simulation with a ~~Nose~~ Hoover ~~chains~~ thermostat, one has to:		*To run an ''NVT''-simulation with a Nosé-Hoover chain thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
	#Set {{TAG\|ISIF}}=2		#Set {{TAG\|ISIF}}=2