MDALGO: Difference between revisions

From VASP Wiki
VisualWikitext
No edit summary
 
(34 intermediate revisions by 5 users not shown)
Line 1: Line 1:
{{TAGDEF|MDALGO|0 {{!}} 1 {{!}} 2 {{!}} 3 {{!}} 11 {{!}} 21 {{!}} 13|0}}
{{TAGDEF|MDALGO|0 {{!}} 1 {{!}} 2 {{!}} 3 {{!}} 4 {{!}} 5 {{!}} 11 {{!}} 21 {{!}} 13 |0}}


Description: {{TAG|MDALGO}} specifies the molecular dynamics simulation protocol (in case {{TAG|IBRION}}=0 and VASP was compiled with [[Precompiler_flags|-Dtbdyn]]).  
Description: Specifies the [[thermostat]] and lattice dynamics for [[molecular-dynamics calculations]] (in case {{TAG|IBRION|0}}).
----
----


== {{TAG|MDALGO}}=0: Standard molecular dynamics ==
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.
Should provide the same results as {{TAG|MDALGO}}=2 ({{TAG|Nose-Hoover thermostat}}). The difference is that it is a different implementation and works also without the precompiler flag [[Precompiler_flags|-Dtbdyn]].


=== NVE ensemble ===
{{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|{{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.}}


*To perform a calculation in the NVE ensemble:
== Options ==
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}.
#Set {{TAG|MDALGO}}=0 and set {{TAG|SMASS}}=-3.


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


For the description of the Andersen thermostat see: {{TAG|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 {{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]].|:}}


The Andersen thermostat is only available for the NVT ensemble.
=== {{TAG|MDALGO|2}}: [[Nosé-Hoover thermostat]] ===


=== Standard molecular dynamics in ===
: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]] ({{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}}).|:}}


*For a standard molecular dynamics run with Anderson thermostat, one has to:
=== {{TAG|MDALGO|3}}: [[Langevin thermostat]] ===
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}.
#Set {{TAG|MDALGO}}=1, and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}


=== Constrained molecular dynamics ===
: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]].
For a description of constrained molecular dynamics see {{TAG|Constrained molecular dynamics}}.
:* [[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 {{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]].


* For a constrained molecular dynamics run with Andersen thermostat, one has to:
:Also see [[stochastic boundary conditions]].
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|MDALGO}}=1, and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}
#Define geometric constraints in the {{FILE|ICONST}}-file, and set the STATUS parameter for the constrained coordinates to 0
#When the free-energy gradient is to be computed, set {{TAG|LBLUEOUT}}=.TRUE.


=== Slow-growth approach ===
=== {{TAG|MDALGO|4}}: [[Nosé-Hoover chain thermostat]] ===
For a description of slow-growth approach see {{TAG|Slow-growth approach}}.
: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}}.  
* For a slow-growth simulation, one has to perform a calcualtion very similar to {{TAG|Constrained molecular dynamics}} but additionally the transformation velocity-related {{TAG|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|MDALGO}}=1, and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}
#Define geometric constraints in the {{FILE|ICONST}}-file, and set the STATUS parameter for the constrained coordinates to 0
#When the free-energy gradient is to be computed, set {{TAG|LBLUEOUT}}=.TRUE.


<ol start="5">
=== {{TAG|MDALGO|5}}: [[CSVR thermostat|Canonical sampling through velocity-rescaling (CSVR thermostat)]] ===
<li>Specify the transformation velocity-related {{TAG|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt>.</li>
{{NB|mind|This option is available as of VASP 6.4.3.|:}}
</ol>
:The [[CSVR thermostat]] can be used to sample an [[NVT ensemble]]. It requires setting {{TAG|CSVR_PERIOD}}.


=== Monitoring geometric parameters ===
=== {{TAG|MDALGO|13}}: Multiple [[Andersen thermostat|Andersen thermostats]] ===
Geometric parameters with <tt>STATUS = 7</tt> in the {{FILE|ICONST}}-file are monitored during the MD simulation.
<div id="multiAnderson"></div>
The corresponding values are written onto the {{FILE|REPORT}}-file, for each MD step, after the lines following the string <tt>Monit_coord</tt>.
: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}}.
 
Sometimes it is desirable to terminate the simulation if all values of monitored parameters get larger that some predefined upper and/or lower limits. These limits can be set by the user by means of the {{TAG|VALUE_MAX}} and {{TAG|VALUE_MIN}}-tags.
 
*To monitor geometric parameters during an MD run:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}.
#Set {{TAG|MDALGO}}=1, and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}.
#Define geometric constraints in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the constrained coordinates to 7.
#Optionally, set the upper and/or lower limits for the coordinates, by means of the {{TAG|VALUE_MAX}} and {{TAG|VALUE_MIN}}-tags, respectively.
 
=== Metadynamics ===
For a description of metadynamics see {{TAG|Metadynamics}}.
 
* For a metadynamics run with Andersen thermostat, one has to:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}.
#Set {{TAG|MDALGO}}=1 (or {{TAG|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}.
#Set the parameters {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, and {{TAG|HILLS_BIN}}.
#Define collective variables in the {{FILE|ICONST}}-file, and set the {{TAG|STATUS}} parameter for the collective variables to 5.
#If needed, define the bias potential in the {{FILE|PENALTYPOT}}-file.
 
The actual time-dependent bias potential is written to the {{FILE|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE|HILLSPOT}} to {{FILE|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.
 
=== Biased molecular dynamics ===
 
For a description of biased molecular dynamics see {{TAG|Biased molecular dynamics}}.
 
* For a biased molecular dynamics run with Andersen thermostat, one has to:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}.
#Set {{TAG|MDALGO}}=1 (or {{TAG|MDALGO}}=11 in VASP 5.x), and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}.
#In order to avoid updating of the bias potential, set {{TAG|HILLS_BIN}}={{TAG|NSW}}.
#Define collective variables in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5.
#Define the bias potential in the {{FILE|PENALTYPOT}}-file if necessary.
 
The values of all collective variables for each MD step are listed in the {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.
 
=== Special case: NVE ensemble ===
 
NVE ensemble calculations can be also run by selecting the Anderson thermostat and setting the update collision probability ({{TAG|ANDERSEN_PROB}}) to zero.
*To run an NVE ensemble:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}.
#Set {{TAG|MDALGO}}=1 and {{TAG|ANDERSEN_PROB}}=0.0.
 
== {{TAG|MDALGO}}=2: Nose-Hoover thermostat==
 
For the description of the Nose-Hoover thermostat see: {{TAG|Nose-Hoover thermostat}}.
 
The Nose-Hoover thermostat is currently only available for the NVT ensemble.
 
=== Standard molecular dynamics ===
 
* For a standard molecular dynamics run with Nose-Hoover thermostat, one has to:
#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}}.
 
=== 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:
#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}}.
#Define geometric constraints in the {{FILE|ICONST}}-file, and set the STATUS parameter for the constrained coordinates to 0.
#When the free-energy gradient is to be computed, set {{TAG|LBLUEOUT}}=.TRUE.
 
=== 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:
#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}}
#Define geometric constraints in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the constrained coordinates to 0
#When the free-energy gradient is to be computed, set {{TAG|LBLUEOUT}}=.TRUE.
<ol start="5">
<li>Specify the transformation velocity-related {{TAG|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt></li>
</ol>
 
=== Monitoring geometric parameters ===
Geometric parameters with <tt>STATUS = 7</tt> in the {{FILE|ICONST}}-file are monitored during the MD simulation.
The corresponding values are written onto the {{FILE|REPORT}}-file, for each MD step, after the lines following the string <tt>Monit_coord</tt>.
 
Sometimes it is desirable to terminate the simulation if all values of monitored parameters get larger that some predefined upper and/or lower limits. These limits can be set by the user by means of the {{TAG|VALUE_MAX}} and {{TAG|VALUE_MIN}}-tags.
 
To monitor geometric parameters during an MD run:
#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}}
#Define geometric constraints in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the constrained coordinates to 7
#Optionally, set the upper and/or lower limits for the coordinates, by means of the {{TAG|VALUE_MAX}} and {{TAG|VALUE_MIN}}-tags, respectively.
<div id="Langevin"></div>
 
== {{TAG|MDALGO}}=3: Langevin thermostat ==
 
For the description of the Langevin thermostat see: {{TAG|Langevin thermostat}}.
 
The Langevin thermostat is available for [[NVT ensemble|NVT]] and [[NpT ensemble|NpT]] ensembles.
 
=== ''NVT''-simulation with Langevin thermostat ===
 
*To run an ''NVT''-simulation with a Langevin thermostat, one has to:
{{Template:NVT_Langevin_thermostat_recipe}}
 
=== ''NpT''-simulation with Langevin thermostat ===
The Langevin dynamics in the isobari-isothermic ensemble is calculated by the method of Parrinello and Rahman{{cite|parrinello:prl:1980}}{{cite|parrinello:jap:1981}} (see {{TAG|NpT ensemble}} for more descriptions) combined with a {{TAG|Langevin thermostat}}.
 
*To run an NpT-simulation (Parinello-Rahman dynamics) with a Langevin thermostat, one has to:
{{Template:NpT_Langevin_thermostat_recipe}}
 
=== Stochastic boundary conditions ===
In some cases it is desirable to study approach of initially non-equilibrium system to equilibrium. Examples of such simulations include the impact problems when a particle with large kinetic energy hits a surface or calculation of friction force between two surfaces sliding with respect to each other. As shown by Toton ''et al.''<ref name="Toton10"/>, this type of problems can be studied using the stochastic boundary conditions (SBC) derived from the generalized Langevin equation by Kantorovich and Rompotis.<ref name="Kantorovich08"/> In this approach, the system of interest is divided into three regions: (a) fixed atoms, (b) the internal (Newtonian) atoms moving according to Newtonian dynamics, and (c) a buffer region of Langevin atoms (''i.e.'', atoms governed by [[#LangevinEOM|Langevin equations of motion]]) located between (a) and (b).
 
The role of the Langevin atoms is to dissipate heat, while the fixed atoms are needed solely to create the correct potential well for the Langevin atoms to move in. The Newtonian region should include all atoms relevant to the process under study: in the case of the impact problem, for instance, the Newtonian region should contain atoms of the molecule hitting the surface and several uppermost layers of the material forming the surface. Performing molecular dynamics with such a setup guarantees that the system (possibly out of equilibrium initially) arrives at the appropriate canonical distribution.
 
*To run a simulation with stochastic boundary conditions, one has to:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|ISIF}}=2
#Set {{TAG|MDALGO}}=3 to invoke the Langevin thermostat
#Prepare the {{FILE|POSCAR}} file in such a way that the Newtonian and Langevin atoms are treated as different species (even if they are chemically identical). In your {{FILE|POSCAR}}, use [[Selective Dynamics]] and the corresponding logical flags to define the frozen and moveable atoms.
#Specify friction coefficients &gamma;, for all species in the {{FILE|POSCAR}} file, by means of the {{TAG|LANGEVIN_GAMMA}}-tag: set the friction coefficients to 0 for all fixed and Newtonian atoms, and choose a proper &gamma; for the Langevin atoms.
 
==== Practical example ====


Consider a system consisting of 16 hydrogen and 48 silicon atoms. Suppose that eight silicon atoms are considered to be Langevin atoms and the remaining 32 Si atoms are either fixed or Newtonian atoms. The Langevin and Newtonian (or fixed) atoms should be considered as different species, ''i.e.'', the {{FILE|POSCAR}}-file should contain the line like this:
=== {{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 {{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).|:}}


Si H Si
=== {{TAG|MDALGO|11}} (deprecated) ===
40 16 8
:For VASP 5.x {{TAGDEF|MDALGO|11}} selects the [[Andersen thermostat]]. This is replaced by {{TAG|MDALGO|1}}.


As only the final eight Si atoms are considered to be Langevin atoms, the {{FILE|INCAR}}-file should contain the following line defining the friction coefficients:
=== {{TAG|MDALGO|21}} (deprecated) ===
:For VASP 5.x it selects the [[Nosé-Hoover thermostat]]. This is replaced by {{TAG|MDALGO|2}}.


LANGEVIN_GAMMA = 0.0  0.0  10.0
== Related tags and articles ==


''i.e.'', for all non-Langevin atoms, &gamma; should be set to zero.
:::{| cellpadding="5" cellspacing="5" style="width: 90%; border-spacing: 5px;"
| style="text-align:center; background-color:#DEC4EB;"| [[thermostats]] || style="text-align:center; background-color:#DEC4EB;"| related [[INCAR tag]]
|-
|style="background-color:#D9F8F5;"| [[Langevin thermostat|Langevin thermostat and dynamics]] ||style="background-color:#D9F8F5;"|  {{TAG|LANGEVIN_GAMMA}}, {{TAG|LANGEVIN_GAMMA_L}}, {{TAG|PMASS}}, {{TAG|PSTRESS}}
|-
|style="background-color:#D9F8F5;"| [[Andersen thermostat]] ||style="background-color:#D9F8F5;"| {{TAG|ANDERSEN_PROB}}
|-
|style="background-color:#D9F8F5;"| Multiple [[Andersen thermostat|Andersen thermostats]] ||style="background-color:#D9F8F5;"| {{TAG|NSUBSYS}}, {{TAG|TSUBSYS}}, {{TAG|PSUBSYS}}
|-
|style="background-color:#D9F8F5;"| [[Nosé-Hoover thermostat]]  ||style="background-color:#D9F8F5;"| {{TAG|SMASS}}
|-
|style="background-color:#D9F8F5;"| [[Nosé-Hoover chain thermostat]]  ||style="background-color:#D9F8F5;"| {{TAG|NHC_NCHAINS}}, {{TAG|NHC_PERIOD}}, {{TAG|NHC_NRESPA}}, {{TAG|NHC_NS}}
|-
|style="background-color:#D9F8F5;"| [[CSVR thermostat]]  ||style="background-color:#D9F8F5;"| {{TAG|CSVR_PERIOD}}
|}


== {{TAG|MDALGO}}=11: Biased-MD and metadynamics with Andersen thermostat ==
General MD-related tags: {{TAG|IBRION}}, {{TAG|NSW}}, {{TAG|POTIM}}, {{TAG| ISIF}}, {{TAG|RANDOM_SEED}}
=== Andersen thermostat ===
For a short description of the Andersen thermostat see [[#Andersen|its section]] under {{TAG|MDALGO}}=1.


<div id="Metadynamics"></div>
MD output: {{FILE|REPORT}}
=== Metadynamics ===
For a description of metadynamics see {{TAG|Metadynamics}}.


* For a metadynamics run with Andersen thermostat, one has to:
{{sc|MDALGO|Howto|Workflows that use this tag}}
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|MDALGO}}=11, and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}
#Set the parameters {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, and {{TAG|HILLS_BIN}}
#Define collective variables in the {{FILE|ICONST}}-file, and set the {{TAG|STATUS}} parameter for the collective variables to 5
#If needed, define the bias potential in the {{FILE|PENALTYPOT}}-file
 
The actual time-dependent bias potential is written to the {{FILE|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE|HILLSPOT}} to {{FILE|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.
 
=== Biased molecular dynamics ===
 
For a description of biased molecular dynamics see {{TAG|Biased molecular dynamics}}.
 
* For a biased molecular dynamics run with Andersen thermostat, one has to:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|MDALGO}}=11, and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}
#In order to avoid updating of the bias potential, set {{TAG|HILLS_BIN}}={{TAG|NSW}}
#Define collective variables in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5
#Define the bias potential in the {{FILE|PENALTYPOT}}-file
 
The values of all collective variables for each MD step are listed in the {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.
 
== {{TAG|MDALGO}}=21: Biased-MD and metadynamics with Nose-Hoover Thermostat ==
Biased-molecular- or {{TAG|Metadynamics}} with Nose-Hoover Thermostat ({{TAG|SMASS}} needs to be specified in the {{FILE|INCAR}} file).
 
=== Metadynamics ===
For a description of metadynamics see {{TAG|Metadynamics}}.
 
* For a metadynamics run with Nose-Hoover thermostat, one has to:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|MDALGO}}=21, and choose an appropriate setting for {{TAG|SMASS}}
#Set the parameters {{TAG|HILLS_H}}, {{TAG|HILLS_W}}, and {{TAG|HILLS_BIN}}
#Define collective variables in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5
#If needed, define the bias potential in the {{FILE|PENALTYPOT}}-file
 
The actual time-dependent bias potential is written to the {{FILE|HILLSPOT}}-file, which is updated after adding a new Gaussian. At the beginning of the simulation, VASP attempts to read the initial bias potential from the {{FILE|PENALTYPOT}}-file. For the continuation of a metadynamics run, copy {{FILE|HILLSPOT}} to {{FILE|PENALTYPOT}}. The values of all collective variables for each MD step are listed in {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.
 
=== 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:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|MDALGO}}=21, and choose an appropriate setting for {{TAG|SMASS}}
#In order to avoid updating of the bias potential, set {{TAG|HILLS_BIN}}={{TAG|NSW}}
#Define collective variables in the {{FILE|ICONST}}-file, and set the <tt>STATUS</tt> parameter for the collective variables to 5
#Define the bias potential in the {{FILE|PENALTYPOT}}-file
 
The values of all collective variables for each MD step are listed in the {{FILE|REPORT}}-file, check the lines after the string <tt>Metadynamics</tt>.
 
<div id="multiAnderson"></div>
 
== {{TAG|MDALGO}}=13: Multiple Anderson thermostats ==
Up to three user-defined atomic subsystems may be coupled with independent Andersen thermostats<ref name="Andersen80"/> (see remarks under {{TAG|MDALGO}}=1 as well).
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:
*{{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&le;{{TAG|PSUBSYS}}&le;1 are allowed.
 
== Related Tags and Sections ==
{{TAG|IBRION}},
{{TAG|ISIF}},
{{TAG|SMASS}},
{{TAG|ANDERSEN_PROB}},
{{TAG|RANDOM_SEED}},
{{TAG|LBLUEOUT}},
{{TAG|SHAKETOL}},
{{TAG|SHAKEMAXITER}},
{{TAG|HILLS_H}},
{{TAG|HILLS_W}},
{{TAG|HILLS_BIN}},
{{TAG|INCREM}},
{{TAG|VALUE_MIN}},
{{TAG|VALUE_MAX}},
{{TAG|LANGEVIN_GAMMA}},
{{TAG|LANGEVIN_GAMMA_L}},
{{TAG|PMASS}},
{{TAG|NSUBSYS}},
{{TAG|TSUBSYS}},
{{TAG|PSUBSYS}},
{{FILE|ICONST}},
{{FILE|PENALTYPOT}},
{{FILE|HILLSPOT}},
{{FILE|REPORT}}
 
{{sc|MDALGO|Examples|Examples that use this tag}}


== References ==
== References ==
<references>
<references>
<ref name="Andersen80">[http://dx.doi.org/10.1063/1.439486 H. C. Andersen, J. Chem. Phys. 72, 2384 (1980).]</ref>
<ref name="Toton10">[http://dx.doi.org/10.1088/0953-8984/22/7/074205 D. Toton, C. D. Lorenz, N. Rompotis, N. Martsinovich, and L. Kantorovich, J. Phys.: Condens. Matter 22, 074205 (2010).]</ref>
<ref name="Kantorovich08">[http://dx.doi.org/10.1103/PhysRevB.78.094305 L. Kantorovich and N. Rompotis, Phys. Rev. B 78, 094305 (2008).]</ref>
</references>
</references>
----


[[Category:INCAR]][[Category:Molecular Dynamics]][[Category:Howto]]
[[Category:INCAR tag]][[Category:Molecular dynamics]]

Latest revision as of 07:47, 24 October 2025

MDALGO = 0 | 1 | 2 | 3 | 4 | 5 | 11 | 21 | 13
Default: MDALGO = 0 

Description: Specifies the thermostat and lattice dynamics for molecular-dynamics calculations (in case IBRION = 0).

The algorithm for the thermostat and lattice dynamics is a crucial choise for any molecular-dynamics (MD) calculations (IBRION = 0). In combination with the selected lattice degrees of freedom (ISIF), MDALGO determines the ensemble that is sampled during the MD run. The main output file is the REPORT file.

MDALGO 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 ICONST file, biased molecular dynamics, and more.

Mind: MDALGO >= 0 requires compilation with the precompiler option -Dtbdyn. This option is present by default in all makefile.include templates since VASP 5.4.4.

Options

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 ANDERSEN_PROB. For an NVE ensemble, set ANDERSEN_PROB = 0.0. This is usually done after thermalization to a certain target temperature.
Tip: Leave the value for TEBEG that was set in the thermalization. For TEBEG < 0.1, some part of the code assumes it is used for structure optimization and not an MD run.

MDALGO = 2: Nosé-Hoover thermostat

The Nosé-Hoover thermostat is currently only available for the NVT ensemble. It requires setting an appropriate value for SMASS.
Tip: The Nosé-Hoover thermostat is a special case of the Nosé-Hoover chain thermostat (MDALGO = 4 with NHC_NCHAINS = 1 ). The control tags for MDALGO = 4 may be more convenient to use than the older implementation (MDALGO = 2).

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[1][2] combined with a Langevin thermostat.
  • NVT ensemble: Set an appropriate value for the friction coefficients (LANGEVIN_GAMMA) for all species in the POSCAR file to enables the Langevin thermostat. Fix the cell shape and volume with ISIF <= 2.
  • NpT ensemble: To enable lattice dynamics set ISIF = 3 and specify a separate set of friction coefficient for the lattice degrees-of-freedom (LANGEVIN_GAMMA_L) as well as a ficticious mass for the lattice degrees-of-freedom (PMASS). At the moment, dynamics with fixed volume+variable shape (ISIF = 4) or fixed shape+variable volume (ISIF = 7) are not available. Optionally, one may define an external pressure (PSTRESS). Like for the NVT ensemble, set an appropriate value for the friction coefficients (LANGEVIN_GAMMA) for all species in the POSCAR file to enables the Langevin thermostat.
Also see stochastic boundary conditions.

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 NHC_NCHAINS as well as choosing an appropriate setting for the thermostat parameter NHC_PERIOD.

MDALGO = 5: Canonical sampling through velocity-rescaling (CSVR thermostat)

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 CSVR_PERIOD.

MDALGO = 13: Multiple Andersen thermostats

Up to three user-defined atomic subsystems may be coupled with independent Andersen thermostats[3] (MDALGO = 1). The 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: NSUBSYS, TSUBSYS, and PSUBSYS.

MDALGO = 0 (deprecated)

Selects a Nosé-Hoover thermostat which allows sampling the NVT ensemble at temperature TEBEG. The Nosé-Hoover thermostat requires an appropriate setting for SMASS. To sample an NVE ensemble set SMASS = -3.
Deprecated: If possible, we recommend using one of the newer Nosé-Hoover thermostat implementations VASP provides (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).

MDALGO = 11 (deprecated)

For VASP 5.x MDALGO = 11  selects the Andersen thermostat. This is replaced by MDALGO = 1.

MDALGO = 21 (deprecated)

For VASP 5.x it selects the Nosé-Hoover thermostat. This is replaced by MDALGO = 2.

Related tags and articles

thermostats related INCAR tag
Langevin thermostat and dynamics LANGEVIN_GAMMA, LANGEVIN_GAMMA_L, PMASS, PSTRESS
Andersen thermostat ANDERSEN_PROB
Multiple Andersen thermostats NSUBSYS, TSUBSYS, PSUBSYS
Nosé-Hoover thermostat SMASS
Nosé-Hoover chain thermostat NHC_NCHAINS, NHC_PERIOD, NHC_NRESPA, NHC_NS
CSVR thermostat CSVR_PERIOD

General MD-related tags: IBRION, NSW, POTIM, ISIF, RANDOM_SEED

MD output: REPORT

Workflows that use this tag

References

  1. ↑ M. Parrinello and A. Rahman, Phys. Rev. Lett. 45, 1196 (1980).
  2. ↑ M. Parrinello and A. Rahman, J. Appl. Phys. 52, 7182 (1981).
  3. ↑ H. C. Andersen, J. Chem. Phys. 72, 2384 (1980).
Retrieved from "https://vasp.at/wiki/index.php?title=MDALGO&oldid=32807"