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{{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 for [[MD calculations]] (in case {{TAGO|IBRION|0}}).
----
----
{{NB|mind|All options except {{TAGO|MDALGO|0}} require a {{VASP}} executable which was compiled with the [[Precompiler options#-Dtbdyn|<code>-Dtbdyn</code>]] precompiler option enabled. This is usually the case because the option is present by default in all shipped [[makefile.include]] templates since {{VASP}} 5.4.4.}}
{{TAG|MDALGO}}=1,2,3,4,5 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]]


== {{TAG|MDALGO}}=0: Standard molecular dynamics ==
The main output file is the {{FILE|REPORT}} file.
Standard molecular dynamics ({{TAG|IBRION}}=0), the same behavior as if VASP were compiled without [[Precompiler_flags|-Dtbdyn]].


== {{TAG|MDALGO}}=1: Andersen thermostat ==
== {{TAGDEF|MDALGO|0}}: Standard molecular dynamics ==
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).}}


For the description of the Andersen thermostat see: {{TAG|Andersen thermostat}}.
== {{TAGDEF|MDALGO|1}}: [[Andersen thermostat]] ==


The Andersen thermostat is only available for the NVT case.
The [[Andersen thermostat]] can be used to sample an [[NVT ensemble]], which requires setting an appropriate value for {{TAG|ANDERSEN_PROB}}.  


=== Standard molecular dynamics in ===
For {{TAGDEF|ANDERSEN_PROB|0.0}}, the thermostat is inactive, such that the [[NVE ensemble]] is sampled. 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 {{TAGDEF|TEBEG|<0.1}}, some part of the code assumes it is used for [[structure optimization]] and not an [[molecular-dynamics calculations|MD run]].}}


*For a standard molecular dynamics run with Anderson thermostat, one has to:
== {{TAGDEF|MDALGO|2}}: [[Nosé-Hoover 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 [[Nosé-Hoover thermostat]] is currently only available for the [[NVT ensemble]]. It requires setting an appropriate value for {{TAG|SMASS}}.
For a description of constrained molecular dynamics see {{TAG|Constrained molecular dynamics}}.
{{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}}).}}


* For a constrained molecular dynamics run with Andersen thermostat, one has to:
== {{TAGDEF|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}}
#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 ===
The [[Langevin thermostat]] is available for sampling an [[NVT ensemble]] as well as sampling an [[NpT ensemble]].
For a description of slow-growth approach see {{TAG|Slow-growth approach}}.
* For an [[NVT ensemble]], fix the cell shape and volume with {{TAGDEF|ISIF|2}} and set an appropriate value for the friction coefficients for all species in the {{FILE|POSCAR}} file by means of the {{TAG|LANGEVIN_GAMMA}} tag.
* 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:
* 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]].
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAGDEF|ISIF|3}} to allow for relaxation of the cell volume and shape. At the moment, dynamics with ''fixed volume+variable shape'' ({{TAG|ISIF}}=4) or ''fixed shape+variable volume'' ({{TAG|ISIF}}=7) are not available.
#Set {{TAG|MDALGO}}=1, and choose an appropriate setting for {{TAG|ANDERSEN_PROB}}
#Specify friction coefficients for all species in the {{FILE|POSCAR}} file by means of the {{TAG|LANGEVIN_GAMMA}} tag.
#Define geometric constraints in the {{FILE|ICONST}}-file, and set the STATUS parameter for the constrained coordinates to 0
#Specify a separate set of friction coefficient for the lattice degrees-of-freedom using the {{TAG|LANGEVIN_GAMMA_L}} tag.
#When the free-energy gradient is to be computed, set {{TAG|LBLUEOUT}}=.TRUE.
#Set a mass for the lattice degrees-of-freedom using the {{TAG|PMASS}} tag.
#Optionally, one may define an external pressure (in kB) by means of the {{TAG|PSTRESS}} tag.


<ol start="5">
Also see [[stochastic boundary conditions]].
<li>Specify the transformation velocity-related {{TAG|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt>.</li>
</ol>


=== Monitoring geometric parameters ===
== {{TAGDEF|MDALGO|4}}: [[Nosé-Hoover chain thermostat]] ==
Geometric parameters with <tt>STATUS = 7</tt> in the {{FILE|ICONST}}-file are monitored during the MD simulation.
The [[Nosé-Hoover chain thermostat]] can be 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 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.
== {{TAG|MDALGO}}=5: [[CSVR thermostat|Canonical sampling through velocity-rescaling (CSVR thermostat)]] ==
{{NB|mind|This option is available as of VASP 6.4.3.}}


*To monitor geometric parameters during an MD run:
The [[CSVR thermostat]] can be used to sample an [[NVT ensemble]]. It requires setting {{TAG|CSVR_PERIOD}}.
#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.
 
=== 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 ==
'''Note:''' Geometric constraints and metadynamics are not available for Langevin dynamics.
 
=== ''NVT''-simulation with Langevin thermostat ===
<span id="LangevinEOM">
The Langevin thermostat<ref name="Allen91"/> maintains the temperature through a modification of Newton's equations of motion
:<math>
\dot{r_i} = p_i/m_i \qquad
\dot{p_i} = F_i - {\gamma}_i\,p_i + f_i,
</math>
</span>
where ''F<sub>i</sub>'' is the force acting on atom ''i'' due to the interaction potential, &gamma;<sub>i</sub> is a friction coefficient, and ''f<sub>i</sub>'' is a random force with dispersion &sigma;<sub>i</sub> related to &gamma;<sub>i</sub> through:
:<math>
\sigma_i^2 = 2\,m_i\,{\gamma}_i\,k_B\,T/{\Delta}t
</math>
with &Delta;''t'' being the time-step used in the MD to integrate the equations of motion. Obviously, Langevin dynamics is identical to the classical Hamiltonian in the limit of vanishing &gamma;.
 
*To run an ''NVT''-simulation with a Langevin thermostat, 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
#Specify friction coefficients for all species in the {{FILE|POSCAR}} file, by means of the {{TAG|LANGEVIN_GAMMA}}-tag.
 
<div id="ParrinelloRahman"></div>
=== ''NpT''-simulation with Langevin thermostat ===
 
In the method of Parrinello and Rahman<ref name="Parrinello80"/><ref name="Parrinello81"/>, the equations of motion for ionic and lattice degrees-of-freedom are derived from the following Lagrangian:
:<math>
{\mathcal{L}}(s,h,\dot{s},\dot{h})=\frac{1}{2}\sum_i^N m_i \dot{s_i}^t\,G \dot{s_i}-V(s,h) +\frac{1}{2}W\,\mathrm{Tr}(\dot{h}^t \dot{h}) - p_\mathrm{ext}\Omega,
</math>
where ''s<sub>i</sub>'' is a position vector in fractional coordinates for atom ''i'', ''h'' is the matrix formed by lattice vectors, the tensor ''G'' is defined as ''G''=''h''<sup>t</sup>''h'', ''p''<sub>ext</sub> is the external pressure, &Omega; is the cell volume (&Omega;=det ''h''), and ''W'' is a constant with the dimensionality of mass. Integrating equations of motion based on the Parrinello-Rahman Lagrangian generates an ''NpH'' ensemble, where the enthalpy <math>H=E+p_\mathrm{ext}\Omega</math> is the constant of motion. The Parrinello-Rahman method can be combined with a Langevin thermostat<ref name="Allen91"/> to generate an ''NpT''-ensemble.
 
*To run an ''NpT''-simulation (Parinello-Rahman dynamics) with a Langevin thermostat, one has to:
#Set the standard MD-related tags: {{TAG|IBRION}}=0, {{TAG|TEBEG}}, {{TAG|POTIM}}, and {{TAG|NSW}}
#Set {{TAG|ISIF}}=3 to allow for relaxation of the cell volume and shape. At the moment, dynamics with ''fixed volume+variable shape'' ({{TAG|ISIF}}=4) or ''fixed shape+variable volume'' ({{TAG|ISIF}}=7) are not available.
#Set {{TAG|MDALGO}}=3 to invoke the Langevin thermostat
#Specify friction coefficients for all species in the {{FILE|POSCAR}} file, by means of the {{TAG|LANGEVIN_GAMMA}}-tag.
#Specify a separate set of friction coefficient for the lattice degrees-of-freedom, using the {{TAG|LANGEVIN_GAMMA_L}}-tag.
#Set a mass for the lattice degrees-of-freedom, using the {{TAG|PMASS}}-tag.
#Optionally, one may define an external pressure (in kB), by means of the {{TAG|PSTRESS}}-tag.
 
The temperatures listed in the {{FILE|OSZICAR}} are computed using the kinetic energy including contribution from both atomic and lattice degrees of freedom. The external pressure for a simulation can be computed as one third of the trace of the stress-tensor corrected for kinetic contributions, listed in the {{FILE|OUTCAR}} file. This can be achieved, ''e.g.'' using the following command:
<code lang="text">
grep "Total+kin" OUTCAR| awk 'BEGIN {p=0.} {p+=($2+$3+$4)/3.} END {print "pressure (kB):",p}'
</code>
 
Important: In Parinello-Rahman<ref name="Parrinello80"/><ref name="Parrinello81"/> dynamics (''NpT''), the stress tensor is used to define forces on lattice degrees-of-freedom. In order to achieve a reasonable quality of sampling (and to avoid numerical problems), it is essential to eliminate [[Energy_vs_volume_Volume_relaxations_and Pulay_stress|Pulay stress]]. Unfortunately, this usually requires a rather large value of {{TAG|ENCUT}}. {{TAG|PREC}}=low, frequently used in ''NVT''-MD is not recommended for molecular dynamics with variable cell volume.
 
=== 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:
 
Si H Si
40 16 8
 
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:
 
LANGEVIN_GAMMA = 0.0  0.0  10.0
 
''i.e.'', for all non-Langevin atoms, &gamma; should be set to zero.
 
== {{TAG|MDALGO}}=11: Biased-MD and metadynamics with Andersen thermostat ==
=== Andersen thermostat ===
For a short description of the Andersen thermostat see [[#Andersen|its section]] under {{TAG|MDALGO}}=1.
 
<div id="Metadynamics"></div>
=== 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}}=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>.


== {{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).
== {{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:  
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]  
*{{TAG|NSUBSYS}}=[int array]  
Line 254: Line 65:
:Collision probability for atoms in each subsystem. Only the values 0&le;{{TAG|PSUBSYS}}&le;1 are allowed.
:Collision probability for atoms in each subsystem. Only the values 0&le;{{TAG|PSUBSYS}}&le;1 are allowed.


== Related Tags and Sections ==
== Related tags and articles ==
{{TAG|IBRION}},
{{TAG|IBRION}},
{{TAG|ISIF}},
{{TAG|ISIF}},
Line 285: Line 96:
<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="Andersen80">[http://dx.doi.org/10.1063/1.439486 H. C. Andersen, J. Chem. Phys. 72, 2384 (1980).]</ref>
<ref name="Allen91">M. P. Allen and D. J. Tildesley, ''Computer simulation of liquids'', Oxford university press: New York, 1991.</ref>
<ref name="Parrinello80">[http://dx.doi.org/10.1103/PhysRevLett.45.1196 M. Parrinello and A. Rahman, Phys. Rev. Lett. 45, 1196 (1980).]</ref>
<ref name="Parrinello81">[http://dx.doi.org/10.1063/1.328693 M. Parrinello and A. Rahman, J. Appl. Phys. 52, 7182 (1981).]</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]][[Category:Advanced molecular-dynamics sampling]][[Category:Howto]]

Latest revision as of 13:46, 21 October 2025

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

Description: Specifies the thermostat for MD calculations (in case IBRION = 0).

Mind: All options except MDALGO = 0 require a VASP executable which was compiled with the -Dtbdyn precompiler option enabled. This is usually the case because the option is present by default in all shipped makefile.include templates since VASP 5.4.4.

MDALGO=1,2,3,4,5 can be applied in the context of

The main output file is the REPORT file.

MDALGO = 0 : Standard molecular dynamics

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 = 1 : Andersen thermostat

The Andersen thermostat can be used to sample an NVT ensemble, which requires setting an appropriate value for ANDERSEN_PROB.

For ANDERSEN_PROB = 0.0 , the thermostat is inactive, such that the NVE ensemble is sampled. 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 an NVT ensemble as well as sampling an NpT ensemble.

  1. Set ISIF = 3  to allow for relaxation of the cell volume and shape. At the moment, dynamics with fixed volume+variable shape (ISIF=4) or fixed shape+variable volume (ISIF=7) are not available.
  2. Specify friction coefficients for all species in the POSCAR file by means of the LANGEVIN_GAMMA tag.
  3. Specify a separate set of friction coefficient for the lattice degrees-of-freedom using the LANGEVIN_GAMMA_L tag.
  4. Set a mass for the lattice degrees-of-freedom using the PMASS tag.
  5. Optionally, one may define an external pressure (in kB) by means of the PSTRESS tag.

Also see stochastic boundary conditions.

MDALGO = 4 : Nosé-Hoover chain thermostat

The Nosé-Hoover chain thermostat can be 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] (see remarks under MDALGO=1 as well). 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 flags must be set by the user:

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 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, NSUBSYS should be defined as follows:
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.
Simulation temperature for each subsystem
Collision probability for atoms in each subsystem. Only the values 0≤PSUBSYS≤1 are allowed.

Related tags and articles

IBRION, ISIF, SMASS, ANDERSEN_PROB, RANDOM_SEED, LBLUEOUT, SHAKETOL, SHAKEMAXITER, HILLS_H, HILLS_W, HILLS_BIN, INCREM, VALUE_MIN, VALUE_MAX, LANGEVIN_GAMMA, LANGEVIN_GAMMA_L, PMASS, NSUBSYS, TSUBSYS, PSUBSYS, ICONST, PENALTYPOT, HILLSPOT, REPORT

Examples 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).
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