MDALGO: Difference between revisions

Revision as of 17:03, 10 April 2014

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

Description: MDALGO specifies the molecular dynamics simulation protocol (in case IBRION=0 and VASP was compiled with -Dtbdyn).

MDALGO=0

Standard molecular dynamics (IBRION=0), the same behavior as if VASP were compiled without -Dtbdyn.

MDALGO=1

NVT-simulation with Andersen thermostat. In the approach proposed by Andersen^[1] the system is thermally coupled to a fictitious heat bath with the desired temperature. The coupling is represented by stochastic impulsive forces that act occasionally on randomly selected particles. The collision probability is defined as an average number of collisions per atom and time-step. This quantity can be controlled by the flag ANDERSEN_PROB. The total number of collisions with the heat-bath is written in the file REPORT for each MD step.

MDALGO=2

Nose-Hoover thermostat (SMASS needs to be specified in the INCAR file).

MDALGO=3

NVT- or NpT-simulation with Langevin thermostat.^[2]

The Langevin thermostat maintains the temperature through a modification of Newton's equations of motion

{\displaystyle \dot{r_i} = p_i/m_i \qquad \dot{p_i} = F_i - {\gamma}_i\,p_i + f_i, }

where F_i is the force acting on atom i due to the interaction potential, γ_i is a friction coefficient, and f_i is a random force with dispersion σ_i related to γ_i through:

{\displaystyle \sigma_i^2 = 2\,m_i\,{\gamma}_i\,k_B\,T/{\Delta}t }

with Δt 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 γ.

To run an NVT-simulation with Langevin thermostat, one has to:

Set the standard MD-related tags: IBRION=0, TEBEG, POTIM, and NSW
Set ISIF=2
Set MDALGO=3 to invoke the Langevin thermostat
Specify friction coefficients for all species in the POSCAR file, by means of the LANGEVIN_GAMMA-tag.

To run an NpT-simulation (Parinello-Rahman dynamics) with a Langevin thermostat, one has to:

Set the standard MD-related tags: IBRION=0, TEBEG, POTIM, and NSW
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.
Set MDALGO=3 to invoke the Langevin thermostat
Specify friction coefficients for all species in the POSCAR file, by means of the LANGEVIN_GAMMA-tag.
Specify a separate set of friction coefficient for the lattice degrees-of-freedom, using the LANGEVIN_GAMMA_L-tag.
Set a mass for the lattice degrees-of-freedom, using the PMASS-tag.
Optionally, one may define an external pressure (in kB), by means of the PSTRESS-tag.

The temperatures listed in the 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 OUTCAR file. This can be achieved, e.g. using the following command:


grep "Total+kin" OUTCAR| awk 'BEGIN {p=0.} {p+=($2+$3+$4)/3.} END {print "pressure (kB):",p}'

Important: In Parinello-Rahman^[3]^[4] dynamicsCite error: Closing </ref> missing for <ref> tag

^[2] ^[3] ^[4] </references>

Contents

↑ Cite error: Invalid <ref> tag; no text was provided for refs named Andersen80
↑ ^a ^b M. P. Allen and D. J. Tildesley, Computer simulation of liquids, Oxford university press: New York, 1991.
↑ ^a ^b M. Parinello and A. Rahman, Phys. Rev. Lett. 45, 1196 (1980).
↑ ^a ^b M. Parrinello and A. Rahman, J. Appl. Phys. 52, 7182 (1981).

[Andersen80-1] Cite error: Invalid <ref> tag; no text was provided for refs named Andersen80

[Allen91-2] M. P. Allen and D. J. Tildesley, Computer simulation of liquids, Oxford university press: New York, 1991.

[Parrinello80-3] M. Parinello and A. Rahman, Phys. Rev. Lett. 45, 1196 (1980).

[Parrinello81-4] M. Parrinello and A. Rahman, J. Appl. Phys. 52, 7182 (1981).

[1]

[2]

[3]

[4]

@@ Line 27: / Line 27: @@
 :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 Langevin dynamics, one has to:
+:*To run an ''NVT''-simulation with 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
@@ Line 33: / Line 33: @@
 :#Specify friction coefficients for all species in the {{FILE|POSCAR}} file, by means of the {{TAG|LANGEVIN_GAMMA}}-tag.
-:To run an ''NpT''-simulation with Langevin dynamics, one has to:
+:*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.
@@ Line 41: / Line 41: @@
 :#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<ref > (''NpT''), the stress tensor is used to define forces on lattice degrees-of-freedom (see Ref. [79,80] for details). In order to achieve a reasonable quality of sampling (or even to avoid numerical problems), it is essential to eliminate Pulay stress. Unfortunately, this usually requires rather large value of ENCUT. The setting with PREC=low (add the corresponding link) frequently used in NVT MD is not recommended for molecular dynamics with variable cell volume. For more details on the Pulay stress see 7.6.
 :'''Note:''' Geometric constraints and metadynamics are not available for Langevin dynamics.
@@ Line 90: / Line 97: @@
 <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. Parinello 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>
 </references>
 ----