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MolecularDynamics

This page gives hints on how to perform a molecular dynamics calculation with the ABINIT package.

Introduction

Three molecular dynamics algorithm (Numerov, Verlet, Blanes and Moanes) allow to perform simulations in real (simulated) time, see ionmov. The displacement of atoms may be computed according to Newton’s law, or by adding a friction force to it. Nose-Hoover thermostat is available with Verlet algorithm. Langevin dynamics is also available.

Specified lattice parameters, or angles, or atomic positions, can be kept fixed if needed, see topic_GeoConstraints.

The trajectories can be analyzed thanks to the APPA postprocessor.

compulsory:

  • dtion Delta Time for IONs
  • ionmov IONic MOVEs
  • mdtemp Molecular Dynamics TEMPeratures

basic:

  • nnos Number of NOSe masses
  • ntime Number of TIME steps
  • qmass Q thermostat MASS
  • vel VELocity
  • vis VIScosity

useful:

  • friction internal FRICTION coefficient
  • nctime NetCdf TIME between output of molecular dynamics informations
  • noseinert NOSE thermostat INERTia factor
  • restartxf RESTART from (X,F) history

expert:

  • bmass Barostat MASS
  • delayperm DELAY between trials to PERMUTE atoms
  • densfor_pred DENSity and FORces PREDictor
  • diismemory Direct Inversion in the Iterative Subspace MEMORY
  • extrapwf flag - EXTRAPolation of the Wave-Functions
  • hmcsst Hybrid Monte Carlo Strain Step Trajectory
  • hmctt Hybrid Monte Carlo Trial Trajectory
  • mdwall Molecular Dynamics WALL location
  • signperm SIGN of PERMutation potential

Selected Input Files

fast:

mpiio:

paral:

v10:

v2:

v3:

v5:

v8:

Tutorials