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Release66:Gaussian Basis AIMD

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where <level of theory> is any Gaussian basis set method in NWChem
where <level of theory> is any Gaussian basis set method in NWChem
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QMD Keywords
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==QMD Keywords==
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dt_nucl -- Nuclear time step
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==dt_nucl -- Nuclear time step==
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This specifies the nuclear time step in atomic units (1 a.u. = 0.02419 fs). Default 10.0 a.u.
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This specifies the nuclear time step in atomic units (1 a.u. = 0.02419 fs). Default 10.0 a.u.
nsteps_nucl -- Simulation steps
nsteps_nucl -- Simulation steps

Revision as of 14:43, 23 September 2015

Overview


This module performs adiabatic ab initio molecular dynamics on finite systems. The nuclei are integrated using the velocity-Verlet algorithm, and the electronic potential can be provided by any of the Gaussian basis set based methods in NWChem, e.g. DFT, TDDFT, TCE, MP2, SCF, MCSCF, etc. If analytic gradients are not available for the selected level of theory, numerical gradients will automatically be used. Initial velocities are randomly selected from the Maxwell-Boltzmann distribution at the specified temperature, unless a restart file (.qmdrst) is present. If a restart file is present, the trajectory information will be read from that file and the trajectory will resume from that point.

For computational details and a case study using the module, please refer to the following paper: S. A. Fischer, T. W. Ueltschi, P. Z. El-Khoury, A. L. Mifflin, W. P. Hess, H.F. Wang, C. J. Cramer, N. Govind "Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The CH Region of DMSO as a Case Study" J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.5b03323 (2015) Publication Date (Web): July 29, 2015

QMD
  [dt_nucl <double default 10.0>]
  [nstep_nucl <integer default 1000>]
  [targ_temp <double default 298.15>]
  [thermostat <string default none> <thermostat parameters>]
  [rand_seed <integer default new one generated for each run>]
  [com_step <integer default 100>]
  [print_xyz <integer default 1>]
  [linear] <logical default false>
END

The module is called as:

task <level of theory> qmd

where <level of theory> is any Gaussian basis set method in NWChem

QMD Keywords

dt_nucl -- Nuclear time step

This specifies the nuclear time step in atomic units (1 a.u. = 0.02419 fs). Default 10.0 a.u.

nsteps_nucl -- Simulation steps

This specifies the number of steps to take in the nuclear dynamics. Default 1000

targ_temp -- Temperature of the system

This specifies the temperature to use with the thermostat. Also it is used in generating initial velocities from the Maxwell-Boltzmann distribution. Default 298.15 K

thermostat -- Thermostat for controling temperature of the simulation

This specifies the thermostat to use for regulating the temperature of the nuclei. Possible options are:
 none 
   No thermostat is used, i.e. an NVE ensemble is simulated. Default
 svr <double default 1000.0>
   Stochastic velocity rescaling thermostat of Bussi, Donadio, and Parrinello J. Chem. Phys. 126, 014101 (2007)
   Number sets the relaxation parameter of the thermostat
 langevin <double default 0.1>
   Langevin dynamics, implementation according to Bussi and Parrinello Phys. Rev. E 75, 056707 (2007)
   Number sets the value of the friction
 berendsen <double default 1000.0>
   Berendsen thermostat, number sets the relaxation parameter of the thermostat
 rescale
   Velocity rescaling, i.e. isokinetic ensemble

rand_seed -- Seed for the random number generator

This specifies the seed for initializing the random number generator. If not given, a unique random seed will be generated. Even without a thermostat, this will influence the initial velocities.

com_step -- How often center-of-mass translations and rotations are removed

This specifies that center-of-mass translations and rotations will be removed every com_step steps. Default 10
COM translations and rotations are removed on startup (either randomized initial velocities or those read from the restart file).

print_xyz -- How often to print trajectory information to xyz file

This specifies that the trajectory information (coordinates, velocities, total energy, step number, dipole (if available)) to the xyz file. The units for the coordinates and velocities in the xyz file are Angstrom and Angstrom/fs, respectively.

linear -- Flag for linear molecules

If present, the code assumes the molecule is linear.


Processing the output of a QMD run