MD
This section defines the whole set of parameters needed perform an MD run. [Edit on GitHub]
Subsections
Keywords
Keyword descriptions
- ANGVEL_TOL
Type: real
Default: [au_t^-1*bohr]
Usage: ANGVEL_TOL 0.1Description: The maximum accepted angular velocity. This option is ignored when the system is periodic. Removes the components of the velocities that project on the external rotational degrees of freedom.
- ANGVEL_ZERO
Type: logical
Default: F
Lone keyword: T
Usage: ANGVEL_ZERO LOGICALDescription: Set the initial angular velocity to zero. This option is ignored when the system is periodic or when initial velocities are defined. Technically, the part of the random initial velocities that projects on the external rotational degrees of freedom is subtracted.
- ANNEALING
Type: real
Default: 1.00000000E+000
Usage: annealingDescription: Specifies the rescaling factor for annealing velocities. Automatically enables the annealing procedure. This scheme works only for ensembles that do not have thermostats on particles.
- ANNEALING_CELL
Type: real
Default: 1.00000000E+000
Usage: ANNEALING_CELLDescription: Specifies the rescaling factor for annealing velocities of the CELL Automatically enables the annealing procedure for the CELL. This scheme works only for ensambles that do not have thermostat on CELLS velocities.
- COMVEL_TOL
Type: real
Default: [au_t^-1*bohr]
Usage: COMVEL_TOL 0.1Description: The maximum accepted velocity of the center of mass. With Shell-Model, comvel may drift if MD%THERMOSTAT%REGION /= GLOBAL
Mentions: ⭐Molecular Dynamics
- DISPLACEMENT_TOL
Type: real
Default: 5.29177209E+001 [angstrom]
Usage: DISPLACEMENT_TOLDescription: This keyword sets a maximum atomic displacement in each Cartesian direction. The maximum velocity is evaluated and if it is too large to remain within the assigned limit, the time step is rescaled accordingly, and the first half step of the velocity verlet is repeated.
- ECONS_START_VAL
Type: real
Default: 0.00000000E+000 [hartree]
Usage: ECONS_START_VALDescription: The starting value of the conserved quantity
- ENSEMBLE
Type: enum
Default: NVE
Usage: ensemble nveDescription: The ensemble/integrator that you want to use for MD propagation
Valid values:
NVEconstant energy (microcanonical)NVTconstant temperature and volume (canonical)NPT_Iconstant temperature and pressure using an isotropic cellNPT_Fconstant temperature and pressure using a flexible cellMSSTsimulate steady shock (uniaxial)MSST_DAMPEDsimulate steady shock (uniaxial) with extra viscosityHYDROSTATICSHOCKsimulate steady shock with hydrostatic pressureISOKINconstant kinetic energyREFTRAJreading frames from a file called reftraj.xyz (e.g. for property calculation)LANGEVINlangevin dynamics (constant temperature)NPE_Fconstant pressure ensemble (no thermostat)NPE_Iconstant pressure ensemble using an isotropic cell (no thermostat)NVT_ADIABATICadiabatic dynamics in constant temperature and volume ensemble (CAFES)NPT_IANPT_I ensemble with frozen atoms in absolute coordinate
References: Evans1983, VandeVondele2002, Minary2003
Mentions: ⭐QM/MM with Built-in Force Field, ⭐Langevin Dynamics, ⭐Molecular Dynamics
- INITIALIZATION_METHOD
Type: enum
Default: DEFAULT
Usage: INITIALIZATION_METHOD DEFAULTDescription: This keyword selects which method to use to initialize MD. If velecities are not set explicitly, DEFAULT optioin will assign random velocities and then scale according to TEMPERATURE; VIBRATIONAL option will then use previously calculated vibrational modes to initialise both the atomic positions and velocities so that the starting point for MD is as close to canonical ensemble as possible, without the need for lengthy equilibration steps. See PRL 96, 115504 (2006). The user input atomic positions in this case are expected to be already geometry optimised. Further options for VIBRATIONAL mode is can be set in INITIAL_VIBRATION subsection. If unspecified, then the DEFAULT mode will be used.
Valid values:
DEFAULTAssign random velocities and then scale according to TEMPERATUREVIBRATIONALInitialise positions and velocities to give canonical ensemble with TEMPERATURE, using the method described in PRL 96, 115504 (2006)
Mentions: ⭐Molecular Dynamics
- MAX_STEPS
Type: integer
Default: 1000000000
Usage: MAX_STEPS 100Description: The number of MD steps to perform, counting from step 1
- SCALE_TEMP_KIND
Type: logical
Default: F
Lone keyword: T
Usage: SCALE_TEMP_KIND LOGICALDescription: When necessary rescale the temperature per each kind separately
- STEPS
Type: integer
Default: 3
Usage: STEPS 100Description: The number of MD steps to perform, counting from step_start_val.
Mentions: ⭐Real-Time Propagation and Ehrenfest MD
- STEP_START_VAL
Type: integer
Default: 0
Usage: STEP_START_VALDescription: The starting step value for the MD
- TEMPERATURE
Type: real
Default: 3.00000000E+002 [K]
Usage: TEMPERATURE 325.0Description: The temperature in K used to initialize the velocities with init and pos restart, and in the NPT/NVT simulations
Mentions: ⭐Langevin Dynamics, ⭐Molecular Dynamics
- TEMPERATURE_ANNEALING
Type: real
Default: 1.00000000E+000
Usage: TEMPERATURE_ANNEALINGDescription: Specifies the rescaling factor for the external temperature. This scheme works only for the Langevin ensemble.
- TEMP_KIND
Type: logical
Default: F
Lone keyword: T
Usage: TEMP_KIND LOGICALDescription: Compute the temperature per each kind separately
- TEMP_TOL
Type: real
Default: 0.00000000E+000 [K]
Aliases: TEMP_TO, TEMPERATURE_TOLERANCE
Usage: TEMP_TOL 0.0Description: The maximum accepted deviation of the (global) temperature from the desired target temperature before a rescaling of the velocities is performed. If it is 0 no rescaling is performed. NOTE: This keyword is obsolescent; Using a CSVR thermostat with a short timeconstant is recommended as a better alternative.
Mentions: ⭐Molecular Dynamics
- TIMESTEP
Type: real
Default: 5.00000000E-001 [fs]
Usage: TIMESTEP 1.0Description: The length of an integration step (in case RESPA the large TIMESTEP)
Mentions: ⭐Real-Time Bethe-Salpeter Propagation, ⭐X-Ray Absorption from RTP and \delta-Kick perturbation, ⭐QM/MM with Built-in Force Field, ⭐Real-Time Propagation and Ehrenfest MD, ⭐Molecular Dynamics
- TIME_START_VAL
Type: real
Default: 0.00000000E+000 [fs]
Usage: TIME_START_VALDescription: The starting timer value for the MD