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rpmd

Performs ab initio ring-polymer molecular dynamics simulation. This command can appear in the global context.

Subcommands

Options

all_quantized

Whether to treat all nuclei quantum mechanically as ring polymers.

  • The type is bool
  • The default is true
bead_positions_file_prefix

Specify common prefix of a series of .xyz files containing the customized ring-polymer positions. (# n_bead) positions files will be required in the the same directory as for the input file, e.g. if n_bead = 4, bead_positions_file_prefix = 'H-G42_bead' -> entos will try to find files H-G42_bead1.xyz, ..., H-G42_bead4.xyz to read positions. MUST be specified if "load_bead_positions" option is true.

  • The type is string
  • There is no default value.
bead_velocities_file_prefix

Specify common prefix of a series of .vel files containing the customized ring-polymer velocities info. (# n_bead) velocities files will be required in the the same directory as for the input file, e.g. if n_bead = 4, bead_velocities_file_prefix = 'H-G42_bead' -> entos will try to find files H-G42_bead1.vel, ..., H-G42_bead4.vel to read velocites. MUST be specified if "load_bead_velocities" option is true.

  • The type is string
  • There is no default value.
free_ring_polymer_cayley

Free ring-polymer evolution using Cayley transform of the exact exponential propagator.

  • The type is bool
  • The default is true
integrator

Specify the algorithm for integrating the equations of motion.

  • The type is string
  • The default is velocity verlet
  • The value must be one of:
load_bead_positions

Specify whether to use customized positions for all the ring-polymer beads to initialize a trajectory

  • The type is bool
  • The default is false
load_bead_velocities

Specify whether to use customized velocities for all the ring-polymer beads to initialize a trajectory

  • The type is bool
  • The default is false
n_beads

Number of ring-polymer beads.

  • The type is int
  • There is no default value.
  • The value must be positive
n_steps

Specify the number of integration steps.

This option is mandatory.

  • The type is int
  • There is no default value.
  • The value must be nonnegative
name

Specify the name of a set of results.

This option is deprecated.

  • The type is string
  • There is no default value.
output_coordinates

Specify name of the xyz file containing the coordinates from snapshots of the simulation.

  • The type is string
  • The default is coordinates
output_energies

Specify name of the txt file containing the energies from snapshots of the simulation.

  • The type is string
  • The default is energies
output_forces

Specify name of the xyz file containing the forces from snapshots of the simulation.

  • The type is string
  • The default is forces
output_metadynamics

Specify name of two metadynamics output files:

  1. with "_bias.txt" suffix, and contains collective variable and instantaneous biasing potential info,
  2. with "_free_energy.txt" suffix, and contains a series of free energy surface scans every every free_energy_scan_steps MD steps.

  • The type is string
  • The default is metadynamics
output_quantum_kinetic_energy

Specify name of the txt file containing the value of primitive kinetic energy estimator from snapshots of the simulation.

  • The type is string
  • The default is primitive_kinetic_energy
output_radius_of_gyration

Specify name of the txt file containing the information about radius of gyration of the ring polymers from snapshots of the simulation.

  • The type is string
  • The default is radius_of_gyration
output_restraint

Specify name of the xyz file containing the restraint potential and forces from snapshots of the simulation.

  • The type is string
  • The default is restraints
output_steps

Number of steps that elapse between outputting simulation information, which includes energies, coordinates, velocities, and forces, etc.

  • The type is int
  • The default is 1
  • The value must be positive
output_velocities

Specify name of the xyz file containing the velocities from snapshots of the simulation.

  • The type is string
  • The default is velocities
print_level

Print level.

  • The type is int
  • There is no default value.
  • The value must be one of:
    • -2 - No output
    • -1 - Minimum output
    • 0 - Output that doesn't scale with system size
    • 1 - Output that scales linearly with system size
    • 2 - (Debugging) output that scales quadratically with system size
    • 3 - (Debugging) output that scales cubically with system size
quantized_nuclei

Specify the indices of nuclei that will be treated as ring polymers.

  • The type is [int]
  • There is no default value.
rng_seed

Seed used to initialize a pseudo-random number generator. By default, rng_seed is set to -1, which uses a pseudo random seed.

  • The type is int
  • The default is -1
save_steps

Whether to save the steps to the results.

If true, output_steps controls the number of steps that elapse between saving a step. The step information contains: energies, coordinates, velocities, and forces.

  • The type is bool
  • The default is false
save_to_file

Whether to write the simulation results to files.

  • The type is bool
  • The default is false
temperature

Specify the temperature for sampling the ring-polmer beads.

  • The type is quantity
  • The default is 300 kelvin
  • The value must be nonnegative
time_step

Specify the time step for integration.

  • The type is quantity
  • The default is 1.0 fs
  • The value must be positive