Parrinello-Rahman Barostat¶

The Parrinello-Rahman scheme integrates the particle positions together with the cell matrix \(\mathbf{h}\), which evolves under the difference between the instantaneous stress and the target external pressure, with a fictitious cell mass. The temperature is controlled by an additional thermostat variable with its own fictitious mass. Individual components of \(\mathbf{h}\) can be frozen or tied together to impose isotropic, anisotropic or partially constrained deformations.

The scheme is enabled by including config_parrinellorahman.msp, which replaces the default numerical_scheme:

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######################################################################################################
######################## Default configuration for Parrinello-Rahman  ################################
######################################################################################################

numerical_scheme_parrinellorahman:
  - force_thermo_state                    # pressure (virial) needed at every step
  - simulation_thermodynamic_state
  - first_push_parrinellorahman: { dt_scale: 1.0 }
  - update_xform_parrinellorahman
  - nbh_dist
  - check_and_update_particles
  - zero_force_energy
  - compute_force
  - force_to_accel
  - convergence_push_parrinellorahman: { dt_scale: 1.0 }

numerical_scheme: numerical_scheme_parrinellorahman

The energies and the virial are computed at every step in this scheme (force_thermo_state), whatever the output frequencies.

init_parrinellorahman¶

Sets the targets and the fictitious masses. It must run once before the time loop, typically in init_prolog.

init_parrinellorahman:
  Text: <float>
  masseNVT: <float>
  Pext: <float>
  masseNPT: <float>
  hmask: <3x3 matrix>
  hblend: <3x3 matrix>

Text:      float, required                  # Target temperature.
masseNVT:  float, required                  # Fictitious mass of the thermostat variable.
Pext:      float, required                  # Target external pressure.
masseNPT:  float, required                  # Fictitious mass of the cell.
hmask:     3x3 matrix, default all ones     # Component-wise factors on the cell velocity and acceleration; a 0 freezes the corresponding component of h.
hblend:    3x3 matrix, default identity     # Blends the diagonal components of the cell velocity (e.g. rows of 1/3 for an isotropic deformation of x, y and z).

The other operators of the scheme are:

• first_push_parrinellorahman (dt_scale): first half of the position, velocity and cell update;
• update_xform_parrinellorahman (file, default "parrinello_rahman.dat"; force_append_thermo): applies the new cell matrix to the domain and writes the cell evolution to file;
• convergence_push_parrinellorahman (dt_scale, epsilon default 1.0e-6, max_iter default 100): second half of the update, solved iteratively until the change between two iterations is below epsilon (at most max_iter iterations).

includes:
  - config_parrinellorahman.msp

init_prolog:
  - deformation_xform:
      defbox: { extension: [ 1.0 , 1.0 , 1.0 ] }
  - init_parrinellorahman:
      Text: 300 K
      masseNVT: 1.0e-14 Da
      Pext: 1.013e5 kg*m^-1*s^-2
      masseNPT: 1.0e2 Da
      hmask: [ [ 1 , 0 , 0 ] , [ 0 , 1 , 0 ] , [ 0 , 0 , 1 ] ]
      hblend: [ [ 1/3 , 1/3 , 1/3 ] , [ 1/3 , 1/3 , 1/3 ] , [ 0 , 0 , 0 ] ]

Other examples (isotropic, anisotropic, in-plane) are available in exaStamp/data/regression_new/numerical_schemes/npt_parrinello_rahman/.