Molecular Dynamics

NVT

A minimal example configuration file for an NVT simulation using janus md is:

arch: mace_mp

ensemble: nvt
struct: "tests/data/NaCl.cif"

An example configuration file with all parameters set for an NVT simulation using janus md is:

arch: mace_mp
device: cpu
model: "tests/models/mace_mp_small.model"
calc_kwargs:
  dispersion: True

ensemble: nvt
struct: "tests/data/NaCl.cif"
steps: 100
timestep: 0.1
temp: 100
equil_steps: 100
minimize: True
minimize_every: 50
minimize_kwargs:
  opt_kwargs:
    maxstep: 0.1
rescale_velocities: True
remove_rot: True
rescale_every: 50

post_process_kwargs:
  rdf_compute: True
correlation_kwargs:
  vaf:
    a: Velocity
    points: 250
  saf:
    a: Stress
    a_kwargs: {'components': ['xy', 'yz', 'zx']}
    points: 250
plumed_input: null
plumed_log: null

friction: 0.005
ensemble_kwargs:
  fixcm: False

temp_start: 0
temp_end: 100
temp_step: 10
temp_time: 1

restart: False
restart_auto: True
restart_stem: nvt-restart
restart_every: 1000
rotate_restart: True
restarts_to_keep: 2

final_file: nvt-final.extxyz
stats_file: nvt-stats.dat
stats_every: 100
traj_file: nvt-traj.extxyz
traj_append: False
traj_start: 10
traj_every: 100

file_prefix: NaCl
read_kwargs:
  index: "0"
write_kwargs:
  invalidate_calc: True

log: nvt-log.yml
summary: nvt-summary.yml
tracker: False
progress_bar: True
update_progress_every: 10

NPT

A minimal example configuration file for an NPT simulation using janus md is:

arch: mace_mp

ensemble: npt
struct: "tests/data/NaCl.cif"

An example configuration file with all parameters set for an NPT simulation using janus md is:

arch: mace_mp
device: cpu
model: "tests/models/mace_mp_small.model"
calc_kwargs:
  dispersion: True

ensemble: npt
struct: "tests/data/NaCl.cif"
steps: 100
timestep: 0.1
temp: 100
equil_steps: 100
minimize: True
minimize_every: 50
minimize_kwargs:
  filter_class: null
rescale_velocities: True
remove_rot: True
rescale_every: 50

post_process_kwargs:
  rdf_compute: True
correlation_kwargs:
  vaf:
    a: Velocity
    points: 250
  saf:
    a: Stress
    a_kwargs: {'components': ['xy', 'yz', 'zx']}
    points: 250
plumed_input: null
plumed_log: null

thermostat_time: 50
barostat_time: 75
bulk_modulus: 1
pressure: 1
ensemble_kwargs:
  mask: [0, 1, 0]

temp_start: 0
temp_end: 100
temp_step: 10
temp_time: 1

restart: False
restart_auto: True
restart_stem: npt-restart
restart_every: 1000
rotate_restart: True
restarts_to_keep: 2

final_file: npt-final.extxyz
stats_file: npt-stats.dat
stats_every: 100
traj_file: npt-traj.extxyz
traj_append: False
traj_start: 10
traj_every: 100

file_prefix: NaCl
read_kwargs:
  index: "0"
write_kwargs:
  invalidate_calc: True

log: npt-log.yml
summary: npt-summary.yml
tracker: False
progress_bar: True
update_progress_every: 10

NVE

A minimal example configuration file for an NVE simulation using janus md is:

arch: mace_mp

ensemble: nve
struct: "tests/data/NaCl.cif"

An example configuration file with all parameters set for an NVE simulation using janus md is:

arch: mace_mp
device: cpu
model: "tests/models/mace_mp_small.model"
calc_kwargs:
  dispersion: True

ensemble: nve
struct: "tests/data/NaCl.cif"
steps: 100
timestep: 0.1
temp: 100
equil_steps: 100
minimize: True
minimize_every: 50
minimize_kwargs:
  opt_kwargs:
    maxstep: 0.1
rescale_velocities: True
remove_rot: True
rescale_every: 50

post_process_kwargs:
  rdf_compute: True
correlation_kwargs:
  vaf:
    a: Velocity
    points: 250
  saf:
    a: Stress
    a_kwargs: {'components': ['xy', 'yz', 'zx']}
    points: 250
plumed_input: null
plumed_log: null

restart: False
restart_auto: True
restart_stem: nve-restart
restart_every: 1000
rotate_restart: True
restarts_to_keep: 2

final_file: nve-final.extxyz
stats_file: nve-stats.dat
stats_every: 100
traj_file: nve-traj.extxyz
traj_append: False
traj_start: 10
traj_every: 100

file_prefix: NaCl
read_kwargs:
  index: "0"
write_kwargs:
  invalidate_calc: True

log: nve-log.yml
summary: nve-summary.yml
tracker: False
progress_bar: True
update_progress_every: 10

NPH

A minimal example configuration file for an NPH simulation using janus md is:

arch: mace_mp

ensemble: nph
struct: "tests/data/NaCl.cif"

An example configuration file with all parameters set for an NPH simulation using janus md is:

arch: mace_mp
device: cpu
model: "tests/models/mace_mp_small.model"
calc_kwargs:
  dispersion: True

ensemble: nph
struct: "tests/data/NaCl.cif"
steps: 100
timestep: 0.1
temp: 100
equil_steps: 100
minimize: True
minimize_every: 50
minimize_kwargs:
  filter_class: null
rescale_velocities: True
remove_rot: True
rescale_every: 50

post_process_kwargs:
  rdf_compute: True
correlation_kwargs:
  vaf:
    a: Velocity
    points: 250
  saf:
    a: Stress
    a_kwargs: {'components': ['xy', 'yz', 'zx']}
    points: 250
plumed_input: null
plumed_log: null

barostat_time: 75
bulk_modulus: 1
pressure: 1
ensemble_kwargs:
  mask: [0, 1, 0]

restart: False
restart_auto: True
restart_stem: nph-restart
restart_every: 1000
rotate_restart: True
restarts_to_keep: 2

final_file: nph-final.extxyz
stats_file: nph-stats.dat
stats_every: 100
traj_file: nph-traj.extxyz
traj_append: False
traj_start: 10
traj_every: 100

file_prefix: NaCl
read_kwargs:
  index: "0"
write_kwargs:
  invalidate_calc: True

log: nph-log.yml
summary: nph-summary.yml
tracker: False
progress_bar: True
update_progress_every: 10

NVT NH

A minimal example configuration file for an NVT NH simulation using janus md is:

arch: mace_mp

ensemble: nvt-nh
struct: "tests/data/NaCl.cif"

An example configuration file with all parameters set for an NVT NH simulation using janus md is:

arch: mace_mp
device: cpu
model: "tests/models/mace_mp_small.model"
calc_kwargs:
  dispersion: True

ensemble: nvt-nh
struct: "tests/data/NaCl.cif"
steps: 100
timestep: 0.1
temp: 100
equil_steps: 100
minimize: True
minimize_every: 50
minimize_kwargs:
  filter_class: null
rescale_velocities: True
remove_rot: True
rescale_every: 50

post_process_kwargs:
  rdf_compute: True
correlation_kwargs:
  vaf:
    a: Velocity
    points: 250
  saf:
    a: Stress
    a_kwargs: {'components': ['xy', 'yz', 'zx']}
    points: 250
plumed_input: null
plumed_log: null

thermostat_time: 50
ensemble_kwargs:
  mask: [0, 1, 0]

temp_start: 0
temp_end: 100
temp_step: 10
temp_time: 1

restart: False
restart_auto: True
restart_stem: nvt-nh-restart
restart_every: 1000
rotate_restart: True
restarts_to_keep: 2

final_file: nvt-nh-final.extxyz
stats_file: nvt-nh-stats.dat
stats_every: 100
traj_file: nvt-nh-traj.extxyz
traj_append: False
traj_start: 10
traj_every: 100

file_prefix: NaCl
read_kwargs:
  index: "0"
write_kwargs:
  invalidate_calc: True

log: nvt-nh-log.yml
summary: nvt-nh-summary.yml
tracker: False
progress_bar: True
update_progress_every: 10

NVT CSVR

A minimal example configuration file for an NVT CSVR simulation using janus md is:

arch: mace_mp

ensemble: nvt-csvr
struct: "tests/data/NaCl.cif"

An example configuration file with all parameters set for an NVT CSVR simulation using janus md is:

arch: mace_mp
device: cpu
model: "tests/models/mace_mp_small.model"
calc_kwargs:
  dispersion: True

ensemble: nvt-csvr
struct: "tests/data/NaCl.cif"
steps: 100
timestep: 0.1
temp: 100
equil_steps: 100
minimize: True
minimize_every: 50
minimize_kwargs:
  opt_kwargs:
    maxstep: 0.1
rescale_velocities: True
remove_rot: True
rescale_every: 50

post_process_kwargs:
  rdf_compute: True
correlation_kwargs:
  vaf:
    a: Velocity
    points: 250
  saf:
    a: Stress
    a_kwargs: {'components': ['xy', 'yz', 'zx']}
    points: 250
plumed_input: null
plumed_log: null

taut: 1000

temp_start: 0
temp_end: 100
temp_step: 10
temp_time: 1

restart: False
restart_auto: True
restart_stem: nvt-csvr-restart
restart_every: 1000
rotate_restart: True
restarts_to_keep: 2

final_file: nvt-csvr-final.extxyz
stats_file: nvt-csvr-stats.dat
stats_every: 100
traj_file: nvt-csvr-traj.extxyz
traj_append: False
traj_start: 10
traj_every: 100

file_prefix: NaCl
read_kwargs:
  index: "0"
write_kwargs:
  invalidate_calc: True

log: nvt-csvr-log.yml
summary: nvt-csvr-summary.yml
tracker: False
progress_bar: True
update_progress_every: 10

NPT MTK

A minimal example configuration file for an NPT MTK simulation using janus md is:

arch: mace_mp

ensemble: npt-mtk
struct: "tests/data/NaCl.cif"

An example configuration file with all parameters set for an NPT MTK simulation using janus md is:

arch: mace_mp
device: cpu
model: "tests/models/mace_mp_small.model"
calc_kwargs:
  dispersion: True

ensemble: npt-mtk
struct: "tests/data/NaCl.cif"
steps: 100
timestep: 0.1
temp: 100
equil_steps: 100
minimize: True
minimize_every: 50
minimize_kwargs:
  opt_kwargs:
    maxstep: 0.1
rescale_velocities: True
remove_rot: True
rescale_every: 50

post_process_kwargs:
  rdf_compute: True
correlation_kwargs:
  vaf:
    a: Velocity
    points: 250
  saf:
    a: Stress
    a_kwargs: {'components': ['xy', 'yz', 'zx']}
    points: 250
plumed_input: null
plumed_log: null

pressure: 1
thermostat_time: 100
barostat_time: 1000
thermostat_chain: 3
barostat_chain: 3
thermostat_substeps: 1
barostat_substeps: 1

temp_start: 0
temp_end: 100
temp_step: 10
temp_time: 1

restart: False
restart_auto: True
restart_stem: npt-mtk-restart
restart_every: 1000
rotate_restart: True
restarts_to_keep: 2

final_file: npt-mtk-final.extxyz
stats_file: npt-mtk-stats.dat
stats_every: 100
traj_file: npt-mtk-traj.extxyz
traj_append: False
traj_start: 10
traj_every: 100

file_prefix: NaCl
read_kwargs:
  index: "0"
write_kwargs:
  invalidate_calc: True

log: npt-mtk-log.yml
summary: npt-mtk-summary.yml
tracker: False
progress_bar: True
update_progress_every: 10