Command line interface

DPTI: An Automatic Workflow Software for Thermodynamic Integration Calculations

usage: dpti [-h] {equi,hti,hti_liq,hti_ice,hti_water,ti,ti_water,gdi,mti} ...

modules

the subcommands of dpti

module

Possible choices: equi, hti, hti_liq, hti_ice, hti_water, ti, ti_water, gdi, mti

module-level help

Sub-commands

equi

equilibration simulations

dpti equi [-h] {gen,extract,stat-bond,compute,run} ...

Positional Arguments

command

Possible choices: gen, extract, stat-bond, compute, run

commands for equilibration simulations

Sub-commands

gen

generate a job

dpti equi gen [-h] [-e ENSEMBLE] [-t TEMPERATURE] [-p PRESSURE] [-a]
              [-c CONF_NPT] [-o OUTPUT]
              PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-e, --ensemble

the ensemble of the simulation

-t, --temperature

the temperature of the system

-p, --pressure

the pressure of the system

-a, --avg-posi

dump the average position of atoms

Default: False

-c, --conf-npt

use conf computed from NPT simulation

-o, --output

the output folder for the job

Default: “new_job”

extract

extract the conf

dpti equi extract [-h] [-o OUTPUT] JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-o, --output

output conf file name

Default: “conf.lmp”

stat-bond

Statistic of the bonds

dpti equi stat-bond [-h] [-s SKIP] JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-s, --skip

skip this number of frames

Default: 1

compute

Compute thermodynamics

dpti equi compute [-h] JOB

Positional Arguments

JOB: folder of the job

run

run the job

dpti equi run [-h] JOB machine

Positional Arguments

JOB: folder of the job
machine: machine.json file for the job

hti

Hamiltonian thermodynamic integration for atomic solid

dpti hti [-h] {gen,compute,run} ...

Positional Arguments

command

Possible choices: gen, compute, run

commands of Hamiltonian thermodynamic integration for atomic solid

Sub-commands

gen

generate a job

dpti hti gen [-h] [-o OUTPUT] [-s {one-step,two-step,three-step}] [-z] PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-o, --output

the output folder for the job

Default: “new_job”

-s, --switch

Possible choices: one-step, two-step, three-step

one-step: switching on DP and switching off spring simultanenously. two-step: 1 switching on DP, 2 switching off spring. three-step: 1 switching on soft LJ, 2 switching on DP, 3 switching off spring and soft LJ.

Default: “one-step”

-z, --meam

whether use meam instead of dp

Default: False

compute

Compute the result of a job

dpti hti compute [-h] [-t {helmholtz,gibbs}] [-m {inte,mbar}] [-s SCHEME]
                 [-g PV] [-G PV_ERR]
                 JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-t, --type

Possible choices: helmholtz, gibbs

the type of free energy

Default: “helmholtz”

-m, --inte-method

Possible choices: inte, mbar

the method of thermodynamic integration

Default: “inte”

-s, --scheme

the numeric integration scheme

Default: “simpson”

-g, --pv

press*vol value override to calculate Gibbs free energy

-G, --pv-err

press*vol error

run

run the job

dpti hti run [-h] [--no-dp] JOB machine task_name

Positional Arguments

JOB: folder of the job
machine: machine.json file for the job
task_name: task name, can be 00, 01, or 02

Named Arguments

--no-dp

whether to use Deep Potential or not

Default: False

hti_liq

Hamiltonian thermodynamic integration for atomic liquid

dpti hti_liq [-h] {gen,compute,run} ...

Positional Arguments

command

Possible choices: gen, compute, run

commands of Hamiltonian thermodynamic integration for atomic liquid

Sub-commands

gen

Generate a job

dpti hti_liq gen [-h] [-o OUTPUT] [-z] PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-o, --output

the output folder for the job

Default: “new_job”

-z, --meam

whether use meam instead of dp

Default: False

compute

Compute the result of a job

dpti hti_liq compute [-h] [-t {helmholtz,gibbs}] [-g PV] [-G PV_ERR] JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-t, --type

Possible choices: helmholtz, gibbs

the type of free energy

Default: “helmholtz”

-g, --pv

press*vol value override to calculate Gibbs free energy

-G, --pv-err

press*vol error

run

run the job

dpti hti_liq run [-h] [--no-dp] JOB machine task_name

Positional Arguments

JOB: folder of the job
machine: machine.json file for the job
task_name: task name, can be 00, 01, or 02

Named Arguments

--no-dp

whether to use Deep Potential or not

Default: False

hti_ice

Hamiltonian thermodynamic integration for ice

dpti hti_ice [-h] {gen,compute,refine,run} ...

Positional Arguments

command

Possible choices: gen, compute, refine, run

commands of Hamiltonian thermodynamic integration for ice

Sub-commands

gen

Generate a job

dpti hti_ice gen [-h] [-o OUTPUT] [-s {one-step,two-step,three-step}] PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-o, --output

the output folder for the job

Default: “new_job”

-s, --switch

Possible choices: one-step, two-step, three-step

one-step: switching on DP and switching off spring simultanenously. two-step: 1 switching on DP, 2 switching off spring.: three-step: 1 switching on soft LJ, 2 switching on DP, 3 switching off spring and soft LJ.

Default: “one-step”

compute

Compute the result of a job

dpti hti_ice compute [-h] [-t {helmholtz,gibbs}] [-m {inte,mbar}] [-d]
                     [-p {3,5}] [-s SCHEME] [-S SHIFT] [-g PV] [-G PV_ERR]
                     [--npt NPT]
                     JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-t, --type

Possible choices: helmholtz, gibbs

the type of free energy

Default: “helmholtz”

-m, --inte-method

Possible choices: inte, mbar

the method of thermodynamic integration

Default: “inte”

-d, --disorder-corr

apply disorder correction for ice

Default: True

-p, --partial-disorder

Possible choices: 3, 5

apply partial disorder correction for ice

-s, --scheme

the numeric integration scheme

Default: “simpson”

-S, --shift

a constant shift in the energy/mole computation, will be removed from FE

Default: 0.0

-g, --pv

press*vol value override to calculate Gibbs free energy

-G, --pv-err

press*vol error

--npt

directory of the npt task; will use PV from npt result, where P is the control variable and V varies.

refine

Refine the grid of a job

dpti hti_ice refine [-h] -i INPUT -o OUTPUT -e ERROR [-p]

Named Arguments

-i, --input

input job

-o, --output

output job

-e, --error

the error required

-p, --print

print the refinement and exit

Default: False

run

run the job

dpti hti_ice run [-h] [--no-dp] JOB machine task_name

Positional Arguments

JOB: folder of the job
machine: machine.json file for the job
task_name: task name, can be 00, 01, or 02

Named Arguments

--no-dp

whether to use Deep Potential or not

Default: False

hti_water

Hamiltonian thermodynamic integration for liquid water

dpti hti_water [-h] {gen,compute,refine,run} ...

Positional Arguments

command

Possible choices: gen, compute, refine, run

commands of Hamiltonian thermodynamic integration for liquid water

Sub-commands

gen

Generate a job

dpti hti_water gen [-h] [-o OUTPUT] PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-o, --output

the output folder for the job

Default: “new_job”

compute

Compute the result of a job

dpti hti_water compute [-h] [-t {helmholtz,gibbs}] [-m {inte,mbar}]
                       [-s SCHEME] [-g PV] [-G PV_ERR] [--npt NPT]
                       JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-t, --type

Possible choices: helmholtz, gibbs

the type of free energy

Default: “helmholtz”

-m, --inte-method

Possible choices: inte, mbar

the method of thermodynamic integration

Default: “inte”

-s, --scheme

the numeric integration scheme

Default: “simpson”

-g, --pv

press*vol value override to calculate Gibbs free energy

-G, --pv-err

press*vol error

--npt

directory of the npt task; will use PV from npt result, where P is the control variable and V varies.

refine

Refine the grid of a job

dpti hti_water refine [-h] -i INPUT -o OUTPUT -e ERROR

Named Arguments

-i, --input: input job
-o, --output: output job
-e, --error: the error required

run

run the job

dpti hti_water run [-h] [--no-dp] JOB machine task_name

Positional Arguments

JOB: folder of the job
machine: machine.json file for the job
task_name: task name, can be 00, 01, or 02

Named Arguments

--no-dp

whether to use Deep Potential or not

Default: False

ti

thermodynamic integration along isothermal or isobaric paths

dpti ti [-h] {gen,compute,refine,run} ...

Positional Arguments

command

Possible choices: gen, compute, refine, run

commands of thermodynamic integration along isothermal or isobaric paths

Sub-commands

gen

Generate a job

dpti ti gen [-h] [-o OUTPUT] [-z] PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-o, --output

the output folder for the job

Default: “new_job”

-z, --meam

whether use meam instead of dp

Default: False

compute

Compute the result of a job

dpti ti compute [-h] [-m {inte,mbar}] [-e EO] [-E EO_ERR] [-t TO] [-s SCHEME]
                [-H HTI]
                JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-m, --inte-method

Possible choices: inte, mbar

the method of thermodynamic integration

Default: “inte”

-e, --Eo

free energy of starting point

Default: 0

-E, --Eo-err

The statistical error of the starting free energy

Default: 0

-t, --To

the starting thermodynamic position

-s, --scheme

the numerical integration scheme

Default: “simpson”

-H, --hti

the HTI job folder; will extract the free energy of the starting point as from the result.json file in this folder

refine

Refine the grid of a job

dpti ti refine [-h] -i INPUT -o OUTPUT -e ERROR

Named Arguments

-i, --input: input job
-o, --output: output job
-e, --error: the error required

run

run the job

dpti ti run [-h] JOB machine

Positional Arguments

JOB: folder of the job
machine: machine.json file for the job

ti_water

thermodynamic integration along isothermal or isobaric paths for water

dpti ti_water [-h] {gen,compute,refine,run} ...

Positional Arguments

command

Possible choices: gen, compute, refine, run

commands of thermodynamic integration along isothermal or isobaric paths for water

Sub-commands

gen

Generate a job

dpti ti_water gen [-h] [-o OUTPUT] PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-o, --output

the output folder for the job

Default: “new_job”

compute

Compute the result of a job

dpti ti_water compute [-h] [-m {inte,mbar}] [-e EO] [-E EO_ERR] [-t TO]
                      [-s SCHEME] [-S SHIFT] [-H HTI]
                      JOB

Positional Arguments

JOB: folder of the job

Named Arguments

-m, --inte-method

Possible choices: inte, mbar

the method of thermodynamic integration

Default: “inte”

-e, --Eo

free energy of starting point

-E, --Eo-err

the statistical error of the starting free energy

-t, --To

the starting thermodynamic position

-s, --scheme

the numerical integration scheme

Default: “simpson”

-S, --shift

a constant shift in the energy/mole computation, will be removed from FE

Default: 0.0

-H, --hti

the HTI job folder; will extract the free energy of the starting point as from the result.json file in this folder

refine

Refine the grid of a job

dpti ti_water refine [-h] -i INPUT -o OUTPUT -e ERROR

Named Arguments

-i, --input: input job
-o, --output: output job
-e, --error: the error required

run

run the job

dpti ti_water run [-h] JOB machine

Positional Arguments

JOB: folder of the job
machine: machine.json file for the job

gdi

compute the phase boundary via Gibbs-Duhem integration

dpti gdi [-h] [-g GDIDATA_JSON] [-b BEGIN] [-e END] [-d {t,p}]
         [-i INITIAL_VALUE] [-s STEP_VALUE [STEP_VALUE ...]] [-a ABS_TOL]
         [-r REL_TOL] [-w] [-o OUTPUT] [-f FIRST_STEP] [-S SHIFT SHIFT] [-v]
         [-z]
         PARAM MACHINE

Positional Arguments

PARAM: json parameter file
MACHINE: json machine file

Named Arguments

-g, --gdidata-json

json gdi integration file

-b, --begin

start of the integration

-e, --end

end of the integration

-d, --direction

Possible choices: t, p

direction of the integration, along T or P

-i, --initial-value

the initial value of T (direction=p) or P (direction=t)

-s, --step-value

the T (direction=t) or P (direction=p) values must be evaluated

-a, --abs-tol

the absolute tolerance of the integration

Default: 10

-r, --rel-tol

the relative tolerance of the integration

Default: 0.01

-w, --if-water

assumes water molecules: nmols = natoms//3

Default: False

-o, --output

the output folder for the job

Default: “new_job”

-f, --first-step

the first step size of the integrator

-S, --shift

the output folder for the job

Default: [0.0, 0.0]

-v, --verbose

print detailed infomation

Default: False

-z, --if-meam

whether use meam instead of dp

Default: False

mti

mass thermodynamic integration: quantum free energy calculation using PIMD

dpti mti [-h] {gen,run,compute} ...

Positional Arguments

command

Possible choices: gen, run, compute

commands of mass thermodynamic integration

Sub-commands

gen

Generate a job

dpti mti gen [-h] [-o OUTPUT] PARAM

Positional Arguments

PARAM: json parameter file

Named Arguments

-o, --output

the output folder for the job

Default: “new_job”

run

run the job

dpti mti run [-h] JOB PARAM machine

Positional Arguments

JOB: folder of the job
PARAM: json parameter file
machine: machine.json file for the job

compute

Compute the result of a job

dpti mti compute [-h] [--natom_mol NATOM_MOL] JOB

Positional Arguments

JOB: folder of the job

Named Arguments

--natom_mol: the number of atoms in the molecule