`calphy` input file#

The inputfile is yaml formatted. In this section the possible keys in the inputfile is discussed. The input file consists of two main keys, and four separate blocks. For a sample of the inputfile see the end of this document. The table below gives a quick overview of all available keywords in calphy.

Main keys
element	mass

`calculations` block
mode	lattice	reference_phase	temperature	pressure
temperature_high	lattice_constant	repeat	n_iterations	n_switching_steps
n_equilibration_steps	pair_style	pair_coeff	n_print_steps	potential_file

`md` block
timestep	n_small_steps	n_every_steps	n_repeat_steps	n_cycles
thermostat_damping	barostat_damping

`queue` block
scheduler	cores	jobname	walltime	queuename
memory	commands	modules	options

`tolerance` block
lattice_constant	spring_constant	solid_fraction	liquid_fraction	pressure

`melting_temperature` block
step	attempts

main keys#

`element`#

type: string/list of strings
default: None
example:

element: 'Cu'
element: ['Cu', 'Zr']

Chemical symbol(s) of the element(s) in the simulation.

`mass`#

type: float/list of floats default: 1.0 example:

mass: 63.546
mass: [63.546, 91.224]

Mass of the element(s) in the simulation. It should follow the same order as that of element, and should be of the same length.

`calculations` block#

Other than these two main keys, all other options are specified in blocks. The first block is the calculations block. This block can list all the calculations that calphy should perform and it can have more than one entry. A sample calculation block is shown below.

calculations:
- mode: ts
  temperature: [1300, 1400]
  pressure: [0]
  lattice: [FCC]
  repeat: [2, 2, 2]
  reference_phase: solid
  n_iterations: 1

The various keys are-

`mode`#

type: string, fe or ts or mts or alchemy or melting_temperature or tscale or pscale
default: None
example:

mode: fe
mode: ts

Calculation mode. A small description of the different modes are given below.

fe performs a direct free energy calculation
ts performs a direct free energy calculation followed by reversible scaling to find temperature dependence.
mts performs only reversible scaling part and can be used for dynamic Clausius-Clapeyron integration.
alchemy is used for switching between two different interatomic potentials, or for integration over concentration.
melting_temperature can be used for automated calculation of melting temperature.
tscale is used for similar purpose as ts, but scales the temperature directly.
pscale calculates the free energy as a function of the pressure.

`temperature`#

type: float or list of floats
default: None
example:

temperature: 1200
temperature: [1200, 1300]

Temperatures for the simulation in Kelvin. The way temperature is used in calphy depends on the selected mode of calculation.

mode ts or tscale or mts, a temperature sweep is carried out. In that case, only two values of temperature should be specified.
mode melting_temperature, if provided it is used as an initial guess temperature. If not, the experimental melting temperature is used as a guess value.
all other modes, a calculation is launched for each temperature on the list.

`pressure`#

type: None or float or list of floats
default: None
example:

pressure: None
pressure: 0
pressure: [0,0,0]
pressure: [0, 10000]
pressure: [[1,1,1], [1000, 1000, 1000]]

Pressure for the simulation in bars. Depending on the pressure input, other options are automatically set. These options are iso and fix_lattice. iso decides if the barostat relaxes the system isotropically or anisotropically. fix_lattice does not relax the lattice at all. A table consistning of possible pressure input options and their effect is below:

`pressure` input options
Type	Example	`iso`	`fix_lattice`	`mode`	Restrictions
`None`	`pressure: None`	True	True	`fe`, `alchemy`	None
scalar	`pressure: 100`	True	False	all except `pscale`	None
`(1,)`	`pressure: [100]`	True	False	all except `pscale`	None
`(2,)`	`pressure: [100, 200]`	True	False	`pscale`	None
`(3,)`	`pressure: [100, 100, 100]`	False	False	all except `pscale`	px=py=pz
`(1,3)`	`pressure: [[100, 100, 100]]`	False	False	all except `pscale`	px=py=pz
`(2,3)`	`pressure: [[100, 100, 100], [200, 200, 200]]`	False	False	`pscale`	px=py=pz

`lattice`#

type: string or list of strings
default: None
example:

lattice: FCC
lattice: [FCC, LQD]
lattice: [FCC, conf.data]

Lattice to be used for the calculations. The lattice option can use either LAMMPS for creation of input structure or use an input file in the LAMMPS data format. To use LAMMPS to create the structure, the keyword specified should be from the following: BCC, FCC, HCP, DIA, SC and LQD. LAMMPS lattice creation can only be used for single species. If LQD is specified, a solid structure will be first created and melted within the MD run. Alternatively, a LAMMPS data file can be specified which contains the configuration.

`reference_phase`#

type: string or list of strings
default: None
example:

state: solid
state: [solid, liquid]

The protocol to be used for the calculation. The reference_phase input is closely related to the lattice command. It should be of the same length as the lattice input. For each of the lattice specified, reference_phase command specifies which reference state to use.

`lattice_constant`#

type: float or list of floats
default: Experimental lattice constant
example:

lattice_constant: 3.68
lattice_constant: [3.68, 5.43]

Lattice constant for input structures. Lattice constant values to be used for initial structure creation. Only required if the structure is created through LAMMPS. If not specified, the experimental lattice constant will be used.

`repeat`#

type: list of ints of length 3
default: [1, 1, 1]
example:

repeat: [3,3,3]

repeat command specifies the number of unit cells required in each x, y and z directions. This is only used if lattice command uses one of the LAMMPS structure keywords.

`n_iterations`#

type: int
example:

n_iterations: 3

The number of backward and forward integrations to be carried out in all modes. If more than one integration cycle is used, the errors can also be evaluated.

`temperature_high`#

type: float
default: 2*temperature
example:

temperature_high: 1600

The temperature used to melt a solid structure to create a liquid. If reference_phase is chosen as liquid, calphy performs a melting cycle to create an equilibrated liquid structure. calphy starts from the given input structure, and heats it using 2 times the highest temperature provided in the temperature option. If the structure is not melted, the temperature is increased progressively. temperature_high keyword can be used to set the temperature to overheat the structure and melt it.

`npt`#

type: bool
default: True
example:

npt: True

npt determines if calculations are carried out in the NPT ensemble. This option is used with modes alchemy, ts and mts. The effect is described below:

for mode ts and mts: the reversible scaling approach is carried out in NPT if npt is True, otherwise the NVT ensemble is used.
for mode alchemy: If npt is False, the NVT ensemble is used, meaning that the calculated work during alchemical transformation is calculated on the equilibrated volume of the first pair style.

`pair_style`#

type: string or list of strings
example:

pair_style: eam/alloy
pair_style: [eam/alloy, eam/alloy]
pair_style: eam/fs
pair_style: pace

The pair style command for LAMMPS. All styles supported in LAMMPS can be used with calphy. Except for mode alchemy, only the first value in the list will be used. For mode alchemy, there should be two pair styles specified, and the alchemical transformation is carried out between the two.

`pair_coeff`#

type: string or list of strings
default: None
example:

pair_coeff: "* * Cu_EAM/Cu01.eam.alloy Cu"
pair_coeff: ["* * Cu_EAM/Cu01.eam.alloy Cu", "* * Cu_EAM/Cu02.eam.alloy Cu"]
pair_coeff: "* * CuZr_EAM/CuZr.eam.fs Cu Zr"

The pair coeff command for LAMMPS. It should be the same length as pair_style. Except for mode alchemy, only the first value in the list will be used. For mode alchemy, there should be two pair styles specified, and the alchemical transformation is carried out between the two.

`potential_file`#

type: string
default: None
example:

pair_coeff: "/home/calc/potential.inp"

If specified, the pair_style and pair_coeff commands are not used, but rather the potential is read in from the provided input file using include command in LAMMPS. This allows the use of more complex or multiple potential files. Due to the hybrid/scaled styles employed in calphy, this option only works with mode ``fe`` and ``reference_phase`` solid.

`n_equilibration_steps`#

type: int
default: 25000
example:

n_equilibration_steps: 10000

The number of time steps for equilibrating the system.

`n_switching_steps`#

type: int or list of ints
default: 50000
example:

n_switching_steps: 10000
n_switching_steps: [10000, 20000]

The number of switching steps. If a list of two integers is provided, the first value is used for mode fe while the second value will be used for all other modes.

`n_print_steps`#

type: int
default: 0
example:

n_print_steps: 100

Record MD trajectory during temperature sweep runs in the given interval of time steps. Default 0, trajectories are never recorded.

`md` block#

MD block consists of the various options required for the MD runs. An example block is given below and the keys are discussed.

md:
  timestep: 0.001
  thermostat_damping: 0.1
  barostat_damping: 0.1

`timestep`#

type: float default: 0.001
example:

timestep: 0.001

The timestep for MD in picoseconds.

`thermostat_damping`#

type: float
default: 0.1
example:

thermostat_damping: 0.1

The thermostat damping constant for MD.

`barostat_damping`#

type: float
default: 0.1
example:

barostat_damping: 0.1

Pressure damping for MD.

`n_small_steps`#

type: int
default: 10000
example:

n_small_steps: 10000

The number of time steps for equilibration cycles to calculate spring constant and average volume.

`n_every_steps`#

type: int
default: 10
example:

n_every_steps: 100

Keywords to tune how often average values are recorded in LAMMPS. Please see here for more details.

`n_repeat_steps`#

type: int
default: 10
example:

n_repeat_steps: 10

Keywords to tune how often average values are recorded in LAMMPS. Please see here for more details.

`n_cycles`#

type: int
default: 100
example:

n_cycles: 100

Number of cycles to try converging the pressure of the system. If the pressure is not converged after n_cycles, an error will be raised. In each n_cycle, n_small_steps MD steps will be run.

`queue` block#

This block consists of the options for specifying the scheduler for carrying out the calculations. An example block is given below-

queue:
  scheduler: local
  cores: 2
  jobname: ti
  walltime: "23:50:00"
  queuename: shorttime
  memory: 3GB
  modules:
    - anaconda/4
  commands:
    - conda activate env

`scheduler`#

type: string
example:

scheduler: slurm

The scheduler to be used for the job. Can be local, slurm or sge. The code has been tested only on local and slurm.

`cores`#

type: int
example:

cores: 4

The number of cores to be used for the job.

`jobname`#

type: string
example:

jobname: cu

Name of the job. Not used for local.

`walltime`#

type: string
example:

walltime: "23:50:00"

Walltime for the job. Not used for local.

`queuename`#

type: string
example:

queuename: "shorttime"

Name of the queue. Not used for local.

`memory`#

type: string
example:

memory: 3GB

Memory to be used per core. Not used for local.

`commands`#

type: list of strings
example:

command:
 - source .bashrc
 - conda activate ace
 - module load lammps

Command that will be run before the actual calculations are carried out. This section can be used to specify commands that need to be run before the actual calculation. If the calculations are run within a conda environment, the activate command for conda should be specified here. If additional modules need to be loaded, that can also be specified here.

`modules`#

type: list of strings
example:

modules:
  - anaconda
  - lammps

List of modules to be loaded before running the calculations. The given module names will be prefixed by module load.

`options`#

type: string
example:

options:
  - memory: 3GB

Extra options to be added to the submission script.

`tolerance` block#

This block helps to tune the internal convergence parameters that calphy uses. Generally, tuning these parameters are not required.

tolerance:
   spring_constant: 0.01
   solid_fraction: 0.7
   liquid_fraction: 0.05
   pressure: 0.5

`spring_constant`#

type: float
default: 0.01
example:

spring_constant: 0.01

tolerance for the convergence of spring constant calculation.

`solid_fraction`#

type: float
default: 0.7
example:

solid_fraction: 0.7

The minimum amount of solid particles that should be there in solid.

`liquid_fraction`#

type: float
default: 0.05
example:

liquid_fraction: 0.05

Maximum fraction of solid atoms allowed in liquid after melting.

`pressure`#

type: float
default: 0.5
example:

pressure: 0.5

tolerance for the convergence of pressure.

`melting_temperature` block#

This block contains keywords that are used only for the mode melting_temperature.

melting_temperature:
   step: 200
   attempts: 5

`step`#

type: int
example:

step: 200

Temperature interval for search of melting temperature. Only used if mode is melting_temperature.

`attempts`#

type: int
example:

attempts: 5

The number of maximum attempts to try find the melting temperature in a automated manner. Only used if mode is melting_temperature.

calphy input file#

main keys#

element#

mass#

calculations block#

mode#

temperature#

pressure#

lattice#

reference_phase#

lattice_constant#

repeat#

n_iterations#

temperature_high#

npt#

pair_style#

pair_coeff#

potential_file#

n_equilibration_steps#

n_switching_steps#

n_print_steps#

md block#

timestep#

thermostat_damping#

barostat_damping#

n_small_steps#

n_every_steps#

n_repeat_steps#

n_cycles#

queue block#

scheduler#

cores#

jobname#

walltime#

queuename#

memory#

commands#

modules#

options#

tolerance block#

spring_constant#

solid_fraction#

liquid_fraction#

pressure#

melting_temperature block#

step#

attempts#

`calphy` input file#

`element`#

`mass`#

`calculations` block#

`mode`#

`temperature`#

`pressure`#

`lattice`#

`reference_phase`#

`lattice_constant`#

`repeat`#

`n_iterations`#

`temperature_high`#

`npt`#

`pair_style`#

`pair_coeff`#

`potential_file`#

`n_equilibration_steps`#

`n_switching_steps`#

`n_print_steps`#

`md` block#

`timestep`#

`thermostat_damping`#

`barostat_damping`#

`n_small_steps`#

`n_every_steps`#

`n_repeat_steps`#

`n_cycles`#

`queue` block#

`scheduler`#

`cores`#

`jobname`#

`walltime`#

`queuename`#

`memory`#

`commands`#

`modules`#

`options`#

`tolerance` block#

`spring_constant`#

`solid_fraction`#

`liquid_fraction`#

`pressure`#

`melting_temperature` block#

`step`#

`attempts`#