Input file tags

This chapter gives a complete list of the tags that can be specified in the xml input file, along with the hierarchy of objects. Note that every xml input file must start with the root tag . See the accompanying “help.xml” file in the “doc/help_files” directory to see the recommended input file structure.

Each section of this chapter describes one of the major input classes used in the i-PI initialization. These sections will start with some normal text which describes the function of this class in detail. After this the attributes of the tag will be listed, enclosed within a frame for clarity. Finally, the fields contained within the tag will be listed in alphabetical order, possibly followed by their attributes. Attribute names will be bold and field names both bold and underlined. Other supplementary information will be in small font and italicized.

al6xxx_kmc

Holds all the information for the KMC dynamics, such as timestep, rates and barriers that control it.

ATTRIBUTES

mode

The KMC algorithm to be used

dtype: string

options: [‘rfkmc’]

default: rfkmc

FIELDS

optimizer

Option for geometry optimization step

nstep

The number of optimization steps.

dtype: integer

default: 10

a0

FCC lattice parameter

dtype: float

dimension: length

default: 1.0

diffusion_barrier_al

Barrier for vacancy diffusion in pure Al.

dtype: float

dimension: energy

default: 0.01

diffusion_prefactor_al

Prefactor for vacancy diffusion in pure Al.

dtype: float

dimension: frequency

default: 2.4188843e-05

diffusion_barrier_mg

Barrier for vacancy-assisted diffusion of Mg.

dtype: float

dimension: energy

default: 0.0

diffusion_prefactor_mg

Prefactor for vacancy-assisted diffusion of Mg.

dtype: float

dimension: frequency

default: 0.0

diffusion_barrier_si

Barrier for vacancy-assisted diffusion of Si.

dtype: float

dimension: energy

default: 0.0

diffusion_prefactor_si

Prefactor for vacancy-assisted diffusion of Si.

dtype: float

dimension: frequency

default: 0.0

neval

The number of parallel force evaluators.

dtype: integer

default: 4

ncell

The number of repeat cells in each direction.

dtype: integer

default: 4

nvac

The number of vacancies.

dtype: integer

default: 4

nsi

The number of silicon atoms.

dtype: integer

default: 4

nmg

The number of magnesium atoms.

dtype: integer

default: 4

idx

The position of the atoms on the lattice, relative to the canonical ordering.

dtype: integer

default: [ ]

tottime

Total KMC time elapsed

dtype: float

dimension: time

default: 0.0

ecache_file

Filename for storing/loading energy cache

dtype: string

default:

qcache_file

Filename for storing/loading positions cache

dtype: string

default:

max_cache_len

Maximum cache length before oldest entry is deleted

dtype: integer

default: 1000

alchemy

Holds all the information for doing Monte Carlo alchemical exchange moves.

ATTRIBUTES

mode

dtype: string

options: [‘dummy’]

default: dummy

FIELDS

names

The names of the atoms to be to exchanged, in the format [name1, name2, … ].

dtype: string

default: [ ]

nxc

The average number of exchanges per step to be attempted

dtype: float

default: 1

ealc

The contribution to the conserved quantity for the alchemical exchanger

dtype: float

default: 0.0

atoms

Deals with a single replica of the system or classical simulations.

FIELDS

natoms

The number of atoms.

dtype: integer

default: 0

q

The positions of the atoms, in the format [x1, y1, z1, x2, … ].

dtype: float

dimension: length

default: [ ]

p

The momenta of the atoms, in the format [px1, py1, pz1, px2, … ].

dtype: float

dimension: momentum

default: [ ]

m

The masses of the atoms, in the format [m1, m2, … ].

dtype: float

dimension: mass

default: [ ]

names

The names of the atoms, in the format [name1, name2, … ].

dtype: string

default: [ ]

atomswap

Holds all the information for doing Monte Carlo atom swap moves.

ATTRIBUTES

mode

Dummy attribute, does nothing.

dtype: string

options: [‘dummy’]

default: dummy

FIELDS

names

The names of the atoms to be to exchanged, in the format [name1, name2, … ].

dtype: string

default: [ ]

nxc

The average number of exchanges per step to be attempted

dtype: float

default: 1

ealc

The contribution to the conserved quantity for the atom swapper

dtype: float

default: 0.0

barostat

Simulates an external pressure bath.

ATTRIBUTES

mode

The type of barostat. ‘isotropic’ implements the Bussi-Zykova-Parrinello barostat [doi:10.1063/1.3073889] that isotropically scales the volume while sampling the isothermal isobaric ensemble. The implementation details are given in [doi:10.1016/j.cpc.2013.10.027]. ‘sc-isotropic’ implements the same for Suzuki-Chin path integral molecular dynamics [10.1021/acs.jctc.8b01297]. This barostat is suitable for simulating liquids. ‘flexible’ implements the path integral version of the Martyna-Tuckerman-Tobias-Klein barostat which incorporates full cell fluctuations while sampling the isothermal isobaric ensemble [doi:10.1063/1.478193]. This is suitable for anisotropic systems such as molecular solids. ‘anisotropic’ implements the Raiteri-Gale-Bussi barostat which enables cell fluctuations at constant external stress [10.1088/0953-8984/23/33/334213]. It is suitable for simulating solids at given external (non-diagonal) stresses and requires specifying a reference cell for estimating strain. Note that this ensemble is valid only within the elastic limit of small strains. For diagonal stresses (or external pressures) the ‘flexible’ and the ‘anisotropic’ modes should give very similar results. ‘dummy’ barostat does not do anything.

dtype: string

options: [‘dummy’, ‘isotropic’, ‘flexible’, ‘anisotropic’, ‘sc-isotropic’]

default: dummy

FIELDS

thermostat

The thermostat for the cell. Keeps the cell velocity distribution at the correct temperature. Note that the ‘pile_l’, ‘pile_g’, ‘nm_gle’ and ‘nm_gle_g’ options will not work for this thermostat.

tau

The time constant associated with the dynamics of the piston.

dtype: float

dimension: time

default: 1.0

p

Momentum (or momenta) of the piston.

dtype: float

dimension: momentum

default: [ ]

h0

Reference cell for Parrinello-Rahman-like barostats. Should be roughly equal to the mean size of the cell averaged over the trajectory. Sampling might be inaccurate if the difference is too large.

dtype: float

dimension: length

default:

[0. 0. 0. 0. 0. 0. 0. 0. 0.]

hfix

A list of the cell entries that should be held fixed (xx, yy, zz, xy, xz, yz). ‘offdiagonal’ is an alias for xy, xz, yz.

dtype: string

default: [ ]

beads

Describes the bead configurations in a path integral simulation.

ATTRIBUTES

natoms

The number of atoms.

dtype: integer

default: 0

nbeads

The number of beads.

dtype: integer

default: 0

FIELDS

q

The positions of the beads. In an array of size [nbeads, 3*natoms].

dtype: float

dimension: length

default: [ ]

p

The momenta of the beads. In an array of size [nbeads, 3*natoms].

dtype: float

dimension: momentum

default: [ ]

m

The masses of the atoms, in the format [m1, m2, … ].

dtype: float

dimension: mass

default: [ ]

names

The names of the atoms, in the format [name1, name2, … ].

dtype: string

default: [ ]

bias

Deals with creating all the necessary forcefield objects.

FIELDS

force

The class that deals with how each forcefield contributes to the overall potential, force and virial calculation.

bosons

Deals with the specification of which atoms are have bosonic indistinguishability. The specified atoms participate in exchange interaction, which forms ring polymers that combine several particles together. The algorithm scales quadratically with the number of atoms and linearly with the number of beads. The implementation is based on Hirshberg et al.’s doi:10.1073/pnas.1913365116 and Feldman and Hirshberg’s doi:10.1063/5.0173749.

dtype: string

ATTRIBUTES

shape

The shape of the array.

dtype: tuple

default: (0,)

mode

If ‘mode’ is ‘manual’, then the array is read in directly, then reshaped according to the ‘shape’ specified in a row-major manner. If ‘mode’ is ‘file’ then the array is read in from the file given.

dtype: string

options: [‘manual’, ‘file’]

default: manual

id

If ‘id’ is ‘index’, then bosonic atoms are specified a list of indices (zero-based). If ‘id’ is ‘label’ then specify a list of labels.

dtype: string

options: [‘index’, ‘label’]

default: index

cell

Describes with the cell parameters. Takes as array which can be used to initialize the cell vector matrix. N.B.: the cell parameters are stored with the lattice vectors in the columns, and the cell must be oriented in such a way that the array is upper-triangular (i.e. with the first vector aligned along x and the second vector in the xy plane).

dtype: float

dimension: length

ATTRIBUTES

units

The units the input data is given in.

dtype: string

default: automatic

shape

The shape of the array.

dtype: tuple

default: (0,)

mode

If ‘mode’ is ‘manual’, then the array is read in directly, then reshaped according to the ‘shape’ specified in a row-major manner. If ‘mode’ is ‘file’ then the array is read in from the file given.

dtype: string

options: [‘manual’, ‘file’]

default: manual

checkpoint

This class defines how a checkpoint file should be output. Optionally, between the checkpoint tags, you can specify one integer giving the current step of the simulation. By default this integer will be zero.

dtype: integer

ATTRIBUTES

filename

A string to specify the name of the file that is output. The file name is given by ‘prefix’.’filename’ + format_specifier. The format specifier may also include a number if multiple similar files are output.

dtype: string

default: restart

stride

The number of steps between successive writes.

dtype: integer

default: 1

overwrite

This specifies whether or not each consecutive checkpoint file will overwrite the old one.

dtype: boolean

default: True

constrained_dynamics

Holds all the information for the MD integrator, such as timestep, the thermostats and barostats that control it.

ATTRIBUTES

mode

The ensemble that will be sampled during the simulation.

dtype: string

options: [‘nve’, ‘nvt’]

default: nve

splitting

The integrator used for sampling the target ensemble.

dtype: string

options: [‘obabo’, ‘baoab’]

default: baoab

FIELDS

thermostat

The thermostat for the atoms, keeps the atom velocity distribution at the correct temperature.

barostat

Simulates an external pressure bath.

timestep

The time step.

dtype: float

dimension: time

default: 1.0

nmts

Number of iterations for each MTS level (including the outer loop, that should in most cases have just one iteration).

dtype: integer

default: [ ]

nsteps_o

The number of sub steps used in the evolution of the thermostat (used in function step_Oc). Relevant only for GLE thermostats

dtype: integer

default: 1

nsteps_geo

The number of sub steps used in the evolution of the geodesic flow (used in function step_Ag).

dtype: integer

default: 1

csolver

Define a numerical method for computing the projection operators associated with the constraint.

constraint

Define a constraint to be applied onto atoms

constraint

Generic input value

ATTRIBUTES

mode

The type of constraint.

dtype: string

options: [‘distance’, ‘angle’, ‘eckart’, ‘multi’, ‘multi’]

default: distance

FIELDS

atoms

List of atoms indices that are to be constrained.

dtype: integer

default: [ ]

values

List of constraint lengths.

dtype: float

dimension: length

default: [ ]

constraint

One or more constraints that have to be considered coupled

csolver

Holds all parameters for the numerical method used to solve the contraint.

FIELDS

tolerance

Tolerance value used in the Quasi-Newton iteration scheme.

dtype: float

default: 0.0001

maxit

Maximum number of steps used in the Quasi-Newton iteration scheme.

dtype: integer

default: 1000

norm_order

Order of norm used to determine termination of the Quasi-newton iteration.

dtype: integer

default: 2

dmd

DrivenMD with external time-dependent driving potential

FIELDS

dmdff

List of names of forcefields that should do driven MD. Accepts ffdmd forcefield types. Currently implemented (2021) for ffdmd only the driving potential similar to the one described in Bowman, .., Brown JCP 119, 646 (2003).

dtype: string

default: [ ]

dynamics

Holds all the information for the MD integrator, such as timestep, the thermostats and barostats that control it.

ATTRIBUTES

mode

The ensemble that will be sampled during the simulation. nve: constant-energy-volume; nvt: constant-temperature-volume; npt: constant-temperature-pressure(isotropic); nst: constant-temperature-stress(anisotropic); sc: Suzuki-Chin high-order NVT; scnpt: Suzuki-Chin high-order NpT; nvt-cc: constrained-centroid NVT;

dtype: string

options: [‘nve’, ‘nvt’, ‘npt’, ‘nst’, ‘sc’, ‘scnpt’, ‘nvt-cc’]

default: nve

splitting

The Louiville splitting used for sampling the target ensemble.

dtype: string

options: [‘obabo’, ‘baoab’]

default: obabo

FIELDS

thermostat

The thermostat for the atoms, keeps the atom velocity distribution at the correct temperature.

barostat

Simulates an external pressure bath.

timestep

The time step.

dtype: float

dimension: time

default: 1.0

nmts

Number of iterations for each MTS level (including the outer loop, that should in most cases have just one iteration).

dtype: integer

default: [ ]

ensemble

Holds all the information that is ensemble specific, such as the temperature and the external pressure.

FIELDS

temperature

The temperature of the system.

dtype: float

dimension: temperature

default: -1.0

pressure

The external pressure.

dtype: float

dimension: pressure

default: -12345.0

stress

The external stress.

dtype: float

dimension: pressure

default:

[-12345. -0. -0. -0. -12345. -0. -0. -0. -12345.]

eens

The ensemble contribution to the conserved quantity.

dtype: float

dimension: energy

default: 0.0

bias

Deals with creating all the necessary forcefield objects.

bias_weights

Bias weights.

dtype: float

default: [ ]

hamiltonian_weights

Hamiltonian weights.

dtype: float

default: [ ]

time

The internal time for this system

dtype: float

dimension: time

default: 0.0

ffcavphsocket

A cavity molecular dynamics driver for vibraitonal strong coupling. In the current implementation, only a single cavity mode polarized along the x and y directions is coupled to the molecules. Check https://doi.org/10.1073/pnas.2009272117 and also examples/lammps/h2o-cavmd/ for details.

ATTRIBUTES

mode

Specifies whether the driver interface will listen onto a internet socket [inet] or onto a unix socket [unix].

dtype: string

options: [‘unix’, ‘inet’]

default: inet

matching

Specifies whether requests should be dispatched to any client, automatically matched to the same client when possible [auto] or strictly forced to match with the same client [lock].

dtype: string

options: [‘auto’, ‘any’, ‘lock’]

default: auto

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial. Should be set to True for FFSockets

dtype: boolean

default: True

FIELDS

charge_array

The partial charges of all the atoms, in the format [Q1, Q2, … ].

dtype: float

dimension: length

default: [ ]

apply_photon

Determines if additional photonic degrees of freedom is included or not.

dtype: boolean

default: False

E0

The value of varepsilon (effective light-matter coupling strength) in atomic units.

dtype: float

default: 0.0

omega_c

This gives the cavity photon frequency at normal incidence.

dtype: float

dimension: frequency

default: 0.01

ph_rep

In the current implementation, two energy-degenerate photon modes polarized along x and y directions are coupled to the molecular system. If ‘loose’, the cavity photons polarized along the x, y directions are represented by two ‘L’ atoms; the x dimension of the first ‘L’ atom is coupled to the molecules, and the y dimension of the second ‘L’ atom is coupled to the molecules. If ‘dense’, the cavity photons polarized along the x, y directions are represented by one ‘L’ atom; the x and y dimensions of this ‘L’ atom are coupled to the molecules.

dtype: string

options: [‘loose’, ‘dense’]

default: loose

address

This gives the server address that the socket will run on.

dtype: string

default: localhost

port

This gives the port number that defines the socket.

dtype: integer

default: 65535

slots

This gives the number of client codes that can queue at any one time.

dtype: integer

default: 4

exit_on_disconnect

Determines if i-PI should quit when a client disconnects.

dtype: boolean

default: False

timeout

This gives the number of seconds before assuming a calculation has died. If 0 there is no timeout.

dtype: float

default: 0.0

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

ffcommittee

Combines multiple forcefields to build a committee model, that can be used to compute uncertainty-quantified machine-learning models. Each forcefield can be any of the other FF objects, and each should be used with a client that generates a slightly different estimation of energy and forces. These are averaged, and the mean used as the actual forcefield. Statistics about the distribution are also returned as extras fields, and can be printed for further postprocessing. It is also possible for a single FF object to return a JSON-formatted string containing entries committee_pot, committee_force and committee_virial, that contain multiple members at once. These will be unpacked and combined with whatever else is present. Also contains options to use it for uncertainty estimation and for active learning in a ML context, based on a committee model. Implements the approaches discussed in [Musil et al.](http://doi.org/10.1021/acs.jctc.8b00959) and [Imbalzano et al.](http://doi.org/10.1063/5.0036522)

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

weights

List of weights to be given to the forcefields. Defaults to 1 for each FF. Note that the components are divided by the number of FF, and so the default corresponds to an average.

dtype: float

default: [ ]

alpha

Scaling of the variance of the model, corresponding to a calibration of the error

dtype: float

default: 1.0

baseline_name

Name of the forcefield object that should be treated as the baseline for a weighted baseline model.

dtype: string

default:

baseline_uncertainty

Corresponds to the expected error of the baseline model. This represents the error on the TOTAL potential energy of the simulation.

dtype: float

dimension: energy

default: -1.0

active_thresh

The uncertainty threshold for active learning. Structure with an uncertainty above this value are printed in the specified output file so they can be used for active learning.

dtype: float

dimension: energy

default: 0.0

active_output

Output filename for structures that exceed the accuracy threshold of the model, to be used in active learning.

dtype: string

default: active_output

parse_json

Tell the model whether to parse extras string looking for committee values of potential, forces, and virials. Default: false.

dtype: boolean

default: False

ffsocket

Deals with the assigning of force calculation jobs to different driver codes, and collecting the data, using a socket for the data communication.

fflj

Simple, internal LJ evaluator without cutoff, neighbour lists or minimal image convention. Expects standard LJ parameters, e.g. { eps: 0.1, sigma: 1.0 }.

ffdebye

Harmonic energy calculator

ffplumed

Direct PLUMED interface

ffyaff

Uses a Yaff force field to compute the forces.

ffsgdml

A SGDML energy calculator

ffdebye

Harmonic energy calculator

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

hessian

Specifies the Hessian of the harmonic potential. Default units are atomic. Units can be specified only by xml attribute. Implemented options are: ‘atomic_unit’, ‘ev/ang^2’

dtype: float

dimension: hessian

default: [ ]

x_reference

Minimum-energy configuration for the harmonic potential

dtype: float

dimension: length

default: [ ]

v_reference

Zero-value of energy for the harmonic potential

dtype: float

dimension: energy

default: 0.0

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

ffdmd

Simple, internal DMD evaluator without without neighbor lists, but with PBC. Expects coupling elements (n*(n-1)/2 of them), oscillating frequency and time step.

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

dmd_coupling

Specifies the coupling between atom pairs (should be size N*(N-1)/2 ordered c21, c32, c31, c43, c42, c41 etc. – in atomic units!)

dtype: float

default: [ ]

dmd_freq

Frequency of the oscillation of the time-dependent term

dtype: float

dimension: frequency

default: 0.0

dmd_dt

Time step of the oscillating potential. Should match time step of simulation

dtype: float

dimension: time

default: 0.0

dmd_step

The current step counter for dmd.

dtype: integer

default: 0

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

fflj

Simple, internal LJ evaluator without cutoff, neighbour lists or minimal image convention. Expects standard LJ parameters, e.g. { eps: 0.1, sigma: 1.0 }.

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

ffplumed

Direct PLUMED interface

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

file

This describes the location to read the reference structure file from.

dtype: string

default:

plumeddat

The PLUMED input file

dtype: string

default: plumed.dat

plumedstep

The current step counter for PLUMED calls

dtype: integer

default: 0

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

ffsgdml

A SGDML energy calculator

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

sGDML_model

This gives the file name of the sGDML model.

dtype: string

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

ffsocket

Deals with the assigning of force calculation jobs to different driver codes, and collecting the data, using a socket for the data communication.

ATTRIBUTES

mode

Specifies whether the driver interface will listen onto a internet socket [inet] or onto a unix socket [unix].

dtype: string

options: [‘unix’, ‘inet’]

default: inet

matching

Specifies whether requests should be dispatched to any client, automatically matched to the same client when possible [auto] or strictly forced to match with the same client [lock].

dtype: string

options: [‘auto’, ‘any’, ‘lock’]

default: auto

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial. Should be set to True for FFSockets

dtype: boolean

default: True

FIELDS

address

This gives the server address that the socket will run on.

dtype: string

default: localhost

port

This gives the port number that defines the socket.

dtype: integer

default: 65535

slots

This gives the number of client codes that can queue at any one time.

dtype: integer

default: 4

exit_on_disconnect

Determines if i-PI should quit when a client disconnects.

dtype: boolean

default: False

timeout

This gives the number of seconds before assuming a calculation has died. If 0 there is no timeout.

dtype: float

default: 0.0

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

ffyaff

Uses a Yaff force field to compute the forces.

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

yaffpara

This gives the file name of the Yaff input parameter file.

dtype: string

default: parameters.txt

yaffsys

This gives the file name of the Yaff input system file.

dtype: string

default: system.chk

yafflog

This gives the file name of the Yaff output log file.

dtype: string

default: yaff.log

rcut

This gives the real space cutoff used by all pair potentials in atomic units.

dtype: float

default: 18.89726133921252

alpha_scale

This gives the alpha parameter in the Ewald summation based on the real-space cutoff: alpha = alpha_scale / rcut. Higher values for this parameter imply a faster convergence of the reciprocal terms, but a slower convergence in real-space.

dtype: float

default: 3.5

gcut_scale

This gives the reciprocale space cutoff based on the alpha parameter: gcut = gcut_scale * alpha. Higher values for this parameter imply a better convergence in the reciprocal space.

dtype: float

default: 1.1

skin

This gives the skin parameter for the neighborlist.

dtype: integer

default: 0

smooth_ei

This gives the flag for smooth truncations for the electrostatic interactions.

dtype: boolean

default: False

reci_ei

This gives the method to be used for the reciprocal contribution to the electrostatic interactions in the case of periodic systems. This must be one of ‘ignore’ or ‘ewald’. The ‘ewald’ option is only supported for 3D periodic systems.

dtype: string

default: ewald

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

file

This is the class to initialize from file.

dtype: string

ATTRIBUTES

mode

The input data format. ‘xyz’ and ‘pdb’ stand for xyz and pdb input files respectively. ‘chk’ stands for initialization from a checkpoint file. ‘ase’ is to read a file with the Atomic Simulation Environment

dtype: string

options: [‘xyz’, ‘pdb’, ‘chk’, ‘ase’]

default: chk

bead

The index of the bead for which the value will be set. If a negative value is specified, then all beads are assumed.

dtype: integer

default: -1

cell_units

The units for the cell dimensions.

dtype: string

default: automatic

force

The class that deals with how each forcefield contributes to the overall potential, force and virial calculation.

ATTRIBUTES

nbeads

If the forcefield is to be evaluated on a contracted ring polymer, this gives the number of beads that are used. If not specified, the forcefield will be evaluated on the full ring polymer.

dtype: integer

default: 0

weight

A scaling factor for this forcefield, to be applied before adding the force calculated by this forcefield to the total force.

dtype: float

default: 1.0

fd_epsilon

The finite displacement to be used for calculaing the Suzuki-Chin contribution of the force. If the value is negative, a centered finite-difference scheme will be used. [in bohr]

dtype: float

default: -0.001

name

An optional name to refer to this force component.

dtype: string

default:

forcefield

Mandatory. The name of the forcefield this force is referring to.

dtype: string

default:

FIELDS

mts_weights

The weight of force in each mts level starting from outer.

dtype: float

dimension: force

default:

[1.]

force_extras

A list of quantities that should be extracted from the ‘extra’ string returned by the forcefield, that are then treated the same way as energy or forces – that is treated as a numerical, physical quantity, interpolated when changing the number of PI replicas. Same quantities from different force components are summed as well. The names should correspond to entries in the JSON-formatted extra string.

dtype: string

default: [ ]

forcefield

Base forcefield class that deals with the assigning of force calculation jobs and collecting the data.

ATTRIBUTES

name

Mandatory. The name by which the forcefield will be identified in the System forces section.

dtype: string

pbc

Applies periodic boundary conditions to the atoms coordinates before passing them on to the driver code.

dtype: boolean

default: True

threaded

Whether the forcefield should use a thread loop to evaluate, or work in serial

dtype: boolean

default: False

FIELDS

latency

The number of seconds the polling thread will wait between exhamining the list of requests.

dtype: float

default: 0.0001

offset

A constant offset that is subtracted from the forcefield energy. Useful when there is a large core energy contribution that is constant throughout a simulation and hides significant changes in the 10th digit.

dtype: float

dimension: energy

default: 0.0

parameters

The parameters of the force field

dtype: dictionary

default: { }

activelist

List with indexes of the atoms that this socket is taking care of. Default: [-1] (corresponding to all)

dtype: integer

default:

[-1]

forces

Deals with creating all the necessary forcefield objects.

FIELDS

force

The class that deals with how each forcefield contributes to the overall potential, force and virial calculation.

frequencies

Provides a compact way of specifying the ring polymer frequencies

dtype: float

dimension: frequency

ATTRIBUTES

units

The units the input data is given in.

dtype: string

default: automatic

shape

The shape of the array.

dtype: tuple

default: (0,)

mode

If ‘mode’ is ‘manual’, then the array is read in directly, then reshaped according to the ‘shape’ specified in a row-major manner. If ‘mode’ is ‘file’ then the array is read in from the file given.

dtype: string

options: [‘manual’, ‘file’]

default: manual

style

Specifies the technique to be used to calculate the dynamical masses. ‘rpmd’ simply assigns the bead masses the physical mass. ‘manual’ sets all the normal mode frequencies except the centroid normal mode manually. ‘pa-cmd’ takes an argument giving the frequency to set all the non-centroid normal modes to. ‘wmax-cmd’ is similar to ‘pa-cmd’, except instead of taking one argument it takes two ([wmax,wtarget]). The lowest-lying normal mode will be set to wtarget for a free particle, and all the normal modes will coincide at frequency wmax.

dtype: string

options: [‘pa-cmd’, ‘wmax-cmd’, ‘manual’, ‘rpmd’]

default: rpmd

gle

This is the class to initialize the thermostat (ethermo and fictitious momenta).

dtype: string

ATTRIBUTES

mode

‘chk’ stands for initialization from a checkpoint file. ‘manual’ means that the value to initialize from is giving explicitly as a vector.

dtype: string

options: [‘chk’, ‘manual’]

default: manual

h0

Describes with the cell parameters. Takes as array which can be used to initialize the cell vector matrix. N.B.: the cell parameters are stored with the lattice vectors in the columns, and the cell must be oriented in such a way that the array is upper-triangular (i.e. with the first vector aligned along x and the second vector in the xy plane).

dtype: float

dimension: length

ATTRIBUTES

units

The units the input data is given in.

dtype: string

default: automatic

shape

The shape of the array.

dtype: tuple

default: (0,)

mode

If ‘mode’ is ‘manual’, then the array is read in directly, then reshaped according to the ‘shape’ specified in a row-major manner. If ‘mode’ is ‘file’ then the array is read in from the file given.

dtype: string

options: [‘manual’, ‘file’]

default: manual

init_cell

This is the class to initialize cell.

dtype: string

ATTRIBUTES

mode

This decides whether the system box is created from a cell parameter matrix, or from the side lengths and angles between them. If ‘mode’ is ‘manual’, then ‘cell’ takes a 9-elements vector containing the cell matrix (row-major, lattice vectors stored in columns). The 1st element define lattice vector a, the 2nd, 5th elements define lattice vector b, and the 3rd, 6th, 9th elements define lattice vector c. The other elements are ignored, as the cell must be aligned so that it is upper triangular. If ‘mode’ is ‘abcABC’, then ‘cell’ takes an array of 6 floats, the first three being the length of the sides of the system parallelopiped, and the last three being the angles (in degrees) between those sides. Angle A corresponds to the angle between sides b and c, and so on for B and C. If mode is ‘abc’, then this is the same as for ‘abcABC’, but the cell is assumed to be orthorhombic. ‘pdb’ and ‘chk’ read the cell from a PDB or a checkpoint file, respectively.

dtype: string

options: [‘manual’, ‘pdb’, ‘chk’, ‘abc’, ‘abcABC’]

default: manual

initialize

Specifies the number of beads, and how the system should be initialized.

ATTRIBUTES

nbeads

The number of beads. Will override any provision from inside the initializer. A ring polymer contraction scheme is used to scale down the number of beads if required. If instead the number of beads is scaled up, higher normal modes will be initialized to zero.

dtype: integer

FIELDS

positions

Initializes atomic positions. Will take a ‘units’ attribute of dimension ‘length’

dtype: string

velocities

Initializes atomic velocities. Will take a ‘units’ attribute of dimension ‘velocity’

dtype: string

momenta

Initializes atomic momenta. Will take a ‘units’ attribute of dimension ‘momentum’

dtype: string

masses

Initializes atomic masses. Will take a ‘units’ attribute of dimension ‘mass’

dtype: string

labels

Initializes atomic labels

dtype: string

cell

Initializes the configuration of the cell. Will take a ‘units’ attribute of dimension ‘length’

dtype: string

file

Initializes everything possible for the given mode. Will take a ‘units’ attribute of dimension ‘length’. The unit conversion will only be applied to the positions and cell parameters. The ‘units’ attribute is deprecated. Append a ‘quantity{units}’ to the comment line of the xyz or to the ‘TITLE’ tag of a pdb.

dtype: string

gle

Initializes the additional momenta in a GLE thermostat.

dtype: string

instanton

A class for instanton calculations

ATTRIBUTES

mode

Defines whether it is an instanton rate or instanton tunneling splitting calculaion

dtype: string

options: [‘rate’, ‘splitting’]

default: rate

FIELDS

tolerances

Convergence criteria for optimization.

biggest_step

The maximum step size during the optimization.

dtype: float

default: 0.4

old_pos

The previous step positions during the optimization.

dtype: float

dimension: length

default: [ ]

old_pot

The previous step potential energy during the optimization

dtype: float

dimension: energy

default: [ ]

old_force

The previous step force during the optimization

dtype: float

dimension: force

default: [ ]

opt

The geometry optimization algorithm to be used. For small system sizes nichols is recomended. Lanczos is tailored for big bigger than nbeads*natoms >~38*64. NR works in both cases given that the initial guess is close to the optimized geometry. Finally lbfgs is used for tunneling splitting calculations.

dtype: string

options: [‘nichols’, ‘NR’, ‘lbfgs’, ‘lanczos’, ‘None’]

default: None

max_e

Evaluate the forces in a reduced ring polymer such that the potential energy between consecutive replicas is smaller that the provided value.

dtype: float

dimension: energy

default: 0.0

max_ms

Evaluate the forces in a reduced ring polymer such that that mass-scaled distance in a.u. between consecutive replicas is smaller that the provided value.

dtype: float

default: 0.0

discretization

Allows to specified non uniform time discretization as proposed in J. Chem. Phys. 134, 184107 (2011)

dtype: float

default: [ ]

alt_out

Alternative output:Prints different formatting of outputs for geometry, hessian and bead potential energies. All quantities are also accessible from typical i-pi output infrastructure. Default to 1, which prints every step. -1 will suppress the output (except the last one). Any other positive number will set the frequency (in steps) with which the quantities are written to file. The instanton geometry is printed in xyz format and the distances are in angrstroms The hessian is printed in one line with the following format: h1_1,h2_1,…,hN_1, h2_2,h2_2,hN_2, …. ,h1_d,h2_d,…,hN_d. Where N represents the total number of replicas, d the number of dimension of each replica (3*n_atoms) and hi_j means the row j of the physical hessian corresponding to the replica i. The physical hessian uses a convention according to the positions convention used in i-pi. Example of 2 particles, the first two rows of the physical hessian reads: ‘H_x1_x1, H_x1_y1, H_x1_z1, H_x1_x2, H_x1_y2,H_x1_z2’ ‘H_x2_x1, H_x2_y1, H_x2_z1, H_x2_x2, H_x2_y2,H_x2_z2’

dtype: integer

default: 1

prefix

Prefix of the output files.

dtype: string

default: instanton

delta

Initial stretch amplitude.

dtype: float

default: 0.1

hessian_init

How to initialize the hessian if it is not fully provided.

dtype: string

options: [‘true’, ‘false’]

default: false

hessian

(Approximate) Hessian.

dtype: float

default: [ ]

hessian_update

How to update the hessian after each step.

dtype: string

options: [‘powell’, ‘recompute’]

default: powell

hessian_asr

Removes the zero frequency vibrational modes depending on the symmetry of the system.

dtype: string

options: [‘none’, ‘poly’, ‘crystal’]

default: none

qlist_lbfgs

List of previous position differences for L-BFGS, if known.

dtype: float

default: [ ]

glist_lbfgs

List of previous gradient differences for L-BFGS, if known.

dtype: float

default: [ ]

old_direction

The previous direction in a CG or SD optimization.

dtype: float

default: [ ]

scale_lbfgs

Scale choice for the initial hessian. 0 identity. 1 Use first member of position/gradient list. 2 Use last member of position/gradient list.

dtype: integer

default: 2

corrections_lbfgs

The number of past vectors to store for L-BFGS.

dtype: integer

default: 20

ls_options

Options for line search methods. Includes: tolerance: stopping tolerance for the search, iter: the maximum number of iterations, step: initial step for bracketing, adaptive: whether to update initial step.

energy_shift

Set the zero of energy.

dtype: float

dimension: energy

default: 0.0

hessian_final

Decide if we are going to compute the final big-hessian by finite difference.

dtype: string

options: [‘false’, ‘true’]

default: false

labels

This is the class to initialize atomic labels.

dtype: string

ATTRIBUTES

mode

The input data format. ‘xyz’ and ‘pdb’ stand for xyz and pdb input files respectively. ‘ase’ is to read a file with the Atomic Simulation Environment. ‘chk’ stands for initialization from a checkpoint file. ‘manual’ means that the value to initialize from is giving explicitly as a vector.

dtype: string

options: [‘manual’, ‘xyz’, ‘pdb’, ‘ase’, ‘chk’]

default: chk

index

The index of the atom for which the value will be set. If a negative value is specified, then all atoms are assumed.

dtype: integer

default: -1

bead

The index of the bead for which the value will be set. If a negative value is specified, then all beads are assumed.

dtype: integer

default: -1

masses

This is the class to initialize atomic masses.

dtype: string

ATTRIBUTES

mode

The input data format. ‘xyz’ and ‘pdb’ stand for xyz and pdb input files respectively. ‘ase’ is to read a file with the Atomic Simulation Environment. ‘chk’ stands for initialization from a checkpoint file. ‘manual’ means that the value to initialize from is giving explicitly as a vector.

dtype: string

options: [‘manual’, ‘xyz’, ‘pdb’, ‘ase’, ‘chk’]

default: chk

index

The index of the atom for which the value will be set. If a negative value is specified, then all atoms are assumed.

dtype: integer

default: -1

bead

The index of the bead for which the value will be set. If a negative value is specified, then all beads are assumed.

dtype: integer

default: -1

metad

MetaDynamics

FIELDS

metaff

List of names of forcefields that should do metadynamics.

dtype: string

default: [ ]

use_energy

Transfer the potential energy value to PLUMED to use as a collective variable. Can only be used with classical simulations because it requires a rather hacky mechanism to transfer the energy of the system to the forcefield.

dtype: boolean

default: False

momenta

This is the class to initialize momenta.

dtype: string

ATTRIBUTES

mode

The input data format. ‘xyz’ and ‘pdb’ stand for xyz and pdb input files respectively. ‘chk’ stands for initialization from a checkpoint file. ‘manual’ means that the value to initialize from is giving explicitly as a vector. ‘thermal’ means that the data is to be generated from a Maxwell-Boltzmann distribution at the given temperature.

dtype: string

options: [‘manual’, ‘xyz’, ‘pdb’, ‘ase’, ‘chk’, ‘thermal’]

default: chk

index

The index of the atom for which the value will be set. If a negative value is specified, then all atoms are assumed.

dtype: integer

default: -1

bead

The index of the bead for which the value will be set. If a negative value is specified, then all beads are assumed.

dtype: integer

default: -1

motion

Allow chosing the type of calculation to be performed. Holds all the information that is calculation specific, such as geometry optimization parameters, etc.

ATTRIBUTES

mode

How atoms should be moved at each step in the simulatio. ‘replay’ means that a simulation is replayed from trajectories provided to i-PI.

dtype: string

options: [‘vibrations’, ‘minimize’, ‘replay’, ‘neb’, ‘string’, ‘dynamics’, ‘constrained_dynamics’, ‘t_ramp’, ‘p_ramp’, ‘alchemy’, ‘atomswap’, ‘planetary’, ‘instanton’, ‘al-kmc’, ‘dummy’, ‘scp’, ‘normalmodes’, ‘multi’]

FIELDS

fixcom

This describes whether the centre of mass of the particles is fixed.

dtype: boolean

default: True

fixatoms

Indices of the atmoms that should be held fixed.

dtype: integer

default: [ ]

optimizer

Option for geometry optimization

neb_optimizer

Option for NEB optimization

string_optimizer

Option for String minimal-energy path optimization

dynamics

Option for (path integral) molecular dynamics

constrained_dynamics

Option for constrained classical molecular dynamics

file

This describes the location to read a trajectory file from. Replay syntax allows using some POSIX wildcards in the filename of trajectory files. If symbols ?*[] are found in a filename, the code expects to find exactly Nbeads files that match the provided pattern. Bead indices will be read from the files, and the files will be ordered ascendingly by their bead indices. Wildcarded files are expected to be in the folder where the simulation runs.

dtype: string

default:

vibrations

Option for phonon computation

normalmodes

Option for solving the vibrational Schroedinger’s equations in normal mode coordinates.

scp

Option for self consistent phonons computation

alchemy

Option for alchemical exchanges

atomswap

Option for Monte Carlo atom swap

t_ramp

Option for temperature ramp

p_ramp

Option for pressure ramp

instanton

Option for Instanton optimization

al6xxx_kmc

Option for Al-6xxx KMC

planetary

Option for planetary model calculator

motion

A motion class that can be included as a member of a ‘multi’ integrator.

neb_optimizer

Contains the required parameters for performing nudged elastic band (NEB) calculations

ATTRIBUTES

mode

The geometry optimization algorithm to optimize NEB path

dtype: string

options: [‘bfgstrm’, ‘damped_bfgs’, ‘fire’]

default: fire

FIELDS

tolerances

Tolerance criteria to stop NEB optimization. If you work with DFT, do not use these defaults.

old_coord

The previous position in an optimization step.

dtype: float

dimension: length

default: [ ]

full_force

The previous full-dimensional force in an optimization step.

dtype: float

dimension: force

default: [ ]

full_pots

Previous physical potentials of all beads.

dtype: float

dimension: energy

default: [ ]

old_nebpotential

Previous NEB potential energy, which includes spring energy.

dtype: float

default: [ ]

old_nebgradient

The previous gradient including NEB spring forces.

dtype: float

default: [ ]

old_direction

The previous direction.

dtype: float

default: [ ]

biggest_step

The maximum atomic displacement in a single step of optimizations within NEB procedure. If requested step is larger, it will be downscaled so that maximal atomic displacement won’t exceed biggest_step.

dtype: float

dimension: length

default: 0.5

scale_lbfgs

Scale choice for the initial hessian. 0 identity. 1 Use first member of position/gradient list. 2 Use last member of position/gradient list.

dtype: integer

default: 2

hessian_bfgs

Approximate Hessian for damped_BFGS, if known.

dtype: float

default: [ ]

qlist_lbfgs

List of previous position differences for L-BFGS, if known.

dtype: float

default: [ ]

glist_lbfgs

List of previous gradient differences for L-BFGS, if known.

dtype: float

default: [ ]

corrections_lbfgs

The number of past vectors to store for L-BFGS.

dtype: integer

default: 5

dtmax_fire

Maximum time interval per step for FIRE.

dtype: float

default: 1.0

v_fire

Current velocity for FIRE

dtype: float

default: [ ]

alpha_fire

velocity mixing factor for FIRE

dtype: float

default: 0.1

N_down_fire

consecutive steps in downhill dierction for FIRE

dtype: integer

default: 0

N_up_fire

consecutive steps in uphill direction

dtype: integer

default: 0

dt_fire

time per step

dtype: float

default: 0.1

endpoints

Geometry optimization of endpoints (not implemented yet)

spring

Uniform or variable spring constants along the elastic band

tangent

How to calculate tangents: simple averaging from the original 1998 paper, or the improved tangent estimate from J. Chem. Phys. 113, 9978 (2000)

dtype: string

options: [‘plain’, ‘improved’]

default: improved

stage

Stage of the NEB pipeline: optimization of endpoints, NEB itself, climbing image

dtype: string

options: [‘endpoints’, ‘neb’, ‘climb’]

default: neb

use_climb

Use climbing image NEB or not

dtype: boolean

default: False

climb_bead

The index of the climbing bead.

dtype: integer

default: -1

normal_modes

Deals with the normal mode transformations, including the adjustment of bead masses to give the desired ring polymer normal mode frequencies if appropriate. Takes as arguments frequencies, of which different numbers must be specified and which are used to scale the normal mode frequencies in different ways depending on which ‘mode’ is specified.

ATTRIBUTES

transform

Specifies whether to calculate the normal mode transform using a fast Fourier transform or a matrix multiplication. For small numbers of beads the matrix multiplication may be faster.

dtype: string

options: [‘fft’, ‘matrix’]

default: fft

propagator

How to propagate the free ring polymer dynamics. Cayley transform is not exact but is strongly stable and avoid potential resonance issues. A bab scheme performs numerical verlet type propagation. All three options work for distinguishable particles. Only the bab propagator can be used with bosonic particles.

dtype: string

options: [‘exact’, ‘cayley’, ‘bab’]

default: exact

FIELDS

frequencies

Specifies normal mode frequencies for a (closed path) calculation

dtype: float

dimension: frequency

default: [ ]

open_paths

Indices of the atoms whose path should be opened (zero-based).

dtype: integer

default: [ ]

bosons

Specify which atoms are bosons.

dtype: string

default: [ ]

nmts

The number of iterations to perform one bab step.

dtype: integer

default: 10

normalmodes

Vibrational self-consistent field class. Approximates the vibrational eigenstates and eigenvalues of a system by performing a normal mode expansion of the potential energy surface.

ATTRIBUTES

mode

The algorithm to be used: independent mode framework (imf) and vibrational self consistent field (vscf).

dtype: string

options: [‘imf’, ‘vscf’]

default: imf

FIELDS

prefix

Prefix of the output files.

dtype: string

default:

asr

Removes the zero frequency vibrational modes depending on the symmetry of the system for general polyatomic molecules, and periodic crystal structures.

dtype: string

options: [‘none’, ‘poly’, ‘crystal’]

default: none

dynmat

Portion of the dynamical matrix known to the current point in the calculation.

dtype: float

default: [ ]

nprim

Number of primitive unit cells in the simulation cell.

dtype: float

default: 1.0

fnmrms

Fraction of harmonic RMS displacement used to sample along normal mode.

dtype: float

default: 1.0

nevib

Multiple of harm vibr energy up to which BO surface is sampled.

dtype: float

default: 25.0

nint

Integration points for Hamiltonian matrix elements.

dtype: integer

default: 101

pair_range

The range of pair combinations of normal modes to be considered.

dtype: integer

default: [ ]

nbasis

Number of SHO states used as basis for anharmonic wvfn.

dtype: integer

default: 10

athresh

Convergence threshold for absolute error in vibr free energy per degree of freedom.

dtype: float

dimension: energy

default: 3.6749322e-06

ethresh

Convergence thresh for fractional error in vibr free energy.

dtype: float

default: 0.01

alpha

The fraction of mean field potential to mix with the result of the previous SCF iteration.

dtype: float

default: 1.0

nkbt

Threshold for (e - e_gs)/(kB T) of vibr state to be incl in the VSCF and partition function.

dtype: float

default: 4.0

nexc

Minimum number of excited n-body states to calculate (also in MP2 correction).

dtype: integer

default: 5

mptwo

Flag determining whether MP2 correction is calculated.

dtype: boolean

default: False

solve

Flag determining whether the VSCF mean field Schroedinger’s equation is solved.

dtype: boolean

default: False

grid

Flag determining whether the coupling potential is gridded or not.

dtype: boolean

default: True

print_mftpot

Flag determining whether MFT potentials are printed to file.

dtype: boolean

default: False

print_1b_map

Flag determining whether the independent mode potentials are printed to file.

dtype: boolean

default: False

print_2b_map

Flag determining whether the two body mapped coupling potentials are printed to file.

dtype: boolean

default: False

print_vib_density

Flag determining whether the vibrational density (psi**2) are printed to file.

dtype: boolean

default: False

threebody

Flag determining whether three-mode coupling terms are accounted for.

dtype: boolean

default: False

nparallel

The number of forces evaluations per i-PI step.

dtype: integer

default: 1

optimizer

A Geometry Optimization class implementing most of the standard methods

ATTRIBUTES

mode

The geometry optimization algorithm to be used

dtype: string

options: [‘sd’, ‘cg’, ‘bfgs’, ‘bfgstrm’, ‘lbfgs’, ‘damped_bfgs’]

default: lbfgs

FIELDS

ls_options

“Options for line search methods. Includes: tolerance: stopping tolerance for the search (as a fraction of the overall energy tolerance), iter: the maximum number of iterations, step: initial step for bracketing, adaptive: whether to update initial step.

exit_on_convergence

Terminates the simulation when the convergence criteria are met.

dtype: boolean

default: True

tolerances

Convergence criteria for optimization. Default values are extremely conservative. Set them to appropriate values for production runs.

biggest_step

The maximum step size for (L)-BFGS line minimizations.

dtype: float

default: 100.0

scale_lbfgs

Scale choice for the initial hessian. 0 identity. 1 Use first member of position/gradient list. 2 Use last member of position/gradient list.

dtype: integer

default: 2

corrections_lbfgs

The number of past vectors to store for L-BFGS.

dtype: integer

default: 6

old_pos

The previous positions in an optimization step.

dtype: float

dimension: length

default: [ ]

old_pot

The previous potential energy in an optimization step.

dtype: float

dimension: energy

default: [ ]

old_force

The previous force in an optimization step.

dtype: float

dimension: force

default: [ ]

old_direction

The previous direction in a CG or SD optimization.

dtype: float

default: [ ]

invhessian_bfgs

Approximate inverse Hessian for BFGS, if known.

dtype: float

default: [ ]

hessian_trm

Approximate Hessian for trm, if known.

dtype: float

default: [ ]

tr_trm

The trust radius in trm.

dtype: float

dimension: length

default: [ ]

qlist_lbfgs

List of previous position differences for L-BFGS, if known.

dtype: float

default: [ ]

glist_lbfgs

List of previous gradient differences for L-BFGS, if known.

dtype: float

default: [ ]

output

This class defines how properties, trajectories and checkpoints should be output during the simulation. May contain zero, one or many instances of properties, trajectory or checkpoint tags, each giving instructions on how one output file should be created and managed.

ATTRIBUTES

prefix

A string that will be prepended to each output file name. The file name is given by ‘prefix’.’filename’ + format_specifier. The format specifier may also include a number if multiple similar files are output.

dtype: string

default: i-pi

FIELDS

properties

Each of the properties tags specify how to create a file in which one or more properties are written, one line per frame.

dtype: string

trajectory

Each of the trajectory tags specify how to create a trajectory file, containing a list of per-atom coordinate properties.

dtype: string

checkpoint

Each of the checkpoint tags specify how to create a checkpoint file, which can be used to restart a simulation.

dtype: integer

p_ramp

PressureRamp Motion class. It just updates the ensemble pressure in steps, between the indicated values, and then holds to the highest value. It should typically be combined with a dynamics class and barostats, using a MultiMotion.

FIELDS

p_start

Initial pressure

dtype: float

dimension: pressure

default: 1.0

p_end

Final pressure

dtype: float

dimension: pressure

default: 1.0

logscale

Change pressure on a logarihthmic scale.

dtype: boolean

default: False

total_steps

Total number of steps for the ramp

dtype: integer

default: 0

current_step

Current step along the ramp

dtype: integer

default: 0

planetary

Holds all the information for the planetary model frequency matrix calculator.

ATTRIBUTES

mode

The constrained-centroid sampling mode.

dtype: string

options: [‘md’]

default: md

FIELDS

thermostat

The thermostat for the atoms, keeps the atom velocity distribution at the correct temperature.

timestep

The time step.

dtype: float

dimension: time

default: 1.0

nmts

Number of iterations for each MTS level (including the outer loop, that should in most cases have just one iteration).

dtype: integer

default: [ ]

nsamples

Number of samples to accumulate for each planetary step.

dtype: integer

default: 0

stride

How often the planetary calculation should actually be triggered.

dtype: integer

default: 1

nbeads

Number of beads for centroid-constrained dynamics (default same as master trajectory)

dtype: integer

default: -1

screen

Screening parameter for path-integral frequency matrix.

dtype: float

dimension: length

default: 0.0

positions

This is the class to initialize positions.

dtype: string

ATTRIBUTES

mode

The input data format. ‘xyz’ and ‘pdb’ stand for xyz and pdb input files respectively. ‘ase’ is to read a file with the Atomic Simulation Environment. ‘chk’ stands for initialization from a checkpoint file. ‘manual’ means that the value to initialize from is giving explicitly as a vector.

dtype: string

options: [‘manual’, ‘xyz’, ‘pdb’, ‘ase’, ‘chk’]

default: chk

index

The index of the atom for which the value will be set. If a negative value is specified, then all atoms are assumed.

dtype: integer

default: -1

bead

The index of the bead for which the value will be set. If a negative value is specified, then all beads are assumed.

dtype: integer

default: -1

prng

Deals with the pseudo-random number generator.

FIELDS

seed

This is the seed number used to generate the initial state of the random number generator.

dtype: integer

default: 123456

state

Gives the state vector for the random number generator. Avoid directly modifying this unless you are very familiar with the inner workings of the algorithm used.

dtype: integer

default: [ ]

has_gauss

Determines whether there is a stored gaussian number or not. A value of 0 means there is none stored.

dtype: integer

default: 0

gauss

The stored Gaussian number.

dtype: float

default: 0.0

set_pos

Gives the position in the state array that the random number generator is reading from.

dtype: integer

default: 0

properties

This class deals with the output of properties to one file. Between each property tag there should be an array of strings, each of which specifies one property to be output.

dtype: string

ATTRIBUTES

shape

The shape of the array.

dtype: tuple

default: (0,)

mode

If ‘mode’ is ‘manual’, then the array is read in directly, then reshaped according to the ‘shape’ specified in a row-major manner. If ‘mode’ is ‘file’ then the array is read in from the file given.

dtype: string

options: [‘manual’, ‘file’]

default: manual

filename

A string to specify the name of the file that is output. The file name is given by ‘prefix’.’filename’ + format_specifier. The format specifier may also include a number if multiple similar files are output.

dtype: string

default: out

stride

The number of steps between successive writes.

dtype: integer

default: 1

flush

How often should streams be flushed. 1 means each time, zero means never.

dtype: integer

default: 1

remd

Replica Exchange

FIELDS

stride

Every how often to try exchanges (on average).

dtype: float

default: 1.0

krescale

Rescale kinetic energy upon exchanges.

dtype: boolean

default: True

swapfile

File to keep track of replica exchanges

dtype: string

default: remd_idx

repindex

List of current indices of the replicas compared to the starting indices

dtype: integer

default: [ ]

scp

Self-consistent phonons class. It variationally optimizes the free energy to calculate the best harmonic approximation to a system.

ATTRIBUTES

mode

The statistics to be used in the calculation of the free energy. Quantum (qn) or classical (cl) Boltzmann statistics.

dtype: string

options: [‘qn’, ‘cl’]

default: qn

FIELDS

prefix

Prefix of the output files.

dtype: string

default:

asr

The method used to project out zero modes coming from continuous symmetries: crystal removes the three translational modes; molecule removes the three rotational modes in addition to the translational ones. none keeps all the modes.

dtype: string

options: [‘none’, ‘crystal’, ‘poly’]

default: none

random_type

Chooses the type of random numbers.

dtype: string

options: [‘sobol’, ‘pseudo’, ‘file’]

default: pseudo

displace_mode

The type of optimisation strategy for obtaining the mean position. sd stands for a steepest descent algorithm. ik stands for a Newton-Raphson scheme that requires the inverse of the force constant matrix iK. nmik stands for a Newton-Raphson scheme that only displaces along normal modes directions with statistically significant forces. rnmik same as nmik but performs several optimization steps using a reweighted sampling.

dtype: string

options: [‘ik’, ‘sd’, ‘nmik’, ‘rnmik’]

default: nmik

dynmat

The dynamical matrix of the trial Hamiltonian.

dtype: float

default: [ ]

max_steps

Maximum number of Monte carlo steps per SCP iteration.

dtype: integer

max_iter

Maximum number of SCP iterations.

dtype: integer

default: 1

tau

Step size along the gradient for the sd displace_mode

dtype: float

default: 1.0

wthreshold

Threshold on minimum Boltzmann weights before more statistics must be accumulated.

dtype: float

default: 0.9

precheck

Flag for checking statistical significance of forces before optimisation of mean position.

dtype: boolean

default: True

checkweights

Flag for checking Boltzmann weights for whether more statistics are required.

dtype: boolean

default: True

chop

Threshold below which frequencies are set to zero.

dtype: float

default: 1e-09

nparallel

The number of Monte Carlo forces to be evaluated (in parallel) per i-PI step.

dtype: integer

default: 1

batch_weight_exponent

The exponent used to suppress low batch weights.

dtype: integer

default: 1

simulation

This is the top level class that deals with the running of the simulation, including holding the simulation specific properties such as the time step and outputting the data.

ATTRIBUTES

verbosity

The level of output on stdout.

dtype: string

options: [‘quiet’, ‘low’, ‘medium’, ‘high’, ‘debug’]

default: medium

threading

Whether multiple-systems execution should be parallel. Makes execution non-reproducible due to the random number generator being used from concurrent threads.

dtype: boolean

default: True

mode

What kind of simulation should be run.

dtype: string

options: [‘md’, ‘static’]

default: md

safe_stride

Consistent simulation states will be saved every this number of steps. Saving state entails a small overhead, so you may want to set this to the smallest output frequency in your simulation to make i-PI faster. Use at your own risk!

dtype: integer

default: 1

floatformat

A format for all printed floats.

dtype: string

default: %16.8e

FIELDS

prng

Deals with the pseudo-random number generator.

output

This class defines how properties, trajectories and checkpoints should be output during the simulation. May contain zero, one or many instances of properties, trajectory or checkpoint tags, each giving instructions on how one output file should be created and managed.

step

The current simulation time step.

dtype: integer

default: 0

total_steps

The total number of steps that will be done. If ‘step’ is equal to or greater than ‘total_steps’, then the simulation will finish.

dtype: integer

default: 1000

total_time

The maximum wall clock time (in seconds).

dtype: float

default: 0

smotion

Options for a ‘super-motion’ step between system replicas

system

This is the class which holds all the data which represents a single state of the system.

system_template

Generic input value

ffsocket

Deals with the assigning of force calculation jobs to different driver codes, and collecting the data, using a socket for the data communication.

fflj

Simple, internal LJ evaluator without cutoff, neighbour lists or minimal image convention. Expects standard LJ parameters, e.g. { eps: 0.1, sigma: 1.0 }.

ffdmd

Simple, internal DMD evaluator without without neighbor lists, but with PBC. Expects coupling elements (n*(n-1)/2 of them), oscillating frequency and time step.

ffdebye

Harmonic energy calculator

ffplumed

Direct PLUMED interface

ffyaff

Uses a Yaff force field to compute the forces.

ffcommittee

Combines multiple forcefields to build a committee model, that can be used to compute uncertainty-quantified machine-learning models. Each forcefield can be any of the other FF objects, and each should be used with a client that generates a slightly different estimation of energy and forces. These are averaged, and the mean used as the actual forcefield. Statistics about the distribution are also returned as extras fields, and can be printed for further postprocessing. It is also possible for a single FF object to return a JSON-formatted string containing entries committee_pot, committee_force and committee_virial, that contain multiple members at once. These will be unpacked and combined with whatever else is present. Also contains options to use it for uncertainty estimation and for active learning in a ML context, based on a committee model. Implements the approaches discussed in [Musil et al.](http://doi.org/10.1021/acs.jctc.8b00959) and [Imbalzano et al.](http://doi.org/10.1063/5.0036522)

ffsgdml

A SGDML energy calculator

ffcavphsocket

A cavity molecular dynamics driver for vibraitonal strong coupling. In the current implementation, only a single cavity mode polarized along the x and y directions is coupled to the molecules. Check https://doi.org/10.1073/pnas.2009272117 and also examples/lammps/h2o-cavmd/ for details.

smotion

Allow chosing the type of smotion to be performed. Holds all the information that is calculation specific, such as replica exchange parameters, etc.

ATTRIBUTES

mode

Kind of smotion which should be performed.

dtype: string

options: [‘dummy’, ‘remd’, ‘metad’, ‘dmd’, ‘multi’]

FIELDS

remd

Option for REMD simulation

metad

Option for REMD simulation

dmd

Option for driven MD simulation

smotion

A smotion class that can be included as a member of a ‘multi’ Smotion.

string_optimizer

Contains the required parameters for performing string minimal energy path optimization.

ATTRIBUTES

mode

The geometry optimization algorithm to optimize MEP string

dtype: string

options: [‘sd’, ‘cg’, ‘bfgs’, ‘bfgstrm’, ‘damped_bfgs’, ‘lbfgs’, ‘fire’, ‘euler’]

default: bfgstrm

FIELDS

tolerances

Tolerance criteria to stop String optimization. If you work with DFT, do not use these defaults.

old_coord

The previous position in an optimization step.

dtype: float

dimension: length

default: [ ]

full_force

The previous full-dimensional force in an optimization step.

dtype: float

dimension: force

default: [ ]

full_pots

Previous physical potentials of all beads.

dtype: float

dimension: energy

default: [ ]

old_stringpotential

Previous string potential energy.

dtype: float

default: [ ]

old_stringgradient

The previous gradient of the string.

dtype: float

default: [ ]

old_direction

The previous direction.

dtype: float

default: [ ]

biggest_step

The maximum atomic displacement in a single step of optimizations within String MEP procedure. If requested step is larger, it will be downscaled so that maximal atomic displacement won’t exceed biggest_step.

dtype: float

dimension: length

default: 0.5

scale_lbfgs

Scale choice for the initial hessian. 0 identity. 1 Use first member of position/gradient list. 2 Use last member of position/gradient list.

dtype: integer

default: 2

hessian_bfgs

Approximate Hessian for damped_BFGS, if known.

dtype: float

default: [ ]

qlist_lbfgs

List of previous position differences for L-BFGS, if known.

dtype: float

default: [ ]

glist_lbfgs

List of previous gradient differences for L-BFGS, if known.

dtype: float

default: [ ]

corrections_lbfgs

The number of past vectors to store for L-BFGS.

dtype: integer

default: 5

tr_trm

Starting value for the trust radius for BFGSTRM.

dtype: float

dimension: length

default:

[1.]

dtmax_fire

Maximum time interval per step for FIRE.

dtype: float

default: 1.0

v_fire

Current velocity for FIRE

dtype: float

default: [ ]

alpha_fire

velocity mixing factor for FIRE

dtype: float

default: 0.1

N_down_fire

consecutive steps in downhill dierction for FIRE

dtype: integer

default: 0

N_up_fire

consecutive steps in uphill direction

dtype: integer

default: 0

dt_fire

time per step

dtype: float

default: 0.1

endpoints

Geometry optimization of endpoints (not implemented yet)

stage

Stage of the String pipeline: optimization of the endpoints, string opt., climbing image opt.

dtype: string

options: [‘endpoints’, ‘string’, ‘climb’]

default: string

use_climb

Use climbing image String MEP or not

dtype: boolean

default: False

climb_bead

The index of the climbing bead.

dtype: integer

default: -1

system

This is the class which holds all the data which represents a single state of the system.

ATTRIBUTES

prefix

Prepend this string to output files generated for this system.

dtype: string

default:

FIELDS

initialize

Specifies the number of beads, and how the system should be initialized.

forces

Deals with creating all the necessary forcefield objects.

ensemble

Holds all the information that is ensemble specific, such as the temperature and the external pressure.

motion

Allow chosing the type of calculation to be performed. Holds all the information that is calculation specific, such as geometry optimization parameters, etc.

beads

Describes the bead configurations in a path integral simulation.

normal_modes

Deals with the normal mode transformations, including the adjustment of bead masses to give the desired ring polymer normal mode frequencies if appropriate. Takes as arguments frequencies, of which different numbers must be specified and which are used to scale the normal mode frequencies in different ways depending on which ‘mode’ is specified.

cell

Describes with the cell parameters. Takes as array which can be used to initialize the cell vector matrix. N.B.: the cell parameters are stored with the lattice vectors in the columns, and the cell must be oriented in such a way that the array is upper-triangular (i.e. with the first vector aligned along x and the second vector in the xy plane).

dtype: float

dimension: length

default:

[0. 0. 0. 0. 0. 0. 0. 0. 0.]

system_template

Generic input value

FIELDS

template

A string that will be read verbatim containing the model for a system to be generated

dtype: string

labels

A list of strings that should be substituted in the template to create multiple systems

dtype: string

instance

A list of strings that should the labels creating one system instance

dtype: string

t_ramp

TemperatureRamp Motion class. It just updates the ensemble temperature in steps, between the indicated temperatures, and then holds to the highest value. It should typically be combined with a dynamics class and thermostats, using a MultiMotion.

FIELDS

t_start

Initial temperature

dtype: float

dimension: energy

default: 1.0

t_end

Final temperature

dtype: float

dimension: energy

default: 1.0

logscale

Change temperature on a logarihthmic scale.

dtype: boolean

default: False

total_steps

Total number of steps for the ramp

dtype: integer

default: 0

current_step

Current step along the ramp

dtype: integer

default: 0

thermostat

Simulates an external heat bath to keep the velocity distribution at the correct temperature.

ATTRIBUTES

mode

The style of thermostatting. ‘langevin’ specifies a white noise langevin equation to be attached to the cartesian representation of the momenta. ‘svr’ attaches a velocity rescaling thermostat to the cartesian representation of the momenta. Both ‘pile_l’ and ‘pile_g’ attaches a white noise langevin thermostat to the normal mode representation, with ‘pile_l’ attaching a local langevin thermostat to the centroid mode and ‘pile_g’ instead attaching a global velocity rescaling thermostat. ‘gle’ attaches a coloured noise langevin thermostat to the cartesian representation of the momenta, ‘nm_gle’ attaches a coloured noise langevin thermostat to the normal mode representation of the momenta and a langevin thermostat to the centroid and ‘nm_gle_g’ attaches a gle thermostat to the normal modes and a svr thermostat to the centroid. ‘cl’ represents a modified langevin thermostat which compensates for additional white noise from noisy forces or for dissipative effects. ‘ffl’ is the fast-forward langevin thermostat, in which momenta are flipped back whenever the action of the thermostat changes its direction. ‘multiple’ is a special thermostat mode, in which one can define multiple thermostats _inside_ the thermostat tag.

dtype: string

options: [‘’, ‘langevin’, ‘svr’, ‘pile_l’, ‘pile_g’, ‘gle’, ‘nm_gle’, ‘nm_gle_g’, ‘cl’, ‘ffl’, ‘multi’]

FIELDS

ethermo

The initial value of the thermostat energy. Used when the simulation is restarted to guarantee continuity of the conserved quantity.

dtype: float

dimension: energy

default: 0.0

tau

The friction coefficient for white noise thermostats.

dtype: float

dimension: time

default: 0.0

pile_lambda

Scaling for the PILE damping relative to the critical damping. (gamma_k=2*lambda*omega_k

dtype: float

default: 1.0

pile_centroid_t

Option to set a different centroid temperature wrt. that of the ensemble. Only used if value other than 0.0.

dtype: float

dimension: temperature

default: 0.0

A

The friction matrix for GLE thermostats.

dtype: float

dimension: frequency

default: [ ]

C

The covariance matrix for GLE thermostats.

dtype: float

dimension: temperature

default: [ ]

s

Input values for the additional momenta in GLE.

dtype: float

dimension: ms-momentum

default: [ ]

intau

The inherent noise time scale for compensating langevin thermostats.

dtype: float

dimension: time

default: 0.0

idtau

The inherent dissipation time scale for compensating langevin thermostats.

dtype: float

dimension: time

default: 0.0

apat

The time scale for automatic adjustment of CL thermostat’s parameters.

dtype: float

dimension: time

default: 0.0

flip

Flipping type for ffl thermostat (‘soft’, ‘hard’, ‘rescale’, ‘none’)

dtype: string

default: rescale

thermostat

The thermostat for the atoms, keeps the atom velocity distribution at the correct temperature.

trajectory

This class defines how one trajectory file should be output. Between each trajectory tag one string should be given, which specifies what data is to be output.

dtype: string

ATTRIBUTES

filename

A string to specify the name of the file that is output. The file name is given by ‘prefix’.’filename’ + format_specifier. The format specifier may also include a number if multiple similar files are output.

dtype: string

default: traj

stride

The number of steps between successive writes.

dtype: integer

default: 1

format

The output file format.

dtype: string

options: [‘xyz’, ‘pdb’, ‘ase’]

default: xyz

cell_units

The units for the cell dimensions.

dtype: string

default:

bead

Print out only the specified bead. A negative value means print only one every -(bead) beads, e.g. -2 means print just the even beads, -4 one every four and so on.

dtype: integer

default: -1

flush

How often should streams be flushed. 1 means each time, zero means never.

dtype: integer

default: 1

extra_type

What extra to print from the different extra strings.

dtype: string

default: raw

velocities

This is the class to initialize velocities.

dtype: string

ATTRIBUTES

mode

The input data format. ‘xyz’ and ‘pdb’ stand for xyz and pdb input files respectively. ‘chk’ stands for initialization from a checkpoint file. ‘manual’ means that the value to initialize from is giving explicitly as a vector. ‘thermal’ means that the data is to be generated from a Maxwell-Boltzmann distribution at the given temperature.

dtype: string

options: [‘manual’, ‘xyz’, ‘pdb’, ‘ase’, ‘chk’, ‘thermal’]

default: chk

index

The index of the atom for which the value will be set. If a negative value is specified, then all atoms are assumed.

dtype: integer

default: -1

bead

The index of the bead for which the value will be set. If a negative value is specified, then all beads are assumed.

dtype: integer

default: -1

vibrations

Dynamical matrix Class. It calculates phonon modes and frequencies in solids as well as normal vibrational modes and frequencies of aperiodic systems.

ATTRIBUTES

mode

The algorithm to be used: finite differences (fd), normal modes finite differences (nmfd), and energy-scaled normal mode finite differences (enmfd).

dtype: string

options: [‘fd’, ‘nmfd’, ‘enmfd’]

default: fd

FIELDS

pos_shift

The finite displacement in position used to compute derivative of force.

dtype: float

default: 0.01

energy_shift

The finite displacement in energy used to compute derivative of force.

dtype: float

default: 0.0

output_shift

Shift by the dynamical matrix diagonally before outputting.

dtype: float

default: 0.0

prefix

Prefix of the output files.

dtype: string

default: phonons

asr

Removes the zero frequency vibrational modes depending on the symmerty of the system.

dtype: string

options: [‘none’, ‘poly’, ‘lin’, ‘crystal’]

default: none

dynmat

Portion of the dynamical matrix known up to now.

dtype: float

default: [ ]

refdynmat

Portion of the refined dynamical matrix known up to now.

dtype: float

default: [ ]