AMS Molecular Dynamics PLAMS jobs¶

AMSMDJob API¶

class AMSMDJob(velocities=None, timestep=None, samplingfreq=None, nsteps=None, checkpointfrequency=None, engineresultsfreq=None, writevelocities=None, writebonds=None, writemolecules=None, writecharges=None, writeenginegradients=None, calcpressure=None, molecule=None, temperature=None, thermostat=None, tau=None, thermostat_region=None, pressure=None, barostat=None, barostat_tau=None, scale=None, equal=None, constantvolume=None, binlog_time=None, binlog_pressuretensor=None, binlog_dipolemoment=None, _enforce_thermostat=False, _enforce_barostat=False, **kwargs)[source]¶

molecule: Molecule

The initial structure

name: str

The name of the job

settings: Settings

Settings for the job. You should normally not populate neither settings.input.ams.MolecularDynamics nor settings.input.ams.Task

velocities: float or AMSJob or str (path/to/ams.rkf) or 2-tuple (path/to/ams.rkf, frame-number)

If float, it is taken as the temperature. If AMSJob or str, the velocities are taken from the EndVelocities section of the corresponding ams.rkf file. If 2-tuple, the first item must be a path to an ams.rkf, and the second item an integer specifying the frame number - the velocities are then read from History%Velocities(framenumber).

timestep: float

Timestep

samplingfreq: int

Sampling frequency

nsteps: int

Length of simulation

Trajectory options:

checkpointfrequency: int

How frequently to write MDStep*.rkf checkpoint files

writevelocitiesbool

Whether to save velocities to ams.rkf (needed for example to restart from individual frames or to calculate velocity autocorrelation functions)

writebonds: bool

Whether to save bonds to ams.rkf

writemolecules: bool

Whether to write molecules to ams.rkf

writeenginegradients: bool

Whether to save engine gradients (negative of atomic forces) to ams.rkf

Thermostat (NVT, NPT) options:

thermostat: str

‘Berendsen’ or ‘NHC’

tau: float

Thermostat time constant (fs)

temperature: float or tuple of floats

Temperature (K). If a tuple/list of floats, the Thermostat.Duration option will be set to evenly divided intervals.

thermostat_region: str

Region for which to apply the thermostat

Barostat (NPT) options:

barostat: str

‘Berendsen’ or ‘MTK’

barostat_tau: float

Barostat time constant (fs)

pressure: float

Barostat pressure (pascal)

equal: str

‘XYZ’ etc.

scale: str

‘XYZ’ etc.

constantvolume: bool

Constant volume?

Other options:

calcpressure: bool

Whether to calculate pressure for each frame.

binlog_time: bool

Whether to log the time at every timestep in the BinLog section on ams.rkf

binlog_pressuretensor: bool

Whether to log the pressure tensor at every timestep in the BinLog section on ams.rkf

get_velocities_from(other_job, frame=None, update_molecule=True)[source]¶

Function to update the InitialVelocities block in self. It is normally not needed, instead use the e.g. AMSNVEJob.restart_from() function.

This function can be called in prerun() methods for MultiJobs

classmethod restart_from(other_job, frame=None, settings=None, use_prerun=False, **kwargs)[source]¶

other_job: AMSJob

The job to restart from.

frame: int

Which frame to read the structure and velocities from. If None, the final structure and end velocities will be used (section Molecule and MDResults%EndVelocities)

settings: Settings

Settings that override any other settings. All settings from other_job (e.g. the engine settings) are inherited by default but they can be overridden here.

use_prerun: bool

If True, the molecule and velocities will only be read from other_job inside the prerun() method. Set this to True to prevent PLAMS from waiting for other_job to finish as soon as the new job is defined.

kwargs: many options

See the docstring for AMSMDJob.

AMSNVEJob API¶

This class uses the same arguments as AMSMDJob.

class AMSNVEJob(**kwargs)[source]¶

A class for running NVE MD simulations

AMSNVTJob API¶

This class uses the same arguments as AMSMDJob.

class AMSNVTJob(**kwargs)[source]¶

A class for running NVT MD simulations

AMSNPTJob API¶

This class uses the same arguments as AMSMDJob.

AMSNPTResults inherits from AMSResults.

class AMSNPTJob(**kwargs)[source]¶

A class for running NPT MD simulations

class AMSNPTResults(*args, **kwargs)[source]¶

get_equilibrated_molecule(equilibration_fraction=0.667, return_index=False)[source]¶

Discards the first equilibration_fraction of the trajectory. Calculates the average density of the rest. Returns the molecule with the closest density to the average density among the remaining trajectory.

AMSNVESpawnerJob API¶

class AMSNVESpawnerJob(previous_job, n_nve=1, name='nvespawnerjob', **kwargs)[source]¶

A class for running multiple NVE simulations with initial structures/velocities taken from an NVT trajectory. The NVT trajectory must contain the velocities!

__init__(previous_job, n_nve=1, name='nvespawnerjob', **kwargs)[source]¶

previous_job: AMSJob

An AMSJob with an MD trajectory. Must contain velocities (WriteVelocities Yes). Note that the trajectory should have been equilibrated before it starts.

n_nveint

The number of NVE simulations to spawn

All other settings can be set as for an AMSNVEJob (e.g. nsteps).

AMSMDScanDensityJob API¶

class AMSMDScanDensityJob(molecule, scan_density_upper=1.4, startstep=None, **kwargs)[source]¶

A class for scanning the density using MD Deformations

AMSRDFJob API¶

class AMSRDFJob(previous_job, atom_indices=None, atom_indices_to=None, rmin=0.5, rmax=6.0, rstep=0.1, **kwargs)[source]¶

__init__(previous_job, atom_indices=None, atom_indices_to=None, rmin=0.5, rmax=6.0, rstep=0.1, **kwargs)[source]¶

previous_job: AMSJob

AMSJob with finished MD trajectory.

atom_indices: List[int]

Atom indices (starting with 1). If None, calculate RDF from all atoms.

atom_indices_to: List[int]

Atom indices (starting with 1). If None, calculate RDF to all atoms.

rmin: float

Minimum distance (angstrom)

rmax: float

Maximum distance (angstrom)

rstep: float

Bin width for the histogram (angstrom)

class AMSRDFResults(job)[source]¶

Results class for AMSRDFJob

get_rdf()[source]¶

Returns a 2-tuple r, rdf.

r: numpy array of float (angstrom) rdf: numpy array of float

AMSMSDJob API¶

class AMSMSDJob(previous_job, max_correlation_time_fs=10000, start_time_fit_fs=2000, atom_indices=None, **kwargs)[source]¶

A convenient class wrapping around the trajectory analysis MSD tool

__init__(previous_job, max_correlation_time_fs=10000, start_time_fit_fs=2000, atom_indices=None, **kwargs)[source]¶

previous_job: AMSJob

An AMSJob with an MD trajectory. Note that the trajectory should have been equilibrated before it starts.

max_correlation_time_fs: float

Maximum correlation time in femtoseconds

start_time_fit_fsfloat

Smallest correlation time for the linear fit

atom_indicesList[int]

If None, use all atoms. Otherwise use the specified atom indices (starting with 1)

kwargs: dict

Other options to AMSAnalysisJob

class AMSMSDResults(job)[source]¶

Results class for AMSMSDJob

get_msd()[source]¶

returns time [fs], msd [ang^2]

get_linear_fit(start_time_fit_fs=None, end_time_fit_fs=None)[source]¶

Fits the MSD between start_time_fit_fs and end_time_fit_fs

Returns a 3-tuple LinRegress.result, fit_x (fs), fit_y (ang^2)

result.slope is given in ang^2/fs

get_diffusion_coefficient(start_time_fit_fs=None, end_time_fit_fs=None)[source]¶

Returns D in m^2/s

AMSVACFJob API¶

class AMSVACFJob(previous_job, max_correlation_time_fs=5000, max_freq=5000, atom_indices=None, **kwargs)[source]¶

A class for calculating the velocity autocorrelation function and its power spectrum

__init__(previous_job, max_correlation_time_fs=5000, max_freq=5000, atom_indices=None, **kwargs)[source]¶

previous_job: AMSJob

An AMSJob with an MD trajectory. Note that the trajectory should have been equilibrated before it starts.

max_correlation_time_fs: float

Maximum correlation time in femtoseconds

max_freq: float

The maximum frequency for the power spectrum in cm^-1

atom_indices: List[int]

Atom indices (starting with 1). If None, use all atoms.

class AMSVACFResults(job)[source]¶

Results class for AMSVACFJob

get_vacf()[source]¶

Extract the velocity autocorrelation function vs. time.

Returns a 2-tuple time, y with time in fs.

get_power_spectrum(max_freq=None)[source]¶

Calculate the power spectrum as the Fourier transform of the velocity autocorrelation function.

max_freq: float, optional

The maximum frequency in cm^-1.

Returns: A 2-tuple freq, y with freq in cm^-1 and y unitless.

AMSViscosityFromBinLogJob API¶

class AMSViscosityFromBinLogJob(previous_job, **kwargs)[source]¶

A convenient class wrapping around the trajectory analysis ViscosityFromBinLog tool. Only runs with default input options (max correlation time 10% of the total trajectory).

__init__(previous_job, **kwargs)[source]¶

previous_job: AMSJob

An AMSJob with an MD trajectory. Note that the trajectory should have been equilibrated before it starts. It must have been run with the BinLog%PressureTensor option set.

kwargs: dict

Other options to AMSAnalysisJob

class AMSViscosityFromBinLogResults(job)[source]¶

Results class for AMSViscosityFromBinLogJob

get_viscosity_integral()[source]¶

Extract the running viscosity integral.

Returns a 2-tuple with 1D numpy arrays time, viscosity_integral, with time in fs and viscosity_integral in Pa*s.

get_double_exponential_fit()[source]¶

Perform a double exponential fit to the viscosity integral.

The fitted function is of the form

A * (lam * (1 - np.exp(-x / tau1)) + (1 - lam) * (1 - np.exp(-x / tau2)))

where A is the limiting value in the infinite time limit.

Returns: a 3-tuple popt, time, prediction, where

• popt is a 4-tuple containing A, lam, tau1, and tau2,

• time is in fs, and

• prediction is the value of the above function vs time.