`pysimm.lmps`¶

Module Contents¶

Classes¶

`Init`	pysimm.lmps.Init
`Region`	pysimm.lmps.Region
`CreateBox`	pysimm.lmps.CreateBox
`Group`	pysimm.lmps.Group
`Velocity`	pysimm.lmps.Velocity
`OutputSettings`	pysimm.lmps.OutputSettings
`Qeq`	pysimm.lmps.MolecularDynamics
`MolecularDynamics`	pysimm.lmps.MolecularDynamics
`SteeredMolecularDynamics`	pysimm.lmps.MolecularDynamics
`Minimization`	pysimm.lmps.Minimization
`CustomInput`	pysimm.lmps.CustomInput
`Simulation`	pysimm.lmps.Simulation
`LogFile`	pysimm.lmps.LogFile

Functions¶

`check_lmps_exec`()
`enqueue_output`(out, queue)	pysimm.lmps.enqueue_output
`call_lammps`(simulation, np, nanohub, prefix='mpiexec')	pysimm.lmps.call_lammps
`qeq`(s, np=None, nanohub=None, **kwargs)	pysimm.lmps.qeq
`quick_md`(s, np=None, nanohub=None, **kwargs)	pysimm.lmps.quick_md
`quick_min`(s, np=None, nanohub=None, **kwargs)	pysimm.lmps.quick_min
`energy`(s, all=False, np=None, **kwargs)	pysimm.lmps.energy
`check_lmps_attr`(s)

Attributes¶

`pd`
`LAMMPS_EXEC`
`verbose`
`templates`
`FF_SETTINGS`

pysimm.lmps.pd[source]¶

pysimm.lmps.LAMMPS_EXEC[source]¶

pysimm.lmps.verbose = False[source]¶

pysimm.lmps.templates[source]¶

pysimm.lmps.FF_SETTINGS[source]¶

pysimm.lmps.check_lmps_exec()[source]¶

class pysimm.lmps.Init(**kwargs)[source]¶

Bases: object

pysimm.lmps.Init

Template object to contain LAMMPS initialization settings

forcefield¶: name of a supported force field; simulation settings will be chosen based on the force field name

units¶: LAMMPS set of units to use during simulation; default=real

atom_style¶: LAMMPS aomt_style to use during simulation; default=full

charge¶: option to define if any particles in system a non-zero charge

kspace_style¶: LAMMPS kspace_style to use during simulation if system has charges; default=pppm 1e-4

cutoff¶: dictionary of cutoff distances for nonbonded interactions; default={‘lj’: 12.0, ‘coul’: 12.0, ‘inner_lj’: 10.0}

pair_style¶: LAMMPS pair_style to use during simulation

bond_style¶: LAMMPS bond_style to use during simulation

angle_style¶: LAMMPS angle_style to use during simulation

dihedral_style¶: LAMMPS dihedral_style to use during simulation

improper_style¶: LAMMPS improper_style to use during simulation

special_bonds¶: LAMMPS special_bonds to use during simulation

pair_modify¶: LAMMPS pair_modify to use during simulation

read_data¶: name of data file to read instead of using System object

write(self, sim=None)[source]¶

pysimm.lmps.Init.write

Prepare LAMMPS input with initialization settings

Parameters: sim – Simulation object reference
Returns: string of LAMMPS input

class pysimm.lmps.Region(name='all', style='block', *args, **kwargs)[source]¶

Bases: pysimm.utils.Item

pysimm.lmps.Region

Template object to create a region in a LAMMPS simulation. See LAMMPS documentation for further information

name¶: name id for region

style¶: LAMMPS region style

\*args: args for given style

\*\*kwargs: optional kwargs for region command

write(self, sim=None)[source]¶

class pysimm.lmps.CreateBox(n=1, region=Region(), *args, **kwargs)[source]¶

Bases: pysimm.utils.Item

pysimm.lmps.CreateBox

Template object to create a box in a LAMMPS simulation. See LAMMPS documentation for further information

n¶: number of atom types

region¶: Region object

\*\*kwargs: optional kwargs for create_box command (replace / with _)

write(self, sim=None)[source]¶

class pysimm.lmps.Group(name='all', style='id', *args, **kwargs)[source]¶

Bases: pysimm.utils.Item

pysimm.lmps.Group

Template object to define a group in a LAMMPS simulation. See LAMMPS documentation for further information

name¶: name for the group

style¶: style for the group

\*args: arguments for the given style

write(self, sim=None)[source]¶

class pysimm.lmps.Velocity(group=Group('all'), style='create', *args, **kwargs)[source]¶

Bases: pysimm.utils.Item

pysimm.lmps.Velocity

Template object to define velocity initialization in a LAMMPS simulation. See LAMMPS documentation for further information

group¶: group for velocity command

style¶: style for the velocity command

\*args: arguments for the given style

write(self, sim=None)[source]¶

class pysimm.lmps.OutputSettings(**kwargs)[source]¶

Bases: object

pysimm.lmps.OutputSettings

Template object to define thermo and dump output settings in a LAMMPS simulation. See LAMMPS documentation for further information

thermo¶: dictionary of settings for thermo output

dump¶: dictionary of settings for dump output

write(self, sim=None)[source]¶

class pysimm.lmps.Qeq(**kwargs)[source]¶

Bases: object

pysimm.lmps.MolecularDynamics

Template object to contain LAMMPS qeq settings

cutoff¶: distance cutoff for charge equilibration

tol¶: tolerance (precision) for charge equilibration

max_iter¶: maximum iterations

qfile¶: file with qeq parameters (leave undefined for defaults)

write(self, sim=None)[source]¶

pysimm.lmps.Qeq.write

Create LAMMPS input for a charge equilibration calculation

Parameters: sim – Simulation object reference
Returns: input string

class pysimm.lmps.MolecularDynamics(**kwargs)[source]¶

Bases: object

pysimm.lmps.MolecularDynamics

Template object to contain LAMMPS MD settings

name¶: name to identify MD

group¶: Group object for integrator

timestep¶: timestep value to use during MD

ensemble¶: ‘nvt’ or ‘npt’ or ‘nve’; default=nve

limit¶: numerical value to use with nve when limiting particle displacement

temperature¶: dictionary of settings for temperature (start, stop, damp)

pressure¶: dictionary of settings for pressure (start, stop, damp)

run¶: length of MD simulation in number of timesteps or False to omit run command

unfix¶: True to include command to unfix integrator after run

rigid¶: dictionary of settings for a rigid simulation

extra_keywords¶: dictionary of extra keywords to append at the end of the LAMMPS fix integrator

write(self, sim=None)[source]¶

pysimm.lmps.MolecularDynamics.write

Create LAMMPS input for a molecular dynamics simulation.

Parameters: sim – pysimm.lmps.Simulation object reference
Returns: input string

class pysimm.lmps.SteeredMolecularDynamics(**kwargs)[source]¶

Bases: MolecularDynamics

pysimm.lmps.MolecularDynamics

Template object to contain LAMMPS MD settings

name¶: name to identify MD

group¶: Group object for integrator

timestep¶: timestep value to use during MD

ensemble¶: ‘nvt’ or ‘npt’ or ‘nve’; default=nve

limit¶: numerical value to use with nve when limiting particle displacement

temperature¶: dictionary of settings for temperature (start, stop, damp)

pressure¶: dictionary of settings for pressure (start, stop, damp)

run¶: length of MD simulation in number of timesteps or False to omit run command

unfix¶: True to include command to unfix integrator after run

rigid¶: dictionary of settings for a rigid simulation

extra_keywords¶: dictionary of extra keywords to append at the end of the LAMMPS fix integrator

write(self, sim=None)[source]¶

pysimm.lmps.SteeredMolecularDynamics.write

Create LAMMPS input for a steered molecular dynamics simulation.

Parameters: sim – Simulation object reference
Returns: input string

class pysimm.lmps.Minimization(**kwargs)[source]¶

Bases: object

pysimm.lmps.Minimization

Template object to contain LAMMPS energy minimization settings.

min_style¶: LAMMPS minimization style default=’sd’

dmax¶: how far any atom can move in a single line search in any dimension

etol¶: energy tolerance default=1e-3

ftol¶: force tolerance default=1e-3

maxiter¶: maximum iterations default=10000

max eval: maximum force evaluations default=100000

write(self, sim=None)[source]¶

pysimm.lmps.Minimization.write

Create LAMMPS input for an energy minimization simulation.

Parameters: sim – Simulation object reference
Returns: input string

class pysimm.lmps.CustomInput(custom_input)[source]¶

Bases: object

pysimm.lmps.CustomInput

Template object to contain custom LAMMPS input.

custom_input¶: custom input string

write(self, sim=None)[source]¶

pysimm.lmps.CustomInput.write

Create LAMMPS input for a custom simulation.

Parameters: sim – pysimm.lmps.Simulation object reference
Returns: input string

class pysimm.lmps.Simulation(s, **kwargs)[source]¶

Bases: object

pysimm.lmps.Simulation

Organizational object for LAMMPS simulation. Should contain combination of MolecularDynamics, Minimization, and/or CustomInput object.

forcefield¶: name of force field for simulation settings

name¶: name for simulation

log¶: LAMMPS log filename

write¶: file name to write final LAMMPS data file default=None

print_to_screen¶: True to have LAMMPS output printed to stdout after simulation ends

debug¶: True to have LAMMPS output streamed to stdout during simulation (WARNING: this may degrade performance)

custom¶: option to flag simulation as purley custom input to skip prepaing initialization

add(self, *args)[source]¶

add_qeq(self, template=None, **kwargs)[source]¶

pysimm.lmps.Simulation.add_qeq

Add Qeq template to simulation

Parameters

template – Qeq object reference
**kwargs – if template is None these are passed to Qeq constructor to create new template

add_md(self, template=None, **kwargs)[source]¶

pysimm.lmps.Simulation.add_md

Add MolecularDyanmics template to simulation

Parameters

template – MolecularDynamics object reference
**kwargs – if template is None these are passed to MolecularDynamics constructor to create new template

add_min(self, template=None, **kwargs)[source]¶

pysimm.lmps.Simulation.add_min

Add Minimization template to simulation

Parameters

template – Minimization object reference
**kwargs – if template is None these are passed to Minimization constructor to create new template

add_custom(self, custom='')[source]¶

pysimm.lmps.Simulation.add_custom

Add custom input string to simulation

Parameters: custom – custom LAMMPS input string to add to Simulation

property input(self)[source]¶

write_input(self, init=True)[source]¶

pysimm.lmps.Simulation.write_input

Creates LAMMPS input string including initialization and input from templates/custom input

Parameters: None –
Returns: None

run(self, np=None, nanohub=None, save_input=True, prefix='mpiexec')[source]¶

pysimm.lmps.Simulation.run

Begin LAMMPS simulation.

Parameters

np – number of threads to use (serial by default) default=None
nanohub – dictionary containing nanohub resource information default=None
init – True to write initialization part of LAMMPS input script (set to False if using complete custom input)
save_input – True to save input as pysimm.sim.in
prefix – prefix for running LAMMPS (i.e. - mpiexec)

pysimm.lmps.enqueue_output(out, queue)[source]¶

pysimm.lmps.enqueue_output

Helps queue output for printing to screen during simulation.

pysimm.lmps.call_lammps(simulation, np, nanohub, prefix='mpiexec')[source]¶

pysimm.lmps.call_lammps

Wrapper to call LAMMPS using executable name defined in pysimm.lmps module.

Parameters

simulation – Simulation object reference
np – number of threads to use
nanohub – dictionary containing nanohub resource information default=None
prefix – prefix for running LAMMPS (i.e. - mpiexec)

Returns

None

pysimm.lmps.qeq(s, np=None, nanohub=None, **kwargs)[source]¶

pysimm.lmps.qeq

Convenience function to call a qeq calculation. kwargs are passed to Qeq constructor

Parameters

s – system to perform simulation on
np – number of threads to use
nanohub – dictionary containing nanohub resource information default=None

Returns

None

pysimm.lmps.quick_md(s, np=None, nanohub=None, **kwargs)[source]¶

pysimm.lmps.quick_md

Convenience function to call an individual MD simulation. kwargs are passed to MD constructor

Parameters

s – system to perform simulation on
np – number of threads to use
nanohub – dictionary containing nanohub resource information default=None

Returns

None

pysimm.lmps.quick_min(s, np=None, nanohub=None, **kwargs)[source]¶

pysimm.lmps.quick_min

Convenience function to call an individual energy minimization simulation. kwargs are passed to min constructor

Parameters

s – system to perform simulation on
np – number of threads to use
nanohub – dictionary containing nanohub resource information default=None

Returns

None

pysimm.lmps.energy(s, all=False, np=None, **kwargs)[source]¶

pysimm.lmps.energy

Convenience function to calculate energy of a given System object.

Parameters

s – system to calculate energy
all – returns decomposition of energy if True (default: False)
np – number of threads to use for simulation

Returns

total energy or disctionary of energy components

pysimm.lmps.check_lmps_attr(s)[source]¶

class pysimm.lmps.LogFile(fname)[source]¶

Bases: object

pysimm.lmps.LogFile

Class to read LAMMPS log file into Pandas DataFrame stored in LogFile.data

fname¶: filename of log file

data¶: resulting DataFrame with log file data

_read(self, fname)[source]¶

pysimm.lmps¶

Module Contents¶

Classes¶

Functions¶

Attributes¶

`pysimm.lmps`¶