matscipy.io.opls

Functions

`read_block`(filename, name)	Read a named data block from a parameter file for a non-reactive potential. Blocks begin with `# name` and are terminated by empty lines. Using the function on a file named `parameterfile` which contains a block named `Bonds` and the following entries :: # Bonds C1-C1 10.0 1.0 H1-H1 20.0 2.0.
`read_cutoffs`(filename)	Read the cutoffs for construction of a non-reactive system from a file. Comments in the file begin with `#`, the file should be structured like this: :: # Cutoffs C1-C1 1.23 # name, cutoff (A) H1-H1 4.56 # name, cutoff (A) C1-H1 7.89 # name, cutoff (A).
`read_extended_xyz`(fileobj)	Read an extended xyz file with labeled atoms. The number of atoms should be given in the first line, the second line contains the cell dimensions and the definition of the columns. The file should contain the following columns: element (1 or 2 characters), x(float), y(float), z (float), molecule id (int), name (1 or 2 characters). A full description of the extended xyz format can be found for example in the ASE documentation. An example for a file defining an H2 molecule is given below. :: 2 Lattice="10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0" Properties=species:S:1:pos:R:3:molid:I:1:type:S:1 H 4.5 5.0 5.0 1 H1 H 5.5 5.0 5.0 1 H1.
`read_lammps_data`(filename[, ...])	Read positions, bonds, angles and dihedrals from a LAMMPS file.
`read_lammps_definitions`(filename)	Reads force field definitions from a LAMMPS parameter file and stores the parameters in `matscipy.opls.LJQData`, `matscipy.opls.BondData`, `matscipy.opls.AnglesData` and `matscipy.opls.DihedralsData` objects.
`read_parameter_file`(filename)	Read the parameters of a non-reactive potential from a file. An example for the file structure is given below. The blocks are separated by empty lines, comments begin with `#`. For more information about the potentials, refer to the documentation of the LAMMPS commands `bond_style harmonic`, `angle_style harmonic`, `dihedral_style harmonic`. The default global cutoffs for Lennard-Jones and Coulomb interactions are 10.0 and 7.4 A. They can be overridden with the optional `Cutoffs-LJ-Coulomb` block. By default, geometric mixing is applied between Lennard-Jones parameters of different particle types and the global cutoff is used for all pairs. This behavior can be overridden using the optional `LJ-pairs` block. :: # Element C1 0.001 3.5 -0.01 # name, LJ-epsilon (eV), LJ-sigma (A), charge (e) H1 0.001 2.5 0.01 # name, LJ-epsilon (eV), LJ-sigma (A), charge (e).
`update_from_lammps_dump`(atoms, filename[, check])	Read simulation cell, positions and velocities from a LAMMPS dump file and use them to update an existing configuration.
`write_lammps`(prefix, atoms)	Convenience function.
`write_lammps_atoms`(prefix, atoms[, units])	Write atoms input for LAMMPS.
`write_lammps_definitions`(prefix, atoms)	Write force field definitions for LAMMPS.
`write_lammps_in`(prefix)	Writes a simple LAMMPS input script for a structure optimization using a non-reactive potential.

matscipy.io.opls.read_extended_xyz(fileobj)

Read an extended xyz file with labeled atoms. The number of atoms should be given in the first line, the second line contains the cell dimensions and the definition of the columns. The file should contain the following columns: element (1 or 2 characters), x(float), y(float), z (float), molecule id (int), name (1 or 2 characters). A full description of the extended xyz format can be found for example in the ASE documentation. An example for a file defining an H2 molecule is given below.

2
Lattice="10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0" Properties=species:S:1:pos:R:3:molid:I:1:type:S:1
H 4.5 5.0 5.0 1 H1
H 5.5 5.0 5.0 1 H1

Parameters:: filename (str) – Name of the file to read from.
Returns:: Atomic structure as defined in the input file.
Return type:: matscipy.opls.OPLSStructure

matscipy.io.opls.read_block(filename, name)

Read a named data block from a parameter file for a non-reactive potential. Blocks begin with # name and are terminated by empty lines. Using the function on a file named parameterfile which contains a block named Bonds and the following entries

# Bonds
C1-C1 10.0 1.0
H1-H1 20.0 2.0

will return the following dictionary:

{'C1-C1': [10., 1.], 'H1-H1': [20., 2.]}

Parameters:

filename (str) – Name of the file to read from.
name (str) – Name of the data block to search for.

Returns:

Name-Value pairs. Each value is a list of arbitrary length.

Return type:

dict

Raises:

RuntimeError – If data block name is not found in the file.

matscipy.io.opls.read_cutoffs(filename)

Read the cutoffs for construction of a non-reactive system from a file. Comments in the file begin with #, the file should be structured like this:

# Cutoffs
C1-C1 1.23  # name, cutoff (A)
H1-H1 4.56  # name, cutoff (A)
C1-H1 7.89  # name, cutoff (A)

Parameters:: filename (str) – Name of the file to read from.
Returns:: Cutoffs.
Return type:: matscipy.opls.CutoffList

matscipy.io.opls.read_parameter_file(filename)

Read the parameters of a non-reactive potential from a file. An example for the file structure is given below. The blocks are separated by empty lines, comments begin with #. For more information about the potentials, refer to the documentation of the LAMMPS commands bond_style harmonic, angle_style harmonic, dihedral_style harmonic. The default global cutoffs for Lennard-Jones and Coulomb interactions are 10.0 and 7.4 A. They can be overridden with the optional Cutoffs-LJ-Coulomb block. By default, geometric mixing is applied between Lennard-Jones parameters of different particle types and the global cutoff is used for all pairs. This behavior can be overridden using the optional LJ-pairs block.

# Element
C1 0.001 3.5 -0.01  # name, LJ-epsilon (eV), LJ-sigma (A), charge (e)
H1 0.001 2.5  0.01  # name, LJ-epsilon (eV), LJ-sigma (A), charge (e)

# Cutoffs-LJ-Coulomb (this block is optional)
LJ 10.0  # distance (A)
C  10.0  # distance (A)

# LJ-pairs (this block is optional)
C1-H1 0.002 2.1 12.0  # name, epsilon (eV), sigma (A), cutoff (A)

# Bonds
C1-C1 10.0 1.0  # name, spring constant*2 (eV/A**2), distance (A)

# Angles
H1-C1-C1 1.0 100.0  # name, spring constant*2 (eV), equilibrium angle

# Dihedrals
H1-C1-C1-H1 0.0 0.0 0.01 0.0  # name, energy (eV), energy (eV), ...

# Cutoffs
C1-C1 1.85  # name, cutoff (A)
C1-H1 1.15  # name, cutoff (A)

Parameters:

filename (str) – Name of the file to read from.

Returns:

cutoffs (matscipy.opls.CutoffList) – Cutoffs.
ljq (matscipy.opls.LJQData) – Lennard-Jones data and atomic charges.
bonds (matscipy.opls.BondData) – Bond coefficients, i.e. spring constants and equilibrium distances.
angles (matscipy.opls.AnglesData) – Angle coefficients.
dihedrals (matscipy.opls.DihedralsData) – Dihedral coefficients.

matscipy.io.opls.write_lammps(prefix, atoms)

Convenience function. The functions matscipy.io.opls.write_lammps_in(), matscipy.io.opls.write_lammps_atoms() and matscipy.io.opls.write_lammps_definitions() are usually called at the same time. This function combines them, filenames will be prefix.in, prefix.atoms and prefix.opls.

Parameters:

prefix (str) – Prefix for filenames.
atoms (matscipy.opls.OPLSStructure) – The atomic structure to be written.

matscipy.io.opls.write_lammps_in(prefix)

Writes a simple LAMMPS input script for a structure optimization using a non-reactive potential. The name of the resulting script is prefix.in, while the atomic structure is defined in prefix.atoms and the definition of the atomic interaction in prefix.opls.

Parameters:: prefix (str) – Prefix for filename.

matscipy.io.opls.write_lammps_atoms(prefix, atoms, units='metal')

Write atoms input for LAMMPS. Filename will be prefix.atoms.

Parameters:

prefix (str) – Prefix for filename.
atoms (matscipy.opls.OPLSStructure) – The atomic structure to be written.
units (str, optional) – The units to be used.

matscipy.io.opls.write_lammps_definitions(prefix, atoms)

Write force field definitions for LAMMPS. Filename will be prefix.opls.

Parameters:

prefix (str) – Prefix for filename.
atoms (matscipy.opls.OPLSStructure) – The atomic structure for which the force field definitions should be written. Must contain at least Lennard-Jones and charge data matscipy.opls.LJQData. Bond-, angle- and dihedral-potentials are optional and are written if they are present: matscipy.opls.BondData, matscipy.opls.AnglesData, matscipy.opls.DihedralsData.

matscipy.io.opls.read_lammps_definitions(filename)

Reads force field definitions from a LAMMPS parameter file and stores the parameters in matscipy.opls.LJQData, matscipy.opls.BondData, matscipy.opls.AnglesData and matscipy.opls.DihedralsData objects. The ‘number’ of the particles, pairs, … for the corresponding interaction parameters is not included in these objects and is output in dicts. Note that there is an offset of one between LAMMPS and python numbering.

Parameter file:

bond_style      harmonic
bond_coeff      1 1.2 3.4 # AA-AA
bond_coeff      2 5.6 7.8 # AA-BB

Returned dictionary:

bond_type_index[0] = 'AA-AA'
bond_type_index[1] = 'AA-BB'

Parameters:

filename (str) – Name of the file to read from.

Returns:

ljq_data (matscipy.opls.LJQData) – Lennard-Jones and charge data.
bond_data (matscipy.opls.BondData) – Parameters of the harmonic bond potentials.
ang_data (matscipy.opls.AnglesData) – Parameters of the harmonic angle potentials.
dih_data (matscipy.opls.DihedralsData) – Parameters of the OPLS dihedral potentials.
particle_type_index (dict) – Indicees of particle types as used by LAMMPS.
bond_type_index (dict) – Indicees of bond types as used by LAMMPS.
ang_type_index (dict) – Indicees of angle types as used by LAMMPS.
dih_type_index (dict) – Indicees of dihedral types as used by LAMMPS.

matscipy.io.opls.read_lammps_data(filename, filename_lammps_params=None)

Read positions, bonds, angles and dihedrals from a LAMMPS file. Optionally, a LAMMPS parameter file can be specified to restore all interactions from a preceding simulation.

Parameters:

filename (str) – Name of the file to read the atomic configuration from.
filename_lammps_params (str, optional) – Name of the file to read the interactions from.

Returns:

Atomic structure as defined in the input file.

Return type:

matscipy.opls.OPLSStructure

matscipy.io.opls.update_from_lammps_dump(atoms, filename, check=True)

Read simulation cell, positions and velocities from a LAMMPS dump file and use them to update an existing configuration.

Parameters:

atoms (matscipy.opls.OPLSStructure) – Atomic structure to be updated.
filename (str) – Name of the file to read the atomic configuration from.
check (bool, optional) – Make sure that the particle types in the input structure and the read-in file are the same.

Returns:

Atomic structure as defined in the input file.

Return type:

matscipy.opls.OPLSStructure