pylammpsmpi.wrapper.concurrent module¶

class pylammpsmpi.wrapper.concurrent.LammpsConcurrent(cores: int = 8, oversubscribe: bool = False, working_directory: str = '.', hostname_localhost: bool | None = None, cmdargs: list[Any] | None = None, executor: BaseExecutor | None = None)¶

Bases: object

close()¶

Close the current lammps object

Parameters:: None
Return type:: None

command(cmd)¶

Send a command to the lammps object

Parameters:: cmd (string, list of strings) – command to be sent
Return type:: None

create_atoms(n, id, type, x, v=None, image=None, shrinkexceed=False) → Future¶

Create atoms on all processors.

Parameters:

n (int) – Number of atoms.
id (list of ints, optional) – IDs of N atoms that need to be created.
type (list of atom types, optional) – Type of N atoms.
x (list of positions) – List of positions for N atoms.
v (list of velocities, optional) – List of velocities for N atoms.
image (list of ints, optional) – List of image flags for N atoms.
shrinkexceed (bool, optional) – Whether to shrink the box if the atoms exceed the box boundaries.

Return type:

None

extract_atom(name: str) → Future¶

Extract a property of the atoms.

Parameters:: name (str) – The property of the atom to be extracted.
Returns:: val – A future object representing the extracted property of the atoms.
Return type:: Future

extract_box() → Future¶

Get the simulation box.

Returns:: box – A future object representing the simulation box.
Return type:: Future

extract_compute(id, style, type, length=0, width=0)¶

Extract compute value from the lammps library

Parameters:

id (string) – id of the compute
style ({0, 1}) – 0 - global data 1 - per atom data
type ({0, 1, 2}) – 0 - scalar 1 - vector 2 - array
length (int, optional. Default 0) – if style is 0 and type is 1 or 2, then length is the length of vector.
width (int, optional. Default 0) – if type is 2, then width is the number of elements in each element along length.

Returns:

data computed by the fix depending on the chosen inputs

Return type:

val

extract_fix(*args) → Future¶

Extract a fix value.

Parameters:: args (tuple) – Variable number of arguments specifying the fix value to extract.
Returns:: value – A future object representing the extracted fix value.
Return type:: Future

extract_global(name: str) → Future¶

Extract value of global simulation parameters.

Parameters:: name (str) – Name of the global simulation parameter.
Returns:: value – A future object representing the value of the requested global parameter.
Return type:: Future

extract_setting(*args)¶

extract_variable(*args) → Future¶

Extract the value of a variable.

Parameters:: args (tuple) – Variable number of arguments specifying the variable to extract.
Returns:: data – A future object representing the value of the variable.
Return type:: Future

file(inputfile: str) → Future¶

Read script from an input file.

Parameters:: inputfile (str) – Name of the input file.
Return type:: None

find_compute_neighlist(*args)¶: Find neighbor list index of compute neighbor list :param computeid: name of compute :type computeid: string :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int

find_fix_neighlist(*args)¶: Find neighbor list index of fix neighbor list :param fixid: name of fix :type fixid: string :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int

find_pair_neighlist(*args)¶: Find neighbor list index of pair style neighbor list Try finding pair instance that matches style. If exact is set, the pair must match style exactly. If exact is 0, style must only be contained. If pair is of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style. Once the pair instance has been identified, multiple neighbor list requests may be found. Every neighbor list is uniquely identified by its request index. Thus, providing this request index ensures that the correct neighbor list index is returned. :param style: name of pair style that should be searched for :type style: string :param exact: controls whether style should match exactly or only must be contained in pair style name, defaults to True :type exact: bool, optional :param nsub: match nsub-th hybrid sub-style, defaults to 0 :type nsub: int, optional :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int

gather_atoms(*args, concat=False, ids=None)¶

Gather atom properties

Parameters:

name ({'x', 'mass', 'id', 'type', 'mask', 'v', 'f',) – ‘molecule’, ‘q’, ‘mu’, ‘omega’, ‘angmom’, ‘torque’, ‘radius’} the property of atom to be extracted
concat (bool, optional. Default False) – If True, gather information from all processors, but not sorted according to Atom ids
ids (list, optional. Default None) – If a list of ids are provided, the required information for only those atoms are returned

Returns:

val – If the requested name has multiple dimensions, output will be a multi-dimensional array.

Return type:

array of length n_atoms sorted by atom ids

Notes

This method gathers information from all processors.

pylammpsmpi.wrapper.concurrent module¶

pylammpsmpi

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