pylammpsmpi.wrapper.concurrent module¶

class pylammpsmpi.wrapper.concurrent.LammpsConcurrent(cores=8, oversubscribe=False, working_directory='.', cmdargs=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)¶

Create atoms on all procs

Parameters:

n (int) – number of atoms
id (list of ints, optional) – ids of N atoms that need to be created if not specified, ids from 1 to N are assigned
type (list of atom types, optional) – type of N atoms, if not specied, all atoms are assigned as type 1
x (list of positions) – list of the type [posx, posy, posz] for N atoms
v (list of velocities) – list of the type [vx, vy, vz] for N atoms
image (list of ints, optional) – if not specified a list of 0s will be used.
shrinkexceed (bool, optional) – default False

Return type:

None

extract_atom(name)¶

Extract a property of the atoms

Parameters:: name ({'x', 'mass', 'id', 'type', 'mask', 'v', 'f',) – ‘molecule’, ‘q’, ‘mu’, ‘omega’, ‘angmom’, ‘torque’, ‘radius’} the property of atom to be extracted
Returns:: val – If the requested name has multiple dimensions, output will be a multi-dimensional array.
Return type:: array of length n_atoms

Notes

This method only gathers information from the current processor. Rest of the values would be zero.

See also

scatter_atoms

extract_box()¶

Get the simulation box

Parameters:: None
Returns:: box – of the form [boxlo,boxhi,xy,yz,xz,periodicity,box_change] where boxlo and boxhi are lower and upper bounds of the box in three dimensions, xy, yz, xz are the box tilts, periodicity is an array which shows if the box is periodic in three dimensions.
Return type:: list

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)¶

Extract a fix value

Parameters:

id (string) – id of the fix
style ({0, 1, 2}) – 0 - global data 1 - per-atom data 2 - local data
type ({0, 1, 2}) – 0 - scalar 1 - vector 2 - array
i (int, optional) – index to select fix output
j (int, optional) – index to select fix output

Returns:

Fix data corresponding to the requested dimensions

Return type:

value

extract_global(name)¶

Extract value of global simulation parameters

Parameters:: name (string) – see notes for a set of possible options

Notes

The possible options for name are- “dt”, “boxlo”, “boxhi”, “boxxlo”, “boxxhi”, “boxylo”, “boxyhi”, “boxzlo”, “boxzhi”, “periodicity”, “xy”, “xz”, “yz”, “natoms”, “nbonds”, “nangles”, “ndihedrals”, “nimpropers”, “nlocal”, “nghost”, “nmax”, “ntypes”, “ntimestep”, “units”, “triclinic”, “q_flag”, “atime”, “atimestep”

Also global constants defined by units can be accessed- “boltz”, “hplanck”, “mvv2e”, “ftm2v”, “mv2d”, “nktv2p”, “qqr2e”, “qe2f”, “vxmu2f”, “xxt2kmu”, “dielectric”, “qqr2e”, “e_mass”, “hhmrr2e”, “mvh2r”, “angstrom”, “femtosecond”, “qelectron”

extract_setting(*args)¶

extract_variable(*args)¶

Extract the value of a variable

Parameters:

name (string) – name of the variable
group (string) – group id (ignored for equal style variables)
flag ({0, 1}) – 0 - equal style variable 1 - atom style variable

Returns:

value of variable depending on the requested dimension

Return type:

data

Notes

Currently only returns the information provided on a single processor

file(inputfile)¶

Read script from an input file

Parameters:: inputfile (string) – name of inputfile
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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