dpdata.md package

Submodules

dpdata.md.msd module

dpdata.md.msd.msd(system, sel=None, begin=0, window=0)

dpdata.md.pbc module

dpdata.md.pbc.apply_pbc(system_coords, system_cells)

dpdata.md.pbc.dir_coord(coord, box)

dpdata.md.pbc.posi_diff(box, r0, r1)

dpdata.md.pbc.posi_shift(box, r0, r1)

dpdata.md.pbc.system_pbc_shift(system)

dpdata.md.rdf module

dpdata.md.rdf.compute_rdf(box, posis, atype, sel_type=[None, None], max_r=5, nbins=100)

dpdata.md.rdf.rdf(sys, sel_type=[None, None], max_r=5, nbins=100)

Compute the rdf of a system.

Parameters:

sysSystem or LabeledSystem

The dpdata system

sel_typelist

List of size 2. The first element specifies the type of the first atom, while the second element specifies the type of the second atom. Both elements can be ints or list of ints. If the element is None, all types are specified. Examples are sel_type = [0, 0], sel_type = [0, [0, 1]] or sel_type = [0, None]

max_rfloat

Maximal range of rdf calculation

nbinsint

Number of bins for rdf calculation

Returns:

xx: np.array

The lattice of r

rdf: np.array

The value of rdf at r

coord: np.array

The coordination number up to r

dpdata.md.water module

dpdata.md.water.compute_bonds(box, posis, atype, oh_sel=[0, 1], max_roh=1.3, uniq_hbond=True)

dpdata.md.water.compute_bonds_ase(box, posis, atype, oh_sel=[0, 1], max_roh=1.3, uniq_hbond=True)

dpdata.md.water.compute_bonds_naive(box, posis, atype, oh_sel=[0, 1], max_roh=1.3, uniq_hbond=True)

dpdata.md.water.find_ions(atype, bonds, oh_sel=[0, 1], ret_h2o=True)

dpdata.md.water.pbc_coords(cells, coords, atom_types, oh_sel=[0, 1], max_roh=1.3)