crys

Angstrom	Convert a string or number to a floating point number, if possible.
FakeASEAtoms([scaled_positions, cell, symbols])	Mimic the basic behavior of ase.Atoms.
Structure([set_all_auto, units])	Container class for representing a single crystal structure (unit cell + atoms).
Trajectory(*args, **kwds)	Like Structure, but all attrs in attrs_nstep have a timeaxis along axis=0 and length nstep:
UnitsHandler()	Base class for Structure, providing unit conversion methods.
_trans(coords, old, new)	Helper for coord_trans().
align_cart(obj[, x, y, vecs, indices, cart, eps])	Align obj w.r.t.
angle(x, y)	Angle between vectors x and y in degrees.
angles(struct[, pbc, mask_val, deg])	Wrapper for _flib.angles(), which accepts a Structure.
atoms2struct(at)	Transform ASE Atoms object to Structure.
call_vmd_measure_gofr(trajfn[, dr, rmax, ...])	Call VMD's "measure gofr" command.
cc2cell(cryst_const)	From crystallographic constants a, b, c, alpha, beta, gamma to cell.
cc2cell3d(cryst_const[, axis])	Same as cc2cell() for 2d arrays (the name "3d" is just to indicate that we work w/ trajectories).
cc2celldm(cryst_const[, fac])	Convert cryst_const to PWscf celldm.
cell2cc(cell)	From cell to crystallographic constants a, b, c, alpha, beta, gamma.
cell2cc3d(cell[, axis])	Same as cell2cc() for 3d arrays.
celldm2cc(celldm[, fac])	Convert PWscf celldm to cryst_const.
center_on_atom(obj_in[, idx, copy])	Shift all coords in obj such that the atom with index idx is at the center of the cell: [0.5,0.5,0.5] fractional coords.
compress(traj[, copy])	Wrapper for Trajectory.compress().
concatenate(lst)	Concatenate Structure or Trajectory objects into one Trajectory.
coord_trans(coords[, old, new, copy, axis])	General-purpose n-dimensional coordinate transformation.
coord_trans3d(coords[, old, new, copy, ...])	Special case version for debugging mostly.
distances(struct[, pbc, squared, fullout])	Wrapper for _flib.distsq_frac().
distances_traj(traj[, pbc])	Cartesian distances along a trajectory.
grid_in_cell(cell[, h, size, minpoints, ...])	For a given cell, generate grid size from grid spacing h or vice versa.
kgrid(cell, **kwds)	Calculate k-point grid for given real-space cell or grid spacing from grid size.
mean(traj)	Mean of Trajectory along timeaxis, like numpy.mean(array,axis=0).
min_image_convention(sij[, copy])	Apply minimum image convention to differences of fractional coords.
mix(st1, st2, alpha)	Linear interpolation between two Structures based on the numbers in alpha.
nearest_neighbors(struct[, idx, skip, ...])	Indices of the nearest neighbor atoms to atom idx, skipping atoms whose symbols are skip.
nearest_neighbors_from_dists(dists, symbols)	Core part of nearest_neighbors(), which accepts pre-calculated distances.
nearest_neighbors_struct(struct, **kwds)	Return Structure with only nearest neighbors.
pbc_wrap(obj[, copy])	Apply periodic boundary conditions to fractional coords.
pbc_wrap_coords(coords_frac[, copy, mask, ...])	Apply periodic boundary conditions to array of fractional coords.
pi	Convert a string or number to a floating point number, if possible.
populated_attrs(lst)	Set with attr names which are not None in all objects in lst.
recip_cell(cell)	Reciprocal lattice vectors {a,b,c}* = 2*pi / V * {b,c,a} x {c,a,b}.
rmax_smith(cell)	Calculate rmax as in [Smith], where rmax = the maximal distance up to which minimum image nearest neighbor distances are correct.
rmsd(traj[, ref_idx])	Root mean square distance over an MD trajectory.
rpdf(trajs[, dr, rmax, amask, tmask, dmask, ...])	Radial pair distribution (pair correlation) function for Structures and Trajectories.
scell(obj, dims[, method])	Build supercell based on dims.
scell3d(traj, dims, **kwds)	Supercell for Trajectory.
scell_mask(nx, ny, nz[, direc])	Build a mask for the creation of a nx x ny x nz supercell (for 3d coordinates).
smooth(traj, kern[, method])	Smooth Trajectory along timeaxis.
struct2atoms(st, **kwds)	Transform Structure to ASE Atoms object.
struct2traj(obj)	Transform Structure to Trajectory with nstep=1.
tensor2voigt(tensor)	Convert stress tensor to Voigt notation.
tensor2voigt3d(tensor)	Same as tensor2voigt() for trajectories.
velocity_traj(arr[, dt, axis, endpoints])	Calculate velocity from arr (usually coordinates) along time`axis` using timestep dt.
vmd_measure_gofr(traj[, dr, rmax, sel, ...])	Call call_vmd_measure_gofr(), accept Structure / Trajectory as input.
voigt2tensor(voigt)	Convert Voigt stress array to stress tensor.
voigt2tensor3d(voigt)	Same as voigt2tensor() for trajectories.
volume_cc(cryst_const)	Volume of the unit cell from crystallographic constants [1]_.
volume_cc3d(cryst_const[, axis])	Same as volume_cc() for 2d arrays (the name "3d" is just to indicate that we work w/ trajectories).
volume_cell(cell)	Volume of the unit cell from cell vectors. Calculates the triple product::.
volume_cell3d(cell[, axis])	Same as volume_cell() for 3d arrays.