ipymd.data_input package

Subpackages

• ipymd.data_input.spacegroup package
  • Submodules
  • ipymd.data_input.spacegroup.cell module
  • ipymd.data_input.spacegroup.spacegroup module
  • Module contents

Submodules

ipymd.data_input.base module

Created on Sun May 1 22:49:20 2016

@author: cjs14

class ipymd.data_input.base.DataInput

Bases: object

Data is divided into two levels; atomic and meta

• atom is a series of tables, one for each timestep, containing variables (columns) for each atom (rows)
• meta is a table containing variables (columns) for each configuration (rows)

count_configs()

return int of total number of atomic configurations

get_atom_data(config=1)

return pandas.DataFrame of atomic data

get_meta_data(config=1)

return pandas.Series of meta data for the atomic configuration

get_meta_data_all(incl_bb=False, **kwargs)

return pandas.DataFrame of meta data for the atomic configuration

incl_bb : bool

whether to include bounding box coordinates in DataFrame

kwargs : dict

kew word arguments relevant to specific input data

setup_data()

a method to setup the data and variables

ipymd.data_input.cif module

Created on Wed May 18 22:24:10 2016

@author: cjs14

adapted from from http://physics.bu.edu/~erikl/research/tools/crystals/read_cif.py

class ipymd.data_input.cif.CIF

Bases: ipymd.data_input.base.DataInput

Data is divided into two levels; atomic and meta

• atom is a series of tables, one for each timestep, containing variables (columns) for each atom (rows)
• meta is a table containing variables (columns) for each configuration (rows)

setup_data(file_path, override_abc=[], ignore_overlaps=False)

Build a crystal from a Crystallographic Information File (.cif)

Parameters:file_path (str) –

path to file override_abc : [] or [a,b,c]

if not empty, will override a, b, c length parameters given in file

Notes

here is a typical example of a CIF file:

_cell_length_a 4.916 _cell_length_b 4.916 _cell_length_c 5.4054 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 120 _cell_volume 113.131 _exptl_crystal_density_diffrn 2.646 _symmetry_space_group_name_H-M ‘P 32 2 1’ loop_ _space_group_symop_operation_xyz

‘x,y,z’ ‘y,x,2/3-z’ ‘-y,x-y,2/3+z’ ‘-x,-x+y,1/3-z’ ‘-x+y,-x,1/3+z’ ‘x-y,-y,-z’

loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z Si 0.46970 0.00000 0.00000 O 0.41350 0.26690 0.11910

ipymd.data_input.crystal module

Created on Mon May 16 01:23:11 2016

@author: cjs14

Adapted from chemlab which, in turn, was adapted from ASE https://wiki.fysik.dtu.dk/ase/ Copyright (C) 2010, Jesper Friis

class ipymd.data_input.crystal.Crystal

Bases: ipymd.data_input.base.DataInput

Data is divided into two levels; atomic and meta

• atom is a series of tables, one for each timestep, containing variables (columns) for each atom (rows)
• meta is a table containing variables (columns) for each configuration (rows)

setup_data(positions, atom_type, group, cellpar=[1.0, 1.0, 1.0, 90, 90, 90], repetitions=[1, 1, 1], mass_map={}, charge_map={})

Build a crystal from atomic positions, space group and cell parameters (in Angstroms)

Parameters:

• positions (list of coordinates) – A list of the fractional atomic positions
• atom_type (list of atom type) – The atom types corresponding to the positions, the atoms will be translated in all the equivalent positions.
• group (int | str) – Space group given as its number in International Tables NB: to see mappings from Hermann–Mauguin notation, etc, use the get_spacegroup_df function in this module
• repetitions – Repetition of the unit cell in each direction
• cellpar – Unit cell parameters (in Angstroms and degrees)
• mass_map (dict of atom masses) – mapping of atom masses to atom types
• charge_map (dict of atom charges) – mapping of atom charges to atom types
• function was taken and adapted from the spacegroup module (This) –

:param found in ASE.: :param The module spacegroup module was originally developed by Jesper: :param Frills.:

Example

from ipymd.data_input import crystal c = crystal.Crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],

[‘Na’, ‘Cl’], 225, cellpar = [5.4, 5.4, 5.4, 90, 90, 90], repetitions = [5, 5, 5])

c.get_atom_data() c.get_simulation_box()

ipymd.data_input.crystal.get_spacegroup_df()

dataframe of spacegroup mappings

ipymd.data_input.lammps module

Created on Mon May 16 01:15:56 2016

@author: cjs14

class ipymd.data_input.lammps.LAMMPS_Input

Bases: ipymd.data_input.base.DataInput

Data is divided into two levels; atomic and meta

• atom is a series of tables, one for each timestep, containing variables (columns) for each atom (rows)
• meta is a table containing variables (columns) for each configuration (rows)

setup_data(atom_path='', atom_style='atomic')

get data from file

Parameters:atom_style ('atomic', 'charge') – defines how atomic data is listed: atomic; atom-ID atom-type x y z charge; atom-ID atom-type q x y z

class ipymd.data_input.lammps.LAMMPS_Output

Bases: ipymd.data_input.base.DataInput

Data is divided into two levels; atomic and meta

• atom is a series of tables, one for each timestep, containing variables (columns) for each atom (rows)
• meta is a table containing variables (columns) for each configuration (rows)

setup_data(atom_path='', sys_path='', sys_sep=' ', atom_map={}, incl_atom_step=False, incl_sys_data=True)

Data divided into two levels; meta and atom

atom_map : dict

mapping of atom level variable names e.g. {‘C_var[1]’:’x’}

sys_sep : str

the separator between variables in the system data file

incl_atom_time : bool

include time according to atom file in column ‘atom_step’ of meta

incl_sys_data : bool

include system data in the single step meta data

Notes

Meta level data created with fix print, e.g.;

fix sys_info all print 100 “${t} ${natoms} ${temp}” & title “time natoms temp” file system.dump screen no

Atom level data created with dump, e.g.;

dump atom_info all custom 100 atom.dump id type x y z mass q OR (file per configuration) dump atom_info all custom 100 atom_*.dump id type xs ys zs mass q

ipymd.data_input.lammps.atoi(text)

ipymd.data_input.lammps.natural_keys(text)

alist.sort(key=natural_keys) sorts in human order, e.g. [‘1’,‘2’,‘100’] instead of [‘1’,‘100’,‘2’] http://nedbatchelder.com/blog/200712/human_sorting.html

Module contents