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util

thmd.util

Modules:

check_installation

Functions:

check_install_ovito()

check_install_googlesearch()

compute_angle

Functions:

angle_vector2vectors(fixVector, arrayVectors, unit='rad')

copmute angles between a vector with set of vectors

compute_distance

Functions:

dist2_point2points(point, points)

Compute bond_len and postion_vetors from 1 point to a list of points

Parameters:

  • point (list array) –

    coordinate of 1 point.

  • points (list array) –

    2d-list of coordinates of points/point.

Returns:

  • df ( DataFrame ) –

    pd.DataFrame constains distance and component of connecting vectors.

dist2_points2line(points, line=[(0, 0, 0), (0, 0, 0)])

Compute bond_len and postion_vetors from 1 point to a list of points Ref: https://stackoverflow.com/questions/39840030/distance-between-point-and-a-line-from-two-points

Parameters:

  • points (list array DataFrame) –

    list of coordinates of points/point.

  • line (list array, default: [(0, 0, 0), (0, 0, 0)] ) –

    2d-array contains coordinates to define a line.

Returns:

  • d ( float list ) –

    distances between points and a line.

closest_points2line(points, line=[(0, 0, 0), (0, 0, 0)], distance=0, Xbound=None, Ybound=None, Zbound=None)

Find all points locate inside a checkin-distance "dist" from a line.

Parameters:

  • points (list array) –

    list of coordinates of points/point.

  • line (list array, default: [(0, 0, 0), (0, 0, 0)] ) –

    [[x1,y1,z1], [x1,y2,z2]]: 2d-list contains coordinates to define a line.

  • distance (float, default: 0 ) –

    the checkin-distance.

  • Xbound (tuple, default: None ) –

    define the boundaries for checking. Xbound='line': use the lengths of lines as bounds. Xbound=None: extend to INF. Xbound = (xlo, xhi)

  • Ybound (tuple, default: None ) –

    define the boundaries for checking.

  • Zbound (tuple, default: None ) –

    define the boundaries for checking.

Returns:

  • ds_idx ( Series ) –

    Series of indices of points within the checkin-distance

closest_points2multilines(points, multilines=[], distance=0, Xbound=None, Ybound=None, Zbound=None)

Find all points locate inside a checkin-distance "dist" from multilines. The Bound is set as the line-lengths.

Parameters:

  • points (list array) –

    list of coordinates of points/point.

  • multilines (list, default: [] ) –

    list of pair-points, each pair-point contains coordinates of 2 points to define a line used in 'closest_points2line'.

  • distance (float, default: 0 ) –

    the checkin-distance.

Returns:

  • ds_idx ( Series ) –

    Series of indices of points within the checkin-distance

compute_tensor

Functions:

ke_tensor(vel, mass, kb)

Compute Kinetic Energy tensors, and Temp Args: vel (array): Nx3 array of per-atom velocity mass (array): Nx3 array of atomic mass inUNIT (str): ['angstrom','ps','amu','eV'], outUNIT=['eV','K'] Returns: Kinetic energy tensor, Kinetic scalar, Temperature scalar

stress_tensor(per_atom_stress_tensor, atomic_volume, unitFac=1)

Compute local pressure/stress Args: per_atom_stress_tensor : Nx6 array of the per-atom stress tensor atomVol : Nx1 vector of atomVol inUNIT=['bar','angstrom'], outUNIT=['bar'] → unitFac=1e-4 for ['GPa'] Returns: pressure scalar Stress tensor

detect_sign_change

Functions:

detect_sign_change(y, x=[])

determine points where line y=y(x) change its sign

Parameters:

  • y –

    Nx1 arrays, contains dependent variable y

  • x –

    (Optinal) Nx1 arrays, contains independent variable x of line y(x)

Returns:

  • idx –

    1d array of indices where sign changes

grid_box

Functions:

  • grid_box_2d –

    devide box into 2d grid, return list of atom-IDs in each slab and list of slab-centers

  • grid_box_1d –

    devide box into 1d slabs, return list of atom-IDs in each slab and list of slab-centers

grid_box_2d(points, box, plane='XY', mode='bin_number', grid_size=[20, 20])

devide box into 2d grid, return list of atom-IDs in each slab and list of slab-centers Args: P : Nx3 array contain positions of atoms box : simulation box mode : "bin_number" or "bin_size" mode_value : corresponding 'Number-of-bins' or 'size-of-bin' plane : on which plane the box will be gridded Returns: atomIDinCell : 1xBinNumber array of 1xM-vector, contain indices of atoms of each Cell cellCenter : 1xBinNumber array of scalar, is center of each slab

grid_box_1d(points, box, axis='Z', mode='bin_number', grid_size=20)

devide box into 1d slabs, return list of atom-IDs in each slab and list of slab-centers Args: P : Nx3 array contain positions of atoms box : simulation box mode : "bin_number" or "bin_size" mode_value : corresponding 'Number-of-bins' or 'size-of-bin' axis : on which axis the box will be slabbed Returns: atomIDinCell : 1xBinNumber array of 1xM arrays, contain indices of atoms of each Slab, array of arrays geoCenter : 1xBinNumber array of scalar, is geometry center of each slab massCenter : 1xBinNumber array of scalar, is mass center of each slab

many_stuff

Functions:

memory_usage()

return the memory usage in MB

natSorted(mylist)

https://stackoverflow.com/questions/4836710/is-there-a-built-in-function-for-string-natural-sort

split_list(a, n)

Should use np.array_split instead Args: a (list): list to be splitted n (int): number of chunks Returns: generator: a generator of splitted list

find_nearest_value(array, value)

row_operation

Functions:

unique_row(X, tol_decimal=2)

find match_indices & mismatch_indices of arr(find_rows) in arr(X), return indices of X Args: X, find_rows : NxN numpy arrays tol_decimal : number of digits for round off input data

match_row(X, find_rows, tol_decimal=2)

find match_indices & mismatch_indices of arr(find_rows) in arr(X), return indices of X Args: X, find_rows : NxN numpy arrays tol_decimal : number of digits for round off input data

asvoid(arr)

Base on: https://stackoverflow.com/questions/38674027/find-the-row-indexes-of-several-values-in-a-numpy-array

string_index

Functions:

string_index(idx_list)

groupSURF index by consecutive-series

unit

This module to convert unit of some physical properties pressure

Consider to use this module: https://unyt.readthedocs.io/en/stable/usage.html

Functions:

  • pressure –

    convert unit of pressure

  • force –

    convert unit of force

  • energy –

    convert unit of energy

  • constant –

    list of constants

pressure(key_word='all_key')

convert unit of pressure Pa: Pascal atm: standard atmosphere at: technical atmosphere

kgf/cm2 = kg/cm2 1 Pa = 1 N/m^2 1 kgf/cm2 = 1

Parameters:

  • key_word (str, default: 'all_key' ) –

    a string to specify units to be converted.

Returns:

  • factor ( float ) –

    multiply factor of conversion

Examples:

key_word='Pa_atm': convert from Pa (Pascal) to atm (Standard atmosphere)

force(key_word='all_key')

convert unit of force N: Newton kgf = m.g: kilogram-force (weight: one kilogram of mass in a 9.80665 m/s2 gravitational field) lbf: pound-force p: pond

1 N = 1 J/m (Work = Force.distance) 1 kcal = 4184 J = 4184 N.m = 4184.10^10 N.Angstrom 69.4786 pN = 1 kcal/mol Angstrom. https://tinyurl.com/yb2gnlhc

Parameters:

  • key_word (str, default: 'all_key' ) –

    a string to specify units to be converted.

Returns:

  • factor ( float ) –

    multiply factor of conversion

energy(key_word='all_key')

convert unit of energy J: Joule W.h: watt-hour cal: calorie (th) hp.h: horsepower hour eV: electron-volt

1 J = 1 N.m (Work = Force.distance) 1J = 1 W.s

Parameters:

  • key_word (str, default: 'all_key' ) –

    a string to specify units to be converted.

Returns:

  • factor ( float ) –

    multiply factor of conversion

Notes 

## convert eV to kcal/mol
eV2J = 1/unit_convert.energy('J_eV')
J2Jmol = unit_convert.constant('1/mol')
kj2kcal = 1/unit_convert.energy('kcal/mol_kJ/mol')
eV2kcalmol = eV2J * J2Jmol * 1e-3 *kj2kcal

constant(key_word='all_key')

list of constants Na = 6.02214076e23 (=1/mol): Avogadro number

Parameters:

  • Ex –

    key_word='Pa_atm': convert from Pa (Pascal) to atm (Standard atmosphere)

Returns: factor: float, multiply factor of conversion