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search_structure2

esta.grrmBag.search_structure2

to get all the possible atomic structures with some constrainds from a list of xyz strs

author: skumar email: sonukumar.physics@gmail.com/sonukumar.icredd.hokudai.ac.jp date: July 2020 place: QCL, ICReDD, Japan

struct

struct class for getting the possible strs with some contraints on atoms locations

read_xyz(xyzfile)

input: 
filename, str, filename xyz file name
output: 
atomic positions: array: rank 2 array of shape (natoms, 3)
atomic labels: list/array of strings: rank 1 array of atomic 
labels no of atoms: scalar

get_str(xyzfile_obj, xyz_file, atoms_list, threshold=None, atoms_list_unwanted=None, threshold_unwanted=None, **kwarg)

get xyz files with constrains mentioned .....

input: 
xyzobj: xyz data object
atoms_list: a list of atleast 2 atoms; e.g. [1,10], or [[1,4], [6,8]]
x lfind: 
threshold: list of scalars depending on list of atoms, scalars are
           distance between atoms in angstrom; if one value given then 
           all atoms pairs have same threshold

atoms_list_unwanted: same as atoms_list, but these are not wanted in search sts
threshold_unwanted:  same as threshold, but atoms with these distances or more
                     are needed in the final xyz str
***kwarg: other keyword arguments
output: 
only xyz files with specific constrains

strInfo

class to just print the str information etc ; it takes as input information of strs from struct class.

get_str_info(filenames, atoms_info, dist_criteria, atoms_info_unwanted=None, dist_criteria_unwanted=None)

get information of all possible atomic strs with input constraints

input: 
filenames: list of all xyz files
atoms_info: list of  index of pair of atoms  (atoms numbering starting from 
            1; like the vesta reads and assigns the atom numbers)
dist_criteria: list of distances for each pair of atoms
  • atoms_info_unwanted: strs with following dist criteria are not needed
  • dist_criteria_unwanted: strs with this critea are not needed ((unwanted means dist = or > is needed )
output: 
3 output files named:
1) "data.dat"    :  all strs with distances between atom pairs 
2) "dat0.dat"    :  contain possible  xyz str with given distance constrains
3) "str_id_info" :  contained id of xyz files; can be used to view the atomic 
                    strs using vesta or other visualization tool