esta.qeBag.read_write_adv
¶
RWpwo
¶
Class to read and write data file for the atomic structures
- read cell parmeters and/or atomic positions
- write this data in xyz, poscar, and qe-str format
get_atm_positions()
¶
find atom positions with labels ...
get_cell_parameters()
¶
return: cell vectors in angstrom or bohr
what is does:
for 'rlx' calculations: search: "lattice parameter (alat)" "crystal axes: (cart. coord. in units of alat)"
for 'vc-relax' calculations: search: 'CELL_PARAMETERS (angstrom)' ...
get_energies_and_kpt()
¶
get the band energies at k point by reading the scf calculation out file
NOTE: Need verbosity ='high' in the scf input file to print the band energies
get_xyz_file()
¶
get xyz file by reading the atomic positions and atomic labels: use method - get_atm_positions(infile)
return:
outfile: write data in xyz file specified by name outfile
IMPORTANT: ordeing same elements together: not done yet .. to be done.. .. so for the time being open the file with Avogadro and save again as xyz file
get_xyz_grouped_file()
¶
get xyz file by reading the atomic positions and atomic labels: use method - get_atm_positions(infile)
return:
outfile: write data in xyz file specified by name outfile
NOTE: similar atoms are grouped together
get_poscar()
¶
write cell_parameters and atomic postions, atom labels etc in poscar file
get_element_label(input_atomic_number)
¶
using mendeleev for it : big database of elemental properties
In [22]: from mendeleev import element
In [21]: for i in [5,6,7,8]:
...: element(i)
...: print (element(i).symbol)
...:
B
C
N
O
get_unique_list(inp)
¶
get unique elements of list
return: string for each type of atoms
get_grouped_list(llist)
¶
get same string elements of list grouped together
get_neach_type(inp)
¶
get number of list entries of each type
return:
list of integers for each type of atoms specifying their number
RWpwi
¶
class to read the pw input file and create poscar file
return: generate poscar file after reading the pw input file
get_unique_list(inp)
¶
get unique elements of list
return: string for each type of atoms
get_grouped_list(llist)
¶
get same string elements of list grouped together
get_neach_type(inp)
¶
get number of list entries of each type
return:
list of integers for each type of atoms specifying their
get_poscar()
¶
write cell_parameters and atomic postions, atom labels etc in poscar file