esta.grrmBag.output_grrm_RxnMap6
¶
grrm
¶
gauss class to extract the xyz file/files from the GRRM17 log file
get_atomic_positions(logfile_name)
¶
not called in case of TS list.log ..........
get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17
get_all_atomic_positions(logfile_name)
¶
get xyz files: atomic positions and atomic labels from "*_TS_list.log" file of GRRM17
get_xyz_file(logfile_name)
¶
get xyz file by reading the atomic positions and atomic labels:
return:
outfile: write data in xyz file specified by name outfile
get_all_xyz_file(logfile_name)
¶
get all xyz file by reading the atomic positions and atomic labels:
return:
outfile: write data in xyz file specified by name outfile
get_energy()
¶
get Energy from *_TS_list.log file of all TS structures
get_energy_general(com_file_name, which_state='EQ')
¶
get Energy of all TS/PT/EQ states from comfile_TS/PT/EQ _list.log file
input:
str: com file name with .com extension
str: choose which states energies to get; EQ/TS/PT
output:
list: energies list of EQ/TS/PT structures
get_connection(logfile_name)
¶
find which TS stats is connected to which EQ states
input:
str: filename
output:
dictionary of TS and connections: {'TS': TS_list, 'Connection': connection}
e.g:
search the following is *TS_list.log file:
Geometry of TS 0, SYMMETRY = C1¶
CONNECTION : 4 - 5
get_map(ts, ts_connection, file_name, layout_is='neato')
¶
input:
list: eq_id
list: connection
get_map2(ts, ts_connection)
¶
input:
list: eq_id
list: connection