Note

GRRM package: This package does processing of the GRRM sofware output files

esta.grrmBag package#

Submodules#

esta.grrmBag.LUPINP module#

get xxx_LUPINP.log file from pos and label variables data

esta.grrmBag.LUPINP.get_LUPINP(atm_pos, label, name_outfile=None)#

get xxx_LUPINP.log file from pos and label variables data

input:

atm_pos: array of shape (no_of_atomic_strs, natoms, 3 ) label: list of shape (no_of_atomic_sts, natoms) name_outfile: prefic of name of the output file, optional

output:
output “name_outfile”+’_LUPINP.log’ file to be used as an initial path

for the LUP calculation

—exampe of XXX_LUPINP.log file: ————

# NODE 0: O 5.490527361273 -7.301039647118 -6.111826190422 H 5.733518415093 -6.371725434573 -5.886303868739 H 5.483149357281 -6.641347567148 -3.750888719682

# NODE 1: O 5.539350619528 -7.324436803847 -6.035948874142 H 5.785226928656 -6.401397049756 -5.821165568507 H 5.502797674893 -6.666317168224 -3.712799145260

esta.grrmBag.a module#

esta.grrmBag.a.get_EQ_IRC(filename, natoms=None)#

get the eq structures from the IRC calculations

filename: str, name of the IRC log file

position: array of shape (2, natoms, 3) ; 2 for two EQ strs label: list of atomic symbols of shape (2, natoms); 2 for eq strs

esta.grrmBag.a.get_EQ_TS_IRC(filename, natoms=None)#

get the EQ and TS structures from the IRC calculations

filename: str, name of the IRC log file

position: array of shape (3, natoms, 3) ; 3 for two EQ and 1 TS strs label: list of atomic symbols of shape (3, natoms); 3 for 2 eq strs and 1 TS strs

esta.grrmBag.a.get_free_energy(filename)#

get free energy of all Geometry strs in Hartree from grrm log file of IRC calculations

esta.grrmBag.a.get_irc_path(filename, path_direction=False)#

read log file or any other file containing IRC path information:

string; filename string;optinal, path_direction can be forward or reversed

default is forward direction

plot the path in png file named filename.png

Reading starts from following …………..

Energy profile along IRC Length (A amu1/2) Energy (Hartree) -61.2536469474 -140.1040646722

30.6359900582 -140.0788979553 30.8934801390 -140.0788985106

Reverse Length (A amu1/2) Energy (Hartree) -30.8934801390 -140.0788985106 -30.6359900582 -140.0788979553 .. .. 60.7900934845 -140.1040632542 61.2536469474 -140.1040646722

esta.grrmBag.a.get_natoms_IRC(filename) → int#

get no. of atoms present in a strs in IRC log file

esta.grrmBag.com2xyz module#

get xyz file from *com file of the GRRM or gaussian input file

esta.grrmBag.com2xyz.get_coord(filename)#

get coord and atomic labesls from com file of gaussian or GRRM17

input filename

scalar; no of atoms list; for atomic labels array; for atomic positions

esta.grrmBag.com2xyz.get_coord_grrm_kin(filename)#

get coord and atomic labesls from com file of GRRM17 com file with kinetic options

input filename

scalar; no of atoms list; for atomic labels array; for atomic positions

esta.grrmBag.com2xyz.get_xyz_file(filename, filetype=None)#

get xyz file from com file

label: string list or string array pos: array of shape (natoms, 3) infile: input file name

xyz file in the present dir; name of file derived from input file

esta.grrmBag.get_IRC_path module#

esta.grrmBag.get_IRC_path.get_EQ_IRC(filename, natoms=None)#

get the eq structures from the IRC calculations

filename: str, name of the IRC log file

position: array of shape (2, natoms, 3) ; 2 for two EQ strs label: list of atomic symbols of shape (2, natoms); 2 for eq strs

esta.grrmBag.get_IRC_path.get_EQ_TS_IRC(filename, natoms=None)#

get the EQ and TS structures from the IRC calculations

filename: str, name of the IRC log file

position: array of shape (3, natoms, 3) ; 3 for two EQ and 1 TS strs label: list of atomic symbols of shape (3, natoms); 3 for 2 eq strs and 1 TS strs

esta.grrmBag.get_IRC_path.get_energy(filename)#
get free energy, electronic, and enthalpies of all Geometry strs in Hartree from grrm log file

of IRC calculations

..note:

Check following matches:: Thermochemistry at 298.150 K, 1.000 Atm Thermochemistry (use all positive eigenvalues) at 298.15 K, 1.00 Atm Thermochemistry (after the above replacements)

esta.grrmBag.get_IRC_path.get_enthalpy(filename)#

get Enthalpie from grrm saddle/saddle+irc log files in Hartree from grrm log file of IRC calculations

..note:

Check following matches:: Thermochemistry at 298.150 K, 1.000 Atm Thermochemistry (use all positive eigenvalues) at 298.15 K, 1.00 Atm Thermochemistry (after the above replacements)

Enthalpie(0K) = -4972.234296259576 Enthalpie = -4972.155864233614

Thermochemistry (use all positive eigenvalues) at 298.15 K, 1.00 Atm Thermochemistry (after the above replacements) at 298.15 K, 1.00 Atm

free_energy[j] = float( lines[i+14].split()[-1] ) elec_energy[j] = float( lines[i+1].split()[-1] ) enthalpy[j] = float( lines[i+8].split()[-1] )

esta.grrmBag.get_IRC_path.get_free_energy(filename)#

get free energy of all Geometry strs in Hartree from grrm log file of IRC calculations

esta.grrmBag.get_IRC_path.get_irc_path(filename, path_direction=False)#

read log file or any other file containing IRC path information:

Parameters

  • filename (string) –

  • path_direction (string (optinal),) – path_direction can be forward or reversed; default is forward direction

Return type

plot the path in png file named filename.png

..note:
Reading starts from following …………..

Energy profile along IRC Length (A amu1/2) Energy (Hartree) -61.2536469474 -140.1040646722

30.6359900582 -140.0788979553 30.8934801390 -140.0788985106

Reverse Length (A amu1/2) Energy (Hartree) -30.8934801390 -140.0788985106 -30.6359900582 -140.0788979553 .. .. 60.7900934845 -140.1040632542 61.2536469474 -140.1040646722

esta.grrmBag.get_IRC_path.get_natoms_IRC(filename) → int#

get no. of atoms present in a strs in IRC log file

esta.grrmBag.get_LUP module#

esta.grrmBag.get_LUP.get_lup_inp(filename)#

read XXX_LUPINP.log file for getting the Path (xyz strs)

Parameters

filename (str) – filename, name of xxx_LUPINP.log file

Returns

  • position_all (array) – array of atomic positions

  • atom_symbol (string) – strings representing atomic symbols

esta.grrmBag.get_LUP.get_lup_out(filename)#

read XXX_LUPIOUTt.log file for getting the Path (xyz strs)

Parameters

filename (str) – filename, name of xxx_LUPINP.log file

Returns

  • position_all (array) – array of atomic positions

  • atom_symbol (string) – strings representing atomic symbols

esta.grrmBag.get_LUPINP module#

esta.grrmBag.get_LUPINP.get_lup_inp(filename, lenergy=None)#

read XXX_LUPINP.log file for getting the Path (xyz strs)

Parameters

  • filename (string) – filename, name of xxx_LUPINP.log file

  • lenergy (logical, optional) – lenergy, whether energy to be extracted from the input filename

Return type

create xyz file containing all xyz strs with energy information in the comment if lenergy is true ..

esta.grrmBag.get_LUP_profile_advv module#

esta.grrmBag.get_LUP_profile_advv.get_lup_profile(filename, natoms)#

extract the LUP path

  • from DS-AFIR calculated log file of GRRM … xxx.log file

  • finally plot the LUP profile

esta.grrmBag.get_LUP_profile_advv.get_lup_profile2(filename)#

extract the LUP path

  • from - from xxx__LUPOUTt.log file

esta.grrmBag.get_nTS_nEQ_nPT module#

get number of EQ, TS, and PT structures from logs of GRRM output

esta.grrmBag.get_nTS_nEQ_nPT.get_nEQ(filename)#
esta.grrmBag.get_nTS_nEQ_nPT.get_nPT(filename)#
esta.grrmBag.get_nTS_nEQ_nPT.get_nTS(filename)#

esta.grrmBag.input_grrm module#

class esta.grrmBag.input_grrm.GenerateCom(xyzfile, charge, multiplicity, cal_type)#

Bases: object

flags_grrm(**kwargs)#

other options in GRRM code for calculation types e.g:

Options sublink=/home/kumarsonu/bin/link_excode_allv3.1_.py Add Interaction Fragm.1=56,57,58,1 Fragm.2=59-62 1 2 Gamma=200.0 END NOFC KeepIntFiles DownDC=12

np = <module 'numpy' from '/home/sonu/anaconda3/envs/py3a/lib/python3.7/site-packages/numpy/__init__.py'>#
read_xyz()#

filename, str, filename xyz file name

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

read_xyz2(xyz2file)#

filename, str, filename xyz file name

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

write_com(**kwargs)#

atomic postions atomic labels no of atoms

com file containing info of atomic structure

write_com_2xyz(xyz2file, **kwargs)#

atomic postions atomic labels no of atoms _________________ –> all of these variable read form 1xyz file ..by

calling self.read_xyz()

str: xyz file name —2nd xyz filename correspinding to product of rxn

com file containing info of atomic structure info of two atomic systems

esta.grrmBag.input_grrm_advv module#

class esta.grrmBag.input_grrm_advv.GenerateCom(xyzfile, charge, multiplicity, cal_type)#

Bases: object

python class to generate input files (*.com file) for different type of calculations for GRRM using:

  • non-supported

  • orca

  • gaussian

Note

Different types of calculation are carried out by the

GRRM software given below:

calculaiton type …. status of Implementation

    • Normal mode analysis (FREQ)

    • Minimum point optimization (MIN) ……DONE

    • Saddle-point optimization (SADDLE)

    • IRC following (IRC)

    • LUP path optimization (LUP) …. DONE

    – to do

    Crossing point (MECI or MESX) optimization …. will not be done Crossing point (MECI or MESX) estimation …. will not be done External atoms (microiterations) Frozen atoms …. DONE

  2. MIN-AFIR calculations … DONE AFIR calculations … DONE DS-AFIR calculations … DONE

    Refinement calculations ….. TODO

author: skumar

email: sonukumar.physics@gmail.com

flags_grrm(**kwargs)#

options in GRRM code for calculation types

Note

Options sublink=/home/kumarsonu/bin/link_excode_allv3.1_.py Add Interaction Fragm.1=56,57,58,1 Fragm.2=59-62 1 2 Gamma=200.0 END NOFC KeepIntFiles DownDC=12

freeze_notfreeze_atoms(fix_atm_list=None)#

xyzfile : name of the xyz file containing xyz coords, and symbols fix_atm_list = [i,j] ; starting atom i to the last last atom j number.

Returns

  • frozen_tuple (tuple) – tuple containg fixed atomic_positins, atomic_symbols, and atom index

  • not_frozen_tuple (tuple) – tuple containg not fixed atomic_positins, atomic_symbols, and atom index

read_xyz()#
Parameters

filename (str) – xyz file name

Returns

  • atomic positions (array) – rank 2 array of shape (natoms, 3)

  • atomic labels (list/array of strings) – rank 1 array of atomic labels

  • strings (string) – string mentioning the units of coordinates

read_xyz2(xyz2file)#
Parameters

  • filename –

  • str –

  • name (filename xyz file) –

Returns

  • 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)

write_com(interface=None, basis=None, solvent=None, log_filename=None, Frozen_dict=None, **kwargs)#

atomic postions atomic labels no of atoms kwargs containing GRRM related parameters

input com GRRM file containing info of atomic structure as well as other GRRM parameteres

write_com_2xyz(xyz2file, interface=None, **kwargs)#

xyz files of products read from command line arguments ….mainly used for creating DS-AFIR input file …

atomic postions atomic labels no of atoms _________________ –> all of these variable read form 1xyz file ..by

calling self.read_xyz()

str: xyz file name —2nd xyz filename correspinding to product of rxn

com file containing info of atomic structure info of two atomic systems

write_inp(xyzfile, charge, multiplicity, ncores=None, memory=None, interface=None)#

generate input file for ORCA like below:

Parameters

  • prefix (string) – name of inp file with .inp extension

  • charge (sclar) – chare on ths system

  • multiplicity (integer) – spin multiplicity (2S+1); for a single electron: S =1/2

Returns

file – inp file for orca containg charge and multiplicity options

Return type

string

Note

! XTB2 NoUseSym @job

  • xyz 0 1

@geometry *

write_input_oniom()#

get input file for the oniom-msm method by suzuki etal. (ICReDD) for:

  • saddle calculations (see general folder for the implementation)

  • EQ/TS sampling calculations (this may not be possible as I tried setting up the calculation, but failed!!)

  • ReStruct calculation ..

esta.grrmBag.output_grrm module#

grrm class to extract the xyz file/files from the GRRM17 log file

class esta.grrmBag.output_grrm.grrm(filename)#

Bases: object

gauss class to extract the xyz file/files from the GRRM17 log file

get_all_atomic_positions_from_EQ_list()#

get xyz files: atomic positions and atomic labels from “*_EQ_list.log” file of GRRM17

get_all_xyz_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

get_all_xyz_in_a_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_energy()#

get Energy from *_EQ_list.log file of all EQ structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_ITR_adv module#

grrm class to extract the xyz file/files from the GRRM17 ITR.log file

class esta.grrmBag.output_grrm_ITR_adv.grrm(filename)#

Bases: object

gauss class to extract the xyz file/files from the GRRM17 log file

get_all_atomic_positions_from_ITR_list()#

get xyz files: atomic positions and atomic labels from “*_ITR_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

get_all_xyz_in_a_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of ITR list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_energy()#

get Energy from *_ITR_list.log file of all TS structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_ITR_adv1 module#

grrm class to process the GRRM Ilog file. Basically process the log file containg ITR keywords (used for min, opt etc in GRRM)

class esta.grrmBag.output_grrm_ITR_adv1.grrm(filename)#

Bases: object

extract the xyz files and energies from the log file

get_all_atomic_positions_from_ITR_list()#

get xyz files: atomic positions and atomic labels from “*_ITR_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

outfile : write data in xyz file specified by name outfile

get_all_xyz_in_a_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of ITR list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_energy()#

get Energy from *_ITR_list.log file of all TS structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_ITR_adv2 module#

grrm class to process the GRRM Ilog file. Basically process the log file containg ITR keywords (used for min, opt etc in GRRM)

class esta.grrmBag.output_grrm_ITR_adv2.grrm(filename)#

Bases: object

extract the xyz files and energies from the log file

get_all_atomic_positions_from_ITR_list()#

get xyz files: atomic positions and atomic labels from “*_ITR_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

outfile : write data in xyz file specified by name outfile

get_all_xyz_in_a_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of ITR list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_bare_energy()#

get Bare Energy from log file of MIN-AFIR calculations

get_energy()#

get Energy from *_ITR_list.log file of all TS structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_ITR_adv3 module#

grrm class to process the GRRM log file. Basically process the log file containg ITR keywords (used for min, opt etc in GRRM)

class esta.grrmBag.output_grrm_ITR_adv3.grrm(filename)#

Bases: object

extract the xyz files and energies from the log file

get_all_atomic_positions_from_ITR_list()#

get xyz files: atomic positions and atomic labels from “*_ITR_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

outfile : write data in xyz file specified by name outfile

get_all_xyz_in_a_file(comment=None, min_afir=None, reverse=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of ITR list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_bare_energy()#

get Bare Energy from log file of MIN-AFIR calculations

get_energy()#

get Energy from *_ITR_list.log file of all TS structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_ITR_adv4 module#

grrm class to process the GRRM log file. Basically process the log file containg ITR keywords (used for min, opt etc in GRRM)

class esta.grrmBag.output_grrm_ITR_adv4.grrm(filename)#

Bases: object

extract the xyz files and energies from the log file

get_all_atomic_positions_from_ITR_list()#

get xyz files: atomic positions and atomic labels from “*_ITR_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

outfile : write data in xyz file specified by name outfile

get_all_xyz_in_a_file(comment=None, min_afir=None, reverse=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of ITR list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_bare_energy()#

get Bare Energy from log file of MIN-AFIR calculations

get_energy()#

get Energy from *_ITR_list.log file of all TS structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_ITR_adv5 module#

grrm class to process the GRRM log file. Basically process the log file containg ITR keywords (used for min, opt etc in GRRM)

class esta.grrmBag.output_grrm_ITR_adv5.grrm(filename)#

Bases: object

extract the xyz files and energies from the log file

get_all_atomic_positions_from_ITR_list()#

get xyz files: atomic positions and atomic labels from “*_ITR_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

outfile : write data in xyz file specified by name outfile

get_all_xyz_in_a_file(comment=None, min_afir=None, reverse=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of ITR list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_bare_energy()#

get Bare Energy from log file of MIN-AFIR calculations

get_energy()#

get Energy from *_ITR_list.log file of all TS structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_PT module#

grrm class to extract the xyz file/files from the GRRM17 PT.log file

class esta.grrmBag.output_grrm_PT.grrm(filename)#

Bases: object

gauss class to extract the xyz file/files from the GRRM17 log file

get_all_atomic_positions_from_PT_list()#

get xyz files: atomic positions and atomic labels from “*_PT_list.log” file of GRRM17

get_all_xyz_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

get_all_xyz_in_a_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of PT list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_energy()#

get Energy from *_PT_list.log file of all PT structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_RxnMap6 module#

class esta.grrmBag.output_grrm_RxnMap6.grrm(comfile)#

Bases: object

gauss class to extract the xyz file/files from the GRRM17 log file

get_all_atomic_positions(logfile_name)#

get xyz files: atomic positions and atomic labels from “*_TS_list.log” file of GRRM17

get_all_xyz_file(logfile_name)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

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_connection(logfile_name)#

find which TS stats is connected to which EQ states

str: filename

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_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

str: com file name with .com extension str: choose which states energies to get; EQ/TS/PT

list: energies list of EQ/TS/PT structures

get_map(ts, ts_connection, file_name, layout_is='neato')#

list: eq_id list: connection

get_map2(ts, ts_connection)#

list: eq_id list: connection

get_xyz_file(logfile_name)#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_TS module#

grrm class to extract the xyz file/files from the GRRM17 TS.log file

class esta.grrmBag.output_grrm_TS.grrm(filename)#

Bases: object

gauss class to extract the xyz file/files from the GRRM17 log file

get_all_atomic_positions_from_TS_list()#

get xyz files: atomic positions and atomic labels from “*_TS_list.log” file of GRRM17

get_all_xyz_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

get_all_xyz_in_a_file(comment=None)#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in a single xyz file specified by name outfile

here outfile = prefix+”_”+’all_’+’.xyz’

Return type

outfile

get_atomic_positions()#

not called in case of TS list.log ……….

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_energy()#

get Energy from *_TS_list.log file of all TS structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.output_grrm_init module#

grrm class to extract the xyz file/files from the GRRM17 log file

class esta.grrmBag.output_grrm_init.grrm(filename)#

Bases: object

gauss class to extract the xyz file/files from the GRRM17 log file

get_all_atomic_positions_from_EQ_list()#

get xyz files: atomic positions and atomic labels from “*_EQ_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

get_atomic_positions()#

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_energy()#

get Energy from *_EQ_list.log file of all EQ structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

esta.grrmBag.plot_strs_energy module#

esta.grrmBag.plot_strs_energy.data_exist()#
esta.grrmBag.plot_strs_energy.process_data()#

  • process data0.dat and EQlist.dat files for plotting

  • generate plot of str vs energy in the e.pdf

esta.grrmBag.search_structure2 module#

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

class esta.grrmBag.search_structure2.strInfo#

Bases: object

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

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 )

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

class esta.grrmBag.search_structure2.struct#

Bases: object

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

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

get xyz files with constrains mentioned …..

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

only xyz files with specific constrains

read_xyz(xyzfile)#

filename, str, filename xyz file name

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

esta.grrmBag.search_structure2_mod module#

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

class esta.grrmBag.search_structure2_mod.strInfo#

Bases: object

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

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 )

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

class esta.grrmBag.search_structure2_mod.struct#

Bases: object

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

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

get xyz files with constrains mentioned …..

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

only xyz files with specific constrains

read_xyz(xyzfile)#

filename, str, filename xyz file name

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

esta.grrmBag.search_structure3 module#

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

class esta.grrmBag.search_structure3.strInfo#

Bases: object

class to just print the str information etc. Iit 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

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 )

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

get_str_info1(filename, atoms_info, dist_criteria, atoms_info_unwanted=None, dist_criteria_unwanted=None)#

get information of all possible atomic strs with input constraints

Parameters

  • filename (str) – file containing all the xyz files

  • atoms_info (list) – list of index of pair of atoms (atoms numbering starting from 1; like the vesta reads and assigns the atom numbers)

  • dist_criteria (list) – list of distances for each pair of atoms

  • atoms_info_unwanted (strs) – strs with following dist criteria are not needed

  • dist_criteria_unwanted (strs) – strs with this critea are not needed ((unwanted means dist = or > is needed )

Returns

data.dat : all strs with distances between atom pairs dat0.dat : contain possible xyz str with given distance constrains str_id_info : contained id of xyz files; can be used to view the atomic

strs using vesta or other visualization tool

Return type

3 output files

class esta.grrmBag.search_structure3.struct#

Bases: object

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

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

get xyz files with constrains mentioned …..

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

only xyz files with specific constrains

read_xyz(xyzfile)#

filename, str, filename xyz file name

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

esta.grrmBag.to_location module#

mv all data files of spectic extensions to newly created directory

esta.grrmBag.to_location.move_to_location(file_ext, loc)#

str: file_ex , eg. xyz str: loc, e.g. ‘xyz_TS’

move all files with file_ext to loc

mv filenames = *xyz to another location (loc);

esta.grrmBag.to_location_adv module#

mv all data files of spectic extensions to newly created directory

esta.grrmBag.to_location_adv.move_to_location(file_prefix, file_ext, loc)#

str: file_predix wihtout ext str: file_ext , eg. xyz str: loc, e.g. ‘xyz_TS’

move all files with file_ext to loc

mv filenames = *xyz to another location (loc);

esta.grrmBag.write_xyz module#

esta.grrmBag.write_xyz.get_all_xyz_file(pos, label, prefix_ofile=None, comment=None)#

get all xyz file given atomic positions and atomic labels:

Returns

write data in xyz file specified by name prefix_ofile

Return type

outfile

esta.grrmBag.write_xyz.get_all_xyz_in_a_file(pos, label, energy=None, prefix_ofile=None, comment=None, reverse=None)#

get all xyz files in a single file …

Parameters

  • pos (rank 2 array) – arry of atomic positions, shape(natoms, 3)

  • label (list of strings) – list of string containing atomic symbols

  • energy (array) – array of energies of all atomic strs

  • prefix_ofile ((optional) string) – string for prefixing the name of the output file

  • comment ((optional) logical) – logical (True/False) for adding commnet in commnet line of the xyz file

  • reverse ((optional) logical) – logical for printing the path in reverse order

Returns

outfile – write data in a single xyz file specified by name outfile here outfile = prefix+”_”+’all_’+’.xyz’

Return type

str

esta.grrmBag.x module#

grrm class to extract the xyz file/files from the GRRM17 log file

class esta.grrmBag.x.grrm(filename)#

Bases: object

gauss class to extract the xyz file/files from the GRRM17 log file

get_all_atomic_positions_from_EQ_list()#

get xyz files: atomic positions and atomic labels from “*_EQ_list.log” file of GRRM17

get_all_xyz_file()#

get all xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

get_atomic_positions()#

get atomic positiions and atomic labels from *_P[0-nproc].log file of GRRM17

get_energy()#

get Energy from *_EQ_list.log file of all EQ structures

get_xyz_file()#

get xyz file by reading the atomic positions and atomic labels:

Returns

write data in xyz file specified by name outfile

Return type

outfile

Module contents#

Note

POINT GROUP package: This package does point group detection of molecules using C program

esta.pointGroup package#

Module contents#