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– -
path_direction–path_direction can be forward or reversed; default is forward direction
Returns:
-
plot the path in png file named filename.png– -
.. note:–Reading starts from following .............. Energy profile along IRC Length (A amu½) 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
get_EQ_IRC(filename, natoms=None)
¶
get the eq structures from the IRC calculations
input:
filename: str, name of the IRC log file
output:
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
get_EQ_TS_IRC(filename, natoms=None)
¶
get the EQ and TS structures from the IRC calculations
input
filename: str name of the IRC log file natoms: integer, optional no. of atoms in the xyz str
output
position: array array of shape (3, natoms, 3) ; 3 for two EQ and 1 TS strs label: list list of atomic symbols of shape (3, natoms); 3 for 2 eq strs and 1 TS strs
get_natoms_IRC(filename) -> int
¶
get no. of atoms present in a strs in IRC log file
get_free_energy(filename)
¶
get free energy of all Geometry strs in Hartree from grrm log file of IRC calculations
.. 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)
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] )
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)