'''Copyright (c) 2022 James Gayvert, Soubhik Mondal
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
'''
import re
import numpy as np
from scipy.linalg import block_diag
import os
class MO:
'''
A class that is internally needed to read file containing MO coefficients.
Used in read_molden function.
...
Attributes
----------
line : str
Line string read from molden file
total_idx : int
Total no of line strings.
'''
def __init__(self,line,total_idx):
'''
Initializes the MO class
Parameters
----------
line : str
Line string
total_idx : int
Total no of such line strings.
'''
irrep_label = line.split('=')[1].lower()
irrep_label = ''.join(c for c in irrep_label if c.isalnum())
first_letter = irrep_label.find(next(filter(str.isalpha, irrep_label)))
self.irrep = irrep_label[first_letter:]
self.orb_num_symm = irrep_label[:first_letter]
self.orb_num_total = total_idx
self.name = str(self.orb_num_symm) + self.irrep
self.coeffs = []
def add_coeff(self,coeff):
self.coeffs.append(coeff)
[docs]class colparser():
'''
A class that parses COLUMBUS electronic structure package generated files
to generate state density and transition density matrices for projected-CAP
calculation on MR-CI level.
'''
def _set_mo_coeff(self,ordering=None):
'''
An internal function to generate mo coffiecients in proper ordering.
Returns
-------
MO coefficients in proper ordering to that of pyopencap internal structure
'''
if ordering is not None:
raise NotImplementedError("Custom ordering NYI.")
else:
mo_coeff = np.zeros((self.nbft,self.nbft))
for i, mo in enumerate(self.mos):
mo_coeff[:,i] = mo.coeffs
self.mo_coeff = mo_coeff
def _read_molden(self,molden_file):
'''
An internal function that parses standard molden file.
Parameters
----------
molden_file : str
molden MO filename (generated in MOLDEN/ folder in COLUMBUS calculation Directory
if 'molden' keyword is invoked in control.run runfile.))
Returns
-------
mos : np.ndarray
MO coefficients.
'''
_SEC_REGEX = re.compile(r'\[[^]]+\]')
irrep_dict = {}
with open(molden_file,'r') as f:
line = f.readline()
while '[MO]' not in line:
line = f.readline()
cur_mo = None
mos = []
line = f.readline()
new_sec = _SEC_REGEX.match(line)
while new_sec is None and len(line.strip())!=0:
if 'sym=' in line.lower():
if cur_mo is not None:
mos.append(cur_mo)
cur_mo = MO(line,len(mos)+1)
if cur_mo.irrep in irrep_dict:
irrep_dict[cur_mo.irrep] = irrep_dict[cur_mo.irrep]+1
else:
irrep_dict[cur_mo.irrep] = 1
elif 'ene=' in line.lower():
pass
elif 'spin' in line.lower():
pass
elif 'occup' in line.lower():
pass
elif len(line.strip())!=0:
coeff = float(line.split()[1])
cur_mo.add_coeff(coeff)
line = f.readline()
new_sec = _SEC_REGEX.match(line)
mos.append(cur_mo)
return mos
[docs] def __init__(self, molden_file, tranls):
'''
Initializes the colparser class
Parameters
----------
molden_file: str
molden MO filename (generated in MOLDEN/ folder in COLUMBUS calculation Directory)
tranls: str
Path to tranls file generated by Columbus in WORK directory
'''
rfile = open(tranls, 'r')
while True:
try:
line=next(rfile)
except StopIteration:
break
if 'transformation information:' in line:
line=next(rfile)
line=next(rfile)
self.nbft = int(re.findall(r'\d+', line)[0])
continue
if 'symmetry blocking information:' in line:
line=next(rfile)
line=next(rfile)
self.slabel = ([str(x) for x in line.split()[2:len(line)]])
line=next(rfile)
self.nbpsy = ([int(x) for x in line.split()[2:len(line)]])
line=next(rfile)
self.nmpsy = ([int(x) for x in line.split()[2:len(line)]])
line=next(rfile)
self.nfcpsy = ([int(x) for x in line.split()[2:len(line)]])
break
self.mos = self._read_molden(molden_file)
self._set_mo_coeff()
[docs] def mo_summary(self):
'''
Prints information about active space and symmetries of MOs.
Returns
-------
str
Total number of basis functions (nbft)
Number of basis functions in each symmetry block (NBPSY).
Number of orbitals in each of the symmetry blocks.(NMPSY<= NBSPSY)
Number of frozen orbitals in each of the symmetry blocks (NFCSY ).
Character labels for the symmetry blocks (SLABEL).
'''
pformat = r' Total number of basis functions: {}' \
' \n Symmetry Label: {}' \
' \n NBPSY: {}'' \n NMPSY: {}' ' \n NFCPSY: {} \n'
return pformat.format(self.nbft, self.slabel, self.nbpsy, self.nmpsy, self.nfcpsy)
def _dm_from_iwfmt(self, finame, state_dm=False):
'''
An internal parser that reads CI densities from user genreated 'iwfmt' density files and
formats them in proper order to generate density matrices.
Parameters
----------
finame : str
File name from where the density elements needs to be read.
state_dm : bool
To specify which kind of density file are being parsed
('True' for State density, 'False' for Transition density).
Returns
-------
dm1_mo: np.ndarray
1 particle density matrix in MO basis
'''
if state_dm:occ = 2.0
else: occ = 0.0
with open(finame,'r') as f:
lines = f.readlines()
dm1_mo = np.zeros((self.nbft,self.nbft))
in_data = False
sym_store = []
symm_indices = []
asymm_store = {}
idx = 4
while True:
try:
line = lines[idx]
except IndexError:
break
if ' 0.000000000000E+00' in line:
if len(line.split()) == 1:
words = last_line.split()
(num,lab1,ibvtyp,itypea,itypeb,ifmt,last,nipv) = [int(word) for word in words]
if itypea==0 and itypeb==7:
in_data=True
sym = 1
elif itypea==2 and itypeb==9:
in_data=True
sym = -1
elif in_data:
words = line.split()
val = float(words[0])
i = int(words[1])-1
j = int(words[2])-1
if sym==1:
sym_store.append(val)
symm_indices.append((i,j))
elif sym==-1:
asymm_store[(i,j)] = val
elif ' ' in line:
pass
elif in_data:
words = line.split()
val = float(words[0])
i = int(words[1])-1
j = int(words[2])-1
if sym==1:
sym_store.append(val)
symm_indices.append((i,j))
elif sym==-1:
asymm_store[(i,j)] = val
idx+=1
last_line = line
k=0
dm_mo=[]
bas_idx = 0
# symmetric block first
for num in self.nbpsy:
arr = np.zeros([num-self.nfcpsy[bas_idx], num-self.nfcpsy[bas_idx]])
if self.nfcpsy[bas_idx]> 0 :
dm_mo=block_diag(dm_mo, occ*np.eye(self.nfcpsy[bas_idx]))
for i in range(num-self.nfcpsy[bas_idx]):
for j in range (i+1) :
arr[i, j]=float(sym_store[k])
if i!=j:
arr[j, i]=arr[i, j]
if symm_indices[k] in asymm_store:
asymm_val = asymm_store[symm_indices[k]]
arr[i,j] -= asymm_val
arr[j,i] += asymm_val
k+=1
bas_idx +=1
dm_mo=block_diag(dm_mo, arr)
dm1_mo = np.delete(dm_mo, (0), axis=0)
return dm1_mo
[docs] def sdm_ao(self, i, DRTn=1, data_dir='.', filename=None):
'''
Returns state density matrix in atomic orbital basis by parsing a Columbus cid1trfl.iwfmt file.
Parameters
----------
i : int
State index
DRTn : int, optional
DRT index
data_dir: str, optional
Directory to search for .iwfmt file. Should not be used in conjunction with `filename` kwarg
filename: str, optional
Path to file to parse. If not specified, the filename is assumed to be cid1trfl.FROMdrt{drtFrom}.state{i}TOdrt{drtTo}.state{i}.iwfmt
in the current directory.
Returns
-------
sdm: np.ndarray
State density matrix in AO basis
'''
if filename is None:
fnameIN =os.path.join(data_dir,'cid1trfl.FROMdrt{}.state{}TOdrt{}.state{}.iwfmt'.format(DRTn, i, DRTn, i))
else:
fnameIN = filename
return self.mo_coeff @ self._dm_from_iwfmt(fnameIN, state_dm=True) @ self.mo_coeff.T
[docs] def tdm_ao(self, iFROM, iTO, drtFrom=1, drtTo=1, data_dir='.', filename=None):
'''
Returns transition density matrix in atomic orbital basis by parsing a Columbus cid1trfl.iwfmt file.
Parameters
----------
iFROM, iTO : int
Initial state index and final state indices respectively.
drtFrom, drtTo : int, optional
DRT indices
data_dir: str, optional
Directory to search for .iwfmt file. Should not be used in conjunction with `filename` kwarg
filename: str, optional
Path to file to parse. If not specified, the filename is assumed to be cid1trfl.FROMdrt{drtFrom}.state{iFrom}TOdrt{drtTo}.state{iTO}.iwfmt
in the current directory.
Returns
-------
tdm: np.ndarray
Transition density matrix in AO basis
'''
if filename is None:
fnameIN =os.path.join(data_dir,'cid1trfl.FROMdrt{}.state{}TOdrt{}.state{}.iwfmt'.format(drtFrom, iFROM, drtTo, iTO))
else:
fnameIN = filename
return self.mo_coeff @ self._dm_from_iwfmt(fnameIN, state_dm=False) @ self.mo_coeff.T
[docs] def sdm_ao_cid1fl(self,i, DRTn):
'''
Read CI state densities from state density cid1fl*.iwfmt files.
Currently NYI.
Parameters
----------
i : int
State index
DRTn : int
DRT index
Raises
-------
NotImplementedError
Returns
-------
np.ndarray
State density matrix in AO basis
'''
raise NotImplementedError()
def _H0_parser(self, str_arg, filename):
'''
An internal parser that parses 'ciudgsm' file and is used by H0 function.
Parameters
----------
str_arg : str
One of the following: {'eci', 'eci+dv1', 'eci+dv2', 'eci+dv3', 'eci+pople' }
filename: str
Path to file
Returns
--------
H0_diag: np.ndarray
Diagonal Hamiltonian with CI energies.
'''
H0_arr=[]
lines = [line for line in open(filename)]
str_in = ['eci', 'eci+dv1', 'eci+dv2', 'eci+dv3', 'eci+pople']
str_search = ['eci =', 'eci+dv1 =', 'eci+dv2 =', 'eci+dv3 =', 'eci+pople =']
str_lookup=str_search[str_in.index(str_arg)]
for line in lines:
if str_lookup in line:
H0_arr = block_diag(H0_arr, float(line.split()[2]))
self.H0_diag=np.delete(H0_arr, (0), axis=0)
return self.H0_diag
[docs] def get_H0(self, correction_type='eci+pople', filename='ciudgsm'):
'''
Parses energies from a Columbus ciudgsm file.
Parameters
----------
correction_type: str, optional
One of {'eci+pople', 'eci', 'eci+dv1', 'eci+dv2', 'eci+dv3' }. Default is 'eci+pople'
filename: str, optional
Path to Columbus ciudgsm file located in WORK directory. If unspecified, assumed to be './ciudgsm'.
Notes
------
See https://aip.scitation.org/doi/pdf/10.1063/1.5144267 for discussion of corrections.
Returns
--------
H0_mat : np.ndarray
Diagonal hamiltonian with CI energies.
'''
str_in = ['eci', 'eci+dv1', 'eci+dv2', 'eci+dv3', 'eci+pople']
if ((correction_type in str_in) == False) or (correction_type==None):
print("The following input args are available (Switching to default 'eci+pople'):" "\n {}".format(str_in))
self.H0_mat = self._H0_parser('eci+pople',filename)
else:
self.H0_mat = self._H0_parser(correction_type,filename)
return self.H0_mat