def parse_gaussian_basis_set(self):
'''
Parses the primitive exponents, coefficients and shell if BSSHOW specified in SEWARD.
'''
basis_map = self._basis_set_map()
linenos = [i[0] + 1 for i in self.regex(_re_prims)]
lisdx = 0
lfsdx = 0
basis_set = pd.DataFrame()
blocks = []
sets = basis_map.groupby('set')
for sdx, seht in sets:
shfunc = 0
lfsdx += len(seht)
starts = linenos[lisdx:lfsdx]
lisdx = lfsdx
prims = []
for i, start in enumerate(starts):
prim = seht['nprim'].values[i]
bas = seht['nbasis'].values[i]
chk1 = len(self[start].split())
chk2 = len(self[start + 1].split())
if chk1 == chk2:
block = self.pandas_dataframe(start, start + prim, bas + 2)
else:
block = self[start:start + 2 * prim]
most = block[::2]
extr = block[1::2]
ncols = len(most[0].split()) + len(extr[0].split())
block = pd.read_csv(StringIO('\n'.join([i + j for i, j in zip(most, extr)])),
delim_whitespace=True, names=range(ncols))
alphas = pd.concat([block[1]] * bas).reset_index(drop=True).str.replace('D', 'E').astype(np.float64)
coeffs = block[list(range(2, bas + 2))].unstack().reset_index(drop=True)
primdf = pd.concat([alphas, coeffs], axis=1)
primdf.columns = ['alpha', 'd']
primdf['L'] = lorder.index(seht['shell'].values[i])
primdf['shell'] = np.repeat(range(shfunc, shfunc + bas), prim)
shfunc += bas
prims.append(primdf)
block = pd.concat(prims)
block['set'] = sdx
blocks.append(block)
gaussian_basis_set = pd.concat(blocks).reset_index(drop=True)
gaussian_basis_set['frame'] = 0
self.gaussian_basis_set = gaussian_basis_set
"""
NWChem Editor
##################
"""
import numpy as np
import pandas as pd
from io import StringIO
from exatomic.container import Universe
from exatomic.editor import Editor as AtomicEditor
from exatomic.basis import BasisSetSummary
try:
from exatomic.algorithms.basis import spher_lml_count, cart_lml_count, rlmap
except ImportError:
from exatomic.algorithms.basis import spher_ml_count, cart_ml_count, lmap, lorder
rlmap = {value: key for key, value in lmap.items() if len(key) == 1}
spher_lml_count = {lorder.index(key): value for key, value in spher_ml_count.items()}
cart_lml_count = {lorder.index(key): value for key, value in cart_ml_count.items()}
class Editor(AtomicEditor):
"""
Base NWChem editor
"""
def _expand_summary(self):
'''
Adds basis set information to the basis set summary table.
Requires a parsed basis set object.
'''
if any('bas_' in col for col in self.basis_set_summary):
return
#lcounts = bfns.apply(lambda y: y['L'].values[0]).value_counts()
