def test_element_data(Z):
# Cycle through the elements and check that
# the info returned from the functions is consistent
data = lut.element_data_from_Z(Z)
assert data[1] == int(Z)
assert data == lut.element_data_from_sym(data[0])
assert data == lut.element_data_from_name(data[2])
assert data[0] == lut.element_sym_from_Z(Z)
assert data[2] == lut.element_name_from_Z(Z)
nsym = lut.element_sym_from_Z(Z, True)
nname = lut.element_name_from_Z(Z, True)
assert int(Z) == lut.element_Z_from_sym(nsym.upper())
# Check capitalization
assert nsym[0] == data[0][0].upper()
assert nname[0] == data[2][0].upper()
split_lines = f.readlines()
all_names = [
'ANO-RCC-MB', 'ANO-RCC-VDZ', 'ANO-RCC-VDZP', 'ANO-RCC-VTZP',
'ANO-RCC-VQZP', 'ANO-RCC-VTZ'
]
split_data = {n: {} for n in all_names}
for l in split_lines:
name, cont = l.split()
el1, name1 = name.split('.')
el2, name2, _, _, cont, _ = cont.split('.')
assert el1 == el2
assert name2 == 'ANO-RCC'
assert name1 in all_names
el = lut.element_Z_from_sym(el1, as_str=True)
assert el not in split_data[name1]
cont = re.findall(r'\d+[a-z]+', cont)
split_data[name1][el] = cont
for name, el_cont_data in split_data.items():
print()
print(name)
new_basis = copy.deepcopy(base_data)
missing_el = []
for el, eldata in new_basis['elements'].items():
if not el in el_cont_data:
missing_el.append(el)
def get_element_number(element):
return lut.element_Z_from_sym(element)
import re
import sys
import copy
from basis_set_exchange import fileio, lut
from basis_set_exchange.readers.helpers import partition_lines, parse_fixed_matrix
with open('ano-r.1.molcas', 'r') as f:
base_data = [x.strip() for x in f.readlines()]
with open('splitmap-ano-r.txt', 'r') as f:
split_data = f.readlines()[2:]
split_data = [x.strip().split() for x in split_data]
split_data = {
lut.element_Z_from_sym(x[0], as_str=True): (x[1], x[2], x[3], x[4])
for x in split_data
}
element_blocks = partition_lines(base_data, lambda x: x.startswith('/'))
names = ['ANO-R0', 'ANO-R1', 'ANO-R2', 'ANO-R3']
for idx, name in enumerate(names):
out_lines = []
print(name)
element_blocks_copy = copy.deepcopy(element_blocks)
for block in element_blocks_copy:
el = re.match(r'/([A-Za-z]+)\..*', block[0]).group(1)
el = lut.element_Z_from_sym(el, as_str=True)
print("basis {} already has element {}. Overwriting...".format(
bn, el),
file=sys.stderr)
all_basis[bn][el] = el_bas_data
if not desired_basis in all_basis:
raise RuntimeError("basis '{}' not found".format(desired_basis))
bas = all_basis[desired_basis]
for el, v in bas.items():
while len(v['links']) > 0:
linkstmp = v['links'].copy()
v['links'] = []
for l in linkstmp:
el2, b2 = l.split(maxsplit=1)
if el2 != el:
raise RuntimeError("bad link")
ldata = all_basis[b2][el2]
v['shells'].extend(ldata['shells'])
v['links'].extend(ldata['links'])
allel = sorted(bas.keys(), key=lambda x: lut.element_Z_from_sym(x))
s = '*\n'
for el in allel:
s += '{} {}\n*\n'.format(el, desired_basis)
s += '\n'.join(bas[el]['shells'])
s += '\n*\n'
print(s)
#!/usr/bin/env python3
import re
import sys
import copy
from basis_set_exchange import fileio, lut
base_data = fileio.read_json_basis('ANO-R.1.json')
with open('splitmap-ano-r.txt', 'r') as f:
split_data = f.readlines()[2:]
split_data = [x.strip().split() for x in split_data]
split_data = {lut.element_Z_from_sym(x[0], as_str=True): (x[1], x[2], x[3], x[4]) for x in split_data}
names = ['ANO-R0', 'ANO-R1', 'ANO-R2', 'ANO-R3']
for idx,name in enumerate(names):
print(name)
new_basis = copy.deepcopy(base_data)
for el,eldata in new_basis['elements'].items():
el_split = split_data[el][idx]
el_split = re.findall(r'\d+[a-z]+', el_split)
print(' -> ', el, el_split)
new_shells = []
# Double and triple check
am = [sh['angular_momentum'] for sh in eldata['electron_shells']]
for a in am:
assert len(a) == 1