def convert_xml(xmlfile):
bsdict = read_xml(xmlfile)
outfile = create_json_filename(xmlfile)
print("New basis file: ", outfile)
bsdict['molssi_bse_magic'] = 1
#print(json.dumps(bsdict, indent=4))
bse.write_json_basis(outfile, bsdict)
def convert_xml_agg(xmlfile):
atom_dict, table_dict = read_basis_xml_agg(xmlfile)
atom_basis_path = create_json_filename(xmlfile, 'element')
table_basis_path = create_json_filename(xmlfile, 'table')
print("Atom basis: ", atom_basis_path)
print("Table basis: ", table_basis_path)
atom_dict['molssi_bse_magic'] = 1
table_dict['molssi_bse_magic'] = 1
table_dict['basisSetRole'] = 'orbital'
bse.write_json_basis(atom_basis_path, atom_dict)
bse.write_json_basis(table_basis_path, table_dict)
newjs['basisSetReferences'] = ref
for el, v in newjs['basisSetElements'].items():
v.pop('elementReferences')
if len(ref) == 0:
refname = "noref"
else:
refname = '_'.join(ref)
new_filename = src_base + "_" + refname + ".json"
print()
print("New filename: ", new_filename)
print("Ref(s): ", ref)
print("Elements in ref: ", elements_in_ref)
bse.write_json_basis(new_filename, newjs)
# Go through all the aggregate files and rename
for el, v in element_files.items():
for z in elements_in_ref:
if z in v['basisSetElements']:
comps = v['basisSetElements'][z]['elementComponents']
if src in comps:
idx = comps.index(src)
comps[idx] = new_filename
# Save all the aggregate files
for k, v in element_files.items():
bse.write_json_basis(k, v)
os.rename(src, src + ".old")
if not cname in added_map:
added_map[cname] = []
added_map[cname].append(k)
# remove only the equivalent shells
celements[k]['elementElectronShells'] = [
x for x in cel['elementElectronShells']
if not x in sel['elementElectronShells']
]
# rewrite the candidate file
if changed:
os.rename(cfile, cfile + ".old")
bse.write_json_basis(cfile, cdata)
# print out the replacement map
for k, v in replaced_map.items():
print("Replaced in {}: {}".format(k, v))
for k, v in added_map.items():
print("Partially replaced in {}: {}".format(k, v))
# Now go through all the atom basis files, doing replacements
for afile in element_files:
adata = bse.read_json_by_path(afile)
changed = False
for k, v in adata['basisSetElements'].items():
for i, c in enumerate(v['elementComponents']):
dest_elements[k] = v
else:
dest_el = dest_elements[k]
dest_el['elementReferences'].extend(v['elementReferences'])
dest_el['elementElectronShells'].extend(v['elementElectronShells'])
# Handle a rename
for f in element_files:
changed = False
data = bse.read_json_by_path(f)
for k, v in data['basisSetElements'].items():
if src_base in v['elementComponents']:
changed = True
print("Found in {} {}".format(f, k))
v['elementComponents'] = [
dest_base if x == src_base else x
for x in v['elementComponents']
]
if changed:
os.rename(f, f + ".old")
bse.write_json_basis(f, data)
# Rename the old file
os.rename(src, src + '.old')
# Rename the old description file
if os.path.isfile(src_base + '.txt'):
src_desc_file = src_base + '.txt'
os.rename(src_desc_file, src_desc_file + '.old')
def create_xml_agg(xmlfile):
# Create from a simple (non-composed) basis
atom_basis_file = create_json_filename(xmlfile, 'element')
table_basis_file = create_json_filename(xmlfile, 'table')
# Needed for the table entry
atom_basis_file = create_json_filename(xmlfile, 'element')
json_file = os.path.basename(create_json_filename(xmlfile))
bs = read_xml(xmlfile)
# May be none
ecp_file = get_ecp_file(xmlfile)
if ecp_file:
ecp_json = create_json_filename(ecp_file)
elementlist = list(bs['basisSetElements'].keys())
atom_elements = {
k: {
'elementComponents': [json_file]
}
for k in elementlist
}
table_elements = {
k: {
'elementEntry': atom_basis_file
}
for k in elementlist
}
# Handle elements with ecp
if ecp_file:
ecp_data = bse.read_json_basis(ecp_json)
ecp_elements = list(ecp_data['basisSetElements'].keys())
for k in ecp_elements:
if not k in atom_elements:
atom_elements[k] = {'elementComponents': [ecp_json]}
else:
atom_elements[k]['elementComponents'].append(ecp_json)
# Create the actual dictionaries
atom_dict = {
'basisSetName': bs['basisSetName'],
'basisSetDescription': bs['basisSetDescription'],
'basisSetElements': atom_elements
}
table_dict = {
'basisSetName': bs['basisSetName'],
'basisSetDescription': bs['basisSetDescription'],
'basisSetElements': table_elements
}
atom_dict['molssi_bse_magic'] = 1
table_dict['molssi_bse_magic'] = 1
table_dict['basisSetRole'] = 'orbital'
bse.write_json_basis(atom_basis_file, atom_dict)
bse.write_json_basis(table_basis_file, table_dict)
reffile = os.path.join(ref_dir, elref + '.json')
file_ref_json = None
if os.path.isfile(reffile):
with open(reffile, 'r') as ftmp:
file_ref_json = json.loads(ftmp.read())
else:
print("Missing file {}".format(reffile))
continue
elref_data = find_Z(file_ref_json, el)
new_references = []
for d in elref_data:
if 'article' in d:
new_references.append(d['article'])
if not d['article'] in refdata:
print("File: ", f)
print("reffile: ", reffile)
raise RuntimeError(
"Reference {} not found in REFERENCES".format(
d['article']))
else:
print("No article: {}".format(reffile))
#print(" Articles: ", new_references)
data['elementReferences'] = new_references
#os.rename(f, f+'.old')
bse.write_json_basis(f, file_data)