def _parse_params_values(parent_tag, units_dict, child_tag, expression=None):
# Tag of type Parameters can exist atmost once
params_dict = {}
if parent_tag.find('Parameters') is None:
return params_dict
for param in parent_tag.find('Parameters').getiterator('Parameter'):
if param.attrib['name'] not in units_dict:
raise ForceFieldParseError(
'Parameters {} with Unknown units found'.format(
param.attrib['name']))
param_name = param.attrib['name']
param_unit = units_dict[param_name]
param_value = u.unyt_quantity(float(param.attrib['value']), param_unit)
params_dict[param_name] = param_value
param_ref_dict = units_dict
if child_tag == 'DihedralType':
if not expression:
raise ForceFieldError(
'Cannot consolidate parameters without an expression')
_consolidate_params(params_dict, expression)
param_ref_dict = _consolidate_params(units_dict,
expression,
update_orig=False)
for param in param_ref_dict:
if param not in params_dict:
raise ForceFieldParseError(
'Parameter {} is in units but cannot be found in parameters list'
.format(param))
return params_dict
def _parse_params_values(parent_tag, units_dict, child_tag, expression=None):
"""Return the values of the parameters."""
# Tag of type Parameters can exist atmost once
params_dict = {}
if parent_tag.find("Parameters") is None:
return params_dict
for param in parent_tag.find("Parameters").getiterator("Parameter"):
if param.attrib["name"] not in units_dict:
raise ForceFieldParseError(
"Parameters {} with Unknown units found".format(
param.attrib["name"]))
param_name = param.attrib["name"]
param_unit = units_dict[param_name]
param_value = u.unyt_quantity(float(param.attrib["value"]), param_unit)
params_dict[param_name] = param_value
param_ref_dict = units_dict
if child_tag == "DihedralType":
if not expression:
raise ForceFieldError(
"Cannot consolidate parameters without an expression")
_consolidate_params(params_dict, expression)
param_ref_dict = _consolidate_params(units_dict,
expression,
update_orig=False)
for param in param_ref_dict:
if param not in params_dict:
raise ForceFieldParseError(
"Parameter {} is in units but cannot be found in parameters list"
.format(param))
return params_dict
def _check_valid_atomtype_names(tag, ref_dict):
at1 = tag.attrib.get('type1', None)
at2 = tag.attrib.get('type2', None)
at3 = tag.attrib.get('type3', None)
at4 = tag.attrib.get('type4', None)
member_types = list(filter(lambda x: x is not None, [at1, at2, at3, at4]))
member_types = ['*' if mem_type == '' else mem_type for mem_type in member_types]
for member in member_types:
if member == '*':
continue
if member not in ref_dict:
raise ForceFieldParseError('AtomTypes {} not present in AtomTypes reference in the xml'.format(member))
return member_types
def _check_atomtype_existence(tag, ref_dict):
at1 = tag.attrib.get('type1', tag.attrib.get('class1', None))
at2 = tag.attrib.get('type2', tag.attrib.get('class2', None))
at3 = tag.attrib.get('type3', tag.attrib.get('class3', None))
at4 = tag.attrib.get('type4', tag.attrib.get('class4', None))
atom_classes_set = set(value.atomclass for value in ref_dict.values()
if value)
member_types = list(filter(lambda x: x is not None, [at1, at2, at3, at4]))
member_types = [
'*' if mem_type == '' else mem_type for mem_type in member_types
]
for member in member_types:
if member == '*':
continue
if member not in ref_dict and member not in atom_classes_set:
raise ForceFieldParseError(
'AtomType/AtomClass {} not present in AtomTypes reference in the xml'
.format(member))
return member_types