def get_indexes(self, rule):
"""Return the atom indexes that match the filter ``rule``
``rule`` can be a function that accepts two arguments: system and an
atom index and that returns True of the atom with index i is of a
given type. On the other hand ``rule`` can be an ATSELECT string that
defines the atoms of interest.
A list of atom indexes is returned.
"""
if isinstance(rule, basestring):
rule = atsel_compile(rule)
return np.array([i for i in xrange(self.natom) if rule(self, i)])
def get_indexes(self, rule):
"""Return the atom indexes that match the filter ``rule``
``rule`` can be a function that accepts two arguments: system and an
atom index and that returns True of the atom with index i is of a
given type. On the other hand ``rule`` can be an ATSELECT string that
defines the atoms of interest.
A list of atom indexes is returned.
"""
if isinstance(rule, str):
rule = atsel_compile(rule)
return np.array([i for i in range(self.natom) if rule(self, i)])
def detect_ffatypes(self, rules):
"""Initialize the ``ffatypes`` attribute based on ATSELECT rules.
**Argument:**
rules
A list of (ffatype, rule) pairs that will be used to initialize
the attributes ``self.ffatypes`` and ``self.ffatype_ids``.
If the system already has FF atom types, they will be overwritten.
"""
with log.section('SYS'):
# Give warning if needed
if self.ffatypes is not None:
if log.do_warning:
log.warn('Overwriting existing FF atom types.')
# Compile all the rules
my_rules = []
for ffatype, rule in rules:
check_name(ffatype)
if isinstance(rule, str):
rule = atsel_compile(rule)
my_rules.append((ffatype, rule))
# Use the rules to detect the atom types
lookup = {}
self.ffatypes = []
self.ffatype_ids = np.zeros(self.natom, int)
for i in range(self.natom):
my_ffatype = None
for ffatype, rule in my_rules:
if rule(self, i):
my_ffatype = ffatype
break
if my_ffatype is None:
raise ValueError(
'Could not detect FF atom type of atom %i.' % i)
ffatype_id = lookup.get(my_ffatype)
if ffatype_id is None:
ffatype_id = len(lookup)
self.ffatypes.append(my_ffatype)
lookup[my_ffatype] = ffatype_id
self.ffatype_ids[i] = ffatype_id
# Make sure all is done well ...
self._init_derived_ffatypes()
def detect_ffatypes(self, rules):
"""Initialize the ``ffatypes`` attribute based on ATSELECT rules.
**Argument:**
rules
A list of (ffatype, rule) pairs that will be used to initialize
the attributes ``self.ffatypes`` and ``self.ffatype_ids``.
If the system already has FF atom types, they will be overwritten.
"""
with log.section('SYS'):
# Give warning if needed
if self.ffatypes is not None:
if log.do_warning:
log.warn('Overwriting existing FF atom types.')
# Compile all the rules
my_rules = []
for ffatype, rule in rules:
check_name(ffatype)
if isinstance(rule, basestring):
rule = atsel_compile(rule)
my_rules.append((ffatype, rule))
# Use the rules to detect the atom types
lookup = {}
self.ffatypes = []
self.ffatype_ids = np.zeros(self.natom, int)
for i in xrange(self.natom):
my_ffatype = None
for ffatype, rule in my_rules:
if rule(self, i):
my_ffatype = ffatype
break
if my_ffatype is None:
raise ValueError('Could not detect FF atom type of atom %i.' % i)
ffatype_id = lookup.get(my_ffatype)
if ffatype_id is None:
ffatype_id = len(lookup)
self.ffatypes.append(my_ffatype)
lookup[my_ffatype] = ffatype_id
self.ffatype_ids[i] = ffatype_id
# Make sure all is done well ...
self._init_derived_ffatypes()