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()