Loading python/lammps.py +88 −4 Original line number Diff line number Diff line Loading @@ -52,6 +52,17 @@ class MPIAbortException(Exception): return repr(self.message) class NeighList: """This is a wrapper class that exposes the contents of a neighbor list It can be used like a regular Python list. Internally it uses the lower-level LAMMPS C-library interface. :param lmp: reference to instance of :class:`lammps` :type lmp: lammps :param idx: neighbor list index :type idx: int """ def __init__(self, lmp, idx): self.lmp = lmp self.idx = idx Loading @@ -64,12 +75,21 @@ class NeighList: @property def size(self): """ :return: number of elements in neighbor list """ return self.lmp.get_neighlist_size(self.idx) def get(self, element): """ :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices :rtype: (int, int, numpy.array) """ iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element) return iatom, numneigh, neighbors # the methods below implement the iterator interface, so NeighList can be used like a regular Python list def __getitem__(self, element): return self.get(element) Loading Loading @@ -169,7 +189,7 @@ class lammps(object): [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_scatter_atoms_subset.restype = None self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int] self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int] self.lib.lammps_find_pair_neighlist.restype = c_int self.lib.lammps_find_fix_neighlist.argtypes = [c_void_p, c_char_p, c_int] Loading Loading @@ -699,29 +719,93 @@ class lammps(object): self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller) def get_neighlist(self, idx): """Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index :param idx: index of neighbor list :type idx: int :return: an instance of :class:`NeighList` wrapping access to neighbor list data :rtype: NeighList """ if idx < 0: return None return NeighList(self, idx) def find_pair_neighlist(self, style, nsub=0, request=0): def find_pair_neighlist(self, style, exact=True, nsub=0, request=0): """Find neighbor list index of pair style neighbor list Try finding pair instance that matches style. If exact is set, the pair must match style exactly. If exact is 0, style must only be contained. If pair is of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style. Once the pair instance has been identified, multiple neighbor list requests may be found. Every neighbor list is uniquely identified by its request index. Thus, providing this request index ensures that the correct neighbor list index is returned. :param style: name of pair style that should be searched for :type style: string :param exact: controls whether style should match exactly or only must be contained in pair style name, defaults to True :type exact: bool, optional :param nsub: match nsub-th hybrid sub-style, defaults to 0 :type nsub: int, optional :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int """ style = style.encode() idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, nsub, request) exact = int(exact) idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, request) return self.get_neighlist(idx) def find_fix_neighlist(self, fixid, request=0): """Find neighbor list index of fix neighbor list :param fixid: name of fix :type fixid: string :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int """ fixid = fixid.encode() idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request) return self.get_neighlist(idx) def find_compute_neighlist(self, computeid, request=0): """Find neighbor list index of compute neighbor list :param computeid: name of compute :type computeid: string :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int """ computeid = computeid.encode() idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request) return self.get_neighlist(idx) def get_neighlist_size(self, idx): """Return the number of elements in neighbor list with the given index :param idx: neighbor list index :type idx: int :return: number of elements in neighbor list with index idx :rtype: int """ return self.lib.lammps_neighlist_num_elements(self.lmp, idx) def get_neighlist_element_neighbors(self, idx, element): """Return data of neighbor list entry :param element: neighbor list index :type element: int :param element: neighbor list element index :type element: int :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices :rtype: (int, int, numpy.array) """ c_iatom = c_int() c_numneigh = c_int() c_neighbors = POINTER(c_int)() Loading Loading
python/lammps.py +88 −4 Original line number Diff line number Diff line Loading @@ -52,6 +52,17 @@ class MPIAbortException(Exception): return repr(self.message) class NeighList: """This is a wrapper class that exposes the contents of a neighbor list It can be used like a regular Python list. Internally it uses the lower-level LAMMPS C-library interface. :param lmp: reference to instance of :class:`lammps` :type lmp: lammps :param idx: neighbor list index :type idx: int """ def __init__(self, lmp, idx): self.lmp = lmp self.idx = idx Loading @@ -64,12 +75,21 @@ class NeighList: @property def size(self): """ :return: number of elements in neighbor list """ return self.lmp.get_neighlist_size(self.idx) def get(self, element): """ :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices :rtype: (int, int, numpy.array) """ iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element) return iatom, numneigh, neighbors # the methods below implement the iterator interface, so NeighList can be used like a regular Python list def __getitem__(self, element): return self.get(element) Loading Loading @@ -169,7 +189,7 @@ class lammps(object): [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_scatter_atoms_subset.restype = None self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int] self.lib.lammps_find_pair_neighlist.argtypes = [c_void_p, c_char_p, c_int, c_int, c_int] self.lib.lammps_find_pair_neighlist.restype = c_int self.lib.lammps_find_fix_neighlist.argtypes = [c_void_p, c_char_p, c_int] Loading Loading @@ -699,29 +719,93 @@ class lammps(object): self.lib.lammps_set_fix_external_callback(self.lmp, fix_name.encode(), cFunc, cCaller) def get_neighlist(self, idx): """Returns an instance of :class:`NeighList` which wraps access to the neighbor list with the given index :param idx: index of neighbor list :type idx: int :return: an instance of :class:`NeighList` wrapping access to neighbor list data :rtype: NeighList """ if idx < 0: return None return NeighList(self, idx) def find_pair_neighlist(self, style, nsub=0, request=0): def find_pair_neighlist(self, style, exact=True, nsub=0, request=0): """Find neighbor list index of pair style neighbor list Try finding pair instance that matches style. If exact is set, the pair must match style exactly. If exact is 0, style must only be contained. If pair is of style pair/hybrid, style is instead matched the nsub-th hybrid sub-style. Once the pair instance has been identified, multiple neighbor list requests may be found. Every neighbor list is uniquely identified by its request index. Thus, providing this request index ensures that the correct neighbor list index is returned. :param style: name of pair style that should be searched for :type style: string :param exact: controls whether style should match exactly or only must be contained in pair style name, defaults to True :type exact: bool, optional :param nsub: match nsub-th hybrid sub-style, defaults to 0 :type nsub: int, optional :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int """ style = style.encode() idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, nsub, request) exact = int(exact) idx = self.lib.lammps_find_pair_neighlist(self.lmp, style, exact, nsub, request) return self.get_neighlist(idx) def find_fix_neighlist(self, fixid, request=0): """Find neighbor list index of fix neighbor list :param fixid: name of fix :type fixid: string :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int """ fixid = fixid.encode() idx = self.lib.lammps_find_fix_neighlist(self.lmp, fixid, request) return self.get_neighlist(idx) def find_compute_neighlist(self, computeid, request=0): """Find neighbor list index of compute neighbor list :param computeid: name of compute :type computeid: string :param request: index of neighbor list request, in case there are more than one, defaults to 0 :type request: int, optional :return: neighbor list index if found, otherwise -1 :rtype: int """ computeid = computeid.encode() idx = self.lib.lammps_find_compute_neighlist(self.lmp, computeid, request) return self.get_neighlist(idx) def get_neighlist_size(self, idx): """Return the number of elements in neighbor list with the given index :param idx: neighbor list index :type idx: int :return: number of elements in neighbor list with index idx :rtype: int """ return self.lib.lammps_neighlist_num_elements(self.lmp, idx) def get_neighlist_element_neighbors(self, idx, element): """Return data of neighbor list entry :param element: neighbor list index :type element: int :param element: neighbor list element index :type element: int :return: tuple with atom local index, number of neighbors and array of neighbor local atom indices :rtype: (int, int, numpy.array) """ c_iatom = c_int() c_numneigh = c_int() c_neighbors = POINTER(c_int)() Loading
