Loading python/lammps.py +81 −0 Original line number Diff line number Diff line Loading @@ -189,6 +189,27 @@ 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_gather.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather.restype = None self.lib.lammps_gather_concat.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_concat.restype = None self.lib.lammps_gather_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_gather_subset.restype = None self.lib.lammps_scatter.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_scatter.restype = None self.lib.lammps_scatter_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_scatter_subset.restype = None 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 Loading Loading @@ -648,6 +669,66 @@ class lammps(object): if name: name = name.encode() self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,data) # return vector of atom/compute/fix properties gathered across procs # 3 variants to match src/library.cpp # name = atom property recognized by LAMMPS in atom->extract() # type = 0 for integer values, 1 for double values # count = number of per-atom valus, 1 for type or charge, 3 for x or f # returned data is a 1d vector - doc how it is ordered? # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes def gather(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) if type == 0: data = ((count*natoms)*c_int)() self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) elif type == 1: data = ((count*natoms)*c_double)() self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) else: return None return data def gather_concat(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) if type == 0: data = ((count*natoms)*c_int)() self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data) elif type == 1: data = ((count*natoms)*c_double)() self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data) else: return None return data def gather_subset(self,name,type,count,ndata,ids): if name: name = name.encode() if type == 0: data = ((count*ndata)*c_int)() self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data) elif type == 1: data = ((count*ndata)*c_double)() self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data) else: return None return data # scatter vector of atom/compute/fix properties across procs # 2 variants to match src/library.cpp # name = atom property recognized by LAMMPS in atom->extract() # type = 0 for integer values, 1 for double values # count = number of per-atom valus, 1 for type or charge, 3 for x or f # assume data is of correct type and length, as created by gather_atoms() # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes def scatter(self,name,type,count,data): if name: name = name.encode() self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) def scatter_subset(self,name,type,count,ndata,ids,data): if name: name = name.encode() self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,data) # create N atoms on all procs # N = global number of atoms # id = ID of each atom (optional, can be None) Loading Loading
python/lammps.py +81 −0 Original line number Diff line number Diff line Loading @@ -189,6 +189,27 @@ 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_gather.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather.restype = None self.lib.lammps_gather_concat.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_gather_concat.restype = None self.lib.lammps_gather_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_gather_subset.restype = None self.lib.lammps_scatter.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_void_p] self.lib.lammps_scatter.restype = None self.lib.lammps_scatter_subset.argtypes = \ [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p] self.lib.lammps_scatter_subset.restype = None 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 Loading Loading @@ -648,6 +669,66 @@ class lammps(object): if name: name = name.encode() self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,data) # return vector of atom/compute/fix properties gathered across procs # 3 variants to match src/library.cpp # name = atom property recognized by LAMMPS in atom->extract() # type = 0 for integer values, 1 for double values # count = number of per-atom valus, 1 for type or charge, 3 for x or f # returned data is a 1d vector - doc how it is ordered? # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes def gather(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) if type == 0: data = ((count*natoms)*c_int)() self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) elif type == 1: data = ((count*natoms)*c_double)() self.lib.lammps_gather_atoms(self.lmp,name,type,count,data) else: return None return data def gather_concat(self,name,type,count): if name: name = name.encode() natoms = self.lib.lammps_get_natoms(self.lmp) if type == 0: data = ((count*natoms)*c_int)() self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data) elif type == 1: data = ((count*natoms)*c_double)() self.lib.lammps_gather_atoms_concat(self.lmp,name,type,count,data) else: return None return data def gather_subset(self,name,type,count,ndata,ids): if name: name = name.encode() if type == 0: data = ((count*ndata)*c_int)() self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data) elif type == 1: data = ((count*ndata)*c_double)() self.lib.lammps_gather_atoms_subset(self.lmp,name,type,count,ndata,ids,data) else: return None return data # scatter vector of atom/compute/fix properties across procs # 2 variants to match src/library.cpp # name = atom property recognized by LAMMPS in atom->extract() # type = 0 for integer values, 1 for double values # count = number of per-atom valus, 1 for type or charge, 3 for x or f # assume data is of correct type and length, as created by gather_atoms() # NOTE: need to insure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes def scatter(self,name,type,count,data): if name: name = name.encode() self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) def scatter_subset(self,name,type,count,ndata,ids,data): if name: name = name.encode() self.lib.lammps_scatter_atoms_subset(self.lmp,name,type,count,ndata,ids,data) # create N atoms on all procs # N = global number of atoms # id = ID of each atom (optional, can be None) Loading
