diff --git a/examples/python/in.fix_python_invoke_neighlist b/examples/python/in.fix_python_invoke_neighlist index 211d444b29..e5445227b1 100644 --- a/examples/python/in.fix_python_invoke_neighlist +++ b/examples/python/in.fix_python_invoke_neighlist @@ -20,7 +20,7 @@ neigh_modify every 20 delay 0 check no python post_force_callback here """ from __future__ import print_function -from lammps import lammps, LAMMPS_INT +from lammps import lammps def post_force_callback(lmp, v): try: @@ -35,14 +35,13 @@ def post_force_callback(lmp, v): #mylist = L.get_neighlist(0) mylist = L.find_pair_neighlist("lj/cut", request=0) print(pid_prefix, mylist) - nlocal = L.extract_global("nlocal", LAMMPS_INT) - nghost = L.extract_global("nghost", LAMMPS_INT) - ntypes = L.extract_global("ntypes", LAMMPS_INT) - mass = L.numpy.extract_atom_darray("mass", ntypes+1) - atype = L.numpy.extract_atom_iarray("type", nlocal+nghost) - x = L.numpy.extract_atom_darray("x", nlocal+nghost, dim=3) - v = L.numpy.extract_atom_darray("v", nlocal+nghost, dim=3) - f = L.numpy.extract_atom_darray("f", nlocal+nghost, dim=3) + nlocal = L.extract_global("nlocal") + nghost = L.extract_global("nghost") + mass = L.numpy.extract_atom("mass") + atype = L.numpy.extract_atom("type", nelem=nlocal+nghost) + x = L.numpy.extract_atom("x", nelem=nlocal+nghost, dim=3) + v = L.numpy.extract_atom("v", nelem=nlocal+nghost, dim=3) + f = L.numpy.extract_atom("f", nelem=nlocal+nghost, dim=3) for iatom, numneigh, neighs in mylist: print(pid_prefix, "- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ", numneigh, "Neighbors") diff --git a/examples/python/py_nve.py b/examples/python/py_nve.py index 27e6d91558..9ff7c0978b 100644 --- a/examples/python/py_nve.py +++ b/examples/python/py_nve.py @@ -39,19 +39,18 @@ class NVE(LAMMPSFixMove): assert(self.group_name == "all") def init(self): - dt = self.lmp.extract_global("dt", LAMMPS_DOUBLE) - ftm2v = self.lmp.extract_global("ftm2v", LAMMPS_DOUBLE) - self.ntypes = self.lmp.extract_global("ntypes", LAMMPS_INT) + dt = self.lmp.extract_global("dt") + ftm2v = self.lmp.extract_global("ftm2v") + self.ntypes = self.lmp.extract_global("ntypes") self.dtv = dt self.dtf = 0.5 * dt * ftm2v def initial_integrate(self, vflag): - nlocal = self.lmp.extract_global("nlocal", LAMMPS_INT) - mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1) - atype = self.lmp.numpy.extract_atom_iarray("type", nlocal) - x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3) - v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3) - f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3) + mass = self.lmp.numpy.extract_atom("mass") + atype = self.lmp.numpy.extract_atom("type") + x = self.lmp.numpy.extract_atom("x") + v = self.lmp.numpy.extract_atom("v") + f = self.lmp.numpy.extract_atom("f") for i in range(x.shape[0]): dtfm = self.dtf / mass[int(atype[i])] @@ -59,11 +58,10 @@ class NVE(LAMMPSFixMove): x[i,:] += self.dtv * v[i,:] def final_integrate(self): - nlocal = self.lmp.extract_global("nlocal", LAMMPS_INT) - mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1) - atype = self.lmp.numpy.extract_atom_iarray("type", nlocal) - v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3) - f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3) + mass = self.lmp.numpy.extract_atom("mass") + atype = self.lmp.numpy.extract_atom("type") + v = self.lmp.numpy.extract_atom("v") + f = self.lmp.numpy.extract_atom("f") for i in range(v.shape[0]): dtfm = self.dtf / mass[int(atype[i])] @@ -77,19 +75,19 @@ class NVE_Opt(LAMMPSFixMove): assert(self.group_name == "all") def init(self): - dt = self.lmp.extract_global("dt", LAMMPS_DOUBLE) - ftm2v = self.lmp.extract_global("ftm2v", LAMMPS_DOUBLE) - self.ntypes = self.lmp.extract_global("ntypes", LAMMPS_INT) + dt = self.lmp.extract_global("dt") + ftm2v = self.lmp.extract_global("ftm2v") + self.ntypes = self.lmp.extract_global("ntypes") self.dtv = dt self.dtf = 0.5 * dt * ftm2v - self.mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1) + self.mass = self.lmp.numpy.extract_atom("mass") def initial_integrate(self, vflag): - nlocal = self.lmp.extract_global("nlocal", LAMMPS_INT) - atype = self.lmp.numpy.extract_atom_iarray("type", nlocal) - x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3) - v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3) - f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3) + nlocal = self.lmp.extract_global("nlocal") + atype = self.lmp.numpy.extract_atom("type") + x = self.lmp.numpy.extract_atom("x") + v = self.lmp.numpy.extract_atom("v") + f = self.lmp.numpy.extract_atom("f") dtf = self.dtf dtv = self.dtv mass = self.mass @@ -102,11 +100,11 @@ class NVE_Opt(LAMMPSFixMove): x[:,d] += dtv * v[:,d] def final_integrate(self): - nlocal = self.lmp.extract_global("nlocal", LAMMPS_INT) - mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1) - atype = self.lmp.numpy.extract_atom_iarray("type", nlocal) - v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3) - f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3) + nlocal = self.lmp.extract_global("nlocal") + mass = self.lmp.numpy.extract_atom("mass") + atype = self.lmp.numpy.extract_atom("type") + v = self.lmp.numpy.extract_atom("v") + f = self.lmp.numpy.extract_atom("f") dtf = self.dtf mass = self.mass