import sys,os,unittest from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL, \ LMP_STYLE_ATOM, LMP_TYPE_VECTOR, LMP_TYPE_SCALAR, LMP_TYPE_ARRAY, \ LMP_VAR_ATOM from ctypes import c_void_p has_manybody=False try: machine=None if 'LAMMPS_MACHINE_NAME' in os.environ: machine=os.environ['LAMMPS_MACHINE_NAME'] lmp=lammps(name=machine) has_manybody = lmp.has_style("pair","sw") lmp.close() except: pass has_full=False try: machine=None if 'LAMMPS_MACHINE_NAME' in os.environ: machine=os.environ['LAMMPS_MACHINE_NAME'] lmp=lammps(name=machine) has_full = lmp.has_style("atom","full") lmp.close() except: pass try: import numpy NUMPY_INSTALLED = True except ImportError: NUMPY_INSTALLED = False @unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available") class PythonNumpy(unittest.TestCase): def setUp(self): machine = None if 'LAMMPS_MACHINE_NAME' in os.environ: machine=os.environ['LAMMPS_MACHINE_NAME'] self.lmp = lammps(name=machine, cmdargs=['-nocite', '-log','none', '-echo','screen']) def tearDown(self): del self.lmp def checkBond(self, vals, btype, batom1, batom2): if ((vals[1] == batom1 and vals[2] == batom2) or (vals[1] == batom2 and vals[2] == batom1)): self.assertEqual(vals[0], btype) return 1 else: return 0 def checkAngle(self, vals, atype, aatom1, aatom2, aatom3): set1 = {aatom1, aatom2, aatom3} set2 = {vals[1], vals[2], vals[3]} if len(set1.intersection(set2)) == 3: self.assertEqual(vals[0], atype) return 1 else: return 0 def checkDihedral(self, vals, dtype, datom1, datom2, datom3, datom4): set1 = {datom1, datom2, datom3, datom4} set2 = {vals[1], vals[2], vals[3], vals[4]} if len(set1.intersection(set2)) == 4: self.assertEqual(vals[0], dtype) return 1 else: return 0 def checkImproper(self, vals, itype, iatom1, iatom2, iatom3, iatom4): set1 = {iatom1, iatom2, iatom3, iatom4} set2 = {vals[1], vals[2], vals[3], vals[4]} if len(set1.intersection(set2)) == 4: self.assertEqual(vals[0], itype) return 1 else: return 0 def testLammpsPointer(self): self.assertEqual(type(self.lmp.lmp), c_void_p) def testExtractComputeGlobalScalar(self): # TODO pass def testExtractComputeGlobalVector(self): self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") self.lmp.command("compute coordsum all reduce sum x y z") natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) values = self.lmp.numpy.extract_compute("coordsum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR) self.assertEqual(len(values), 3) self.assertEqual(values[0], 2.0) self.assertEqual(values[1], 2.0) self.assertEqual(values[2], 2.5) def testExtractComputeGlobalArray(self): # TODO pass def testExtractComputePerAtomVector(self): self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") self.lmp.command("compute ke all ke/atom") natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) values = self.lmp.numpy.extract_compute("ke", LMP_STYLE_ATOM, LMP_TYPE_VECTOR) self.assertEqual(len(values), 2) self.assertEqual(values[0], 0.0) self.assertEqual(values[1], 0.0) def testExtractComputePerAtomArray(self): # TODO pass def testExtractComputeLocalVector(self): self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") self.lmp.command("mass 1 1.0") self.lmp.command("pair_style lj/cut 1.9") self.lmp.command("pair_coeff 1 1 1.0 1.0") self.lmp.command("compute r0 all pair/local dist") self.lmp.command("run 0 post no") values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_VECTOR) self.assertEqual(values.ndim, 1) self.assertEqual(values.size, 2) self.assertEqual(values[0], 0.5) self.assertEqual(values[1], 1.5) def testExtractComputeLocalArray(self): self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("create_atoms 1 single 1.0 1.0 1.0") self.lmp.command("create_atoms 1 single 1.0 1.0 1.5") self.lmp.command("mass 1 1.0") self.lmp.command("pair_style lj/cut 1.9") self.lmp.command("pair_coeff 1 1 1.0 1.0") self.lmp.command("compute r0 all pair/local dist dx dy dz") self.lmp.command("run 0 post no") values = self.lmp.numpy.extract_compute("r0", LMP_STYLE_LOCAL, LMP_TYPE_ARRAY) self.assertEqual(values.ndim, 2) self.assertEqual(values.size, 8) self.assertEqual(values[0,0], 0.5) self.assertEqual(values[0,3], -0.5) self.assertEqual(values[1,0], 1.5) self.assertEqual(values[1,3], 1.5) def testExtractAtomDeprecated(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal", LAMMPS_INT) self.assertEqual(nlocal, 2) ident = self.lmp.numpy.extract_atom_iarray("id", nlocal, dim=1) self.assertEqual(len(ident), 2) ntypes = self.lmp.extract_global("ntypes", LAMMPS_INT) self.assertEqual(ntypes, 1) x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3) v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3) self.assertEqual(len(x), 2) self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all()) self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) self.assertEqual(len(v), 2) def testExtractAtom(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 2) ident = self.lmp.numpy.extract_atom("id") self.assertEqual(len(ident), 2) ntypes = self.lmp.extract_global("ntypes") self.assertEqual(ntypes, 1) x = self.lmp.numpy.extract_atom("x") v = self.lmp.numpy.extract_atom("v") self.assertEqual(len(x), 2) self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all()) self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all()) self.assertEqual(len(v), 2) @unittest.skipIf(not has_full,"Gather bonds test") def testGatherBond_newton_on(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton on on") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") bonds = self.lmp.numpy.gather_bonds() self.assertEqual(len(bonds),24) count = 0 for bond in bonds: count += self.checkBond(bond, 5, 1, 2) count += self.checkBond(bond, 3, 1, 3) count += self.checkBond(bond, 2, 3, 4) count += self.checkBond(bond, 2, 3, 5) count += self.checkBond(bond, 1, 6, 3) count += self.checkBond(bond, 3, 6, 8) count += self.checkBond(bond, 4, 6, 7) count += self.checkBond(bond, 5, 8, 9) count += self.checkBond(bond, 5, 27, 28) count += self.checkBond(bond, 5, 29, 27) self.assertEqual(count,10) @unittest.skipIf(not has_full,"Gather bonds test") def testGatherBond_newton_off(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton off off") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") bonds = self.lmp.numpy.gather_bonds() self.assertEqual(len(bonds),24) count = 0 for bond in bonds: count += self.checkBond(bond, 5, 1, 2) count += self.checkBond(bond, 3, 1, 3) count += self.checkBond(bond, 2, 3, 4) count += self.checkBond(bond, 2, 3, 5) count += self.checkBond(bond, 1, 6, 3) count += self.checkBond(bond, 3, 6, 8) count += self.checkBond(bond, 4, 6, 7) count += self.checkBond(bond, 5, 8, 9) count += self.checkBond(bond, 5, 27, 28) count += self.checkBond(bond, 5, 29, 27) self.assertEqual(count,10) @unittest.skipIf(not has_full,"Gather angles test") def testGatherAngle_newton_on(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton on on") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") angles = self.lmp.numpy.gather_angles() self.assertEqual(len(angles),30) count = 0 for angle in angles: count += self.checkAngle(angle, 4, 2, 1, 3) count += self.checkAngle(angle, 4, 1, 3, 6) count += self.checkAngle(angle, 2, 4, 3, 6) count += self.checkAngle(angle, 3, 7, 6, 8) count += self.checkAngle(angle, 3, 8, 10, 16) count += self.checkAngle(angle, 2, 8, 10, 11) count += self.checkAngle(angle, 1, 12, 10, 16) count += self.checkAngle(angle, 2, 10, 12, 14) count += self.checkAngle(angle, 1, 19, 18, 20) count += self.checkAngle(angle, 1, 28, 27, 29) self.assertEqual(count,10) @unittest.skipIf(not has_full,"Gather angles test") def testGatherAngle_newton_off(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton off off") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") angles = self.lmp.numpy.gather_angles() self.assertEqual(len(angles),30) count = 0 for angle in angles: count += self.checkAngle(angle, 4, 2, 1, 3) count += self.checkAngle(angle, 4, 1, 3, 6) count += self.checkAngle(angle, 2, 4, 3, 6) count += self.checkAngle(angle, 3, 7, 6, 8) count += self.checkAngle(angle, 3, 8, 10, 16) count += self.checkAngle(angle, 2, 8, 10, 11) count += self.checkAngle(angle, 1, 12, 10, 16) count += self.checkAngle(angle, 2, 10, 12, 14) count += self.checkAngle(angle, 1, 19, 18, 20) count += self.checkAngle(angle, 1, 28, 27, 29) self.assertEqual(count,10) @unittest.skipIf(not has_full,"Gather dihedrals test") def testGatherDihedral_newton_on(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton on on") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") dihedrals = self.lmp.numpy.gather_dihedrals() self.assertEqual(len(dihedrals),31) count = 0 for dihedral in dihedrals: count += self.checkDihedral(dihedral, 2, 2, 1, 3, 6) count += self.checkDihedral(dihedral, 3, 2, 1, 3, 5) count += self.checkDihedral(dihedral, 1, 1, 3, 6, 7) count += self.checkDihedral(dihedral, 5, 4, 3, 6, 7) count += self.checkDihedral(dihedral, 4, 3, 6, 8, 9) count += self.checkDihedral(dihedral, 2, 6, 8, 10, 16) count += self.checkDihedral(dihedral, 5, 8, 10, 12, 13) count += self.checkDihedral(dihedral, 1, 8, 10, 12, 14) count += self.checkDihedral(dihedral, 2, 11, 10, 16, 17) count += self.checkDihedral(dihedral, 5, 16, 10, 12, 14) self.assertEqual(count,10) @unittest.skipIf(not has_full,"Gather dihedrals test") def testGatherDihedral_newton_off(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton off off") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") dihedrals = self.lmp.numpy.gather_dihedrals() self.assertEqual(len(dihedrals),31) count = 0 for dihedral in dihedrals: count += self.checkDihedral(dihedral, 2, 2, 1, 3, 6) count += self.checkDihedral(dihedral, 3, 2, 1, 3, 5) count += self.checkDihedral(dihedral, 1, 1, 3, 6, 7) count += self.checkDihedral(dihedral, 5, 4, 3, 6, 7) count += self.checkDihedral(dihedral, 4, 3, 6, 8, 9) count += self.checkDihedral(dihedral, 2, 6, 8, 10, 16) count += self.checkDihedral(dihedral, 5, 8, 10, 12, 13) count += self.checkDihedral(dihedral, 1, 8, 10, 12, 14) count += self.checkDihedral(dihedral, 2, 11, 10, 16, 17) count += self.checkDihedral(dihedral, 5, 16, 10, 12, 14) self.assertEqual(count,10) @unittest.skipIf(not has_full,"Gather impropers test") def testGatherImproper_newton_on(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton on on") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") impropers = self.lmp.numpy.gather_impropers() self.assertEqual(len(impropers),2) count = 0 for improper in impropers: count += self.checkImproper(improper, 1, 6, 3, 8, 7) count += self.checkImproper(improper, 2, 8, 6, 10, 9) self.assertEqual(count,2) @unittest.skipIf(not has_full,"Gather impropers test") def testGatherImproper_newton_off(self): self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR']) self.lmp.command("newton off off") self.lmp.file("in.fourmol") self.lmp.command("run 0 post no") impropers = self.lmp.numpy.gather_impropers() self.assertEqual(len(impropers),2) count = 0 for improper in impropers: count += self.checkImproper(improper, 1, 6, 3, 8, 7) count += self.checkImproper(improper, 2, 8, 6, 10, 9) self.assertEqual(count,2) def testNeighborListSimple(self): self.lmp.commands_string(""" units lj atom_style atomic atom_modify map array boundary f f f region box block 0 2 0 2 0 2 create_box 1 box""") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 2) self.lmp.commands_string(""" mass 1 1.0 velocity all create 3.0 87287 pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.1 bin neigh_modify every 20 delay 0 check no run 0 post no""") idx = self.lmp.find_pair_neighlist("lj/cut") self.assertNotEqual(idx, -1) nlist = self.lmp.numpy.get_neighlist(idx) self.assertEqual(len(nlist), 2) atom_i, neighbors_i = nlist[0] atom_j, neighbors_j = nlist[1] self.assertEqual(atom_i, 0) self.assertEqual(atom_j, 1) self.assertEqual(len(neighbors_i), 1) self.assertEqual(len(neighbors_j), 0) self.assertIn(1, neighbors_i) self.assertNotIn(0, neighbors_j) def testNeighborListHalf(self): self.lmp.commands_string(""" boundary f f f units real region box block -5 5 -5 5 -5 5 create_box 1 box mass 1 1.0 pair_style lj/cut 4.0 pair_coeff 1 1 0.2 2.0 """) x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0 ] tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) self.lmp.command("run 0 post no") self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),0) nlist = self.lmp.numpy.get_neighlist(0) self.assertEqual(nlist.size, 7) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(idx,i) self.assertEqual(neighs.size,nlocal-1-i) # look up neighbor list by atom index neighs = nlist.find(2) self.assertEqual(neighs.size,4) self.assertIsNotNone(neighs,None) # this one will fail neighs = nlist.find(10) self.assertIsNone(neighs,None) @unittest.skipIf(not has_manybody,"Full neighbor list test for manybody potential") def testNeighborListFull(self): self.lmp.commands_string(""" boundary f f f units metal region box block -5 5 -5 5 -5 5 create_box 1 box mass 1 1.0 pair_style sw pair_coeff * * Si.sw Si """) x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0 ] tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) self.lmp.command("run 0 post no") self.assertEqual(self.lmp.find_pair_neighlist("sw"),0) nlist = self.lmp.numpy.get_neighlist(0) self.assertEqual(nlist.size, 7) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(idx,i) self.assertEqual(neighs.size,nlocal-1) @unittest.skipIf(not has_manybody,"Hybrid neighbor list test for manybody potential") def testNeighborListHybrid(self): self.lmp.commands_string(""" boundary f f f units metal region box block -5 5 -5 5 -5 5 create_box 2 box mass * 1.0 pair_style hybrid/overlay morse 4.0 lj/cut 4.0 lj/cut 4.0 sw pair_coeff * * sw Si.sw Si NULL pair_coeff 1 2 morse 0.2 2.0 2.0 pair_coeff 2 2 lj/cut 1 0.1 2.0 pair_coeff * * lj/cut 2 0.01 2.0 """) x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0 ] tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 2, 2, 2] self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) self.lmp.command("run 0 post no") # valid and invalid lookups self.assertNotEqual(self.lmp.find_pair_neighlist("sw"),-1) self.assertNotEqual(self.lmp.find_pair_neighlist("morse"),-1) self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=1),-1) self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=2),-1) self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) self.assertEqual(self.lmp.find_pair_neighlist("hybrid/overlay"),-1) self.assertNotEqual(self.lmp.numpy.get_neighlist(4).size,0) self.assertEqual(self.lmp.numpy.get_neighlist(5).size,-1) # full neighbor list for 4 type 1 atoms # all have 3 type 1 atom neighbors nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("sw")) self.assertEqual(nlist.size, 4) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(idx,i) self.assertEqual(neighs.size,3) # half neighbor list for all pairs between type 1 and type 2 # 4 type 1 atoms with 3 type 2 neighbors and 3 type 2 atoms without neighbors nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("morse")) self.assertEqual(nlist.size, 7) for i in range(0,nlist.size): idx, neighs = nlist.get(i) if (i < 4): self.assertEqual(neighs.size,3) else: self.assertEqual(neighs.size,0) # half neighbor list between type 2 atoms only # 3 pairs with 2, 1, 0 neighbors nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=1)) self.assertEqual(nlist.size, 3) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(neighs.size,2-i) # half neighbor list between all pairs. same as simple lj/cut case nlist = self.lmp.numpy.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=2)) self.assertEqual(nlist.size, 7) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(neighs.size,nlocal-1-i) def testNeighborListZeroHalf(self): self.lmp.commands_string(""" boundary f f f units real region box block -5 5 -5 5 -5 5 create_box 1 box mass 1 1.0 pair_style zero 4.0 pair_coeff 1 1 """) x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0 ] tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) self.lmp.command("run 0 post no") self.assertEqual(self.lmp.find_pair_neighlist("zero"),0) nlist = self.lmp.numpy.get_neighlist(0) self.assertEqual(nlist.size, 7) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(idx,i) self.assertEqual(neighs.size,nlocal-1-i) # look up neighbor list by atom index neighs = nlist.find(2) self.assertEqual(neighs.size,4) self.assertIsNotNone(neighs,None) # this one will fail neighs = nlist.find(10) self.assertIsNone(neighs,None) def testNeighborListZeroFull(self): self.lmp.commands_string(""" boundary f f f units metal region box block -5 5 -5 5 -5 5 create_box 1 box mass 1 1.0 pair_style zero 4.0 full pair_coeff * * """) x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0 ] tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) self.lmp.command("run 0 post no") self.assertEqual(self.lmp.find_pair_neighlist("zero"),0) nlist = self.lmp.numpy.get_neighlist(0) self.assertEqual(nlist.size, 7) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(idx,i) self.assertEqual(neighs.size,nlocal-1) def testNeighborListCompute(self): self.lmp.commands_string(""" boundary f f f units real region box block -5 5 -5 5 -5 5 create_box 1 box mass 1 1.0 pair_style lj/cut 4.0 pair_coeff 1 1 0.2 2.0 compute dist all pair/local dist fix dist all ave/histo 1 1 1 0.0 3.0 4 c_dist mode vector thermo_style custom f_dist[*] """) x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0 ] tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) self.lmp.command("run 0 post no") # check compute data from histogram summary nhisto = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=0) nskip = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=1) minval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=2) maxval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=3) # 21 pair distances counted, none skipped, smallest 1.0, largest 2.1 self.assertEqual(nhisto,21) self.assertEqual(nskip,0) self.assertEqual(minval,1.0) self.assertEqual(maxval,2.1) self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1) self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1) self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1) self.assertEqual(self.lmp.find_fix_neighlist("dist"),-1) # the compute has a half neighbor list nlist = self.lmp.numpy.get_neighlist(self.lmp.find_compute_neighlist("dist")) self.assertEqual(nlist.size, 7) for i in range(0,nlist.size): idx, neighs = nlist.get(i) self.assertEqual(idx,i) self.assertEqual(neighs.size,nlocal-1-i) def test_extract_variable_equalstyle(self): self.lmp.command("variable a equal 100") a = self.lmp.numpy.extract_variable("a") self.assertEqual(a, 100) self.lmp.command("variable a equal 3.14") a = self.lmp.numpy.extract_variable("a") self.assertEqual(a, 3.14) def test_extract_variable_atomstyle(self): self.lmp.command("units lj") self.lmp.command("atom_style atomic") self.lmp.command("atom_modify map array") self.lmp.command("boundary f f f") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) self.lmp.command("variable a atom x*x+y*y+z*z") a = self.lmp.numpy.extract_variable("a", "all", LMP_VAR_ATOM) self.assertIs(type(a), numpy.ndarray) self.assertEqual(a[0], x[0]*x[0]+x[1]*x[1]+x[2]*x[2]) self.assertEqual(a[1], x[3]*x[3]+x[4]*x[4]+x[5]*x[5]) if __name__ == "__main__": unittest.main()