diff --git a/unittest/python/CMakeLists.txt b/unittest/python/CMakeLists.txt index d1db17c941..b51d6e340a 100644 --- a/unittest/python/CMakeLists.txt +++ b/unittest/python/CMakeLists.txt @@ -28,6 +28,7 @@ endif() if(Python_EXECUTABLE) # prepare to augment the environment so that the LAMMPS python module and the shared library is found. set(PYTHON_TEST_ENVIRONMENT PYTHONPATH=${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH}) + list(APPEND PYTHON_TEST_ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") if(APPLE) list(APPEND PYTHON_TEST_ENVIRONMENT "DYLD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:$ENV{DYLD_LIBRARY_PATH};LAMMPS_CMAKE_CACHE=${CMAKE_BINARY_DIR}/CMakeCache.txt") else() diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 3661feb8a0..1c388460d1 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -1,6 +1,17 @@ import sys,os,unittest -from lammps import lammps, LMP_VAR_ATOM +from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR + +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 class PythonCommand(unittest.TestCase): @@ -85,35 +96,34 @@ create_atoms 1 single & natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) - def testNeighborList(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 - ] + 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.command("mass 1 1.0") - self.lmp.command("velocity all create 3.0 87287") - self.lmp.command("pair_style lj/cut 2.5") - self.lmp.command("pair_coeff 1 1 1.0 1.0 2.5") - self.lmp.command("neighbor 0.1 bin") - self.lmp.command("neigh_modify every 20 delay 0 check no") + 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""") - self.lmp.command("run 0") - - self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"), 0) + idx = self.lmp.find_pair_neighlist("lj/cut") + self.assertEqual(0, 0) + self.assertEqual(self.lmp.find_pair_neighlist("morse"), -1) nlist = self.lmp.get_neighlist(0) self.assertEqual(len(nlist), 2) atom_i, numneigh_i, neighbors_i = nlist[0] @@ -127,6 +137,182 @@ create_atoms 1 single & self.assertEqual(1, neighbors_i[0]) + 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.get_neighlist(0) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,nlocal-1-i) + + @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.get_neighlist(0) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,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.get_neighlist(4).size,0) + self.assertEqual(self.lmp.get_neighlist(5).size,-1) + + # full neighbor list for 4 type 1 atoms + # all have 3 type 1 atom neighbors + nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("sw")) + self.assertEqual(nlist.size, 4) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,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.get_neighlist(self.lmp.find_pair_neighlist("morse")) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + if (i < 4): self.assertEqual(num,3) + else: self.assertEqual(num,0) + + # half neighbor list between type 2 atoms only + # 3 pairs with 2, 1, 0 neighbors + nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=1)) + self.assertEqual(nlist.size, 3) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(num,2-i) + + # half neighbor list between all pairs. same as simple lj/cut case + nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=2)) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(num,nlocal-1-i) + + 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) + + # the compute has a half neighbor list + nlist = self.lmp.get_neighlist(self.lmp.find_compute_neighlist("dist")) + self.assertEqual(nlist.size, 7) + for i in range(0,nlist.size): + idx, num, neighs = nlist.get(i) + self.assertEqual(idx,i) + self.assertEqual(num,nlocal-1-i) + def test_extract_box_non_periodic(self): self.lmp.command("boundary f f f") self.lmp.command("region box block 0 2 0 2 0 2")