import sys,os,unittest from lammps import lammps, LMP_VAR_ATOM class PythonCommand(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', '-var','zpos','1.5', '-var','x','2']) # create demo input strings and files # a few commands to set up a box with a single atom self.demo_input=""" region box block 0 $x 0 2 0 2 create_box 1 box create_atoms 1 single 1.0 1.0 ${zpos} """ # another command to add an atom and use a continuation line self.cont_input=""" create_atoms 1 single & 0.2 0.1 0.1 """ self.demo_file='in.test' with open(self.demo_file,'w') as f: f.write(self.demo_input) self.cont_file='in.cont' with open(self.cont_file,'w') as f: f.write(self.cont_input) # clean up temporary files def tearDown(self): if os.path.exists(self.demo_file): os.remove(self.demo_file) if os.path.exists(self.cont_file): os.remove(self.cont_file) ############################## def testFile(self): """Test reading commands from a file""" natoms = self.lmp.get_natoms() self.assertEqual(natoms,0) self.lmp.file(self.demo_file) natoms = self.lmp.get_natoms() self.assertEqual(natoms,1) self.lmp.file(self.cont_file) natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) def testNoFile(self): """Test (not) reading commands from no file""" self.lmp.file(None) natoms = self.lmp.get_natoms() self.assertEqual(natoms,0) def testCommand(self): """Test executing individual commands""" natoms = self.lmp.get_natoms() self.assertEqual(natoms,0) cmds = self.demo_input.splitlines() for cmd in cmds: self.lmp.command(cmd) natoms = self.lmp.get_natoms() self.assertEqual(natoms,1) def testCommandsList(self): """Test executing commands from list of strings""" natoms = self.lmp.get_natoms() self.assertEqual(natoms,0) cmds = self.demo_input.splitlines()+self.cont_input.splitlines() self.lmp.commands_list(cmds) natoms = self.lmp.get_natoms() self.assertEqual(natoms,2) def testCommandsString(self): """Test executing block of commands from string""" natoms = self.lmp.get_natoms() self.assertEqual(natoms,0) self.lmp.commands_string(self.demo_input+self.cont_input) 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 ] 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.command("run 0") self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"), 0) nlist = self.lmp.get_neighlist(0) self.assertEqual(len(nlist), 2) atom_i, numneigh_i, neighbors_i = nlist[0] atom_j, numneigh_j, _ = nlist[1] self.assertEqual(atom_i, 0) self.assertEqual(atom_j, 1) self.assertEqual(numneigh_i, 1) self.assertEqual(numneigh_j, 0) self.assertEqual(1, neighbors_i[0]) 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") self.lmp.command("create_box 1 box") boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box() self.assertEqual(boxlo, [0.0, 0.0, 0.0]) self.assertEqual(boxhi, [2.0, 2.0, 2.0]) self.assertEqual(xy, 0.0) self.assertEqual(yz, 0.0) self.assertEqual(xz, 0.0) self.assertEqual(periodicity, [0, 0, 0]) self.assertEqual(box_change, 0) def test_extract_box_periodic(self): self.lmp.command("boundary p p p") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box() self.assertEqual(boxlo, [0.0, 0.0, 0.0]) self.assertEqual(boxhi, [2.0, 2.0, 2.0]) self.assertEqual(xy, 0.0) self.assertEqual(yz, 0.0) self.assertEqual(xz, 0.0) self.assertEqual(periodicity, [1, 1, 1]) self.assertEqual(box_change, 0) def test_extract_box_triclinic(self): self.lmp.command("boundary p p p") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("change_box all triclinic") self.lmp.command("change_box all xy final 0.1 yz final 0.2 xz final 0.3") boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box() self.assertEqual(boxlo, [0.0, 0.0, 0.0]) self.assertEqual(boxhi, [2.0, 2.0, 2.0]) self.assertEqual(xy, 0.1) self.assertEqual(yz, 0.2) self.assertEqual(xz, 0.3) self.assertEqual(periodicity, [1, 1, 1]) self.assertEqual(box_change, 0) def test_reset_box(self): self.lmp.command("boundary p p p") self.lmp.command("region box block 0 2 0 2 0 2") self.lmp.command("create_box 1 box") self.lmp.command("change_box all triclinic") self.lmp.command("change_box all xy final 0.1 yz final 0.2 xz final 0.3") self.lmp.reset_box([0,0,0], [1,1,1], 0, 0, 0) boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box() self.assertEqual(boxlo, [0.0, 0.0, 0.0]) self.assertEqual(boxhi, [1.0, 1.0, 1.0]) self.assertEqual(xy, 0) self.assertEqual(yz, 0) self.assertEqual(xz, 0) self.assertEqual(periodicity, [1, 1, 1]) self.assertEqual(box_change, 0) def test_extract_variable_equalstyle(self): self.lmp.command("variable a equal 100") a = self.lmp.extract_variable("a") self.assertEqual(a, 100) self.lmp.command("variable a equal 3.14") a = self.lmp.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.extract_variable("a", "all", LMP_VAR_ATOM) 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]) def test_get_thermo(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.lmp.create_atoms(2, id=None, type=types, x=x) state = { "step": 0, "dt" : 0.005, "time" : 0.0, "atoms" : 2.0, "vol" : 8.0, "lx" : 2.0, "ly" : 2.0, "lz" : 2.0, "xlo" : 0, "xhi" : 2.0, "ylo" : 0, "yhi" : 2.0, "zlo" : 0, "zhi" : 2.0 } for key, value in state.items(): result = self.lmp.get_thermo(key) self.assertEqual(value, result, key) def test_extract_global_double(self): self.lmp.command("region box block -1 1 -2 2 -3 3") self.lmp.command("create_box 1 box") self.assertEqual(self.lmp.extract_global("boxxlo"), -1.0) self.assertEqual(self.lmp.extract_global("boxxhi"), 1.0) self.assertEqual(self.lmp.extract_global("boxylo"), -2.0) self.assertEqual(self.lmp.extract_global("boxyhi"), 2.0) self.assertEqual(self.lmp.extract_global("boxzlo"), -3.0) self.assertEqual(self.lmp.extract_global("boxzhi"), 3.0) self.assertEqual(self.lmp.extract_global("boxlo"), [-1.0, -2.0, -3.0]) self.assertEqual(self.lmp.extract_global("boxhi"), [1.0, 2.0, 3.0]) self.assertEqual(self.lmp.extract_global("sublo"), [-1.0, -2.0, -3.0]) self.assertEqual(self.lmp.extract_global("subhi"), [1.0, 2.0, 3.0]) self.assertEqual(self.lmp.extract_global("periodicity"), [1,1,1]) # only valid for triclinic box self.lmp.command("change_box all triclinic") self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0]) self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0]) ############################## if __name__ == "__main__": unittest.main()