import sys,os,unittest,ctypes from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL from lammps import LMP_TYPE_VECTOR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS from lammps import LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT 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): 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 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) self.assertEqual(self.lmp.find_pair_neighlist("morse"), -1) nlist = self.lmp.get_neighlist(idx) 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 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) # look up neighbor list by atom index num, neighs = nlist.find(2) self.assertEqual(num,4) self.assertIsNotNone(neighs,None) # this one will fail num, neighs = nlist.find(10) self.assertEqual(num,-1) 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.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) ndist1 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_VECTOR) ndist2 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_ROWS) ndist3 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_COLS) self.assertEqual(ndist1,21) self.assertEqual(ndist2,21) self.assertEqual(ndist3,0) 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.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") 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 prism 0 2 0 2 0 2 0.1 0.2 0.3") 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, 0.1) self.assertEqual(xz, 0.2) self.assertEqual(yz, 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(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("units"), "lj") self.assertEqual(self.lmp.extract_global("ntimestep"), 0) self.assertEqual(self.lmp.extract_global("dt"), 0.005) 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]) self.assertEqual(self.lmp.extract_global("triclinic"), 0) self.assertEqual(self.lmp.extract_global("sublo_lambda"), None) self.assertEqual(self.lmp.extract_global("subhi_lambda"), None) self.assertEqual(self.lmp.extract_global("respa_levels"), None) self.assertEqual(self.lmp.extract_global("respa_dt"), None) # set and initialize r-RESPA self.lmp.command("run_style respa 3 5 2 pair 2 kspace 3") self.lmp.command("mass * 1.0") self.lmp.command("run 1 post no") self.assertEqual(self.lmp.extract_global("ntimestep"), 1) self.assertEqual(self.lmp.extract_global("respa_levels"), 3) self.assertEqual(self.lmp.extract_global("respa_dt"), [0.0005, 0.0025, 0.005]) # checks only for triclinic boxes self.lmp.command("change_box all triclinic") self.assertEqual(self.lmp.extract_global("triclinic"), 1) 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]) def test_create_atoms(self): self.lmp.command("boundary f p m") self.lmp.command("region box block 0 10 0 10 0 10") self.lmp.command("create_box 2 box") # second atom is outside the box -> dropped self.lmp.create_atoms(2, [1,2], [1,1], [1.0, 1.0, 3.0, 5.0, 8.0, 12.0]) self.assertEqual(self.lmp.get_natoms(),1) # non-zero velocities self.lmp.create_atoms(2, None, [2,2], [2.0, 2.0, 1.0, 3.0, 4.0, 6.0], v=[0.1, 0.2, 0.3, -0.1, -0.2, -0.3]) self.assertEqual(self.lmp.get_natoms(),3) # first atom is dropped, extend shrinkwrapped box for second atom, third atoms is wrapped around PBC. self.lmp.create_atoms(3, [5,8,10], [1,2,1], [-1.0, 1.0, 3.0, 5.0, 8.0, 12.0, 1.0, -1.0, 1.0], shrinkexceed=True) self.assertEqual(self.lmp.get_natoms(),5) # set image flags self.lmp.create_atoms(1, None, [2], [5.0, 8.0, 1.0], image=[self.lmp.encode_image_flags(1,0,-1)]) self.assertEqual(self.lmp.get_natoms(),6) tag = self.lmp.extract_atom("id") typ = self.lmp.extract_atom("type") pos = self.lmp.extract_atom("x",LAMMPS_DOUBLE_2D) vel = self.lmp.extract_atom("v",LAMMPS_DOUBLE_2D) img = self.lmp.extract_atom("image",LAMMPS_AUTODETECT) # expected results: tag, type, x, v, image result = [ [ 1, 1, [1.0, 1.0, 3.0], [ 0.0, 0.0, 0.0], [0, 0, 0]],\ [ 2, 2, [2.0, 2.0, 1.0], [ 0.1, 0.2, 0.3], [0, 0, 0]],\ [ 3, 2, [3.0, 4.0, 6.0], [-0.1, -0.2, -0.3], [0, 0, 0]],\ [ 8, 2, [5.0, 8.0, 12.0], [ 0.0, 0.0, 0.0], [0, 0, 0]],\ [10, 1, [1.0, 9.0, 1.0], [ 0.0, 0.0, 0.0], [0, 0, 0]],\ [11, 2, [5.0, 8.0, 1.0], [ 0.0, 0.0, 0.0], [1, 0, -1]] ] for i in range(len(result)): self.assertEqual(tag[i],result[i][0]) self.assertEqual(typ[i],result[i][1]) for j in range(3): self.assertEqual(pos[i][0:3],result[i][2]) self.assertEqual(vel[i][0:3],result[i][3]) self.assertEqual(self.lmp.decode_image_flags(img[i]), result[i][4]) ############################## if __name__ == "__main__": unittest.main()