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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,
"elapsed" : 0.0,
"elaplong": 0,
"dt" : 0.005,
"time" : 0.0,
"atoms" : 2.0,
"temp" : 0,
"press" : 0,
"pe" : 0.0,
"ke" : 0.0,
"etotal" : 0.0,
"enthalpy" : 0.0,
"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)
##############################
if __name__ == "__main__":
unittest.main()
|
