98 lines
3.4 KiB
Python
98 lines
3.4 KiB
Python
import os,unittest
|
|
from lammps import lammps
|
|
|
|
try:
|
|
import numpy
|
|
NUMPY_INSTALLED = True
|
|
except ImportError:
|
|
NUMPY_INSTALLED = False
|
|
|
|
@unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available")
|
|
class PythonCmdWrapper(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'])
|
|
self.lmp.cmd.units("lj")
|
|
self.lmp.cmd.atom_style("atomic")
|
|
self.lmp.cmd.atom_modify("map array")
|
|
|
|
if 'LAMMPS_CMAKE_CACHE' in os.environ:
|
|
self.cmake_cache = {}
|
|
|
|
with open(os.environ['LAMMPS_CMAKE_CACHE'], 'r') as f:
|
|
for line in f:
|
|
line = line.strip()
|
|
if not line or line.startswith('#') or line.startswith('//'): continue
|
|
parts = line.split('=')
|
|
key, value_type = parts[0].split(':')
|
|
if len(parts) > 1:
|
|
value = parts[1]
|
|
if value_type == "BOOL":
|
|
value = (value.upper() == "ON")
|
|
else:
|
|
value = None
|
|
self.cmake_cache[key] = value
|
|
|
|
def tearDown(self):
|
|
self.lmp.close()
|
|
del self.lmp
|
|
|
|
def test_version(self):
|
|
self.assertGreaterEqual(self.lmp.version(), 20200824)
|
|
|
|
def test_create_atoms(self):
|
|
self.lmp.cmd.region("box block", 0, 2, 0, 2, 0, 2)
|
|
self.lmp.cmd.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, atomid=None, atype=types, x=x), 2)
|
|
self.assertEqual(self.lmp.extract_global("natoms"), 2)
|
|
pos = self.lmp.numpy.extract_atom("x")
|
|
self.assertEqual(pos.shape[0], 2)
|
|
numpy.testing.assert_array_equal(pos[0], tuple(x[0:3]))
|
|
numpy.testing.assert_array_equal(pos[1], tuple(x[3:6]))
|
|
|
|
def test_thermo_capture(self):
|
|
self.lmp.cmd.lattice("fcc", 0.8442),
|
|
self.lmp.cmd.region("box block", 0, 4, 0, 4, 0, 4)
|
|
self.lmp.cmd.create_box(1, "box")
|
|
self.lmp.cmd.create_atoms(1, "box")
|
|
self.lmp.cmd.mass(1, 1.0)
|
|
self.lmp.cmd.velocity("all create", 1.44, 87287, "loop geom")
|
|
self.lmp.cmd.pair_style("lj/cut", 2.5)
|
|
self.lmp.cmd.pair_coeff(1, 1, 1.0, 1.0, 2.5)
|
|
self.lmp.cmd.neighbor(0.3, "bin")
|
|
self.lmp.cmd.neigh_modify("delay 0 every 20 check no")
|
|
self.lmp.cmd.fix("1 all nve")
|
|
|
|
current_run = {}
|
|
|
|
def append_thermo_data(lmp):
|
|
for k, v in lmp.last_thermo().items():
|
|
current_run.setdefault(k, []).append(v)
|
|
|
|
# thermo data is only captured during a run if PYTHON package is enabled
|
|
# without it, it will only capture the final thermo at completion
|
|
nvalues = 1
|
|
if self.lmp.has_package("PYTHON"):
|
|
self.lmp.cmd.fix("myfix", "all", "python/invoke", 10, "end_of_step", append_thermo_data)
|
|
nvalues = 2
|
|
|
|
self.lmp.cmd.run(10)
|
|
append_thermo_data(self.lmp)
|
|
|
|
for k in ('Step', 'Temp', 'E_pair', 'E_mol', 'TotEng', 'Press'):
|
|
self.assertIn(k, current_run)
|
|
self.assertEqual(len(current_run[k]), nvalues)
|
|
|
|
if __name__ == "__main__":
|
|
unittest.main()
|