143 lines
6.1 KiB
Python
143 lines
6.1 KiB
Python
import os,unittest
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from lammps import PyLammps
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try:
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import numpy
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NUMPY_INSTALLED = True
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except ImportError:
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NUMPY_INSTALLED = False
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@unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available")
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class PythonPyLammps(unittest.TestCase):
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def setUp(self):
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machine = None
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if 'LAMMPS_MACHINE_NAME' in os.environ:
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machine=os.environ['LAMMPS_MACHINE_NAME']
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self.pylmp = PyLammps(name=machine, cmdargs=['-nocite', '-log','none', '-echo', 'screen'])
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self.pylmp.units("lj")
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self.pylmp.atom_style("atomic")
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self.pylmp.atom_modify("map array")
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if 'LAMMPS_CMAKE_CACHE' in os.environ:
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self.cmake_cache = {}
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with open(os.environ['LAMMPS_CMAKE_CACHE'], 'r') as f:
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for line in f:
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line = line.strip()
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if not line or line.startswith('#') or line.startswith('//'): continue
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parts = line.split('=')
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key, value_type = parts[0].split(':')
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if len(parts) > 1:
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value = parts[1]
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if value_type == "BOOL":
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value = (value.upper() == "ON")
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else:
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value = None
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self.cmake_cache[key] = value
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def tearDown(self):
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self.pylmp.close()
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del self.pylmp
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def test_version(self):
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self.assertGreaterEqual(self.pylmp.version(), 20200824)
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def test_create_atoms(self):
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self.pylmp.region("box block", 0, 2, 0, 2, 0, 2)
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self.pylmp.create_box(1, "box")
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x = [
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1.0, 1.0, 1.0,
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1.0, 1.0, 1.5
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]
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types = [1, 1]
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self.assertEqual(self.pylmp.lmp.create_atoms(2, id=None, type=types, x=x), 2)
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self.assertEqual(self.pylmp.system.natoms, 2)
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self.assertEqual(len(self.pylmp.atoms), 2)
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numpy.testing.assert_array_equal(self.pylmp.atoms[0].position, tuple(x[0:3]))
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numpy.testing.assert_array_equal(self.pylmp.atoms[1].position, tuple(x[3:6]))
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self.assertEqual(self.pylmp.last_run, None)
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def test_write_script(self):
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outfile = 'in.test_write_script'
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self.pylmp.write_script(outfile)
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self.assertTrue(os.path.exists(outfile))
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os.remove(outfile)
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def test_runs(self):
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self.pylmp.lattice("fcc", 0.8442),
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self.pylmp.region("box block", 0, 4, 0, 4, 0, 4)
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self.pylmp.create_box(1, "box")
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self.pylmp.create_atoms(1, "box")
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self.pylmp.mass(1, 1.0)
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self.pylmp.velocity("all create", 1.44, 87287, "loop geom")
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self.pylmp.pair_style("lj/cut", 2.5)
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self.pylmp.pair_coeff(1, 1, 1.0, 1.0, 2.5)
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self.pylmp.neighbor(0.3, "bin")
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self.pylmp.neigh_modify("delay 0 every 20 check no")
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self.pylmp.fix("1 all nve")
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self.pylmp.variable("fx atom fx")
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self.pylmp.run(10)
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# thermo data is only captured during a run if PYTHON package is enabled
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# without it, it will only capture the final thermo at completion
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if self.pylmp.lmp.has_package("PYTHON"):
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self.assertEqual(len(self.pylmp.runs), 1)
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self.assertEqual(self.pylmp.last_run, self.pylmp.runs[0])
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self.assertEqual(len(self.pylmp.last_run.thermo.Step), 2)
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self.assertEqual(len(self.pylmp.last_run.thermo.Temp), 2)
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self.assertEqual(len(self.pylmp.last_run.thermo.E_pair), 2)
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self.assertEqual(len(self.pylmp.last_run.thermo.E_mol), 2)
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self.assertEqual(len(self.pylmp.last_run.thermo.TotEng), 2)
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self.assertEqual(len(self.pylmp.last_run.thermo.Press), 2)
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else:
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self.assertEqual(len(self.pylmp.runs), 1)
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self.assertEqual(self.pylmp.last_run, self.pylmp.runs[0])
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self.assertEqual(len(self.pylmp.last_run.thermo.Step), 1)
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self.assertEqual(len(self.pylmp.last_run.thermo.Temp), 1)
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self.assertEqual(len(self.pylmp.last_run.thermo.E_pair), 1)
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self.assertEqual(len(self.pylmp.last_run.thermo.E_mol), 1)
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self.assertEqual(len(self.pylmp.last_run.thermo.TotEng), 1)
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self.assertEqual(len(self.pylmp.last_run.thermo.Press), 1)
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def test_info_queries(self):
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self.pylmp.lattice("fcc", 0.8442),
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self.pylmp.region("box block", 0, 4, 0, 4, 0, 4)
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self.pylmp.create_box(1, "box")
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self.pylmp.variable("a equal 10.0")
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self.pylmp.variable("b string value")
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self.assertEqual(self.pylmp.variables['a'].value, 10.0)
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self.assertEqual(self.pylmp.variables['b'].value, 'value')
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self.assertEqual(len(self.pylmp.variables),2)
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self.assertEqual(self.pylmp.system.units,'lj')
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self.assertEqual(self.pylmp.system.atom_style,'atomic')
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self.assertEqual(self.pylmp.system.ntypes,1)
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self.assertEqual(self.pylmp.system.natoms,0)
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self.assertEqual(self.pylmp.communication.comm_style,'brick')
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self.assertEqual(self.pylmp.communication.comm_layout,'uniform')
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self.assertEqual(self.pylmp.communication.nprocs,1)
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self.assertEqual(len(self.pylmp.computes),3)
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self.assertEqual(self.pylmp.computes[0]['name'], 'thermo_temp')
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self.assertEqual(self.pylmp.computes[0]['style'], 'temp')
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self.assertEqual(self.pylmp.computes[0]['group'], 'all')
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self.assertEqual(self.pylmp.computes[1]['name'], 'thermo_press')
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self.assertEqual(self.pylmp.computes[1]['style'], 'pressure')
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self.assertEqual(self.pylmp.computes[1]['group'], 'all')
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self.assertEqual(self.pylmp.computes[2]['name'], 'thermo_pe')
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self.assertEqual(self.pylmp.computes[2]['style'], 'pe')
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self.assertEqual(self.pylmp.computes[2]['group'], 'all')
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self.assertEqual(len(self.pylmp.dumps),0)
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self.pylmp.fix('one','all','nve')
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self.assertEqual(len(self.pylmp.fixes),1)
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self.assertEqual(self.pylmp.fixes[0]['name'], 'one')
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self.assertEqual(self.pylmp.fixes[0]['style'], 'nve')
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self.assertEqual(self.pylmp.fixes[0]['group'], 'all')
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self.pylmp.group('none','empty')
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self.assertEqual(len(self.pylmp.groups),2)
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if __name__ == "__main__":
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unittest.main()
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