class TestRPMD(ForceBalanceTestCase):
""" RPMD unit test that runs a short RPMD simulation
and compares calculated potential energies from
MD with postprocessed potential energies as an
internal consistency check.
"""
def setUp(self):
self.logger.debug('\nBuilding OpenMM engine...\n')
os.chdir(os.path.join('test','files','rpmd_files'))
openmm = False
try:
import simtk.openmm
openmm = True
except: logger.warn("OpenMM cannot be imported. Make sure it's installed!")
print os.getcwd()
if openmm:
self.ommEngine = OpenMM(ffxml='qtip4pf.xml', coords='liquid.pdb', pbc=True, platname='CUDA', precision='double')
def test_rpmd_simulation(self):
self.logger.debug('\nRunning MD...\n')
if not os.path.exists('temp'): os.mkdir('temp')
os.chdir('temp')
# We're in the temp directory so need to copy the force field file here.
shutil.copy2('../qtip4pf.xml','./qtip4pf.xml')
self.addCleanup(os.system, 'cd .. ; rm -rf temp')
MD_data = self.ommEngine.molecular_dynamics(nsteps=1000, nsave=100, timestep=0.5, temperature=300, pressure=1.0, verbose=False, save_traj=True, rpmd_opts=['32','9'])
# Line below performs same MD run, but using verbose option
#MD_data = self.ommEngine.molecular_dynamics(nsteps=1000, nsave=100, timestep=0.5, temperature=300, pressure=1.0, verbose=True, save_traj=True, rpmd_opts=['32','9'])
postprocess_potentials = self.ommEngine.evaluate_(traj=self.ommEngine.xyz_rpmd, dipole=True)
self.assertEqual(MD_data['Dips'].all(), postprocess_potentials['Dipole'].all())
self.assertEqual(MD_data['Potentials'].all(), postprocess_potentials['Energy'].all())
