def testScientificPython(self):
""" Test ScientificPython parsing """
import parmed.amber as amber
if utils.has_scientific():
amber.use("Scientific")
from parmed.amber.netcdffiles import NetCDFTraj, NetCDFRestart
traj = NetCDFTraj.open_old(get_fn("tz2.truncoct.nc"))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn("ncinpcrd.rst7"))
self._check_rst(rst)
else:
self.assertRaises(ImportError, lambda: amber.use("Scientific"))
def testRemdFiles(self):
""" Test proper reading and writing of NetCDF files with REMD info """
rstfn = get_fn('restart.ncrst', written=True)
trjfn = get_fn('traj.nc', written=True)
# Do the restart with T-REMD first
traj = NetCDFRestart.open_new(
rstfn,
100,
True,
True,
'Restart w/ REMD',
remd='Temperature',
temp=300,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
traj.box = [40, 40, 40, 90, 90, 90]
traj.close()
traj = NetCDFRestart.open_old(rstfn)
self.assertEqual(traj.temp0, 300)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFRestart.open_new(
rstfn,
100,
False,
True,
'Restart w/ REMD',
remd='Multi',
remd_dimtypes=[1, 3, 3, 3],
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.remd_indices = remd_indices
traj.close()
traj = NetCDFRestart.open_old(rstfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices)
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
# Do the restart with T-REMD first
traj = NetCDFTraj.open_new(
trjfn,
100,
True,
True,
True,
title='Traj w/ REMD',
remd='Temperature',
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.add_coordinates(crd)
traj.add_velocities(vel)
traj.add_temp0(300)
traj.add_box([40, 40, 40, 90, 90, 90])
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_equal(traj.temp0, [300])
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFTraj.open_new(
trjfn,
100,
False,
True,
title='Traj w/ REMD',
remd='Multi',
remd_dimension=4,
vels=True,
frcs=True,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
frc = np.random.rand(100, 3)
traj.remd_dimtype = [1, 3, 3, 3]
traj.add_coordinates(crd * u.angstroms)
traj.add_velocities(vel * u.angstroms / u.picosecond)
traj.add_forces(frc * u.kilocalories_per_mole / u.angstrom)
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.add_remd_indices(remd_indices)
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_allclose(frc, traj.forces.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices.squeeze())
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
def testRemdFiles(self):
""" Test proper reading and writing of NetCDF files with REMD info """
rstfn = get_fn('restart.ncrst', written=True)
trjfn = get_fn('traj.nc', written=True)
# Do the restart with T-REMD first
traj = NetCDFRestart.open_new(
rstfn, 100, True, True, 'Restart w/ REMD', remd='Temperature',
temp=300,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
traj.box = [40, 40, 40, 90, 90, 90]
traj.close()
traj = NetCDFRestart.open_old(rstfn)
self.assertEqual(traj.temp0, 300)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFRestart.open_new(
rstfn, 100, False, True, 'Restart w/ REMD', remd='Multi',
remd_dimtypes=[1, 3, 3, 3],
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.remd_indices = remd_indices
traj.close()
traj = NetCDFRestart.open_old(rstfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices)
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
# Do the restart with T-REMD first
traj = NetCDFTraj.open_new(
trjfn, 100, True, True, True, title='Traj w/ REMD',
remd='Temperature',
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.add_coordinates(crd)
traj.add_velocities(vel)
traj.add_temp0(300)
traj.add_box([40, 40, 40, 90, 90, 90])
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_equal(traj.temp0, [300])
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFTraj.open_new(
trjfn, 100, False, True, title='Traj w/ REMD', remd='Multi',
remd_dimension=4, vels=True, frcs=True,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
frc = np.random.rand(100, 3)
traj.remd_dimtype = [1, 3, 3, 3]
traj.add_coordinates(crd*u.angstroms)
traj.add_velocities(vel*u.angstroms/u.picosecond)
traj.add_forces(frc*u.kilocalories_per_mole/u.angstrom)
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.add_remd_indices(remd_indices)
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_allclose(frc, traj.forces.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices.squeeze())
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
def testNetCDF(self):
""" Test scipy NetCDF parsing """
traj = NetCDFTraj.open_old(get_fn('tz2.truncoct.nc'))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn('ncinpcrd.rst7'))
self._check_rst(rst)
# Now try writing files
ntraj = NetCDFTraj.open_new(get_fn('test.nc', written=True),
traj.atom,
box=True)
for crd in traj.coordinates:
ntraj.add_coordinates(crd)
for box in traj.box:
ntraj.add_box(box)
ntraj.close()
traj = NetCDFTraj.open_old(get_fn('test.nc', written=True))
self._check_traj(traj, written=True)
nrst = NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
rst.atom,
rst.hasbox,
rst.hasvels,
title=rst.title)
nrst.coordinates = rst.coordinates
nrst.velocities = rst.velocities
nrst.time = rst.time
nrst.box = rst.box
nrst.close()
rst = NetCDFRestart.open_old(get_fn('test.ncrst', written=True))
self._check_rst(rst, written=True)
# Now write NetCDF trajectory without any optional attributes/variables
# and check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(nframe, natom, 3) * 20 - 10
coords = np.array(coords, dtype='f')
nctraj = NetCDFFile(get_fn('test2.nc', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBER'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial', ))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'f',
('frame', 'atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFTraj.open_old(get_fn('test2.nc', written=True))
np.testing.assert_allclose(traj2.coordinates, coords)
# Now write NetCDF restart without any optional attributes/variables and
# check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(natom, 3) * 20 - 10
nctraj = NetCDFFile(get_fn('test2.ncrst', written=True),
'w',
mmap=False)
nctraj.Conventions = 'AMBERRESTART'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial', ))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'd', ('atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFRestart.open_old(get_fn('test2.ncrst', written=True))
np.testing.assert_allclose(traj2.coordinates[0], coords)
def testNetCDF(self):
""" Test scipy NetCDF parsing """
traj = NetCDFTraj.open_old(get_fn('tz2.truncoct.nc'))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn('ncinpcrd.rst7'))
self._check_rst(rst)
# Now try writing files
ntraj = NetCDFTraj.open_new(get_fn('test.nc', written=True),
traj.atom, box=True)
for crd in traj.coordinates:
ntraj.add_coordinates(crd)
for box in traj.box:
ntraj.add_box(box)
ntraj.close()
traj = NetCDFTraj.open_old(get_fn('test.nc', written=True))
self._check_traj(traj, written=True)
nrst = NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
rst.atom, rst.hasbox, rst.hasvels,
title=rst.title)
nrst.coordinates = rst.coordinates
nrst.velocities = rst.velocities
nrst.time = rst.time
nrst.box = rst.box
nrst.close()
rst = NetCDFRestart.open_old(get_fn('test.ncrst', written=True))
self._check_rst(rst, written=True)
# Now write NetCDF trajectory without any optional attributes/variables
# and check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(nframe, natom, 3) * 20 - 10
coords = np.array(coords, dtype='f')
nctraj = NetCDFFile(get_fn('test2.nc', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBER'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial',))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'f', ('frame', 'atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFTraj.open_old(get_fn('test2.nc', written=True))
np.testing.assert_allclose(traj2.coordinates, coords)
# Now write NetCDF restart without any optional attributes/variables and
# check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(natom, 3) * 20 - 10
nctraj = NetCDFFile(get_fn('test2.ncrst', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBERRESTART'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial',))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'd', ('atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFRestart.open_old(get_fn('test2.ncrst', written=True))
np.testing.assert_allclose(traj2.coordinates[0], coords)