예제 #1
0
    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"))
예제 #2
0
    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)
예제 #3
0
    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)
예제 #4
0
    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)
예제 #5
0
    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)