def test_velocity_traj():
# Test Trajectory.get_velocity() against velocities output from CP2K. The
# agreement is very good. Works only for fixed-cell MDs, however!
dr = 'files/cp2k/md/nvt_print_low'
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
tr = io.read_cp2k_md(fn)
# read from data file
v1 = tr.velocity.copy()
# If tr.velocity != None, then get_velocity() doesn't calculate it. Then,
# it simply returns tr.velocity, which is what we of course usually want.
tr.velocity = None
# calculate from coords + time step, b/c of central diffs, only steps 1:-1
# are the same
v2 = tr.get_velocity()
print ">>>> np.abs(v1).max()", np.abs(v1).max()
print ">>>> np.abs(v1).min()", np.abs(v1).min()
print ">>>> np.abs(v2).max()", np.abs(v2).max()
print ">>>> np.abs(v2).min()", np.abs(v2).min()
print ">>>> np.abs(v1-v2).max()", np.abs(v1-v2).max()
print ">>>> np.abs(v1-v2).min()", np.abs(v1-v2).min()
assert np.allclose(v1[1:-1,...], v2[1:-1,...], atol=1e-4)
##from pwtools import mpl
##fig,ax = mpl.fig_ax()
##ax.plot(v1[1:-1,:,0], 'b')
##ax.plot(v2[1:-1,:,0], 'r')
##mpl.plt.show()
shape = (100,10,3)
arr = np.random.rand(*shape)
assert crys.velocity_traj(arr, axis=0).shape == shape
assert crys.velocity_traj(arr, axis=0, endpoints=False).shape == (98,10,3)
def test_velocity_traj():
# Test Trajectory.get_velocity() against velocities output from CP2K. The
# agreement is very good. Works only for fixed-cell MDs, however!
dr = 'files/cp2k/md/nvt_print_low'
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr)))
tr = io.read_cp2k_md(fn)
# read from data file
v1 = tr.velocity.copy()
# If tr.velocity != None, then get_velocity() doesn't calculate it. Then,
# it simply returns tr.velocity, which is what we of course usually want.
tr.velocity = None
# calculate from coords + time step, b/c of central diffs, only steps 1:-1
# are the same
v2 = tr.get_velocity()
print(">>>> np.abs(v1).max()", np.abs(v1).max())
print(">>>> np.abs(v1).min()", np.abs(v1).min())
print(">>>> np.abs(v2).max()", np.abs(v2).max())
print(">>>> np.abs(v2).min()", np.abs(v2).min())
print(">>>> np.abs(v1-v2).max()", np.abs(v1-v2).max())
print(">>>> np.abs(v1-v2).min()", np.abs(v1-v2).min())
assert np.allclose(v1[1:-1,...], v2[1:-1,...], atol=1e-4)
##from pwtools import mpl
##fig,ax = mpl.fig_ax()
##ax.plot(v1[1:-1,:,0], 'b')
##ax.plot(v2[1:-1,:,0], 'r')
##mpl.plt.show()
shape = (100,10,3)
arr = np.random.rand(*shape)
assert crys.velocity_traj(arr, axis=0).shape == shape
assert crys.velocity_traj(arr, axis=0, endpoints=False).shape == (98,10,3)
def test_cp2k_txt_vs_dcd():
# Two exactly equal NPT runs, nstep=16, natoms=57. The dcd run uses
# motion/print/trajectory format dcd_aligned_cell
# the other the default xyz format. So we have
# PROJECT-pos-1.dcd
# PROJECT-pos-1.xyz
# Since the cell changes and we use dcd_aligned_cell, the coords from the
# xyz run are NOT the same as the coords in the dcd file, which HAS to be
# like this. Only coords_frac can be compared, and coords after the xyz
# run's cell has been aligned to [[x,0,0],[xy,y,0],[xz,yz,z]].
dir_xyz = unpack_compressed('files/cp2k/dcd/npt_xyz.tgz')
dir_dcd = unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
tr_xyz = io.read_cp2k_md(pj(dir_xyz, 'cp2k.out'))
tr_dcd = io.read_cp2k_md_dcd(pj(dir_dcd, 'cp2k.out'))
for name in ['natoms', 'nstep', 'timestep', 'symbols']:
assert getattr(tr_xyz, name) == getattr(tr_dcd, name)
assert tr_xyz.timestep == 1.0
assert tr_xyz.natoms == 57
assert tr_xyz.nstep == 16
# coords are 32bit float in dcd files (single prec, so coords_frac can only
# be accurate to that precision, which ~1e-8). cryst_const is double
# precision in the dcd file, so atol can be lower
assert np.allclose(tr_xyz.coords_frac,
tr_dcd.coords_frac,
rtol=0,
atol=1.5e-7)
assert np.allclose(tr_xyz.cryst_const,
tr_dcd.cryst_const,
rtol=0,
atol=7e-10)
assert not np.allclose(tr_xyz.coords, tr_dcd.coords, rtol=0, atol=5e-6)
assert not np.allclose(tr_xyz.cell, tr_dcd.cell, rtol=0, atol=7e-10)
# align xyz cell, now cell and coords are the same
tr_xyz.coords = None
tr_xyz.cell = None
tr_xyz.set_all()
assert np.allclose(tr_xyz.coords_frac,
tr_dcd.coords_frac,
rtol=0,
atol=1.5e-7)
assert np.allclose(tr_xyz.cryst_const,
tr_dcd.cryst_const,
rtol=0,
atol=7e-10)
assert np.allclose(tr_xyz.coords, tr_dcd.coords, rtol=0, atol=5e-6)
assert np.allclose(tr_xyz.cell, tr_dcd.cell, rtol=0, atol=7e-10)
def test_cp2k_md():
attr_lst = parse.Cp2kMDOutputFile().attr_lst
# This parser and others have get_econst(), but not all, so ATM it's not
# part of the Trajectory API
attr_lst.pop(attr_lst.index('econst'))
for dr in ['files/cp2k/md/npt_f_print_low', 'files/cp2k/md/nvt_print_low']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' % dr
print("testing: %s" % fn)
print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base, dr)))
tr = io.read_cp2k_md(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst)
pp = parse.Cp2kMDOutputFile(fn)
forces_outfile = pp._get_forces_from_outfile() * Ha / Bohr / eV * Ang
assert np.allclose(forces_outfile, tr.forces, rtol=1e-3)
def test_cp2k_md():
attr_lst = parse.Cp2kMDOutputFile().attr_lst
# This parser and others have get_econst(), but not all, so ATM it's not
# part of the Trajectory API
attr_lst.pop(attr_lst.index('econst'))
for dr in ['files/cp2k/md/npt_f_print_low', 'files/cp2k/md/nvt_print_low']:
base = os.path.dirname(dr)
fn = '%s/cp2k.out' %dr
print "testing: %s" %fn
print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
tr = io.read_cp2k_md(fn)
assert_attrs_not_none(tr, attr_lst=attr_lst)
pp = parse.Cp2kMDOutputFile(fn)
forces_outfile = pp._get_forces_from_outfile()*Ha/Bohr/eV*Ang
assert np.allclose(forces_outfile, tr.forces, rtol=1e-3)
def test_cp2k_txt_vs_dcd():
# Two exactly equal NPT runs, nstep=16, natoms=57. The dcd run uses
# motion/print/trajectory format dcd_aligned_cell
# the other the default xyz format. So we have
# PROJECT-pos-1.dcd
# PROJECT-pos-1.xyz
# Since the cell changes and we use dcd_aligned_cell, the coords from the
# xyz run are NOT the same as the coords in the dcd file, which HAS to be
# like this. Only coords_frac can be compared, and coords after the xyz
# run's cell has been aligned to [[x,0,0],[xy,y,0],[xz,yz,z]].
dir_xyz = unpack_compressed('files/cp2k/dcd/npt_xyz.tgz')
dir_dcd = unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
tr_xyz = io.read_cp2k_md(pj(dir_xyz, 'cp2k.out'))
tr_dcd = io.read_cp2k_md_dcd(pj(dir_dcd, 'cp2k.out'))
for name in ['natoms', 'nstep', 'timestep', 'symbols']:
assert getattr(tr_xyz,name) == getattr(tr_dcd, name)
assert tr_xyz.timestep == 1.0
assert tr_xyz.natoms == 57
assert tr_xyz.nstep == 16
# coords are 32bit float in dcd files (single prec, so coords_frac can only
# be accurate to that precision, which ~1e-8). cryst_const is double
# precision in the dcd file, so atol can be lower
assert np.allclose(tr_xyz.coords_frac, tr_dcd.coords_frac, rtol=0,
atol=1.5e-7)
assert np.allclose(tr_xyz.cryst_const, tr_dcd.cryst_const, rtol=0,
atol=7e-10)
assert not np.allclose(tr_xyz.coords, tr_dcd.coords, rtol=0,
atol=5e-6)
assert not np.allclose(tr_xyz.cell, tr_dcd.cell, rtol=0,
atol=7e-10)
# align xyz cell, now cell and coords are the same
tr_xyz.coords = None; tr_xyz.cell=None; tr_xyz.set_all()
assert np.allclose(tr_xyz.coords_frac, tr_dcd.coords_frac, rtol=0,
atol=1.5e-7)
assert np.allclose(tr_xyz.cryst_const, tr_dcd.cryst_const, rtol=0,
atol=7e-10)
assert np.allclose(tr_xyz.coords, tr_dcd.coords, rtol=0,
atol=5e-6)
assert np.allclose(tr_xyz.cell, tr_dcd.cell, rtol=0,
atol=7e-10)
