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 run(filename, none_attrs=[]):
# filename = 'files/cpmd/md_bo/cpmd.bo.out'
# basename = 'cpmd.bo.out'
# archive = 'files/cpmd/md_bo.tgz'
bar = '=' * 78
print(bar)
print("@@testing: %s" % filename)
print(bar)
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + '.tgz'
workdir = unpack_compressed(archive)
pp = CpmdMDOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=none_attrs)
traj = pp.get_traj()
attrs3d = [
'coords',
'coords_frac',
'forces',
'cell',
'stress',
]
for attr_name in traj.attr_lst:
attr = getattr(traj, attr_name)
if attr_name not in none_attrs:
if hasattr(attr, 'ndim'):
print("%s: ndim: %s, shape: %s" %
(attr_name, attr.ndim, attr.shape))
assert attr is not None, "FAILED - None: %s" % attr_name
if attr_name in attrs3d:
assert attr.ndim == 3, "FAILED - not 3d: %s" % attr_name
def test_pw_md_out():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
alat = 5.9098 # Bohr
pp1 = PwMDOutputFile(filename=filename, use_alat=True)
pp1.parse()
none_attrs = [\
'coords_frac',
]
assert_attrs_not_none(pp1, none_attrs=none_attrs)
assert np.allclose(pp1.timestep, 150.0) # tryd
traj1 = pp1.get_traj()
assert_attrs_not_none(traj1)
pp2 = PwMDOutputFile(filename=filename,
use_alat=False,
units={'length': alat*Bohr/Ang})
pp2.parse()
assert np.allclose(pp2.timestep, 150.0) # tryd
assert_attrs_not_none(pp2, none_attrs=none_attrs)
# Skip coords and cell b/c they are modified by self.alat and
# pp1.alat = 1.0, pp2.alat = 5.9098
attr_lst = common.pop_from_list(pp1.attr_lst, ['coords', 'cell'])
adae(pp1.__dict__, pp2.__dict__, keys=attr_lst)
traj2 = pp2.get_traj()
adae(traj1.__dict__, traj2.__dict__, keys=traj1.attr_lst)
pp3 = PwMDOutputFile(filename=filename)
assert alat == pp3.get_alat() # self.use_alat=True default
def run(filename, none_attrs=[]):
# filename = 'files/cpmd/md_bo/cpmd.bo.out'
# basename = 'cpmd.bo.out'
# archive = 'files/cpmd/md_bo.tgz'
bar = '='*78
print bar
print "@@testing: %s" %filename
print bar
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + '.tgz'
workdir = unpack_compressed(archive)
pp = CpmdMDOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=none_attrs)
traj = pp.get_traj()
attrs3d = ['coords',
'coords_frac',
'forces',
'cell',
'stress',
]
for attr_name in traj.attr_lst:
attr = getattr(traj, attr_name)
if attr_name not in none_attrs:
if hasattr(attr, 'ndim'):
print "%s: ndim: %s, shape: %s" %(attr_name, attr.ndim, attr.shape)
assert attr is not None, "FAILED - None: %s" %attr_name
if attr_name in attrs3d:
assert attr.ndim == 3, "FAILED - not 3d: %s" %attr_name
def test_pw_md_out():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
alat = 5.9098 # Bohr
pp1 = PwMDOutputFile(filename=filename, use_alat=True)
pp1.parse()
none_attrs = [\
'coords_frac',
]
assert_attrs_not_none(pp1, none_attrs=none_attrs)
assert np.allclose(pp1.timestep, 150.0) # tryd
traj1 = pp1.get_traj()
assert_attrs_not_none(traj1)
pp2 = PwMDOutputFile(filename=filename,
use_alat=False,
units={'length': alat * Bohr / Ang})
pp2.parse()
assert np.allclose(pp2.timestep, 150.0) # tryd
assert_attrs_not_none(pp2, none_attrs=none_attrs)
# Skip coords and cell b/c they are modified by self.alat and
# pp1.alat = 1.0, pp2.alat = 5.9098
attr_lst = common.pop_from_list(pp1.attr_lst, ['coords', 'cell'])
adae(pp1.__dict__, pp2.__dict__, keys=attr_lst)
traj2 = pp2.get_traj()
adae(traj1.__dict__, traj2.__dict__, keys=traj1.attr_lst)
pp3 = PwMDOutputFile(filename=filename)
assert alat == pp3.get_alat() # self.use_alat=True default
def test_pw_scf_no_forces_stress():
fn = unpack_compressed('files/pw.scf_no_forces_stress.out.gz')
pp = PwSCFOutputFile(fn)
assert pp.get_forces() is None
assert pp.get_stress() is None
st = io.read_pw_scf(fn)
assert st.stress is None
assert st.forces is None
def test_pw_scf_no_forces_stress():
fn = unpack_compressed('files/pw.scf_no_forces_stress.out.gz')
pp = PwSCFOutputFile(fn)
assert pp.get_forces() is None
assert pp.get_stress() is None
st = io.read_pw_scf(fn)
assert st.stress is None
assert st.forces is None
def test_cpmd_scf():
filename = "files/cpmd/scf/cpmd.out"
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + ".tgz"
workdir = unpack_compressed(archive)
pp = CpmdSCFOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=[])
def test_cpmd_scf():
filename = 'files/cpmd/scf/cpmd.out'
basename = os.path.basename(filename)
archive = os.path.dirname(filename) + '.tgz'
workdir = unpack_compressed(archive)
pp = CpmdSCFOutputFile(filename=pj(workdir, basename))
pp.parse()
assert_attrs_not_none(pp, none_attrs=[])
def test_read_matdyn_freq_disp():
# Parse matdyn frequency file. In QE 5.x the path_norm and band structure
# is also directly written to a file with suffix ".gp", i.e.
# "matdyn.freq.disp.gp"
fn = unpack_compressed('files/qe_matdyn_disp/matdyn.freq.disp.gz')
kk, ff = pwscf.read_matdyn_freq(fn)
d = np.loadtxt('files/qe_matdyn_disp/matdyn.freq.disp.gp.gz')
assert np.allclose(kpath.get_path_norm(kk), d[:,0])
assert np.allclose(ff, d[:,1:])
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_pdos():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
pp = parse.PwMDOutputFile(filename=filename)
traj = pp.get_traj()
# timestep dt
# -----------
# Only needed in pd.*_pdos(), not in pd.velocity(). Here is why:
#
# vacf_pdos, direct_pdos:
# If we compute the *normalized* VCAF, then dt is a factor:
# <v_x(0) v_x(t)> = 1/dt^2 <dx(0) dx(t)>
# which cancels in the normalization. dt is not needed in the velocity
# calculation, hence not
# V=velocity(coords, dt=dt)
# only
# V=velocity(coords).
V = traj.velocity # Ang / fs
mass = traj.mass # amu
dt = traj.timestep # fs
timeaxis = traj.timeaxis
assert np.allclose(150.0, dt * constants.fs / constants.tryd) # dt=150 Rydberg time units
fd, dd = pd.direct_pdos(V, m=mass, dt=dt, npad=1, tonext=False)
fv, dv = pd.vacf_pdos(V, m=mass, dt=dt, mirr=True)
np.testing.assert_array_almost_equal(fd, fv, err_msg="freq not equal")
np.testing.assert_array_almost_equal(dd, dv, err_msg="dos not equal")
assert np.allclose(fd, np.loadtxt('files/ref_test_pdos/fd.txt.gz'))
assert np.allclose(fv, np.loadtxt('files/ref_test_pdos/fv.txt.gz'))
assert np.allclose(dd, np.loadtxt('files/ref_test_pdos/dd.txt.gz'))
assert np.allclose(dv, np.loadtxt('files/ref_test_pdos/dv.txt.gz'))
df = fd[1] - fd[0]
print "Nyquist freq: %e" %(0.5/dt)
print "df: %e:" %df
print "timestep: %f fs = %f tryd" %(dt, dt * constants.fs / constants.tryd)
print "timestep pw.out: %f tryd" %(pp.timestep)
# API
fd, dd, ffd, fdd, si = pd.direct_pdos(V, m=mass, dt=dt, full_out=True)
fv, dv, ffv, fdv, si, vacf, fft_vacf = pd.vacf_pdos(V, m=mass, dt=dt,
mirr=True, full_out=True)
# Test padding for speed.
fd, dd, ffd, fdd, si = pd.direct_pdos(V, m=mass, dt=dt, npad=1, tonext=True, \
full_out=True)
assert len(fd) == len(dd)
assert len(ffd) == len(fdd)
# If `tonext` is used, full fft array lengths must be a power of two.
assert len(ffd) >= 2*V.shape[timeaxis] - 1
assert np.log2(len(ffd)) % 1.0 == 0.0
def test_pdos():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
pp = parse.PwMDOutputFile(filename=filename)
traj = pp.get_traj()
# timestep dt
# -----------
# Only needed in pd.*_pdos(), not in pd.velocity(). Here is why:
#
# vacf_pdos, direct_pdos:
# If we compute the *normalized* VCAF, then dt is a factor:
# <v_x(0) v_x(t)> = 1/dt^2 <dx(0) dx(t)>
# which cancels in the normalization. dt is not needed in the velocity
# calculation, hence not
# V=velocity(coords, dt=dt)
# only
# V=velocity(coords).
V = traj.velocity # Ang / fs
mass = traj.mass # amu
dt = traj.timestep # fs
timeaxis = traj.timeaxis
assert np.allclose(150.0, dt * constants.fs / constants.tryd) # dt=150 Rydberg time units
fd, dd = pd.direct_pdos(V, m=mass, dt=dt, npad=1, tonext=False)
fv, dv = pd.vacf_pdos(V, m=mass, dt=dt, mirr=True)
np.testing.assert_array_almost_equal(fd, fv, err_msg="freq not equal")
np.testing.assert_array_almost_equal(dd, dv, err_msg="dos not equal")
assert np.allclose(fd, np.loadtxt('files/ref_test_pdos/fd.txt.gz'))
assert np.allclose(fv, np.loadtxt('files/ref_test_pdos/fv.txt.gz'))
assert np.allclose(dd, np.loadtxt('files/ref_test_pdos/dd.txt.gz'))
assert np.allclose(dv, np.loadtxt('files/ref_test_pdos/dv.txt.gz'))
df = fd[1] - fd[0]
print("Nyquist freq: %e" %(0.5/dt))
print("df: %e:" %df)
print("timestep: %f fs = %f tryd" %(dt, dt * constants.fs / constants.tryd))
print("timestep pw.out: %f tryd" %(pp.timestep))
# API
fd, dd, ffd, fdd, si = pd.direct_pdos(V, m=mass, dt=dt, full_out=True)
fv, dv, ffv, fdv, si, vacf, fft_vacf = pd.vacf_pdos(V, m=mass, dt=dt,
mirr=True, full_out=True)
# Test padding for speed.
fd, dd, ffd, fdd, si = pd.direct_pdos(V, m=mass, dt=dt, npad=1, tonext=True, \
full_out=True)
assert len(fd) == len(dd)
assert len(ffd) == len(fdd)
# If `tonext` is used, full fft array lengths must be a power of two.
assert len(ffd) >= 2*V.shape[timeaxis] - 1
assert np.log2(len(ffd)) % 1.0 == 0.0
def test_save_object():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
dumpfile = os.path.join(testdir, 'pw.md.pk')
c = PwMDOutputFile(filename=filename)
print ">>> parsing ..."
c.parse()
print ">>> ... done"
print ">>> saving %s ..." %dumpfile
c.dump(dumpfile)
print ">>> ... done"
print ">>> loading ..."
c2 = PwMDOutputFile()
c2.load(dumpfile)
print ">>> ... done"
print ">>> checking equalness of attrs in loaded object ..."
known_fails = {'fd': 'closed/uninitialized file',
'cont': 'container object'}
arr_t = type(np.array([1]))
dict_t = type({})
for attr in c.__dict__.iterkeys():
c_val = getattr(c, attr)
c2_val = getattr(c2, attr)
dotest = True
for name, string in known_fails.iteritems():
if name == attr:
print "known fail: %s: %s: %s" %(name, string, attr)
dotest = False
if dotest:
print "testing:", attr, type(c_val), type(c2_val)
type_c = type(c_val)
type_c2 = type(c2_val)
assert type_c is type_c2, "attr: %s: types differ: %s, %s" \
%(attr, str(type_c), str(type_c2))
if type(c_val) is arr_t:
assert (c_val == c2_val).all(), "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
elif type(c_val) is dict_t:
ade(c_val, c2_val)
else:
assert c_val == c2_val, "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
def test_save_object():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
dumpfile = os.path.join(testdir, 'pw.md.pk')
c = PwMDOutputFile(filename=filename)
print(">>> parsing ...")
c.parse()
print(">>> ... done")
print(">>> saving %s ..." %dumpfile)
c.dump(dumpfile)
print(">>> ... done")
print(">>> loading ...")
c2 = io.read_pickle(dumpfile)
print(">>> ... done")
print(">>> checking equalness of attrs in loaded object ...")
known_fails = {'fd': 'closed/uninitialized file',
'cont': 'container object'}
arr_t = type(np.array([1]))
dict_t = type({})
for attr in c.__dict__.keys():
c_val = getattr(c, attr)
c2_val = getattr(c2, attr)
dotest = True
for name, string in known_fails.items():
if name == attr:
print("known fail: %s: %s: %s" %(name, string, attr))
dotest = False
if dotest:
print("testing:", attr, type(c_val), type(c2_val))
type_c = type(c_val)
type_c2 = type(c2_val)
assert type_c is type_c2, "attr: %s: types differ: %s, %s" \
%(attr, str(type_c), str(type_c2))
if type(c_val) is arr_t:
assert (c_val == c2_val).all(), "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
elif type(c_val) is dict_t:
ade(c_val, c2_val)
else:
assert c_val == c2_val, "fail: %s: %s, %s" \
%(attr, c_val, c2_val)
def test_pw_scf_one_atom():
fn = unpack_compressed('files/pw.scf_one_atom.out.gz')
pp = PwSCFOutputFile(fn)
pp.parse()
not_none = [\
'coords',
'symbols',
'stress',
'etot',
'forces',
'nstep_scf',
'cell',
'natoms',
'nkpoints',
]
tools.assert_attrs_not_none(pp, attr_lst=not_none)
assert pp.forces.shape == (1, 3)
assert pp.coords.shape == (1, 3)
assert pp.stress.shape == (3, 3)
assert pp.cell.shape == (3, 3)
def test_pw_scf_one_atom():
fn = unpack_compressed('files/pw.scf_one_atom.out.gz')
pp = PwSCFOutputFile(fn)
pp.parse()
not_none = [\
'coords',
'symbols',
'stress',
'etot',
'forces',
'nstep_scf',
'cell',
'natoms',
'nkpoints',
]
tools.assert_attrs_not_none(pp, attr_lst=not_none)
assert pp.forces.shape == (1,3)
assert pp.coords.shape == (1,3)
assert pp.stress.shape == (3,3)
assert pp.cell.shape == (3,3)
def test_get_cont():
filename = tools.unpack_compressed('files/pw.md.out.gz', prefix=__file__)
pp = parse.PwMDOutputFile(filename=filename)
tr1 = pp.get_traj()
# Need new parser instance, since pp.cont is already used, i.e. set_all()
# called -> all attrs set. Also units are already applied, thus won't be
# applied again since self.units_applied=True.
pp = parse.PwMDOutputFile(filename=filename)
tr2 = pp.get_traj(auto_calc=False)
# specific for the used pw.out file, None is everything which is not parsed
# since nothing is calculated from parsed data
none_attrs = [
'coords_frac',
'cryst_const',
'pressure',
'velocity',
'volume',
'mass',
'mass_unique',
'nspecies',
'ntypat',
'order',
'symbols_unique',
'typat',
'time',
'znucl',
'znucl_unique',
]
for name in tr1.attr_lst:
a1 = getattr(tr1, name)
a2 = getattr(tr2, name)
if name in none_attrs:
assert a1 is not None, ("a1 %s is None" % name)
assert a2 is None, ("a2 %s is not None" % name)
else:
tools.assert_all_types_equal(a1, a2)
def run(dr):
dr = dr[:-1] if dr.endswith('/') else dr
workdir = unpack_compressed(dr + '.tgz')
exe = os.path.join(os.path.dirname(__file__), '../../bin/cut-cpmd.sh')
cmd = '{e} {w} 20 > {w}/cut-cpmd.log'.format(e=exe, w=workdir)
sp.run(cmd, check=True, shell=True)
def run(dr, none_attrs=[]):
dr = dr[:-1] if dr.endswith('/') else dr
archive = dr + '.tgz'
workdir = unpack_compressed(archive)
common.system('../bin/cut-cpmd.sh %s 20 > %s/cut-cpmd.log' %(workdir,
workdir))
def test_dcd():
# nstep = 101
# natoms = 16
dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
fn_lmp = pj(dir_lmp, 'lmp.out.dcd')
# nstep = 16
# natoms = 57
dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')
# read headers
hdr_lmp = dcd.read_dcd_header(fn_lmp)
hdr_cp2k = dcd.read_dcd_header(fn_cp2k)
print ">>> comparing headers"
for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
tools.assert_dict_with_all_types_equal(ref, dct, keys=ref.keys(),
strict=True)
# compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
# implementations
# cc = cryst_const
# co = coords
print ">>> comparing data"
for fn,convang,nstephdr,nstep,natoms in [(fn_lmp,True,True,101,16),
(fn_lmp,True,False,101,16),
(fn_cp2k,False,False,16,57)]:
cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
cc_f, co_f = dcd.read_dcd_data_f(fn, convang=convang, nstephdr=nstephdr)
print ">>> ... cryst_const"
tools.assert_array_equal(cc_py, cc_f)
print ">>> ... coords"
tools.assert_array_equal(co_py, co_f)
print ">>> ... shapes"
assert cc_f.shape == (nstep,6)
assert co_f.shape == (nstep,natoms,3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print ">>> ... angles"
assert (cc_py[:,3:] > 50).all()
# compare slow and fast python versions
# cc = cryst_const
# co = coords
print ">>> comparing data"
for fn,convang,nstep,natoms in [(fn_lmp,True,101,16),
(fn_lmp,True,101,16),
(fn_cp2k,False,16,57)]:
cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
print ">>> ... cryst_const"
tools.assert_array_equal(cc_py_fast, cc_py_ref)
print ">>> ... coords"
tools.assert_array_equal(co_py_fast, co_py_ref)
print ">>> ... shapes"
assert cc_py_ref.shape == (nstep,6)
assert co_py_ref.shape == (nstep,natoms,3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print ">>> ... angles"
assert (cc_py_fast[:,3:] > 50).all()
def test_dcd():
# nstep = 101
# natoms = 16
dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
fn_lmp = pj(dir_lmp, 'lmp.out.dcd')
# nstep = 16
# natoms = 57
dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')
# read headers
hdr_lmp = dcd.read_dcd_header(fn_lmp)
hdr_cp2k = dcd.read_dcd_header(fn_cp2k)
print(">>> comparing headers")
for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
tools.assert_dict_with_all_types_equal(ref,
dct,
keys=list(ref.keys()),
strict=True)
# compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
# implementations
# cc = cryst_const
# co = coords
print(">>> comparing data")
for fn, convang, nstephdr, nstep, natoms in [
(fn_lmp, True, True, 101, 16), (fn_lmp, True, False, 101, 16),
(fn_cp2k, False, False, 16, 57)
]:
cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
cc_f, co_f = dcd.read_dcd_data_f(fn,
convang=convang,
nstephdr=nstephdr)
print(">>> ... cryst_const")
tools.assert_array_equal(cc_py, cc_f)
print(">>> ... coords")
tools.assert_array_equal(co_py, co_f)
print(">>> ... shapes")
assert cc_f.shape == (nstep, 6)
assert co_f.shape == (nstep, natoms, 3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print(">>> ... angles")
assert (cc_py[:, 3:] > 50).all()
# compare slow and fast python versions
# cc = cryst_const
# co = coords
print(">>> comparing data")
for fn, convang, nstep, natoms in [(fn_lmp, True, 101, 16),
(fn_lmp, True, 101, 16),
(fn_cp2k, False, 16, 57)]:
cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
print(">>> ... cryst_const")
tools.assert_array_equal(cc_py_fast, cc_py_ref)
print(">>> ... coords")
tools.assert_array_equal(co_py_fast, co_py_ref)
print(">>> ... shapes")
assert cc_py_ref.shape == (nstep, 6)
assert co_py_ref.shape == (nstep, natoms, 3)
# lmp angles are around 60, cp2k around 90 degree, cosines are between
# -1 and 1, make sure the angle conversion works
print(">>> ... angles")
assert (cc_py_fast[:, 3:] > 50).all()
def test_return_3d_if_no_cell_unit():
filename = tools.unpack_compressed('files/pw.vc_relax_no_cell_unit.out.gz',
prefix=__file__)
pp = PwMDOutputFile(filename=filename)
pp.parse()
assert np.allclose(pp.cell, _cell*pp.get_alat())
