def run(tgz, skip=[], atol_map={}):
tgz_path = os.path.dirname(tgz)
unpack_path = tgz.replace('.tgz', '')
common.system("tar -C {0} -xzf {1}".format(tgz_path, tgz))
tr1 = io.read_lammps_md_txt("{0}/log.lammps".format(unpack_path))
tr2 = io.read_lammps_md_dcd("{0}/log.lammps".format(unpack_path))
for name in tr1.attr_lst:
if name in skip:
continue
elif name in atol_map:
set_atol(atol_map[name])
else:
set_atol()
x1 = getattr(tr1, name)
x2 = getattr(tr2, name)
print(name)
tools.assert_all_types_almost_equal(x1, x2)
# stress
assert (tr1.stress[:, 0, 1] == tr1.stress[:, 1, 0]).all()
assert (tr1.stress[:, 0, 2] == tr1.stress[:, 2, 0]).all()
assert (tr1.stress[:, 1, 2] == tr1.stress[:, 2, 1]).all()
def run(tgz, skip=[], atol_map={}):
tgz_path = os.path.dirname(tgz)
unpack_path = tgz.replace('.tgz','')
common.system("tar -C {0} -xzf {1}".format(tgz_path,tgz))
tr1 = io.read_lammps_md_txt("{0}/log.lammps".format(unpack_path))
tr2 = io.read_lammps_md_dcd("{0}/log.lammps".format(unpack_path))
for name in tr1.attr_lst:
if name in skip:
continue
elif atol_map.has_key(name):
set_atol(atol_map[name])
else:
set_atol()
x1 = getattr(tr1, name)
x2 = getattr(tr2, name)
print name
tools.assert_all_types_almost_equal(x1, x2)
# stress
assert (tr1.stress[:,0,1] == tr1.stress[:,1,0]).all()
assert (tr1.stress[:,0,2] == tr1.stress[:,2,0]).all()
assert (tr1.stress[:,1,2] == tr1.stress[:,2,1]).all()
# create structure file
st = crys.Structure(coords_frac=np.array([[0.0]*3, [.5]*3]),
cryst_const=np.array([2.85]*3 + [60]*3),
symbols=['Al','N'])
io.write_lammps('lmp.struct', crys.scell(st,(3,3,3)))
# write lmp.in for nvt or npt
common.file_write('lmp.in', lmp_in_templ.format(ensemble=ens_txt))
# run lammps
common.system("mpirun -np 2 lammps < lmp.in", wait=True)
# read trajectory
trtxt_orig = io.read_lammps_md_txt('log.lammps')
trdcd = io.read_lammps_md_dcd('log.lammps')
# plotting
plots = mpl.prepare_plots(['coords', 'coords_frac', 'velocity',
'cryst_const', 'cell'])
for name,pl in plots.iteritems():
trtxt = trtxt_orig.copy()
print name
xtxt = getattr(trtxt, name)
setattr(trtxt, name, None)
xcalc = eval('trtxt.get_%s()' %name)
if name == 'cell':
sl = np.s_[Ellipsis]
func = lambda x: np.reshape(x, (x.shape[0], 9))
elif name in trtxt.attrs_nstep_3d:
# coords_frac and coords: only x-coord (index=0)
# create structure file
st = crys.Structure(coords_frac=np.array([[0.0]*3, [.5]*3]),
cryst_const=np.array([2.85]*3 + [60]*3),
symbols=['Al','N'])
io.write_lammps('lmp.struct', crys.scell(st,(3,3,3)))
# write lmp.in for nvt or npt
common.file_write('lmp.in', lmp_in_templ.format(ensemble=ens_txt))
# run lammps
common.system("mpirun -np 2 lammps < lmp.in", wait=True)
# read trajectory
trtxt_orig = io.read_lammps_md_txt('log.lammps')
trdcd = io.read_lammps_md_dcd('log.lammps')
# plotting
plots = mpl.prepare_plots(['coords', 'coords_frac', 'velocity',
'cryst_const', 'cell'])
for name,pl in plots.items():
trtxt = trtxt_orig.copy()
print(name)
xtxt = getattr(trtxt, name)
setattr(trtxt, name, None)
xcalc = eval('trtxt.get_%s()' %name)
if name == 'cell':
sl = np.s_[Ellipsis]
func = lambda x: np.reshape(x, (x.shape[0], 9))
elif name in trtxt.attrs_nstep_3d:
# coords_frac and coords: only x-coord (index=0)
