def test_scf_cell():
filename = 'files/pw.vc_relax_coords_fixed.out'
common.system('gunzip %s.gz' %filename)
pp = parse.PwSCFOutputFile(filename, use_alat=False)
cell_2d_red = pp.get_cell()
assert np.allclose(cell_2d_red, cell_2d_red_ref, atol=1e-15, rtol=0)
pp = parse.PwSCFOutputFile(filename, use_alat=True)
assert np.allclose(pp.get_cell(),
cell_2d_red*pp.get_alat(),
atol=1e-15,
rtol=0)
st = io.read_pw_scf(filename)
tr = io.read_pw_md(filename)
# tr is from a vc-relax w/ fixed fractional coords, check that
assert np.allclose(np.zeros((tr.nstep,tr.natoms,3)),
tr.coords_frac - tr.coords_frac[0,...].copy(),
rtol=0, atol=1e-15)
# check if scf parser gets the same coords_frac as the trajectory parser
# Note: this and the next test have the same max error of
# 4.33868466709e-08 (b/c of limited accuracy in printed numbers in
# pwscf output)
assert np.allclose(st.coords_frac,tr.coords_frac[0,...], atol=1e-7, rtol=0)
# same test, plus test of concatenate() works
trcat = crys.concatenate((st,tr))
assert np.allclose(np.zeros((trcat.nstep,trcat.natoms,3)),
trcat.coords_frac - trcat.coords_frac[0,...].copy(),
rtol=0, atol=1e-7)
def test_scf_cell():
filename = 'files/pw.vc_relax_coords_fixed.out'
common.system('gunzip %s.gz' % filename)
pp = parse.PwSCFOutputFile(filename, use_alat=False)
cell_2d_red = pp.get_cell()
assert np.allclose(cell_2d_red, cell_2d_red_ref, atol=1e-15, rtol=0)
pp = parse.PwSCFOutputFile(filename, use_alat=True)
assert np.allclose(pp.get_cell(),
cell_2d_red * pp.get_alat(),
atol=1e-15,
rtol=0)
st = io.read_pw_scf(filename)
tr = io.read_pw_md(filename)
# tr is from a vc-relax w/ fixed fractional coords, check that
assert np.allclose(np.zeros((tr.nstep, tr.natoms, 3)),
tr.coords_frac - tr.coords_frac[0, ...].copy(),
rtol=0,
atol=1e-15)
# check if scf parser gets the same coords_frac as the trajectory parser
# Note: this and the next test have the same max error of
# 4.33868466709e-08 (b/c of limited accuracy in printed numbers in
# pwscf output)
assert np.allclose(st.coords_frac,
tr.coords_frac[0, ...],
atol=1e-7,
rtol=0)
# same test, plus test of concatenate() works
trcat = crys.concatenate((st, tr))
assert np.allclose(np.zeros((trcat.nstep, trcat.natoms, 3)),
trcat.coords_frac - trcat.coords_frac[0, ...].copy(),
rtol=0,
atol=1e-7)
import os
import numpy as np
from matplotlib import pyplot as plt
from pwtools import parse, crys, constants, common, io
pj = os.path.join
if __name__ == '__main__':
tmpdir = '/tmp/rpdf_vmd_test/'
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
dct = {}
common.system("gunzip pw.out.gz")
traj = io.read_pw_md('pw.out')
common.system("gzip pw.out")
symbols = np.array(traj.symbols)
# O_Ca
msk1 = symbols=='O'
msk2 = symbols=='Ca'
amask = [msk1, msk2]
tmask = np.s_[-1]
dct['O:Ca:-1:-1'] = {'amask': amask, 'tmask': tmask}
tmask = np.s_[0:]
dct['O:Ca:0:-1'] = {'amask': amask, 'tmask': tmask}
# Ca_O
msk1 = symbols=='Ca'
msk2 = symbols=='O'
import os
import numpy as np
from matplotlib import pyplot as plt
from pwtools import parse, crys, constants, common, io
pj = os.path.join
if __name__ == '__main__':
tmpdir = '/tmp/rpdf_vmd_test/'
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
dct = {}
common.system("gunzip pw.out.gz")
traj = io.read_pw_md('pw.out')
common.system("gzip pw.out")
symbols = np.array(traj.symbols)
# O_Ca
msk1 = symbols == 'O'
msk2 = symbols == 'Ca'
amask = [msk1, msk2]
tmask = np.s_[-1]
dct['O:Ca:-1:-1'] = {'amask': amask, 'tmask': tmask}
tmask = np.s_[0:]
dct['O:Ca:0:-1'] = {'amask': amask, 'tmask': tmask}
# Ca_O
msk1 = symbols == 'Ca'
msk2 = symbols == 'O'