def read_results(self):
self.results = {}
assert os.path.exists(self.outfile), "%s missing" % self.outfile
st = io.read_pw_scf(self.outfile)
self.results['energy'] = st.etot
self.results['forces'] = st.forces
self.results['stress'] = stress_pwtools2ase(st.stress)
def read_results(self):
self.results = {}
assert os.path.exists(self.outfile), "%s missing" %self.outfile
st = io.read_pw_scf(self.outfile)
self.results['energy'] = st.etot
self.results['forces'] = st.forces
self.results['stress'] = stress_pwtools2ase(st.stress)
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_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 get_atoms_with_calc_lammps():
st_start = io.read_pw_scf('files/ase/pw.scf.out.start.wz-AlN')
at = st_start.get_ase_atoms(pbc=True)
label = pj(testdir, prefix, 'calc_dir', 'lmp')
calc = Lammps(label=label,
pair_style='tersoff',
pair_coeff='* * AlN.tersoff Al N',
command='lammps < lmp.in > lmp.out 2>&1',
backup=True,
)
at.set_calculator(calc)
return at
def get_atoms_with_calc_lammps():
st_start = io.read_pw_scf('files/ase/pw.scf.out.start.wz-AlN')
at = st_start.get_ase_atoms(pbc=True)
label = pj(testdir, prefix, 'calc_dir', 'lmp')
calc = Lammps(label=label,
pair_style='tersoff',
pair_coeff='* * AlN.tersoff Al N',
command='lammps < lmp.in > lmp.out 2>&1',
backup=True,
)
at.set_calculator(calc)
return at
def get_atoms_with_calc_pwscf(pseudo_dir):
st_start = io.read_pw_scf('files/ase/pw.scf.out.start.rs-AlN')
at = st_start.get_ase_atoms(pbc=True)
label = pj(testdir, prefix, 'calc_dir', 'pw')
calc = Pwscf(label=label,
kpts=1/0.9,
ecutwfc=30,
conv_thr=1e-5,
pp='pbe-n-kjpaw_psl.0.1.UPF',
pseudo_dir=pseudo_dir,
calc_name='my_calc',
outdir=pj(testdir, prefix, 'scratch'),
command='pw.x < pw.in > pw.out 2>&1',
backup=True,
)
at.set_calculator(calc)
return at
def get_atoms_with_calc_pwscf(pseudo_dir):
st_start = io.read_pw_scf('files/ase/pw.scf.out.start.rs-AlN')
at = st_start.get_ase_atoms(pbc=True)
label = pj(testdir, prefix, 'calc_dir', 'pw')
calc = Pwscf(label=label,
kpts=1/0.9,
ecutwfc=30,
conv_thr=1e-5,
pp='pbe-n-kjpaw_psl.0.1.UPF',
pseudo_dir=pseudo_dir,
calc_name='my_calc',
outdir=pj(testdir, prefix, 'scratch'),
command='pw.x < pw.in > pw.out 2>&1',
backup=True,
)
at.set_calculator(calc)
return at
def test_pwscf_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_pwx():
skip("no pw.x found, skipping test")
else:
pseudo_dir = pj(testdir, prefix, 'pseudo')
print(common.backtick("mkdir -pv {p}; cp files/qe_pseudos/*.gz {p}/; \
gunzip {p}/*".format(p=pseudo_dir)))
at = get_atoms_with_calc_pwscf(pseudo_dir)
print("scf")
# trigger calculation here
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_pw_scf(at.calc.label + '.out')
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa)
# files/ase/pw.scf.out.start is a norm-conserving LDA struct,
# calculated with pz-vbc.UPF, so the PBE vc-relax will make the cell
# a bit bigger
print("vc-relax")
from ase.optimize import BFGS
from ase.constraints import UnitCellFilter
opt = BFGS(UnitCellFilter(at))
cell = parse.arr2d_from_txt("""
-1.97281509 0. 1.97281509
0. 1.97281509 1.97281509
-1.97281509 1.97281509 0.""")
assert np.allclose(cell, at.get_cell())
opt.run(fmax=0.05) # run only 2 steps
cell = parse.arr2d_from_txt("""
-2.01837531 0. 2.01837531
0. 2.01837531 2.01837531
-2.01837531 2.01837531 0""")
assert np.allclose(cell, at.get_cell())
# at least 1 backup files must exist: pw.*.0 is the SCF run, backed up
# in the first iter of the vc-relax
assert os.path.exists(at.calc.infile + '.0')
def test_pwscf_calculator():
if not have_ase():
skip("no ASE found, skipping test")
elif not have_pwx():
skip("no pw.x found, skipping test")
else:
pseudo_dir = pj(testdir, prefix, 'pseudo')
print common.backtick("mkdir -pv {p}; cp files/qe_pseudos/*.gz {p}/; \
gunzip {p}/*".format(p=pseudo_dir))
at = get_atoms_with_calc_pwscf(pseudo_dir)
print "scf"
# trigger calculation here
forces = at.get_forces()
etot = at.get_potential_energy()
stress = at.get_stress(voigt=False) # 3x3
st = io.read_pw_scf(at.calc.label + '.out')
assert np.allclose(forces, st.forces)
assert np.allclose(etot, st.etot)
assert np.allclose(st.stress, -stress * constants.eV_by_Ang3_to_GPa)
# files/ase/pw.scf.out.start is a norm-conserving LDA struct,
# calculated with pz-vbc.UPF, so the PBE vc-relax will make the cell
# a bit bigger
print "vc-relax"
from ase.optimize import BFGS
from ase.constraints import UnitCellFilter
opt = BFGS(UnitCellFilter(at))
cell = parse.arr2d_from_txt("""
-1.97281509 0. 1.97281509
0. 1.97281509 1.97281509
-1.97281509 1.97281509 0.""")
assert np.allclose(cell, at.get_cell())
opt.run(fmax=0.05) # run only 2 steps
cell = parse.arr2d_from_txt("""
-2.01837531 0. 2.01837531
0. 2.01837531 2.01837531
-2.01837531 2.01837531 0""")
assert np.allclose(cell, at.get_cell())
# at least 1 backup files must exist: pw.*.0 is the SCF run, backed up
# in the first iter of the vc-relax
assert os.path.exists(at.calc.infile + '.0')
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)
sp_points_frac = np.array([\
[0,0,0],
[.5,0,0],
[1/2., 1/2., 0],
[0,0.5,0],
[0,0,0],
[0,0,.5],
[0.5,0,.5],
[0.5,0.5,.5],
[0.0,0.5,.5],
[0,0,.5],
])
# recip. cell in 2*pi/alat units, need this to make QE happy, q-points in
# matdyn.in and matdyn.freq output file are cartesian in 2*pi/alat
st = io.read_pw_scf('pw.out')
rcell_reduced = crys.recip_cell(st.cell) / 2.0 / np.pi * st.cryst_const[0]
sp_points = np.dot(sp_points_frac, rcell_reduced)
# fine path: use N=500 for nice LO-TO split jumps [see below for more comments
# on that]
ks_path = kpath.kpath(sp_points, N=50)
# call matdyn.x
templ_txt = """
&input
asr='crystal',
XXXMASS
flfrc='q2r.fc',
flfrq='XXXFNFREQ'
/
sp_points_frac = np.array([\
[0,0,0],
[.5,0,0],
[1/2., 1/2., 0],
[0,0.5,0],
[0,0,0],
[0,0,.5],
[0.5,0,.5],
[0.5,0.5,.5],
[0.0,0.5,.5],
[0,0,.5],
])
# recip. cell in 2*pi/alat units, need this to make QE happy, q-points in
# matdyn.in and matdyn.freq output file are cartesian in 2*pi/alat
st = io.read_pw_scf('pw.out')
rcell_reduced = crys.recip_cell(st.cell) / 2.0 / np.pi * st.cryst_const[0]
sp_points = np.dot(sp_points_frac, rcell_reduced)
# fine path: use N=500 for nice LO-TO split jumps [see below for more comments
# on that]
ks_path = kpath.kpath(sp_points, N=50)
# call matdyn.x
templ_txt = """
&input
asr='crystal',
XXXMASS
flfrc='q2r.fc',
flfrq='XXXFNFREQ'
/
#!/usr/bin/python
# Parse each pw.out and write results/idx/struct.pk
from pwtools import sql, io
db = sql.SQLiteDB('calc.db', table='calc')
for idx in db.get_list1d("select idx from calc"):
print(idx)
st = io.read_pw_scf('calc/%i/pw.out' % idx)
st.dump('results/%i/struct.pk' % idx)
