def analyze(self, guard=True):
if not self.initialized:
return
#end if
log_filepath = os.path.join(self.path, self.outfile_name)
if not os.path.exists(log_filepath):
self.error(
'RMG analysis cannot be completed.\nLog file does not exist at path provided.\nPath provided: {}'
.format(log_filepath))
#end if
logfile = TextFile(log_filepath)
self.setup_info = obj()
self.results = obj()
if guard:
try:
self.read_setup_info(logfile)
except:
None
#end try
try:
self.read_results(logfile)
except:
None
#end try
else:
self.read_setup_info(logfile)
self.read_results(logfile)
def read(self, filepath=None):
if filepath is None:
filepath = self.location
#end if
if not os.path.exists(filepath):
self.error('file does not exist: {0}'.format(filepath))
#end if
file = TextFile(filepath)
self.read_file(file)
def get_output(self, filetag):
filename = self.info.files[filetag]
outfile = os.path.join(self.info.path, filename)
if os.path.exists(outfile):
filepath = outfile
elif os.path.exists(filename):
filepath = filename
elif self.info.exit:
self.error(
'output file does not exist at either of the locations below:\n {0}\n {1}'
.format(outfile, filename))
else:
return None
#end if
try:
return TextFile(filepath)
except:
return None
def test_textfile():
from fileio import TextFile
files = get_files()
# test empty initialization
empty = TextFile()
# test read
f = TextFile(files['scf.in'])
assert(len(f.read())==1225)
assert(len(f.lines())==55)
assert(len(f.tokens())==125)
assert(f.readline()=='&CONTROL\n')
assert(f.readline()==" calculation = 'scf'\n")
assert(f.readline('celldm')=='celldm(1) = 1.0\n')
assert(f.readtokens('ecutwfc')==['ecutwfc', '=', '272'])
val = f.readtokensf('CELL_PARAMETERS',float,float,float)
ref = [28.34589199, 0.0, 0.0]
assert(value_eq(val,ref))
f.close()
def analyze(self):
path = self.path
infile_name = self.infile_name
outfile_name = self.outfile_name
pw2c_outfile_name = self.pw2c_outfile_name
nx = 0
outfile = os.path.join(path, outfile_name)
try:
# perform MD analysis
f = TextFile(outfile)
n = 0
md_res = []
while f.seek('!', 1) != -1:
E = float(f.readtokens()[-2])
f.seek('P=', 1)
P = float(f.readtokens()[-1])
f.seek('time =', 1)
t = float(f.readtokens()[-2])
f.seek('kinetic energy', 1)
K = float(f.readtokens()[-2])
f.seek('temperature', 1)
T = float(f.readtokens()[-2])
md_res.append((E, P, t, K, T))
n += 1
#end while
md_res = array(md_res, dtype=float).T
quantities = ('total_energy', 'pressure', 'time', 'kinetic_energy',
'temperature')
md = obj()
for i, q in enumerate(quantities):
md[q] = md_res[i]
#end for
md.potential_energy = md.total_energy - md.kinetic_energy
self.md_data = md
self.md_stats = self.md_statistics()
if self.info.md_only:
return
#end if
except:
nx += 1
if self.info.warn:
self.warn('MD analysis failed')
#end if
#end try
try:
lines = open(outfile, 'r').read().splitlines()
except:
nx += 1
if self.info.warn:
self.warn('file read failed')
#end if
#end try
try:
fermi_energies = []
for l in lines:
if l.find('Fermi energ') != -1:
toks = l.split()[::-1]
assert toks[0] == 'ev'
for tok in toks[1:]:
try:
ef1 = float(tok)
fermi_energies.append(ef1)
except ValueError:
fermi_energies = fermi_energies[::-1]
break
#end try
#end for
#end if
#end for
if len(fermi_energies) == 0:
self.Ef = 0.0
else:
self.Ef = fermi_energies[-1]
#end if
self.fermi_energies = array(fermi_energies)
except:
nx += 1
if self.info.warn:
self.warn('fermi energy read failed')
#end if
#end try
try:
energies = []
for l in lines:
if l.find('! ') != -1:
energies.append(float(l.split('=')[1].split()[0]))
#end if
#end for
if len(energies) == 0:
self.E = 0.0
else:
self.E = energies[-1]
#end if
self.energies = array(energies)
except:
nx += 1
if self.info.warn:
self.warn('total energy read failed')
#end if
#end try
try:
# get bands and occupations
nfound = 0
index = -1
bands = obj()
bands.up = obj()
bands.down = obj()
polarized = False
if self.input.system.nspin > 1:
polarized = True
#end if
read_kpoints = False
read_2pi_alat = False
read_rel = False
for i in range(len(lines)):
l = lines[i]
if 'End of self-consistent calculation' in l:
# Initialize each time in case a hybrid functional was used
if nfound > 0:
nfound = 0
index = -1
bands = obj()
bands.up = obj()
bands.down = obj()
#end if
#end if
if '- SPIN UP -' in l:
up_spin = True
elif '- SPIN DOWN -' in l:
up_spin = False
index = -1
#end if
if 'number of k points=' in l:
try:
num_kpoints = int(l.strip().split()[4])
except:
print(
"Number of k-points {0} is not an integer".format(
num_kpoints))
#end try
kpoints_2pi_alat = lines[i + 2:i + 2 + num_kpoints]
kpoints_rel = lines[i + 4 + num_kpoints:i + 4 +
2 * num_kpoints]
kpoints_2pi_alat = array([
k.strip().split()[4:6] + [k.strip().split()[6][0:-2]]
for k in kpoints_2pi_alat
],
dtype=float)
kpoints_rel = array([
k.strip().split()[4:6] + [k.strip().split()[6][0:-2]]
for k in kpoints_rel
],
dtype=float)
#end if
if 'bands (ev)' in l:
index += 1
nfound += 1
i_occ = -1
j = i
while i_occ == -1:
j += 1
if 'occupation numbers' in lines[j]:
i_occ = j
#end if
#end while
seigs = ''
for j in range(i + 1, i_occ):
seigs += lines[j]
#end for
seigs = seigs.replace(
'-', ' -'
) # For cases where the eigenvalues "touch", e.g. -144.9938-144.9938 -84.3023
seigs = seigs.strip()
eigs = array(seigs.split(), dtype=float)
soccs = ''
for j in range(i_occ + 1, i_occ + 1 + (i_occ - i) - 2):
soccs += lines[j]
#end for
occs = array(soccs.split(), dtype=float)
bk = obj(
index=index,
kpoint_2pi_alat=kpoints_2pi_alat[index],
kpoint_rel=kpoints_rel[index],
eigs=eigs,
occs=occs,
pol='none',
)
band_channel = bands.up
if polarized:
if up_spin:
bk.pol = 'up'
elif not up_spin:
bk.pol = 'down'
band_channel = bands.down
#end if
else:
index = nfound - 1
#end if
band_channel.append(bk)
#if nfound==1:
# bands.up = obj(
# eigs = eigs,
# occs = occs
# )
#elif nfound==2:
# bands.down = obj(
# eigs = eigs,
# occs = occs
# )
#end if
#end if
#end for
vbm = obj(energy=-1.0e6)
cbm = obj(energy=1.0e6)
direct_gap = obj(energy=1.0e6)
for band_channel in bands:
for b in band_channel:
e_val = max(b.eigs[b.occs > 0.5])
e_cond = min(b.eigs[b.occs < 0.5])
if e_val > vbm.energy:
vbm.energy = e_val
vbm.kpoint_rel = b.kpoint_rel
vbm.kpoint_2pi_alat = b.kpoint_2pi_alat
vbm.index = b.index
vbm.pol = b.pol
vbm.band_number = max(where(b.occs > 0.5))
#end if
if e_cond < cbm.energy:
cbm.energy = e_cond
cbm.kpoint_rel = b.kpoint_rel
cbm.kpoint_2pi_alat = b.kpoint_2pi_alat
cbm.index = b.index
cbm.pol = b.pol
cbm.band_number = min(where(b.occs < 0.5))
#end if
if (e_cond - e_val) < direct_gap.energy:
direct_gap.energy = e_cond - e_val
direct_gap.kpoint_rel = b.kpoint_rel
direct_gap.kpoint_2pi_alat = b.kpoint_2pi_alat
direct_gap.index = b.index
direct_gap.pol = [vbm.pol, cbm.pol]
#end if
#end for
#end for
electronic_structure = ''
if (vbm.energy + 0.025) >= cbm.energy:
if vbm.band_number == cbm.band_number:
electronic_structure = 'metallic'
else:
electronic_structure = 'semi-metal'
#end if
else:
electronic_structure = 'insulating'
if not equal(vbm.kpoint_rel, cbm.kpoint_rel).all():
indirect_gap = obj(energy=round(cbm.energy - vbm.energy,
3),
kpoints=obj(vbm=vbm, cbm=cbm))
bands.indirect_gap = indirect_gap
#end if
bands.electronic_structure = electronic_structure
bands.vbm = vbm
bands.cbm = cbm
bands.direct_gap = direct_gap
if nfound > 0:
self.bands = bands
#end if
# Kayahan edited --end
except:
nx += 1
if self.info.warn:
self.warn('band read failed')
#end if
#end try
try:
# read structures
structures = obj()
i = 0
found = False
cont = False
while i < len(lines):
l = lines[i]
if l.find('CELL_PARAMETERS') != -1 and l.strip().startswith(
'CELL'):
conf = obj()
axes = []
cont = True
for d in (0, 1, 2):
i += 1
axes.append(array(lines[i].split(), dtype=float))
#end for
conf.axes = array(axes)
#end if
if l.find('ATOMIC_POSITIONS') != -1:
found = True
if not cont:
conf = obj()
#end if
atoms = []
positions = []
i += 1
tokens = lines[i].split()
while len(tokens) > 0 and tokens[0].lower() != 'end' and (
len(tokens) == 4 or
(len(tokens) == 7 and tokens[-1] in '01')):
atoms.append(tokens[0])
positions.append(array(tokens[1:4], dtype=float))
i += 1
tokens = lines[i].split()
#end while
conf.atoms = atoms
conf.positions = array(positions)
if 'crystal' in l.lower() and 'axes' in conf:
conf.positions = dot(conf.positions, conf.axes)
#end if
nconf = len(structures)
structures[nconf] = conf
cont = False
#end if
i += 1
#end while
if found:
self.structures = structures
#end if
except:
nx += 1
if self.info.warn:
self.warn('structure read failed')
#end if
#end try
#begin added by Yubo "Paul" Yang: cell, stress, pressure and volume
# 01/21/2016: grab cells in a vc-relax run, one at each optimization step
# 09/29/2016: obselete after rev7131
# grab stress, pressure and volume
try:
press = 0.
vol = 0.
for l in lines:
if l.find('unit-cell volume') != -1:
#vol = float( l.split('=')[-1].split()[-2] )
vol = l.split('=')[-1].split()[-2]
# end if
if (l.find('total') != -1) and (l.find('stress') != -1):
press = l.split('=')[-1]
# end if
# end for
self.pressure = float(press)
self.volume = float(vol)
except:
nx += 1
if self.info.warn:
self.warn('pressure/volume read failed')
#end if
#end try
try:
stress = []
nlines = len(lines)
i = 0
while i < nlines:
l = lines[i]
if l.find('total stress') != -1:
for j in range(3):
i += 1
stress.append(
list(np.array(lines[i].split(), dtype=float)))
#end for
#end if
i += 1
#end while
self.stress = stress
except:
nx += 1
if self.info.warn:
self.warn('stress read failed')
#end if
#end try
#end added by Yubo "Paul" Yang
try:
forces = []
tot_forces = []
i = 0
found = False
nlines = len(lines)
while i < nlines:
l = lines[i]
if l.find('Forces acting on atoms') != -1:
found = True
conf = obj()
aforces = []
found_atom = False
for j in range(10):
i += 1
if i < nlines and 'atom' in lines[i]:
found_atom = True
break
#end if
#end for
if found_atom:
tokens = lines[i].split()
while len(tokens) == 9 and tokens[4] == 'force':
aforces.append(tokens[6:])
i += 1
tokens = lines[i].split()
#end while
#end if
forces.append(aforces)
i += 1
elif 'Total force' in l:
tokens = l.split()
if len(tokens) == 9 and tokens[1] == 'force':
tot_forces.append(float(tokens[3]))
#end if
#end if
i += 1
#end while
if found:
self.forces = array(forces, dtype=float)
self.tot_forces = array(tot_forces)
max_forces = []
for f in self.forces:
if len(f.shape) == 2:
max_forces.append((sqrt((f**2).sum(1))).max())
#end if
#end for
self.max_forces = array(max_forces)
#end if
except:
nx += 1
if self.info.warn:
self.warn('force read failed')
#end if
#end try
try:
tc = 0.
tw = 0.
for l in lines:
if l.find('PWSCF :') != -1:
t1 = l.split(':')[1].split('CPU')
tc = pwscf_time(t1[0])
tw = pwscf_time(t1[1].replace('WALL', ''))
break
#end if
#end for
self.cputime = tc
self.walltime = tw
except:
nx += 1
if self.info.warn:
self.warn('time read failed')
#end if
#end try
try:
# read symmetrized k-points
nkpoints = None
i = 0
for l in lines:
if 'number of k points' in l:
tokens = l.replace('=', ' ').split()
nkpoints = int(tokens[4])
break
#end if
i += 1
#end for
if nkpoints is not None:
i += 2
klines_cart = lines[i:i + nkpoints]
i += nkpoints + 2
klines_unit = lines[i:i + nkpoints]
kpoints_cart = []
for l in klines_cart:
tokens = l.replace('= (', ':').replace('), wk =',
':').split(':')
kpoints_cart.append(tokens[1].split())
#end for
kpoints_unit = []
kweights = []
for l in klines_unit:
tokens = l.replace('= (', ':').replace('), wk =',
':').split(':')
kpoints_unit.append(tokens[1].split())
kweights.append(tokens[2])
#end for
self.kpoints_cart = array(kpoints_cart, dtype=float)
self.kpoints_unit = array(kpoints_unit, dtype=float)
self.kweights = array(kweights, dtype=float)
#end if
except:
nx += 1
if self.info.warn:
self.warn('symmetrized kpoint read failed')
#end if
#end try
try:
if pw2c_outfile_name != None:
lines = open(os.path.join(path, pw2c_outfile_name),
'r').readlines()
for l in lines:
if l.find('Kinetic') != -1:
tokens = l.split()
self.K = eval(tokens[5])
break
#end if
#end for
#end if
except:
nx += 1
if self.info.warn:
self.warn('pw2casino read failed')
#end if
#end try
if nx > 0 and self.info.warn:
self.warn(
'encountered an exception, some quantities will not be available'
)
#end try
if self.info.xml:
self.xmldata = obj(data=None, kpoints=None, failed=False)
try:
cont = self.input.control
datadir = os.path.join(self.path, cont.outdir,
cont.prefix + '.save')
data_file = os.path.join(datadir, 'data-file.xml')
if not os.path.exists(data_file):
datadir = os.path.join(self.path, cont.outdir)
data_file = os.path.join(datadir, cont.prefix + '.xml')
#end if
data = read_qexml(data_file)
kpdata = data.root.eigenvalues.k_point
kpoints = obj()
for ki, kpd in kpdata.items():
kp = obj(kpoint=kpd.k_point_coords, weight=kpd.weight)
kpoints[ki] = kp
for si, dfile in kpd.datafile.items():
efilepath = os.path.join(datadir, dfile.iotk_link)
if os.path.exists(efilepath):
edata = read_qexml(efilepath)
eunits = edata.root.units_for_energies.units.lower(
)
if eunits.startswith('ha'):
units = 'Ha'
elif eunits.startswith('ry'):
units = 'Ry'
elif eunits.startswith('ev'):
units = 'eV'
else:
units = 'Ha'
#end if
spin = obj(units=units,
eigenvalues=edata.root.eigenvalues,
occupations=edata.root.occupations)
if si == 1:
kp.up = spin
elif si == 2:
kp.down = spin
#end if
else:
self.xmldata.failed = True
#end if
#end for
#end for
self.xmldata.set(data=data, kpoints=kpoints)
except Exception as e:
if self.info.warn:
self.warn(
'encountered an exception during xml read, this data will not be available\nexception encountered: '
+ str(e))
#end if
self.xmldata.failed = True
def open_log(self):
logfile = os.path.join(self.info.path, self.info.outfile)
self.log = TextFile(logfile)