def inUnit(self, unit):
unitStr = self.unit + '-' + unit
if not unitStr.lower() == 'eh-eh':
self.Et, self.unit = qtk.convE(self.Et, unitStr)
if hasattr(self, 'energies'):
for key in self.energies.keys():
self.energies[key], _ = qtk.convE(self.energies[key], unitStr)
return self
def inUnit(self, unit):
unitStr = self.unit + '-' + unit
if not unitStr.lower() == 'eh-eh':
self.Et, self.unit = qtk.convE(self.Et, unitStr)
if hasattr(self, 'energies'):
for key in self.energies.keys():
self.energies[key], _ = qtk.convE(self.energies[key],
unitStr)
return self
def __sub__(self, other):
out = copy.deepcopy(self)
if isinstance(other, qtk.QM.general_io.GenericQMOutput):
if self.unit == other.unit:
out.Et = self.Et - other.Et
else:
unitStr = self.unit + '-' + other.unit
out.Et = self.Et + qtk.convE(other.Et, unitStr, '-')
out.scf_step = max(self.scf_step, other.scf_step)
elif (type(other) is int) or (type(other) is float):
out.Et = self.Et - other
else:
out.Et = np.nan
return out
def __sub__(self, other):
out = copy.deepcopy(self)
if isinstance(other, qtk.QM.general_io.GenericQMOutput):
if self.unit == other.unit:
out.Et = self.Et - other.Et
else:
unitStr = self.unit + '-' + other.unit
out.Et = self.Et + qtk.convE(other.Et, unitStr, '-')
out.scp_step = max(self.scf_step, other.scf_step)
elif (type(other) is int) or (type(other) is float):
out.Et = self.Et - other
else:
out.Et = np.nan
return out
def unfold(self,
k_path,
folds,
epsilon=1E-5,
WFK=None,
overwrite=False,
shift=None,
**kwargs):
path = self.path
cwd = os.getcwd()
os.chdir(path)
f2b_list = sorted(glob.glob('*.f2b'))
if not f2b_list or overwrite:
if not WFK:
WFK_card = '%s/*_WFK' % path
WFK_list = sorted(glob.glob(WFK_card))
if len(WFK_list) > 0:
WFK = WFK_list[-1]
else:
qtk.exit('wavefunction file not found.')
exe = qtk.setting.abinit_f2b_exe
log_name = '%s_f2b.log' % self.name
log = open(log_name, 'w')
fold_str = [str(f) for f in folds]
cmd_str = "%s %s %s" % (exe, WFK, ':'.join(fold_str))
run = sp.Popen(cmd_str, shell=True, stdout=log)
run.wait()
log.close()
f2b_list = sorted(glob.glob('*.f2b'))
f2b = f2b_list[0]
k_path = np.asarray(k_path)
def dp2l_vec(X0_list, p0, p1):
eps = epsilon
denom = p1 - p0
denomabs = np.linalg.norm(denom)
if denomabs < eps:
return False
numer = np.cross(X0_list - p0[np.newaxis, :],
X0_list - p1[np.newaxis, :])
return np.linalg.norm(numer, axis=1) / denomabs
_data = read_csv(f2b,
delim_whitespace=True,
dtype='float64',
header=None).values
os.chdir(cwd)
KEIG = _data[:, :3]
EIG = np.array(_data[:, 3]) * qtk.convE(1, 'Ha-ev')[0]
if not hasattr(self, 'fermi_index'):
self.fermi_index = self.molecule.getValenceElectrons() / 2 - 1
if not shift:
EIG = EIG - np.max(self.band[:, self.fermi_index])
else:
EIG = EIG - shift
EIG = EIG.tolist()
W = _data[:, 4]
L = []
ENE = []
WGHT = []
G = self.G_lattice.copy()
for i in range(3):
G[i, :] = G[i, :] * folds[i]
k_path = k_path.dot(G)
KEIG = KEIG.dot(G)
itr_test = 0
dl = 0
for ikp in range(len(k_path) - 1):
itr = 0
p0 = k_path[ikp, :]
p1 = k_path[ikp + 1, :]
B = p0 - p1
dk = np.linalg.norm(B)
dist_vec = dp2l_vec(KEIG, p0, p1)
ind1 = (dist_vec < epsilon)
A_vec = (p0[np.newaxis, :] - KEIG)[ind1]
x_vec = A_vec.dot(B.T) / dk
ind2 = (x_vec > 0) * ((x_vec - dk) < epsilon)
L.extend((x_vec[ind2] + dl).tolist())
ENE.extend(np.asarray(EIG)[ind1][ind2].tolist())
WGHT.extend(np.asarray(W)[ind1][ind2].tolist())
dl = dl + dk
L = np.array(L, dtype='float64')
ENE = np.array(ENE, dtype='float64')
WGHT = np.array(WGHT, dtype='float64')
return L, ENE, WGHT
def __init__(self, qmout, **kwargs):
PlanewaveOutput.__init__(self, qmout, **kwargs)
out_file = open(qmout)
data = out_file.readlines()
out_file.close()
EStrList = filter(lambda x: 'Etotal' in x, data)
EList = filter(lambda x: 'ETOT' in x, data)
self.scf_step = len(EList)
if self.scf_step > 0:
Et_list = [float(filter(None, s.split(' '))[2]) for s in EList]
self.Et = Et_list[-1]
elif len(EStrList) > 0:
EStr = EStrList[-1]
self.Et = float(EStr.split(' ')[-1])
if len(EStrList) > 0:
EStr = EStrList[-1]
detailInd = data.index(EStr)
self.detail = data[detailInd - 7:detailInd]
GStr = filter(lambda x: 'G(1)' in x, data)[-1]
ind_g = len(data) - data[::-1].index(GStr) - 1
G_lattice = []
for i in range(3):
G_lattice.append(
np.fromstring(data[ind_g + i].split('=')[-1], sep=' '))
self.G_lattice = np.array(G_lattice)
xangst = filter(lambda x: 'xangst' in x, data)[-1]
angst_n = len(data) - data[::-1].index(xangst) - 1
xcart = filter(lambda x: 'xcart' in x, data)[-1]
cart_n = len(data) - data[::-1].index(xcart) - 1
Rstr = copy.deepcopy(data[angst_n:cart_n])
Rstr[0] = Rstr[0].replace('xangst', '')
R = [[float(r) for r in filter(None, s.split(' '))] for s in Rstr]
N = len(R)
ZstrOriginal = filter(lambda x: ' typat' in x, data)[-1]
Zstr = ZstrOriginal.replace('typat', '')
Zind = [int(z) for z in filter(None, Zstr.split(' '))]
ZindItr = data.index(ZstrOriginal)
while len(Zind) != N:
ZindItr += 1
ZindNewStr = filter(None, data[ZindItr].split(' '))
ZindNew = [int(z) for z in ZindNewStr]
Zind.extend(ZindNew)
NZnuc = filter(lambda x: 'ntypat' in x, data)[-1]
NZnuc = int(filter(None, NZnuc.split(' '))[-1])
Znuc = filter(lambda x: 'znucl ' in x, data)[-1]
line_znuc = len(data) - data[::-1].index(Znuc)
Znuc = filter(None, Znuc.replace('znucl', '').split(' '))
Znuc = [float(z) for z in Znuc]
while len(Znuc) < NZnuc:
Znuc_new = filter(None, data[line_znuc].split(' '))
Znuc_new = [float(z) for z in Znuc_new]
Znuc.extend(Znuc_new)
line_znuc = line_znuc + 1
build = []
for i in range(N):
Z = [Znuc[Zind[i] - 1]]
Z.extend(R[i])
build.append(Z)
self.molecule = qtk.Molecule()
self.molecule.build(build)
if self.scf_step > 0:
fStr = filter(lambda x: 'tesian forces (hartree/b' in x, data)[-1]
fInd = data.index(fStr)
fData = data[fInd + 1:fInd + 1 + N]
force = []
for f in fData:
fStr = filter(None, f.split(' '))[1:]
force.append([float(fs) for fs in fStr])
self.force = np.array(force)
self.occupation = []
try:
r1p = re.compile(r'^[ a-z]{17} +[ 0-9.E+-]+$')
r2p = re.compile(r'^ +[a-z]+ +.*$')
report = filter(r2p.match, filter(r1p.match, data))
occ_ptn_lst = filter(lambda x: ' occ ' in x, report)
if len(occ_ptn_lst) > 0:
occ_pattern = occ_ptn_lst[-1]
occ_pattern_ind = len(report) - report[::-1].index(occ_pattern)
occ_pattern_end = report[occ_pattern_ind]
occ_ind_start = len(data) - data[::-1].index(occ_pattern) - 1
occ_ind_end = len(data) - data[::-1].index(occ_pattern_end) - 1
for i in range(occ_ind_start, occ_ind_end):
for occ in filter(None, data[i].split(' ')):
try:
self.occupation.append(float(occ))
except Exception as err:
pass
except Exception as err:
qtk.warning("error when extracting occupation number with" +\
" error message: %s" % str(err))
cell_pattern = re.compile(r'^ R.*=.* G.*=.*$')
cell_list = filter(cell_pattern.match, data)
cell = []
for cstr in cell_list:
cell.append([float(c) for c in filter(None, cstr.split(' '))[1:4]])
self.lattice = np.array(cell) / 1.889726124993
self.celldm = qtk.lattice2celldm(self.lattice)
self.molecule.R_scale = qtk.xyz2fractional(self.molecule.R,
self.celldm)
eigStr = os.path.join(os.path.split(qmout)[0], '*_EIG')
eigFileList = sorted(glob.glob(eigStr))
if len(eigFileList) != 0:
if 'eig_index' in kwargs:
eig_i = kwargs['eig_index']
else:
eig_i = -1
if len(eigFileList) > 1:
qtk.warning(
"more than one o_EIG files found " + \
"loading last file with name: %s" % eigFileList[eig_i]
)
eigFile = open(eigFileList[eig_i])
eigData = eigFile.readlines()
eigFile.close()
unitStr = filter(lambda x: 'Eigenvalues' in x, eigData)[0]
unitStr = unitStr.replace('(', '').replace(')', '')
unit = filter(None, unitStr.split(' '))[1]
spinList = filter(lambda x: 'SPIN' in x, eigData)
if len(spinList) != 0:
spinFactor = 2
maxInd = eigData.index(spinList[-1])
else:
spinFactor = 1
maxInd = len(eigData)
ind = []
for kStr in filter(lambda x: 'kpt#' in x, eigData):
ind.append(eigData.index(kStr))
band = []
kpoints = []
if spinFactor == 1:
for i in range(len(ind)):
wcoord = eigData[ind[i]].split('wtk=')[-1].split(', kpt=')
weight = float(wcoord[0])
cStr = filter(None, wcoord[1].split('(')[0].split(' '))
coord = [float(c) for c in cStr]
coord.append(weight)
kpoints.append(coord)
s = ind[i] + 1
if i < len(ind) - 1:
e = ind[i + 1]
else:
e = len(eigData)
eig_i = filter(None, ''.join(eigData[s:e]).split(' '))
band.append([
qtk.convE(float(ew), '%s-eV' % unit)[0] for ew in eig_i
])
self.band = np.array(band)
self.kpoints = np.array(kpoints)
self.mo_eigenvalues = np.array(band[0]).copy()
if len(self.occupation) > 0:
diff = np.diff(self.occupation)
ind = np.array(range(len(diff)))
pos = diff[np.where(abs(diff) > 0.5)]
mask = np.in1d(diff, pos)
if len(ind[mask]) > 0:
N_state = ind[mask][0]
else:
qtk.warning("occupation number not available... " + \
"try to use molecule object with closed shell assumption"
)
N_state = self.molecule.getValenceElectrons() / 2 - 1
vb = max(self.band[:, N_state])
cb = min(self.band[:, N_state + 1])
vb_pos = np.argmax(self.band[:, N_state])
cb_pos = np.argmin(self.band[:, N_state + 1])
self.Eg = cb - vb
if vb_pos == cb_pos:
self.Eg_direct = True
else:
self.Eg_direct = False
self.fermi_index = N_state
else:
qtk.warning("spin polarized band data " +\
"extraction is not yet implemented")
else:
qtk.warning('no k-point information (o_EIG file) found')
def __init__(self, qmout, **kwargs):
PlanewaveOutput.__init__(self, qmout, **kwargs)
out_file = open(qmout)
data = out_file.readlines()
out_file.close()
Et_pattern = re.compile("^.*total energy *=.*$")
f_pattern = re.compile("^.*atom.*type.*force.*=.*$")
Et_list = filter(Et_pattern.match, data)
f_list = filter(f_pattern.match, data)
if len(Et_list) > 0:
Et_str = filter(Et_pattern.match, data)[-1]
Et = float(Et_str.split()[-2])
self.Et, self.unit = qtk.convE(Et, 'Ry-Eh')
out_folder = os.path.split(os.path.abspath(qmout))[0]
save = glob.glob(os.path.join(out_folder, '*.save'))
# extract force information
if len(f_list) > 0:
fstr = [filter(None, fstr.split('=')[-1].split(' '))
for fstr in f_list]
# atomic unit force, HF/au, converted from Ry/au
self.force = 0.5 * np.array(
[[float(comp) for comp in atm] for atm in fstr]
)
# extract band structure from xml files
if save:
save = save[0]
try:
data_xml = os.path.join(save, 'data-file.xml')
xml_file = open(data_xml)
tree = ET.parse(xml_file)
xml_file.close()
self.xml = tree.getroot()
kpoints = []
band = []
# extract celldm
celldm = []
cellVec = []
for i in range(1, 4):
cellvStr = filter(None,
self.xml[2][4][i].text.replace('\n', '').split(' ')
)
cellVec.append([float(v) for v in cellvStr])
self.celldm = qtk.cellVec2celldm(cellVec)
# extract structure
R = []
N = int(self.xml[3][0].text.replace('\n', ''))
Nsp = int(self.xml[3][1].text.replace('\n', ''))
for i in range(N):
RiStr = self.xml[3][5+Nsp+i].get('tau')
Ri = [float(r) * 0.529177249 for r in RiStr.split(' ')]
ni = self.xml[3][5+Nsp+i].get('SPECIES')
Z = [qtk.n2Z(ni)]
Z.extend(Ri)
R.append(Z)
self.molecule = qtk.Molecule()
self.molecule.build(R)
# access data for each kpoint
for k in self.xml[-2]:
k_str = k[0].text
coord = [float(c) for c in k_str.split()]
weight = float(k[1].text.split()[0])
coord.append(weight)
kpoints.append(coord)
ev_file = os.path.join(save, k[2].attrib['iotk_link'])
k_xml_file = open(ev_file)
k_xml = ET.parse(k_xml_file)
k_xml_file.close()
ev_k = k_xml.getroot()
ev_str = ev_k[2].text.split()
ev = [qtk.convE(float(entry), 'Eh-eV')[0]\
for entry in ev_str]
band.append(ev)
occ_str = ev_k[3].text.split()
occ = [float(entry) for entry in occ_str]
self.kpoints = np.array(kpoints)
self.mo_eigenvalues = copy.deepcopy(band[0])
self.band = np.array(band)
self.occupation = occ
diff = np.diff(occ)
pos = diff[np.where(abs(diff) > 0.5)]
mask = np.in1d(diff, pos)
ind = np.array(range(len(diff)))
if len(ind[mask]) > 0:
N_state = ind[mask][0]
vb = max(self.band[:, N_state])
cb = min(self.band[:, N_state + 1])
vb_pos = np.argmax(self.band[:, N_state])
cb_pos = np.argmin(self.band[:, N_state + 1])
self.Eg = cb - vb
if vb_pos == cb_pos:
self.Eg_direct = True
else:
self.Eg_direct = False
cell = []
for i in range(1, 4):
vec = filter(
None,
self.xml[2][4][i].text.replace('\n', '').split(' '))
cell.append([float(v) for v in vec])
self.lattice = np.array(cell) / 1.889726124993
self.celldm = qtk.lattice2celldm(self.lattice)
self.molecule.R_scale = qtk.xyz2fractional(
self.molecule.R, self.celldm)
except IOError:
qtk.warning('xml file of job %s not found' % qmout)
else:
qtk.warning('job %s not finished' % qmout)
def __init__(self, qmout, **kwargs):
PlanewaveOutput.__init__(self, qmout, **kwargs)
out_file = open(qmout)
data = out_file.readlines()
out_file.close()
Et_pattern = re.compile("^.*total energy *=.*$")
f_pattern = re.compile("^.*atom.*type.*force.*=.*$")
Et_list = filter(Et_pattern.match, data)
f_list = filter(f_pattern.match, data)
if len(Et_list) > 0:
Et_str = filter(Et_pattern.match, data)[-1]
Et = float(Et_str.split()[-2])
self.Et, self.unit = qtk.convE(Et, 'Ry-Eh')
out_folder = os.path.split(os.path.abspath(qmout))[0]
save = glob.glob(os.path.join(out_folder, '*.save'))
# extract force information
if len(f_list) > 0:
fstr = [
filter(None,
fstr.split('=')[-1].split(' ')) for fstr in f_list
]
# atomic unit force, HF/au, converted from Ry/au
self.force = 0.5 * np.array([[float(comp) for comp in atm]
for atm in fstr])
# extract band structure from xml files
if save:
save = save[0]
try:
data_xml = os.path.join(save, 'data-file.xml')
xml_file = open(data_xml)
tree = ET.parse(xml_file)
xml_file.close()
self.xml = tree.getroot()
kpoints = []
band = []
# extract celldm
celldm = []
cellVec = []
for i in range(1, 4):
cellvStr = filter(
None,
self.xml[2][4][i].text.replace('\n',
'').split(' '))
cellVec.append([float(v) for v in cellvStr])
self.celldm = qtk.cellVec2celldm(cellVec)
# extract structure
R = []
N = int(self.xml[3][0].text.replace('\n', ''))
Nsp = int(self.xml[3][1].text.replace('\n', ''))
for i in range(N):
RiStr = self.xml[3][5 + Nsp + i].get('tau')
Ri = [float(r) * 0.529177249 for r in RiStr.split(' ')]
ni = self.xml[3][5 + Nsp + i].get('SPECIES')
Z = [qtk.n2Z(ni)]
Z.extend(Ri)
R.append(Z)
self.molecule = qtk.Molecule()
self.molecule.build(R)
# access data for each kpoint
for k in self.xml[-2]:
k_str = k[0].text
coord = [float(c) for c in k_str.split()]
weight = float(k[1].text.split()[0])
coord.append(weight)
kpoints.append(coord)
ev_file = os.path.join(save, k[2].attrib['iotk_link'])
k_xml_file = open(ev_file)
k_xml = ET.parse(k_xml_file)
k_xml_file.close()
ev_k = k_xml.getroot()
ev_str = ev_k[2].text.split()
ev = [qtk.convE(float(entry), 'Eh-eV')[0]\
for entry in ev_str]
band.append(ev)
occ_str = ev_k[3].text.split()
occ = [float(entry) for entry in occ_str]
self.kpoints = np.array(kpoints)
self.mo_eigenvalues = copy.deepcopy(band[0])
self.band = np.array(band)
self.occupation = occ
diff = np.diff(occ)
pos = diff[np.where(abs(diff) > 0.5)]
mask = np.in1d(diff, pos)
ind = np.array(range(len(diff)))
if len(ind[mask]) > 0:
N_state = ind[mask][0]
vb = max(self.band[:, N_state])
cb = min(self.band[:, N_state + 1])
vb_pos = np.argmax(self.band[:, N_state])
cb_pos = np.argmin(self.band[:, N_state + 1])
self.Eg = cb - vb
if vb_pos == cb_pos:
self.Eg_direct = True
else:
self.Eg_direct = False
cell = []
for i in range(1, 4):
vec = filter(
None,
self.xml[2][4][i].text.replace('\n',
'').split(' '))
cell.append([float(v) for v in vec])
self.lattice = np.array(cell) / 1.889726124993
self.celldm = qtk.lattice2celldm(self.lattice)
self.molecule.R_scale = qtk.xyz2fractional(
self.molecule.R, self.celldm)
except IOError:
qtk.warning('xml file of job %s not found' % qmout)
else:
qtk.warning('job %s not finished' % qmout)
def __init__(self, qmout, **kwargs):
PlanewaveOutput.__init__(self, qmout, **kwargs)
out_file = open(qmout)
data = out_file.readlines()
out_file.close()
EStrList = filter(lambda x: 'Etotal' in x, data)
EList = filter(lambda x: 'ETOT' in x, data)
self.scf_step = len(EList)
if self.scf_step > 0:
Et_list = [float(filter(None, s.split(' '))[2]) for s in EList]
self.Et = Et_list[-1]
elif len(EStrList) > 0:
EStr = EStrList[-1]
self.Et = float(EStr.split(' ')[-1])
if len(EStrList) > 0:
EStr = EStrList[-1]
detailInd = data.index(EStr)
self.detail = data[detailInd-7:detailInd]
xangst = filter(lambda x: 'xangst' in x, data)[-1]
angst_n = len(data) - data[::-1].index(xangst) - 1
xcart = filter(lambda x: 'xcart' in x, data)[-1]
cart_n = len(data) - data[::-1].index(xcart) - 1
Rstr = copy.deepcopy(data[angst_n:cart_n])
Rstr[0] = Rstr[0].replace('xangst', '')
R = [[float(r) for r in filter(None, s.split(' '))] for s in Rstr]
N = len(R)
ZstrOriginal = filter(lambda x: ' typat' in x, data)[-1]
Zstr = ZstrOriginal.replace('typat', '')
Zind = [int(z) for z in filter(None, Zstr.split(' '))]
ZindItr = data.index(ZstrOriginal)
while len(Zind) != N:
ZindItr += 1
ZindNewStr = filter(None, data[ZindItr].split(' '))
ZindNew = [int(z) for z in ZindNewStr]
Zind.extend(ZindNew)
Znuc = filter(lambda x: 'znucl ' in x, data)[-1]
Znuc = filter(None, Znuc.replace('znucl', '').split(' '))
Znuc = [float(z) for z in Znuc]
build = []
for i in range(N):
Z = [Znuc[Zind[i]-1]]
Z.extend(R[i])
build.append(Z)
self.molecule = qtk.Molecule()
self.molecule.build(build)
if self.scf_step > 0:
fStr = filter(lambda x: 'tesian forces (hartree/b' in x, data)[-1]
fInd = data.index(fStr)
fData = data[fInd+1:fInd+1+N]
force = []
for f in fData:
fStr = filter(None, f.split(' '))[1:]
force.append([float(fs) for fs in fStr])
self.force = np.array(force)
self.occupation = []
try:
r1p = re.compile(r'^[ a-z]{17} +[ 0-9.E+-]+$')
r2p = re.compile(r'^ +[a-z]+ +.*$')
report = filter(r2p.match, filter(r1p.match, data))
occ_pattern = filter(lambda x: ' occ ' in x, report)[-1]
occ_pattern_ind = len(report) - report[::-1].index(occ_pattern)
occ_pattern_end = report[occ_pattern_ind]
occ_ind_start = len(data) - data[::-1].index(occ_pattern) - 1
occ_ind_end = len(data) - data[::-1].index(occ_pattern_end) - 1
for i in range(occ_ind_start, occ_ind_end):
for occ in filter(None, data[i].split(' ')):
try:
self.occupation.append(float(occ))
except:
pass
except Exception as err:
qtk.warning("error when extracting occupation number with" +\
" error message: %s" % str(err))
cell_pattern = re.compile(r'^ R.*=.* G.*=.*$')
cell_list = filter(cell_pattern.match, data)
cell = []
for cstr in cell_list:
cell.append(
[float(c) for c in filter(None, cstr.split(' '))[1:4]])
self.lattice = np.array(cell) / 1.889726124993
self.celldm = qtk.lattice2celldm(self.lattice)
self.molecule.R_scale = qtk.xyz2fractional(
self.molecule.R, self.celldm)
eigStr = os.path.join(os.path.split(qmout)[0], '*_EIG')
eigFileList = glob.glob(eigStr)
if len(eigFileList) != 0:
if len(eigFileList) > 1:
qtk.warning("more than one o_EIG files found")
eigFile = open(eigFileList[0])
eigData = eigFile.readlines()
eigFile.close()
spinList = filter(lambda x: 'SPIN' in x, eigData)
if len(spinList) != 0:
spinFactor = 2
maxInd = eigData.index(spinList[-1])
else:
spinFactor = 1
maxInd = len(eigData)
ind = []
for kStr in filter(lambda x: 'kpt#' in x, eigData):
ind.append(eigData.index(kStr))
band = []
kpoints = []
if spinFactor == 1:
for i in range(len(ind)):
wcoord = eigData[ind[i]].split('wtk=')[-1].split(', kpt=')
weight = float(wcoord[0])
cStr = filter(None, wcoord[1].split('(')[0].split(' '))
coord = [float(c) for c in cStr]
coord.append(weight)
kpoints.append(coord)
s = ind[i] + 1
if i < len(ind) - 1:
e = ind[i+1]
else:
e = len(eigData)
eig_i = filter(None, ''.join(eigData[s:e]).split(' '))
band.append([qtk.convE(float(ew), 'Eh-eV')[0]
for ew in eig_i])
self.band = np.array(band)
self.kpoints = np.array(kpoints)
self.mo_eigenvalues = np.array(band[0]).copy()
if len(self.occupation) > 0:
diff = np.diff(self.occupation)
ind = np.array(range(len(diff)))
pos = diff[np.where(abs(diff) > 0.5)]
mask = np.in1d(diff, pos)
if len(ind[mask]) > 0:
N_state = ind[mask][0]
vb = max(self.band[:, N_state])
cb = min(self.band[:, N_state + 1])
vb_pos = np.argmax(self.band[:, N_state])
cb_pos = np.argmin(self.band[:, N_state + 1])
self.Eg = cb - vb
if vb_pos == cb_pos:
self.Eg_direct = True
else:
self.Eg_direct = False
else:
qtk.warning("spin polarized band data " +\
"extraction is not yet implemented")
else:
qtk.warning('no k-point information (o_EIG file) found')
def __init__(self, qmoutXML, **kwargs):
PlanewaveOutput.__init__(self, qmoutXML, **kwargs)
if qmoutXML:
#xml_file = open(qmoutXML)
tree = ET.parse(qmoutXML)
#xml_file.close()
self.xml = tree.getroot()
self.Et, self.unit = qtk.convE(float(self.xml[-2][-5][1].text),
'eV-Eh', '-')
self.info = self.xml[0][1].text
self.SCFStep = len(self.xml[-2]) - 9
try:
# kpoints and band structure data
kpoints = []
band = []
occ = []
ktag = self.xml[2]
if ktag.tag != 'kpoints':
qtk.exit("vasp xml structure for kpoints unexpected")
if ktag[0].tag == 'generation':
k_ind = 1
elif ktag[0].tag == 'varray':
k_ind = 0
else:
qtk.exit("vasp xml for kpointss has unexpected tag: %s" %
ktag[0].tag)
for i in range(len(ktag[k_ind])):
k_str = ktag[k_ind][i].text
weight = float(ktag[k_ind + 1][i].text)
band_k = []
occ_k = []
bk_xml = self.xml[-2][-3][0][5][0][i]
for b_xml in bk_xml:
b, o = [float(c) for c in b_xml.text.split()]
band_k.append(b)
occ_k.append(o)
coord = [float(c) for c in k_str.split()]
coord.append(weight)
kpoints.append(coord)
band.append(band_k)
occ.append(occ_k)
self.mo_eigenvalues = copy.deepcopy(band[0])
self.kpoints = np.array(kpoints)
self.band = np.array(band)
self.occupation = occ[0]
diff = np.diff(occ[0])
pos = diff[np.where(abs(diff) > 0.5)]
mask = np.in1d(diff, pos)
ind = np.array(range(len(diff)))
if len(ind[mask]) > 0:
N_state = ind[mask][0]
vb = max(self.band[:, N_state])
cb = min(self.band[:, N_state + 1])
vb_pos = np.argmax(self.band[:, N_state])
cb_pos = np.argmin(self.band[:, N_state + 1])
self.Eg = cb - vb
if vb_pos == cb_pos:
self.Eg_direct = True
else:
self.Eg_direct = False
ind = np.arange(len(self.kpoints))[self.kpoints[:, -1] == 0]
if len(ind > 0):
ind_w = np.arange(len(
self.kpoints))[self.kpoints[:, -1] != 0]
self.band_weighted = self.band[ind_w]
self.kpoints_weighted = self.kpoints[ind_w]
self.band = self.band[ind]
self.kpoints = self.kpoints[ind]
# DOS data
dos = []
self.E_fermi = float(self.xml[-2][-1][0].text)
for dos_xml in self.xml[-2][-1][1][0][5][0]:
dos_lst = filter(None, dos_xml.text.split(' '))
dos_E = [float(d) for d in dos_lst]
dos.append(dos_E)
self.dos = np.array(dos)
except Exception as err:
qtk.warning("error when accessing kpoint data for %s with err: %s"\
% (self.name, err))
def __init__(self, qmoutXML, **kwargs):
PlanewaveOutput.__init__(self, qmoutXML, **kwargs)
if qmoutXML:
#xml_file = open(qmoutXML)
tree = ET.parse(qmoutXML)
#xml_file.close()
self.xml = tree.getroot()
self.Et, self.unit = qtk.convE(float(self.xml[-2][-5][1].text),
'eV-Eh', '-')
self.info = self.xml[0][1].text
self.SCFStep = len(self.xml[-2])-9
try:
# kpoints and band structure data
kpoints = []
band = []
occ = []
for i in range(len(self.xml[2][1])):
k_str = self.xml[2][1][i].text
weight = float(self.xml[2][2][i].text)
band_k = []
occ_k = []
bk_xml = self.xml[-2][-3][0][5][0][i]
for b_xml in bk_xml:
b, o = [float(c) for c in b_xml.text.split()]
band_k.append(b)
occ_k.append(o)
coord = [float(c) for c in k_str.split()]
coord.append(weight)
kpoints.append(coord)
band.append(band_k)
occ.append(occ_k)
self.mo_eigenvalues = copy.deepcopy(band[0])
self.kpoints = np.array(kpoints)
self.band = np.array(band)
self.occupation = occ[0]
diff = np.diff(occ[0])
pos = diff[np.where(abs(diff) > 0.5)]
mask = np.in1d(diff, pos)
ind = np.array(range(len(diff)))
if len(ind[mask]) > 0:
N_state = ind[mask][0]
vb = max(self.band[:, N_state])
cb = min(self.band[:, N_state + 1])
vb_pos = np.argmax(self.band[:, N_state])
cb_pos = np.argmin(self.band[:, N_state + 1])
self.Eg = cb - vb
if vb_pos == cb_pos:
self.Eg_direct = True
else:
self.Eg_direct = False
# DOS data
dos = []
self.E_fermi = float(self.xml[-2][-1][0].text)
print self.E_fermi
for dos_xml in self.xml[-2][-1][1][0][5][0]:
dos_lst = filter(None, dos_xml.text.split(' '))
dos_E = [float(d) for d in dos_lst]
dos.append(dos_E)
self.dos = np.array(dos)
except:
qtk.warning("error when accessing kpoint data for %s"\
% self.name)
def findBonds(self, ratio=setting.bond_ratio, **kwargs):
del self.segments
del self.bond_types
self.segments = []
self.bond_types = {}
if 'no_report' not in kwargs or not kwargs['no_report']:
qtk.report("Molecule",
"finding bonds with cutoff ratio",
ratio)
def to_graph(l):
G = networkx.Graph()
for part in l:
# each sublist is a bunch of nodes
G.add_nodes_from(part)
# it also imlies a number of edges:
G.add_edges_from(to_edges(part))
return G
def to_edges(l):
"""
treat `l` as a Graph and returns it's edges
to_edges(['a','b','c','d']) -> [(a,b), (b,c),(c,d)]
"""
it = iter(l)
last = next(it)
for current in it:
yield last, current
last = current
itr = 0
bond_list = []
bonded = [False for i in range(self.N)]
for i in xrange(self.N):
for j in xrange(i+1, self.N):
d_ij = np.linalg.norm(self.R[i,:] - self.R[j,:])
atom_i = getattr(pt, self.type_list[i])
atom_j = getattr(pt, self.type_list[j])
Ri = atom_i.covalent_radius + \
atom_i.covalent_radius_uncertainty
Rj = atom_j.covalent_radius + \
atom_j.covalent_radius_uncertainty
Dij = (Ri+Rj) * float(ratio)
if d_ij < Dij:
bonded[i] = True
bonded[j] = True
if self.Z[i] < self.Z[j]:
atom_begin = self.Z[i]
atom_end = self.Z[j]
index_begin = i
index_end = j
else:
atom_begin = self.Z[j]
atom_end = self.Z[i]
index_begin = j
index_end = i
self.bonds[itr] = {'atom_begin' : atom_begin,
'index_begin' : index_begin,
'atom_end' : atom_end,
'index_end' : index_end,
'length' : d_ij}
bond_list.append([i, j])
type_begin = qtk.Z2n(atom_begin)
type_end = qtk.Z2n(atom_end)
bond_table = qtk.data.elements.bond_table
bond_keys = []
bond_keys = [
type_begin + _ + type_end for _ in ['-', '=', '#']
]
try:
bond_type_ind = np.argmin(
abs(
np.array([
bond_table[k][0] for k in bond_keys
if k in bond_table.keys()
]) - d_ij
)
)
except Exception as _e:
self.write_xyz()
qtk.exit(
"error while processing bond" +\
str(bond_keys) + "with error message %s" % str(_e))
bond_type = bond_keys[bond_type_ind]
self.bonds[itr]['name'] = bond_type
bond_energy = \
bond_table[bond_keys[bond_type_ind]][1] * \
qtk.convE(1, 'kj-kcal')[0]
self.bonds[itr]['energy'] = bond_energy
if np.isnan(bond_energy):
qtk.warning("Non-tabliated covalent bond %s" % bond_type)
if bond_type in self.bond_types:
self.bond_types[bond_type] += 1
else:
self.bond_types[bond_type] = 1
itr += 1
segments = list(connected_components(to_graph(bond_list)))
for s in range(len(segments)):
segment = list(segments[s])
new_mol = self.getSegment(segment, **kwargs)
ns = len(self.segments)
new_mol.name = new_mol.name + '_%d' % ns
self.segments.append(new_mol)
for s in [i for i in range(self.N) if not bonded[i]]:
segment = [s]
new_mol = self.getSegment(segment, **kwargs)
ns = len(self.segments)
new_mol.name = new_mol.name + '_%d' % ns
self.segments.append(new_mol)
def findBonds(self, ratio=setting.bond_ratio, **kwargs):
del self.segments
del self.bond_types
self.segments = []
self.bond_types = {}
if 'no_report' not in kwargs or not kwargs['no_report']:
qtk.report("Molecule",
"finding bonds with cutoff ratio",
ratio)
def to_graph(l):
G = networkx.Graph()
for part in l:
# each sublist is a bunch of nodes
G.add_nodes_from(part)
# it also imlies a number of edges:
G.add_edges_from(to_edges(part))
return G
def to_edges(l):
"""
treat `l` as a Graph and returns it's edges
to_edges(['a','b','c','d']) -> [(a,b), (b,c),(c,d)]
"""
it = iter(l)
last = next(it)
for current in it:
yield last, current
last = current
itr = 0
bond_list = []
bonded = [False for i in range(self.N)]
for i in xrange(self.N):
for j in xrange(i+1, self.N):
d_ij = np.linalg.norm(self.R[i,:] - self.R[j,:])
atom_i = getattr(pt, self.type_list[i])
atom_j = getattr(pt, self.type_list[j])
Ri = atom_i.covalent_radius + \
atom_i.covalent_radius_uncertainty
Rj = atom_j.covalent_radius + \
atom_j.covalent_radius_uncertainty
Dij = (Ri+Rj) * float(ratio)
if d_ij < Dij:
bonded[i] = True
bonded[j] = True
if self.Z[i] < self.Z[j]:
atom_begin = self.Z[i]
atom_end = self.Z[j]
index_begin = i
index_end = j
else:
atom_begin = self.Z[j]
atom_end = self.Z[i]
index_begin = j
index_end = i
self.bonds[itr] = {'atom_begin' : atom_begin,
'index_begin' : index_begin,
'atom_end' : atom_end,
'index_end' : index_end,
'length' : d_ij}
bond_list.append([i, j])
type_begin = qtk.Z2n(atom_begin)
type_end = qtk.Z2n(atom_end)
bond_table = qtk.data.elements.bond_table
bond_keys = []
bond_keys = [
type_begin + _ + type_end for _ in ['-', '=', '#']
]
try:
bond_type_ind = np.argmin(
abs(
np.array([
bond_table[k][0] for k in bond_keys
if k in bond_table.keys()
]) - d_ij
)
)
except Exception as _e:
qtk.warning(
"error while processing bond" +\
str(bond_keys) + "with error message %s" % str(_e))
bond_type_ind = -1
bond_type = bond_keys[bond_type_ind]
self.bonds[itr]['name'] = bond_type
try:
bond_energy = \
bond_table[bond_keys[bond_type_ind]][1] * \
qtk.convE(1, 'kj-kcal')[0]
except:
bond_energy = np.nan
self.bonds[itr]['energy'] = bond_energy
if np.isnan(bond_energy):
qtk.warning("Non-tabliated covalent bond %s" % bond_type)
if bond_type in self.bond_types:
self.bond_types[bond_type] += 1
else:
self.bond_types[bond_type] = 1
itr += 1
segments = list(connected_components(to_graph(bond_list)))
for s in range(len(segments)):
segment = list(segments[s])
new_mol = self.getSegment(segment, **kwargs)
ns = len(self.segments)
new_mol.name = new_mol.name + '_%d' % ns
self.segments.append(new_mol)
for s in [i for i in range(self.N) if not bonded[i]]:
segment = [s]
new_mol = self.getSegment(segment, **kwargs)
ns = len(self.segments)
new_mol.name = new_mol.name + '_%d' % ns
self.segments.append(new_mol)
