def setCelldm(self, celldm=None, **kwargs):
if not self.celldm:
if not celldm:
if not self.periodic:
if 'margin' not in kwargs:
margin = qtk.setting.box_margin
else:
margin = kwargs['margin']
self.box = self.getSize() + \
2*np.array([margin, margin, margin])
self.celldm = copy.deepcopy(self.box)
self.celldm.extend([0, 0, 0])
else:
self.periodic = True
self.celldm = celldm
self.box = celldm[:3]
self.R_scale = qtk.xyz2fractional(self.R, celldm)
else:
if celldm:
self.periodic = True
for i in range(len(celldm)):
self.celldm[i] = celldm[i]
self.box = celldm[:3]
for i in range(self.N):
for j in range(3):
if self.scale:
self.R[i, j] = self.R_scale[i, j] * \
self.celldm[j] / float(self.scale[j])
else:
self.R[i, j] = self.R_scale[i, j] * celldm[j]
return self.celldm
def setCelldm(self, celldm=None, **kwargs):
if not self.celldm:
if not celldm:
if not self.periodic:
if 'margin' not in kwargs:
margin = qtk.setting.box_margin
else:
margin = kwargs['margin']
self.box = self.getSize() + \
2*np.array([margin, margin, margin])
self.celldm = copy.deepcopy(self.box)
self.celldm.extend([0, 0, 0])
else:
self.periodic = True
self.celldm = celldm
self.box = celldm[:3]
self.R_scale = qtk.xyz2fractional(self.R, celldm)
else:
if celldm:
self.periodic = True
for i in range(len(celldm)):
self.celldm[i] = celldm[i]
self.box = celldm[:3]
for i in range(self.N):
for j in range(3):
if self.scale:
self.R[i, j] = self.R_scale[i, j] * \
self.celldm[j] / float(self.scale[j])
else:
self.R[i, j] = self.R_scale[i, j] * celldm[j]
return self.celldm
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')
