def _get_econt_info(self, out_log):
"""
extract energy contour information from out_log file
:param out_log: file that is parsed
:retuns: econt (dict), dictionary containing the energy contour info
:note: econt contains the following keys
* 'emin', bottom of energy contour
* 'Nepts', number of points in energy contour
* 'epts', list of complex valued energy points
* 'weights', list of complex valued weights for energy integration
"""
from aiida_kkr.tools.common_functions import search_string
from numpy import array
f = open(out_log)
tmptxt = f.readlines()
f.close()
econt = {}
itmp = search_string('[read_energy] number of energy points', tmptxt)
if itmp >= 0: econt['Nepts'] = int(tmptxt.pop(itmp).split()[-1])
itmp = search_string('energies and weights are:', tmptxt)
if itmp >= 0:
tmp = []
for ie in range(econt['Nepts']):
tmpline = tmptxt[itmp + 4 + ie].split()[1:]
tmp.append([
float(tmpline[0]),
float(tmpline[1]),
float(tmpline[2]),
float(tmpline[3])
])
tmp = array(tmp)
econt['epts'] = tmp[:, :2]
econt['weights'] = tmp[:, 2:]
econt['emin'] = tmp[0, 0]
return econt
def test_set_rmtcore(self):
#test rmtcore
from numpy import array
from aiida_kkr.tools.common_functions import search_string
para_dict = dict([
(u'INS', 0), (u'RCLUSTZ', 1.69), (u'LMAX', 2), (u'GMAX', 65.0),
(u'<RMTCORE>',
[0.3535533906, 0.3535533906, 0.3535533906, 0.3535533906]),
(u'RMAX', 7.0), (u'NSPIN', 1)
])
zatom = array([47., 47., 47., 47.])
alat = 7.8692316414074615
natom = 4
positions = array([[0., 0., 0.], [0., 0.5, 0.5], [0.5, 0., 0.5],
[0.5, 0.5, 0.]])
bravais = array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]])
k = kkrparams(**para_dict)
k.set_multiple_values(ZATOM=zatom,
NAEZ=natom,
ALATBASIS=alat,
RBASIS=positions,
BRAVAIS=bravais)
k.fill_keywords_to_inputfile()
txt = open('inputcard').readlines()
naez = int(txt[search_string('NAEZ', txt)].split()[-1])
rmtcore = []
l_offset = search_string('RMTCORE', txt)
for iatom in range(naez):
rmtcore_at = float(txt[l_offset + 1 + iatom].split()[-1])
rmtcore.append(rmtcore_at)
maxdiff = (max(abs(array(para_dict['<RMTCORE>']) - array(rmtcore))))
assert maxdiff < 10**-6
def get_symmetries(outfile_0init):
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
try:
itmp = search_string('symmetries found for this lattice:', tmptxt)
nsym = int(tmptxt[itmp].split(':')[1].split()[0])
except IndexError:
itmp = search_string('< FINDGROUP > : Finding symmetry operations', tmptxt)
tmptxt2 = tmptxt[itmp:]
itmp = search_string('found for this lattice:', tmptxt2)
nsym = int(tmptxt2[itmp].split(':')[1].split()[0])
itmp = search_string('symmetries will be used', tmptxt)
nsym_used = int(tmptxt[itmp].split()[3])
itmp = search_string('<SYMTAUMAT>', tmptxt)
tmpdict = {}
for isym in range(nsym_used):
tmpval = tmptxt[itmp+5+isym].replace('0-', '0 -').replace('1-', '1 -').split() # bugfix for -120 degree euler angle
desc = tmpval[1]
inversion = int(tmpval[2])
euler = [float(tmpval[3]), float(tmpval[4]), float(tmpval[5])]
unitary = int(tmpval[6].replace('T', '1').replace('F', '0'))
tmpdict[desc] = {'has_inversion':inversion, 'is_unitary':unitary, 'euler_angles':euler}
desc = tmpdict
return nsym, nsym_used, desc
def test_search_string(self):
txt = open('files/kkr/kkr_run_dos_output/output.0.txt',
'r').readlines()
alatline = search_string('ALAT', txt)
noline = search_string('ALT', txt)
assert alatline == 23
assert noline == -1
def get_alat(inpfile):
f = open(inpfile)
txt = f.readlines()
f.close()
itmp = search_string('ALATBASIS', txt)
result = float(txt[itmp].split('ALATBASIS')[1].split('=')[1].split()[0])
return result
def get_spinmom_per_atom(outfile, natom, nonco_out_file=None):
"""
Extract spin moment information from outfile and nonco_angles_out (if given)
"""
from numpy import array
f = open(outfile)
tmptxt = f.readlines()
f.close()
itmp = 0
result = []
while itmp >= 0:
itmp = search_string('m_spin', tmptxt)
if itmp>=0:
tmpline = tmptxt.pop(itmp)
tmparray = []
for iatom in range(natom):
tmpline = tmptxt.pop(itmp)
tmparray.append(float(tmpline.split()[3]))
result.append(tmparray)
# if the file is there, i.e. NEWSOSOL is used, then extract also direction of spins (angles theta and phi)
if nonco_out_file is not None and result != []:
from numpy import loadtxt
from numpy import shape
angles = loadtxt(nonco_out_file)
if len(shape(angles))==1:
angles = array([angles])
vec = angles_to_vec(result[-1], angles[:,0], angles[:,1])
else:
vec, angles = [],[]
return array(result), vec, angles
def extract_timings(outfile):
from numpy import array
f = open(outfile)
tmptxt = f.readlines()
f.close()
itmp = 0
res = []
search_keys = ['main0',
'main1a - tbref',
'main1a ', # two spaces to differentiate from following key
'main1b - calctref13',
'main1b ', # two spaces!
'main1c - serial part',
'main1c ',# two spaces!
'main2',
'Time in Iteration']
while itmp>=0:
tmpvals = []
for isearch in search_keys:
itmp = search_string(isearch, tmptxt)
if itmp>=0:
tmpval = [isearch, float(tmptxt.pop(itmp).split()[-1])]
tmpvals.append(tmpval)
if len(tmpvals)>0:
res.append(tmpvals)
#print(res)
res = array(res[0])
#print(dict(res))
return dict(res)
def _extract_timings(self, outfile):
"""
Extract timings for the different parts in the KKRimp code
:param outfile: timing file of the KKRimp run
:returns: res (dict) timings in seconds, averaged over iterations
"""
from aiida_kkr.tools.common_functions import search_string
f = open(outfile)
tmptxt = f.readlines()
f.close()
search_keys = [
'time until scf starts', 'vpot->tmat', 'gref->gmat',
'gonsite->density', 'energyloop', 'Iteration number',
'Total running time'
]
res = {}
for isearch in search_keys:
tmpval = []
itmp = 0
while itmp >= 0:
itmp = search_string(isearch, tmptxt)
if itmp >= 0:
tmpval.append(float(tmptxt.pop(itmp).split()[-1]))
if len(tmpval) > 0:
res[isearch] = tmpval
# average over iterations
niter = len(res.get(search_keys[-2], []))
if niter > 0:
for key in search_keys[1:6]:
res[key] = sum(res[key]) / niter
for key in [search_keys[0], search_keys[-1]]:
res[key] = res[key][0]
return res
def get_alatinfo(outfile_0init):
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
itmp = search_string('Lattice constants :', tmptxt)
alat = float(tmptxt[itmp].split(':')[1].split('=')[1].split()[0])
twopialat = float(tmptxt[itmp].split(':')[1].split('=')[2].split()[0])
return alat, twopialat
def startpot_jellium(outfile):
f = open(outfile)
tmptxt = f.readlines()
f.close()
itmp = search_string('JELLSTART POTENTIALS', tmptxt)
if itmp ==-1:
return False
else:
return True
def get_shape_array(outfile, atominfo):
f = open(outfile)
txt = f.readlines()
f.close()
#naez/natyp number of items either one number (=ishape without cpa or two =[iatom, ishape] with CPA)
# read in naez and/or natyp and then find ishape array (1..natyp[=naez without CPA])
itmp = search_string('NAEZ= ', txt)
if itmp>=0:
tmp = txt[itmp]
ipos = tmp.find('NAEZ=')
naez = int(tmp[ipos+5:].split()[0])
else:
naez = -1
itmp = search_string('NATYP= ', txt)
if itmp>=0:
tmp = txt[itmp]
ipos = tmp.find('NATYP=')
natyp = int(tmp[ipos+6:].split()[0])
else:
natyp = -1
# consistency check
if naez==-1 and natyp>0:
naez = natyp
elif natyp==-1 and naez>0:
natyp = naez
elif natyp==-1 and naez==-1:
raise ValueError('Neither NAEZ nor NATYP found in %s'%outfile)
# read shape index from atominfo file
f = open(atominfo)
tmptxt = f.readlines()
f.close()
itmp = search_string('<SHAPE>', tmptxt) + 1
ishape = []
for iatom in range(natyp):
txt = tmptxt[itmp+iatom]
if natyp>naez: #CPA option
ishape.append(int(txt.split()[1]))
else:
ishape.append(int(txt.split()[0]))
return natyp, naez, ishape
def get_nspin(outfile_0init):
"""
extract NSPIN value from output.0.txt
"""
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
itmp = search_string('NSPIN', tmptxt)
nspin = int(tmptxt[itmp+1].split()[0])
return nspin
def get_volumes(outfile):
f = open(outfile)
tmptxt = f.readlines()
f.close()
itmp = search_string('Total volume (alat^3)', tmptxt)
if itmp>=0:
Vtot = float(tmptxt.pop(itmp).split()[-1])
itmp = 0
results = []
while itmp>=0:
itmp = search_string(' Volume(alat^3) :', tmptxt)
if itmp>=0:
tmpstr = tmptxt.pop(itmp)
tmpstr = tmpstr.split()
tmpstr = [int(tmpstr[2]), float(tmpstr[5])]
results.append(tmpstr)
return Vtot, results
def get_natom(outfile_0init):
"""
extract NATYP value from output.0.txt
"""
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
itmp = search_string('NATYP', tmptxt)
natom = int(tmptxt[itmp+1].split()[0])
return natom
def get_scfinfo(outfile_0init, outfile_000, outfile):
f = open(outfile_000)
tmptxt = f.readlines()
f.close()
itmp = search_string('ITERATION :', tmptxt)
tmpval = tmptxt[itmp].split(':')[1].split()
niter = int(tmpval[0])
nitermax = int(tmpval[3])
f = open(outfile)
tmptxt = f.readlines()
f.close()
itmp1 = search_string('SCF ITERATION CONVERGED', tmptxt)
itmp2 = search_string('NUMBER OF SCF STEPS EXHAUSTED', tmptxt)
if itmp1>=0:
converged = True
else:
converged = False
if itmp2>=0:
nmax_reached = True
else:
nmax_reached = False
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
itmp = search_string('STRMIX FCM QBOUND', tmptxt)
tmpval = tmptxt[itmp+1].split()
strmix = float(tmpval[0])
fcm = float(tmpval[1])
qbound = float(tmpval[2])
tmpval = tmptxt[itmp+4].split()
brymix = float(tmpval[0])
itmp = search_string('IMIX IGF ICC', tmptxt)
imix = int(tmptxt[itmp+1].split()[0])
idtbry = int(tmptxt[itmp+4].split()[0])
mixinfo = [imix, strmix, qbound, fcm, idtbry, brymix]
return niter, nitermax, converged, nmax_reached, mixinfo
def use_newsosol(outfile_0init):
"""
extract NEWSOSOL info from output.0.txt
"""
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
itmp = search_string('NEWSOSOL', tmptxt)
newsosol = False
if itmp>=0:
newsosol = True
return newsosol
def get_fpradius(naez, atominfo):
f = open(atominfo)
txt = f.readlines()
f.close()
itmp = search_string('<FPRADIUS>', txt) + 1
results = []
for iatom in range(naez):
#ZAT LMXC KFG <CLS> <REFPOT> <NTC> FAC <IRNS> <RMTREF> <FPRADIUS>
# 0.00 1 3 3 0 0 1 1 1 1. 199 2.3166000 0.4696902
tmpline = float(txt[itmp+iatom].split()[-1])
results.append(tmpline)
return results
def get_econt_info(outfile_0init):
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
itmp = search_string('E min', tmptxt)
emin = float(tmptxt[itmp].split('min')[1].split('=')[1].split()[0])
itmp = search_string('Temperature', tmptxt)
tempr = float(tmptxt[itmp].split('Temperature')[1].split('=')[1].split()[0])
itmp = search_string('Number of energy points', tmptxt)
Nepts = int(tmptxt[itmp].split(':')[1].split()[0])
doscalc = search_string('Density-of-States calculation', tmptxt)
if doscalc == -1:
# npol
itmp = search_string('poles =', tmptxt)
Npol = int(tmptxt[itmp].split('=')[1].split()[0])
# npt1, npt2, npt3
itmp = search_string('contour:', tmptxt)
tmp = tmptxt[itmp].replace(',','').split(':')[1].split()
N1 = int(tmp[2])
N2 = int(tmp[5])
N3 = int(tmp[8])
else:
Npol, N1, N2, N3 = 0, 0, Nepts, 0
return emin, tempr, Nepts, Npol, N1, N2, N3
def _get_nspin(self, file):
"""
Extract nspin from file
:param file: file that is parsed
:returns: 1 if calculation is paramagnetic, 2 otherwise
"""
from aiida_kkr.tools.common_functions import search_string
f = open(file)
tmptxt = f.readlines()
f.close()
itmp = search_string('NSPIN', tmptxt)
nspin = int(tmptxt.pop(itmp).split()[-1])
return nspin
def get_radial_meshpoints(potfile):
f = open(potfile)
txt = f.readlines()
f.close()
itmp = 0
result = []
while itmp >= 0:
itmp = search_string('exc:', txt)
if itmp >= 0:
txt.pop(itmp)# remove header line
tmp = txt.pop(itmp+3) # extract meshpoints
result.append(float(tmp))
return result
def get_ewald(outfile_0init):
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
itmp = search_string('setting bulk Madelung coefficients', tmptxt)
if itmp>=0:
info = '3D'
else:
info = '2D'
if info == '3D':
itmp = search_string('< LATTICE3D >', tmptxt)
tmpval = tmptxt[itmp+7].split()[2:]
rsum = float(tmpval[2]), int(tmpval[0]), int(tmpval[1])
tmpval = tmptxt[itmp+8].split()[2:]
gsum = float(tmpval[2]), int(tmpval[0]), int(tmpval[1])
else:
itmp = search_string('< LATTICE2D >', tmptxt)
tmpval = tmptxt[itmp+13].split()[2:]
rsum = float(tmpval[2]), int(tmpval[0]), int(tmpval[1])
tmpval = tmptxt[itmp+14].split()[2:]
gsum = float(tmpval[2]), int(tmpval[0]), int(tmpval[1])
return rsum, gsum, info
def _get_natom(self, file):
"""
Extract number of atoms in impurity cluster
:param file: file that is parsed to find number of atoms
:returns: natom (int), number of atoms in impurity cluster
"""
from aiida_kkr.tools.common_functions import search_string
f = open(file)
tmptxt = f.readlines()
f.close()
itmp = search_string('NATOM is', tmptxt)
natom = int(tmptxt.pop(itmp).split()[-1])
return natom
def find_warnings(outfile):
from numpy import array
f = open(outfile)
tmptxt = f.readlines()
tmptxt_caps = [txt.upper() for txt in tmptxt]
f.close()
itmp = 0
res = []
while itmp>=0:
itmp = search_string('WARNING', tmptxt_caps)
if itmp>=0:
tmpval = tmptxt_caps.pop(itmp)
tmpval = tmptxt.pop(itmp)
res.append(tmpval.strip())
return array(res)
def get_kmeshinfo(outfile_0init, outfile_000):
"""
Extract kmesh info from output.0.txt and output.000.txt
"""
# first get info from output.0.txt
f = open(outfile_0init)
tmptxt = f.readlines()
f.close()
nkmesh = []
itmp = search_string('number of different k-meshes', tmptxt)
nkmesh.append( int(tmptxt[itmp].split(':')[1].split()[0]) )
itmp = search_string('k-mesh NofKs', tmptxt)
nofks, nkx, nky, nkz = [],[],[],[]
for ik in range(nkmesh[0]):
tmpval = tmptxt[itmp+2+ik].split()
nofks.append(int(tmpval[1]))
nkx.append(int(tmpval[2]))
nky.append(int(tmpval[3]))
nkz.append(int(tmpval[4]))
tmpdict = {'number_of_kpts':nofks, 'n_kx':nkx, 'n_ky':nky, 'n_kz':nkz}
nkmesh.append(tmpdict)
#next get kmesh_ie from output.000.txt
f = open(outfile_000)
tmptxt = f.readlines()
f.close()
kmesh_ie = []
itmp = 0
while itmp>=0:
itmp = search_string('KMESH =', tmptxt)
if itmp>=0:
tmpval = int(tmptxt.pop(itmp).split()[-1])
kmesh_ie.append(tmpval)
return nkmesh, kmesh_ie
def get_single_particle_energies(outfile_000):
"""
extracts single particle energies from outfile_000 (output.000.txt)
returns the valence contribution of the single particle energies
"""
from numpy import array
f = open(outfile_000)
tmptxt = f.readlines()
f.close()
itmp = 0
res = []
while itmp>=0:
itmp = search_string('band energy per atom', tmptxt)
if itmp>=0:
tmpval = float(tmptxt.pop(itmp).split()[-1])
res.append(tmpval)
return array(res)
def _get_Etot(self, file):
"""
Extract total energy file
:param file: file that is parsed
:returns: Etot (list), values of the total energy in Ry for all iterations
"""
from aiida_kkr.tools.common_functions import search_string
f = open(file)
tmptxt = f.readlines()
f.close()
itmp = 0
Etot = []
while itmp >= 0:
itmp = search_string('TOTAL ENERGY', tmptxt)
if itmp >= 0:
Etot.append(float(tmptxt.pop(itmp).split()[-1]))
return Etot
def _get_newsosol(self, file):
"""
Check if spin orbit coupling solver is used
:param file: absolute path to out_log.000.txt of KKRimp calculation
:returns: True(False) if SOC solver is (not) used
"""
from aiida_kkr.tools.common_functions import search_string
f = open(file)
tmptxt = f.readlines()
f.close()
itmp = search_string('Spin orbit coupling used?', tmptxt)
itmp = int(tmptxt.pop(itmp).split()[-1])
if itmp == 1:
newsosol = True
else:
newsosol = False
return newsosol
def get_cls_info(outfile):
f = open(outfile)
tmptxt = f.readlines()
f.close()
itmp = 0
Ncls = 0
Natom = 0
cls_all = []
results = []
while itmp>=0:
itmp = search_string('CLSGEN_TB: Atom', tmptxt)
if itmp>=0:
tmpstr = tmptxt.pop(itmp)
tmpstr = tmpstr.split()
tmp = [int(tmpstr[2]), int(tmpstr[4]), float(tmpstr[6]), int(tmpstr[8]), int(tmpstr[10])]
results.append(tmp)
if int(tmpstr[8]) not in cls_all:
Ncls += 1
cls_all.append(int(tmpstr[8]))
Natom += 1
return Ncls, Natom, results
def get_orbmom(outfile, natom):
"""
read orbmom info from outfile and return array (iteration, atom)=orbmom
"""
from numpy import array
f = open(outfile)
tmptxt = f.readlines()
f.close()
itmp = 0
result = []
while itmp >= 0:
itmp = search_string('m_spin', tmptxt)
if itmp>=0:
tmpline = tmptxt.pop(itmp)
tmparray = []
for iatom in range(natom):
tmpline = tmptxt.pop(itmp)
tmparray.append(float(tmpline.split()[4]))
result.append(tmparray)
return array(result)#, vec, angles
def test_set_potname_empty(self):
p = kkrparams()
p.set_multiple_values(RMAX=1,
GMAX=1,
NSPIN=1,
RBASIS=[0, 0, 0],
LMAX=2,
RCLUSTZ=1.2,
NAEZ=1,
ZATOM=[0],
BRAVAIS=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
ALATBASIS=1,
FILES=['', 'shapenew'])
p.fill_keywords_to_inputfile()
from aiida_kkr.tools.common_functions import search_string
txt = open('inputcard').readlines()
itmp = search_string('FILES', txt)
potname = txt[itmp + 2].split()[0]
shapename = txt[itmp + 4].split()[0]
assert 'potential' == potname
assert 'shapenew' == shapename
