def output(self):
"""Outputs BMDL input file as a formatted string
Creates a long string containing the batch
job script which will later be written on disk.
:returns: batch script input file
:rtype: str
"""
mdlfile = "bmdl/"
prnfile = "bmdl/"
now = datetime.datetime.now()
line = "BMDL HP......=N "\
+ str(now.day) + "." + str(now.month) + "." + str(now.year) + "\n"
JOBNAMline = "JOBNAM...=" + self.jobname_lat
MSGLline = "MSGL.= " + str(self.msgl)
NPRNline = "NPRN.= " + str(self.nprn)
line = line + \
"{0:21s}{1:9s} {2:9s}".format(
JOBNAMline, MSGLline, NPRNline) + "\n"
line = line + "DIR001=" + mdlfile + "\n"
line = line + "DIR006=" + prnfile + "\n"
line = line + "Madelung potential for {0}".format(
self.jobname_lat) + "\n"
line = line + "NL.....={0:2d}".format(self.bmdl_nl) + "\n"
line = line + "LAMDA....= {0:4.2f} AMAX....= {1:4.2f} BMAX....= {2:4.2f}"\
.format(self.lamda, self.amax, self.bmax) + "\n"
line = line + "NQ....={0:3d} LAT...={1:2d} IPRIM.= {2} NQR2..= {3}"\
.format(self.nq, common.lat_to_ibz(self.lat), self.iprim, self.nqr2) + "\n"
line = line + "A........={0:10.8f} B.......={1:10.8f} C.......={2:10.8f}"\
.format(self.latparams[0], self.latparams[1], self.latparams[2]) + "\n"
if self.iprim == 1:
line = line + "ALPHA....={0:10.6f} BETA....={1:10.6f} GAMMA...={2:10.6f}"\
.format(self.latvectors[0], self.latvectors[1], self.latvectors[2]) + "\n"
elif self.iprim == 0:
line = line + "BSX......={0:10.7f} BSY.....={1:10.7f} BSZ.....={2:10.7f}"\
.format(self.latvectors[0][0], self.latvectors[0][1], self.latvectors[0][2]) + "\n"
line = line + "BSX......={0:10.7f} BSY.....={1:10.7f} BSZ.....={2:10.7f}"\
.format(self.latvectors[1][0], self.latvectors[1][1], self.latvectors[1][2]) + "\n"
line = line + "BSX......={0:10.7f} BSY.....={1:10.7f} BSZ.....={2:10.7f}"\
.format(self.latvectors[2][0], self.latvectors[2][1], self.latvectors[2][2]) + "\n"
for i in range(self.nq):
line = line + "QX({3:03})..={0:10.7f} QY({3:03}).={1:10.7f} QZ({3:03}).={2:10.7f}"\
.format(self.basis[i,0], self.basis[i,1], self.basis[i,2], i + 1) + "\n"
return line
def generate_prims(self, angles):
"""Generates the primitive lattice vectors from the angle and Bravais-lattice
type information.
"""
deg_to_rad = np.pi / 180.0
alpha = angles[0] * deg_to_rad
beta = angles[1] * deg_to_rad
gamma = angles[2] * deg_to_rad
ibz = common.lat_to_ibz(self.lat)
boa = self.latparams[1] / self.latparams[0]
coa = self.latparams[2] / self.latparams[0]
#
if ibz == 1:
prims = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
elif ibz == 2:
prims = np.array([[0.5, 0.5, 0.0], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5]])
elif ibz == 3:
prims = np.array([[0.5, 0.5, -0.5], [-0.5, 0.5, 0.5],
[0.5, -0.5, 0.5]])
elif ibz == 4:
prims = np.array([[1.0, 0.0, 0.0], [-0.5, 0.5 * np.sqrt(3.0), 0.0],
[0.0, 0.0, coa]])
elif ibz == 5:
prims = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, coa]])
elif ibz == 6:
prims = np.array([[-0.5, 0.5, 0.5 * coa], [0.5, -0.5, 0.5 * coa],
[0.5, 0.5, -0.5 * coa]])
elif ibz == 7:
prims = np.array([[0.0, 1.0, coa],
[-0.5 * np.sqrt(3.0), -0.5, coa],
[0.5 * np.sqrt(3.0), -0.5, coa]])
elif ibz == 8:
prims = np.array([[1.0, 0.0, 0.0], [0.0, boa, 0.0],
[0.0, 0.0, coa]])
elif ibz == 9:
prims = np.array([[0.5, -0.5 * boa, 0.0], [0.5, 0.5 * boa, 0.0],
[0.0, 0.0, coa]])
elif ibz == 10:
prims = np.array([[0.5, -0.5 * boa, 0.5 * coa],
[0.5, 0.5 * boa, -0.5 * coa],
[-0.5, 0.5 * boa, 0.5 * coa]])
elif ibz == 11:
prims = np.array([[0.5, 0.0, 0.5 * coa], [0.5, 0.5 * boa, 0.0],
[0.0, 0.5 * boa, 0.5 * coa]])
elif ibz == 12:
prims = np.array([[1.0, 0.0, 0.0],
[boa * np.cos(gamma), boa * np.sin(gamma), 0.0],
[0.0, 0.0, coa]])
elif ibz == 13:
prims = np.array(
[[0.0, -boa, 0.0],
[0.5 * np.sin(gamma), -0.5 * np.cos(gamma), -0.5 * coa],
[0.5 * np.sin(gamma), -0.5 * np.cos(gamma), 0.5 * coa]])
elif ibz == 14:
tmp1 = (np.cos(alpha) -
np.cos(beta) * np.cos(gamma)) / np.sin(gamma)
tmp2 = np.sqrt((1.0 - np.cos(gamma)**2 - np.cos(alpha)**2 -
np.cos(beta)**2 + 2.0 * np.cos(alpha) *
np.cos(beta) * np.cos(gamma))) / np.sin(gamma)
prims = np.array([[1.0, 0.0, 0.0],
[boa * np.cos(gamma), boa * np.sin(gamma), 0.0],
[coa * np.cos(beta), coa * tmp1, coa * tmp2]])
#print('generated prims:')
#print(prims)
return prims
def output(self, index):
"""Outputs KSTR input file as a formatted string.
:param index:
:type index:
:returns: KSTR input file string
:rtype: str
"""
slope = 'kstr/'
prn = 'kstr/'
boolean = {True: "Y", False: "N"}
if index == 1:
kappaw = self.kappaw[0]
jobname_lat = self.jobname_lat
elif index == 2:
kappaw = self.kappaw[1]
jobname_lat = self.jobname_lat2
now = datetime.datetime.now()
line = "KSTR HP......=N "\
+ str(now.day) + "." + str(now.month) + "." + str(now.year) + "\n"
JOBNAMline = "JOBNAM...=" + jobname_lat
MSGLline = "MSGL.= " + str(self.msgl)
line = line + "{0:21s}{1:9s}".format(JOBNAMline, MSGLline) +\
" MODE...={0} STORE..={1} HIGH...={2}"\
.format(self.mode, self.store, self.high) + "\n"
line = line + "DIR001=" + slope + "\n"
line = line + "DIR006=" + prn + "\n"
line = line + "Slope matrices, {0:10}, (kappa*w)^2= {1:5.1f}"\
.format(jobname_lat, kappaw) + "\n"
line = line + "NL.....={0:2d} NLH...={1:2d} NLW...={2:2d} "\
.format(self.kstr_nl, self.nlh, self.nlw) +\
"NDER..={0:2d} ITRANS={1:2d} NPRN..={2:2d}"\
.format(self.nder, self.itrans, self.nprn) + "\n"
line = line + "(K*W)^2..={0:10.6f} DMAX....={1:10.4f} RWATS...={2:10.2f}"\
.format(kappaw, self.dmax, self.rwats) + "\n"
line = line + "NQ3...={0:3d} LAT...={1:2d} IPRIM.={2:2d} NGHBP.={3:2d} NQR2..={4:2d}"\
.format(self.nq, common.lat_to_ibz(self.lat), self.iprim, self.nghbp, self.nqr2) + "\n"
line = line + "A........={0:10.8f} B.......={1:10.8f} C.......={2:10.8f}"\
.format(self.latparams[0], self.latparams[1], self.latparams[2]) + "\n"
if self.iprim == 1:
line = line + "ALPHA....={0:10.6f} BETA....={1:10.6f} GAMMA...={2:10.6f}"\
.format(self.latvectors[0], self.latvectors[1], self.latvectors[2]) + "\n"
elif self.iprim == 0:
line = line + "BSX......={0:10.7f} BSY.....={1:10.7f} BSZ.....={2:10.7f}"\
.format(self.latvectors[0][0], self.latvectors[0][1], self.latvectors[0][2]) + "\n"
line = line + "BSX......={0:10.7f} BSY.....={1:10.7f} BSZ.....={2:10.7f}"\
.format(self.latvectors[1][0], self.latvectors[1][1], self.latvectors[1][2]) + "\n"
line = line + "BSX......={0:10.7f} BSY.....={1:10.7f} BSZ.....={2:10.7f}"\
.format(self.latvectors[2][0], self.latvectors[2][1], self.latvectors[2][2]) + "\n"
for i in range(self.nq):
#line = line + "QX.......={0:10.7f} QY......={1:10.7f} QZ(...={2:10.7f}"\
line = line + "QX({3:03})..={0:10.7f} QY({3:03}).={1:10.7f} QZ({3:03}).={2:10.7f}"\
.format(self.basis[i,0], self.basis[i,1], self.basis[i,2], i+1) + "\n"
for i in range(self.nq):
line = line + "a/w(IQ)..= {0:4.2f} {1:4.2f} {2:4.2f} {3:4.2f}"\
.format(*self.awIQ[i, :]) + "\n"
line = line + "LAMDA....={0:10.7f} AMAX....={1:10.7f} BMAX....={2:10.7f}"\
.format(self.lamda, self.amax, self.bmax) + "\n"
return line
def check_input_file(self):
"""Perform various checks on the class data
Makes sure that all necessary data exists
before we attempt to write the input file to disk.
:returns: None
:rtype: None
"""
# Mission critical arguments
if self.jobname is None:
sys.exit('Kgrn: \'jobname\' has to be given!')
if self.latname is None:
sys.exit('Kgrn: \'latname\' has to be given!')
if self.ibz is None:
try:
self.ibz = common.lat_to_ibz(self.latname)
except KeyError:
sys.exit('Kgrn: \'ibz\' has to be given for \'latname\'={0}!'.
format(self.latname))
if self.latpath is None:
self.latpath = './'
if self.sws is None or self.sws == 0.0:
sys.exit('Kgrn: \'sws\' has to be given!')
if self.atomblock is None:
sys.exit('Kgrn: Some atomic information is missing =>' +
' self.atomblock has not been constructed!')
if self.atconf is None:
sys.exit('Kgrn: Some atomic information is missing =>' +
' self.atconf has not been constructed!')
else:
if isinstance(self.atconf[0], list):
pass
else:
self.atconf = [self.atconf]
# Arguments for which reasonable default values exist
if self.strt is None:
self.strt = 'A'
if self.msgl is None:
self.msgl = 1
if self.expan is None:
self.expan = 'S'
if self.fcd is None:
self.fcd = 'Y'
if self.func is None:
self.func = 'SCA'
if self.niter is None:
self.niter = 100
if self.nlin is None:
self.nlin = 31
if self.nprn is None:
self.nprn = 0
if self.ncpa is None:
self.ncpa = 7
if self.mode is None:
self.mode = '3D'
if self.frc is None:
self.frc = 'N'
if self.dos is None:
self.dos = 'N'
if self.ops is None:
self.ops = 'N'
if self.afm is None:
self.afm = 'P'
for i in range(len(self.splts)):
if not self.splts[i] == 0.0:
self.afm = 'F'
break
if self.crt is None:
self.crt = 'M'
if self.lmaxh is None:
self.lmaxh = 8
if self.lmaxt is None:
self.lmaxt = 4
if self.kgrn_nfi is None:
self.kgrn_nfi = 31
if self.fixg is None:
self.fixg = 2
if self.shf is None:
self.shf = 0
if self.sofc is None:
self.sofc = 'N'
if self.kmsh is None:
self.kmsh = 'G'
if self.nkx is None:
self.nkx = 0
if self.nky is None:
if self.ibz == 2:
self.nky = 13
elif self.ibz == 3:
self.nky = 17
elif self.ibz == 4:
self.nky = 13
self.nkz = 9
else:
self.nky = 13
if self.nkz is None:
self.nkz = 0
if self.fbz is None:
self.fbz = 'N'
if self.kmsh2 is None:
self.kmsh2 = 'G'
if self.ibz2 is None:
self.ibz2 = 1
if self.nkx2 is None:
self.nkx2 = 4
if self.nky2 is None:
self.nky2 = 0
if self.nkz2 is None:
self.nkz2 = 51
if self.zmsh is None:
self.zmsh = 'C'
if self.nz1 is None:
self.nz1 = 16
if self.nz2 is None:
self.nz2 = 8
if self.nz3 is None:
self.nz3 = 8
if self.nres is None:
self.nres = 4
if self.nzd is None:
self.nzd = 1500
if self.depth is None:
self.depth = 1.0
if self.imagz is None:
self.imagz = 0.020
if self.eps is None:
self.eps = 0.2
if self.elim is None:
self.elim = -1.0
if self.amix is None:
self.amix = 0.05
if self.efmix is None:
self.efmix = 1.0
if self.vmtz is None:
self.vmtz = 0.0
if self.mmom is None:
self.mmom = 0.0
if self.tole is None:
self.tole = 1.0e-7
if self.tolef is None:
self.tolef = 1.0e-7
if self.tolcpa is None:
self.tolcpa = 1.0e-6
if self.tfermi is None:
self.tfermi = 500.0
if self.nsws is None:
self.nsws = 1
if self.dsws is None:
self.dsws = 0.05
if self.alpcpa is None:
self.alpcpa = 0.6020
if self.efgs is None:
self.efgs = 0.0
if self.hx is None:
self.hx = 0.1
if self.nx is None:
self.nx = 5
if self.nz0 is None:
self.nz0 = 6
if self.stmp is None:
self.stmp = 'N'
if self.iex is None:
self.iex = 4
if self.dirac_np is None:
self.dirac_np = 251
if self.nes is None:
self.nes = 15
if self.dirac_niter is None:
self.dirac_niter = 100
if self.iwat is None:
self.iwat = 0
if self.nprna is None:
self.nprna = 0
if self.vmix is None:
self.vmix = 0.3
if self.rwat is None:
self.rwat = 3.5
if self.rmax is None:
self.rmax = 20.0
if self.dx is None:
self.dx = 0.03
if self.dr1 is None:
self.dr1 = 0.002
if self.test is None:
self.test = 1.0e-12
if self.teste is None:
self.teste = 1.0e-12
if self.testy is None:
self.testy = 1.0e-12
if self.testv is None:
self.testv = 1.0e-12
if self.FOR001 is None:
self.FOR001 = self.latpath + '/kstr/' + self.latname + '.tfh'
self.FOR001_2 = self.latpath + '/kstr/' + self.latname + '2.tfh'
self.FOR001 = common.cleanup_path(self.FOR001)
self.FOR001_2 = common.cleanup_path(self.FOR001_2)
if self.DIR002 is None:
self.DIR002 = 'kgrn/'
if self.DIR003 is None:
self.DIR003 = 'kgrn/'
if self.FOR004 is None:
self.FOR004 = self.latpath + '/bmdl/' + self.latname + '.mdl'
self.FOR004 = common.cleanup_path(self.FOR004)
if self.DIR006 is None:
self.DIR006 = 'kgrn/'
if self.DIR009 is None:
self.DIR009 = 'kgrn/'
if self.DIR010 is None:
self.DIR010 = 'kgrn/'
if self.DIR011 is None:
self.DIR011 = 'kgrn/tmp/'
if self.CQNA is None:
self.CQNA = 'N'
if self.ncpu is None:
self.ncpu = 1