def readisordk(filename="AOONEINT"):
"""Read data under label ISORDK in AOONEINT"""
header = readhead(filename)
INT = header["int_fmt"]
FLOAT = header["float_fmt"]
aooneint = FortranBinary(filename)
aooneint.find("ISORDK")
aooneint.next()
aooneint.next()
sizeofi = struct.calcsize(INT)
sizeofd = struct.calcsize(FLOAT)
mxcent_ = (len(aooneint.data) - sizeofi) // (4 * sizeofd)
chrn_ = aooneint.readbuf(mxcent_, FLOAT)
nucdep = aooneint.readbuf(1, INT)[0]
cooo_ = aooneint.readbuf(3 * mxcent_, FLOAT)
isordk_ = {
# "table":table1,
"chrn": chrn_,
"nucdep": nucdep,
"cooo": cooo_,
}
aooneint.close()
return isordk_
def test_1(self):
"""Read int, float
integer, parameter :: n = 3
double precision x(n)
x = (/ 1.0D0, 2.0D0, 3.0D0 /)
open(1, file='fort.1', status='new', form='unformatted')
write(1) n
write(1) x
close(1)
end
"""
ffile = os.path.join(self.tdir, 'fort.1')
fb = FortranBinary(ffile)
# first record is int 3
next(fb)
n = fb.readbuf(1, 'i')[0]
self.assertEqual(n, 3)
# first record is float 1. 2. 3.
next(fb)
xref = (1., 2., 3.)
x = fb.readbuf(n, 'd')
np.testing.assert_allclose(x, xref)
fb.close()
def test_1(self):
"""Read int, float
integer, parameter :: n = 3
double precision x(n)
x = (/ 1.0D0, 2.0D0, 3.0D0 /)
open(1, file='fort.1', status='new', form='unformatted')
write(1) n
write(1) x
close(1)
end
"""
ffile = os.path.join(self.tdir, 'fort.1')
fb = FortranBinary(ffile)
# first record is int 3
next(fb)
n = fb.readbuf(1, 'i')[0]
self.assertEqual(n, 3)
# first record is float 1. 2. 3.
next(fb)
xref = (1., 2., 3.)
x = fb.readbuf(n, 'd')
np.testing.assert_allclose(x, xref)
fb.close()
def test_3b(self):
"""Read vecs
integer, parameter :: nx = 3, ny=3
double precision x(nx), y(ny)
x = (/ 1.0D0, 2.0D0, 3.0D0 /)
y = (/ 5.0D0, 6.0D0, 7.0D0 /)
open(3, file='fort.3', status='new', form='unformatted')
write(3) nx, ny
write(3) x
write(3) y
close(3)
end
"""
ffile = os.path.join(self.tdir, 'fort.3')
fb = FortranBinary(ffile)
# first record is int 3
fb.next()
x = []
for rec in fb:
x += list(fb.readbuf(3, 'd'))
xref = (1., 2., 3., 5., 6., 7.)
np.testing.assert_allclose(x, xref)
fb.close()
def test_3b(self):
"""Read vecs
integer, parameter :: nx = 3, ny=3
double precision x(nx), y(ny)
x = (/ 1.0D0, 2.0D0, 3.0D0 /)
y = (/ 5.0D0, 6.0D0, 7.0D0 /)
open(3, file='fort.3', status='new', form='unformatted')
write(3) nx, ny
write(3) x
write(3) y
close(3)
end
"""
ffile = os.path.join(self.tdir, 'fort.3')
fb = FortranBinary(ffile)
# first record is int 3
fb.next()
x=[]
for rec in fb:
x += list(fb.readbuf(3, 'd'))
xref = (1., 2., 3., 5., 6., 7.)
np.testing.assert_allclose(x, xref)
fb.close()
def read(*args, **kwargs):
"""Read response vector given property"""
if "freqs" in kwargs:
# linear response/one frequency
bfreqs = kwargs.get("freqs")
else:
# non-linear response/two frequencies
bfreqs = kwargs.get("bfreqs", (0.0, ))
cfreqs = kwargs.get("cfreqs", (0.0, ))
propfile = kwargs.get("propfile", "RSPVEC")
lr_vecs = kwargs.get("lr_vecs", False)
rspvec = FortranBinary(propfile)
vecs = {}
for rec in rspvec:
for lab in args:
try:
lab1 = bytes(lab.ljust(16), "utf-8")
except TypeError:
lab1 = bytes(lab.ljust(16))
# alternative label with permuted labels
lab2 = lab1[8:] + lab1[:8]
if lab1 in rec or lab2 in rec:
if lab1 in rec:
rec.read(16, "c")
bfreq, cfreq = rec.read(2, "d")
elif lab2 in rec:
rec.read(16, "c")
cfreq, bfreq = rec.read(2, "d")
if bfreq in bfreqs and cfreq in cfreqs:
_rec = next(rspvec)
kzyvar = len(_rec) // 8
buffer_ = rspvec.readbuf(kzyvar, "d")
vecs[(lab, bfreq, cfreq)] = \
np.array(buffer_).view(full.matrix)
vecs[(lab1, bfreq, bfreq)] = vecs[(lab, bfreq, cfreq)]
vecs[(lab2, cfreq, bfreq)] = vecs[(lab, bfreq, cfreq)]
# now check that all required vectors are saved
for _l in args:
for b in bfreqs:
for c in cfreqs:
if (_l, b, c) not in vecs:
raise RspVecError(
"Response vector N(%s,%g,%g) not found on file %s" %
(_l, b, c, propfile))
# complement dict with lr pointers
if cfreqs == (0.0, ):
vecs.update({(_l, b): vecs[(_l, b, 0.0)]
for _l in args for b in bfreqs})
if bfreqs == (0.0, ):
vecs.update({_l: vecs[(_l, 0.0, 0.0)] for _l in args})
if lr_vecs:
keys = ((a, w) for a in args for w in bfreqs)
return {k: vecs[k] for k in keys}
else:
return vecs
def readall(property_label, propfile="RSPVEC"):
"""Read response all vectors given property"""
import numpy
_rspvec = FortranBinary(propfile)
found = []
while _rspvec.find(property_label) is not None:
_rspvec.rec.read(16, "c")
vfreq = _rspvec.rec.read(1, "d")[0]
_rec = next(_rspvec)
kzyvar = len(_rec) // 8
buffer_ = _rspvec.readbuf(kzyvar, "d")
mat = numpy.array(buffer_).view(full.matrix)
found.append((mat, vfreq))
return found
def readscfinp(filename="AOONEINT"):
"""Read data under labl SCFINP in AOONEINT"""
header = readhead(filename)
INT = header["int_fmt"]
FLOAT = header["float_fmt"]
aooneint = FortranBinary(filename)
aooneint.find("SCFINP")
import collections
scfinp_ = collections.OrderedDict()
aooneint.next()
title = aooneint.data.decode()
aooneint.next()
scfinp_["ttitle"] = title
nsym = aooneint.readbuf(1, INT)[0]
scfinp_["nsym"] = nsym
scfinp_["naos"] = aooneint.readbuf(nsym, INT)
scfinp_["potnuc"] = aooneint.readbuf(1, FLOAT)[0]
kmax = aooneint.readbuf(1, INT)[0]
scfinp_["kmax"] = kmax
scfinp_["ncent"] = aooneint.readbuf(kmax, INT)
nbasis = aooneint.readbuf(1, INT)[0]
scfinp_["nbasis"] = nbasis
scfinp_["jtran"] = aooneint.readbuf(nbasis, INT)
scfinp_["itran"] = aooneint.readbuf(8 * nbasis, INT)
scfinp_["ctran"] = aooneint.readbuf(8 * nbasis, FLOAT)
scfinp_["nbasis"] = aooneint.readbuf(1, INT)[0]
scfinp_["inamn"] = aooneint.readbuf(nbasis, INT)
scfinp_["iptyp"] = aooneint.readbuf(nbasis, INT)
scfinp_["dpnuc"] = aooneint.readbuf(3, FLOAT)
nucdep = aooneint.readbuf(1, INT)[0]
scfinp_["nucdep"] = nucdep
scfinp_["cooo"] = aooneint.readbuf(3 * nucdep, FLOAT)
scfinp_["ifxyz"] = aooneint.readbuf(3, INT)
scfinp_["dummy"] = aooneint.readbuf(1, FLOAT)[0]
scfinp_["qpol"] = aooneint.readbuf(6, FLOAT)
scfinp_["qq"] = aooneint.readbuf(3, FLOAT)
scfinp_["jfxyz"] = aooneint.readbuf(3, INT)
aooneint.close()
return scfinp_
class SirIfc:
"""Read data from dalton interface file"""
ifclabel = "SIR IPH "
def __init__(self, name="SIRIFC"):
self.name = name
self.file = FortranBinary(name)
self._cmo = None
self._dv = None
self._pv = None
self._fock = None
self._fc = None
self._fv = None
self._orbdiag = None
if not self.file.find(self.ifclabel):
raise RuntimeError("Label %s not found on %s" %
(self.ifclabel, name))
rec = next(self.file)
# Integer size from first record, 4 floats, 5 ints
# 1) POTNUC,EMY,EACTIV,EMCSCF,ISTATE,ISPIN,NACTEL,LSYM,MS2
try:
self.INT = get_intcode(len(rec), 4, 5)
except KeyError: # pragma no cover
# Allow Dalton 2013 version
self.INT = get_intcode(len(rec), 4, 4)
self.FLOAT = "d"
self.potnuc, self.emy, self.eactive, self.emcscf = self.file.readbuf(
4, self.FLOAT)
self.istate, self.ispin, self.nactel, self.lsym = \
self.file.readbuf(4, self.INT)
self.file.next()
self.nisht, self.nasht, self.nocct, self.norbt, self.nbast,\
self.nconf, self.nwopt, self.nwoph, self.ncdets,\
self.ncmot, self.nnashx, self.nnashy, self.nnorbt,\
self.n2orbt, self.nsym = \
self.file.readbuf(15, self.INT)
self.muld2h = numpy.array(self.file.readbuf(64, self.INT)).reshape(
(8, 8))
self.nrhf = numpy.array(self.file.readbuf(8, self.INT))
self.nfro = numpy.array(self.file.readbuf(8, self.INT))
self.nish = numpy.array(self.file.readbuf(8, self.INT))
self.nash = numpy.array(self.file.readbuf(8, self.INT))
self.norb = numpy.array(self.file.readbuf(8, self.INT))
self.nbas = numpy.array(self.file.readbuf(8, self.INT))
self.nelmn1, self.nelmx1, self.nelmn3, self.nelmx3, self.mctype = \
self.file.readbuf(5, self.INT)
self.nas1 = numpy.array(self.file.readbuf(8, self.INT))
self.nas2 = numpy.array(self.file.readbuf(8, self.INT))
self.nas3 = numpy.array(self.file.readbuf(8, self.INT))
self.file.close()
return
@property
def cmo(self):
"""Read MO coefficients"""
if self._cmo is None:
with FortranBinary(self.name) as fb:
fb.find(self.ifclabel)
for _ in range(3):
fb.next()
ncmot4 = max(self.ncmot, 4)
dbl = fb.readbuf(ncmot4, self.FLOAT)
n = 0
self._cmo = blocked.BlockDiagonalMatrix(self.nbas, self.norb)
for isym in range(8):
for mo in range(self.norb[isym]):
for ao in range(self.nbas[isym]):
self._cmo.subblock[isym][ao, mo] = dbl[n]
n += 1
assert n == self.ncmot
return self._cmo
@property
def dv(self):
"""Get active density matrix"""
if self._dv is None:
with FortranBinary(self.name) as fb:
fb.find(self.ifclabel)
for _ in range(5):
fb.next()
# mmashx = max(self.nnashx, 4)
dbl = fb.readbuf(self.nnashx, self.FLOAT)
self._dv = full.triangular.init(dbl)
return self._dv
@property
def pv(self):
"""Get two-electron density"""
if self._pv is None:
with FortranBinary(self.name) as fb:
fb.find(self.ifclabel)
for i in range(7):
fb.next()
m2ashy = max(self.nnashx**2, 4)
dbl = fb.readbuf(m2ashy, self.FLOAT)
self._pv = full.matrix((self.nnashx, self.nnashx))
n = 0
for i in range(self.nnashx):
for j in range(self.nnashx):
self._pv[j, i] = dbl[n]
n += 1
assert n == self.nnashx**2
return self._pv
@property
def fock(self):
"""Read Fock matrix (MO)"""
if self._fock is None:
with FortranBinary(self.name) as fb:
fb.find(self.ifclabel)
for i in range(6):
fb.next()
m2orbt = max(self.n2orbt, 4)
dbl = fb.readbuf(m2orbt, self.FLOAT)
self._fock = blocked.BlockDiagonalMatrix(self.norb, self.norb)
n = 0
for isym in range(8):
for i in range(self.norb[isym]):
for j in range(self.norb[isym]):
self._fock.subblock[isym][j, i] = dbl[n]
n += 1
assert n == self.n2orbt
return self._fock
@property
def fc(self):
"""Read inactive Fock matrix (MO)"""
if self._fc is None:
with FortranBinary(self.name) as fb:
fb.find(self.ifclabel)
for i in range(8):
fb.next()
mmorbt = max(self.nnorbt, 4)
dbl = fb.readbuf(mmorbt, self.FLOAT)
self._fc = blocked.triangular(self.norb)
n = 0
for isym in range(8):
ij = 0
for i in range(self.norb[isym]):
for j in range(i + 1):
self._fc.subblock[isym][i, j] = dbl[ij]
ij += 1
n += ij
assert n == self.nnorbt
return self._fc
@property
def fv(self):
"""Get active Fock matrix"""
if self._fv is None:
with FortranBinary(self.name) as fb:
fb.find(self.ifclabel)
for i in range(9):
fb.next()
mmorbt = max(self.nnorbt, 4)
dbl = fb.readbuf(mmorbt, self.FLOAT)
self._fv = blocked.triangular(self.norb)
n = 0
for isym in range(8):
ij = 0
for i in range(self.norb[isym]):
for j in range(i + 1):
self._fv.subblock[isym][i, j] = dbl[ij]
ij += 1
n += ij
assert n == self.nnorbt
return self._fv
@property
def orbdiag(self):
"""Get orbital Hessian diagonal"""
if self._orbdiag is None:
with FortranBinary(self.name) as fb:
if fb.find("ORBDIAG"):
rec = next(fb)
self._orbdiag = rec.read(self.nwopt, self.FLOAT)
else:
raise LabelNotFound("ORBDIAG not found")
return numpy.array(self._orbdiag)
def __str__(self):
retstr = ""
retstr += "Nuclear Potential Energy: %12.6f\n" % self.potnuc
retstr += "Electronic energy : %12.6f\n" % self.emy
retstr += "Active energy : %12.6f\n" % self.eactive
retstr += "MCSCF energy : %12.6f\n" % self.emcscf
retstr += "State : %d\n" % self.istate
retstr += "Spin : %d\n" % self.ispin
retstr += "Active electrons : %d\n" % self.nactel
retstr += "Symmetry : %d\n" % self.lsym
retstr += "NISHT : %d\n" % self.nisht
retstr += "NASHT : %d\n" % self.nasht
retstr += "NOCCT : %d\n" % self.nocct
retstr += "NORBT : %d\n" % self.norbt
retstr += "NBAST : %d\n" % self.nbast
retstr += "NCONF : %d\n" % self.nconf
retstr += "NWOPT : %d\n" % self.nwopt
retstr += "NWOPH : %d\n" % self.nwoph
retstr += "NCDETS : %d\n" % self.ncdets
retstr += "NCMOT : %d\n" % self.ncmot
retstr += "NNASHX : %d\n" % self.nnashx
retstr += "NNASHY : %d\n" % self.nnashy
retstr += "NNORBT : %d\n" % self.nnorbt
retstr += "N2ORBT : %d\n" % self.n2orbt
retstr += "NSYM : %d\n" % self.nsym
retstr += "MULD2H:\n"
for i in range(8):
retstr += " "
for j in range(8):
retstr += " %d" % self.muld2h[i, j]
retstr += "\n"
def strvec(lab, vec):
""" String representation of vector"""
locstr = lab + ":"
for i in range(8):
locstr += " %d" % vec[i]
return locstr + "\n"
retstr += strvec("NRHF", self.nrhf)
retstr += strvec("NFRO", self.nfro)
retstr += strvec("NISH", self.nish)
retstr += strvec("NASH", self.nash)
retstr += strvec("NORB", self.norb)
retstr += strvec("NBAS", self.nbas)
retstr += "NELMN1 : %d\n" % self.nelmn1
retstr += "NELMX1 : %d\n" % self.nelmx1
retstr += "NELMN3 : %d\n" % self.nelmn3
retstr += "NELMX3 : %d\n" % self.nelmx3
retstr += "MCTYPE : %d\n" % self.mctype
retstr += strvec("NAS1", self.nas1)
retstr += strvec("NAS2", self.nas2)
retstr += strvec("NAS3", self.nas3)
retstr += "CMO" + str(self.cmo)
retstr += "DV\n" + str(self.dv) + "\n"
retstr += "FOCK" + str(self.fock)
retstr += "PV\n" + str(self.pv) + "\n"
retstr += "FC" + str(self.fc)
retstr += "FV" + str(self.fv)
return retstr
def xindx(self):
from itertools import combinations
ms2 = self.ispin - 1
na = (self.nactel + ms2) // 2
nb = (self.nactel - ms2) // 2
astrings = tuple(combinations(range(self.nasht)[::-1], na))[::-1]
bstrings = tuple(combinations(range(self.nasht)[::-1], nb))[::-1]
return ((adet[::-1], bdet[::-1]) for bdet in bstrings
for adet in astrings)