def _write(gobj, gtensor, title, level=logger.INFO):
if gobj.verbose >= level:
w, v = numpy.linalg.eigh(numpy.dot(gtensor, gtensor.T))
idxmax = abs(v).argmax(axis=0)
v[:, v[idxmax, [0, 1, 2]] < 0] *= -1 # format phase
sorted_axis = numpy.argsort(idxmax)
v = v[:, sorted_axis]
if numpy.linalg.det(v) < 0: # ensure new axes in RHS
v[:, 2] *= -1
g2 = reduce(numpy.dot, (v.T, gtensor, v))
gobj.stdout.write('%s %s\n' % (title, g2.diagonal()))
if gobj.verbose >= logger.DEBUG:
rhf_nmr._write(gobj.stdout, gtensor, title + ' tensor')
def _write(gobj, gtensor, title):
gobj.stdout.write('%s %s\n' % (title, gtensor.diagonal()))
if gobj.verbose >= logger.DEBUG:
rhf_nmr._write(gobj.stdout, gtensor, title+' tensor')
w = numpy.linalg.svd(gtensor)[1]
gobj.stdout.write('sqrt(ggT) %s\n' % w)
def _write(obj, tensor, title):
obj.stdout.write('%s %s\n' % (title, tensor.diagonal()))
rhf_nmr._write(obj.stdout, tensor, title + ' tensor')
w = numpy.linalg.eigvals(tensor)
obj.stdout.write('eigenvalues: %s\n' % w)
def shielding(self, mo1=None):
cput0 = (time.clock(), time.time())
self.dump_flags()
if self.verbose >= logger.WARN:
self.check_sanity()
t0 = (time.clock(), time.time())
unit_ppm = nist.ALPHA**2 * 1e6
msc_dia = self.dia() * unit_ppm
t0 = logger.timer(self, 'h11', *t0)
msc_para, para_pos, para_neg, para_occ = \
[x*unit_ppm for x in self.para(mo10=mo1)]
e11 = msc_para + msc_dia
logger.timer(self, 'NMR shielding', *cput0)
if self.verbose > logger.QUIET:
for i, atm_id in enumerate(self.shielding_nuc):
rhf_nmr._write(self.stdout, e11[i],
'\ntotal shielding of atom %d %s'
% (atm_id, self.mol.atom_symbol(atm_id)))
rhf_nmr._write(self.stdout, msc_dia[i], 'dia-magnetism')
rhf_nmr._write(self.stdout, msc_para[i], 'para-magnetism')
if self.verbose >= logger.INFO:
rhf_nmr._write(self.stdout, para_occ[i], 'occ part of para-magnetism')
rhf_nmr._write(self.stdout, para_pos[i], 'vir-pos part of para-magnetism')
rhf_nmr._write(self.stdout, para_neg[i], 'vir-neg part of para-magnetism')
return e11
def shielding(self, mo1=None):
cput0 = (logger.process_clock(), logger.perf_counter())
self.dump_flags()
if self.verbose >= logger.WARN:
self.check_sanity()
t0 = (logger.process_clock(), logger.perf_counter())
unit_ppm = nist.ALPHA**2 * 1e6
msc_dia = self.dia() * unit_ppm
t0 = logger.timer(self, 'h11', *t0)
msc_para, para_pos, para_neg, para_occ = \
[x*unit_ppm for x in self.para(mo10=mo1)]
e11 = msc_para + msc_dia
logger.timer(self, 'NMR shielding', *cput0)
if self.verbose > logger.QUIET:
for i, atm_id in enumerate(self.shielding_nuc):
rhf_nmr._write(
self.stdout, e11[i], '\ntotal shielding of atom %d %s' %
(atm_id, self.mol.atom_symbol(atm_id)))
rhf_nmr._write(self.stdout, msc_dia[i], 'dia-magnetism')
rhf_nmr._write(self.stdout, msc_para[i], 'para-magnetism')
if self.verbose >= logger.INFO:
rhf_nmr._write(self.stdout, para_occ[i],
'occ part of para-magnetism')
rhf_nmr._write(self.stdout, para_pos[i],
'vir-pos part of para-magnetism')
rhf_nmr._write(self.stdout, para_neg[i],
'vir-neg part of para-magnetism')
return e11
def _write(gobj, gtensor, title):
gobj.stdout.write('%s %s\n' % (title, gtensor.diagonal()))
if gobj.verbose >= logger.DEBUG:
rhf_nmr._write(gobj.stdout, gtensor, title+' tensor')
w = numpy.linalg.svd(gtensor)[1]
gobj.stdout.write('sqrt(ggT) %s\n' % w)