def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename)
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace('\n', '')
self.name = s.split()[1]
self.xc = f.readline().replace('\n', '').split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f, txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f, txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
l = f.readline().split()
E = float(l[0])
me = [float(l[1]), float(l[2]), float(l[3])]
self.append(LrTDDFTExcitation(e=E, m=me))
if fh is None:
f.close()
# update own variables
self.istart = self.Om.fullkss.istart
self.jend = self.Om.fullkss.jend
def forced_update(self):
"""Recalc yourself."""
nonselfconsistent_xc = None
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
# nonselfconsistent_xc = HybridXC('PBE0', alpha=5.0)
else:
Om = ApmB
name = 'LrTDDFThyb'
self.kss = KSSingles(calculator=self.calculator,
nspins=self.nspins,
nonselfconsistent_xc=nonselfconsistent_xc,
eps=self.eps,
istart=self.istart,
jend=self.jend,
energy_range=self.energy_range,
txt=self.txt)
self.Om = Om(self.calculator, self.kss,
self.xc, self.derivative_level, self.numscale,
finegrid=self.finegrid, eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
def forced_update(self):
"""Recalc yourself."""
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
else:
Om = ApmB
name = 'LrTDDFThyb'
self.kss = KSSingles(calculator=self.calculator,
nspins=self.nspins,
eps=self.eps,
istart=self.istart,
jend=self.jend,
energy_range=self.energy_range,
txt=self.txt)
self.Om = Om(self.calculator, self.kss,
self.xc, self.derivative_level, self.numscale,
finegrid=self.finegrid, eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
def update(self,
calculator=None,
nspins=None,
eps=0.001,
istart=0,
jend=None,
energy_range=None,
xc=None,
derivative_level=None,
numscale=0.001):
changed = False
if self.calculator != calculator or \
self.nspins != nspins or \
self.eps != eps or \
self.istart != istart or \
self.jend != jend :
changed = True
if not changed: return
self.calculator = calculator
self.nspins = nspins
self.eps = eps
self.istart = istart
self.jend = jend
self.xc = xc
self.derivative_level = derivative_level
self.numscale = numscale
self.kss = KSSingles(calculator=calculator,
nspins=nspins,
eps=eps,
istart=istart,
jend=jend,
energy_range=energy_range,
txt=self.txt)
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
else:
Om = ApmB
name = 'LrTDDFThyb'
self.Om = Om(self.calculator,
self.kss,
self.xc,
self.derivative_level,
self.numscale,
finegrid=self.finegrid,
eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
def update(self,
calculator=None,
nspins=None,
eps=0.001,
istart=0,
jend=None,
energy_range=None,
xc=None,
derivative_level=None,
numscale=0.001):
changed = False
if self.calculator != calculator or \
self.nspins != nspins or \
self.eps != eps or \
self.istart != istart or \
self.jend != jend :
changed = True
if not changed: return
self.calculator = calculator
self.nspins = nspins
self.eps = eps
self.istart = istart
self.jend = jend
self.xc = xc
self.derivative_level = derivative_level
self.numscale = numscale
self.kss = KSSingles(calculator=calculator,
nspins=nspins,
eps=eps,
istart=istart,
jend=jend,
energy_range=energy_range,
txt=self.txt)
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
else:
Om = ApmB
name = 'LrTDDFThyb'
self.Om = Om(self.calculator, self.kss,
self.xc, self.derivative_level, self.numscale,
finegrid=self.finegrid, eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
class LrTDDFT(ExcitationList):
"""Linear Response TDDFT excitation class
Input parameters:
calculator:
the calculator object after a ground state calculation
nspins:
number of spins considered in the calculation
Note: Valid only for unpolarised ground state calculation
eps:
Minimal occupation difference for a transition (default 0.001)
istart:
First occupied state to consider
jend:
Last unoccupied state to consider
xc:
Exchange-Correlation approximation in the Kernel
derivative_level:
0: use Exc, 1: use vxc, 2: use fxc if available
filename:
read from a file
"""
def __init__(self,
calculator=None,
nspins=None,
eps=0.001,
istart=0,
jend=None,
energy_range=None,
xc=None,
derivative_level=1,
numscale=0.00001,
txt=None,
filename=None,
finegrid=2,
force_ApmB=False, # for tests
eh_comm=None # parallelization over eh-pairs
):
self.nspins = None
self.istart = None
self.jend = None
if isinstance(calculator, str):
ExcitationList.__init__(self, None, txt)
return self.read(calculator)
else:
ExcitationList.__init__(self, calculator, txt)
if filename is not None:
return self.read(filename)
self.filename = None
self.calculator = None
self.eps = None
self.xc = None
self.derivative_level = None
self.numscale = numscale
self.finegrid = finegrid
self.force_ApmB = force_ApmB
if eh_comm is None:
eh_comm = mpi.serial_comm
elif isinstance(eh_comm, (mpi.world.__class__,
mpi.serial_comm.__class__)):
# Correct type already.
pass
else:
# world should be a list of ranks:
eh_comm = mpi.world.new_communicator(np.asarray(eh_comm))
self.eh_comm = eh_comm
if calculator is not None:
calculator.converge_wave_functions()
if calculator.density.nct_G is None:
calculator.set_positions()
self.update(calculator, nspins, eps,
istart, jend, energy_range,
xc, derivative_level, numscale)
def analyse(self, what=None, out=None, min=0.1):
"""Print info about the transitions.
Parameters:
1. what: I list of excitation indicees, None means all
2. out : I where to send the output, None means sys.stdout
3. min : I minimal contribution to list (0<min<1)
"""
if what is None:
what = range(len(self))
elif isinstance(what, int):
what = [what]
if out is None:
out = sys.stdout
for i in what:
print >> out, str(i) + ':', self[i].analyse(min=min)
def update(self,
calculator=None,
nspins=None,
eps=0.001,
istart=0,
jend=None,
energy_range=None,
xc=None,
derivative_level=None,
numscale=0.001):
changed = False
if self.calculator != calculator or \
self.nspins != nspins or \
self.eps != eps or \
self.istart != istart or \
self.jend != jend :
changed = True
if not changed: return
self.calculator = calculator
self.nspins = nspins
self.eps = eps
self.istart = istart
self.jend = jend
self.xc = xc
self.derivative_level = derivative_level
self.numscale = numscale
self.kss = KSSingles(calculator=calculator,
nspins=nspins,
eps=eps,
istart=istart,
jend=jend,
energy_range=energy_range,
txt=self.txt)
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
else:
Om = ApmB
name = 'LrTDDFThyb'
self.Om = Om(self.calculator, self.kss,
self.xc, self.derivative_level, self.numscale,
finegrid=self.finegrid, eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
## self.diagonalize()
def diagonalize(self, istart=None, jend=None, energy_range=None):
self.istart = istart
self.jend = jend
self.Om.diagonalize(istart, jend, energy_range)
# remove old stuff
while len(self): self.pop()
for j in range(len(self.Om.kss)):
self.append(LrTDDFTExcitation(self.Om,j))
def get_Om(self):
return self.Om
def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename)
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace('\n','')
self.name = s.split()[1]
self.xc = f.readline().replace('\n','').split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f,
txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f,
txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
l = f.readline().split()
E = float(l[0])
me = [float(l[1]), float(l[2]), float(l[3])]
self.append(LrTDDFTExcitation(e=E, m=me))
if fh is None:
f.close()
# update own variables
self.istart = self.Om.fullkss.istart
self.jend = self.Om.fullkss.jend
def singlets_triplets(self):
"""Split yourself into a singlet and triplet object"""
slr = LrTDDFT(None, self.nspins, self.eps,
self.istart, self.jend, self.xc,
self.derivative_level, self.numscale)
tlr = LrTDDFT(None, self.nspins, self.eps,
self.istart, self.jend, self.xc,
self.derivative_level, self.numscale)
slr.Om, tlr.Om = self.Om.singlets_triplets()
for lr in [slr, tlr]:
lr.kss = lr.Om.fullkss
return slr, tlr
def single_pole_approximation(self, i, j):
"""Return the excitation according to the
single pole approximation. See e.g.:
Grabo et al, Theochem 501 (2000) 353-367
"""
for ij, kss in enumerate(self.kss):
if kss.i == i and kss.j == j:
return sqrt(self.Om.full[ij][ij]) * Hartree
return self.Om.full[ij][ij] / kss.energy * Hartree
def __str__(self):
string = ExcitationList.__str__(self)
string += '# derived from:\n'
string += self.kss.__str__()
return string
def write(self, filename=None, fh=None):
"""Write current state to a file.
'filename' is the filename. If the filename ends in .gz,
the file is automatically saved in compressed gzip format.
'fh' is a filehandle. This can be used to write into already
opened files.
"""
if mpi.rank == mpi.MASTER:
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename,'wb')
except:
f = open(filename, 'w')
else:
f = open(filename, 'w')
else:
f = fh
f.write('# ' + self.name + '\n')
xc = self.xc
if xc is None: xc = 'RPA'
if self.calculator is not None:
xc += ' ' + self.calculator.get_xc_functional()
f.write(xc + '\n')
f.write('%g %d %g %d' % (self.eps, int(self.derivative_level),
self.numscale, int(self.finegrid)) + '\n')
self.kss.write(fh=f)
self.Om.write(fh=f)
if len(self):
f.write('# Eigenvalues\n')
istart = self.istart
if istart is None:
istart = self.kss.istart
jend = self.jend
if jend is None:
jend = self.kss.jend
f.write('%d %d %d'%(len(self), istart, jend) + '\n')
for ex in self:
f.write(ex.outstring())
f.write('# Eigenvectors\n')
for ex in self:
for w in ex.f:
f.write('%g '%w)
f.write('\n')
if fh is None:
f.close()
def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename)
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace('\n','')
self.name = s.split()[1]
self.xc = f.readline().replace('\n','').split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f,
txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f,
txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
l = f.readline().split()
E = float(l[0])
me = [float(l[1]), float(l[2]), float(l[3])]
self.append(LrTDDFTExcitation(e=E, m=me))
if fh is None:
f.close()
# update own variables
self.istart = self.Om.fullkss.istart
self.jend = self.Om.fullkss.jend
class LrTDDFT(ExcitationList):
"""Linear Response TDDFT excitation class
Input parameters:
calculator:
the calculator object after a ground state calculation
nspins:
number of spins considered in the calculation
Note: Valid only for unpolarised ground state calculation
eps:
Minimal occupation difference for a transition (default 0.001)
istart:
First occupied state to consider
jend:
Last unoccupied state to consider
xc:
Exchange-Correlation approximation in the Kernel
derivative_level:
0: use Exc, 1: use vxc, 2: use fxc if available
filename:
read from a file
"""
def __init__(self, calculator=None, **kwargs):
self.timer = Timer()
self.set(**kwargs)
if isinstance(calculator, str):
ExcitationList.__init__(self, None, self.txt)
self.filename = calculator
else:
ExcitationList.__init__(self, calculator, self.txt)
if self.filename is not None:
return self.read(self.filename)
if self.eh_comm is None:
self.eh_comm = mpi.serial_comm
elif isinstance(self.eh_comm, (mpi.world.__class__,
mpi.serial_comm.__class__)):
# Correct type already.
pass
else:
# world should be a list of ranks:
self.eh_comm = mpi.world.new_communicator(np.asarray(eh_comm))
if calculator is not None and calculator.initialized:
if calculator.wfs.kpt_comm.size > 1:
err_txt = "Spin parallelization with Linear response "
err_txt += "TDDFT. Use parallel = {'domain' : 'domain_only'} "
err_txt += "calculator parameter."
raise NotImplementedError(err_txt)
if self.xc == 'GS':
self.xc = calculator.hamiltonian.xc.name
calculator.converge_wave_functions()
if calculator.density.nct_G is None:
spos_ac = calculator.initialize_positions()
calculator.wfs.initialize(calculator.density,
calculator.hamiltonian, spos_ac)
self.update(calculator)
def set(self, **kwargs):
defaults = {
'nspins' : None,
'eps' : 0.001,
'istart' : 0,
'jend' : None,
'energy_range' : None,
'xc' : 'GS',
'derivative_level' : 1,
'numscale' : 0.00001,
'txt' : None,
'filename' : None,
'finegrid' : 2,
'force_ApmB' : False, # for tests
'eh_comm' : None # parallelization over eh-pairs
}
changed = False
for key, value in defaults.items():
if hasattr(self, key):
value = getattr(self, key) # do not overwrite
setattr(self, key, kwargs.pop(key, value))
if value != getattr(self, key):
changed = True
for key in kwargs:
raise KeyError('Unknown key ' + key)
return changed
def set_calculator(self, calculator):
self.calculator = calculator
# self.force_ApmB = parameters['force_ApmB']
self.force_ApmB = None # XXX
def analyse(self, what=None, out=None, min=0.1):
"""Print info about the transitions.
Parameters:
1. what: I list of excitation indicees, None means all
2. out : I where to send the output, None means sys.stdout
3. min : I minimal contribution to list (0<min<1)
"""
if what is None:
what = range(len(self))
elif isinstance(what, int):
what = [what]
if out is None:
out = sys.stdout
for i in what:
print >> out, str(i) + ':', self[i].analyse(min=min)
def update(self, calculator=None, **kwargs):
changed = self.set(**kwargs)
if calculator is not None:
changed = True
self.set_calculator(calculator)
if not changed:
return
self.forced_update()
def forced_update(self):
"""Recalc yourself."""
nonselfconsistent_xc = None
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
# nonselfconsistent_xc = HybridXC('PBE0', alpha=5.0)
else:
Om = ApmB
name = 'LrTDDFThyb'
self.kss = KSSingles(calculator=self.calculator,
nspins=self.nspins,
nonselfconsistent_xc=nonselfconsistent_xc,
eps=self.eps,
istart=self.istart,
jend=self.jend,
energy_range=self.energy_range,
txt=self.txt)
self.Om = Om(self.calculator, self.kss,
self.xc, self.derivative_level, self.numscale,
finegrid=self.finegrid, eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
def diagonalize(self, istart=None, jend=None,
energy_range=None, TDA=False):
self.timer.start('diagonalize')
self.timer.start('omega')
self.Om.diagonalize(istart, jend, energy_range, TDA)
self.timer.stop('omega')
# remove old stuff
self.timer.start('clean')
while len(self): self.pop()
self.timer.stop('clean')
print >> self.txt, 'LrTDDFT digonalized:'
self.timer.start('build')
for j in range(len(self.Om.kss)):
self.append(LrTDDFTExcitation(self.Om, j))
print >> self.txt, ' ', str(self[-1])
self.timer.stop('build')
self.timer.stop('diagonalize')
def get_Om(self):
return self.Om
def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename)
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace('\n','')
self.name = s.split()[1]
self.xc = f.readline().replace('\n','').split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f,
txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f,
txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
self.append(LrTDDFTExcitation(string=f.readline()))
# load the eigenvectors
f.readline()
for i in range(n):
values = f.readline().split()
weights = [float(val) for val in values]
self[i].f = np.array(weights)
self[i].kss = self.kss
if fh is None:
f.close()
# update own variables
self.istart = self.Om.fullkss.istart
self.jend = self.Om.fullkss.jend
def singlets_triplets(self):
"""Split yourself into a singlet and triplet object"""
slr = LrTDDFT(None, nspins=self.nspins, eps=self.eps,
istart=self.istart, jend=self.jend, xc=self.xc,
derivative_level=self.derivative_level,
numscale=self.numscale)
tlr = LrTDDFT(None, nspins=self.nspins, eps=self.eps,
istart=self.istart, jend=self.jend, xc=self.xc,
derivative_level=self.derivative_level,
numscale=self.numscale)
slr.Om, tlr.Om = self.Om.singlets_triplets()
for lr in [slr, tlr]:
lr.kss = lr.Om.fullkss
return slr, tlr
def single_pole_approximation(self, i, j):
"""Return the excitation according to the
single pole approximation. See e.g.:
Grabo et al, Theochem 501 (2000) 353-367
"""
for ij, kss in enumerate(self.kss):
if kss.i == i and kss.j == j:
return sqrt(self.Om.full[ij][ij]) * Hartree
return self.Om.full[ij][ij] / kss.energy * Hartree
def __str__(self):
string = ExcitationList.__str__(self)
string += '# derived from:\n'
string += self.Om.kss.__str__()
return string
def write(self, filename=None, fh=None):
"""Write current state to a file.
'filename' is the filename. If the filename ends in .gz,
the file is automatically saved in compressed gzip format.
'fh' is a filehandle. This can be used to write into already
opened files.
"""
if mpi.rank == mpi.MASTER:
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename,'wb')
except:
f = open(filename, 'w')
else:
f = open(filename, 'w')
else:
f = fh
f.write('# ' + self.name + '\n')
xc = self.xc
if xc is None: xc = 'RPA'
if self.calculator is not None:
xc += ' ' + self.calculator.get_xc_functional()
f.write(xc + '\n')
f.write('%g %d %g %d' % (self.eps, int(self.derivative_level),
self.numscale, int(self.finegrid)) + '\n')
self.kss.write(fh=f)
self.Om.write(fh=f)
if len(self):
f.write('# Eigenvalues\n')
istart = self.istart
if istart is None:
istart = self.kss.istart
jend = self.jend
if jend is None:
jend = self.kss.jend
f.write('%d %d %d'%(len(self), istart, jend) + '\n')
for ex in self:
f.write(ex.outstring())
f.write('# Eigenvectors\n')
for ex in self:
for w in ex.f:
f.write('%g '%w)
f.write('\n')
if fh is None:
f.close()
class LrTDDFT(ExcitationList):
"""Linear Response TDDFT excitation class
Input parameters:
calculator:
the calculator object after a ground state calculation
nspins:
number of spins considered in the calculation
Note: Valid only for unpolarised ground state calculation
eps:
Minimal occupation difference for a transition (default 0.001)
istart:
First occupied state to consider
jend:
Last unoccupied state to consider
xc:
Exchange-Correlation approximation in the Kernel
derivative_level:
0: use Exc, 1: use vxc, 2: use fxc if available
filename:
read from a file
"""
def __init__(
self,
calculator=None,
nspins=None,
eps=0.001,
istart=0,
jend=None,
energy_range=None,
xc=None,
derivative_level=1,
numscale=0.00001,
txt=None,
filename=None,
finegrid=2,
force_ApmB=False, # for tests
eh_comm=None # parallelization over eh-pairs
):
self.nspins = None
self.istart = None
self.jend = None
if isinstance(calculator, str):
ExcitationList.__init__(self, None, txt)
return self.read(calculator)
else:
ExcitationList.__init__(self, calculator, txt)
if filename is not None:
return self.read(filename)
self.filename = None
self.calculator = None
self.eps = None
self.xc = None
self.derivative_level = None
self.numscale = numscale
self.finegrid = finegrid
self.force_ApmB = force_ApmB
if eh_comm is None:
eh_comm = mpi.serial_comm
elif isinstance(eh_comm,
(mpi.world.__class__, mpi.serial_comm.__class__)):
# Correct type already.
pass
else:
# world should be a list of ranks:
eh_comm = mpi.world.new_communicator(np.asarray(eh_comm))
self.eh_comm = eh_comm
if calculator is not None:
calculator.converge_wave_functions()
if calculator.density.nct_G is None:
calculator.set_positions()
self.update(calculator, nspins, eps, istart, jend, energy_range,
xc, derivative_level, numscale)
def analyse(self, what=None, out=None, min=0.1):
"""Print info about the transitions.
Parameters:
1. what: I list of excitation indicees, None means all
2. out : I where to send the output, None means sys.stdout
3. min : I minimal contribution to list (0<min<1)
"""
if what is None:
what = range(len(self))
elif isinstance(what, int):
what = [what]
if out is None:
out = sys.stdout
for i in what:
print >> out, str(i) + ':', self[i].analyse(min=min)
def update(self,
calculator=None,
nspins=None,
eps=0.001,
istart=0,
jend=None,
energy_range=None,
xc=None,
derivative_level=None,
numscale=0.001):
changed = False
if self.calculator != calculator or \
self.nspins != nspins or \
self.eps != eps or \
self.istart != istart or \
self.jend != jend :
changed = True
if not changed: return
self.calculator = calculator
self.nspins = nspins
self.eps = eps
self.istart = istart
self.jend = jend
self.xc = xc
self.derivative_level = derivative_level
self.numscale = numscale
self.kss = KSSingles(calculator=calculator,
nspins=nspins,
eps=eps,
istart=istart,
jend=jend,
energy_range=energy_range,
txt=self.txt)
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
else:
Om = ApmB
name = 'LrTDDFThyb'
self.Om = Om(self.calculator,
self.kss,
self.xc,
self.derivative_level,
self.numscale,
finegrid=self.finegrid,
eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
## self.diagonalize()
def diagonalize(self, istart=None, jend=None, energy_range=None):
self.istart = istart
self.jend = jend
self.Om.diagonalize(istart, jend, energy_range)
# remove old stuff
while len(self):
self.pop()
for j in range(len(self.Om.kss)):
self.append(LrTDDFTExcitation(self.Om, j))
def get_Om(self):
return self.Om
def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename)
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace('\n', '')
self.name = s.split()[1]
self.xc = f.readline().replace('\n', '').split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f, txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f, txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
l = f.readline().split()
E = float(l[0])
me = [float(l[1]), float(l[2]), float(l[3])]
self.append(LrTDDFTExcitation(e=E, m=me))
if fh is None:
f.close()
# update own variables
self.istart = self.Om.fullkss.istart
self.jend = self.Om.fullkss.jend
def singlets_triplets(self):
"""Split yourself into a singlet and triplet object"""
slr = LrTDDFT(None, self.nspins, self.eps, self.istart, self.jend,
self.xc, self.derivative_level, self.numscale)
tlr = LrTDDFT(None, self.nspins, self.eps, self.istart, self.jend,
self.xc, self.derivative_level, self.numscale)
slr.Om, tlr.Om = self.Om.singlets_triplets()
for lr in [slr, tlr]:
lr.kss = lr.Om.fullkss
return slr, tlr
def single_pole_approximation(self, i, j):
"""Return the excitation according to the
single pole approximation. See e.g.:
Grabo et al, Theochem 501 (2000) 353-367
"""
for ij, kss in enumerate(self.kss):
if kss.i == i and kss.j == j:
return sqrt(self.Om.full[ij][ij]) * Hartree
return self.Om.full[ij][ij] / kss.energy * Hartree
def __str__(self):
string = ExcitationList.__str__(self)
string += '# derived from:\n'
string += self.kss.__str__()
return string
def write(self, filename=None, fh=None):
"""Write current state to a file.
'filename' is the filename. If the filename ends in .gz,
the file is automatically saved in compressed gzip format.
'fh' is a filehandle. This can be used to write into already
opened files.
"""
if mpi.rank == mpi.MASTER:
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename, 'wb')
except:
f = open(filename, 'w')
else:
f = open(filename, 'w')
else:
f = fh
f.write('# ' + self.name + '\n')
xc = self.xc
if xc is None: xc = 'RPA'
if self.calculator is not None:
xc += ' ' + self.calculator.get_xc_functional()
f.write(xc + '\n')
f.write('%g %d %g %d' % (self.eps, int(self.derivative_level),
self.numscale, int(self.finegrid)) + '\n')
self.kss.write(fh=f)
self.Om.write(fh=f)
if len(self):
f.write('# Eigenvalues\n')
istart = self.istart
if istart is None:
istart = self.kss.istart
jend = self.jend
if jend is None:
jend = self.kss.jend
f.write('%d %d %d' % (len(self), istart, jend) + '\n')
for ex in self:
f.write(ex.outstring())
f.write('# Eigenvectors\n')
for ex in self:
for w in ex.f:
f.write('%g ' % w)
f.write('\n')
if fh is None:
f.close()
def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith(".gz"):
try:
import gzip
f = gzip.open(filename)
except:
f = open(filename, "r")
else:
f = open(filename, "r")
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace("\n", "")
self.name = s.split()[1]
self.xc = f.readline().replace("\n", "").split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == "LrTDDFT":
self.Om = OmegaMatrix(kss=self.kss, filehandle=f, txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f, txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != "# Eigenvalues\n":
# go back to previous position
f.seek(p)
else:
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
self.append(LrTDDFTExcitation(string=f.readline()))
# load the eigenvectors
f.readline()
for i in range(n):
values = f.readline().split()
weights = [float(val) for val in values]
self[i].f = np.array(weights)
self[i].kss = self.kss
if fh is None:
f.close()
# update own variables
self.istart = self.Om.fullkss.istart
self.jend = self.Om.fullkss.jend
class LrTDDFT(ExcitationList):
"""Linear Response TDDFT excitation class
Input parameters:
calculator:
the calculator object after a ground state calculation
nspins:
number of spins considered in the calculation
Note: Valid only for unpolarised ground state calculation
eps:
Minimal occupation difference for a transition (default 0.001)
istart:
First occupied state to consider
jend:
Last unoccupied state to consider
xc:
Exchange-Correlation approximation in the Kernel
derivative_level:
0: use Exc, 1: use vxc, 2: use fxc if available
filename:
read from a file
"""
default_parameters = {
'nspins': None,
'eps': 0.001,
'istart': 0,
'jend': sys.maxsize,
'energy_range': None,
'xc': 'GS',
'derivative_level': 1,
'numscale': 0.00001,
'txt': None,
'filename': None,
'finegrid': 2,
'force_ApmB': False, # for tests
'eh_comm': None} # parallelization over eh-pairs
def __init__(self, calculator=None, **kwargs):
self.timer = Timer()
self.diagonalized = False
changed = self.set(**kwargs)
if isinstance(calculator, str):
ExcitationList.__init__(self, None, self.txt)
self.filename = calculator
else:
ExcitationList.__init__(self, calculator, self.txt)
if self.filename is not None:
self.read(self.filename)
if set(['istart', 'jend', 'energy_range']) & set(changed):
# the user has explicitely demanded these
self.diagonalize()
return
if self.eh_comm is None:
self.eh_comm = mpi.serial_comm
elif isinstance(self.eh_comm, (mpi.world.__class__,
mpi.serial_comm.__class__)):
# Correct type already.
pass
else:
# world should be a list of ranks:
self.eh_comm = mpi.world.new_communicator(
np.asarray(self.eh_comm))
if calculator is not None and calculator.initialized:
if not isinstance(calculator.wfs, FDWaveFunctions):
raise RuntimeError(
'Linear response TDDFT supported only in real space mode')
if calculator.wfs.kd.comm.size > 1:
err_txt = 'Spin parallelization with Linear response '
err_txt += "TDDFT. Use parallel={'domain': world.size} "
err_txt += 'calculator parameter.'
raise NotImplementedError(err_txt)
if self.xc == 'GS':
self.xc = calculator.hamiltonian.xc.name
if calculator.parameters.mode != 'lcao':
calculator.converge_wave_functions()
if calculator.density.nct_G is None:
spos_ac = calculator.initialize_positions()
calculator.wfs.initialize(calculator.density,
calculator.hamiltonian, spos_ac)
self.update(calculator)
def set(self, **kwargs):
"""Change parameters."""
changed = []
for key, value in LrTDDFT.default_parameters.items():
if hasattr(self, key):
value = getattr(self, key) # do not overwrite
setattr(self, key, kwargs.pop(key, value))
if value != getattr(self, key):
changed.append(key)
for key in kwargs:
raise KeyError('Unknown key ' + key)
return changed
def set_calculator(self, calculator):
self.calculator = calculator
# self.force_ApmB = parameters['force_ApmB']
self.force_ApmB = None # XXX
def analyse(self, what=None, out=None, min=0.1):
"""Print info about the transitions.
Parameters:
1. what: I list of excitation indicees, None means all
2. out : I where to send the output, None means sys.stdout
3. min : I minimal contribution to list (0<min<1)
"""
if what is None:
what = range(len(self))
elif isinstance(what, numbers.Integral):
what = [what]
if out is None:
out = sys.stdout
for i in what:
print(str(i) + ':', self[i].analyse(min=min), file=out)
def update(self, calculator=None, **kwargs):
changed = self.set(**kwargs)
if calculator is not None:
changed = True
self.set_calculator(calculator)
if not changed:
return
self.forced_update()
def forced_update(self):
"""Recalc yourself."""
if not self.force_ApmB:
Om = OmegaMatrix
name = 'LrTDDFT'
if self.xc:
xc = XC(self.xc)
if hasattr(xc, 'hybrid') and xc.hybrid > 0.0:
Om = ApmB
name = 'LrTDDFThyb'
else:
Om = ApmB
name = 'LrTDDFThyb'
self.kss = KSSingles(calculator=self.calculator,
nspins=self.nspins,
eps=self.eps,
istart=self.istart,
jend=self.jend,
energy_range=self.energy_range,
txt=self.txt)
self.Om = Om(self.calculator, self.kss,
self.xc, self.derivative_level, self.numscale,
finegrid=self.finegrid, eh_comm=self.eh_comm,
txt=self.txt)
self.name = name
def diagonalize(self, **kwargs):
self.set(**kwargs)
self.timer.start('diagonalize')
self.timer.start('omega')
self.Om.diagonalize(self.istart, self.jend, self.energy_range)
self.timer.stop('omega')
self.diagonalized = True
# remove old stuff
self.timer.start('clean')
while len(self):
self.pop()
self.timer.stop('clean')
print('LrTDDFT digonalized:', file=self.txt)
self.timer.start('build')
for j in range(len(self.Om.kss)):
self.append(LrTDDFTExcitation(self.Om, j))
print(' ', str(self[-1]), file=self.txt)
self.timer.stop('build')
self.timer.stop('diagonalize')
def get_Om(self):
return self.Om
def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename, 'rt')
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace('\n', '')
self.name = s.split()[1]
self.xc = f.readline().replace('\n', '').split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f,
txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f,
txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
self.diagonalized = True
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
self.append(LrTDDFTExcitation(string=f.readline()))
# load the eigenvectors
f.readline()
for i in range(n):
values = f.readline().split()
weights = [float(val) for val in values]
self[i].f = np.array(weights)
self[i].kss = self.kss
if fh is None:
f.close()
def singlets_triplets(self):
"""Split yourself into a singlet and triplet object"""
slr = LrTDDFT(None, nspins=self.nspins, eps=self.eps,
istart=self.istart, jend=self.jend, xc=self.xc,
derivative_level=self.derivative_level,
numscale=self.numscale)
tlr = LrTDDFT(None, nspins=self.nspins, eps=self.eps,
istart=self.istart, jend=self.jend, xc=self.xc,
derivative_level=self.derivative_level,
numscale=self.numscale)
slr.Om, tlr.Om = self.Om.singlets_triplets()
for lr in [slr, tlr]:
lr.kss = lr.Om.fullkss
return slr, tlr
def single_pole_approximation(self, i, j):
"""Return the excitation according to the
single pole approximation. See e.g.:
Grabo et al, Theochem 501 (2000) 353-367
"""
for ij, kss in enumerate(self.kss):
if kss.i == i and kss.j == j:
return sqrt(self.Om.full[ij][ij]) * Hartree
return self.Om.full[ij][ij] / kss.energy * Hartree
def __str__(self):
string = ExcitationList.__str__(self)
string += '# derived from:\n'
string += self.Om.kss.__str__()
return string
def write(self, filename=None, fh=None):
"""Write current state to a file.
'filename' is the filename. If the filename ends in .gz,
the file is automatically saved in compressed gzip format.
'fh' is a filehandle. This can be used to write into already
opened files.
"""
if self.calculator is None:
rank = mpi.world.rank
else:
rank = self.calculator.wfs.world.rank
if rank == 0:
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename, 'wt')
except:
f = open(filename, 'w')
else:
f = open(filename, 'w')
else:
f = fh
f.write('# ' + self.name + '\n')
xc = self.xc
if xc is None:
xc = 'RPA'
if self.calculator is not None:
xc += ' ' + self.calculator.get_xc_functional()
f.write(xc + '\n')
f.write('%g %d %g %d' % (self.eps, int(self.derivative_level),
self.numscale, int(self.finegrid)) + '\n')
self.kss.write(fh=f)
self.Om.write(fh=f)
if len(self):
f.write('# Eigenvalues\n')
istart = self.istart
if istart is None:
istart = self.kss.istart
jend = self.jend
if jend is None:
jend = self.kss.jend
f.write('%d %d %d' % (len(self), istart, jend) + '\n')
for ex in self:
f.write(ex.outstring())
f.write('# Eigenvectors\n')
for ex in self:
for w in ex.f:
f.write('%g ' % w)
f.write('\n')
if fh is None:
f.close()
mpi.world.barrier()
def __getitem__(self, i):
if not self.diagonalized:
self.diagonalize()
return list.__getitem__(self, i)
def __iter__(self):
if not self.diagonalized:
self.diagonalize()
return list.__iter__(self)
def __len__(self):
if not self.diagonalized:
self.diagonalize()
return list.__len__(self)
def read(self, filename=None, fh=None):
"""Read myself from a file"""
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename, 'rt')
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
# get my name
s = f.readline().replace('\n', '')
self.name = s.split()[1]
self.xc = f.readline().replace('\n', '').split()[0]
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
self.kss = KSSingles(filehandle=f)
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f,
txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f,
txt=self.txt)
self.Om.Kss(self.kss)
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
self.diagonalized = True
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
self.append(LrTDDFTExcitation(string=f.readline()))
# load the eigenvectors
f.readline()
for i in range(n):
values = f.readline().split()
weights = [float(val) for val in values]
self[i].f = np.array(weights)
self[i].kss = self.kss
if fh is None:
f.close()
def read(self, filename=None, fh=None):
"""Read myself from a file"""
timer = self.timer
timer.start('name')
if fh is None:
if filename.endswith('.gz'):
try:
import gzip
f = gzip.open(filename, 'rt')
except:
f = open(filename, 'r')
else:
f = open(filename, 'r')
self.filename = filename
else:
f = fh
self.filename = None
timer.stop('name')
timer.start('header')
# get my name
s = f.readline().strip()
self.name = s.split()[1]
self.xc = XC(f.readline().strip().split()[0])
values = f.readline().split()
self.eps = float(values[0])
if len(values) > 1:
self.derivative_level = int(values[1])
self.numscale = float(values[2])
self.finegrid = int(values[3])
else:
# old writing style, use old defaults
self.numscale = 0.001
timer.stop('header')
timer.start('init_kss')
self.kss = KSSingles(filehandle=f)
timer.stop('init_kss')
timer.start('init_obj')
if self.name == 'LrTDDFT':
self.Om = OmegaMatrix(kss=self.kss, filehandle=f, txt=self.txt)
else:
self.Om = ApmB(kss=self.kss, filehandle=f, txt=self.txt)
self.Om.fullkss = self.kss
timer.stop('init_obj')
timer.start('read diagonalized')
# check if already diagonalized
p = f.tell()
s = f.readline()
if s != '# Eigenvalues\n':
# go back to previous position
f.seek(p)
else:
self.diagonalized = True
# load the eigenvalues
n = int(f.readline().split()[0])
for i in range(n):
self.append(LrTDDFTExcitation(string=f.readline()))
# load the eigenvectors
timer.start('read eigenvectors')
f.readline()
for i in range(n):
self[i].f = np.array([float(x) for x in f.readline().split()])
self[i].kss = self.kss
timer.stop('read eigenvectors')
timer.stop('read diagonalized')
if fh is None:
f.close()