def HLC_generic(A=0.009170, B=0.004455, C=0.009155, D=0.001947):
'''calculate High Level Correction term
from alpha and beta VALENCE electron count.
'''
global Ehlc
say('HLC.')
nClosed = nwchem.rtdb_get("scf:nclosed")
nOpen = nwchem.rtdb_get("scf:nopen")
nElec = nwchem.rtdb_get("scf:nelec")
nFrozen = sum_core_orbitals()
# According to Curtiss,
# nBeta = num valence pairs
# nAlpha = num unpaired or remaining valence electrons
# subject to the constraint that nAlpha >= nBeta
nBeta = nClosed - nFrozen
nAlpha = nElec - (nFrozen * 2) - nBeta
debug('\nclosed=%d open=%d frozen=%d nAlpha=%d nBeta=%d\n' %
(nClosed,nOpen,nFrozen,nAlpha,nBeta))
if nAlpha < nBeta:
nAlpha, nBeta = nBeta, nAlpha
if is_molecule():
Ehlc = -(A * nBeta) - B * (nAlpha - nBeta)
else: # it's an atom, calc is different
Ehlc = -(C * nBeta) - D * (nAlpha - nBeta)
return False
def E_hlc ():
# E_hlc = High Level Correction
global Ehlc
# Correction coefficients in milli Hartrees
# closed shell
A = 0.009472
# open shell
Ap = 0.009769
B = 0.003179
# atoms and atom ions
C = 0.009741
D = 0.002115
# single electron pair species
# e.g.: Li2, Na2, LiNa, BeH2, BeH+
E = 0.002379
say('HLC.')
nClosed = nwchem.rtdb_get("scf:nclosed")
nOpen = nwchem.rtdb_get("scf:nopen")
nElec = nwchem.rtdb_get("scf:nelec")
nFrozen = sum_core_orbitals()
# According to Curtiss,
# nBeta = num valence pairs
# nAlpha = num unpaired or remaining valence electrons
# subject to the constraint that nAlpha >= nBeta
nBeta = nClosed - nFrozen
nAlpha = nElec - nFrozen - nClosed
debug ('\nclosed=%d open=%d frozen=%d nAlpha=%d nBeta=%d\n' % \
(nClosed,nOpen,nFrozen,nAlpha,nBeta))
if nAlpha < nBeta:
nAlpha,nBeta = nBeta,nAlpha
# test for single (valence) electron pair species
if (nOpen == 0) and (nClosed - nFrozen) == 1 and \
(nAlpha == 1) and (nBeta == 1):
hlc = E
elif is_atom():
hlc = -C * (nBeta) - D * (nAlpha-nBeta)
elif Multiplicity > 1:
hlc = -Ap * (nBeta) - B * (nAlpha-nBeta)
else: # USUAL CASE: singlet, closed shell
hlc = -A * (nBeta)
Ehlc = hlc
return False
def E_hlc(self):
"""E_hlc = High Level Correction
"""
# Correction coefficients in milli Hartrees
# closed shell
A = 0.009472
# open shell
Ap = 0.009769
B = 0.003179
# atoms and atom ions
C = 0.009741
D = 0.002115
# single electron pair species
# e.g.: Li2, Na2, LiNa, BeH2, BeH+
E = 0.002379
self.say('HLC.')
nClosed = nwchem.rtdb_get("scf:nclosed")
nOpen = nwchem.rtdb_get("scf:nopen")
nElec = nwchem.rtdb_get("scf:nelec")
self.nFrozen = self.sum_core_orbitals()
# According to Curtiss,
# nBeta = num valence pairs
# nAlpha = num unpaired or remaining valence electrons
# subject to the constraint that nAlpha >= nBeta
self.nBeta = nClosed - self.nFrozen
self.nAlpha = nElec - self.nFrozen - nClosed
self.debug('\nclosed=%d open=%d frozen=%d nAlpha=%d nBeta=%d\n' % \
(nClosed, nOpen, self.nFrozen, self.nAlpha, self.nBeta))
if self.nAlpha < self.nBeta:
self.nAlpha, self.nBeta = self.nBeta, self.nAlpha
#self.say('** a<->b swap: nAlpha=%d nBeta=%d\n' % (self.nAlpha,self.nBeta))
# test for single (valence) electron pair species
if (nOpen == 0) and (nClosed - self.nFrozen) == 1 and \
(self.nAlpha == 1) and (self.nBeta == 1):
hlc = E
elif self.is_atom():
hlc = -C * (self.nBeta) - D * (self.nAlpha - self.nBeta)
elif self.multiplicity != "singlet":
hlc = -Ap * (self.nBeta) - B * (self.nAlpha - self.nBeta)
else: # USUAL CASE: singlet, closed shell
hlc = -A * (self.nBeta)
self.Ehlc = hlc
def set_atoms_list():
global AtomsList
global NumAtoms
# rtdb_get() returns a string if only one atom
# or a list of atoms (i.e., tags).
# Absent type handling,
# len('CU') is the same as len(['C','U'])
#
tags = nwchem.rtdb_get("geometry:geometry:tags")
tag_type = type(tags).__name__
if type(tags).__name__ == 'str':
AtomsList.append(tags)
debug('AtomsList: %s\n' % tags)
elif tag_type == 'list':
AtomsList.extend(tags)
if debug_flag:
atmstr = ''
for atm in tags:
atmstr += ' ' + atm
debug('AtomsList: %s\n' % atmstr)
else:
AtomsList = []
NumAtoms = len(AtomsList)
debug('NumAtoms=%d\n' % NumAtoms)
def init_g3mp2(charge=0, mult='singlet', use_qcisdt_f=False):
'''say hello
'''
set_charge(charge)
set_multiplicity(mult)
if get_multiplicity() > 1:
set_HFtype('uhf')
else:
set_HFtype('rhf')
if use_qcisdt_f:
use_qcisdt()
else:
use_ccsdt()
if QCISDT_flag:
ccstring = 'QCISD(T)'
else:
ccstring = 'CCSD(T)'
title = nwchem.rtdb_get("title")
say(" %s -- NWChem G3(MP2,%s) Composite Method\n" % (title, ccstring))
return False
def set_atoms_list():
global AtomsList
global NumAtoms
# rtdb_get() returns EITHER
# a string if only one atom, or
# a list of atoms (i.e., tags).
#
# Without type handling,
# len('CU') is the same as len(['C','U'])
#
tags = nwchem.rtdb_get("geometry:geometry:tags")
tag_type = type(tags).__name__
if tag_type == "str":
AtomsList.append(tags)
debug("AtomsList: %s\n" % tags)
elif tag_type == "list":
AtomsList.extend(tags)
if debug_flag:
atmstr = ""
for atm in tags:
atmstr += " " + atm
debug("AtomsList: %s\n" % atmstr)
else:
AtomsList = []
NumAtoms = len(AtomsList)
debug("NumAtoms=%d\n" % NumAtoms)
def init_g4mp2(self):
"""Say hello.
"""
title = nwchem.rtdb_get("title")
self.say(" %s -- NWChem G4(MP2) Composite Method\n" % (title))
return False
def get_theory():
theory = nwchem.rtdb_get('task:theory').lower()
if theory == 'dft':
scf = nwchem.rtdb_get('dft:scftype').lower()
else:
scf = nwchem.rtdb_get('scf:scftype').lower()
if theory == 'scf':
return scf
elif theory == 'dft':
if scf == 'uhf':
return 'uks'
elif scf == 'rhf':
return 'rks'
# if here, it wasn't handled
raise NotImplementedError('%s %s' % (theory, scf))
def get_theory():
theory = nwchem.rtdb_get('task:theory').lower()
if theory == 'dft':
scf = nwchem.rtdb_get('dft:scftype').lower()
else:
scf = nwchem.rtdb_get('scf:scftype').lower()
if theory == 'scf':
return scf
elif theory == 'dft':
if scf == 'uhf':
return 'uks'
elif scf =='rhf':
return 'rks'
# if here, it wasn't handled
raise NotImplementedError('%s %s' % (theory, scf))
def geometry_hash(self):
"""Produce a hashed geometry identifier from the geometry in the
RTDB. This is useful to generate file names for writing and reading
geometry to/from disk.
:return: sha1 hex digest of geometry
:rtype : str
"""
keys = [nwchem.rtdb_first()]
while True:
try:
keys.append(nwchem.rtdb_next())
except nwchem.NWChemError:
break
ckey = [k for k in keys if "coords" in k and "geometry" in k][0]
tkey = [k for k in keys if "tags" in k and "geometry" in k][0]
coords = nwchem.rtdb_get(ckey)
tags = nwchem.rtdb_get(tkey)
fused = " ".join([str(c) for c in coords]) + " ".join([str(t) for t in tags])
result = hashlib.sha1(fused).hexdigest()
return result
def init_g4mp2(charge=0, mult="singlet"):
"""say hello
"""
set_charge(charge)
set_multiplicity(mult)
if get_multiplicity() > 1:
set_HFtype("uhf")
else:
set_HFtype("rhf")
title = nwchem.rtdb_get("title")
say(" %s -- NWChem G4(MP2) Composite Method\n" % (title))
return False
def init_g4mp2(charge=0,mult='singlet'):
'''say hello
'''
set_charge(charge)
set_multiplicity(mult)
if get_multiplicity() > 1:
set_HFtype('uhf')
else:
set_HFtype('rhf')
title = nwchem.rtdb_get("title")
say(" %s -- NWChem G4(MP2) Composite Method\n" % (title))
return False
def initialize_atoms_list(self):
"""Use NWChem's RTDB geometry to initialize self.atoms,
e.g. CH3OH gives ['C','H','H','H','O''H']
"""
# rtdb_get() returns a string if only one atom
# or a list of atoms (i.e., tags).
# Absent type handling,
# len('CU') is the same as len(['C','U'])
tags = nwchem.rtdb_get("geometry:geometry:tags")
if type(tags) == str:
self.atoms.append(tags)
self.debug('AtomsList: %s\n' % tags)
else:
self.atoms.extend(tags)
if self.debug_flag:
atmstr=''
for atm in tags:
atmstr += ' '+atm
self.debug('AtomsList: %s\n' % atmstr)
self.debug('NumAtoms={0}\n'.format(len(self.atoms)))
def get_scftype():
if nwchem.rtdb_get('task:theory').lower() == 'dft':
return nwchem.rtdb_get('dft:scftype')
else:
return nwchem.rtdb_get('scf:scftype')
def get_spin_multiplicity():
return nwchem.rtdb_get('dft:mult')
def get_dipole():
return nwchem.rtdb_get('%s:dipole' % _PROPERTYGROUP)
def prep():
global _PROPERTYGROUP
nwchem.rtdb_open('perm/mol.db', 'old')
_PROPERTYGROUP = nwchem.rtdb_get('task:theory')
def get_atomic_numbers():
return map(int, nwchem.rtdb_get('geometry:geometry:charges'))
def get_atom_names():
return nwchem.rtdb_get('geometry:geometry:tags')
def get_atom_names():
return nwchem.rtdb_get('geometry:geometry:tags')
def get_total_charge():
return int(nwchem.rtdb_get('charge'))
def get_converged():
return 1 == nwchem.rtdb_get('%s:converged' % _PROPERTYGROUP)
def get_functional():
return nwchem.rtdb_get('dft:xc_spec')
def get_symmetry():
return nwchem.rtdb_get('geometry:geometry:group name')
def get_basis():
return nwchem.rtdb_get('basis:ao basis:star bas type')
def get_scftype():
if nwchem.rtdb_get('task:theory').lower() == 'dft':
return nwchem.rtdb_get('dft:scftype')
else:
return nwchem.rtdb_get('scf:scftype')
def get_potential_energy():
return nwchem.rtdb_get('%s:energy' % _PROPERTYGROUP)
def HF_zpe():
''' run hessian on equilibrium geometry
get zero point energy.
n
note: linear tri-atomics and larger
give high ZPE values in NWChem @ HF/6-31G*
'''
global Ezpe
global Ethermal
global Hthermal
global AtomsList
#AUKCAL = 627.5093314 # bogus
AUKCAL = kCalPerHartree
c = 2.99792458E+10
h = 6.62606957E-27
kgas = 1.3806488E-16 # cgs units
Rgas = 1.9872041 / 1000.0 / AUKCAL # atomic units
temperature = T298
say("zpe.")
if is_atom():
Ezpe = 0.0
Ethermal = 1.5 * Rgas * temperature
Hthermal = Ethermal + (Rgas * temperature)
# Ethermal = 0.001416 # 3/2 * RT
# Hthermal = 0.002360 # Ethermal + kT
return False
# run hessian on equilibrium geometry
# ignore ZPE, calculate it from vibrations list
zpe, vibs, intens = nwchem.task_freq("scf")
# Handroll the ZPE because NWChem's zpe accumulates
# truncation error from 3 sigfig physical constants.
vibsum = 0.0
for freq in vibs:
if (freq > 0.1):
vibsum += freq
cm2Ha = 219474.6 # cm-1 to Hartree conversion
Ezpe = vibsum / (2.0 * cm2Ha)
# get total thermal energy, enthalpy
eth = nwchem.rtdb_get("vib:ethermal")
hth = nwchem.rtdb_get("vib:hthermal")
debug("NWChem zpe,E,H thermal= %.6f, %.6f, %.6f\n" % (Ezpe,eth, hth))
eth = 0.0
hth = 0.0
xdum = 0.0
for freq in vibs:
if (freq > 0.1):
# freqency temperature in Kelvin from cm-1
thetav = freq * (h * c / kgas)
if (temperature > 0.0):
xdum = math.exp(-thetav / temperature)
else:
xdum = 0.0
xdum = xdum / (1.0 - xdum)
eth = eth + thetav * (0.5 + xdum)
# linear boolean is available only after task_freq('scf') runs
# NWChem only writes the flag if molecule is linear
eth = eth * Rgas
try:
is_linear = nwchem.rtdb_get("vib:linear")
except:
is_linear = False
if (is_linear and QCISDT_flag):
# translational(3/2RT) and rotation(2/2RT) thermal corrections
eth = eth + 2.5 * Rgas * temperature
else:
# translational(3/2RT) and rotation(3/2RT) thermal corrections
eth = eth + 3.0 * Rgas * temperature
# Hthermal = eth+pV=eth+RT, since pV=RT
hth = eth + Rgas * temperature
debug("RgasT= %.9f, kT_298_perMol= %.9f\n" %
(Rgas * temperature, kT_298_perMol))
debug("Handrolled E,H thermal= %.6f, %.6f\n" % (eth, hth))
Ethermal = eth
Hthermal = hth
return False
def get_spin_multiplicity():
try:
return nwchem.rtdb_get('dft:mult')
except SystemError:
return None
def get_atom_masses():
return nwchem.rtdb_get('geometry:geometry:masses')
def get_positions():
return _reshape_atom_vector(nwchem.rtdb_get('geometry:geometry:coords'))
def get_converged():
return 1 == nwchem.rtdb_get('%s:converged' % _PROPERTYGROUP)
def get_atom_masses():
return nwchem.rtdb_get('geometry:geometry:masses')
def get_forces():
try:
forces = nwchem.rtdb_get('%s:gradient' % _PROPERTYGROUP)
return _reshape_atom_vector([-f for f in forces])
except SystemError:
return None
def get_functional():
try:
return nwchem.rtdb_get('dft:xc_spec')
except SystemError:
return None
def prep():
global _PROPERTYGROUP
nwchem.rtdb_open('perm/mol.db', 'old')
_PROPERTYGROUP = nwchem.rtdb_get('task:theory')
def get_dipole():
try:
return nwchem.rtdb_get('%s:dipole' % _PROPERTYGROUP)
except SystemError:
return None
def get_atomic_numbers():
return map(int, nwchem.rtdb_get('geometry:geometry:charges'))
def get_potential_energy():
return nwchem.rtdb_get('%s:energy' % _PROPERTYGROUP)
def get_positions():
return _reshape_atom_vector(nwchem.rtdb_get('geometry:geometry:coords'))
def get_total_charge():
return int(nwchem.rtdb_get('charge'))
def E_zpe(self):
"""Run hessian on equilibrium geometry, get zero point energy.
n
Note: linear tri-atomics and larger give high ZPE values in
NWChem @ HF/6-31G*
"""
self.say('ZPE.')
AUKCAL = 627.5093314
c = 2.99792458E+10
h = 6.62606957E-27
kgas = 1.3806488E-16 # cgs units
Rgas = 1.9872041/1000.0/AUKCAL # atomic units
temperature = 298.15
if self.is_atom():
self.Ezpe = 0.0
self.Ethermal = 1.5 * Rgas * temperature # 3/2 * RT
self.Hthermal = self.Ethermal + (Rgas * temperature)
return False
# run hessian on equilibrium geometry
# ignore ZPE, calculate it from vibrations list
zpe, vibs, intens = nwchem.task_freq("dft")
# Handroll the ZPE because NWChem's zpe accumulates
# truncation error from 3 sigfig physical constants.
vibsum = 0.0
for freq in vibs:
if (freq > 0.1):
vibsum += freq
cm2Ha = 219474.6 # cm-1 to Hartree conversion
self.Ezpe = vibsum / (2.0 * cm2Ha)
# shamelessly swipe code from NWCHEM/src/vib_wrtFreq.F
eth = 0.0
hth = 0.0
xdum = 0.0
for freq in vibs:
if (freq > 0.1):
thetav = freq * (h * c / kgas) #freqency temperature in Kelvin from cm-1
if (temperature > 0.0):
xdum = math.exp(-thetav/temperature)
else:
xdum = 0.0
xdum = xdum / (1.0 - xdum)
eth = eth + thetav * (0.5 + xdum)
eth = eth * Rgas
# linear boolean is available only after task_freq('scf') runs
# NWChem only writes the flag if molecule is linear
try:
is_linear = nwchem.rtdb_get("vib:linear")
except:
is_linear = False
if (is_linear):
# translational(3/2RT) and rotation(2/2RT) thermal corrections
eth = eth + 2.5 * Rgas * temperature
else:
# translational(3/2RT) and rotation(3/2RT) thermal corrections
eth = eth + 3.0 * Rgas * temperature
# Hthermal = eth+pV=eth+RT, since pV=RT
hth = eth + Rgas * temperature
self.debug("Handrolled E,H thermal= %.6f, %.6f\n" % (eth,hth))
self.Ethermal = eth
self.Hthermal = hth
thetav = freq * (h * c / kgas) # freqency temperature in Kelvin from cm-1
if temperature > 0.0:
xdum = math.exp(-thetav / temperature)
else:
xdum = 0.0
xdum = xdum / (1.0 - xdum)
eth = eth + thetav * (0.5 + xdum)
eth = eth * Rgas
# linear boolean is available only after task_freq('???') runs
# NWChem only writes the flag if molecule is linear
try:
is_linear = nwchem.rtdb_get("vib:linear")
except:
is_linear = False
if is_linear:
# translational(3/2RT) and rotation(2/2RT) thermal corrections
eth = eth + 2.5 * Rgas * temperature
else:
# translational(3/2RT) and rotation(3/2RT) thermal corrections
eth = eth + 3.0 * Rgas * temperature
# Hthermal = eth+pV=eth+RT, since pV=RT
hth = eth + Rgas * temperature
debug("ZPE,E,H thermal= %.6f, %.6f, %.6f\n" % (Ezpe, eth, hth))
def get_basisname():
return nwchem.rtdb_get('basis:ao basis:star bas type')
def get_symmetry():
return nwchem.rtdb_get('geometry:geometry:group name')
def get_forces():
try:
forces = nwchem.rtdb_get('%s:gradient' % _PROPERTYGROUP)
return _reshape_atom_vector([-f for f in forces])
except:
return None