def E_zpe():
say("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
# these identifiers replicate those used in NWChem freq calculations
# AUKCAL = 627.5093314 # WRONG!
AUKCAL = kCalPerHartree
c = 2.99792458e10
h = 6.62606957e-27
kgas = 1.3806488e-16 # cgs units
Rgas = 1.9872041 / 1000.0 / AUKCAL # atomic units
temperature = 298.15
if is_atom():
Ezpe = 0.0
Ethermal = 1.5 * Rgas * temperature # 3/2 * RT
Hthermal = Ethermal + (Rgas * temperature)
return False
# run hessian on equilibrium geometry
# ignore ZPE, calculate it from vibrations list
try:
zpe, vibs, intens = nwchem.task_freq("dft")
except NWChemError, message:
report("NWChem error: %s\n" % message)
report("FAILED: Zero Point Energy calculation")
return True
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
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
