def test():
from Ints import getbasis, getints
from hartree_fock import rhf
from Molecule import Molecule
# Make a test molecule for the calculation
h2 = Molecule('h2', [(1, (1., 0, 0)), (1, (-1., 0, 0))])
# Get a basis set and compute the integrals.
# normally the routine will do this automatically, but we
# do it explicitly here so that we can pass the same set
# of integrals into the CI code and thus not recompute them.
bfs = getbasis(h2)
S, h, Ints = getints(bfs, h2)
# Compute the HF wave function for our molecule
en, orbe, orbs = rhf(h2, integrals=(S, h, Ints))
print "SCF completed, E = ", en
print " orbital energies ", orbe
# Compute the occupied and unoccupied orbitals, used in the
# CIS program to generate the excitations
nclosed, nopen = h2.get_closedopen()
nbf = len(bfs)
nocc = nclosed + nopen
nvirt = nbf - nocc
# Call the CI program:
Ecis = CIS(Ints, orbs, orbe, nocc, nvirt, en)
print "Ecis = ", Ecis
def test():
from hartree_fock import rhf
from Molecule import Molecule
# Make a test molecule for the calculation
h2 = Molecule('h2',[(1,(1.,0,0)),(1,(-1.,0,0))])
# Get a basis set and compute the integrals.
# normally the routine will do this automatically, but we
# do it explicitly here so that we can pass the same set
# of integrals into the CI code and thus not recompute them.
bfs = getbasis(h2)
S,h,Ints = getints(bfs,h2)
# Compute the HF wave function for our molecule
en,orbe,orbs = rhf(h2,
integrals=(S,h,Ints)
)
print "SCF completed, E = ",en
print " orbital energies ",orbe
# Compute the occupied and unoccupied orbitals, used in the
# CIS program to generate the excitations
nclosed,nopen = h2.get_closedopen()
nbf = len(bfs)
nocc = nclosed+nopen
nvirt = nbf-nocc
# Call the CI program:
Ecis = CIS(Ints,orbs,orbe,nocc,nvirt,en)
print "Ecis = ",Ecis
def rhf_dyn(atoms, **kwargs):
"""\
Uses RHF derived forces to compute dynamics.
Options: Value Description
-------- ----- -----------
job pydyn Descriptive job name
nsteps 100 number of dynamics steps to take
dt 0.1 time step size in picoseconds
units matter! we assume atom positions are
stored in bohrs, velocities are in bohr/ps,
acceleration is in bohr/ps^2
and forces are in hartree/bohr
Hartree-Fock options copied from hartree_fock.py -> rhf
rhf(atoms,**kwargs) - Closed-shell HF driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
ETemp False Use ETemp value for finite temperature DFT (default)
float Use (float) for the electron temperature
bfs None The basis functions to use. List of CGBF's
basis_data None The basis data to use to construct bfs
integrals None The one- and two-electron integrals to use
If not None, S,h,Ints
orbs None If not none, the guess orbitals
"""
#dynamics options
job = kwargs.get('job', settings.DynJob)
nsteps = kwargs.get('nsteps', settings.DynSteps)
dt = kwargs.get('dt', settings.DynTStep)
#save any given RHF options
cc = kwargs.get('ConvCriteria', settings.ConvergenceCriteria)
maxit = kwargs.get('MaxIter', settings.MaxIters)
doavg = kwargs.get('DoAveraging', settings.Averaging)
temp = kwargs.get('ETemp', settings.ElectronTemperature)
bfcns = kwargs.get('bfs')
if not bfcns:
bdat = kwargs.get('basis_data')
ints = kwargs.get('integrals')
init_orbs = kwargs.get('orbs')
#open data file to store energy info
edat = open(job + '.edat', 'w')
edat.write("#Step Time PE KE TE\n")
#open trajectory file to store xyz info
xyz = open(job + '.xyz', 'w')
#xyz.write("#RHF molecular dynamics done by PyQuante\n")
#xyz.write("#job: %s nsteps: %d dt:%f\n"%(job,nsteps,dt))
xyz.write(xyz_str(atoms))
t = 0.
for n in xrange(nsteps):
t += n * dt
pe,orben,coefs = rhf(atoms,ConvCriteria=cc,MaxIter=maxit,\
DoAveraging=doavg,ETemp=temp,bfs=bfcns,\
basis_data=bdat,integrals=ints,orbs=init_orbs)
ncl, nop = atoms.get_closedopen()
wf = Wavefunction(orbs=coefs,
orbe=orben,
restricted=True,
nclosed=ncl,
nopen=nop)
hf_force(atoms, wf, bdat)
ke = leapfrog(atoms, t, dt)
te = ke + pe
bl = atoms[0].dist(atoms[1])
edat.write('%d %f %f %f %f %f\n' %
(n, t, bl, pe, ke, te))
xyz.write(xyz_str(atoms))
edat.close()
xyz.close()
return
def RHFEnergyFunction(atomlist,**kwargs):
from hartree_fock import rhf
return rhf(atomlist,**kwargs)[0]
def rhf_dyn(atoms,**kwargs):
"""\
Uses RHF derived forces to compute dynamics.
Options: Value Description
-------- ----- -----------
job pydyn Descriptive job name
nsteps 100 number of dynamics steps to take
dt 0.1 time step size in picoseconds
units matter! we assume atom positions are
stored in bohrs, velocities are in bohr/ps,
acceleration is in bohr/ps^2
and forces are in hartree/bohr
Hartree-Fock options copied from hartree_fock.py -> rhf
rhf(atoms,**kwargs) - Closed-shell HF driving routine
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS for accelerated convergence (default)
False No convergence acceleration
ETemp False Use ETemp value for finite temperature DFT (default)
float Use (float) for the electron temperature
bfs None The basis functions to use. List of CGBF's
basis_data None The basis data to use to construct bfs
integrals None The one- and two-electron integrals to use
If not None, S,h,Ints
orbs None If not none, the guess orbitals
"""
#dynamics options
job = kwargs.get('job',settings.DynJob)
nsteps = kwargs.get('nsteps',settings.DynSteps)
dt = kwargs.get('dt',settings.DynTStep)
#save any given RHF options
cc = kwargs.get('ConvCriteria',settings.ConvergenceCriteria)
maxit = kwargs.get('MaxIter',settings.MaxIters)
doavg = kwargs.get('DoAveraging',settings.Averaging)
temp = kwargs.get('ETemp',settings.ElectronTemperature)
bfcns = kwargs.get('bfs')
if not bfcns:
bdat = kwargs.get('basis_data')
ints = kwargs.get('integrals')
init_orbs = kwargs.get('orbs')
#open data file to store energy info
edat = open(job+'.edat', 'w')
edat.write("#Step Time PE KE TE\n")
#open trajectory file to store xyz info
xyz = open(job+'.xyz', 'w')
#xyz.write("#RHF molecular dynamics done by PyQuante\n")
#xyz.write("#job: %s nsteps: %d dt:%f\n"%(job,nsteps,dt))
xyz.write(xyz_str(atoms))
t=0.
for n in xrange(nsteps):
t+=n*dt
pe,orben,coefs = rhf(atoms,ConvCriteria=cc,MaxIter=maxit,\
DoAveraging=doavg,ETemp=temp,bfs=bfcns,\
basis_data=bdat,integrals=ints,orbs=init_orbs)
ncl,nop = atoms.get_closedopen()
wf = Wavefunction(orbs=coefs,orbe=orben,restricted=True,nclosed=ncl,nopen=nop)
hf_force(atoms,wf,bdat)
ke = leapfrog(atoms,t,dt)
te = ke+pe
bl = atoms[0].dist(atoms[1])
edat.write('%d %f %f %f %f %f\n' %(n,t,bl,pe,ke,te))
xyz.write(xyz_str(atoms))
edat.close()
xyz.close()
return
import numpy as np
import psi4
import sys
sys.path.insert(0, '../../3/misiewicz')
import hartree_fock
sys.path.insert(0, '../../6/misiewicz')
import utility
def mp2(C, evals, int_tensor, nocc):
dim = C.shape[0]
nvir = dim - nocc
C_occ = C[:,:nocc].conjugate() # Grab the columns for occupied orbitals.
C_vir = C[:,nocc:] # Grab the columns for virtual orbitals.
aint = utility.tensor_basis_transform(int_tensor, C_occ, C_vir)
e = 0
for i, j, a, b in itertools.product(range(nocc), range(nocc), range(nvir), range(nvir)):
e += aint[i,j,a,b] * (
np.conjugate(2 * aint[i,j,a,b] - aint[i,j,b,a])) / (
evals[i] + evals[j] - evals[nocc+a] - evals[nocc+b])
return e
if __name__ == "__main__":
psi4.set_memory('500 MB')
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
hf_data = hartree_fock.rhf(h2o)[2:] # Throw away first two data points...
print(mp2(*hf_data))
