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 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 fixedocc_uhf_dyn(atoms, occa, occb, **kwargs):
"""\
Uses Fixed occupation UHF derived forces to compute dynamics.
occa and occb represent the orbital occupation arrays for
the calculating spin orbitals with holes
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 -> uhf
uhf(atoms,**kwargs) - Unrestriced Open Shell Hartree Fock
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS averaging for convergence acceleration
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.DynTSteps)
#save any given UHF options
cc = kwargs.get('ConvCriteria', settings.ConvergenceCriteria)
maxit = kwargs.get('MaxIter', settings.MaxIter)
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,(orbea,orbeb),(coefsa,coefsb) = uhf_fixed_occ(atoms,occa,occb, ConvCriteria=cc,MaxIter=maxit,\
DoAveraging=doavg,ETemp=temp,bfs=bfcns,\
basis_data=bdat,integrals=ints,orbs=init_orbs)
na, nb = atoms.get_alphabeta()
wf = Wavefunction(orbs_a=coefsa,orbs_b=coefsb,\
orbe_a=orbea,orbe_b=orbeb,\
occs_a=occa,occs_b=occb,\
fixedocc=True,nalpha=na,nbeta=nb)
hf_force(atoms, wf, bdat)
bl = atoms[0].dist(atoms[1]) #testing with H2
ke = leapfrog(atoms, t, dt)
te = ke + pe
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 fixedocc_uhf_dyn(atoms,occa,occb,**kwargs):
"""\
Uses Fixed occupation UHF derived forces to compute dynamics.
occa and occb represent the orbital occupation arrays for
the calculating spin orbitals with holes
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 -> uhf
uhf(atoms,**kwargs) - Unrestriced Open Shell Hartree Fock
atoms A Molecule object containing the molecule
Options: Value Description
-------- ----- -----------
ConvCriteria 1e-4 Convergence Criteria
MaxIter 20 Maximum SCF iterations
DoAveraging True Use DIIS averaging for convergence acceleration
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.DynTSteps)
#save any given UHF options
cc = kwargs.get('ConvCriteria',settings.ConvergenceCriteria)
maxit = kwargs.get('MaxIter',settings.MaxIter)
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,(orbea,orbeb),(coefsa,coefsb) = uhf_fixed_occ(atoms,occa,occb, ConvCriteria=cc,MaxIter=maxit,\
DoAveraging=doavg,ETemp=temp,bfs=bfcns,\
basis_data=bdat,integrals=ints,orbs=init_orbs)
na,nb = atoms.get_alphabeta()
wf = Wavefunction(orbs_a=coefsa,orbs_b=coefsb,\
orbe_a=orbea,orbe_b=orbeb,\
occs_a=occa,occs_b=occb,\
fixedocc=True,nalpha=na,nbeta=nb)
hf_force(atoms,wf,bdat)
bl = atoms[0].dist(atoms[1]) #testing with H2
ke = leapfrog(atoms,t,dt)
te = ke+pe
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