def NumericForces(atomlist,EnergyFunction): "Return the forces on each atom in atomlist via finite differences" Forces = [] dx = 1e-4 nat = len(atomlist) for i in xrange(nat): plus_x_geo = shift_geo(copy.deepcopy(atomlist),i,0,dx) minus_x_geo = shift_geo(copy.deepcopy(atomlist),i,0,-dx) plus_y_geo = shift_geo(copy.deepcopy(atomlist),i,1,dx) minus_y_geo = shift_geo(copy.deepcopy(atomlist),i,1,-dx) plus_z_geo = shift_geo(copy.deepcopy(atomlist),i,2,dx) minus_z_geo = shift_geo(copy.deepcopy(atomlist),i,2,-dx) fx = (EnergyFunction(plus_x_geo)-EnergyFunction(minus_x_geo))/(2*dx) fy = (EnergyFunction(plus_y_geo)-EnergyFunction(minus_y_geo))/(2*dx) fz = (EnergyFunction(plus_z_geo)-EnergyFunction(minus_z_geo))/(2*dx) Forces.append((fx,fy,fz)) return array(Forces)
def split_guess_lines(guess_lines): from PyQuante.Util import parseline from PyQuante.NumWrap import transpose, array import re orbpat = re.compile('Orbital Energy') orb = [] orbe = [] occs = [] orbs = [] for line in guess_lines: if orbpat.search(line): orbei, occi = parseline(line, 'xxxfxf') orbe.append(orbei) occs.append(occi) orb = [] orbs.append(orb) else: orb.extend(map(float, line.split())) orbs = transpose(array(orbs)) return occs, orbe, orbs
def split_guess_lines(guess_lines): from PyQuante.Util import parseline from PyQuante.NumWrap import transpose,array import re orbpat = re.compile('Orbital Energy') orb = [] orbe = [] occs = [] orbs = [] for line in guess_lines: if orbpat.search(line): orbei,occi = parseline(line,'xxxfxf') orbe.append(orbei) occs.append(occi) orb = [] orbs.append(orb) else: orb.extend(map(float,line.split())) orbs = transpose(array(orbs)) return occs,orbe,orbs
def oep_hf_an(atoms,orbs,**opts): """oep_hf - Form the optimized effective potential for HF exchange. Implementation of Wu and Yang's Approximate Newton Scheme from J. Theor. Comp. Chem. 2, 627 (2003). oep_hf(atoms,orbs,**opts) atoms A Molecule object containing a list of the atoms orbs A matrix of guess orbitals Options ------- bfs None The basis functions to use for the wfn pbfs None The basis functions to use for the pot 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 """ maxiter = opts.get('maxiter',100) tol = opts.get('tol',1e-5) bfs = opts.get('bfs',None) if not bfs: basis = opts.get('basis',None) bfs = getbasis(atoms,basis) # The basis set for the potential can be set different from # that used for the wave function pbfs = opts.get('pbfs',None) if not pbfs: pbfs = bfs npbf = len(pbfs) integrals = opts.get('integrals',None) if integrals: S,h,Ints = integrals else: S,h,Ints = getints(bfs,atoms) nel = atoms.get_nel() nocc,nopen = atoms.get_closedopen() Enuke = atoms.get_enuke() # Form the OEP using Yang/Wu, PRL 89 143002 (2002) nbf = len(bfs) norb = nbf bp = zeros(nbf,'d') bvec = opts.get('bvec',None) if bvec: assert len(bvec) == npbf b = array(bvec) else: b = zeros(npbf,'d') # Form and store all of the three-center integrals # we're going to need. # These are <ibf|gbf|jbf> (where 'bf' indicates basis func, # as opposed to MO) # N^3 storage -- obviously you don't want to do this for # very large systems Gij = [] for g in range(npbf): gmat = zeros((nbf,nbf),'d') Gij.append(gmat) gbf = pbfs[g] for i in range(nbf): ibf = bfs[i] for j in range(i+1): jbf = bfs[j] gij = three_center(ibf,gbf,jbf) gmat[i,j] = gij gmat[j,i] = gij # Compute the Fermi-Amaldi potential based on the LDA density. # We're going to form this matrix from the Coulombic matrix that # arises from the input orbitals. D0 and J0 refer to the density # matrix and corresponding Coulomb matrix D0 = mkdens(orbs,0,nocc) J0 = getJ(Ints,D0) Vfa = (2*(nel-1.)/nel)*J0 H0 = h + Vfa b = zeros(nbf,'d') eold = 0 for iter in range(maxiter): Hoep = get_Hoep(b,H0,Gij) orbe,orbs = geigh(Hoep,S) D = mkdens(orbs,0,nocc) Vhf = get2JmK(Ints,D) energy = trace2(2*h+Vhf,D)+Enuke if abs(energy-eold) < tol: break else: eold = energy logging.debug("OEP AN Opt: %d %f" % (iter,energy)) dV_ao = Vhf-Vfa dV = matrixmultiply(transpose(orbs),matrixmultiply(dV_ao,orbs)) X = zeros((nbf,nbf),'d') c = zeros(nbf,'d') Gkt = zeros((nbf,nbf),'d') for k in range(nbf): # This didn't work; in fact, it made things worse: Gk = matrixmultiply(transpose(orbs),matrixmultiply(Gij[k],orbs)) for i in range(nocc): for a in range(nocc,norb): c[k] += dV[i,a]*Gk[i,a]/(orbe[i]-orbe[a]) for l in range(nbf): Gl = matrixmultiply(transpose(orbs),matrixmultiply(Gij[l],orbs)) for i in range(nocc): for a in range(nocc,norb): X[k,l] += Gk[i,a]*Gl[i,a]/(orbe[i]-orbe[a]) # This should actually be a pseudoinverse... b = solve(X,c) logging.info("Final OEP energy = %f" % energy) return energy,orbe,orbs
def oep(atoms,orbs,energy_func,grad_func=None,**opts): """oep - Form the optimized effective potential for a given energy expression oep(atoms,orbs,energy_func,grad_func=None,**opts) atoms A Molecule object containing a list of the atoms orbs A matrix of guess orbitals energy_func The function that returns the energy for the given method grad_func The function that returns the force for the given method Options ------- verbose False Output terse information to stdout (default) True Print out additional information 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 """ verbose = opts.get('verbose',False) ETemp = opts.get('ETemp',False) opt_method = opts.get('opt_method','BFGS') bfs = opts.get('bfs',None) if not bfs: basis = opts.get('basis',None) bfs = getbasis(atoms,basis) # The basis set for the potential can be set different from # that used for the wave function pbfs = opts.get('pbfs',None) if not pbfs: pbfs = bfs npbf = len(pbfs) integrals = opts.get('integrals',None) if integrals: S,h,Ints = integrals else: S,h,Ints = getints(bfs,atoms) nel = atoms.get_nel() nocc,nopen = atoms.get_closedopen() Enuke = atoms.get_enuke() # Form the OEP using Yang/Wu, PRL 89 143002 (2002) nbf = len(bfs) norb = nbf bp = zeros(nbf,'d') bvec = opts.get('bvec',None) if bvec: assert len(bvec) == npbf b = array(bvec) else: b = zeros(npbf,'d') # Form and store all of the three-center integrals # we're going to need. # These are <ibf|gbf|jbf> (where 'bf' indicates basis func, # as opposed to MO) # N^3 storage -- obviously you don't want to do this for # very large systems Gij = [] for g in range(npbf): gmat = zeros((nbf,nbf),'d') Gij.append(gmat) gbf = pbfs[g] for i in range(nbf): ibf = bfs[i] for j in range(i+1): jbf = bfs[j] gij = three_center(ibf,gbf,jbf) gmat[i,j] = gij gmat[j,i] = gij # Compute the Fermi-Amaldi potential based on the LDA density. # We're going to form this matrix from the Coulombic matrix that # arises from the input orbitals. D0 and J0 refer to the density # matrix and corresponding Coulomb matrix D0 = mkdens(orbs,0,nocc) J0 = getJ(Ints,D0) Vfa = (2*(nel-1.)/nel)*J0 H0 = h + Vfa b = fminBFGS(energy_func,b,grad_func, (nbf,nel,nocc,ETemp,Enuke,S,h,Ints,H0,Gij), logger=logging) energy,orbe,orbs = energy_func(b,nbf,nel,nocc,ETemp,Enuke, S,h,Ints,H0,Gij,return_flag=1) return energy,orbe,orbs
def oep_hf_an(atoms, orbs, **opts): """oep_hf - Form the optimized effective potential for HF exchange. Implementation of Wu and Yang's Approximate Newton Scheme from J. Theor. Comp. Chem. 2, 627 (2003). oep_hf(atoms,orbs,**opts) atoms A Molecule object containing a list of the atoms orbs A matrix of guess orbitals Options ------- bfs None The basis functions to use for the wfn pbfs None The basis functions to use for the pot 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 """ maxiter = opts.get('maxiter', 100) tol = opts.get('tol', 1e-5) bfs = opts.get('bfs', None) if not bfs: basis = opts.get('basis', None) bfs = getbasis(atoms, basis) # The basis set for the potential can be set different from # that used for the wave function pbfs = opts.get('pbfs', None) if not pbfs: pbfs = bfs npbf = len(pbfs) integrals = opts.get('integrals', None) if integrals: S, h, Ints = integrals else: S, h, Ints = getints(bfs, atoms) nel = atoms.get_nel() nocc, nopen = atoms.get_closedopen() Enuke = atoms.get_enuke() # Form the OEP using Yang/Wu, PRL 89 143002 (2002) nbf = len(bfs) norb = nbf bp = zeros(nbf, 'd') bvec = opts.get('bvec', None) if bvec: assert len(bvec) == npbf b = array(bvec) else: b = zeros(npbf, 'd') # Form and store all of the three-center integrals # we're going to need. # These are <ibf|gbf|jbf> (where 'bf' indicates basis func, # as opposed to MO) # N^3 storage -- obviously you don't want to do this for # very large systems Gij = [] for g in xrange(npbf): gmat = zeros((nbf, nbf), 'd') Gij.append(gmat) gbf = pbfs[g] for i in xrange(nbf): ibf = bfs[i] for j in xrange(i + 1): jbf = bfs[j] gij = three_center(ibf, gbf, jbf) gmat[i, j] = gij gmat[j, i] = gij # Compute the Fermi-Amaldi potential based on the LDA density. # We're going to form this matrix from the Coulombic matrix that # arises from the input orbitals. D0 and J0 refer to the density # matrix and corresponding Coulomb matrix D0 = mkdens(orbs, 0, nocc) J0 = getJ(Ints, D0) Vfa = (2 * (nel - 1.) / nel) * J0 H0 = h + Vfa b = zeros(nbf, 'd') eold = 0 for iter in xrange(maxiter): Hoep = get_Hoep(b, H0, Gij) orbe, orbs = geigh(Hoep, S) D = mkdens(orbs, 0, nocc) Vhf = get2JmK(Ints, D) energy = trace2(2 * h + Vhf, D) + Enuke if abs(energy - eold) < tol: break else: eold = energy logging.debug("OEP AN Opt: %d %f" % (iter, energy)) dV_ao = Vhf - Vfa dV = matrixmultiply(transpose(orbs), matrixmultiply(dV_ao, orbs)) X = zeros((nbf, nbf), 'd') c = zeros(nbf, 'd') Gkt = zeros((nbf, nbf), 'd') for k in xrange(nbf): # This didn't work; in fact, it made things worse: Gk = matrixmultiply(transpose(orbs), matrixmultiply(Gij[k], orbs)) for i in xrange(nocc): for a in xrange(nocc, norb): c[k] += dV[i, a] * Gk[i, a] / (orbe[i] - orbe[a]) for l in xrange(nbf): Gl = matrixmultiply(transpose(orbs), matrixmultiply(Gij[l], orbs)) for i in xrange(nocc): for a in xrange(nocc, norb): X[k, l] += Gk[i, a] * Gl[i, a] / (orbe[i] - orbe[a]) # This should actually be a pseudoinverse... b = solve(X, c) logger.info("Final OEP energy = %f" % energy) return energy, orbe, orbs
def oep(atoms, orbs, energy_func, grad_func=None, **opts): """oep - Form the optimized effective potential for a given energy expression oep(atoms,orbs,energy_func,grad_func=None,**opts) atoms A Molecule object containing a list of the atoms orbs A matrix of guess orbitals energy_func The function that returns the energy for the given method grad_func The function that returns the force for the given method Options ------- verbose False Output terse information to stdout (default) True Print out additional information 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 """ verbose = opts.get('verbose', False) ETemp = opts.get('ETemp', False) opt_method = opts.get('opt_method', 'BFGS') bfs = opts.get('bfs', None) if not bfs: basis = opts.get('basis', None) bfs = getbasis(atoms, basis) # The basis set for the potential can be set different from # that used for the wave function pbfs = opts.get('pbfs', None) if not pbfs: pbfs = bfs npbf = len(pbfs) integrals = opts.get('integrals', None) if integrals: S, h, Ints = integrals else: S, h, Ints = getints(bfs, atoms) nel = atoms.get_nel() nocc, nopen = atoms.get_closedopen() Enuke = atoms.get_enuke() # Form the OEP using Yang/Wu, PRL 89 143002 (2002) nbf = len(bfs) norb = nbf bp = zeros(nbf, 'd') bvec = opts.get('bvec', None) if bvec: assert len(bvec) == npbf b = array(bvec) else: b = zeros(npbf, 'd') # Form and store all of the three-center integrals # we're going to need. # These are <ibf|gbf|jbf> (where 'bf' indicates basis func, # as opposed to MO) # N^3 storage -- obviously you don't want to do this for # very large systems Gij = [] for g in xrange(npbf): gmat = zeros((nbf, nbf), 'd') Gij.append(gmat) gbf = pbfs[g] for i in xrange(nbf): ibf = bfs[i] for j in xrange(i + 1): jbf = bfs[j] gij = three_center(ibf, gbf, jbf) gmat[i, j] = gij gmat[j, i] = gij # Compute the Fermi-Amaldi potential based on the LDA density. # We're going to form this matrix from the Coulombic matrix that # arises from the input orbitals. D0 and J0 refer to the density # matrix and corresponding Coulomb matrix D0 = mkdens(orbs, 0, nocc) J0 = getJ(Ints, D0) Vfa = (2 * (nel - 1.) / nel) * J0 H0 = h + Vfa b = fminBFGS(energy_func, b, grad_func, (nbf, nel, nocc, ETemp, Enuke, S, h, Ints, H0, Gij), logger=logging) energy, orbe, orbs = energy_func(b, nbf, nel, nocc, ETemp, Enuke, S, h, Ints, H0, Gij, return_flag=1) return energy, orbe, orbs