def test_evaluate_basis_pyscf():
"""Test gbasis.evals.eval.evaluate_basis against pyscf results."""
pytest.importorskip("pyscf")
from pyscf import gto
from gbasis.wrappers import from_pyscf
mol = gto.Mole()
mol.build(atom="H 0 0 0; He 0.8 0 0", basis="ano-rcc", spin=1)
basis = from_pyscf(mol)
grid_1d = np.linspace(-2, 2, num=5)
grid_x, grid_y, grid_z = np.meshgrid(grid_1d, grid_1d, grid_1d)
grid_3d = np.vstack([grid_x.ravel(), grid_y.ravel(), grid_z.ravel()]).T
pyscf_eval_sph = gto.eval_gto(mol, "GTOval_sph", grid_3d)
pyscf_eval_cart = gto.eval_gto(mol, "GTOval_cart", grid_3d)
# s orbitals
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[:6],
pyscf_eval_cart.T[:6])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[46:53],
pyscf_eval_cart.T[46:53])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[:6],
pyscf_eval_sph.T[:6])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[40:47],
pyscf_eval_sph.T[40:47])
# p orbitals
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[6:18],
pyscf_eval_cart.T[6:18])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[53:65],
pyscf_eval_cart.T[53:65])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[6:18],
pyscf_eval_sph.T[6:18])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[47:59],
pyscf_eval_sph.T[47:59])
# d orbitals are off by some constant for the cartesian case
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[18:33],
pyscf_eval_sph.T[18:33])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[59:74],
pyscf_eval_sph.T[59:74])
# f orbitals are off by some constant for the cartesian case
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[33:40],
pyscf_eval_sph.T[33:40])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="spherical")[74:88],
pyscf_eval_sph.T[74:88])
def MolDensity(self,samps,m,p=[0.0,0.0,0.0],tag=None):
Ps = np.zeros(len(samps))
mol = gto.Mole()
pyscfatomstring=''
if (tag==None):
for j in range(len(m.atoms)):
pyscfatomstring=pyscfatomstring+"H@"+str(m.atoms[j])+" "+str(m.coords[j,0])+" "+str(m.coords[j,1])+" "+str(m.coords[j,2])+(";" if j!= len(m.atoms)-1 else "")
else:
for j in range(len(m.atoms)):
if (j == tag):
print("Tagging atom", j)
pyscfatomstring=pyscfatomstring+"N@0"+" "+str(m.coords[j,0])+" "+str(m.coords[j,1])+" "+str(m.coords[j,2])+(";" if j!= len(m.atoms)-1 else "")
else:
pyscfatomstring=pyscfatomstring+"H@"+str(m.atoms[j])+" "+str(m.coords[j,0])+" "+str(m.coords[j,1])+" "+str(m.coords[j,2])+(";" if j!= len(m.atoms)-1 else "")
mol.atom = pyscfatomstring
mol.basis = TOTAL_SENSORY_BASIS
mol.verbose = 0
if (len(m.atoms)%2 == 0):
mol.spin = 0
else:
mol.spin = 1
try:
mol.build()
except Exception as Ex:
print(mol.atom, mol.basis, m.atoms, m.coords)
raise Ex
return np.sum(gto.eval_gto('GTOval_sph',mol._atm,mol._bas,mol._env,samps*1.889725989),axis=1)
def AtomEmbedAtomCentered(self, samps, m, p, i=-1):
mol = gto.Mole()
MaxEmbedded = 30
SensedAtoms = [a for a in m.AtomsWithin(30.0, p) if a != i]
if (len(SensedAtoms) > MaxEmbedded):
SensedAtoms = SensedAtoms[:MaxEmbedded]
if (len(SensedAtoms) == 0):
raise Exception("NoAtomsInSensoryRadius")
mol.atom = "C " + str(p[0]) + " " + str(p[1]) + " " + str(p[2]) + ";"
na = 0
for j in SensedAtoms:
mol.atom = mol.atom + "H@" + str(m.atoms[j]) + " " + str(
m.coords[j, 0]) + " " + str(m.coords[j, 1]) + " " + str(
m.coords[j, 2]) + (";" if j != SensedAtoms[-1] else "")
na = na + 1
#print mol.atom
#print self.atoms
#print self.coords
#print "Basis Atom",[mol.bas_atom(i) for i in range(mol.nbas)]
if (na % 2 == 0):
mol.spin = 0
else:
mol.spin = 1
if (TOTAL_SENSORY_BASIS == None):
raise ("missing sensory basis")
mol.basis = TOTAL_SENSORY_BASIS
nsaos = 0
try:
mol.build()
except Exception as Ex:
print mol.atom, mol.basis, m.atoms, m.coords, SensedAtoms, p
raise Ex
nsaos = gto.nao_nr_range(mol, 0, mol.atom_nshells(0))[1]
nbas = gto.nao_nr(mol)
print "nAtoms: ", m.NAtoms(), " nsaos: ", nsaos, " nbas ", nbas
S = mol.intor('cint1e_ovlp_sph',
shls_slice=(0, mol.atom_nshells(0), 0,
mol.atom_nshells(0)))
Sinv = MatrixPower(S, -1.0)
SBFs = gto.eval_gto('GTOval_sph',
mol._atm,
mol._bas,
mol._env,
samps * 1.889725989,
comp=1,
shls_slice=(0, mol.atom_nshells(0)))
print "SBFs.shape", SBFs.shape
Cs = mol.intor('cint1e_ovlp_sph',
shls_slice=(0, mol.atom_nshells(0), mol.atom_nshells(0),
mol.nbas))
print "Cs.shape", Cs.shape
# for i in range(len(Cs[0])):
# tmp = np.dot(SBFs,np.dot(Sinv,Cs[:,i]))
# GridstoRaw(tmp*tmp,150,"Atoms"+str(i))
# exit(0)
Sd = np.sum(np.dot(SBFs, np.dot(Sinv, Cs)), axis=1)
print "Sd.shape", Sd.shape
return Sd
def Populate(self):
print("Populating Grids... ")
#
# Populate output Bases
#
self.GauGrid = MakeUniform([0,0,0],self.GridRange*.8,self.NGau)
self.Grid = MakeUniform([0,0,0],self.GridRange,self.NPts)
self.dx=(np.max(self.Grid[:,0])-np.min(self.Grid[:,0]))/self.NPts*1.889725989
self.dy=(np.max(self.Grid[:,1])-np.min(self.Grid[:,1]))/self.NPts*1.889725989
self.dz=(np.max(self.Grid[:,2])-np.min(self.Grid[:,2]))/self.NPts*1.889725989
return
mol = gto.Mole()
mol.atom = ''.join(["H@0 "+str(self.GauGrid[iii,0])+" "+str(self.GauGrid[iii,1])+" "+str(self.GauGrid[iii,2])+";" for iii in range(len(self.GauGrid))])[:-1]
if (self.NGau3%2==0):
mol.spin = 0
else:
mol.spin = 1
if (ATOM_BASIS == None):
raise("missing ATOM_BASIS")
mol.basis = ATOM_BASIS
try:
mol.build()
except Exception as Ex:
print(mol.atom)
raise Ex
# All this shit could be Pre-Computed...
# Really any grid could be used.
orbs=gto.eval_gto('GTOval_sph',mol._atm,mol._bas,mol._env,self.Grid*1.889725989)
nbas=orbs.shape[1]
if (nbas!=self.NGau3):
raise Exception("insanity")
S=mol.intor('cint1e_ovlp_sph')
#S = np.zeros(shape=(nbas,nbas))
#for i in range(nbas):
# for j in range(nbas):
# S[i,j] += np.sum(orbs[:,i]*orbs[:,j])
C = MatrixPower(S,-0.5)
if (0):
for i in range(nbas):
CM = np.dot(self.Grid.T,orbs[:,i])
print("Centers of Mass, i", np.dot(self.Grid.T,orbs[:,i]*orbs[:,i])*self.dx*self.dy*self.dz, self.GauGrid[i])
Rsq = np.array(map(np.linalg.norm,self.Grid-CM))
print("Rsq of Mass, i", np.sqrt(np.dot(Rsq,orbs[:,i]*orbs[:,i]))*self.dx*self.dy*self.dz)
for j in range(nbas):
print("Normalization of grid i.", np.sum(orbs[:,i]*orbs[:,j])*self.dx*self.dy*self.dz)
self.OBFs = np.zeros(shape=(self.NGau3,self.NPts3))
for i in range(nbas):
for j in range(nbas):
self.OBFs[i,:] += (C.T[i,j]*orbs[:,j]).T
# Populate Sensory bases.
self.PopulateSense()
if (not self.Spherical):
self.BuildIsometries()
print("Using ", len(self.Isometries), " isometries.")
print("Grid storage cost: ",self.OBFs.size*64/1024/1024, "Mb")
def TestGridGauEmbedding(self,samps,m,p,i):
mol = gto.Mole()
MaxEmbedded = 15
SensedAtoms = [a for a in m.AtomsWithin(10.0,p) if a != i]
if (len(SensedAtoms)>MaxEmbedded):
SensedAtoms=SensedAtoms[:MaxEmbedded]
if (len(SensedAtoms)==0):
raise Exception("NoAtomsInSensoryRadius")
GauGrid = MakeUniform([0,0,0],3.5,self.NGau)
#pyscfatomstring="C "+str(p[0])+" "+str(p[1])+" "+str(p[2])+";"
mol.atom = ''.join(["H@0 "+str(GauGrid[iii,0])+" "+str(GauGrid[iii,1])+" "+str(GauGrid[iii,2])+";" for iii in range(len(GauGrid))])
na = len(GauGrid)
#na=0
for j in SensedAtoms:
mol.atom=mol.atom+"H@"+str(m.atoms[j])+" "+str(m.coords[j,0])+" "+str(m.coords[j,1])+" "+str(m.coords[j,2])+(";" if j!=SensedAtoms[-1] else "")
na=na+1
#print mol.atom
#print self.atoms
#print self.coords
#print "Basis Atom",[mol.bas_atom(i) for i in range(mol.nbas)]
if (na%2 == 0):
mol.spin = 0
else:
mol.spin = 1
if (TOTAL_SENSORY_BASIS == None):
raise("missing sensory basis")
mol.basis = TOTAL_SENSORY_BASIS
nsaos = 0
try:
mol.build()
except Exception as Ex:
print(mol.atom, mol.basis, m.atoms, m.coords, SensedAtoms, p)
raise Ex
nsaos = len(GauGrid)
nbas = gto.nao_nr(mol)
print("nAtoms: ",m.NAtoms()," nsaos: ", nsaos, " nbas ", nbas)
S = mol.intor('cint1e_ovlp_sph',shls_slice=(0,nsaos,0,nsaos))
Sinv = MatrixPower(S,-1.0)
SBFs = gto.eval_gto('GTOval_sph',mol._atm,mol._bas,mol._env,samps*1.889725989,comp=1,shls_slice=(0,nsaos))
print("SBFs.shape", SBFs.shape)
Cs = mol.intor('cint1e_ovlp_sph',shls_slice=(0,nsaos,nsaos,mol.nbas))
print("Cs.shape", Cs.shape)
Sd = np.sum(np.dot(SBFs,np.dot(Sinv,Cs)),axis=1)
print("Sd.shape", Sd.shape)
return Sd
def SenseOnGrid(self,p,grd_):
mol = gto.Mole()
mol.atom =''
if (not self.Spherical):
tmpgrid = self.SenseGrid + p
mol.atom = ''.join(["H@0 "+str(tmpgrid[iii,0])+" "+str(tmpgrid[iii,1])+" "+str(tmpgrid[iii,2])+";" for iii in range(len(tmpgrid))])
else:
mol.atom = ''.join("C "+str(p[0])+" "+str(p[1])+" "+str(p[2])+";")
mol.spin = 0
if (TOTAL_SENSORY_BASIS == None):
raise("missing sensory basis")
mol.basis = TOTAL_SENSORY_BASIS
mol.build()
return gto.eval_gto('GTOval_sph',mol._atm,mol._bas,mol._env,grd_*1.889725989)
def test_evaluate_basis_pyscf_cart_norm():
"""Test gbasis.evals.eval.evaluate_basis against pyscf results.
These cases fail because pyscf seems to have a different normalization constant for the d and f
orbitals.
"""
pytest.importorskip("pyscf")
from pyscf import gto
from gbasis.wrappers import from_pyscf
mol = gto.Mole()
mol.build(atom="H 0 0 0; He 0.8 0 0", basis="ano-rcc", spin=1)
basis = from_pyscf(mol)
grid_1d = np.linspace(-2, 2, num=5)
grid_x, grid_y, grid_z = np.meshgrid(grid_1d, grid_1d, grid_1d)
grid_3d = np.vstack([grid_x.ravel(), grid_y.ravel(), grid_z.ravel()]).T
pyscf_eval_cart = gto.eval_gto(mol, "GTOval_cart", grid_3d)
# d orbitals are all off by some scalar factor
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[18:36],
pyscf_eval_cart.T[18:36])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[65:83],
pyscf_eval_cart.T[65:83])
# f orbitals are all off by some scalar factor
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[36:46],
pyscf_eval_cart.T[36:46])
assert np.allclose(
evaluate_basis(basis, grid_3d, coord_type="cartesian")[83:103],
pyscf_eval_cart.T[83:103])