def int_beta(self):
logger.info(self, '* Go with inside betasphere')
xcoor = numpy.zeros(3)
coords = numpy.empty((self.bnpang, 3))
nrad = self.bnrad
iqudr = self.biqudr
mapr = self.bmapr
r0 = 0
rfar = self.brad
rad = self.rad
t0 = time.clock()
rmesh, rwei, dvol, dvoln = grids.rquad(nrad, r0, rfar, rad, iqudr, mapr)
coordsang = grids.lebgrid(self.bnpang)
rprops = 0.0
for n in range(nrad):
r = rmesh[n]
for j in range(self.bnpang): # j-loop can be changed to map
cost = coordsang[j, 0]
sintcosp = coordsang[j, 1] * coordsang[j, 2]
sintsinp = coordsang[j, 1] * coordsang[j, 3]
xcoor[0] = r * sintcosp
xcoor[1] = r * sintsinp
xcoor[2] = r * cost
p = self.xnuc + xcoor
coords[j] = p
val = numint.eval_rho(self, coords)
props = numpy.einsum('i,i->', val, coordsang[:, 4])
rprops += props * dvol[n] * rwei[n]
logger.info(self, '*--> Electron density inside bsphere %8.5f ', rprops)
logger.timer(self, 'Bsphere build', t0)
return rprops
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Read info
logger.info(self, 'Reading HDF5 file')
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.coords = f['molecule/coords'].value
self.nmo = f['basis/nmo'].value
self.nprims = f['basis/nprims'].value
self.icen = f['basis/icen'].value
self.ityp = f['basis/ityp'].value
self.oexp = f['basis/oexp'].value
self.mo_coeff = f['basis/mo_coeff'].value
self.mo_occ = f['basis/mo_occ'].value
self.ngroup = f['basis/ngroup'].value
self.nzexp = f['basis/nzexp'].value
self.nuexp = f['basis/nuexp'].value
self.rcutte = f['basis/rcutte'].value
self.nshells = f['basis/nshells'].value
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
logger.info(self, 'Finish with HDF5 file')
logger.timer(self, 'Info readed', t0)
logger.info(self, '')
return self
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Read info
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.coords = f['molecule/coords'].value
self.charges = f['molecule/charges'].value
self.symbols = f['molecule/symbols'].value
self.nmo = f['basis/nmo'].value
self.nprims = f['basis/nprims'].value
self.icen = f['basis/icen'].value
self.ityp = f['basis/ityp'].value
self.oexp = f['basis/oexp'].value
self.mo_coeff = f['basis/mo_coeff'].value
self.mo_occ = f['basis/mo_occ'].value
self.ngroup = f['basis/ngroup'].value
self.nzexp = f['basis/nzexp'].value
self.nuexp = f['basis/nuexp'].value
self.rcutte = f['basis/rcutte'].value
# 2) Build cube data
coords = self.coords
margin = self.margin
resolution = self.resolution
self.box = numpy.max(coords, axis=0) - numpy.min(coords,
axis=0) + margin * 2
self.boxorig = numpy.min(coords, axis=0) - margin
nx = self.nx
ny = self.ny
nz = self.nz
if resolution is not None:
nx, ny, nz = numpy.ceil(self.box / resolution).astype(int)
self.nx = nx
self.ny = ny
self.nz = nz
# .../(nx-1) to get symmetric mesh
# see also the discussion on https://github.com/sunqm/pyscf/issues/154
self.xs = numpy.arange(nx) * (self.box[0] / (nx - 1))
self.ys = numpy.arange(ny) * (self.box[1] / (ny - 1))
self.zs = numpy.arange(nz) * (self.box[2] / (nz - 1))
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
density(self)
logger.timer(self, 'Cube done', t0)
logger.info(self, '')
return self
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Build grid
self.grids.verbose = self.verbose
self.grids.stdout = self.stdout
self.grids.max_memory = self.max_memory
self.grids.scratch = self.scratch
self.grids.build()
# 2) Read info
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.coords = f['molecule/coords'].value
self.charges = f['molecule/charges'].value
self.symbols = f['molecule/symbols'].value
self.nmo = f['basis/nmo'].value
self.nprims = f['basis/nprims'].value
self.icen = f['basis/icen'].value
self.ityp = f['basis/ityp'].value
self.oexp = f['basis/oexp'].value
self.mo_coeff = f['basis/mo_coeff'].value
self.mo_occ = f['basis/mo_occ'].value
self.ngroup = f['basis/ngroup'].value
self.nzexp = f['basis/nzexp'].value
self.nuexp = f['basis/nuexp'].value
self.rcutte = f['basis/rcutte'].value
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
# 3) Qualitie of grid
out = numint.eval_rho_gradmod(self,self.grids.coords)
rhoval = numpy.einsum('i,i->',out[:,0],self.grids.weights)
logger.info(self,'Integral of rho %.6f' % rhoval)
# 4) Dispersion energy, TODO: prune rho points
f_vv10(self,out[:,0],out[:,1])
logger.timer(self,'VV10 integration done', t0)
logger.info(self,'')
return self
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Read info
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.coords = f['molecule/coords'].value
self.charges = f['molecule/charges'].value
self.symbols = f['molecule/symbols'].value
self.nmo = f['basis/nmo'].value
self.nprims = f['basis/nprims'].value
self.icen = f['basis/icen'].value
self.ityp = f['basis/ityp'].value
self.oexp = f['basis/oexp'].value
self.mo_coeff = f['basis/mo_coeff'].value
self.mo_occ = f['basis/mo_occ'].value
self.ngroup = f['basis/ngroup'].value
self.nzexp = f['basis/nzexp'].value
self.nuexp = f['basis/nuexp'].value
self.rcutte = f['basis/rcutte'].value
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
# 2) Test
logger.info(self, 'Testing orthogonality of orbitals')
s = gto.eval_overlap(self)
s = numpy.dot(s, self.mo_coeff)
s = numpy.dot(self.mo_coeff.T, s)
tools.dump_tri(self.stdout, s)
logger.info(self, '')
logger.timer(self, 'Integrals done', t0)
logger.info(self, '')
return self
def out_beta(self):
logger.info(self, '* Go outside betasphere')
xcoor = numpy.zeros(3)
nrad = self.nrad
iqudr = self.iqudr
mapr = self.mapr
r0 = self.brad
rfar = self.rmax
rad = self.rad
t0 = time.clock()
rmesh, rwei, dvol, dvoln = grids.rquad(nrad, r0, rfar, rad, iqudr, mapr)
coordsang = self.agrids
rprops = 0.0
for n in range(nrad):
r = rmesh[n]
coords = []
weigths = []
for j in range(self.npang):
inside = True
inside = inbasin(self, r, j)
if (inside == True):
cost = coordsang[j, 0]
sintcosp = coordsang[j, 1] * coordsang[j, 2]
sintsinp = coordsang[j, 1] * coordsang[j, 3]
xcoor[0] = r * sintcosp
xcoor[1] = r * sintsinp
xcoor[2] = r * cost
p = self.xyzrho + xcoor
coords.append(p)
weigths.append(coordsang[j, 4])
coords = numpy.array(coords)
weigths = numpy.array(weigths)
val = numint.eval_rho(self, coords)
props = numpy.einsum('i,i->', val, weigths)
rprops += props * dvol[n] * rwei[n]
logger.info(self, '*--> Electron density outside bsphere %8.5f ', rprops)
logger.timer(self, 'Out Bsphere build', t0)
return rprops
def build(self, **kwargs):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Read info
logger.info(self,'Reading HDF5 file')
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.xyz = f['molecule/coords'].value
self.charges = f['molecule/charges'].value
self.symbols = f['molecule/symbols'].value
# 2) Dump info
if self.verbose > logger.NOTE:
self.dump_flags()
# 3) Gen grids
atom_grids_tab = gen_atomic_grids(self,self.atom_grid,
self.radi_method,
self.level,
self.prune, **kwargs)
self.coords, self.weights = \
gen_partition(self,atom_grids_tab,
self.radii_adjust, self.atomic_radii,
self.becke_scheme)
# 4) Save
logger.info(self,'Finish with grids')
logger.info(self,'Tot grids %d', len(self.weights))
logger.info(self,'Write HDF5 grid file')
grid_dic = {'coords':self.coords,
'weights':self.weights}
chkfile.save(self.chkfile, 'becke', grid_dic)
logger.info(self,'Grid saved')
logger.timer(self,'Becke grid build', t0)
logger.info(self,'')
return self
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Read info
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.coords = f['molecule/coords'].value
self.charges = f['molecule/charges'].value
self.nmo = f['basis/nmo'].value
self.nprims = f['basis/nprims'].value
self.icen = f['basis/icen'].value
self.ityp = f['basis/ityp'].value
self.oexp = f['basis/oexp'].value
self.mo_coeff = f['basis/mo_coeff'].value
self.mo_occ = f['basis/mo_occ'].value
self.ngroup = f['basis/ngroup'].value
self.nzexp = f['basis/nzexp'].value
self.nuexp = f['basis/nuexp'].value
self.rcutte = f['basis/rcutte'].value
# 2) Setup basis info and grids
if (self.ntrial % 2 == 0): self.ntrial += 1
geofac = numpy.power(((self.rmaxsurf - 0.1) / self.rprimer),
(1.0 / (self.ntrial - 1.0)))
self.rpru = numpy.zeros((self.ntrial))
for i in range(self.ntrial):
self.rpru[i] = self.rprimer * numpy.power(geofac, (i + 1) - 1)
self.rsurf = numpy.zeros((self.npang, self.ntrial))
self.nlimsurf = numpy.zeros((self.npang), dtype=numpy.int32)
self.grids = grids.lebgrid(self.npang)
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
# 3) Check rho nuclear atractors
t = time.time()
step = self.step
self.xyzrho = numpy.zeros((self.natm, 3))
for i in range(self.natm):
coords = self.coords[i]
self.xyzrho[i], gradmod = gradrho(self, coords, step)
if (gradmod > 1e-4):
if (self.charges[i] > 2.0):
logger.info(self, 'Good rho position %.6f %.6f %.6f',
*self.xyzrho[i])
else:
raise RuntimeError('Failed finding nucleus:',
*self.xyzrho[i])
else:
logger.info(self, 'Check rho position %.6f %.6f %.6f',
*self.xyzrho[i])
logger.info(self, 'Setting xyrho for atom to imput coords')
self.xyzrho[i] = self.coords[i]
self.xnuc = numpy.asarray(self.xyzrho[self.inuc])
logger.info(self,
'Time finding nucleus %.3f (sec)' % (time.time() - t))
t = time.time()
backend = 1
ct_ = numpy.asarray(self.grids[:, 0], order='C')
st_ = numpy.asarray(self.grids[:, 1], order='C')
cp_ = numpy.asarray(self.grids[:, 2], order='C')
sp_ = numpy.asarray(self.grids[:, 3], order='C')
angw_ = numpy.asarray(self.grids[:, 4], order='C')
# 4) Compute surface
feval = 'gsurf_driver'
drv = getattr(libgsurf, feval)
drv(ctypes.c_int(self.nmo), ctypes.c_int(self.nprims),
self.ityp.ctypes.data_as(ctypes.c_void_p),
self.oexp.ctypes.data_as(ctypes.c_void_p),
self.ngroup.ctypes.data_as(ctypes.c_void_p),
self.nzexp.ctypes.data_as(ctypes.c_void_p),
self.nuexp.ctypes.data_as(ctypes.c_void_p),
self.rcutte.ctypes.data_as(ctypes.c_void_p),
self.mo_coeff.ctypes.data_as(ctypes.c_void_p),
self.mo_occ.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.natm),
self.coords.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(self.npang), ctypes.c_int((self.inuc)),
self.xyzrho.ctypes.data_as(ctypes.c_void_p),
ct_.ctypes.data_as(ctypes.c_void_p),
st_.ctypes.data_as(ctypes.c_void_p),
cp_.ctypes.data_as(ctypes.c_void_p),
sp_.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(backend),
ctypes.c_int(self.ntrial), ctypes.c_double(self.epsiscp),
ctypes.c_double(self.epsroot), ctypes.c_double(self.rmaxsurf),
ctypes.c_double(self.epsilon),
self.rpru.ctypes.data_as(ctypes.c_void_p),
ctypes.c_double(self.step), ctypes.c_int(self.mstep),
self.nlimsurf.ctypes.data_as(ctypes.c_void_p),
self.rsurf.ctypes.data_as(ctypes.c_void_p))
logger.info(self,
'Time finding surface %.3f (sec)' % (time.time() - t))
self.rmin = 1000.0
self.rmax = 0.0
for i in range(self.npang):
nsurf = self.nlimsurf[i]
self.rmin = numpy.minimum(self.rmin, self.rsurf[i, 0])
self.rmax = numpy.maximum(self.rmax, self.rsurf[i, nsurf - 1])
logger.info(self, 'Rmin for surface %.6f', self.rmin)
logger.info(self, 'Rmax for surface %.6f', self.rmax)
# 5) Safe surface
logger.info(self, 'Finish with surface')
logger.info(self, 'Write HDF5 surface file')
atom_dic = {
'inuc': self.inuc,
'xnuc': self.xnuc,
'xyzrho': self.xyzrho,
'coords': self.grids,
'npang': self.npang,
'ntrial': self.ntrial,
'rmin': self.rmin,
'rmax': self.rmax,
'nlimsurf': self.nlimsurf,
'rsurf': self.rsurf
}
chkfile.save(self.chkfile, 'atom' + str(self.inuc), atom_dic)
logger.info(self, 'Surface of atom %d saved', self.inuc)
logger.timer(self, 'BaderSurf build', t0)
logger.info(self, '')
return self
logger.info(self, '')
return self
kernel = build
if __name__ == '__main__':
name = 'h2o.wfn.h5'
becke = Becke(name)
becke.verbose = 4
becke.grids.atom_grid = {'H': (510, 5810), 'O': (510, 5810)}
becke.grids.prune = None
becke.kernel()
from pyscf import lib, dft
from pyscf.dft import numint
t0 = time.clock()
logger.TIMER_LEVEL = 3
chkname = 'h2o.chk'
mol = lib.chkfile.load_mol(chkname)
mf_mo_coeff = lib.chkfile.load(chkname, 'scf/mo_coeff')
mf_mo_occ = lib.chkfile.load(chkname, 'scf/mo_occ')
coords = numpy.reshape(becke.grids.coords, (-1, 3))
ao = dft.numint.eval_ao(mol, coords, deriv=1)
rho = dft.numint.eval_rho2(mol, ao, mf_mo_coeff, mf_mo_occ, xctype='GGA')
rho = numpy.einsum('i,i->', rho[0], becke.grids.weights)
logger.info(mol, 'Integral of rho %.6f' % rho)
logger.timer(mol, 'CPU integration done', t0)
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Build info
idx = 'atom' + str(self.inuc)
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.coords = f['molecule/coords'].value
self.charges = f['molecule/charges'].value
self.symbols = f['molecule/symbols'].value
self.nmo = f['basis/nmo'].value
self.nprims = f['basis/nprims'].value
self.icen = f['basis/icen'].value
self.ityp = f['basis/ityp'].value
self.oexp = f['basis/oexp'].value
self.mo_coeff = f['basis/mo_coeff'].value
self.mo_occ = f['basis/mo_occ'].value
self.ngroup = f['basis/ngroup'].value
self.nzexp = f['basis/nzexp'].value
self.nuexp = f['basis/nuexp'].value
self.rcutte = f['basis/rcutte'].value
self.inuc = f[idx + '/inuc'].value
self.xnuc = f[idx + '/xnuc'].value
self.xyzrho = f[idx + '/xyzrho'].value
self.agrids = f[idx + '/coords'].value
self.npang = f[idx + '/npang'].value
self.ntrial = f[idx + '/ntrial'].value
self.rmin = f[idx + '/rmin'].value
self.rmax = f[idx + '/rmax'].value
self.nlimsurf = f[idx + '/nlimsurf'].value
self.rsurf = f[idx + '/rsurf'].value
if self.charges[self.inuc] == 1:
self.rad = grids.BRAGG[self.charges[self.inuc]]
else:
self.rad = grids.BRAGG[self.charges[self.inuc]] * 0.5
self.brad = self.rmin * self.betafac
if (self.iqudr == 'legendre'):
self.iqudr = 1
if (self.biqudr == 'legendre'):
self.biqudr = 1
if (self.mapr == 'becke'):
self.mapr = 1
elif (self.mapr == 'exp'):
self.mapr = 2
elif (self.mapr == 'none'):
self.mapr = 0
if (self.bmapr == 'becke'):
self.bmapr = 1
elif (self.bmapr == 'exp'):
self.bmapr = 2
elif (self.bmapr == 'none'):
self.bmapr = 0
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
# 2) Compute integrals
brprops = int_beta(self)
rprops = out_beta(self)
#logger.info(self,'Write info to HDF5 file')
#atom_dic = {'inprops':brprops,
# 'outprops':rprops,
# 'totprops':(brprops+rprops)}
#chkfile.save(self.surfile, 'atom_props'+str(self.inuc), atom_dic)
logger.info(self, '*-> Total density density %8.5f ',
(rprops + brprops))
logger.info(self, '')
logger.info(self, 'Basim properties of atom %d done', self.inuc)
logger.timer(self, 'Basin build', t0)
logger.info(self, '')
return self
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
# 1) Build grid
self.grids.verbose = self.verbose
self.grids.stdout = self.stdout
self.grids.max_memory = self.max_memory
self.grids.scratch = self.scratch
self.grids.build()
# 2) Read info
with h5py.File(self.chkfile) as f:
self.natm = f['molecule/natm'].value
self.coords = f['molecule/coords'].value
self.charges = f['molecule/charges'].value
self.symbols = f['molecule/symbols'].value
self.nmo = f['basis/nmo'].value
self.nprims = f['basis/nprims'].value
self.icen = f['basis/icen'].value
self.ityp = f['basis/ityp'].value
self.oexp = f['basis/oexp'].value
self.mo_coeff = f['basis/mo_coeff'].value
self.mo_occ = f['basis/mo_occ'].value
self.ngroup = f['basis/ngroup'].value
self.nzexp = f['basis/nzexp'].value
self.nuexp = f['basis/nuexp'].value
self.rcutte = f['basis/rcutte'].value
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
# 3) Qualitie of grid
rho = numint.eval_rho(self, self.grids.coords)
rhoval = numpy.einsum('i,i->', rho, self.grids.weights)
logger.info(self, 'Integral of rho %.6f' % rhoval)
# 4) Promolecular density and weights
logger.info(self, 'Getting atomic data from tabulated densities')
npoints = len(self.grids.weights)
output = numpy.zeros(npoints)
promol = numpy.zeros(npoints)
ftmp = misc.H5TmpFile()
rhoat = 0.0
for i in range(self.natm):
libfapi.atomic(ctypes.c_int(npoints),
ctypes.c_int(self.charges[i]),
self.coords[i].ctypes.data_as(ctypes.c_void_p),
self.grids.coords.ctypes.data_as(ctypes.c_void_p),
output.ctypes.data_as(ctypes.c_void_p))
h5dat = ftmp.create_dataset('atom' + str(i), (npoints, ), 'f8')
h5dat[:] = output[:]
rhoa = numpy.einsum('i,i->', output, self.grids.weights)
rhoat += rhoa
promol += output
logger.info(self, 'Integral of rho for atom %d %.6f' % (i, rhoa))
logger.info(self, 'Integral of rho promolecular %.6f' % rhoat)
for i in range(self.natm):
h5dat = ftmp.create_dataset('weight' + str(i), (npoints, ), 'f8')
h5dat[:] = ftmp['atom' + str(i)][:] / (promol + param.HMINIMAL)
# 5) Atomic partition
atomq = numpy.zeros(self.natm)
hirshfeld = numpy.zeros(npoints)
for i in range(self.natm):
hirshfeld[:] = ftmp['weight' + str(i)]
atomq[i] = numpy.einsum('i,i->', rho,
self.grids.weights * hirshfeld)
logger.info(self, 'Charge of atom %d %.6f' % (i, atomq[i]))
logger.timer(self, 'Becke integration done', t0)
logger.info(self, '')
return self
def build(self):
t0 = time.clock()
logger.TIMER_LEVEL = 3
title, symbols, numbers, coords, icen, ityp, oexp, \
mo_count, mo_occ, mo_energy, mo_coeff = wfn.load_wfn(self.wfnfile)
nprims, nmo = mo_coeff.shape
self.natm = coords.shape[0]
self.nelectrons = mo_occ.sum()
self.symbols = symbols
self.coords = coords
self.charges = numbers
self.nmo = nmo
self.icen = icen
self.ityp = ityp
self.oexp = oexp
self.mo_occ = mo_occ
self.mo_coeff = mo_coeff
self.nprims = nprims
self.lang = numpy.empty(self.nprims, dtype=numpy.int32)
self.npc = numpy.zeros(self.natm, dtype=numpy.int32)
# 1) Purge repeated primitives
purge_prims(self)
# 2) Classifie basis set
get_shells(self)
# 3) Get cutdistances for each shell
get_shells_eps(self)
# 4) In case for correlated build natural orbitals
if (self.corr): get_nat_orbs(self)
# Dump info
if self.verbose > logger.NOTE:
self.dump_input()
# 5) Write info to file
logger.info(self, 'Write HDF5 file')
mol_dic = {
'natm': self.natm,
'symbols': self.symbols,
'corr': self.corr,
'coords': self.coords,
'charges': self.charges,
'nelectrons': self.nelectrons
}
chkfile.save(self.chkfile, 'molecule', mol_dic)
bas_dic = {
'cuttz': self.cuttz,
'nmo': self.nmo,
'nprims': self.nprims,
'icen': self.icen,
'ityp': self.ityp,
'oexp': self.oexp,
'lang': self.lang,
'lmax': self.lmax,
'npc': self.npc,
'mo_coeff': self.mo_coeff,
'mo_occ': self.mo_occ,
'ngroup': self.ngroup,
'nzexp': self.nzexp,
'nuexp': self.nuexp,
'rcutte': self.rcutte,
'nshells': self.nshells
}
chkfile.save(self.chkfile, 'basis', bas_dic)
logger.timer(self, 'Basis info build', t0)
logger.info(self, '')
return self