1252 lines
46 KiB
Python
1252 lines
46 KiB
Python
import numpy as np
|
|
from functools import reduce
|
|
|
|
|
|
def memoize(f):
|
|
memo = {}
|
|
def helper(x):
|
|
if x not in memo:
|
|
memo[x] = f(x)
|
|
return memo[x]
|
|
return helper
|
|
|
|
@memoize
|
|
def idx2_tri(iijj):
|
|
'''
|
|
iijj should be a 2-tuple
|
|
return triangular compound index for (0-indexed counting)
|
|
'''
|
|
ij1=min(iijj)
|
|
ij2=max(iijj)
|
|
return ij1+(ij2*(ij2+1))//2
|
|
# return ij1+(ij2*(ij2-1))//2
|
|
|
|
def pad(arr_in,outshape):
|
|
arr_out = np.zeros(outshape,dtype=np.complex128)
|
|
dataslice = tuple(slice(0,arr_in.shape[dim]) for dim in range(len(outshape)))
|
|
arr_out[dataslice] = arr_in
|
|
return arr_out
|
|
|
|
def xyzcount(s):
|
|
return list(map(s.count,['x','y','z']))
|
|
|
|
def idx40(i,j,k,l):
|
|
return idx2_tri((idx2_tri((i,k)),idx2_tri((j,l))))
|
|
|
|
def idx4(i,j,k,l):
|
|
return idx2_tri((idx2_tri((i-1,k-1)),idx2_tri((j-1,l-1))))+1
|
|
|
|
def stri4(i,j,k,l):
|
|
return (4*'{:5d}').format(i,j,k,l)
|
|
|
|
def stri4z(i,j,k,l,zr,zi):
|
|
return (4*'{:5d}'+2*'{:25.16e}').format(i,j,k,l,zr,zi)
|
|
|
|
def stri2z(i,j,zr,zi):
|
|
return (2*'{:5d}'+2*'{:25.16e}').format(i,j,zr,zi)
|
|
|
|
def strijklikjli4z(i,j,k,l,zr,zi):
|
|
return ('{:10d}'+ 2*'{:8d}'+4*'{:5d}'+2*'{:25.16e}').format(idx4(i,j,k,l),idx2_tri((i-1,k-1))+1,idx2_tri((j-1,l-1))+1,i,j,k,l,zr,zi)
|
|
|
|
|
|
def makesq(vlist,n1,n2):
|
|
'''
|
|
make hermitian matrices of size (n2 x n2) from from lower triangles
|
|
vlist is n1 lower triangles in flattened form
|
|
given: ([a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t],2,4)
|
|
output a 2x4x4 array, where each 4x4 is the square constructed from the lower triangle
|
|
[
|
|
[
|
|
[a b* d* g*]
|
|
[b c e* h*]
|
|
[d e f i*]
|
|
[g h i j ]
|
|
],
|
|
[
|
|
[k l* n* q*]
|
|
[l m o* r*]
|
|
[n o p s*]
|
|
[q r s t ]
|
|
]
|
|
]
|
|
'''
|
|
out=np.zeros([n1,n2,n2],dtype=np.complex128)
|
|
n0 = vlist.shape[0]
|
|
lmask=np.tri(n2,dtype=bool)
|
|
for i in range(n0):
|
|
out[i][lmask] = vlist[i].conj()
|
|
out2=out.transpose([0,2,1])
|
|
for i in range(n0):
|
|
out2[i][lmask] = vlist[i]
|
|
return out2
|
|
|
|
|
|
def makesq3(vlist,n2):
|
|
'''
|
|
make hermitian matrices of size (n2 x n2) from from lower triangles
|
|
vlist is n1 lower triangles in flattened form
|
|
given: ([a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t],2,4)
|
|
output a 2x4x4 array, where each 4x4 is the square constructed from the lower triangle
|
|
[
|
|
[
|
|
[a b* d* g*]
|
|
[b c e* h*]
|
|
[d e f i*]
|
|
[g h i j ]
|
|
],
|
|
[
|
|
[k l* n* q*]
|
|
[l m o* r*]
|
|
[n o p s*]
|
|
[q r s t ]
|
|
]
|
|
]
|
|
'''
|
|
n0 = vlist.shape[0]
|
|
out=np.zeros([n0,n2,n2],dtype=np.complex128)
|
|
lmask=np.tri(n2,dtype=bool)
|
|
for i in range(n0):
|
|
out[i][lmask] = vlist[i].conj()
|
|
out2=out.transpose([0,2,1])
|
|
for i in range(n0):
|
|
out2[i][lmask] = vlist[i]
|
|
return out2
|
|
|
|
def makesq2(vlist,n1,n2):
|
|
out=np.zeros([n1,n2,n2],dtype=np.complex128)
|
|
lmask=np.tri(n2,dtype=bool)
|
|
tmp=np.zeros([n2,n2],dtype=np.complex128)
|
|
tmp2=np.zeros([n2,n2],dtype=np.complex128)
|
|
for i in range(n1):
|
|
tmp[lmask] = vlist[i].conj()
|
|
tmp2=tmp.T
|
|
tmp2[lmask] = vlist[i]
|
|
out[i] = tmp2.copy()
|
|
return out
|
|
|
|
def get_supcellPhase(cell, kpts=[], kmesh=[]):
|
|
'''
|
|
The unitary transformation that transforms the supercell basis k-mesh
|
|
adapted basis.
|
|
'''
|
|
from pyscf.pbc import tools
|
|
from pyscf import lib
|
|
|
|
latt_vec = cell.lattice_vectors()
|
|
if not bool(kmesh):
|
|
# Guess kmesh
|
|
scaled_k = cell.get_scaled_kpts(kpts).round(8)
|
|
kmesh = (len(np.unique(scaled_k[:,0])),
|
|
len(np.unique(scaled_k[:,1])),
|
|
len(np.unique(scaled_k[:,2])))
|
|
|
|
R_rel_a = np.arange(kmesh[0])
|
|
R_rel_b = np.arange(kmesh[1])
|
|
R_rel_c = np.arange(kmesh[2])
|
|
R_vec_rel = lib.cartesian_prod((R_rel_a, R_rel_b, R_rel_c))
|
|
R_vec_abs = np.einsum('nu, uv -> nv', R_vec_rel, latt_vec)
|
|
|
|
NR = len(R_vec_abs)
|
|
phase = np.exp(1j*np.einsum('Ru, ku -> Rk', R_vec_abs, kpts))
|
|
phase /= np.sqrt(NR) # normalization in supercell
|
|
|
|
# R_rel_mesh has to be construct exactly same to the Ts in super_cell function
|
|
scell = tools.super_cell(cell, kmesh)
|
|
return scell,phase
|
|
|
|
def qp2rename():
|
|
import shutil
|
|
qp2names={}
|
|
qp2names['mo_coef_complex'] = 'C.qp'
|
|
qp2names['bielec_ao_complex'] = 'W.qp'
|
|
|
|
qp2names['kinetic_ao_complex'] = 'T.qp'
|
|
qp2names['ne_ao_complex'] = 'V.qp'
|
|
qp2names['overlap_ao_complex'] = 'S.qp'
|
|
|
|
|
|
for old,new in qp2names.items():
|
|
shutil.move(old,new)
|
|
shutil.copy('e_nuc','E.qp')
|
|
|
|
def print_mo_bi(mf,kconserv=None,outfilename='W.mo.qp',cas_idx=None,bielec_int_threshold = 1E-8):
|
|
|
|
cell = mf.cell
|
|
kpts = mf.kpts
|
|
#nao = mf.cell.nao
|
|
#Nk = kpts.shape[0]
|
|
|
|
mo_coeff = mf.mo_coeff
|
|
# Mo_coeff actif
|
|
mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
|
|
|
|
Nk, nao, nmo = mo_k.shape
|
|
|
|
if (kconserv is None):
|
|
from pyscf.pbc import tools
|
|
kconserv = tools.get_kconserv(cell, kpts)
|
|
|
|
with open(outfilename,'w') as outfile:
|
|
for d, kd in enumerate(kpts):
|
|
for c, kc in enumerate(kpts):
|
|
if c > d: break
|
|
#idx2_cd = idx2_tri((c,d))
|
|
for b, kb in enumerate(kpts):
|
|
if b > d: break
|
|
a = kconserv[b,c,d]
|
|
if a > d: continue
|
|
#if idx2_tri((a,b)) > idx2_cd: continue
|
|
#if ((c==d) and (a>b)): continue
|
|
ka = kpts[a]
|
|
eri_4d_mo_kpt = mf.with_df.ao2mo([mo_k[a], mo_k[b], mo_k[c], mo_k[d]],
|
|
[ka,kb,kc,kd],compact=False).reshape((nmo,)*4)
|
|
eri_4d_mo_kpt *= 1./Nk
|
|
for l in range(nmo):
|
|
ll=l+d*nmo
|
|
for j in range(nmo):
|
|
jj=j+c*nmo
|
|
if jj>ll: break
|
|
idx2_jjll = idx2_tri((jj,ll))
|
|
for k in range(nmo):
|
|
kk=k+b*nmo
|
|
if kk>ll: break
|
|
for i in range(nmo):
|
|
ii=i+a*nmo
|
|
if idx2_tri((ii,kk)) > idx2_jjll: break
|
|
if ((jj==ll) and (ii>kk)): break
|
|
v=eri_4d_mo_kpt[i,k,j,l]
|
|
if (abs(v) > bielec_int_threshold):
|
|
outfile.write(stri4z(ii+1,jj+1,kk+1,ll+1,
|
|
v.real,v.imag)+'\n')
|
|
|
|
|
|
def print_ao_bi(mf,kconserv=None,outfilename='W.ao.qp',bielec_int_threshold = 1E-8):
|
|
|
|
cell = mf.cell
|
|
kpts = mf.kpts
|
|
nao = mf.cell.nao
|
|
Nk = kpts.shape[0]
|
|
|
|
if (kconserv is None):
|
|
from pyscf.pbc.tools import get_kconserv
|
|
kconserv = get_kconserv(cell, kpts)
|
|
|
|
with open(outfilename,'w') as outfile:
|
|
for d, kd in enumerate(kpts):
|
|
for c, kc in enumerate(kpts):
|
|
if c > d: break
|
|
#idx2_cd = idx2_tri((c,d))
|
|
for b, kb in enumerate(kpts):
|
|
if b > d: break
|
|
a = kconserv[b,c,d]
|
|
if a > d: continue
|
|
#if idx2_tri((a,b)) > idx2_cd: continue
|
|
#if ((c==d) and (a>b)): continue
|
|
ka = kpts[a]
|
|
|
|
eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],
|
|
compact=False).reshape((nao,)*4)
|
|
eri_4d_ao_kpt *= 1./Nk
|
|
for l in range(nao):
|
|
ll=l+d*nao
|
|
for j in range(nao):
|
|
jj=j+c*nao
|
|
if jj>ll: break
|
|
idx2_jjll = idx2_tri((jj,ll))
|
|
for k in range(nao):
|
|
kk=k+b*nao
|
|
if kk>ll: break
|
|
for i in range(nao):
|
|
ii=i+a*nao
|
|
if idx2_tri((ii,kk)) > idx2_jjll: break
|
|
if ((jj==ll) and (ii>kk)): break
|
|
v=eri_4d_ao_kpt[i,k,j,l]
|
|
if (abs(v) > bielec_int_threshold):
|
|
outfile.write(stri4z(ii+1,jj+1,kk+1,ll+1,
|
|
v.real,v.imag)+'\n')
|
|
|
|
|
|
def print_kcon_chem_to_phys(kcon,fname):
|
|
'''
|
|
input: kconserv in chem notation kcon_c[a,b,c] = d
|
|
where (ab|cd) is allowed by symmetry
|
|
output: kconserv in phys notation kcon_p[i,j,k] = l
|
|
where <ij|kl> is allowed by symmetry
|
|
(printed to file)
|
|
'''
|
|
Nk,n2,n3 = kcon.shape
|
|
if (n2!=n3 or Nk!=n2):
|
|
raise Exception('print_kcon_chem_to_phys called with non-cubic array')
|
|
|
|
with open(fname,'w') as outfile:
|
|
for a in range(Nk):
|
|
for b in range(Nk):
|
|
for c in range(Nk):
|
|
d = kcon[a,b,c]
|
|
outfile.write(stri4(a+1,c+1,b+1,d+1)+'\n')
|
|
|
|
def print_kpts_unblocked(ints_k,outfilename,thresh):
|
|
'''
|
|
for ints_k of shape (Nk,n1,n2),
|
|
print the elements of the corresponding block-diagonal matrix of shape (Nk*n1,Nk*n2) in file
|
|
'''
|
|
Nk,n1,n2 = ints_k.shape
|
|
with open(outfilename,'w') as outfile:
|
|
for ik in range(Nk):
|
|
shift1 = ik*n1+1
|
|
shift2 = ik*n2+1
|
|
for i1 in range(n1):
|
|
for i2 in range(n2):
|
|
int_ij = ints_k[ik,i1,i2]
|
|
if abs(int_ij) > thresh:
|
|
outfile.write(stri2z(i1+shift1, i2+shift2, int_ij.real, int_ij.imag)+'\n')
|
|
return
|
|
|
|
def print_kpts_unblocked_upper(ints_k,outfilename,thresh):
|
|
'''
|
|
for hermitian ints_k of shape (Nk,n1,n1),
|
|
print the elements of the corresponding block-diagonal matrix of shape (Nk*n1,Nk*n1) in file
|
|
(only upper triangle is printed)
|
|
'''
|
|
Nk,n1,n2 = ints_k.shape
|
|
if (n1!=n2):
|
|
raise Exception('print_kpts_unblocked_upper called with non-square matrix')
|
|
|
|
with open(outfilename,'w') as outfile:
|
|
for ik in range(Nk):
|
|
shift = ik*n1+1
|
|
for i1 in range(n1):
|
|
for i2 in range(i1,n1):
|
|
int_ij = ints_k[ik,i1,i2]
|
|
if abs(int_ij) > thresh:
|
|
outfile.write(stri2z(i1+shift, i2+shift, int_ij.real, int_ij.imag)+'\n')
|
|
return
|
|
|
|
|
|
|
|
def get_kin_ao(mf):
|
|
nao = mf.cell.nao_nr()
|
|
Nk = len(mf.kpts)
|
|
return np.reshape(mf.cell.pbc_intor('int1e_kin',1,1,kpts=mf.kpts),(Nk,nao,nao))
|
|
|
|
def get_ovlp_ao(mf):
|
|
nao = mf.cell.nao_nr()
|
|
Nk = len(mf.kpts)
|
|
return np.reshape(mf.get_ovlp(cell=mf.cell,kpts=mf.kpts),(Nk,nao,nao))
|
|
|
|
def get_pot_ao(mf):
|
|
nao = mf.cell.nao_nr()
|
|
Nk = len(mf.kpts)
|
|
|
|
if mf.cell.pseudo:
|
|
v_kpts_ao = np.reshape(mf.with_df.get_pp(kpts=mf.kpts),(Nk,nao,nao))
|
|
else:
|
|
v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=mf.kpts),(Nk,nao,nao))
|
|
|
|
if len(mf.cell._ecpbas) > 0:
|
|
from pyscf.pbc.gto import ecp
|
|
v_kpts_ao += np.reshape(ecp.ecp_int(mf.cell, mf.kpts),(Nk,nao,nao))
|
|
|
|
return v_kpts_ao
|
|
|
|
def ao_to_mo_1e(ao_kpts,mo_coef):
|
|
return np.einsum('kim,kij,kjn->kmn',mo_coef.conj(),ao_kpts,mo_coef)
|
|
|
|
def get_j3ao_old(fname,nao,Nk):
|
|
'''
|
|
returns list of Nk_pair arrays of shape (naux,nao,nao)
|
|
if naux is the same for each pair, returns numpy array
|
|
if naux is not the same for each pair, returns array of arrays
|
|
'''
|
|
import h5py
|
|
with h5py.File(fname,'r') as intfile:
|
|
j3c = intfile.get('j3c')
|
|
j3ckeys = list(j3c.keys())
|
|
j3ckeys.sort(key=lambda strkey:int(strkey))
|
|
|
|
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
|
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
|
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
|
j3clist = [j3c.get(i+'/0') for i in j3ckeys]
|
|
#if j3clist==[None]*len(j3clist):
|
|
if not(any(j3clist)):
|
|
# if using older version, stop before last level
|
|
j3clist = [j3c.get(i) for i in j3ckeys]
|
|
|
|
naosq = nao*nao
|
|
naotri = (nao*(nao+1))//2
|
|
nkinvsq = 1./np.sqrt(Nk)
|
|
|
|
# dimensions are (kikj,iaux,jao,kao), where kikj is compound index of kpts i and j
|
|
# output dimensions should be reversed (nao, nao, naux, nkptpairs)
|
|
return np.array([(i.value.reshape([-1,nao,nao]) if (i.shape[1] == naosq) else makesq3(i.value,nao)) * nkinvsq for i in j3clist])
|
|
|
|
def get_j3ao(fname,nao,Nk):
|
|
'''
|
|
returns padded df AO array
|
|
fills in zeros when functions are dropped due to linear dependency
|
|
last AO index corresponds to smallest kpt index?
|
|
(k, mu, i, j) where i.kpt >= j.kpt
|
|
'''
|
|
import h5py
|
|
with h5py.File(fname,'r') as intfile:
|
|
j3c = intfile.get('j3c')
|
|
j3ckeys = list(j3c.keys())
|
|
nkpairs = len(j3ckeys)
|
|
|
|
# get num order instead of lex order
|
|
j3ckeys.sort(key=lambda strkey:int(strkey))
|
|
|
|
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
|
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
|
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
|
keysub = '/0' if bool(j3c.get('0/0',getclass=True)) else ''
|
|
|
|
naux = max(map(lambda k: j3c[k+keysub].shape[0],j3c.keys()))
|
|
|
|
naosq = nao*nao
|
|
naotri = (nao*(nao+1))//2
|
|
nkinvsq = 1./np.sqrt(Nk)
|
|
|
|
j3arr = np.zeros((nkpairs,naux,nao,nao),dtype=np.complex128)
|
|
|
|
for i,kpair in enumerate(j3ckeys):
|
|
iaux,dim2 = j3c[kpair+keysub].shape
|
|
if (dim2==naosq):
|
|
j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]) * nkinvsq
|
|
#j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
|
|
else:
|
|
j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()],nao) * nkinvsq
|
|
#j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()].conj(),nao) * nkinvsq
|
|
|
|
return j3arr
|
|
|
|
def get_j3ao_big(fname,nao,Nk):
|
|
'''
|
|
returns padded df AO array
|
|
fills in zeros when functions are dropped due to linear dependency
|
|
last AO index corresponds to largest kpt index?
|
|
(k, mu, j, i) where i.kpt >= j.kpt
|
|
'''
|
|
import h5py
|
|
with h5py.File(fname,'r') as intfile:
|
|
j3c = intfile.get('j3c')
|
|
j3ckeys = list(j3c.keys())
|
|
nkpairs = len(j3ckeys)
|
|
|
|
# get num order instead of lex order
|
|
j3ckeys.sort(key=lambda strkey:int(strkey))
|
|
|
|
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
|
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
|
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
|
#keysub = '/0' if bool(j3c.get('0/0',getclass=True)) else ''
|
|
|
|
#naux = max(map(lambda k: j3c[k+keysub].shape[0],j3c.keys()))
|
|
naux = max(map(lambda k: j3c[k]['0'].shape[0],j3c.keys()))
|
|
|
|
naosq = nao*nao
|
|
naotri = (nao*(nao+1))//2
|
|
nkinvsq = 1./np.sqrt(Nk)
|
|
|
|
j3arr = np.zeros((nkpairs,naux,nao,nao),dtype=np.complex128)
|
|
|
|
for i,kpair in enumerate(j3ckeys):
|
|
#iaux,dim2 = j3c[kpair+keysub].shape
|
|
tmpdat = np.concatenate([j3c[kpair][ii][()] for ii in j3c[kpair]],axis=1)
|
|
iaux,dim2 = tmpdat.shape
|
|
if (dim2==naosq):
|
|
#j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
|
|
j3arr[i,:iaux,:,:] = tmpdat.reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
|
|
else:
|
|
#j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()].conj(),nao) * nkinvsq
|
|
j3arr[i,:iaux,:,:] = makesq3(tmpdat.conj(),nao) * nkinvsq
|
|
|
|
return j3arr
|
|
|
|
|
|
def get_j3ao_new(fname,nao,Nk):
|
|
'''
|
|
returns padded df AO array
|
|
fills in zeros when functions are dropped due to linear dependency
|
|
last AO index corresponds to largest kpt index?
|
|
(k, mu, j, i) where i.kpt >= j.kpt
|
|
'''
|
|
import h5py
|
|
with h5py.File(fname,'r') as intfile:
|
|
j3c = intfile.get('j3c')
|
|
j3ckeys = list(j3c.keys())
|
|
nkpairs = len(j3ckeys)
|
|
|
|
# get num order instead of lex order
|
|
j3ckeys.sort(key=lambda strkey:int(strkey))
|
|
|
|
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
|
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
|
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
|
keysub = '/0' if bool(j3c.get('0/0',getclass=True)) else ''
|
|
|
|
naux = max(map(lambda k: j3c[k+keysub].shape[0],j3c.keys()))
|
|
#naux = max(map(lambda k: j3c[k]['0'].shape[0],j3c.keys()))
|
|
|
|
naosq = nao*nao
|
|
naotri = (nao*(nao+1))//2
|
|
nkinvsq = 1./np.sqrt(Nk)
|
|
|
|
j3arr = np.zeros((nkpairs,naux,nao,nao),dtype=np.complex128)
|
|
|
|
for i,kpair in enumerate(j3ckeys):
|
|
iaux,dim2 = j3c[kpair+keysub].shape
|
|
#tmpdat = np.concatenate([j3c[kpair][ii][()] for ii in j3c[kpair]],axis=1)
|
|
#iaux,dim2 = tmpdat.shape
|
|
if (dim2==naosq):
|
|
j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
|
|
#j3arr[i,:iaux,:,:] = tmpdat.reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
|
|
else:
|
|
j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()].conj(),nao) * nkinvsq
|
|
#j3arr[i,:iaux,:,:] = makesq3(tmpdat.conj(),nao) * nkinvsq
|
|
|
|
return j3arr
|
|
|
|
def print_df(j3arr,fname,thresh):
|
|
with open(fname,'w') as outfile:
|
|
for k,kpt_pair in enumerate(j3arr):
|
|
for iaux,dfbasfunc in enumerate(kpt_pair):
|
|
for i,i0 in enumerate(dfbasfunc):
|
|
for j,v in enumerate(i0):
|
|
if (abs(v) > thresh):
|
|
outfile.write(stri4z(i+1,j+1,iaux+1,k+1,v.real,v.imag)+'\n')
|
|
return
|
|
|
|
def df_pad_ref_test(j3arr,nao,naux,nkpt_pairs):
|
|
df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
|
|
for k,kpt_pair in enumerate(j3arr):
|
|
for iaux,dfbasfunc in enumerate(kpt_pair):
|
|
for i,i0 in enumerate(dfbasfunc):
|
|
for j,v in enumerate(i0):
|
|
df_ao_tmp[i,j,iaux,k]=v
|
|
return df_ao_tmp
|
|
|
|
|
|
def df_ao_to_mo(j3ao,mo_coef):
|
|
from itertools import product
|
|
Nk = mo_coef.shape[0]
|
|
kpair_list = ((i,j,idx2_tri((i,j))) for (i,j) in product(range(Nk),repeat=2) if (i>=j))
|
|
return np.array([
|
|
np.einsum('mij,ik,jl->mkl',j3ao[kij],mo_coef[ki].conj(),mo_coef[kj])
|
|
for ki,kj,kij in kpair_list])
|
|
|
|
|
|
def df_ao_to_mo_new(j3ao,mo_coef):
|
|
#TODO: fix this (C/F ordering, conj, transpose, view cmplx->float)
|
|
|
|
from itertools import product
|
|
Nk = mo_coef.shape[0]
|
|
return np.array([
|
|
np.einsum('mji,ik,jl->mlk',j3ao[idx2_tri((ki,kj))],mo_coef[ki].conj(),mo_coef[kj])
|
|
for ki,kj in product(range(Nk),repeat=2) if (ki>=kj)],dtype=np.complex128)
|
|
|
|
def df_ao_to_mo_test(j3ao,mo_coef):
|
|
from itertools import product
|
|
Nk = mo_coef.shape[0]
|
|
return np.array([
|
|
np.einsum('mij,ik,jl->mkl',j3ao[idx2_tri((ki,kj))],mo_coef[ki].conj(),mo_coef[kj])
|
|
for ki,kj in product(range(Nk),repeat=2) if (ki>=kj)])
|
|
|
|
def pyscf2QP2_mo(cell,mf,kpts,kmesh=None,cas_idx=None, int_threshold = 1E-8,qph5path='qpdat.h5'):
|
|
pyscf2QP2(cell,mf,kpts,kmesh,cas_idx,int_threshold,qph5path,
|
|
print_ao_ints_df=False,
|
|
print_mo_ints_df=True,
|
|
print_ao_ints_mono=False,
|
|
print_mo_ints_mono=True)
|
|
return
|
|
|
|
|
|
|
|
def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
|
qph5path = 'qpdat.h5', sp_twist=None,
|
|
print_ao_ints_bi=False,
|
|
print_mo_ints_bi=False,
|
|
print_ao_ints_df=True,
|
|
print_mo_ints_df=False,
|
|
print_ao_ints_mono=True,
|
|
print_mo_ints_mono=False,
|
|
print_debug=False):
|
|
'''
|
|
kpts = List of kpoints coordinates. Cannot be null, for gamma is other script
|
|
kmesh = Mesh of kpoints (optional)
|
|
cas_idx = List of active MOs. If not specified all MOs are actives
|
|
int_threshold = The integral will be not printed in they are bellow that
|
|
'''
|
|
|
|
# from pyscf.pbc import ao2mo
|
|
from pyscf.pbc import tools
|
|
import h5py
|
|
# import scipy
|
|
from scipy.linalg import block_diag
|
|
|
|
mo_coef_threshold = int_threshold
|
|
ovlp_threshold = int_threshold
|
|
kin_threshold = int_threshold
|
|
ne_threshold = int_threshold
|
|
bielec_int_threshold = int_threshold
|
|
thresh_mono = int_threshold
|
|
loc_cell,phase=get_supcellPhase(cell=cell,kmesh=kmesh,kpts=kpts)
|
|
|
|
|
|
# qph5path = 'qpdat.h5'
|
|
# create hdf5 file, delete old data if exists
|
|
with h5py.File(qph5path,'w') as qph5:
|
|
qph5.create_group('nuclei')
|
|
qph5.create_group('electrons')
|
|
qph5.create_group('ao_basis')
|
|
qph5.create_group('mo_basis')
|
|
qph5.create_group('qmcpack')
|
|
#qph5.create_group('pseudo')
|
|
#qph5['pseudo'].attrs['do_pseudo']=False
|
|
|
|
#if mf.cell.cart:
|
|
# mo_coeff = mf.mo_coeff.copy()
|
|
#else:
|
|
# # normalized can be one of ['all','sp',None]
|
|
# # we can either normalize here or after qp
|
|
# c2s = mf.cell.cart2sph_coeff(normalized='sp')
|
|
# mo_coeff = list(map(lambda x: np.dot(c2s,x),mf.mo_coeff))
|
|
mo_coeff = mf.mo_coeff
|
|
# Mo_coeff actif
|
|
mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
|
|
e_k = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
|
|
|
|
Nk, nao, nmo = mo_k.shape
|
|
|
|
print("n Kpts", Nk)
|
|
print("n active Mos per kpt", nmo)
|
|
print("n AOs per kpt", nao)
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclei #
|
|
# #
|
|
##########################################
|
|
|
|
natom = cell.natm
|
|
|
|
print('n_atom per kpt', natom)
|
|
|
|
#BY DEFAULT SEEMS TO BE IN BOHR
|
|
atom_xyz = mf.cell.atom_coords()
|
|
|
|
unit_bohr=1.0
|
|
if not(mf.cell.unit.startswith(('B','b','au','AU'))):
|
|
from pyscf.data.nist import BOHR
|
|
# atom_xyz *= BOHR # always convert to au
|
|
# atom_xyz /= BOHR # always convert to au
|
|
unit_bohr=BOHR
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['kpt_num']=Nk
|
|
|
|
if len(kpts)!=0:
|
|
nbatom=loc_cell.natm
|
|
qph5['nuclei'].attrs['nucl_num']=nbatom
|
|
MyPos=qph5.create_dataset('nuclei/nucl_coord',(nbatom,3),dtype="f8")
|
|
for x in range(nbatom):
|
|
MyPos[x:]=loc_cell.atom_coord(x)/unit_bohr
|
|
qph5.create_dataset('nuclei/nucl_charge',data=loc_cell.atom_charges())
|
|
strtype=h5py.special_dtype(vlen=str)
|
|
atom_dset=qph5.create_dataset('nuclei/nucl_label',(nbatom,),dtype=strtype)
|
|
for i in range(nbatom):
|
|
atom_dset[i] = loc_cell.atom_pure_symbol(i)
|
|
else:
|
|
qph5['nuclei'].attrs['nucl_num']=natom
|
|
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
|
|
qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
|
|
strtype=h5py.special_dtype(vlen=str)
|
|
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
|
|
for i in range(natom):
|
|
atom_dset[i] = mf.cell.atom_pure_symbol(i)
|
|
|
|
##########################################
|
|
# #
|
|
# Basis #
|
|
# #
|
|
##########################################
|
|
|
|
# nucleus on which each AO is centered
|
|
ao_nucl=[i[0] for i in mf.cell.ao_labels(fmt=False,base=1)]
|
|
|
|
|
|
nprim_max = 0
|
|
nfunc_tot = 0
|
|
for iatom, (sh0,sh1,ao0,ao1) in enumerate(cell.aoslice_by_atom()):
|
|
for ib in range(sh0,sh1): # sets of contracted exponents
|
|
nprim = cell.bas_nprim(ib)
|
|
nfunc_tot += cell.bas_nctr(ib)
|
|
if (nprim > nprim_max):
|
|
nprim_max = nprim
|
|
|
|
qp_prim_num = np.zeros((nfunc_tot),dtype=int)
|
|
qp_coef = np.zeros((nfunc_tot,nprim_max))
|
|
qp_expo = np.zeros((nfunc_tot,nprim_max))
|
|
qp_nucl = np.zeros((nfunc_tot),dtype=int)
|
|
qp_lbas = np.zeros((nfunc_tot),dtype=int)
|
|
|
|
clabels = cell.cart_labels(fmt=False)
|
|
|
|
tmp_idx=0
|
|
for iatom, (sh0,sh1,ao0,ao1) in enumerate(cell.aoslice_by_atom()):
|
|
# shell start,end; AO start,end (sph or cart) for each atom
|
|
for ib in range(sh0,sh1): # sets of contracted exponents
|
|
l = cell.bas_angular(ib) # angular momentum
|
|
nprim = cell.bas_nprim(ib) # numer of primitives
|
|
es = cell.bas_exp(ib) # exponents
|
|
cs = cell.bas_ctr_coeff(ib) # coeffs
|
|
nctr = cell.bas_nctr(ib) # number of contractions
|
|
print(iatom,ib,l,nprim,nctr,tmp_idx)
|
|
#if cell.cart:
|
|
# nfuncmax = ((l+1)*(l+2))//2
|
|
#else:
|
|
# nfuncmax = 2*l+1
|
|
for ic in range(nctr): # sets of contraction coeffs
|
|
qp_expo[tmp_idx,:nprim] = es[:]
|
|
qp_coef[tmp_idx,:nprim] = cs[:,ic]
|
|
qp_nucl[tmp_idx] = iatom
|
|
qp_lbas[tmp_idx] = l
|
|
qp_prim_num[tmp_idx] = nprim
|
|
tmp_idx += 1
|
|
#for nfunc in range(nfuncmax):
|
|
#for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
|
|
# qp_expo[tmp_idx,:nprim] = es[:]
|
|
# qp_coef[tmp_idx,:nprim] = cs[:,ic]
|
|
# qp_nucl[tmp_idx] = iatom + 1
|
|
# qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3])
|
|
# qp_prim_num[tmp_idx] = nprim
|
|
# tmp_idx += 1
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['mo_basis'].attrs['mo_num']=Nk*nmo
|
|
qph5['ao_basis'].attrs['ao_num']=Nk*nao
|
|
|
|
#qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
|
qph5['ao_basis'].attrs['ao_basis']="dummy basis"
|
|
|
|
qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
|
|
|
|
qph5['qmcpack'].attrs['qmc_nshell']=nfunc_tot
|
|
qph5['qmcpack'].attrs['qmc_prim_num_max']=nprim_max
|
|
qph5.create_dataset('qmcpack/qmc_nucl',data=qp_nucl)
|
|
qph5.create_dataset('qmcpack/qmc_prim_num',data=qp_prim_num)
|
|
qph5.create_dataset('qmcpack/qmc_expo',data=qp_expo.T)
|
|
qph5.create_dataset('qmcpack/qmc_coef',data=qp_coef.T)
|
|
qph5.create_dataset('qmcpack/qmc_lbas',data=qp_lbas)
|
|
|
|
|
|
|
|
# with h5py.File(qph5path,'a') as qph5:
|
|
# qph5['mo_basis'].attrs['mo_num']=Nk*nmo
|
|
# qph5['ao_basis'].attrs['ao_num']=Nk*nao
|
|
#
|
|
# #qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
|
# qph5['ao_basis'].attrs['ao_basis']="dummy basis"
|
|
#
|
|
# qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
|
|
|
|
##########################################
|
|
# #
|
|
# Electrons #
|
|
# #
|
|
##########################################
|
|
|
|
nelec = cell.nelectron
|
|
neleca,nelecb = cell.nelec
|
|
|
|
print('num_elec per kpt', nelec)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
#in old version: param << nelec*Nk, nmo*Nk, natom*Nk
|
|
qph5['electrons'].attrs['elec_alpha_num']=neleca*Nk
|
|
qph5['electrons'].attrs['elec_beta_num']=nelecb*Nk
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclear Repulsion #
|
|
# #
|
|
##########################################
|
|
|
|
#Total energy shift due to Ewald probe charge = -1/2 * Nelec*madelung/cell.vol =
|
|
shift = tools.pbc.madelung(cell, kpts)*cell.nelectron * -.5
|
|
e_nuc = (cell.energy_nuc() + shift)*Nk
|
|
|
|
print('nucl_repul', e_nuc)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['nuclear_repulsion']=e_nuc
|
|
|
|
##########################################
|
|
# #
|
|
# MO Coef #
|
|
# #
|
|
##########################################
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
# k,mo,ao(,2)
|
|
mo_coef_f = np.array(mo_k.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
#mo_coef_blocked=block_diag(*mo_k)
|
|
mo_coef_blocked_f = block_diag(*mo_coef_f)
|
|
qph5.create_dataset('mo_basis/mo_coef_complex',data=mo_coef_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nao,2)))
|
|
qph5.create_dataset('mo_basis/mo_coef_kpts',data=mo_coef_f.view(dtype=np.float64).reshape((Nk,nmo,nao,2)))
|
|
|
|
if print_debug:
|
|
print_kpts_unblocked(mo_k,'C.qp',mo_coef_threshold)
|
|
|
|
##########################################
|
|
# #
|
|
# Integrals Mono #
|
|
# #
|
|
##########################################
|
|
|
|
ne_ao = get_pot_ao(mf)
|
|
kin_ao = get_kin_ao(mf)
|
|
ovlp_ao = get_ovlp_ao(mf)
|
|
|
|
if print_ao_ints_mono:
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
kin_ao_f = np.array(kin_ao.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ovlp_ao_f = np.array(ovlp_ao.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ne_ao_f = np.array(ne_ao.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
|
|
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_kpts',data=kin_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
|
|
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_kpts',data=ovlp_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
|
|
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_kpts', data=ne_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
|
|
|
|
if print_debug:
|
|
for fname,ints in zip(('S.qp','V.qp','T.qp'),
|
|
(ovlp_ao, ne_ao, kin_ao)):
|
|
print_kpts_unblocked_upper(ints,fname,thresh_mono)
|
|
|
|
if print_mo_ints_mono:
|
|
kin_mo = ao_to_mo_1e(kin_ao,mo_k)
|
|
ovlp_mo = ao_to_mo_1e(ovlp_ao,mo_k)
|
|
ne_mo = ao_to_mo_1e(ne_ao,mo_k)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
kin_mo_f = np.array(kin_mo.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ovlp_mo_f = np.array(ovlp_mo.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ne_mo_f = np.array(ne_mo.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
|
|
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_kpts',data=kin_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
|
|
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_kpts',data=ovlp_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
|
|
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_kpts', data=ne_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
|
|
if print_debug:
|
|
for fname,ints in zip(('S.mo.qp','V.mo.qp','T.mo.qp'),
|
|
(ovlp_mo, ne_mo, kin_mo)):
|
|
print_kpts_unblocked_upper(ints,fname,thresh_mono)
|
|
|
|
|
|
##########################################
|
|
# #
|
|
# k-points #
|
|
# #
|
|
##########################################
|
|
|
|
kconserv = tools.get_kconserv(cell, kpts)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
kcon_f_phys = np.array(kconserv.transpose((1,2,0)),order='c')
|
|
qph5.create_dataset('nuclei/kconserv',data=kcon_f_phys+1)
|
|
qph5.create_dataset('nuclei/kpts',data=kpts)
|
|
|
|
if print_debug:
|
|
print_kcon_chem_to_phys(kconserv,'K.qp')
|
|
|
|
##########################################
|
|
# #
|
|
# Integrals Bi #
|
|
# #
|
|
##########################################
|
|
|
|
try:
|
|
j3ao_new = get_j3ao_new(mf.with_df._cderi,nao,Nk)
|
|
print('using old get_j3ao_new')
|
|
except ValueError:
|
|
j3ao_new = get_j3ao_big(mf.with_df._cderi,nao,Nk)
|
|
print('using new get_j3ao_big')
|
|
except:
|
|
print('unhandled error in get_j3ao?')
|
|
|
|
# test? nkpt_pairs should be (Nk*(Nk+1))//2
|
|
nkpt_pairs, naux, _, _ = j3ao_new.shape
|
|
|
|
print("n df fitting functions", naux)
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_group('ao_two_e_ints')
|
|
qph5['ao_two_e_ints'].attrs['df_num']=naux
|
|
|
|
if print_ao_ints_df:
|
|
if print_debug:
|
|
print_df(j3ao_new,'D.qp',bielec_int_threshold)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_dataset('ao_two_e_ints/df_ao_integrals',data=j3ao_new.view(dtype=np.float64).reshape((nkpt_pairs,naux,nao,nao,2)))
|
|
|
|
if print_mo_ints_df:
|
|
|
|
j3mo_new = df_ao_to_mo_new(j3ao_new,mo_k)
|
|
|
|
if print_debug:
|
|
print_df(j3mo_new,'D.mo.qp',bielec_int_threshold)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_dataset('mo_two_e_ints/df_mo_integrals',data=j3mo_new.view(dtype=np.float64).reshape((nkpt_pairs,naux,nmo,nmo,2)))
|
|
|
|
if (print_ao_ints_bi):
|
|
print_ao_bi(mf,kconserv,'W.qp',bielec_int_threshold)
|
|
if (print_mo_ints_bi):
|
|
print_mo_bi(mf,kconserv,'W.mo.qp',cas_idx,bielec_int_threshold)
|
|
|
|
|
|
##########################################
|
|
# #
|
|
# PBC DATA To transfer to qmc #
|
|
# #
|
|
##########################################
|
|
|
|
if len(kpts)== 0:
|
|
sp_twist=[0.0,0.0,0.0]
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['qmcpack'].attrs['PBC']=True
|
|
qph5['qmcpack'].attrs['cart']=cell.cart
|
|
qph5['qmcpack'].attrs['Pseudo']=cell.has_ecp()
|
|
qph5.create_dataset('qmcpack/Super_Twist',(1,3),dtype="f8",data=sp_twist)
|
|
if len(kpts)!= 0:
|
|
qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=loc_cell.lattice_vectors())
|
|
else:
|
|
qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors())
|
|
qph5.create_dataset('qmcpack/eigenval',(1,Nk*nmo),dtype="f8",data=e_k)
|
|
qph5.create_dataset('qmcpack/qmc_phase',data=phase.view(dtype=float))
|
|
|
|
return
|
|
|
|
def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
|
|
qph5path = 'qpdat.h5',
|
|
print_debug=False):
|
|
'''
|
|
cas_idx = List of active MOs. If not specified all MOs are actives
|
|
int_threshold = The integral will be not printed in they are bellow that
|
|
norm should be one of 'sp', 'all', or None
|
|
'''
|
|
|
|
import h5py
|
|
|
|
norm='sp'
|
|
mol = mf.mol
|
|
nao_c = mol.nao_cart()
|
|
|
|
mo_coef_threshold = int_threshold
|
|
ovlp_threshold = int_threshold
|
|
kin_threshold = int_threshold
|
|
ne_threshold = int_threshold
|
|
bielec_int_threshold = int_threshold
|
|
thresh_mono = int_threshold
|
|
|
|
|
|
# qph5path = 'qpdat.h5'
|
|
# create hdf5 file, delete old data if exists
|
|
with h5py.File(qph5path,'w') as qph5:
|
|
qph5.create_group('nuclei')
|
|
qph5.create_group('electrons')
|
|
qph5.create_group('ao_basis')
|
|
qph5.create_group('mo_basis')
|
|
qph5.create_group('pseudo')
|
|
qph5['pseudo'].attrs['do_pseudo']=False
|
|
|
|
if mf.mol.cart:
|
|
mo_coeff = mf.mo_coeff.copy()
|
|
else:
|
|
#c2s = mol.cart2sph_coeff(normalized=norm)
|
|
c2s = mol.cart2sph_coeff(normalized='sp')
|
|
#c2s = mol.cart2sph_coeff(normalized='all')
|
|
#c2s = mol.cart2sph_coeff(normalized=None)
|
|
mo_coeff = np.dot(c2s,mf.mo_coeff)
|
|
#TODO: clean this up; use mol.cart_labels(fmt=False)
|
|
dnormlbl1=["dxx","dyy","dzz"]
|
|
dnormfac1 = 2.0*np.sqrt(np.pi/5)
|
|
|
|
dnormlbl2=["dxy","dxz","dyz"]
|
|
dnormfac2 = 2.0*np.sqrt(np.pi/15)
|
|
|
|
fnormlbl1=["fxxx","fyyy","fzzz"]
|
|
fnormfac1 = 2.0*np.sqrt(np.pi/7)
|
|
|
|
fnormlbl2=["fxxy","fxxz","fxyy","fxzz","fyyz","fyzz"]
|
|
fnormfac2 = 2.0*np.sqrt(np.pi/35)
|
|
|
|
fnormlbl3=["fxyz"]
|
|
fnormfac3 = 2.0*np.sqrt(np.pi/105)
|
|
|
|
gnormlbl1=["gxxxx","gyyyy","gzzzz"]
|
|
gnormfac1 = 2.0*np.sqrt(np.pi/9)
|
|
|
|
gnormlbl2=["gxxxy","gxxxz","gxyyy","gxzzz","gyyyz","gyzzz"]
|
|
gnormfac2 = 2.0*np.sqrt(np.pi/63)
|
|
|
|
gnormlbl3=["gxxyy","gxxzz","gyyzz"]
|
|
gnormfac3 = 2.0*np.sqrt(np.pi/105)
|
|
|
|
gnormlbl4=["gxxyz","gxyyz","gxyzz"]
|
|
gnormfac4 = 2.0*np.sqrt(np.pi/315)
|
|
|
|
hnormlbl1=["hxxxxx","hyyyyy","hzzzzz"]
|
|
hnormfac1 = 2.0*np.sqrt(np.pi/11)
|
|
|
|
hnormlbl2=["hxxxxy","hxxxxz","hxyyyy","hxzzzz","hyyyyz","hyzzzz"]
|
|
hnormfac2 = 2.0*np.sqrt(np.pi/99)
|
|
|
|
hnormlbl3=["hxxxyy","hxxxzz","hxxyyy","hxxzzz","hyyyzz","hyyzzz"]
|
|
hnormfac3 = 2.0*np.sqrt(np.pi/231)
|
|
|
|
hnormlbl4=["hxxxyz","hxyyyz","hxyzzz"]
|
|
hnormfac4 = 2.0*np.sqrt(np.pi/693)
|
|
|
|
hnormlbl5=["hxxyyz","hxxyzz","hxyyzz"]
|
|
hnormfac5 = 2.0*np.sqrt(np.pi/1155)
|
|
|
|
for i_lbl,mo_lbl in enumerate(mol.cart_labels()):
|
|
if any(i in mo_lbl for i in dnormlbl1):
|
|
mo_coeff[i_lbl,:] *= dnormfac1
|
|
elif any(i in mo_lbl for i in dnormlbl2):
|
|
mo_coeff[i_lbl,:] *= dnormfac2
|
|
elif any(i in mo_lbl for i in fnormlbl1):
|
|
mo_coeff[i_lbl,:] *= fnormfac1
|
|
elif any(i in mo_lbl for i in fnormlbl2):
|
|
mo_coeff[i_lbl,:] *= fnormfac2
|
|
elif any(i in mo_lbl for i in fnormlbl3):
|
|
mo_coeff[i_lbl,:] *= fnormfac3
|
|
elif any(i in mo_lbl for i in gnormlbl1):
|
|
mo_coeff[i_lbl,:] *= gnormfac1
|
|
elif any(i in mo_lbl for i in gnormlbl2):
|
|
mo_coeff[i_lbl,:] *= gnormfac2
|
|
elif any(i in mo_lbl for i in gnormlbl3):
|
|
mo_coeff[i_lbl,:] *= gnormfac3
|
|
elif any(i in mo_lbl for i in gnormlbl4):
|
|
mo_coeff[i_lbl,:] *= gnormfac4
|
|
elif any(i in mo_lbl for i in hnormlbl1):
|
|
mo_coeff[i_lbl,:] *= hnormfac1
|
|
elif any(i in mo_lbl for i in hnormlbl2):
|
|
mo_coeff[i_lbl,:] *= hnormfac2
|
|
elif any(i in mo_lbl for i in hnormlbl3):
|
|
mo_coeff[i_lbl,:] *= hnormfac3
|
|
elif any(i in mo_lbl for i in hnormlbl4):
|
|
mo_coeff[i_lbl,:] *= hnormfac4
|
|
elif any(i in mo_lbl for i in hnormlbl5):
|
|
mo_coeff[i_lbl,:] *= hnormfac5
|
|
|
|
# Mo_coeff actif
|
|
mo_c = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
|
|
e_c = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
|
|
|
|
nao, nmo = mo_c.shape
|
|
|
|
print("n active MOs", nmo)
|
|
print("n AOs", nao)
|
|
assert nao==nao_c, "wrong number of AOs"
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclei #
|
|
# #
|
|
##########################################
|
|
|
|
natom = mol.natm
|
|
print('n_atom', natom)
|
|
|
|
atom_xyz = mol.atom_coords(unit='Bohr')
|
|
#if not(mol.unit.startswith(('B','b','au','AU'))):
|
|
# from pyscf.data.nist import BOHR
|
|
# atom_xyz /= BOHR # always convert to au
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['nucl_num']=natom
|
|
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
|
|
qph5.create_dataset('nuclei/nucl_charge',data=mol.atom_charges())
|
|
|
|
strtype=h5py.special_dtype(vlen=str)
|
|
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
|
|
for i in range(natom):
|
|
atom_dset[i] = mol.atom_pure_symbol(i)
|
|
|
|
##########################################
|
|
# #
|
|
# ECP #
|
|
# #
|
|
##########################################
|
|
|
|
if (mol.has_ecp()):
|
|
#atsymb = [mol.atom_pure_symbol(i) for i in range(natom)]
|
|
#pyecp = mol._ecp
|
|
## nelec to remove for each atom
|
|
#nuc_z_remov = [pyecp[i][0] for i in atsymb]
|
|
#nl_per_atom = [len(pyecp[i][1]) for i in atsymb]
|
|
## list of l-values for channels of each atom
|
|
#ecp_l = [[pyecp[i][1][j][0] for j in range(len(pyecp[i][1]))] for i in atsymb]
|
|
## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
|
|
#ecp_ac = [[pyecp[i][1][j][1] for j in range(len(pyecp[i][1]))] for i in atsymb]
|
|
pyecp = [mol._ecp[mol.atom_pure_symbol(i)] for i in range(natom)]
|
|
nzrmv=[0]*natom
|
|
lmax=0
|
|
klocmax=0
|
|
knlmax=0
|
|
for i,(nz,dat) in enumerate(pyecp):
|
|
nzrmv[i]=nz
|
|
for lval,ac in dat:
|
|
if (lval==-1):
|
|
klocmax=max(sum(len(j) for j in ac),klocmax)
|
|
else:
|
|
lmax=max(lval,lmax)
|
|
knlmax=max(sum(len(j) for j in ac),knlmax)
|
|
#psd_nk = np.zeros((natom,klocmax),dtype=int)
|
|
#psd_vk = np.zeros((natom,klocmax),dtype=float)
|
|
#psd_dzk = np.zeros((natom,klocmax),dtype=float)
|
|
#psd_nkl = np.zeros((natom,knlmax,lmax+1),dtype=int)
|
|
#psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
|
|
#psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
|
|
klnlmax=max(klocmax,knlmax)
|
|
psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int)
|
|
psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float)
|
|
psd_dz = np.zeros((lmax+2,klnlmax,natom),dtype=float)
|
|
for i,(_,dat) in enumerate(pyecp):
|
|
for lval,ac in dat:
|
|
count=0
|
|
for ri,aici in enumerate(ac):
|
|
for ai,ci in aici:
|
|
psd_n[lval+1,count,i] = ri-2
|
|
psd_v[lval+1,count,i] = ci
|
|
psd_dz[lval+1,count,i] = ai
|
|
count += 1
|
|
psd_nk = psd_n[0,:klocmax]
|
|
psd_vk = psd_v[0,:klocmax]
|
|
psd_dzk = psd_dz[0,:klocmax]
|
|
psd_nkl = psd_n[1:,:knlmax]
|
|
psd_vkl = psd_v[1:,:knlmax]
|
|
psd_dzkl = psd_dz[1:,:knlmax]
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['pseudo'].attrs['do_pseudo']=True
|
|
qph5['pseudo'].attrs['pseudo_lmax']=lmax
|
|
qph5['pseudo'].attrs['pseudo_klocmax']=klocmax
|
|
qph5['pseudo'].attrs['pseudo_kmax']=knlmax
|
|
qph5.create_dataset('pseudo/nucl_charge_remove',data=nzrmv)
|
|
qph5.create_dataset('pseudo/pseudo_n_k',data=psd_nk)
|
|
qph5.create_dataset('pseudo/pseudo_n_kl',data=psd_nkl)
|
|
qph5.create_dataset('pseudo/pseudo_v_k',data=psd_vk)
|
|
qph5.create_dataset('pseudo/pseudo_v_kl',data=psd_vkl)
|
|
qph5.create_dataset('pseudo/pseudo_dz_k',data=psd_dzk)
|
|
qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl)
|
|
|
|
## nelec to remove for each atom
|
|
#nuc_z_remov = [i[0] for i in pyecp]
|
|
#nl_per_atom = [len(i[1]) for i in pyecp]
|
|
## list of l-values for channels of each atom
|
|
#ecp_l = [[ j[0] for j in i[1] ] for i in pyecp]
|
|
#lmax = max(map(max,ecp_l))
|
|
## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
|
|
#ecp_ac = [[ j[1] for j in i[1] ] for i in pyecp]
|
|
|
|
|
|
##########################################
|
|
# #
|
|
# Basis #
|
|
# #
|
|
##########################################
|
|
|
|
# nucleus on which each AO is centered
|
|
ao_nucl=[i[0] for i in mf.mol.ao_labels(fmt=False,base=1)]
|
|
|
|
|
|
nprim_max = 0
|
|
for iatom, (sh0,sh1,ao0,ao1) in enumerate(mol.aoslice_by_atom()):
|
|
for ib in range(sh0,sh1): # sets of contracted exponents
|
|
nprim = mol.bas_nprim(ib)
|
|
if (nprim > nprim_max):
|
|
nprim_max = nprim
|
|
|
|
qp_prim_num = np.zeros((nao),dtype=int)
|
|
qp_coef = np.zeros((nao,nprim_max))
|
|
qp_expo = np.zeros((nao,nprim_max))
|
|
qp_nucl = np.zeros((nao),dtype=int)
|
|
qp_pwr = np.zeros((nao,3),dtype=int)
|
|
|
|
clabels = mol.cart_labels(fmt=False)
|
|
|
|
tmp_idx=0
|
|
for iatom, (sh0,sh1,ao0,ao1) in enumerate(mol.aoslice_by_atom()):
|
|
# shell start,end; AO start,end (sph or cart) for each atom
|
|
for ib in range(sh0,sh1): # sets of contracted exponents
|
|
l = mol.bas_angular(ib) # angular momentum
|
|
nprim = mol.bas_nprim(ib) # numer of primitives
|
|
es = mol.bas_exp(ib) # exponents
|
|
cs = mol.bas_ctr_coeff(ib) # coeffs
|
|
nctr = mol.bas_nctr(ib) # number of contractions
|
|
print(iatom,ib,l,nprim,nctr,tmp_idx)
|
|
for ic in range(nctr): # sets of contraction coeffs
|
|
for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
|
|
qp_expo[tmp_idx,:nprim] = es[:]
|
|
qp_coef[tmp_idx,:nprim] = cs[:,ic]
|
|
qp_nucl[tmp_idx] = iatom + 1
|
|
qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3])
|
|
qp_prim_num[tmp_idx] = nprim
|
|
tmp_idx += 1
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['mo_basis'].attrs['mo_num']=nmo
|
|
qph5['ao_basis'].attrs['ao_num']=nao
|
|
|
|
#qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
|
qph5['ao_basis'].attrs['ao_basis']="dummy basis"
|
|
|
|
qph5.create_dataset('ao_basis/ao_nucl',data=qp_nucl)
|
|
qph5.create_dataset('ao_basis/ao_prim_num',data=qp_prim_num)
|
|
qph5.create_dataset('ao_basis/ao_expo',data=qp_expo.T)
|
|
qph5.create_dataset('ao_basis/ao_coef',data=qp_coef.T)
|
|
qph5.create_dataset('ao_basis/ao_power',data=qp_pwr.T)
|
|
|
|
##########################################
|
|
# #
|
|
# Electrons #
|
|
# #
|
|
##########################################
|
|
|
|
nelec = mol.nelectron
|
|
neleca,nelecb = mol.nelec
|
|
|
|
print('num_elec', nelec)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['electrons'].attrs['elec_alpha_num']=neleca
|
|
qph5['electrons'].attrs['elec_beta_num']=nelecb
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclear Repulsion #
|
|
# #
|
|
##########################################
|
|
|
|
e_nuc = mol.energy_nuc()
|
|
|
|
print('nucl_repul', e_nuc)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['nuclear_repulsion']=e_nuc
|
|
|
|
##########################################
|
|
# #
|
|
# MO Coef #
|
|
# #
|
|
##########################################
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_dataset('mo_basis/mo_coef',data=mo_c.T)
|
|
|
|
return
|