From b91c9ebad13c0a19f8fb54332ad5aa55acd06afa Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 7 May 2018 12:06:25 +0200 Subject: [PATCH] Merge Anouar (#69) * Converter for Pyscf * Scripts to read integrals and metadata and generates fake ezfio * update README * Trying to fix jbuilder bug in OCaml installation * Do AO->MO transformation from pyscf in QP * Optimization of reader due to format creux * Optimization of reader due to format creux 2 --- plugins/QMC/qp_convert_qmcpack_to_ezfio.py | 41 +++++- plugins/pyscf/NEEDED_CHILDREN_MODULES | 1 + plugins/pyscf/PyscfToQp.py | 137 ++++++++++++++++++ plugins/pyscf/README.rst | 21 +++ plugins/pyscf/pyscf.main.irp.f | 38 +++++ .../read_integral/Gen_Ezfio_from_integral.sh | 17 +++ plugins/read_integral/README.rst | 1 + plugins/read_integral/create_ezfio.py | 48 ++++++ .../read_integrals_achocol.irp.f | 47 ++++++ .../read_integrals_mo_chocol.irp.f | 86 +++++++++++ 10 files changed, 432 insertions(+), 5 deletions(-) create mode 100644 plugins/pyscf/NEEDED_CHILDREN_MODULES create mode 100644 plugins/pyscf/PyscfToQp.py create mode 100644 plugins/pyscf/README.rst create mode 100644 plugins/pyscf/pyscf.main.irp.f create mode 100755 plugins/read_integral/Gen_Ezfio_from_integral.sh create mode 100755 plugins/read_integral/create_ezfio.py create mode 100644 plugins/read_integral/read_integrals_achocol.irp.f create mode 100644 plugins/read_integral/read_integrals_mo_chocol.irp.f diff --git a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py index 54f6b5b5..b6237476 100755 --- a/plugins/QMC/qp_convert_qmcpack_to_ezfio.py +++ b/plugins/QMC/qp_convert_qmcpack_to_ezfio.py @@ -333,11 +333,14 @@ if do_pseudo: # |_/ (/_ |_ # + psi_coef = ezfio.get_determinants_psi_coef() psi_det = ezfio.get_determinants_psi_det() bit_kind = ezfio.get_determinants_bit_kind() +nexcitedstate = ezfio.get_determinants_n_states() + print "" print "BEGIN_DET" print "" @@ -349,7 +352,11 @@ if "QP_STATE" in os.environ: state = int(os.environ["QP_STATE"])-1 else: state = 0 -psi_coef = psi_coef[state] + +psi_coef_small = psi_coef[state] + + + encode = 8*bit_kind @@ -359,11 +366,35 @@ def bindigits(n, bits): decode = lambda det: ''.join(bindigits(i,encode)[::-1] for i in det)[:mo_num] -for coef, (det_a, det_b) in zip(psi_coef, psi_det): +MultiDetAlpha = [] +MultiDetBeta = [] +for coef, (det_a, det_b) in zip(psi_coef_small, psi_det): print coef - print decode(det_a) - print decode(det_b) + MyDetA=decode(det_a) + MyDetB=decode(det_b) + print MyDetA + print MyDetB print '' - + MultiDetAlpha.append( det_a ) + MultiDetBeta.append( det_b ) print "END_DET" + +import h5py +H5_qmcpack=h5py.File('MultiDet.h5','w') +groupMultiDet=H5_qmcpack.create_group("MultiDet") +groupMultiDet.create_dataset("NbDet",(1,),dtype="f8",data=len(psi_coef_small)) + +groupMultiDet.create_dataset("Coeff",(len(psi_coef_small),),dtype="f8",data=psi_coef) +groupMultiDet.create_dataset("nstate",(1,),dtype="i4",data=len(MyDetA)) +groupMultiDet.create_dataset("nexcitedstate",(1,),dtype="i4",data=nexcitedstate) +groupMultiDet.create_dataset("Nbits",(1,),dtype="i4",data=len(det_a)) + +print "temp=",MultiDetAlpha[0] +mylen="S"+str(len(MyDetA)) +groupMultiDet.create_dataset("CI_Alpha",(len(psi_coef_small),len(det_a)),dtype='i8',data=MultiDetAlpha) + +mylen="S"+str(len(MyDetB)) +groupMultiDet.create_dataset("CI_Beta",(len(psi_coef_small),len(det_b)),dtype='i8',data=MultiDetBeta) + +H5_qmcpack.close() diff --git a/plugins/pyscf/NEEDED_CHILDREN_MODULES b/plugins/pyscf/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/plugins/pyscf/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ + diff --git a/plugins/pyscf/PyscfToQp.py b/plugins/pyscf/PyscfToQp.py new file mode 100644 index 00000000..74ef951c --- /dev/null +++ b/plugins/pyscf/PyscfToQp.py @@ -0,0 +1,137 @@ + +import numpy,re,sys + +def pyscf2QP(cell,mf, kpts=[], int_threshold = 1E-15): + # The integral will be not printed in they are bellow that + + + PBC=False + ComputeMode= re.split('[. ]', str(mf)) + print 'ComputeMode=',ComputeMode + + for n in ComputeMode: + if n in ("UHF","KUHF","UKS"): + sys.exit('Unrestricted calculation unsupported in Quantum Package') + if n == "pbc": + PBC=True + + if PBC and len(kpts) == 0: + sys.exit("ERROR (read!): You need to specify explicit the list of K-point (including gamma)") + + print 'Performing PBC?:',PBC + if PBC: + from pyscf.pbc import ao2mo + from pyscf.pbc import tools + else: + from pyscf import ao2mo + + natom = len(cell.atom_coords()) + print 'n_atom', natom + print 'num_elec', cell.nelectron + print 'nucl_num', len(cell.atom_coords()) + + + print '' + mo_coeff = mf.mo_coeff # List of mo_coeff for each k-point + if not PBC: + nmo = mo_coeff.shape[1] + else: + nmo = mo_coeff[0].shape[1] + + + # Wrote all the parameter need to creat a dummy EZFIO folder who will containt the integral after. + # More an implentation detail than a real thing + with open('param','w') as f: + f.write(' '.join(map(str,(cell.nelectron, nmo, natom)))) + # _ + # |\ | _ | _ _. ._ |_) _ ._ | _ o _ ._ + # | \| |_| (_ | (/_ (_| | | \ (/_ |_) |_| | _> | (_) | | + # | + + print 'mf, cell', mf.energy_nuc(), cell.energy_nuc() + shift = tools.pbc.madelung(cell, numpy.zeros(3))*cell.nelectron * -.5 if PBC else 0 + e_nuc = cell.energy_nuc() + shift + + print 'nucl_repul', e_nuc + with open('e_nuc','w') as f: + f.write(str(e_nuc)) + + + from itertools import product + + # ___ + # | ._ _|_ _ _ ._ _. | _ |\/| _ ._ _ + # _|_ | | |_ (/_ (_| | (_| | _> | | (_) | | (_) + # _| + + if PBC: + h_ao = ('kinetic', mf.get_hcore(kpts=kpts) ) # Give only one k point ? + dummy_ao = ('nuclear', numpy.zeros( (len(kpts),nmo,nmo), dtype=numpy.float )) + else: + h_ao = ('kinetic', mf.get_hcore() ) + dummy_ao = ('nuclear', numpy.zeros( (nmo,nmo), dtype=numpy.float )) + + def gen_mono_MO(mo_coeff,l_int,shift=0): + # 2Id transfortion Transformation. For now we handle only one or zero K point. + print 'l_int.shape=',l_int.shape + + l_int_mo = reduce(numpy.dot, (mo_coeff.T, l_int, mo_coeff)) #This formula is only right for one kpt. + + print 'l_int_mo=',l_int_mo + + for i,j in product(range(nmo), repeat=2): + int_ = l_int_mo[i,j] + yield (i+1+shift,j+1+shift, int_) + + # Print + for name, ao in (h_ao,dummy_ao): + with open('%s_mo' % name,'w') as f: + print '%s_mo' % name + if not PBC: + for mono in gen_mono_MO(mo_coeff,ao): + f.write('%s %s %s\n'% mono) + else: + for i,(m,a) in enumerate(zip(mo_coeff,ao)): + for mono in gen_mono_MO(m,a,i): + f.write('%s %s %s\n'% mono) + + # ___ _ + # | ._ _|_ _ _ ._ _. | _ |_) o + # _|_ | | |_ (/_ (_| | (_| | _> |_) | + # _| + # + + def ao2mo_amazing(mo_coeff): + if PBC: + eri_4d= mf.with_df.ao2mo(mo_coeff,compact=False) + else: + eri_4d= ao2mo.kernel(cell,mo_coeff,compact=False) + + return eri_4d.reshape((nmo,)*4) + + + def write_amazing(eri_4d, shift=0): + + # HANDLE 8 FOLD by Scemama way. Maybe we can use compact=True + for l in range(nmo): + for k in range(nmo): + for j in range(l,nmo): + for i in range(max(j,k),nmo): + v = eri_4d[i,k,j,l] + if abs(v) > int_threshold: + f.write('%s %s %s %s %s\n' % (i+1+shift,j+1+shift,k+1+shift,l+1+shift,v)) + + + if PBC: + eri_4d= mf.with_df.ao2mo(mo_coeff[0],compact=False) + else: #Molecular + eri_4d= ao2mo.kernel(cell,mo_coeff,compact=False) + + eri_4d = eri_4d.reshape((nmo,)*4) + + f = open('bielec_mo','w') + for i,mc in enumerate(mo_coeff): + eri = ao2mo_amazing(mc) + write_amazing(eri, nmo*i) + + diff --git a/plugins/pyscf/README.rst b/plugins/pyscf/README.rst new file mode 100644 index 00000000..6588ef08 --- /dev/null +++ b/plugins/pyscf/README.rst @@ -0,0 +1,21 @@ +===== +pyscf +===== +Converter from Pyscf to Quatum Package for Molecules AND Solids +Import this script in your Pyscf input. + + +Use as follow: +``` + from MolPyscfToQP import pyscf2QP + pyscf2QP(cell,mf,kpts=kpts,int_threshold = 1E-15) + +``` +Needed Modules +============== +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. +Documentation +============= +.. Do not edit this section It was auto-generated +.. by the `update_README.py` script. diff --git a/plugins/pyscf/pyscf.main.irp.f b/plugins/pyscf/pyscf.main.irp.f new file mode 100644 index 00000000..dc2013c2 --- /dev/null +++ b/plugins/pyscf/pyscf.main.irp.f @@ -0,0 +1,38 @@ +program pyscf + implicit none + BEGIN_DOC +! TODO + END_DOC + print *, ' _/ ' + print *, ' -:\_?, _Jm####La ' + print *, 'J"(:" > _]#AZ#Z#UUZ##, ' + print *, '_,::./ %(|i%12XmX1*1XL _?, ' + print *, ' \..\ _\(vmWQwodY+ia%lnL _",/ ( ' + print *, ' .:< ]J=mQD?WXn|,)nr" ' + print *, ' 4XZ#Xov1v}=)vnXAX1nnv;1n" ' + print *, ' ]XX#ZXoovvvivnnnlvvo2*i7 ' + print *, ' "23Z#1S2oo2XXSnnnoSo2>v" ' + print *, ' miX#L -~`""!!1}oSoe|i7 ' + print *, ' 4cn#m, v221=|v[ ' + print *, ' ]hI3Zma,;..__wXSe=+vo ' + print *, ' ]Zov*XSUXXZXZXSe||vo2 ' + print *, ' ]Z#>=|< ' + print *, ' -ziiiii||||||+||==+> ' + print *, ' -%|+++||=|=+|=|==/ ' + print *, ' -a>====+|====-:- ' + print *, ' "~,- -- /- ' + print *, ' -. )> ' + print *, ' .~ +- ' + print *, ' . .... : . ' + print *, ' -------~ ' + print *, '' +end diff --git a/plugins/read_integral/Gen_Ezfio_from_integral.sh b/plugins/read_integral/Gen_Ezfio_from_integral.sh new file mode 100755 index 00000000..d190ffae --- /dev/null +++ b/plugins/read_integral/Gen_Ezfio_from_integral.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +ezfio=$1 +# Create the integral +echo 'Create Integral' + +echo 'Create EZFIO' +read nel nmo natom <<< $(cat param) +read e_nucl <<< $(cat e_nuc) +./create_ezfio.py $ezfio $nel $natom $nmo $e_nucl +#Handle the orbital consitensy check +qp_edit -c $ezfio &> /dev/null +cp $ezfio/{ao,mo}_basis/ao_md5 + +#Read the integral +echo 'Read Integral' +qp_run read_integrals_mo $ezfio diff --git a/plugins/read_integral/README.rst b/plugins/read_integral/README.rst index 02b63512..a027ede8 100644 --- a/plugins/read_integral/README.rst +++ b/plugins/read_integral/README.rst @@ -3,6 +3,7 @@ read_integral ============= Warning: CAN NOT CHANGE THE NUMBER OF MO ! +Scripts to read integrals and metadata and generates fake ezfio Needed Modules ============== diff --git a/plugins/read_integral/create_ezfio.py b/plugins/read_integral/create_ezfio.py new file mode 100755 index 00000000..acad3441 --- /dev/null +++ b/plugins/read_integral/create_ezfio.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python +from ezfio import ezfio + +import sys +filename = sys.argv[1] +num_elec, nucl_num, mo_tot_num = map(int,sys.argv[2:5]) + +nuclear_repulsion = float(sys.argv[5]) +ezfio.set_file(filename) + +#Important ! +import math +ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.)) +ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.)) + + +#Important +ezfio.set_nuclei_nucl_num(nucl_num) +ezfio.set_nuclei_nucl_charge([0.]*nucl_num) +ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num ) +ezfio.set_nuclei_nucl_label( ['He'] * nucl_num ) + +ezfio.set_nuclei_disk_access_nuclear_repulsion('Read') +ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion) + +# Ao num +ao_num = mo_tot_num +ezfio.set_ao_basis_ao_basis("Dummy one. We read MO") +ezfio.set_ao_basis_ao_num(ao_num) +ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff + +#Just need one +ao_prim_num_max = 5 + +d = [ [0] *ao_prim_num_max]*ao_num +ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num) +ezfio.set_ao_basis_ao_power(d) +ezfio.set_ao_basis_ao_coef(d) +ezfio.set_ao_basis_ao_expo(d) + +#Dummy one +ao_md5 = '3b8b464dfc95f282129bde3efef3c502' +ezfio.set_ao_basis_ao_md5(ao_md5) +ezfio.set_mo_basis_ao_md5(ao_md5) + + +ezfio.set_mo_basis_mo_tot_num(mo_tot_num) +ezfio.set_mo_basis_mo_coef([ [0]*mo_tot_num] * ao_num) diff --git a/plugins/read_integral/read_integrals_achocol.irp.f b/plugins/read_integral/read_integrals_achocol.irp.f new file mode 100644 index 00000000..d6b51b25 --- /dev/null +++ b/plugins/read_integral/read_integrals_achocol.irp.f @@ -0,0 +1,47 @@ +program read_integrals + + PROVIDE ezfio_filename + call ezfio_set_integrals_monoelec_disk_access_ao_one_integrals("None") + call run +end + +subroutine run + use map_module + implicit none + + integer :: iunit + integer :: getunitandopen + + integer ::i,j,k,l + double precision :: integral + double precision, allocatable :: A(:,:) + + integer :: n_integrals + integer(key_kind), allocatable :: buffer_i(:) + real(integral_kind), allocatable :: buffer_values(:) + integer(key_kind) :: key + + call ezfio_set_integrals_monoelec_disk_access_ao_one_integrals("Read") + + allocate(buffer_i(ao_num**4/8), buffer_values(ao_num**4/8)) + + iunit = getunitandopen('bielec_ao','r') + n_integrals=0 + do + read (iunit,*,end=13) i,j,k,l, integral + n_integrals += 1 + call bielec_integrals_index(i, j, k, l, buffer_i(n_integrals) ) + buffer_values(n_integrals) = integral + enddo + 13 continue + close(iunit) + + call insert_into_ao_integrals_map(n_integrals,buffer_i,buffer_values) + + call map_sort(ao_integrals_map) + call map_unique(ao_integrals_map) + + call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map) + call ezfio_set_integrals_bielec_disk_access_ao_integrals('Read') + +end diff --git a/plugins/read_integral/read_integrals_mo_chocol.irp.f b/plugins/read_integral/read_integrals_mo_chocol.irp.f new file mode 100644 index 00000000..8e5fde8e --- /dev/null +++ b/plugins/read_integral/read_integrals_mo_chocol.irp.f @@ -0,0 +1,86 @@ +program read_integrals + BEGIN_DOC +! Reads the integrals from the following files: +! - kinetic_mo +! - nuclear_mo +! - bielec_mo + END_DOC + + integer :: iunit + integer :: getunitandopen + integer :: i,j,n + + PROVIDE ezfio_filename + call ezfio_set_integrals_monoelec_disk_access_mo_one_integrals("None") + + logical :: has + call ezfio_has_mo_basis_mo_tot_num(has) + if (.not.has) then + + iunit = getunitandopen('nuclear_mo','r') + n=0 + do + read (iunit,*,end=12) i + n = max(n,i) + enddo + 12 continue + close(iunit) + call ezfio_set_mo_basis_mo_tot_num(n) + + call ezfio_has_ao_basis_ao_num(has) + mo_label = "None" + if (has) then + call huckel_guess + else + call ezfio_set_ao_basis_ao_num(n) + endif + endif + call run +end + +subroutine run + use map_module + implicit none + + integer :: iunit + integer :: getunitandopen + + integer ::i,j,k,l + double precision :: integral + double precision, allocatable :: A(:,:) + + integer :: n_integrals + integer(key_kind), allocatable :: buffer_i(:) + real(integral_kind), allocatable :: buffer_values(:) + integer(key_kind) :: key + + call ezfio_get_mo_basis_mo_tot_num(mo_tot_num) + + allocate (A(mo_tot_num,mo_tot_num)) + A = 0.d0 + + iunit = getunitandopen('kinetic_mo','r') + do + read (iunit,*,end=10) i,j, integral + A(i,j) = integral + enddo + 10 continue + close(iunit) + call write_one_e_integrals('mo_kinetic_integral', A, size(A,1), size(A,2)) + + + iunit = getunitandopen('nuclear_mo','r') + do + read (iunit,*,end=12) i,j, integral + A(i,j) = integral + enddo + 12 continue + close(iunit) + call write_one_e_integrals('mo_ne_integral', A, size(A,1), size(A,2)) + + call write_one_e_integrals('mo_pseudo_integral', mo_pseudo_integral,& + size(mo_pseudo_integral,1), size(mo_pseudo_integral,2)) + + + call ezfio_set_integrals_monoelec_disk_access_mo_one_integrals("Read") +end