mirror of
https://github.com/pfloos/quack
synced 2024-09-27 03:50:53 +02:00
ERI dat -> binary
This commit is contained in:
Abdallah Ammar
parent
1de213dc89
commit
567e77dd4a
23
PyDuck.py
23
PyDuck.py
@ -18,6 +18,7 @@ parser.add_argument('-b', '--basis', type=str, required=True, help='Name of the
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parser.add_argument('--bohr', default='Angstrom', action='store_const', const='Bohr', help='By default QuAcK assumes that the xyz files are in Angstrom. Add this argument if your xyz file is in Bohr.')
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parser.add_argument('-c', '--charge', type=int, default=0, help='Total charge of the molecule. Specify negative charges with "m" instead of the minus sign, for example m1 instead of -1. Default is 0')
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parser.add_argument('--cartesian', default=False, action='store_true', help='Add this option if you want to use cartesian basis functions.')
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parser.add_argument('--print_2e', default=False, action='store_true', help='Add this option if you want to print 2e-integrals.')
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parser.add_argument('-fc', '--frozen_core', type=bool, default=False, help='Freeze core MOs. Default is false')
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parser.add_argument('-m', '--multiplicity', type=int, default=1, help='Spin multiplicity. Default is 1 therefore singlet')
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parser.add_argument('--working_dir', type=str, default=QuAcK_dir, help='Set a working directory to run the calculation.')
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@ -32,6 +33,7 @@ frozen_core=args.frozen_core
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multiplicity=args.multiplicity
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xyz=args.xyz + '.xyz'
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cartesian=args.cartesian
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print_2e=args.print_2e
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working_dir=args.working_dir
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#Read molecule
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@ -90,11 +92,10 @@ t1e = mol.intor('int1e_kin') #Kinetic energy matrix elements
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dipole = mol.intor('int1e_r') #Matrix elements of the x, y, z operators
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x,y,z = dipole[0],dipole[1],dipole[2]
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norb = len(ovlp)
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norb = len(ovlp) # nBAS_AOs
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subprocess.call(['rm', working_dir + '/int/nBas.dat'])
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f = open(working_dir+'/int/nBas.dat','w')
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f.write(str(norb))
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f.write(' ')
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f.write(" {} ".format(str(norb)))
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f.close()
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@ -122,7 +123,6 @@ write_matrix_to_file(y,norb,working_dir+'/int/y.dat')
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subprocess.call(['rm', working_dir + '/int/z.dat'])
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write_matrix_to_file(z,norb,working_dir+'/int/z.dat')
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#Write two-electron integrals
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eri_ao = mol.intor('int2e')
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def write_tensor_to_file(tensor,size,file,cutoff=1e-15):
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@ -132,12 +132,23 @@ def write_tensor_to_file(tensor,size,file,cutoff=1e-15):
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for k in range(i,size):
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for l in range(j,size):
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if abs(tensor[i][k][j][l]) > cutoff:
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#f.write(str(i+1)+' '+str(j+1)+' '+str(k+1)+' '+str(l+1)+' '+"{:.16E}".format(tensor[i][k][j][l]))
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f.write(str(i+1)+' '+str(j+1)+' '+str(k+1)+' '+str(l+1)+' '+"{:.16E}".format(tensor[i][k][j][l]))
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f.write('\n')
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f.close()
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subprocess.call(['rm', working_dir + '/int/ERI.dat'])
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write_tensor_to_file(eri_ao,norb,working_dir+'/int/ERI.dat')
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# Write two-electron integrals
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if print_2e:
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# (formatted)
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subprocess.call(['rm', working_dir + '/int/ERI.dat'])
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write_tensor_to_file(eri_ao,norb,working_dir+'/int/ERI.dat')
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else:
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# (binary)
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subprocess.call(['rm', working_dir + '/int/ERI.bin'])
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# chem -> phys notation
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eri_ao = eri_ao.transpose(0, 2, 1, 3)
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eri_ao.tofile('int/ERI.bin')
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#Execute the QuAcK fortran program
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subprocess.call(QuAcK_dir+'/bin/QuAcK')
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@ -15,7 +15,7 @@ program QuAcK
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logical :: doG0W0,doevGW,doqsGW,doufG0W0,doufGW,doSRGqsGW
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logical :: doG0T0pp,doevGTpp,doqsGTpp,doufG0T0pp,doG0T0eh,doevGTeh,doqsGTeh
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integer :: nNuc,nBas
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integer :: nNuc,nBas_AOs
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integer :: nC(nspin)
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integer :: nO(nspin)
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integer :: nV(nspin)
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@ -120,15 +120,15 @@ program QuAcK
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doACFDT,exchange_kernel,doXBS, &
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dophBSE,dophBSE2,doppBSE,dBSE,dTDA)
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!------------------------------------------------!
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!---------------------------------------------------!
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! Read input information !
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!------------------------------------------------!
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!---------------------------------------------------!
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! nC = number of core orbitals !
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! nO = number of occupied orbitals !
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! nV = number of virtual orbitals (see below) !
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! nR = number of Rydberg orbitals !
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! nBas = number of basis functions (see below) !
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!------------------------------------------------!
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! nBas_AOs = number of basis functions in AOs !
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!---------------------------------------------------!
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call read_molecule(nNuc,nO,nC,nR)
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allocate(ZNuc(nNuc),rNuc(nNuc,ncart))
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@ -141,7 +141,7 @@ program QuAcK
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! Read basis set information from PySCF !
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!---------------------------------------!
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call read_basis_pyscf(nBas,nO,nV)
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call read_basis_pyscf(nBas_AOs, nO, nV)
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!--------------------------------------!
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! Read one- and two-electron integrals !
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@ -149,26 +149,31 @@ program QuAcK
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! Memory allocation for one- and two-electron integrals
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allocate(S(nBas,nBas),T(nBas,nBas),V(nBas,nBas),Hc(nBas,nBas),X(nBas,nBas), &
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ERI_AO(nBas,nBas,nBas,nBas),dipole_int_AO(nBas,nBas,ncart))
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allocate(S(nBas_AOs,nBas_AOs))
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allocate(T(nBas_AOs,nBas_AOs))
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allocate(V(nBas_AOs,nBas_AOs))
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allocate(Hc(nBas_AOs,nBas_AOs))
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allocate(X(nBas_AOs,nBas_AOs))
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allocate(ERI_AO(nBas_AOs,nBas_AOs,nBas_AOs,nBas_AOs))
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allocate(dipole_int_AO(nBas_AOs,nBas_AOs,ncart))
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! Read integrals
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call wall_time(start_int)
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call read_integrals(nBas,S,T,V,Hc,ERI_AO)
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call read_dipole_integrals(nBas,dipole_int_AO)
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call read_integrals(nBas_AOs, S(1,1), T(1,1), V(1,1), Hc(1,1), ERI_AO(1,1,1,1))
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call read_dipole_integrals(nBas_AOs, dipole_int_AO)
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call wall_time(end_int)
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t_int = end_int - start_int
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write(*,*)
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write(*,'(A65,1X,F9.3,A8)') 'Total CPU time for reading integrals = ',t_int,' seconds'
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write(*,'(A65,1X,F9.3,A8)') 'Total wall time for reading integrals = ',t_int,' seconds'
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write(*,*)
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! Compute orthogonalization matrix
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call orthogonalization_matrix(nBas,S,X)
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call orthogonalization_matrix(nBas_AOs, S, X)
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!---------------------!
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! Choose QuAcK branch !
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@ -200,7 +205,7 @@ program QuAcK
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dodrCCD,dorCCD,docrCCD,dolCCD,doCIS,doCIS_D,doCID,doCISD,doFCI,dophRPA,dophRPAx,docrRPA,doppRPA, &
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doG0F2,doevGF2,doqsGF2,doufG0F02,doG0F3,doevGF3,doG0W0,doevGW,doqsGW,doufG0W0,doufGW,doSRGqsGW, &
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doG0T0pp,doevGTpp,doqsGTpp,doufG0T0pp,doG0T0eh,doevGTeh,doqsGTeh, &
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nNuc,nBas,nC,nO,nV,nR,ENuc,ZNuc,rNuc, &
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nNuc,nBas_AOs,nC,nO,nV,nR,ENuc,ZNuc,rNuc, &
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S,T,V,Hc,X,dipole_int_AO,ERI_AO,maxSCF_HF,max_diis_HF,thresh_HF,level_shift, &
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guess_type,mix,reg_MP,maxSCF_CC,max_diis_CC,thresh_CC,spin_conserved,spin_flip,TDA, &
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maxSCF_GF,max_diis_GF,renorm_GF,thresh_GF,lin_GF,reg_GF,eta_GF,maxSCF_GW,max_diis_GW,thresh_GW, &
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@ -216,7 +221,7 @@ program QuAcK
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dodrCCD,dorCCD,docrCCD,dolCCD,doCIS,doCIS_D,doCID,doCISD,doFCI,dophRPA,dophRPAx,docrRPA,doppRPA, &
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doG0F2,doevGF2,doqsGF2,doufG0F02,doG0F3,doevGF3,doG0W0,doevGW,doqsGW,doufG0W0,doufGW,doSRGqsGW, &
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doG0T0pp,doevGTpp,doqsGTpp,doufG0T0pp,doG0T0eh,doevGTeh,doqsGTeh, &
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nNuc,nBas,nC,nO,nV,nR,ENuc,ZNuc,rNuc, &
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nNuc,nBas_AOs,nC,nO,nV,nR,ENuc,ZNuc,rNuc, &
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S,T,V,Hc,X,dipole_int_AO,ERI_AO,maxSCF_HF,max_diis_HF,thresh_HF,level_shift, &
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guess_type,mix,reg_MP,maxSCF_CC,max_diis_CC,thresh_CC,spin_conserved,spin_flip,TDA, &
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maxSCF_GF,max_diis_GF,renorm_GF,thresh_GF,lin_GF,reg_GF,eta_GF,maxSCF_GW,max_diis_GW,thresh_GW, &
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@ -231,7 +236,7 @@ program QuAcK
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call GQuAcK(doGtest,doGHF,dostab,dosearch,doMP2,doMP3,doCCD,dopCCD,doDCD,doCCSD,doCCSDT, &
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dodrCCD,dorCCD,docrCCD,dolCCD,dophRPA,dophRPAx,docrRPA,doppRPA, &
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doG0W0,doevGW,doqsGW,doG0F2,doevGF2,doqsGF2, &
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nNuc,nBas,sum(nC),sum(nO),sum(nV),sum(nR),ENuc,ZNuc,rNuc,S,T,V,Hc,X,dipole_int_AO,ERI_AO, &
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nNuc,nBas_AOs,sum(nC),sum(nO),sum(nV),sum(nR),ENuc,ZNuc,rNuc,S,T,V,Hc,X,dipole_int_AO,ERI_AO, &
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maxSCF_HF,max_diis_HF,thresh_HF,level_shift,guess_type,mix,reg_MP, &
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maxSCF_CC,max_diis_CC,thresh_CC,TDA,maxSCF_GF,max_diis_GF,thresh_GF,lin_GF,reg_GF,eta_GF, &
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maxSCF_GW,max_diis_GW,thresh_GW,TDA_W,lin_GW,reg_GW,eta_GW, &
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@ -256,7 +261,7 @@ program QuAcK
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call wall_time(end_QuAcK)
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t_QuAcK = end_QuAcK - start_QuAcK
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write(*,'(A65,1X,F9.3,A8)') 'Total CPU time for QuAcK = ',t_QuAcK,' seconds'
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write(*,'(A65,1X,F9.3,A8)') 'Total wall time for QuAcK = ',t_QuAcK,' seconds'
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write(*,*)
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end program
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@ -1,4 +1,4 @@
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subroutine read_basis_pyscf(nBas,nO,nV)
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subroutine read_basis_pyscf(nBas_AOs, nO, nV)
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! Read basis set information from PySCF
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@ -14,23 +14,23 @@ subroutine read_basis_pyscf(nBas,nO,nV)
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! Output variables
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integer,intent(out) :: nV(nspin)
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integer,intent(out) :: nBas
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integer,intent(out) :: nBas_AOs
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!------------------------------------------------------------------------
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! Primary basis set information
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!------------------------------------------------------------------------
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open(unit=3,file='int/nBas.dat')
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read(3,*) nBas
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read(3, *) nBas_AOs
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close(unit=3)
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write(*,'(A28)') '------------------'
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write(*,'(A28,1X,I16)') 'Number of basis functions',nBas
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write(*,'(A28)') '------------------'
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write(*,'(A38)') '--------------------------------------'
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write(*,'(A38,1X,I16)') 'Number of basis functions (AOs)', nBas_AOs
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write(*,'(A38)') '--------------------------------------'
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write(*,*)
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! Number of virtual orbitals
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nV(:) = nBas - nO(:)
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nV(:) = nBas_AOs - nO(:)
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end subroutine
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@ -1,4 +1,4 @@
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subroutine read_integrals(nBas,S,T,V,Hc,G)
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subroutine read_integrals(nBas_AOs, S, T, V, Hc, G)
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! Read one- and two-electron integrals from files
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@ -7,7 +7,7 @@ subroutine read_integrals(nBas,S,T,V,Hc,G)
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! Input variables
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integer,intent(in) :: nBas
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integer,intent(in) :: nBas_AOs
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! Local variables
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@ -18,11 +18,11 @@ subroutine read_integrals(nBas,S,T,V,Hc,G)
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! Output variables
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double precision,intent(out) :: S(nBas,nBas)
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double precision,intent(out) :: T(nBas,nBas)
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double precision,intent(out) :: V(nBas,nBas)
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double precision,intent(out) :: Hc(nBas,nBas)
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double precision,intent(out) :: G(nBas,nBas,nBas,nBas)
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double precision,intent(out) :: S(nBas_AOs,nBas_AOs)
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double precision,intent(out) :: T(nBas_AOs,nBas_AOs)
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double precision,intent(out) :: V(nBas_AOs,nBas_AOs)
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double precision,intent(out) :: Hc(nBas_AOs,nBas_AOs)
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double precision,intent(out) :: G(nBas_AOs,nBas_AOs,nBas_AOs,nBas_AOs)
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! Open file with integrals
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@ -35,7 +35,6 @@ subroutine read_integrals(nBas,S,T,V,Hc,G)
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open(unit=8 ,file='int/Ov.dat')
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open(unit=9 ,file='int/Kin.dat')
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open(unit=10,file='int/Nuc.dat')
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open(unit=11,file='int/ERI.dat')
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open(unit=21,file='int/x.dat')
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open(unit=22,file='int/y.dat')
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@ -75,31 +74,29 @@ subroutine read_integrals(nBas,S,T,V,Hc,G)
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Hc(:,:) = T(:,:) + V(:,:)
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! Read nuclear integrals
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! Read 2e-integrals
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G(:,:,:,:) = 0d0
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do
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read(11,*,end=11) mu,nu,la,si,ERI
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! ! formatted file
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! open(unit=11, file='int/ERI.dat')
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! G(:,:,:,:) = 0d0
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! do
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! read(11,*,end=11) mu, nu, la, si, ERI
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! ERI = lambda*ERI
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! G(mu,nu,la,si) = ERI ! <12|34>
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! G(la,nu,mu,si) = ERI ! <32|14>
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! G(mu,si,la,nu) = ERI ! <14|32>
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! G(la,si,mu,nu) = ERI ! <34|12>
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! G(si,mu,nu,la) = ERI ! <41|23>
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! G(nu,la,si,mu) = ERI ! <23|41>
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! G(nu,mu,si,la) = ERI ! <21|43>
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! G(si,la,nu,mu) = ERI ! <43|21>
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! end do
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! 11 close(unit=11)
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ERI = lambda*ERI
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! <12|34>
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G(mu,nu,la,si) = ERI
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! <32|14>
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G(la,nu,mu,si) = ERI
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! <14|32>
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G(mu,si,la,nu) = ERI
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! <34|12>
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G(la,si,mu,nu) = ERI
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! <41|23>
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G(si,mu,nu,la) = ERI
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! <23|41>
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G(nu,la,si,mu) = ERI
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! <21|43>
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G(nu,mu,si,la) = ERI
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! <43|21>
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G(si,la,nu,mu) = ERI
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end do
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11 close(unit=11)
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! binary file
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open(unit=11, file='int/ERI.bin', form='unformatted', access='stream')
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read(11) G
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close(11)
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! Print results
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@ -107,24 +104,24 @@ subroutine read_integrals(nBas,S,T,V,Hc,G)
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write(*,'(A28)') '----------------------'
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write(*,'(A28)') 'Overlap integrals'
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write(*,'(A28)') '----------------------'
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call matout(nBas,nBas,S)
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call matout(nBas_AOs,nBas_AOs,S)
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write(*,*)
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write(*,'(A28)') '----------------------'
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write(*,'(A28)') 'Kinetic integrals'
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write(*,'(A28)') '----------------------'
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call matout(nBas,nBas,T)
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call matout(nBas_AOs,nBas_AOs,T)
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write(*,*)
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write(*,'(A28)') '----------------------'
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write(*,'(A28)') 'Nuclear integrals'
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write(*,'(A28)') '----------------------'
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call matout(nBas,nBas,V)
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call matout(nBas_AOs,nBas_AOs,V)
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write(*,*)
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write(*,'(A28)') '----------------------'
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write(*,'(A28)') 'Electron repulsion integrals'
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write(*,'(A28)') '----------------------'
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do la=1,nBas
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do si=1,nBas
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call matout(nBas,nBas,G(1,1,la,si))
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do la=1,nBas_AOs
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do si=1,nBas_AOs
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call matout(nBas_AOs, nBas_AOs, G(1,1,la,si))
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end do
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end do
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write(*,*)
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