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RUQT.f90
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RUQT.f90
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program RUQT
Use InterfaceMod
Use FunctionMod
!Use InterfaceMod2
Use TypeMod
implicit none
real(8),allocatable,dimension(:,:) :: H_one,H_Two,OneInts,H_Two_le,H_Two_re,H_Two_cen,H_Two_le_trans,H_Two_re_trans
real(8), allocatable, dimension(:) :: TwoIntsCompact,transm,transm_curr,current,energy_list,mo_ener,B0_coeff
real(8), allocatable, dimension(:,:) :: Smat_le,Smat_re,Smat_cen,Smat,coupling_mat,mo_coeff,mo_coeff2
complex(8), allocatable, dimension(:,:) :: gfc_r,gfc_a,current_temp,Sigma_l,Sigma_r,Gamma_L,Gamma_R
complex(8),allocatable,dimension(:) :: voltage
real(8) :: coupling_r,coupling_l,energy,energy_start,energy_end,delta_en,volt_start,volt_end,delta_volt,corr_ener
integer :: size_l,size_r,size_c,size_lc,size_lcr,numatomic,num_threads,numfcore,numfvirt
character(len=100) :: inputfile,outfile,option
logical :: libint,gamess,rdm_flag,invert,doubles,currentflag,cisd_flag,qchem,hf_flag
logical :: dft_flag,pyscf,maple,use_b0,molcas,write_ruqt_data
integer :: i,j,k,counter,counter2,current_values,norb,numact,energy_val,volt_val,ioerror,numocc,numvirt
character(len=40) :: ElectrodeType,CalcType,functional,inputcode,b0_type
real(8) :: KT,current_con,Fermi_enl,Fermi_enR,localden_fermi,localden_fermi_l,localden_fermi_r,temp
real(8) :: fermi_l,fermi_r
complex(8), allocatable, dimension(:,:) :: test
type(B1) :: B1data,l1data
type(B2) :: B2data,l2data
type(energr) :: G_S
real(8) :: time_start,time_end
integer :: state_num
call cpu_time(time_start)
invert=.true.
currentflag=.false.
write(*,*) "Just getting started"
Call Get_Command_Argument(1,inputfile)
Call ReadInput(inputfile,norb,numfcore,numfvirt,numocc,numvirt,size_l,size_r,size_c,energy_start,energy_end,delta_en,volt_start,volt_end,delta_volt,inputcode,KT,ElectrodeType,Fermi_enl,Fermi_enR,CalcType,localden_fermi_l,localden_fermi_r,doubles,numatomic,functional,num_threads,use_b0,b0_type,write_ruqt_data,state_num)
write(*,*) "Input File Read"
write(*,*) "Using the following parameters for the transport calculation"
write(*,*) "Number of OpenMP Threads:",num_threads
write(*,*) "Number of Molecular and Atomic Orbitals:",norb,numatomic
write(*,*) "Number of Active Orbitals:",norb-numfcore-numfvirt
write(*,*) "Number of Occupied Orbitals:",numocc
write(*,*) "Number of Virtual Orbitals:",numvirt
write(*,*) "Orbitals in left electrode:",size_l
write(*,*) "Orbitals in device region:",size_c
write(*,*) "Orbitals in right electrode:",size_r
write(*,*) "Transmission Energy Window(eV) and dE:",energy_start,energy_end,delta_en
write(*,*) "Voltage Window and dV:",volt_start,volt_end,delta_volt
write(*,*) "Fermi Density:",localden_fermi_l,localden_fermi_r
write(*,*) "KT:",KT
write(*,*) "Transport Calculated for State ",state_num
size_lc = size_l + size_c
size_lcr = size_l + size_c + size_r
libint=.false.
Call Flag_set(inputcode,functional,cisd_flag,rdm_flag,hf_flag,dft_flag,qchem,gamess,pyscf,maple,molcas)
if(qchem.eqv..true.) then
write(*,*) 'Using Qchem data for this run'
Call Get_HF_Qchem(inputfile,norb,H_Two,Smat)
elseif(molcas.eqv..true.) then
Call Get_HF_Molcas2("MolEl.dat",norb,H_Two,Smat,state_num)
elseif(libint.eqv..true.) then
Call Get_HF_libint(inputfile,norb,numact,H_one,Smat,mo_coeff,OneInts,TwoIntsCompact)
elseif(gamess.eqv..true.) then
Call Get_HF_GAMESS(inputfile,numatomic,H_Two,Smat,norb)
write(*,*) 'Using GAMESS data for this run'
elseif(pyscf.eqv..true.) then
write(*,*) 'Using PySCF data for this run'
Call Get_HF_PySCF(inputfile,numatomic,H_Two,Smat,norb)
!Call Get_HF_Psi4()
elseif(maple.eqv..true.) then
write(*,*) "Using Maple+QuantumChemistry data for this run"
Call Get_HF_PySCF(inputfile,numatomic,H_Two,Smat,norb)
end if
write(*,*) 'This run using:'
if(rdm_flag.eqv..true.) then
write(*,*) 'The Lehmann representation of a'
if(doubles.eqv..true.) then
write(*,*) 'p2-RDM Greens function'
elseif(doubles.eqv..false.) then
write(*,*) 'HF Greens function'
end if
elseif(qchem.eqv..true.) then
write(*,*) 'QCHEM HF/DFT Greens function'
elseif(molcas.eqv..true.) then
write(*,*) 'Using Molcas Fock Matrix: FOCK_AO'
elseif(pyscf.eqv..true.) then
write(*,*) 'PYSCF HF/DFT Greens Function'
end if
!CALL OMP_SET_NUM_THREADS(num_threads)
!Here we want to parition the Smatrix and H matrix into electrodes and
!the device
if(trim(ElectrodeType).eq."Metal_WBL") then
write(*,*) 'Starting Metal WBL calculation'
allocate(Sigma_l(1:size_c,1:size_c))
allocate(Sigma_r(1:size_c,1:size_c))
Call PartitionHS_MetalWBL(Smat,H_Two,size_l,size_r,size_c,size_lc,size_lcr,Smat_le,Smat_re,Smat_cen,H_Two_le,H_Two_re,H_Two_cen,H_Two_le_trans,H_Two_re_trans,write_ruqt_data,inputfile)
write(*,*) 'Getting Electrodes'
Call Electrodes_MetalWBL(Sigma_l,Sigma_r,Smat_re,Smat_le,H_Two_le,H_Two_re,localden_fermi_l,localden_fermi_r,size_c,size_lc,size_lcr,size_l,size_r,H_Two_le_trans,H_Two_re_trans,write_ruqt_data,inputfile)
allocate(Gamma_L(1:size_c,1:size_c))
allocate(Gamma_R(1:size_c,1:size_c))
Gamma_L=-(DIMAG(Sigma_L)-DIMAG(adjoint(Sigma_L,size_c)))!,1E-12,8)
Gamma_R=-(DIMAG(Sigma_R)-DIMAG(adjoint(Sigma_R,size_c)))!,1E-12,8)
if(trim(CalcType).eq."current".or.trim(CalcType).eq."Current") then
write(*,*) "Starting Current Calculation"
volt_val = abs(int((volt_end - volt_start)/delta_volt)+1)
energy_val = abs(int((energy_start-energy_end)/delta_en)+1)
current_values = volt_val
allocate(gfc_r(1:size_c,1:size_c))
allocate(gfc_a(1:size_c,1:size_c))
allocate(current(1:current_values))
allocate(voltage(1:current_values))
allocate(transm(1:energy_val))
allocate(transm_curr(1:energy_val))
allocate(current_temp(1:size_c,1:size_c))
allocate(energy_list(1:energy_val))
transm=0
transm_curr=0
current_temp=0
energy = energy_start
current_con = 2*1.6021766E-19*(4.135667E-15)**(-1)
counter = 1
do k=1,energy_val
transm(k) = 0
current_temp=0
energy = energy_start + (k-1)*delta_en
energy_list(k) = energy
if((hf_flag.eqv..true.).or.(dft_flag.eqv..true.)) then
gfc_r = 0
gfc_a = 0
gfc_r = energy*Smat_cen-H_Two_cen
gfc_r = gfc_r - Sigma_l - Sigma_r
gfc_r = inv(gfc_r)
gfc_a = adjoint(gfc_r,size_c)
else if((cisd_flag.eqv..true.).or.(rdm_flag.eqv..true.)) then
gfc_r = 0
gfc_a = 0
Call Build_G_SD_Invert(gfc_r,Sigma_l,Sigma_r,energy,size_l,size_c,size_lc,size_lcr,norb,inputfile,numocc,numvirt,counter,B1data,B2data,mo_ener,mo_coeff,mo_coeff2,doubles,currentflag,energy_val,k,G_S,corr_ener,numatomic,B0_coeff,use_b0,gamess,maple,numfcore,numfvirt,b0_type)
gfc_a = adjoint(gfc_r,size_c)
counter=2
end if
current_temp = matmul_zgemm(Gamma_R,gfc_a)
current_temp = matmul_zgemm(gfc_r,current_temp)
current_temp = matmul_zgemm(Gamma_L,current_temp)
do i=1,size_c
transm(k) = transm(k) + real(current_temp(i,i))
end do
end do
do j=1,energy_val
write(*,*) 'Transm vs Energy curve',real(energy_list(j)),real(transm(j))
end do
outfile = trim(inputfile) // ".negf_dat"
open(unit=7,file=outfile,action='write',iostat=ioerror)
write(7,*) energy_val
do j=1,energy_val
write(7,*) real(energy_list(j)),real(transm(j))
end do
! close(7)
currentflag=.true.
do j=1,volt_val
temp = (j-1)*delta_volt + volt_start
voltage(j) = temp
current(j) = 0
transm_curr=0
do k=1,energy_val
! transm(k) = 0
energy = energy_start + (k-1)*delta_en
! current_temp = 0
! if((hf_flag.eqv..true.).or.(dft_flag.eqv..true.)) then
! gfc_r = 0
! gfc_a = 0
! gfc_r = energy*Smat_cen-H_Two_cen
! gfc_r = gfc_r - Sigma_l - Sigma_r
! gfc_r = inv(gfc_r)
! gfc_a = adjoint(gfc_r,size_c)
! else if((cisd_flag.eqv..true.).or.(rdm_flag.eqv..true.)) then
! gfc_r = 0
! gfc_a = 0
! Call Build_G_SD_Invert(gfc_r,Sigma_l,Sigma_r,energy,size_l,size_c,size_lc,size_lcr,norb,inputfile,numocc,numvirt,counter,B1data,B2data,mo_ener,mo_coeff,mo_coeff2,doubles,currentflag,energy_val,k,G_S,corr_ener,numatomic,B0_coeff,use_b0,gamess,maple,numfcore,numfvirt,b0_type)
! gfc_a = adjoint(gfc_r,size_c)
! counter=2
!
!
! end if
! current_temp = matmul_zgemm(Gamma_R,gfc_a)
! current_temp = matmul_zgemm(gfc_r,current_temp)
! current_temp = matmul_zgemm(Gamma_L,current_temp)
!do i=1,size_c
! transm(k) = transm(k) + real(current_temp(i,i))
!end do
fermi_l=fermi_function(energy-temp*0.5,fermi_enL,KT)
fermi_r=fermi_function(energy+temp*0.5,fermi_enR,KT)
!write(*,*) k,fermi_l,fermi_r
transm_curr(k) = transm(k)*(fermi_l-fermi_r)
end do
!write(*,*) temp,KT,transm_curr(1)
do k=1,energy_val
current(j) = current(j) + delta_en*current_con*transm_curr(k)
end do
!write(*,*) 'Done with current at voltage:',real(voltage(j))
end do
do j=1,volt_val
write(*,*) 'IV curve',real(voltage(j)),real(current(j))
end do
!outfile = trim(inputfile) // ".negf_dat"
!open(unit=7,file=outfile,action='append',iostat=ioerror)
write(7,*) volt_val
do j=1,volt_val
write(7,*) real(voltage(j)),real(current(j))
end do
close(7)
elseif(trim(CalcType).eq."Transmission".or.trim(CalcType).eq."transmission") then
write(*,*) "Starting Transmission Calculation at Energy"
energy_val = abs(int((energy_start-energy_end)/delta_en))
allocate(gfc_r(1:size_c,1:size_c))
allocate(gfc_a(1:size_c,1:size_c))
allocate(transm(1:energy_val))
allocate(energy_list(1:energy_val))
allocate(current_temp(1:size_c,1:size_c))
energy = energy_start
counter=1
do k=1,energy_val
transm(k) = 0
current_temp = 0
energy = energy_start + (k-1)*delta_en
energy_list(k) = energy
if((hf_flag.eqv..true.).or.(dft_flag.eqv..true.)) then
gfc_r = 0
gfc_a = 0
gfc_r = energy*Smat_cen-H_Two_cen
gfc_r = gfc_r - Sigma_l - Sigma_r
gfc_r = inv(gfc_r)
gfc_a = adjoint(gfc_r,size_c)
else if((cisd_flag.eqv..true.).or.(rdm_flag.eqv..true.)) then
gfc_r = 0
gfc_a = 0
Call Build_G_SD_Invert(gfc_r,Sigma_l,Sigma_r,energy,size_l,size_c,size_lc,size_lcr,norb,inputfile,numocc,numvirt,counter,B1data,B2data,mo_ener,mo_coeff,mo_coeff2,doubles,currentflag,energy_val,k,G_S,corr_ener,numatomic,B0_coeff,use_b0,gamess,maple,numfcore,numfvirt,b0_type)
gfc_a = adjoint(gfc_r,size_c)
counter=2
end if
current_temp = matmul_zgemm(Gamma_L,gfc_r)
current_temp = matmul_zgemm(current_temp,Gamma_R)
current_temp = matmul_zgemm(current_temp,gfc_a)
do i=1,size_c
transm(k) = transm(k) + real(current_temp(i,i))
end do
write(*,*) 'Done with transmission function at energy:',transm(k)
end do
do j=1,energy_val
write(*,*) 'Transm vs Energy curve',real(energy_list(j)),real(transm(j))
end do
outfile = trim(inputfile) // ".negf_dat"
open(unit=7,file=outfile,action='write',iostat=ioerror)
write(7,*) energy_val
do j=1,energy_val
write(7,*) real(energy_list(j)),real(transm(j))
end do
close(7)
end if
else if(trim(ElectrodeType).eq."Molecule_WBL") then
write(*,*) 'Using Molecule WBL Electrodes'
write(*,*) "***This option only supports DFT/HF calcs and is outdated/buggy***"
write(*,*) "***Slated for removal and likely to be incorrect***"
write(*,*) "***Use at own risk***"
allocate(Sigma_l(1:norb,1:norb))
allocate(Sigma_r(1:norb,1:norb))
Sigma_l = 0
Sigma_r = 0
write(*,*) 'Calculating Coupling'
Call Calculate_Coupling_MoleculeWBL(Coupling_R,Coupling_L,localden_fermi)
write(*,*) 'Calculating Electrodes'
Call Electrodes_MoleculeWBL(Sigma_l,Sigma_r,Smat,Coupling_R,Coupling_L,size_c,size_lc,size_lcr)
allocate(Gamma_L(1:size_c,1:size_c))
allocate(Gamma_R(1:size_c,1:size_c))
Gamma_L=DIMAG(Sigma_L)-DIMAG(adjoint(Sigma_L,norb))
Gamma_R=DIMAG(Sigma_R)-DIMAG(adjoint(Sigma_R,norb))
if(trim(CalcType).eq."current".or.trim(CalcType).eq."Current") then
write(*,*) "Starting Current Calculation"
volt_val = abs(int((volt_end - volt_start)/delta_volt))
energy_val = abs(int((energy_start-energy_end)/delta_en))
current_values = volt_val
allocate(gfc_r(1:norb,1:norb))
allocate(gfc_a(1:norb,1:norb))
allocate(current(1:current_values))
allocate(voltage(1:current_values))
allocate(transm(1:energy_val))
allocate(current_temp(1:norb,1:norb))
energy = energy_start
current_con = 1.6021766E-19*4.135667E-15**(-1)
counter = 1
current_temp = 0
gfc_r = 0
gfc_a = 0
gfc_r = energy*Smat-H_Two
gfc_r = gfc_r - Sigma_l - Sigma_r
gfc_r = inv(gfc_r)
gfc_a = adjoint(gfc_r,norb)
current_temp = matmul_zgemm(Gamma_R,gfc_a)
current_temp = matmul_zgemm(gfc_r,current_temp)
current_temp = matmul_zgemm(Gamma_L,current_temp)
do j=1,volt_val
temp = (j-1)*delta_volt + volt_start
voltage(j) = temp
current(j) = 0
do k=1,energy_val
transm(k) = 0
energy = energy_start + (k-1)*delta_en
! current_temp = 0
! gfc_r = 0
! gfc_a = 0
! gfc_r = energy*Smat-H_Two
! gfc_r = gfc_r - Sigma_l - Sigma_r
! gfc_r = inv(gfc_r)
! gfc_a = adjoint(gfc_r,norb)
! current_temp = matmul_zgemm(Gamma_R,gfc_a)
! current_temp = matmul_zgemm(gfc_r,current_temp)
! current_temp = matmul_zgemm(Gamma_L,current_temp)
do i=1,norb
transm(k) = transm(k) + real(current_temp(i,i))
end do
transm(k) = transm(k)*(fermi_function(energy+temp*0.5,fermi_enL,KT)-fermi_function(energy-temp*0.5,fermi_enR,KT))
end do
do k=1,energy_val
current(j) = current(j) + delta_en*current_con*transm(k)
end do
end do
do j=1,volt_val
write(*,*) 'IV curve',real(voltage(j)),real(current(j))
end do
outfile = trim(inputfile) // ".negf_dat"
open(unit=7,file=outfile,action='write',iostat=ioerror)
write(7,*) volt_val
do j=1,volt_val
write(7,*) real(voltage(j)),real(current(j))
end do
close(7)
elseif(trim(CalcType).eq."Transmission".or.trim(CalcType).eq."transmission") then
write(*,*) "Starting Transmission Calculation at Energy"
energy_val = abs(int((energy_start-energy_end)/delta_en))
allocate(gfc_r(1:norb,1:norb))
allocate(gfc_a(1:norb,1:norb))
allocate(transm(1:energy_val))
allocate(energy_list(1:energy_val))
allocate(current_temp(1:norb,1:norb))
energy = energy_start
temp = volt_start
do k=1,energy_val
transm(k) = 0
energy = energy_start + (k-1)*delta_en
energy_list(k) = energy
gfc_r = 0
gfc_a = 0
gfc_r = energy*Smat-H_Two
gfc_r = gfc_r - Sigma_l - Sigma_r
gfc_r = inv(gfc_r)
gfc_a = adjoint(gfc_r,norb)
current_temp = matmul_zgemm(Gamma_R,gfc_a)
current_temp = matmul_zgemm(gfc_r,current_temp)
current_temp = matmul_zgemm(Gamma_L,current_temp)
do i=1,norb
transm(k) = transm(k) + real(current_temp(i,i))
end do
end do
do j=1,energy_val
write(*,*) 'Transm vs Energy curve',real(energy_list(j)),real(transm(j))
end do
outfile = trim(inputfile) // ".dat"
open(unit=7,file=outfile,action='write',iostat=ioerror)
do j=1,energy_val
write(7,*) real(energy_list(j)),real(transm(j))
end do
close(7)
end if
end if
call cpu_time(time_end)
write(*,*) 'CPU Time:',time_end-time_start
end program
function adjoint(A,norb)
implicit none
complex(8),allocatable,dimension(:,:) :: A,adjoint
integer :: i,j,norb
allocate(adjoint(1:norb,1:norb))
do i=1,norb
do j=1,norb
adjoint(j,i) = DCONJG(A(i,j))
end do
end do
end function
subroutine Get_HF_QChem(inputfile,norb,H_two,Smat)
!Use InterfaceMod
implicit none
character(len=100) :: inputfile,datafile
real(8),allocatable,dimension(:,:) :: H_Two,Smat
integer :: norb,ioerror,i,j
20 format(A)
!write(*,*) inputfile
allocate(H_two(1:norb,1:norb))
allocate(Smat(1:norb,1:norb))
H_two=0
Smat=0
datafile = trim(inputfile) // "_Smat"
open(unit=2,file=datafile,action='READ', iostat = ioerror)
do i=1,norb
do j=1,norb
read(2,*) Smat(i,j)
end do
end do
close(2)
write(*,*) 'Start Htwo'
datafile = trim(inputfile) // "_Htwo"
open(unit=3,file=datafile,action='READ', iostat = ioerror)
do i=1,norb
do j=1,norb
read(3,*) H_Two(i,j)
end do
end do
close(3)
write(*,*) 'Done Getting HF Values'
end subroutine
subroutine Get_HF_Molcas(inputfile,norb,H_two,Smat,state_num)
!Use InterfaceMod
implicit none
character(len=100) :: inputfile,datafile
real(8),allocatable,dimension(:,:) :: H_Two,Smat
integer :: norb,ioerror,i,j,x,y
real(8) :: readtemp
integer :: state_num
character(len=100) :: state_char
20 format(A)
!write(*,*) inputfile
allocate(H_two(1:norb,1:norb))
allocate(Smat(1:norb,1:norb))
H_two=0
Smat=0
datafile = "Overlap"
open(unit=2,file=datafile,action='READ', iostat = ioerror)
do i=1,norb
do j=i,norb
read(2,*) x,y,readtemp
Smat(x,y)=readtemp
Smat(y,x)=readtemp
end do
end do
close(2)
write(*,*) 'Start Fock Matrix'
write(*,*) state_num
if(state_num.lt.10) then
write(state_char,"(I1)") state_num
else
write(state_char,"(I2)") state_num
end if
datafile = "FOCK_AO_"//trim(state_char)
write(*,*) datafile
open(unit=3,file=datafile,action='READ', iostat = ioerror)
do i=1,norb
do j=1,norb
read(3,*) x,y,readtemp
H_Two(x,y)=readtemp
end do
end do
close(3)
write(*,*) 'Done Getting HF Values'
end subroutine
subroutine Get_HF_Molcas2(datafile,norb,H_two,Smat,state_num)
!Use InterfaceMod
implicit none
character(len=9) :: datafile
real(8),allocatable,dimension(:,:) :: H_Two,Smat
integer :: norb,ioerror,i,j,x,y
real(8) :: readtemp
integer :: state_num,num_states,norb_2,nelec_2,actorb,actel
character(len=100) :: state_char,readtemp_str
20 format(A)
!write(*,*) inputfile
allocate(H_two(1:norb,1:norb))
allocate(Smat(1:norb,1:norb))
H_two=0
Smat=0
open(unit=2,file=datafile,action='READ', iostat = ioerror)
read(2,*) readtemp_str
read(2,*) num_states,norb_2,nelec_2,actorb,actel
read(2,*) readtemp_str
if(norb_2.ne.norb) then
write(*,*) "Your orbital count is incorrect. Please check your input and MolEl.dat files"
stop
end if
do i=1,norb
do j=i,norb
read(2,*) x,y,readtemp
Smat(x,y)=readtemp
Smat(y,x)=readtemp
end do
end do
do while (trim(readtemp_str).ne."Effective")
read(2,*) readtemp_str
end do
x=0
do while (trim(readtemp_str).ne."State".and.x.ne.state_num)
read(2,*) readtemp_str,x
end do
write(*,*) "Reading Fock Matrix for ",state_num
do i=1,norb
do j=1,norb
read(2,*) x,y,readtemp
H_Two(x,y)=readtemp
end do
end do
close(2)
write(*,*) 'Done Getting HF Values'
end subroutine
Subroutine Get_HF_GAMESS(inputfile,numatomic,H_two,Smat,norb)
use FunctionMod
implicit none
character(len=100) :: inputfile,datafile
real(8),allocatable,dimension(:,:) :: H_Two,Smat,mo_data,mo_data2,ECP_m,ECP_a,ECP_temp
integer :: numatomic,ioerror,i,j,norb
20 format(A)
allocate(H_two(1:numatomic,1:numatomic))
allocate(Smat(1:numatomic,1:numatomic))
H_two=0
Smat=0
datafile = trim(inputfile) // "_Smat"
open(unit=2,file=datafile,action='READ', iostat = ioerror)
do i=1,numatomic
do j=1,numatomic
read(2,*) Smat(i,j)
end do
end do
close(2)
write(*,*) 'Start Htwo'
datafile = trim(inputfile) // "_Htwo"
open(unit=3,file=datafile,action='READ', iostat = ioerror)
do i=1,numatomic
do j=1,numatomic
read(3,*) H_Two(i,j)
end do
end do
close(3)
write(*,*) 'Get ECP'
datafile = trim(inputfile) // "_ecp"
open(unit=4,file=datafile,status='OLD',action='READ', iostat = ioerror)
if(ioerror.eq.0) then
write(*,*) 'ECP found'
allocate(ECP_m(1:norb,1:norb))
allocate(ECP_temp(1:numatomic,1:norb))
allocate(ECP_a(1:numatomic,1:numatomic))
allocate(mo_data(1:numatomic,1:norb))
allocate(mo_data2(1:norb,1:numatomic))
do i=1,norb
do j=1,norb
read(4,*) ECP_m(i,j)
end do
end do
close(5)
datafile = trim(inputfile) // ".mo_dat"
open(unit=6,file=datafile,action='READ', iostat = ioerror)
do i=1,numatomic
do j=1,norb
read(6,*) mo_data(i,j)
end do
end do
close(6)
mo_data2 = transpose(mo_data)
ECP_temp=matmul_dgemm(mo_data,ECP_m)
ECP_a=matmul_dgemm(ECP_temp,mo_data2)
H_two=H_two-ECP_a
else
write(*,*) "No removal of ECP"
end if
write(*,*) 'H_Two',size(H_Two)
write(*,*) 'Smat',size(Smat)
!stop
write(*,*) 'Done Getting HF Values from GAMESS'
end subroutine
Subroutine Get_HF_PySCF(inputfile,numatomic,H_two,Smat,norb)
!Use InterfaceMod
use FunctionMod
implicit none
character(len=100) :: inputfile,datafile,readtemp
real(8),allocatable,dimension(:,:) :: H_Two,Smat,mo_data,mo_data2,ECP_m,ECP_a,ECP_temp
integer :: numatomic,ioerror,i,j,norb,tempx,tempy
real(8) :: tempval
20 format(A)
allocate(H_two(1:numatomic,1:numatomic))
allocate(Smat(1:numatomic,1:numatomic))
H_two=0
Smat=0
datafile = trim(inputfile) // ".scf_dat"
open(unit=2,file=datafile,action='READ', iostat = ioerror)
do while(trim(readtemp)/="Overlap Matrix")
read(2,'(A)') readtemp
end do
do i=1,numatomic
do j=1,numatomic
read(2,*) tempx,tempy,tempval
Smat(tempx,tempy)=tempval
end do
end do
do while(trim(readtemp)/="Fock Matrix")
read(2,'(A)') readtemp
end do
do i=1,numatomic
do j=1,numatomic
read(2,*) tempx,tempy,tempval
H_Two(tempx,tempy)=tempval
end do
end do
close(2)
end subroutine
subroutine Get_HF_libint(inputfile,norb,numact,H_one,Smat,mo_coeff,OneInts,TwoIntsCompact)
use TypeMod
use FunctionMod
implicit none
character(len=100) :: inputfile,datafile
real(8),allocatable,dimension(:,:) :: H_one,H_Two,Smat,OneInts,mo_coeff
real(8),allocatable,dimension(:) :: TwoIntsCompact
integer :: norb,numact,ioerror,i,j,k,l
integer(8) :: index1,index2,compindex1
integer, dimension(1:4) :: orbind
real(8) :: integral
allocate(H_one(1:norb,1:norb))
allocate(Smat(1:norb,1:norb))
allocate(mo_coeff(1:norb,1:norb))
allocate(OneInts(1:numact,1:numact))
allocate(TwoIntsCompact(1:numact*(numact+1)/2*(numact*(numact+1)/2+1)/2))
20 format(A)
datafile = inputfile // ".Hone"
open(unit=1,file=datafile,action='READ', iostat = ioerror)
do i=1,norb
do j=1,norb
read(1,20) H_one(i,j)
end do
end do
close(1)
datafile = inputfile // ".Smat"
open(unit=2,file=datafile,action='READ', iostat = ioerror)
do i=1,norb
do j=1,norb
read(2,20) Smat(i,j)
end do
end do
close(2)
open(unit=6,file=datafile,action='READ',iostat= ioerror)
do i=1,norb
do j=1,norb
read(6,20) mo_coeff(i,j)
end do
end do
datafile = inputfile // ".OneInts"
open(unit=4,file=datafile,action='READ', iostat = ioerror)
do i=1,norb
do j=1,norb
read(4,20) OneInts(i,j)
end do
end do
close(4)
datafile = inputfile // ".TwoInts"
open(unit=5,file=datafile,action='READ', iostat = ioerror)
do while(orbind(1).ne.0)
read(5,*) orbind(1),orbind(2),orbind(3),orbind(4),integral
i = orbind(1)
k = orbind(2)
j = orbind(3)
l = orbind(4)
index1 = FirstIndex(i,k)
index2 = FirstIndex(j,l)
compindex1 = CompositeIndex(index1,index2)
TwoIntsCompact(compindex1) = integral
end do
end subroutine
subroutine IntTransform(TwoIntsCompact,mo_coeff)
use TypeMod
implicit none
real(8), allocatable,dimension(:,:) :: mo_coeff
real(8), allocatable,dimension(:) :: TwoIntsCompact
!There is nothing here yet!
end subroutine
subroutine Calculate_Coupling_MoleculeWBL(Coupling_R,Coupling_L,localden_fermi)
implicit none
real(8) :: Coupling_R,Coupling_L,localden_fermi
Coupling_R = 0.2
Coupling_L = 0.2
end subroutine
subroutine Electrodes_MoleculeWBL(Sigma_l,Sigma_r,Smat,Coupling_R,Coupling_L,size_c,size_lc,size_lcr)
implicit none
integer :: size_lc,size_c,size_lcr,i,j
real(8) :: Coupling_R,Coupling_L,temp
complex(8), allocatable, dimension(:,:) :: Sigma_L,Sigma_R
real(8), allocatable, dimension(:,:) :: Smat_LE,Smat_RE,Smat
do i = size_c+1,size_lc
do j = 1,size_c
Sigma_L(i,j) = CMPLX(0,-0.5*Coupling_L*Smat(i,j),8)
Sigma_L(j,i) = CMPLX(0,-0.5*Coupling_L*Smat(j,i),8)
end do
end do
do i=size_lc+1,size_lcr
do j= 1,size_c
Sigma_R(i,j) = CMPLX(0,-0.5*Coupling_R*Smat(i,j),8)
Sigma_R(j,i) = CMPLX(0,-0.5*Coupling_R*Smat(j,i),8)
end do
end do
end subroutine
subroutine Electrodes_MetalWBL(Sigma_l,Sigma_r,Smat_re,Smat_le,H_Two_le,H_Two_re,localden_fermi_l,localden_fermi_r,size_c,size_lc,size_lcr,size_l,size_r,H_Two_le_trans,H_Two_re_trans,write_ruqt_data,inputfile)
use FunctionMod
implicit none
integer :: size_lc,size_c,size_lcr,i,j,size_l,size_r,ioerror
real(8) :: Coupling_R,Coupling_L,temp,localden_fermi_l,localden_fermi_r,pi
complex(8), allocatable, dimension(:,:) :: Sigma_L,Sigma_R
real(8), allocatable, dimension(:,:) :: Smat_LE,Smat_RE,Smat,H_Two_re,H_Two_le,Sigma_L_temp,Sigma_R_temp,Sigma_R_temp2,Sigma_L_temp2,sigma_r_temp3,sigma_l_temp3,H_Two_le_trans,H_Two_re_trans
logical :: write_ruqt_data
character(len=100) :: inputfile,outfile
pi = 3.14159265359
allocate(sigma_l_temp(1:size_l,1:size_l))
allocate(sigma_l_temp2(1:size_c,1:size_l))
allocate(sigma_l_temp3(1:size_c,1:size_c))
write(*,*) 'alloc l done'
Sigma_L_temp = -pi*localden_fermi_l*Smat_le
call matmul_dgemm2(H_Two_le_trans,Sigma_L_temp,Sigma_L_temp2)
call matmul_dgemm2(Sigma_L_temp2,H_Two_le,Sigma_L_temp3)
Sigma_L = CMPLX(0,sigma_l_temp3,8)
write(*,*) 'l done'
deallocate(sigma_l_temp)
deallocate(sigma_l_temp2)
deallocate(sigma_l_temp3)
allocate(sigma_r_temp(1:size_r,1:size_r))
allocate(sigma_r_temp2(1:size_c,1:size_r))
allocate(sigma_r_temp3(1:size_c,1:size_c))
Sigma_R_temp = -pi*localden_fermi_r*Smat_re
call matmul_dgemm2(H_Two_re_trans,Sigma_R_temp,Sigma_R_temp2)
call matmul_dgemm2(Sigma_R_temp2,H_Two_re,Sigma_R_temp3)
Sigma_R = CMPLX(0,Sigma_R_temp3,8)
deallocate(Sigma_R_temp)
deallocate(Sigma_R_temp2)
deallocate(Sigma_R_temp3)
if(write_ruqt_data) then
outfile = trim(inputfile) // ".Sigma"
open(unit=8,file=outfile,action='write',iostat=ioerror)
write(8,*) size_l,size_c,size_r
write(8,*) "RUQT Sigma Matrices"
do j=1,size_c
do i=1,size_c
write(8,*) j,i,Sigma_R(j,i)
end do
end do
do j=1,size_c
do i=1,size_c
write(8,*) j,i,Sigma_R(j,i)
end do
end do
close(8)
end if
write(*,*) 'Sigma Calculated'
end subroutine
subroutine PartitionHS_MetalWBL(Smat,H_Two,size_l,size_r,size_c,size_lc,size_lcr,Smat_le,Smat_re,Smat_cen,H_Two_le,H_Two_re,H_Two_cen,H_Two_le_trans,H_Two_re_trans,write_ruqt_data,inputfile)
implicit none
real(8), allocatable, dimension(:,:) :: Smat,Smat_le,Smat_re,Smat_cen,H_Two,H_Two_cen,H_Two_re,H_Two_le,temp,H_Two_le_trans,H_Two_re_trans
real(8), allocatable, dimension(:) :: eigen,work
integer :: size_l,size_c,size_r,size_lc,size_lcr,info,lwork,i,j,ioerror
logical :: write_ruqt_data
character(len=100) :: inputfile,outfile
allocate(Smat_le(1:size_l,1:size_l))
allocate(Smat_re(1:size_r,1:size_r))
allocate(Smat_cen(1:size_c,1:size_c))
Smat_le(1:size_l,1:size_l)=Smat(1:size_l,1:size_l)
Smat_re(1:size_r,1:size_r)=Smat(size_lc+1:size_lcr,size_lc+1:size_lcr)
Smat_cen(1:size_c,1:size_c)=Smat(size_l+1:size_lc,size_l+1:size_lc)
write(*,*) 'Done partitioning S Matrix'
deallocate(Smat)
allocate(H_Two_le(1:size_l,1:size_c))
allocate(H_Two_re(1:size_r,1:size_c))
allocate(H_Two_cen(1:size_c,1:size_c))
allocate(H_Two_le_trans(1:size_c,1:size_l))
allocate(H_Two_re_trans(1:size_c,1:size_r))
H_Two_le(1:size_l,1:size_c)=27.2114*H_Two(1:size_l,size_l+1:size_lc)
H_Two_re(1:size_r,1:size_c)=27.2114*H_Two(size_lc+1:size_lcr,size_l+1:size_lc)
H_Two_cen(1:size_c,1:size_c)=27.2114*H_Two(size_l+1:size_lc,size_l+1:size_lc)
H_Two_le_trans(1:size_c,1:size_l) = 27.2114*H_Two(size_l+1:size_lc,1:size_l) !transpose(H_Two_le)
H_Two_re_trans(1:size_c,1:size_r) = 27.2114*H_Two(size_l+1:size_lc,size_lc+1:size_lcr)!transpose(H_Two_re)
write(*,*) 'Done partitioning Fock Matrix'
deallocate(H_Two)
if(write_ruqt_data) then
outfile = trim(inputfile) // ".partdat"
open(unit=8,file=outfile,action='write',iostat=ioerror)
write(8,*) size_l,size_c,size_r
write(8,*) "RUQT Overlap Matrices"
do j=1,size_l
do i=1,size_l
write(8,*) j,i,Smat_le(j,i)
end do
end do
do j=1,size_c
do i=1,size_c
write(8,*) j,i,Smat_cen(j,i)
end do
end do
do j=1,size_r
do i=1,size_r
write(8,*) j,i, Smat_re(j,i)
end do
end do
write(8,*) "RUQT Fock Matrices"
do j=1,size_l
do i=1,size_c
write(8,*) j,i,H_Two_le(j,i)/27.2114
end do
end do
do j=1,size_r
do i=1,size_c
write(8,*) j,i,H_Two_re(j,i)/27.2114
end do
end do
do j=1,size_c
do i=1,size_c
write(8,*) j,i,H_Two_cen(j,i)/27.2114
end do
end do
close(8)
end if
end subroutine
function fermi_function(energy,fermi_energy,KT)