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s_qep_tem.f90
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!--------------------------------------------------------------------------------
!
! Copyright (C) 2017 L. J. Allen, H. G. Brown, A. J. D’Alfonso, S.D. Findlay, B. D. Forbes
!
! This program is free software: you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation, either version 3 of the License, or
! (at your option) any later version.
!
! This program is distributed in the hope that it will be useful,
! but WITHOUT ANY WARRANTY; without even the implied warranty of
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
! GNU General Public License for more details.
!
! You should have received a copy of the GNU General Public License
! along with this program. If not, see <http://www.gnu.org/licenses/>.
!
!--------------------------------------------------------------------------------
function qep_tem_GPU_memory(n_qep_grates, quick_shift, phase_ramp_shift) result(required_memory)
use m_precision, only: fp_kind
use global_variables, only: nopiy, nopix, ifactory, ifactorx, on_the_fly
use m_lens, only: imaging,imaging_ndf
use m_multislice
implicit none
integer*4,intent(in)::n_qep_grates
logical,intent(in)::quick_shift,phase_ramp_shift
real(fp_kind) :: required_memory
real(fp_kind) :: array_size
integer :: array_count
array_size = 4.0_fp_kind * nopiy * nopix
array_count = 2*(3 + n_slices + n_slices*n_qep_grates) + 3
array_count = array_count + 2 + 1 +imaging_ndf
if (on_the_fly.or.quick_shift.or.phase_ramp_shift) array_count = array_count + 2
if (phase_ramp_shift) array_count = array_count + 2
required_memory = array_count * array_size
if (phase_ramp_shift) required_memory = required_memory + 8.0_fp_kind*(nopiy*ifactory + nopix*ifactorx)
end function
subroutine qep_tem
use m_precision, only: fp_kind
use m_numerical_tools
use global_variables
use m_lens
use cufft_wrapper
#ifdef GPU
use cudafor, only: dim3
use cuda_ms, only: get_sum
use cuda_potential, only: cuda_setup_many_phasegrate, ccd_slice_array, cuda_fph_make_potential
use cuda_setup, only: GPU_memory_message
use cuda_array_library
#endif
use output, only: output_prefix, binary_out, binary_out_unwrap,timing
use m_tilt, only: tilt_wave_function
use m_multislice!, only: make_qep_grates, setup_propagators
use m_potential
use m_string
implicit none
!dummy variables
integer(4) :: i_cell, i_slice, i_qep_pass,i,j,ntilt
integer(4) :: shifty, shiftx,length,z_indx(1)
!random variables
integer(4) :: idum
!real(fp_kind) :: ran1
!probe variables
complex(fp_kind),dimension(nopiy,nopix,n_slices)::prop
complex(fp_kind),dimension(nopiy,nopix,n_qep_grates,n_slices)::projected_potential,qep_grates
complex(fp_kind),dimension(nopiy,nopix) :: psi,psi_initial,psi_out,psi_temp,trans
complex(fp_kind),dimension(nopiy,nopix,imaging_ndf)::ctf
complex(fp_kind)::psi_elastic(nopiy,nopix,nz)
!output
real(fp_kind),dimension(nopiy,nopix,nz) :: cbed,total_intensity
real(fp_kind)::tem_image(nopiy,nopix,nz,imaging_ndf)
real(fp_kind),dimension(nopiy,nopix) :: image,temp
character*120 ::fnam_df
integer :: lengthdf
!diagnostic variables
real(fp_kind) :: intensity, t1, delta
#ifdef GPU
!device variables
integer :: plan
complex(fp_kind),device,dimension(nopiy,nopix) :: psi_d, psi_initial_d,psi_out_d,psi_temp_d
complex(fp_kind),device :: psi_elastic_d(nopiy,nopix,nz)
complex(fp_kind),device,allocatable :: prop_d(:,:,:), transf_d(:,:,:,:), ctf_d(:,:,:), shift_arrayx_d(:,:), shift_arrayy_d(:,:), shift_array_d(:,:), trans_d(:,:)
real(fp_kind),device,allocatable :: tem_image_d(:,:,:,:)
real(fp_kind),device,dimension(nopiy,nopix) :: temp_d,temp_image_d
real(fp_kind),device,dimension(nopiy,nopix,nz) :: cbed_d, total_intensity_d
!device variables for on the fly potentials
complex(fp_kind),device,allocatable,dimension(:,:) :: bwl_mat_d, inverse_sinc_d
complex(fp_kind),device,allocatable,dimension(:,:,:) :: fz_d
#endif
real(fp_kind) :: qep_tem_GPU_memory
character*100::filename
#ifdef GPU
call GPU_memory_message(qep_tem_GPU_memory(), on_the_fly)
#endif
call command_line_title_box('Pre-calculation setup')
call precalculate_scattering_factors
idum = seed_rng()
#ifdef GPU
if (on_the_fly) then
call cuda_setup_many_phasegrate
else
#endif
!DMH if(.not. load_grates) projected_potential = make_qep_grates(idum)
if(.not. load_grates) then
projected_potential = make_qep_grates(idum)
endif
call load_save_add_grates(idum,projected_potential,nopiy,nopix,n_qep_grates,n_slices,nt,nat_slice)
#ifdef GPU
endif
#else
on_the_fly=.false.
#endif
if(pw_illum) then
do i=1,imaging_ndf
ctf(:,:,i) = make_ctf([0.0_fp_kind,0.0_fp_kind,0.0_fp_kind],imaging_df(i),imaging_cutoff,imaging_aberrations,imaging_apodisation)
enddo
#ifdef GPU
allocate(ctf_d(nopiy,nopix,imaging_ndf))
ctf_d = ctf
allocate(tem_image_d(nopiy,nopix,nz,imaging_ndf))
tem_image_d = 0.0_fp_kind
#endif
endif
call command_line_title_box('Calculation running')
#ifdef GPU
if (fp_kind.eq.8)then
call cufftPlan(plan,nopix,nopiy,CUFFT_Z2Z)
else
call cufftPlan(plan,nopix,nopiy,CUFFT_C2C)
endif
allocate(prop_d(nopiy,nopix,n_slices))
prop_d = prop
if (on_the_fly) then
if(allocated(bwl_mat_d)) deallocate(bwl_mat_d)
if(allocated(inverse_sinc_d)) deallocate(inverse_sinc_d)
if(allocated(fz_d)) deallocate(fz_d)
allocate(bwl_mat_d(nopiy,nopix))
allocate(inverse_sinc_d(nopiy,nopix))
allocate(fz_d(nopiy,nopix,nt))
fz_d = fz
inverse_sinc_d = inverse_sinc
bwl_mat_d = bwl_mat
else
allocate(transf_d(nopiy,nopix,n_qep_grates,n_slices))
transf_d = qep_grates
if (qep_mode == 3) then
allocate(shift_array_d(nopiy,nopix))
allocate(shift_arrayx_d(nopix,ifactorx))
allocate(shift_arrayy_d(nopiy,ifactory))
shift_arrayx_d=shift_arrayx
shift_arrayy_d=shift_arrayy
endif
endif
if (any([on_the_fly,quick_shift,phase_ramp_shift])) allocate(trans_d(nopiy,nopix))
#endif
t1 = secnds(0.0)
if (pw_illum) then
psi_initial = 1.0_fp_kind / sqrt(float(npixels))
else
psi_initial = make_ctf(probe_initial_position,probe_df(1),probe_cutoff,probe_aberrations,probe_apodisation)
call ifft2(nopiy, nopix, psi_initial, nopiy, psi_initial, nopiy)
psi_initial = psi_initial/sqrt(sum(abs(psi_initial)**2))
endif
call tilt_wave_function(psi_initial)
do ntilt = 1,n_tilts_total
do i = 1, n_slices
call make_propagator(nopiy,nopix,prop(:,:,i),prop_distance(i),Kz(ntilt),ss,ig1,ig2,claue(:,ntilt),ifactorx,ifactory)
prop(:,:,i) = prop(:,:,i) * bwl_mat
if(.not.on_the_fly) then
qep_grates(:,:,:,i) = exp(ci*pi*a0_slice(3,i)/Kz(ntilt)*projected_potential(:,:,:,i))
do j=1,n_qep_grates
call fft2(nopiy,nopix,qep_grates(:,:,j,i),nopiy,psi,nopiy)
if(qep_mode == 3) qep_grates(:,:,j,i)= psi*bwl_mat
if(qep_mode .ne. 3) call ifft2(nopiy,nopix,psi*bwl_mat,nopiy,qep_grates(:,:,j,i),nopiy)
enddo
endif
enddo
#ifdef GPU
prop_d=prop
!DMH if(.not.on_the_fly) transf_d = qep_grates
if(.not.on_the_fly) then
transf_d = qep_grates
endif
psi_initial_d = psi_initial
! Set accumulators to zero
cbed_d = 0.0_fp_kind
psi_elastic_d = 0.0_fp_kind
total_intensity_d = 0.0_fp_kind
do i_qep_pass = 1, n_qep_passes
! Reset wavefunction
psi_d = psi_initial_d
do i_cell = 1,maxval(ncells)
do i_slice = 1, n_slices
! Transmit
if (on_the_fly) then
call cuda_fph_make_potential(trans_d,ccd_slice_array(i_slice),tau_slice,nat_slice(:,i_slice),i_slice,prop_distance(i_slice),idum,plan,fz_d,inverse_sinc_d,bwl_mat_d)
call cuda_multiplication<<<blocks,threads>>>(psi_d,trans_d, psi_d,1.0_fp_kind,nopiy,nopix)
elseif (qep_mode == 2) then
nran = floor(n_qep_grates*ran1(idum)) + 1
shiftx = floor(ifactorx*ran1(idum)) * nopix_ucell
shifty = floor(ifactory*ran1(idum)) * nopiy_ucell
call cuda_cshift<<<blocks,threads>>>(transf_d(:,:,nran,i_slice),trans_d,nopiy,nopix,shifty,shiftx)
call cuda_multiplication<<<blocks,threads>>>(psi_d,trans_d, psi_d,1.0_fp_kind,nopiy,nopix)
elseif (qep_mode == 3) then
nran = floor(n_qep_grates*ran1(idum)) + 1
shiftx = floor(ifactorx*ran1(idum)) + 1
shifty = floor(ifactory*ran1(idum)) + 1
call cuda_make_shift_array<<<blocks,threads>>>(shift_array_d,shift_arrayy_d(:,shifty),shift_arrayx_d(:,shiftx),nopiy,nopix)
call cuda_multiplication<<<blocks,threads>>>(transf_d(:,:,nran,i_slice),shift_array_d, trans_d,1.0_fp_kind,nopiy,nopix)
call cufftExec(plan,trans_d,trans_d,CUFFT_INVERSE)
call cuda_multiplication<<<blocks,threads>>>(psi_d,trans_d, psi_d,sqrt(normalisation),nopiy,nopix)
else
nran = floor(n_qep_grates*ran1(idum)) + 1
call cuda_multiplication<<<blocks,threads>>>(psi_d,transf_d(:,:,nran,i_slice), psi_d,1.0_fp_kind,nopiy,nopix)
endif
! Propagate
call cufftExec(plan, psi_d, psi_d, CUFFT_FORWARD)
call cuda_multiplication<<<blocks,threads>>>(psi_d,prop_d(:,:,i_slice), psi_d, normalisation, nopiy, nopix)
call cufftExec(plan, psi_d, psi_d, CUFFT_INVERSE)
enddo ! End loop over slices
!If this thickness is an output thickness then accumulate relevent TEM images and diffraction patterns
if (any(i_cell==ncells)) then
!Transform into diffraction space
call cufftExec(plan,psi_d,psi_out_d,CUFFT_FORWARD)
call cuda_mod<<<blocks,threads>>>(psi_out_d,temp_d,normalisation,nopiy,nopix)
z_indx = minloc(abs(ncells-i_cell))
! Accumulate elastic wave function
call cuda_addition<<<blocks,threads>>>(psi_elastic_d(:,:,z_indx(1)),psi_d,psi_elastic_d(:,:,z_indx(1)),1.0_fp_kind,nopiy,nopix)
! Accumulate exit surface intensity
call cuda_mod<<<blocks,threads>>>(psi_d, temp_image_d, 1.0_fp_kind, nopiy, nopix)
call cuda_addition<<<blocks,threads>>>(total_intensity_d(:,:,z_indx(1)), temp_image_d, total_intensity_d(:,:,z_indx(1)), 1.0_fp_kind, nopiy, nopix)
! Accumulate diffaction pattern
call cuda_mod<<<blocks,threads>>>(psi_out_d,temp_d,normalisation,nopiy,nopix)
call cuda_addition<<<blocks,threads>>>(cbed_d(:,:,z_indx(1)),temp_d,cbed_d(:,:,z_indx(1)),1.0_fp_kind,nopiy,nopix)
if(pw_illum) then
! Accumulate image
do i=1,imaging_ndf
psi_temp_d = psi_out_d
call cuda_multiplication<<<blocks,threads>>>(psi_temp_d, ctf_d(:,:,i), psi_temp_d, sqrt(normalisation), nopiy, nopix)
call cufftExec(plan, psi_temp_d, psi_temp_d, CUFFT_INVERSE)
call cuda_mod<<<blocks,threads>>>(psi_temp_d, temp_image_d, normalisation, nopiy, nopix)
call cuda_addition<<<blocks,threads>>>(tem_image_d(:,:,z_indx(1),i), temp_image_d, tem_image_d(:,:,z_indx(1),i), 1.0_fp_kind, nopiy, nopix)
enddo
endif
endif
enddo ! End loop over cells
intensity = get_sum(psi_d)
write(6,900,advance='no') achar(13), i_qep_pass, n_qep_passes, intensity
900 format(a1, 1x, 'QEP pass:', i4, '/', i4, ' Intensity: ', f8.3)
!DMH
call flush(6)
#else
cbed = 0.0_fp_kind
psi_elastic = 0.0_fp_kind
total_intensity = 0.0_fp_kind
do i_qep_pass = 1, n_qep_passes
! Reset wavefunction
psi = psi_initial
do i_cell = 1,maxval(ncells)
do i_slice = 1, n_slices
! Phase grate
nran = floor(n_qep_grates*ran1(idum)) + 1
call qep_multislice_iteration(psi,prop(:,:,i_slice),qep_grates(:,:,:,i_slice),nopiy,nopix,ifactory,ifactorx,idum,n_qep_grates,qep_mode,shift_arrayy,shift_arrayx)
enddo ! End loop over slices
!If this thickness is an output thickness then accumulate relevent TEM images and diffraction patterns
if (any(i_cell==ncells)) then
!Transform into diffraction space
call fft2(nopiy,nopix,psi,nopiy,psi_out,nopiy)
temp = abs(psi_out)**2
z_indx = minloc(abs(ncells-i_cell))
! Accumulate elastic wave function
psi_elastic(:,:,z_indx(1)) = psi_elastic(:,:,z_indx(1)) + psi
! Accumulate exit surface intensity
total_intensity(:,:,z_indx(1)) = total_intensity(:,:,z_indx(1)) + abs(psi)**2
! Accumulate diffaction pattern
temp=abs(psi_out)**2
cbed(:,:,z_indx(1)) = cbed(:,:,z_indx(1)) + temp
! Accumulate image
if(pw_illum) then
do i=1,imaging_ndf
psi_temp = ctf(:,:,i)*psi_out
call ifft2(nopiy,nopix,psi_temp,nopiy,psi_temp,nopiy)
tem_image(:,:,z_indx(1),i) = tem_image(:,:,z_indx(1),i)+abs(psi_temp)**2
enddo
endif
endif
enddo ! End loop over cells
intensity = sum(abs(psi)**2)
write(6,900) i_qep_pass, n_qep_passes, intensity
900 format(1h+, 'QEP pass:', i4, '/', i4, ' Intensity: ', f8.3)
#endif
enddo ! End loop over QEP passes
#ifdef GPU
cbed = cbed_d
psi_elastic = psi_elastic_d
total_intensity = total_intensity_d
if(pw_illum) tem_image = tem_image_d
#endif
delta = secnds(t1)
write(*,*)
write(*,*)
write(*,*) 'Calculation is finished.'
write(*,*)
write(*,*) 'Time elapsed: ', delta, ' seconds.'
write(*,*)
if(timing) then
open(unit=9834, file=trim(adjustl(output_prefix))//'_timing.txt', access='append')
write(9834, '(a, g, a, /)') 'The multislice calculation took ', delta, 'seconds.'
close(9834)
endif
if (fp_kind.eq.8) then
write(*,*) 'The following files were outputted (as 64-bit big-endian floating point):'
else
write(*,*) 'The following files were outputted (as 32-bit big-endian floating point):'
endif
write(*,*)
cbed = cbed / n_qep_passes
psi_elastic = psi_elastic / n_qep_passes
if(pw_illum) then
total_intensity = total_intensity / n_qep_passes
tem_image = tem_image / n_qep_passes
length = ceiling(log10(maxval(zarray)))
lengthdf = ceiling(log10(maxval(abs(imaging_df))))
if(any(imaging_df<0)) lengthdf = lengthdf+1
endif
do i=1,nz
filename = trim(adjustl(output_prefix))
if(nz>1) filename=trim(adjustl(filename))//'_z='//zero_padded_int(int(zarray(i)),length)//'_A'
if(.not.output_thermal) then
call binary_out_unwrap(nopiy, nopix, cbed(:,:,i), trim(filename)//'_DiffPlane')
if(pw_illum) call binary_out(nopiy, nopix, total_intensity(:,:,i), trim(filename)//'_ExitSurface_Intensity')
else
call binary_out_unwrap(nopiy, nopix, cbed(:,:,i), trim(filename)//'_DiffPlaneTotal')
call fft2(nopiy, nopix, psi_elastic(:,:,i), nopiy, psi, nopiy)
image = abs(psi)**2
call binary_out_unwrap(nopiy, nopix, image, trim(filename)//'_DiffPlaneElastic')
image = cbed(:,:,i) - image
call binary_out_unwrap(nopiy, nopix, image, trim(filename)//'_DiffPlaneTDS')
if(pw_illum) then
call binary_out(nopiy, nopix, abs(psi_elastic(:,:,i))**2, trim(filename)//'_ExitSurface_IntensityElastic')
call binary_out(nopiy, nopix, atan2(imag(psi_elastic(:,:,i)), real(psi_elastic(:,:,i))), trim(filename)//'_ExitSurface_PhaseElastic')
call binary_out(nopiy, nopix, total_intensity(:,:,i), trim(filename)//'_ExitSurface_IntensityTotal')
total_intensity(:,:,i) = total_intensity(:,:,i) - abs(psi_elastic(:,:,i))**2
call binary_out(nopiy, nopix, total_intensity(:,:,i), trim(filename)//'_ExitSurface_IntensityTDS')
endif
endif
if(pw_illum) then
do j=1,imaging_ndf
! Elastic image
call fft2 (nopiy, nopix, psi_elastic(:,:,i), nopiy, psi, nopiy)
psi = psi * ctf(:,:,j)
call ifft2 (nopiy, nopix, psi, nopiy, psi, nopiy)
image = abs(psi)**2
if(imaging_ndf>1) then
fnam_df = trim(adjustl(filename))//'_Defocus_'//zero_padded_int(int(imaging_df(j)),lengthdf)//'_Ang'
else
fnam_df = trim(adjustl(filename))
endif
if(output_thermal) then
call binary_out(nopiy, nopix, image, trim(fnam_df)//'_Image_Elastic')
! Inelastic image
image = tem_image(:,:,i,j) - image
call binary_out(nopiy, nopix, image, trim(fnam_df)//'_Image_TDS')
! Total image
call binary_out(nopiy, nopix, tem_image(:,:,i,j), trim(fnam_df)//'_Image_Total')
else
call binary_out(nopiy, nopix, tem_image(:,:,i,j), trim(fnam_df)//'_Image')
endif
enddo
endif
enddo
enddo !end loop over tilts
end subroutine qep_tem