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s_absorptive_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 absorptive_tem_GPU_memory() result(required_memory)
use m_precision, only: fp_kind
use global_variables, only: nopiy, nopix
use m_multislice
implicit none
real(fp_kind) :: required_memory
real(fp_kind) :: array_size
integer :: array_count
array_size = 4.0_fp_kind * nopiy * nopix
array_count = 4 + 4*n_slices
required_memory = array_count * array_size
end function
subroutine absorptive_tem
use global_variables
use m_lens
use m_user_input
use m_absorption
use m_precision
use output
use cufft_wrapper
#ifdef GPU
use CUFFT
use cuda_array_library
use cudafor
use cuda_ms
use cuda_potential
use cuda_setup
#endif
use m_tilt
use m_multislice
use m_potential
use m_string
implicit none
!dummy variables
integer(4) :: i_cell,i_slice,z_indx(1),lengthz,lengthdf,i,idum,ntilt
!random variables
integer(4) :: count
!probe variables
complex(fp_kind),dimension(nopiy,nopix) :: psi,psi_initial,psi_out
complex(fp_kind) :: lens_ctf(nopiy,nopix,imaging_ndf)
complex(fp_kind),dimension(nopiy,nopix,n_slices)::projected_potential,prop,transf_absorptive
!output
real(fp_kind),dimension(nopiy,nopix) :: cbed,image,tem_image,temp_image
!diagnostic variables
real(fp_kind) :: intensity, t1, delta
!output variables
character(120) :: filename,fnam_df
#ifdef GPU
!device variables
integer :: plan
complex(fp_kind),device,allocatable :: prop_d(:,:,:),transf_d(:,:,:)
complex(fp_kind),device,dimension(nopiy,nopix) :: psi_d, psi_out_d
!device variables for on the fly potentials
complex(fp_kind),device,allocatable,dimension(:,:) :: bwl_mat_d,inverse_sinc_d,trans_d
complex(fp_kind),device,allocatable,dimension(:,:,:) :: fz_d,fz_dwf_d,fz_abs_d
real(fp_kind) :: absorptive_tem_GPU_memory
call GPU_memory_message(absorptive_tem_GPU_memory(), on_the_fly)
#else
on_the_fly=.false.
#endif
call command_line_title_box('Pre-calculation setup')
do i=1,imaging_ndf
if(pw_illum) lens_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
! Precalculate the scattering factors on a grid
call precalculate_scattering_factors()
if (pw_illum) then
psi_initial = 1.0_fp_kind/sqrt(float(nopiy*nopix))
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)
!DMH if(.not.load_grates) projected_potential = make_absorptive_grates(nopiy,nopix,n_slices)
if(.not.load_grates) then
projected_potential = make_absorptive_grates(nopiy,nopix,n_slices)
endif
call load_save_add_grates(projected_potential,nopiy,nopix,n_slices)
t1 = secnds(0.0)
#ifdef GPU
! Plan the fourier transforms
if (fp_kind.eq.8)then
call cufftPlan(plan,nopix,nopiy,CUFFT_Z2Z)
else
call cufftPlan(plan,nopix,nopiy,CUFFT_C2C)
endif
!Copy host arrays to the device
if (on_the_fly) then
allocate(bwl_mat_d(nopiy,nopix),inverse_sinc_d(nopiy,nopix))
allocate(trans_d(nopiy,nopix),fz_d(nopiy,nopix,nt))
allocate(fz_dwf_d(nopiy,nopix,nt),fz_abs_d(nopiy,nopix,nt))
fz_d=fz
fz_dwf_d=fz_dwf
fz_abs_d = ci*absorptive_scattering_factors(ig1,ig2,ifactory,ifactorx,nopiy,nopix,nt,a0,ss,atf,nat, ak, relm, orthog, 0.0_8, 4.0d0*atan(1.0d0))*2*ak !make the potential absorptive
inverse_sinc_d=inverse_sinc
bwl_mat_d = bwl_mat
else
allocate(transf_d(nopiy,nopix,n_slices))
endif
allocate(prop_d(nopiy,nopix,n_slices))
#endif
call command_line_title_box('Calculation running')
do ntilt=1,n_tilts_total
!For each specimen tilt we have to redo the transmission function
!and propagators
#ifdef GPU
if (on_the_fly) call cuda_setup_many_phasegrate
#endif
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
!DMH if(.not.on_the_fly) transf_absorptive(:,:,i) = exp(ci*pi*a0_slice(3,i)/Kz(ntilt)*projected_potential(:,:,i))
if(.not.on_the_fly) then
transf_absorptive(:,:,i) = exp(ci*pi*a0_slice(3,i)/Kz(ntilt)*projected_potential(:,:,i))
endif
! Bandwith limit the phase grate, psi is used for temporary storage
call fft2(nopiy, nopix, transf_absorptive(:,:,i), nopiy, psi, nopiy)
psi = psi * bwl_mat
call ifft2(nopiy, nopix, psi, nopiy, transf_absorptive(:,:,i), nopiy)
enddo
lengthz = ceiling(log10(maxval(abs(zarray))))
lengthdf = ceiling(log10(maxval(abs(imaging_df))))
if(any(imaging_df<0)) lengthdf = lengthdf+1
#ifdef GPU
!DMH if(.not.on_the_fly) transf_d=transf_absorptive
if(.not.on_the_fly) then
transf_d=transf_absorptive
endif
psi_d = psi_initial
prop_d = prop
do i_cell = 1, maxval(ncells)
do i_slice = 1, n_slices
if(on_the_fly) then
call cuda_make_abs_potential(trans_d,ccd_slice_array(i_slice),tau_slice(:,:,:,i_slice),nat_slice(:,i_slice),prop_distance(i_slice),plan,fz_d,fz_dwf_d,fz_abs_d,inverse_sinc_d,bwl_mat_d,Volume_array(i_slice))
call cuda_multiplication<<<blocks,threads>>>(psi_d,trans_d, psi_out_d,1.0_fp_kind,nopiy,nopix)
else
call cuda_multiplication<<<blocks,threads>>>(psi_d,transf_d(:,:,i_slice), psi_out_d,1.0_fp_kind,nopiy,nopix)
endif
call cufftExec(plan,psi_out_d,psi_d,CUFFT_FORWARD)
call cuda_multiplication<<<blocks,threads>>>(psi_d,prop_d(:,:,i_slice), psi_out_d,normalisation,nopiy,nopix)
call cufftExec(plan,psi_out_d,psi_d,CUFFT_INVERSE)
enddo ! End loop over slices
!If this thickness corresponds to any of the output values then output images
if (any(i_cell==ncells)) then
psi = psi_d
call fft2(nopiy, nopix, psi, nopiy, psi, nopiy)
cbed = abs(psi)**2
z_indx = minloc(abs(ncells-i_cell))
filename = trim(adjustl(output_prefix))
if (nz>1) filename = trim(adjustl(filename))//'_z='//zero_padded_int(int(zarray(z_indx(1))),lengthz)//'_A'
if (n_tilts_total>1) filename = trim(adjustl(filename))//tilt_description(claue(:,ntilt),ak1,ss,ig1,ig2)
call binary_out_unwrap(nopiy, nopix, cbed, trim(adjustl(filename))//'_DiffractionPattern')
if(pw_illum) then
do i=1,imaging_ndf
psi = psi_d
call fft2(nopiy, nopix, psi, nopiy, psi, nopiy)
psi = psi*lens_ctf(:,:,i)
call ifft2(nopiy, nopix, psi, nopiy, psi, nopiy)
tem_image = abs(psi)**2
fnam_df = trim(adjustl(filename))// '_Image'
if(imaging_ndf>1) fnam_df = trim(adjustl(fnam_df))//'_Defocus_'//zero_padded_int(int(imaging_df(i)),lengthdf)//'_Ang'
call binary_out(nopiy, nopix, tem_image, fnam_df)
enddo
endif
endif
intensity = get_sum(psi_d)
write(6,900,advance='no') achar(13), i_cell, intensity
900 format(a1, 1x, 'Cell: ', i5, ' Intensity: ', f12.6)
#else
psi = psi_initial
do i_cell = 1, maxval(ncells)
do i_slice = 1, n_slices
call multislice_iteration(psi,prop(:,:,i_slice),transf_absorptive(:,:,i_slice),nopiy,nopix);
enddo ! End loop over slices
!If this thickness corresponds to any of the output values then output images
if (any(i_cell==ncells)) then
call fft2(nopiy, nopix, psi, nopiy, psi_out, nopiy)
cbed = abs(psi_out)**2
z_indx = minloc(abs(ncells-i_cell))
filename = trim(adjustl(output_prefix))
if (nz>1) filename = trim(adjustl(filename))//'_z='//zero_padded_int(int(zarray(z_indx(1))),lengthz)//'_A'
if (n_tilts_total>1) filename = trim(adjustl(filename))//tilt_description(claue(:,ntilt),ak1,ss,ig1,ig2)
call binary_out_unwrap(nopiy, nopix, cbed, trim(adjustl(filename))//'_DiffractionPattern')
if(pw_illum) then
call binary_out(nopiy, nopix, abs(psi)**2, trim(adjustl(filename))//'_exit_surface_intensity')
call binary_out(nopiy, nopix, atan2(imag(psi),real(psi)), trim(adjustl(filename))//'_exit_surface_phase')
do i=1,imaging_ndf
call fft2(nopiy, nopix, psi, nopiy, psi_out, nopiy)
psi_out = psi_out*lens_ctf(:,:,i)
call ifft2(nopiy, nopix, psi_out, nopiy, psi_out, nopiy)
tem_image = abs(psi_out)**2
fnam_df = trim(adjustl(filename))// '_Image'
if(imaging_ndf>1) fnam_df = trim(adjustl(fnam_df))//'_Defocus_'//zero_padded_int(int(imaging_df(i)),lengthdf)//'_Ang'
call binary_out(nopiy, nopix, tem_image, fnam_df)
enddo
endif
endif
intensity = sum(abs(psi)**2)
if(n_tilts_total<2) write(6,900) i_cell, intensity
if(n_tilts_total>1) write(6,901) i_cell, ntilt,n_tilts_total, intensity
900 format(1h+,1x, 'Cell: ', i5, ' Intensity: ', f12.6)
901 format(1h+,1x, 'Cell: ', i5, ' tilt:',i5,'/',i5,' Intensity: ', f12.6)
#endif
enddo ! End loop over cells
enddo ! End loop over tilts
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
end subroutine absorptive_tem