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s_qep_stem.f90
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s_qep_stem.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_stem_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, ndet
use m_lens, only: imaging
use m_multislice
implicit none
logical,intent(in)::quick_shift,phase_ramp_shift
integer*4,intent(in)::n_qep_grates
real(fp_kind) :: required_memory
real(fp_kind) :: array_size
integer :: array_count
array_size = 4.0_fp_kind * nopiy * nopix
array_count = 2*(4 + n_slices + n_slices*n_qep_grates) + 2 + ndet
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
! if (ionization) array_count = array_count + 1 + n_slices
!if (eels) array_count = array_count + 1
! Temporary array used in cuda_stem_detector()
array_count = array_count + 1
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_stem(STEM,ionization,PACBED)
use global_variables
use m_lens
use m_user_input
use m_precision
use output
#ifdef GPU
use cuda_array_library
use cudafor
use cuda_ms
use CUFFT
use cuda_potential
use cuda_setup
#endif
use cufft_wrapper
use m_crystallography
use m_tilt
use m_string
use m_multislice!, only: make_qep_grates, output_probe_intensity, output_cell_list, cell_map, output_thickness_list, setup_propagators
use m_potential
use m_numerical_tools
implicit none
logical,intent(in)::STEM,ionization,PACBED
!dummy variables
integer(4) :: i,j,l,m,i_qep_pass,iz,k,ii,jj,ntilt
integer(4) :: count
integer(4) :: shifty,shiftx
integer(4) :: ny,nx,i_df,idet
integer(4) :: total_slices
!random variables
integer(4) :: idum,nsliceoutput,z_indx(1)
!real(fp_kind) :: ran1
complex(fp_kind) :: temp_transf(nopiy,nopix),prop(nopiy,nopix,n_slices)
!probe variables
complex(fp_kind),dimension(nopiy,nopix) :: psi,trans,psi_initial,psi_out,temp_image
complex(fp_kind),dimension(nopiy,nopix,nz)::psi_elastic
complex(fp_kind),dimension(nopiy,nopix,n_qep_grates,n_slices)::projected_potential,qep_grates
!output
real(fp_kind),dimension(nopiy,nopix) :: image,temp
!STEM image variables
real(fp_kind) :: masks(nopiy,nopix,ndet),cbed(nopiy,nopix,nz) !detector masks
real(fp_kind),dimension(nysample,nxsample,probe_ndf,ndet,nz) :: stem_image,stem_elastic_image&
&,stem_inelastic_image
real(fp_kind),dimension(nysample,nxsample,probe_ndf,nz) :: eels_correction_image
real(fp_kind),allocatable :: ion_image(:,:,:),stem_ion_image(:,:,:,:,:),pacbed_pattern(:,:,:),pacbed_elastic(:,:,:)
!diagnostic variables
real(fp_kind) :: intensity
real(fp_kind) :: t1, delta
!output variables
character(120) :: fnam, fnam_temp, fnam_det
#ifdef GPU
!device variables
integer :: plan
complex(fp_kind),device,dimension(nopiy,nopix) :: psi_d,psi_out_d,psi_initial_d,trans_d
complex(fp_kind),device,dimension(nopiy,nopix,nz)::psi_elastic_d
real(fp_kind),device :: cbed_d(nopiy,nopix,nz),temp_d(nopiy,nopix)
complex(fp_kind),device,allocatable :: prop_d(:,:,:),transf_d(:,:,:,:)
complex(fp_kind),device,allocatable,dimension(:,:) ::shift_arrayx_d,shift_arrayy_d,shift_array_d
real(fp_kind),device,allocatable,dimension(:,:,:) :: masks_d,ion_image_d,pacbed_pattern_d
real(fp_kind),device,allocatable :: eels_correction_detector_d(:,:),ion_potential_d(:,:,:,:)
!device variables for on the fly potentials
complex(fp_kind),device,allocatable,dimension(:,:) :: bwl_mat_d,inverse_sinc_d,fz_dwf_d
complex(fp_kind),device,allocatable,dimension(:,:,:) :: fz_d,fz_mu_d
real(fp_kind),device,allocatable :: inelastic_potential_d(:,:)
#endif
real(fp_kind),allocatable :: probe_intensity(:,:,:)
character(1024) :: filename
real(fp_kind)::qep_stem_GPU_memory,const
logical::elfourd
integer*4::length,lengthdf
#ifdef GPU
call GPU_memory_message(qep_stem_GPU_memory(), on_the_fly)
#endif
call command_line_title_box('Pre-calculation setup')
if(pacbed) then
allocate(pacbed_pattern(nopiy,nopix,nz))
pacbed_pattern=0
if(output_thermal) then
allocate(pacbed_elastic(nopiy,nopix,nz))
pacbed_elastic = 0
endif
elfourd = fourdSTEM.and.output_thermal
length = ceiling(log10(maxval(zarray)))
endif
! Precalculate the scattering factors on a grid
call precalculate_scattering_factors()
idum = seed_rng()
#ifdef GPU
if (on_the_fly) then
call cuda_setup_many_phasegrate() !setup the atom co-ordinate for on the fly potentials (the arguments are simply so that
else
#else
!Generally not practical for CPU calculations
on_the_fly = .false.
if (.not.on_the_fly) then
#endif
projected_potential = make_qep_grates(idum)
if(.not. load_grates) call load_save_add_grates(idum,projected_potential,nopiy,nopix,n_qep_grates,n_slices,nt,nat_slice)
call make_local_inelastic_potentials(ionization) !setup the REAL space inelastic potential (ionization and adf) for QUEP ADF is disabled
endif
if(stem) then
do i=1,ndet/nseg
do j=1,nseg
if(nseg>1) masks(:,:,(i-1)*nseg+j) = make_detector(nopiy,nopix,ifactory,ifactorx,ss,inner(i),outer(i),2*pi*j/nseg-seg_det_offset,2*pi/nseg)
if(nseg==1) masks(:,:,(i-1)*nseg+j) = make_detector(nopiy,nopix,ifactory,ifactorx,ss,inner(i),outer(i))
enddo
enddo
endif
t1 = secnds(0.0)
call command_line_title_box('Calculation running')
if(stem) stem_image = 0.0_fp_kind
if(stem) stem_elastic_image = 0.0_fp_kind
#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 (stem.and.(ndet.gt.0)) then
allocate(masks_d(nopiy,nopix,ndet))
masks_d = masks
endif
if (ionization) then
allocate(ion_image_d(nopiy,nopix,num_ionizations))
if(.not.EDX) then
allocate(eels_correction_detector_d(nopiy,nopix))
eels_correction_detector_d=eels_correction_detector
endif
endif
if(pacbed) then
allocate(pacbed_pattern_d(nopiy,nopix,nz))
pacbed_pattern_d=0
endif
allocate(prop_d(nopiy,nopix,n_slices))
prop_d = prop
if (on_the_fly) then
allocate(bwl_mat_d(nopiy,nopix),inverse_sinc_d(nopiy,nopix),fz_d(nopiy,nopix,nt))
fz_d = fz
if(ionization) then
allocate(inelastic_potential_d(nopiy,nopix))
allocate(fz_mu_d(nopiy,nopix,num_ionizations))
fz_mu_d = ionization_mu
endif
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 (ionization) then
allocate(ion_potential_d(nopiy,nopix,num_ionizations,n_slices))
ion_potential_d = ionization_potential
endif
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
#else
if (ionization) allocate(ion_image(nopiy,nopix,num_ionizations))
#endif
if (ionization) then
allocate(stem_ion_image(nysample,nxsample,probe_ndf,nz,num_ionizations))
stem_ion_image = 0.0_fp_kind
if (.not.EDX) eels_correction_image = 0.0_fp_kind
!call binary_out_unwrap(nopiy,nopix,eels_correction_detector,'eels_correction_detector')
endif
if (output_probe_intensity) allocate(probe_intensity(nopiy,nopix,size(output_thickness_list)))
intensity = 1.0d0
do ntilt=1,n_tilts_total
do i = 1, n_slices
call make_propagator(nopiy,nopix,prop(:,:,i),prop_distance(i),Kz(1),ss,ig1,ig2,claue(:,1),ifactorx,ifactory)
prop(:,:,i) = prop(:,:,i) * bwl_mat
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.eq.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
enddo
#ifdef GPU
prop_d=prop
if(.not.on_the_fly) transf_d = qep_grates
#endif
lengthdf = ceiling(log10(maxval(abs(probe_df))))
if(any(probe_df<0)) lengthdf = lengthdf+1
do i_df = 1, probe_ndf
do ny = 1, nysample
do nx = 1, nxsample
#ifdef GPU
write(6,903,ADVANCE='NO') achar(13), i_df, probe_ndf, ny, nysample, nx, nxsample, intensity
903 format(a1,' df:',i3,'/',i3,' y:',i3,'/',i3,' x:',i3,'/',i3,' Intensity:', f6.3, ' (to monitor BWL)')
!DMH
call flush(6)
#else
write(6,900) i_df, probe_ndf, ny, nysample, nx, nxsample, intensity
900 format(1h+,1x,' df:',i3,'/',i3,' y:',i3,'/',i3,' x:',i3,'/',i3,' Intensity:', f6.3, ' (to monitor BWL)')
#endif
!Make STEM probe
psi_initial = make_ctf(probe_positions(:,ny,nx),probe_df(i_df),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))
call tilt_wave_function(psi_initial)
if (output_probe_intensity) probe_intensity = 0.0_fp_kind
cbed=0_fp_kind
#ifdef GPU
cbed_d=0.0_fp_kind
psi_elastic_d=0.0_fp_kind
psi_initial_d = psi_initial
do i_qep_pass = 1, n_qep_passes
! Reset wavefunction
psi_d = psi_initial_d
if (ionization) ion_image_d=0.0_fp_kind
do i = 1,maxval(ncells)
do j = 1, n_slices
! Accumulate ionization cross section
if(ionization) then
do ii=1,num_ionizations
call cuda_mod<<<blocks,threads>>>(psi_d,temp_d,1.0_fp_kind,nopiy,nopix)
if(on_the_fly) then
call cuda_make_ion_potential(inelastic_potential_d,tau_slice(:,atm_indices(ii),:,j),nat_slice(atm_indices(ii),j),plan,&
&fz_mu_d(:,:,ii),inverse_sinc_d,Volume_array(j))
call cuda_multiplication<<<blocks,threads>>>(temp_d,inelastic_potential_d, temp_d,prop_distance(j),nopiy,nopix)
else
call cuda_multiplication<<<blocks,threads>>>(temp_d,ion_potential_d(:,:,ii,j), temp_d,prop_distance(j),nopiy,nopix) !overlap
endif
call cuda_addition<<<blocks,threads>>>(temp_d,ion_image_d(:,:,ii),ion_image_d(:,:,ii),1.0_fp_kind,nopiy,nopix) !depth sum
enddo
endif
! Phase grate
nran = floor(n_qep_grates*ran1(idum)) + 1
if(on_the_fly) then
call cuda_fph_make_potential(trans_d,ccd_slice_array(j),tau_slice,nat_slice(:,j),j,prop_distance(j),idum,plan,fz_d,inverse_sinc_d,bwl_mat_d)
call cuda_multiplication<<<blocks,threads>>>(psi_d,trans_d, psi_out_d,1.0_fp_kind,nopiy,nopix)
elseif(qep_mode == 2) then
shiftx = floor(ifactorx*ran1(idum)) * nopix_ucell
shifty = floor(ifactory*ran1(idum)) * nopiy_ucell
call cuda_cshift<<<blocks,threads>>>(transf_d(:,:,nran,j),trans_d,nopiy,nopix,shifty,shiftx)
call cuda_multiplication<<<blocks,threads>>>(psi_d,trans_d, psi_out_d,1.0_fp_kind,nopiy,nopix)
elseif(qep_mode == 3) then !randomly shift phase grate
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) !make the qspace shift array
call cuda_multiplication<<<blocks,threads>>>(transf_d(:,:,nran,j),shift_array_d, trans_d,1.0_fp_kind,nopiy,nopix) !multiply by the qspace shift array
call cufftExec(plan,trans_d,trans_d,CUFFT_INVERSE)!inverse fourier transform
call cuda_multiplication<<<blocks,threads>>>(psi_d,trans_d, psi_out_d,sqrt(normalisation),nopiy,nopix) !do the phase grate multiplication
else
call cuda_multiplication<<<blocks,threads>>>(psi_d,transf_d(:,:,nran,j), psi_out_d,1.0_fp_kind,nopiy,nopix)
endif
! Propagate
call cufftExec(plan,psi_out_d,psi_d,CUFFT_FORWARD)
call cuda_multiplication<<<blocks,threads>>>(psi_d,prop_d(:,:,j), psi_out_d,normalisation,nopiy,nopix)
call cufftExec(plan,psi_out_d,psi_d,CUFFT_INVERSE)
if (output_probe_intensity) then
k = (i-1)*n_slices+j
if (output_cell_list(k)) then
psi = psi_d
probe_intensity(:,:,cell_map(k)) = probe_intensity(:,:,cell_map(k)) + abs(psi)**2
endif
endif
enddo ! End loop over slices
!If this thickness corresponds to any of the output values then accumulate diffraction pattern
if (any(i==ncells)) then
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))
! 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 diffaction pattern
!call cufftExec(plan,psi_d,psi_out_d,CUFFT_FORWARD)
call cuda_addition<<<blocks,threads>>>(cbed_d(:,:,z_indx(1)),temp_d,cbed_d(:,:,z_indx(1)),1.0_fp_kind,nopiy,nopix)
if(ionization) then
do ii=1,num_ionizations
stem_ion_image(ny,nx,i_df,z_indx(1),ii) = stem_ion_image(ny,nx,i_df,z_indx(1),ii)+get_sum(ion_image_d(:,:,ii))
enddo
endif
endif
enddo ! End loop over cells
enddo ! End loop over QEP passes
intensity = get_sum(psi_d)
cbed= cbed_d
if (output_thermal.and.fourDSTEM) psi_elastic=psi_elastic_d
do iz=1,nz
! Integrate the diffraction pattern
do idet = 1, ndet
stem_image(ny,nx,i_df,idet,iz) = cuda_stem_detector(cbed_d(:,:,iz),masks_d(:,:,idet))
enddo
if (ionization.and.(.not.EDX)) eels_correction_image(ny,nx,i_df,iz) = cuda_stem_detector(cbed_d(:,:,iz),eels_correction_detector_d)
! Integrate the elastic diffraction pattern
call cufftExec(plan,psi_elastic_d(:,:,iz),psi_out_d,CUFFT_FORWARD)
call cuda_mod<<<blocks,threads>>>(psi_out_d,temp_d,normalisation,nopiy,nopix)
do idet = 1, ndet
stem_elastic_image(ny,nx,i_df,idet,iz)=cuda_stem_detector(temp_d,masks_d(:,:,idet))
enddo
psi_out = psi_out_d*sqrt(normalisation)
#else
psi_elastic=0_fp_kind
do i_qep_pass = 1, n_qep_passes
if (ionization) ion_image=0.0_fp_kind
! Reset wavefunction
psi = psi_initial
do i = 1,maxval(ncells)
do j = 1, n_slices
! Accumulate ionization cross section
if(ionization) then
do ii=1,num_ionizations
temp = abs(psi)**2 * ionization_potential(:,:,ii,j) * prop_distance(j)
ion_image(:,:,ii) = temp+ion_image(:,:,ii)
enddo
endif
call qep_multislice_iteration(psi,prop(:,:,j),qep_grates(:,:,:,j),nopiy,nopix,ifactory,ifactorx,idum,n_qep_grates,qep_mode,shift_arrayy,shift_arrayx)
if (output_probe_intensity) then
k = (i-1)*n_slices+j
if (output_cell_list(k)) then
probe_intensity(:,:,cell_map(k)) = probe_intensity(:,:,cell_map(k)) + abs(psi)**2
endif
endif
enddo ! End loop over slices
!If this thickness corresponds to any of the output values then accumulate diffration pattern
if (any(i==ncells)) then
z_indx = minloc(abs(ncells-i))
! Accumulate elastic wave function - this will be Fourier transformed later
psi_elastic(:,:,z_indx(1)) = psi_elastic(:,:,z_indx(1)) + psi
!Transform into diffraction space
call fft2(nopiy,nopix,psi,nopiy,psi_out,nopiy)
! Accumulate diffaction pattern
temp = abs(psi_out)**2
cbed(:,:,z_indx(1)) = cbed(:,:,z_indx(1)) + temp
if(ionization) stem_ion_image(ny,nx,i_df,z_indx(1),:) = stem_ion_image(ny,nx,i_df,z_indx(1),:)+ sum(sum(ion_image,dim=2),dim=1)
endif
enddo ! End loop over cells
enddo !End loop over QEP passes
intensity = sum(abs(psi)**2)
do iz=1,nz
! Integrate the elastic diffraction pattern
call fft2(nopiy,nopix,psi_elastic(:,:,iz),nopiy,psi_out,nopiy)
if(stem) stem_image(ny,nx,i_df,1:ndet,iz) = sum(sum(spread(cbed(:,:,iz),dim=3,ncopies=ndet)*masks(:,:,:),dim=1),dim=1)
if(stem) stem_elastic_image(ny,nx,i_df,1:ndet,iz)= sum(sum(spread(abs(psi_out)**2,dim=3,ncopies =ndet)*masks(:,:,1:ndet),dim=1),dim=1)
if(ionization.and.(.not.EDX)) eels_correction_image(ny,nx,i_df,z_indx(1)) = sum(cbed(:,:,iz)*eels_correction_detector)
#endif
if(pacbed) then
!Output 4D STEM diffraction pattern
if(fourDSTEM) then
!Output total (elastic and inelastic) diffraction pattern
filename = trim(adjustl(output_prefix))
if (probe_ndf>1) filename = trim(adjustl(filename))//defocus_string(probe_df(i_df),lengthdf)
if (nz>1) filename = trim(adjustl(filename))//'_z='//to_string(int(zarray(iz)))//'_A'
call binary_out_unwrap(nopiy, nopix, cbed(:,:,iz)/n_qep_passes, trim(adjustl(filename)) //'_pp_'//&
&to_string(nx)//'_'//to_string(ny)//'_Diffraction_pattern',write_to_screen=.false.&
&,nopiyout=nopiyout,nopixout=nopixout)
endif
if(i_df==1) pacbed_pattern(:,:,iz) = pacbed_pattern(:,:,iz) + cbed(:,:,iz)/n_qep_passes
if(output_thermal) pacbed_elastic(:,:,iz) =pacbed_elastic(:,:,iz) + abs(psi_out)**2/n_qep_passes**2
if (output_thermal.and.fourDSTEM) then
!Output elastic only diffraction pattern
filename = trim(adjustl(output_prefix))
if (probe_ndf>1) filename = trim(adjustl(filename))//defocus_string(probe_df(i_df),lengthdf)
if (nz>1) filename = trim(adjustl(filename))//'_z='//to_string(int(zarray(iz)))//'_A'
filename = trim(adjustl(filename))//'_pp_'//to_string(nx)//'_'//to_string(ny)//'_Elastic_Diffraction_pattern'
call binary_out_unwrap(nopiy, nopix, abs(psi_out)**2/n_qep_passes**2, filename,write_to_screen=.false.&
&,nopiyout=nopiyout,nopixout=nopixout)
endif
endif
enddo
if (output_probe_intensity) call probe_intensity_to_file(probe_intensity,i_df,ny,nx,n_qep_passes,probe_ndf,nysample,nxsample)
enddo ! End loop over x probe positions
enddo ! End loop over y probe positions
enddo ! End loop over defocus series
! QEP normalisation
if(ionization) then
stem_ion_image = stem_ion_image/float(n_qep_passes)
if(.not.EDX) eels_correction_image = eels_correction_image/float(n_qep_passes)
endif
if (ndet.gt.0) then
stem_image = stem_image/float(n_qep_passes)
stem_elastic_image = stem_elastic_image/float(n_qep_passes*n_qep_passes)
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(*,*)
fnam = trim(adjustl(output_prefix))
if (n_tilts_total>1) fnam = trim(adjustl(output_prefix))//tilt_description(claue(:,ntilt),ak1,ss,ig1,ig2)
stem_inelastic_image = stem_image - stem_elastic_image
do idet = 1, ndet
if(output_thermal) then
fnam_temp = trim(adjustl(fnam)) // '_DiffPlaneElastic_Detector'
call add_zero_padded_int(fnam_temp, fnam_det, idet, 2)
call output_stem_image(stem_elastic_image(:,:,:,idet,:),fnam_det,probe_df)
fnam_temp = trim(adjustl(fnam)) // '_DiffPlaneTDS_Detector'
call add_zero_padded_int(fnam_temp, fnam_det, idet, 2)
call output_stem_image(stem_inelastic_image(:,:,:,idet,:),fnam_det,probe_df)
fnam_temp = trim(adjustl(fnam)) // '_DiffPlaneTotal_Detector'
else
fnam_temp = trim(adjustl(fnam)) // '_DiffPlane_Detector'
endif
call add_zero_padded_int(fnam_temp, fnam_det, idet, 2)
call output_stem_image(stem_image(:,:,:,idet,:),fnam_det,probe_df)
enddo
!ionization
if(ionization) then
do ii=1,num_ionizations
if(EDX) then
filename = trim(adjustl(fnam)) // '_'//trim(adjustl(substance_atom_types(atm_indices(ii))))//'_'//trim(adjustl(Ion_description(ii)))//'_shell_EDX'
call output_stem_image(stem_ion_image(:,:,:,:,ii), filename,probe_df)
else
filename = trim(adjustl(fnam))// '_'//trim(adjustl(substance_atom_types(atm_indices(ii))))//'_'//trim(adjustl(Ion_description(ii)))//'_orbital_EELS'
call output_stem_image(stem_ion_image(:,:,:,:,ii), filename,probe_df)
stem_ion_image(:,:,:,:,ii) = stem_ion_image(:,:,:,:,ii)*eels_correction_image
filename = trim(adjustl(fnam)) //'_'//trim(adjustl(substance_atom_types(atm_indices(ii))))//'_'//trim(adjustl(Ion_description(ii)))//'_orbital_EELS_Corrected'
call output_stem_image(stem_ion_image(:,:,:,:,ii), filename,probe_df)
endif
enddo
if(.not.EDX) then
filename = trim(adjustl(fnam)) // '_EELS_CorrectionMap'
call output_stem_image(eels_correction_image, filename,probe_df)
endif
endif
if(pacbed) then
const = float(nysample*nxsample)
do i=1,nz
filename = trim(adjustl(output_prefix))
if (n_tilts_total>1) fnam = trim(adjustl(output_prefix))//tilt_description(claue(:,ntilt),ak1,ss,ig1,ig2)
if(nz>1) filename=trim(adjustl(filename))//'_z='//zero_padded_int(int(zarray(i)),length)//'_A_'
call binary_out_unwrap(nopiy,nopix,pacbed_pattern(:,:,i)/const,trim(adjustl(filename))//'_PACBED_Pattern')
if(output_thermal) then
call binary_out_unwrap(nopiy,nopix,PACBED_elastic(:,:,i)/const,trim(adjustl(filename))//'_elastic_PACBED_Pattern')
call binary_out_unwrap(nopiy,nopix,pacbed_pattern(:,:,i)/const-PACBED_elastic(:,:,i)/const,trim(adjustl(filename))//'_thermal_PACBED_Pattern')
endif
enddo
endif
enddo
end subroutine qep_stem