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muSTEM.f90
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muSTEM.f90
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!--------------------------------------------------------------------------------
! Program: MU_STEM (GPU VERSION)
!
! Description: Calculate (S)TEM images and diffraction patterns using the
! multislice approach.
! Includes the contributions of TDS using either the Hall & Hirsch
! absorptive model or the Quantum Excitation of Phonons model.
! Both plane wave and convergent beam illumination may be used.
! STEM EDX/EELS images can be calculated within the local approximation.
!
! Outputs are big-endian floating point numbers in either
! 32-bit or 64-bit precision, depending on which precision
! is chosen in mod_precision.f90.
!
! Maintainer: Hamish Brown
! Email: [email protected]
! Date: August 2017
! Requirements: PGI Fortran
!
! version: 5.1
!
! 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/>.
!
!--------------------------------------------------------------------------------
program MU_STEM
use m_user_input
use global_variables!, only: high_accuracy, nt, atf, nat, atomf, volts, ss, qep, adf, constants, nopiy, nopix,output_thermal,ionic
use m_lens
#ifdef GPU
use cuda_setup, only: setup_GPU
use cuda_array_library, only: set_blocks
#endif
use output, only: setup_output_prefix,timing
use m_tilt, only: prompt_tilt
use m_absorption
use m_potential
use m_multislice
use m_string
use m_electron
implicit none
integer :: i_illum, i_tds_model, i_cb_menu, i_cb_calc_type,ifile,nfiles,i_arg,idum,i
logical :: nopause = .false.,there,ionization,stem,pacbed
character(512)::command_argument
character(120)::fnam
character(2):: symb
108 write(6,109)
109 format(&
&1x,'|----------------------------------------------------------------------------|',/,&
&1x,'| Melbourne University (scanning) transmission electron |',/,&
&1x,'| microscopy computing suite |',/,&
&1x,'| __ __ __ __ ______ ________ ________ __ __ |',/,&
&1x,'| | \ / \| \ | \ / \| \| \| \ / \ |',/,&
&1x,'| | $$\ / $$| $$ | $$| $$$$$$\\$$$$$$$$| $$$$$$$$| $$\ / $$ |',/,&
&1x,'| | $$$\ / $$$| $$ | $$| $$___\$$ | $$ | $$__ | $$$\ / $$$ |',/,&
&1x,'| | $$$$\ $$$$| $$ | $$ \$$ \ | $$ | $$ \ | $$$$\ $$$$ |',/,&
&1x,'| | $$\$$ $$ $$| $$ | $$ _\$$$$$$\ | $$ | $$$$$ | $$\$$ $$ $$ |',/,&
&1x,'| | $$ \$$$| $$| $$__/ $$| \__| $$ | $$ | $$_____ | $$ \$$$| $$ |',/,&
&1x,'| | $$ \$ | $$ \$$ $$ \$$ $$ | $$ | $$ \| $$ \$ | $$ |',/,&
&1x,'| \$$ \$$ \$$$$$$ \$$$$$$ \$$ \$$$$$$$$ \$$ \$$ |',/,&
&1x,'| |',/,&
&1x,"| Copyright (C) 2017 L.J. Allen, H.G. Brown, A.J. D'Alfonso, |",/,&
&1x,'| S.D. Findlay, B.D. Forbes |',/,&
&1x,'| email: [email protected] |',/,&
&1x,'| This program comes with ABSOLUTELY NO WARRANTY; |',/,&
&1x,'| |',/,&
&1x,'| This program is licensed to you under the terms of the GNU |',/,&
&1x,'| General Public License Version 3 as published by the Free |',/,&
&1x,'| Software Foundation. |',/,&
&1x,'| |',/,&
#ifdef GPU
&1x,'| GPU Version 5.3 |',/,&
#else
&1x,'| CPU only Version 5.3 |',/,&
#endif
&1x,'| |',/,&
&1x,'| Note: pass the argument "nopause" (without quotation marks) |',/,&
&1x,'| e.g. muSTEM.exe nopause |',/,&
&1x,'| to avoid pauses. |',/,&
&1x,'| |',/,&
&1x,'|----------------------------------------------------------------------------|',/)
! Process command line arguments
! Process command line arguments
do i_arg = 1, command_argument_count()
call get_command_argument(i_arg, command_argument)
select case (trim(adjustl(command_argument)))
case ('nopause')
nopause = .true.
case ('timing')
timing = .true.
case ('ionic')
ionic = .true.
end select
enddo
if (.not. nopause) then
write(*,*) ' Press enter to continue.'
read(*,*)
endif
! Set up user input routines, nfiles is the number
! of user input files to play if "play all" is inputted
nfiles = init_input()
do ifile=1,nfiles
!If play or play all open relevant user input file.
if(input_file_number.ne.5) then
fnam = get_driver_file(ifile)
inquire(file=fnam,exist = there)
if (there) then
open(unit=in_file_number, file=fnam, status='old')
else
write(*,*) "Couldn't find user input file: ",trim(adjustl(fnam))
cycle
endif
endif
! Set up CPU multithreading
call setup_threading
#ifdef GPU
! Set up GPU
call setup_GPU
#else
!DMH open(6,carriagecontrol='fortran')
open(6)
#endif
call command_line_title_box('Dataset output')
! Ask for the prefix for dataset output
call setup_output_prefix
call command_line_title_box('Specimen details')
! Read in the xtl file
call set_xtl_global_params
call validate_xtl
! Calculate the mean inner potential
call set_volts(nt, atf, nat, atomf, volts, ss)
! Set electron quantities
call constants
! Ask for slicing scheme
call setup_slicing_depths
! Ask for thickness
call setup_specimen_thickness
! Set up the potential calculation method
call prompt_high_accuracy
! Set the unit cell tiling and grid size
call set_tiling_grid
i_illum = -1
do while(i_illum<1.or.i_illum>2)
call command_line_title_box('Illumination')
write(*,*) '<1> Plane wave (including HRTEM images and diffraction patterns)'
write(*,*) '<2> Convergent-beam (including STEM images and CBED patterns)'
call get_input('Calculation type', i_illum)
write(*,*)
enddo
! Set illumination flags
pw_illum = (i_illum == 1)
cb_illum = .not. pw_illum
! For convergent-beam, set up the probe forming lens
if (cb_illum) call setup_lens_parameters('Probe',probe_aberrations,probe_cutoff)
i_tds_model=-1
do while(i_tds_model<1.or.i_tds_model>2)
call command_line_title_box('Thermal scattering model')
write(*,*) '<1> Quantum Excitation of Phonons (QEP) model'
write(*,*) ' (Accurately accounts for inelastic scattering'
write(*,*) ' due to phonon excitation)'
write(*,*) '<2> Absorptive model'
write(*,*) ' (Calculates faster than QEP but only approximates'
write(*,*) ' inelastic scattering due to phonon excitation)'
call get_input('<1> QEP <2> ABS', i_tds_model)
write(*,*)
enddo
! Set TDS model flags
complex_absorption = (i_tds_model == 2)
qep = .not. complex_absorption
! Prompt for including absorptive potential
if (complex_absorption) call prompt_include_absorption
if((complex_absorption.and.include_absorption).or.qep) then
write(*,*) ' Options for output of inelastically and elastically scattered components'
write(*,*) ' <1> Only output total signal (ie that measured in experiment)'
write(*,*) ' <2> Seperately output elastic, inelastic and total signal'
if(complex_absorption.and.include_absorption) write(*,*) 'Note: option <2> only applies to STEM imaging'
write(*,*)
call get_input('Elastic and inelastic scattering output choice', i_tds_model)
write(*,*)
output_thermal = i_tds_model==2
endif
! Prompt user for a tilt for either kind of illumination
call prompt_tilt
#ifdef GPU
! Setup the CUDA thread hierachy for nopiy, nopix arrays
call set_blocks(nopiy, nopix)
#endif
! Calculate the slices of the supercell
call calculate_slices
! Calculate the bandwidth limiting matrix
call make_bwl_mat
! Ask for QEP parameters
if (qep) call setup_qep_parameters(n_qep_grates,n_qep_passes,nran,quick_shift,ifactory,ifactorx)
! Save/load transmission functions
call prompt_save_load_grates
! Set up the imaging lens
if (pw_illum) then
call setup_lens_parameters('Image',imaging_aberrations,imaging_cutoff)
else
imaging_ndf = 1
endif
! Choose the convergent-beam calculation type
if (cb_illum) then
call command_line_title_box('Calculation type')
write(*,*) 'Choose a calculation type:'
115 write(*,*) '<1> CBED pattern'
write(*,*) '<2> STEM (BF/ABF/ADF/EELS/EDX/PACBED/4D-STEM)'
call get_input('<1> CBED <2> STEM/PACBED', i_cb_calc_type)
write(*,*)
select case (i_cb_calc_type)
case (1)
! CBED pattern
call place_probe(probe_initial_position)
case (2)
! STEM images
call STEM_options(STEM,ionization,PACBED)
fourdSTEM= .false.
if(pacbed) call fourD_STEM_options(fourdSTEM,nopiyout,nopixout,nopiy,nopix)
call setup_probe_scan(PACBED.and.(.not.(ionization.or.STEM)))
call prompt_output_probe_intensity
if(STEM) call setup_integration_measurements
adf = STEM.and.(.not.qep)
! Precalculate the scattering factors on a grid
call precalculate_scattering_factors()
if(ionization) call setup_inelastic_ionization_types
case default
goto 115
end select
endif
! Start simulation
if (pw_illum .and. qep) then
! Plane wave QEP
call qep_tem
elseif (pw_illum .and. complex_absorption) then
! Plane wave absorptive
call absorptive_tem
elseif (cb_illum .and. qep .and. i_cb_calc_type.eq.1) then
! Convergent-beam QEP CBED
call qep_tem
elseif (cb_illum .and. qep .and. i_cb_calc_type.eq.2) then
! Convergent-beam QEP STEM
call qep_stem(STEM,ionization,PACBED)
elseif (cb_illum .and. complex_absorption .and. i_cb_calc_type.eq.1) then
! Convergent-beam absorptive CBED
call absorptive_tem
elseif (cb_illum .and. complex_absorption .and. i_cb_calc_type.eq.2) then
! Convergent-beam absorptive STEM
call absorptive_stem(STEM,ionization,PACBED)
endif
write(*,*)
close(in_file_number)
call reset_allocatable_variables
enddo
if (.not. nopause) then
write(*,*) ' Press enter to exit.'
read(*,*)
endif
end program Mu_STEM
subroutine setup_threading()
use m_string, only: to_string,command_line_title_box
implicit none
integer*4 :: num_threads
integer*4 :: omp_get_max_threads, omp_get_num_procs
num_threads = omp_get_num_procs()
call omp_set_num_threads(num_threads)
call command_line_title_box('CPU multithreading')
write(*,*) 'The number of threads being used on the CPU is: ' // to_string(num_threads)
write(*,*)
end subroutine
subroutine reset_allocatable_variables()
!The downside of using global variables... :(
use global_variables
use m_lens
use m_potential
use m_multislice
#ifdef GPU
use cuda_potential
#endif
if(allocated(Kz) ) deallocate(Kz)
if(allocated(claue) ) deallocate(claue)
if(allocated(nat) ) deallocate(nat)
if(allocated(tau) ) deallocate(tau)
if(allocated(atf) ) deallocate(atf)
if(allocated(atomf) ) deallocate(atomf)
if(allocated(fx) ) deallocate(fx)
if(allocated(dz) ) deallocate(dz)
if(allocated(zarray) ) deallocate(zarray)
if(allocated(ncells) ) deallocate(ncells)
if(allocated(fz ) ) deallocate(fz)
if(allocated(fz_DWF) ) deallocate(fz_DWF)
if(allocated(sinc) ) deallocate(sinc)
if(allocated(inverse_sinc) ) deallocate(inverse_sinc)
if(allocated(substance_atom_types )) deallocate(substance_atom_types)
if(allocated(outer )) deallocate(outer)
if(allocated(inner )) deallocate(inner)
if(allocated(a0_slice )) deallocate(a0_slice )
if(allocated(nat_slice )) deallocate(nat_slice )
if(allocated(nat_slice_unitcell )) deallocate(nat_slice_unitcell)
if(allocated(tau_slice )) deallocate(tau_slice )
if(allocated(tau_slice_unitcell )) deallocate(tau_slice_unitcell)
if(allocated(prop_distance )) deallocate(prop_distance )
if(allocated(depths )) deallocate(depths )
if(allocated(ss_slice )) deallocate(ss_slice )
if(allocated(probe_df )) deallocate(probe_df )
if(allocated(imaging_df )) deallocate(imaging_df )
if(allocated(atm_indices )) deallocate(atm_indices )
if(allocated(ion_description )) deallocate(ion_description )
if(allocated(ionization_mu )) deallocate(ionization_mu )
if(allocated(fz_adf )) deallocate(fz_adf )
if(allocated(adf_potential )) deallocate(adf_potential )
if(allocated(ionization_potential )) deallocate(ionization_potential )
if(allocated(eels_correction_detector)) deallocate(eels_correction_detector)
#ifdef GPU
if(allocated(ccd_slice_array )) deallocate(ccd_slice_array)
if(allocated(Volume_array )) deallocate(Volume_array)
#endif
end subroutine