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m_lens.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/>.
!
!--------------------------------------------------------------------------------
module m_lens
use m_precision, only: fp_kind
implicit none
logical :: pw_illum, cb_illum
logical :: imaging = .false.
type aberration_coefficient
character(len=2)::Haider
character(len=10)::Krivanek
character(len=17)::Description
real(fp_kind)::amplitude,angle
integer*4::m,n
contains
procedure :: initialise
procedure :: set
end type aberration_coefficient
!Future work: make a lens object that contains the aberrations, defocus, cutoff and apodisation
!and has calculate ctf as a bound method
! Probe forming lens
type(aberration_coefficient)::probe_aberrations(14),imaging_aberrations(14)
real(fp_kind),allocatable :: probe_df(:),imaging_df(:)
real(fp_kind)::probe_cutoff,imaging_cutoff
real(fp_kind)::probe_apodisation,imaging_apodisation
integer :: probe_ndf,imaging_ndf
integer(4) :: nxsample, nysample !number of probe positions
real(fp_kind), allocatable :: probe_positions(:,:,:) !matrix containing the probe position
real(fp_kind) :: delx, dely !stepsize for the probe position in x and y
real(fp_kind) :: probe_initial_position(3) = [0.0_fp_kind, 0.0_fp_kind, 0.0_fp_kind]
contains
subroutine initialise(ab,Krivanek,Haider,description,amplitude,angle,n,m)
class(aberration_coefficient),intent(out)::ab
character(len=*),intent(in)::Krivanek
character(len=2),intent(in)::Haider
character(len=*),intent(in)::Description
real(fp_kind),intent(in)::amplitude,angle
integer*4,intent(in)::m,n
ab%Haider = Haider
ab%Krivanek = trim(adjustl(Krivanek))
ab%Description = trim(adjustl(Description))
ab%amplitude = amplitude
ab%angle = angle
ab%m = m
ab%n =n
end subroutine
subroutine set(ab)
use m_user_input, only: get_input
class(aberration_coefficient),intent(inout)::ab
character(:),allocatable::tag
tag = trim(adjustl(ab%description))
write(6,*)' Enter the amplitude of '//tag//' in '//char(143)//':'
call get_input(tag//' coefficient', ab%amplitude)
write(*,*)
if(ab%m>0) then
write(6,*)' Enter the azimuthal orientation of '//tag//' ('//char(237)//') in radians:'
call get_input(tag//' azimuth', ab%angle)
endif
write(*,*)
end subroutine
function chi(ab,q,phi,df)
! Calculate the aberration function chi(q) for the transfer function \exp[-i chi(q)]
use global_variables, only: pi, ak1
implicit none
real(fp_kind) :: chi
type(aberration_coefficient),intent(in)::ab(14)
real(fp_kind),intent(in) :: q,phi, df
integer*4:: naberrations,i
real(fp_kind) :: q2
q2 = q**2
chi = pi*df*q2/ak1
do i=1,14
chi = chi + 2*pi*ak1*(sqrt(q2)/ak1)**(ab(i)%n+1)*ab(i)%amplitude/(ab(i)%n+1)*cos(ab(i)%m*(phi-ab(i)%angle))
enddo
end function
subroutine setup_lens_parameters(string,aberrations,cutoff)
use global_variables, only: ak1,nopiy,nopix
use m_user_input, only: get_input
use output
use CUFFT_wrapper
use m_string
implicit none
integer(4) nflag
character*(*),intent(in) :: string
type(aberration_coefficient),intent(out)::aberrations(14)
real(fp_kind),intent(out):: cutoff
real(fp_kind) :: stigmatism(2),cs_mm,c5_mm,xyposn(3),scherzer_df,cs,apodisation
real(fp_kind),allocatable :: df(:)
integer(4) ::input,ndf,i
complex(fp_kind)::probe(nopiy,nopix)
character(120)::set_defocus
call command_line_title_box(string)
call aberrations(1 )%initialise('C12' ,'A1','2-Fold astig. ',0.0_fp_kind,0.0_fp_kind,1,2)
call aberrations(2 )%initialise('C21' ,'B2','Axial coma ',0.0_fp_kind,0.0_fp_kind,2,1)
call aberrations(3 )%initialise('C23' ,'A2','3-Fold astig. ',0.0_fp_kind,0.0_fp_kind,2,3)
call aberrations(4 )%initialise('C30 = CS' ,'C3','3rd order spher. ',0.0_fp_kind,0.0_fp_kind,3,0)
call aberrations(5 )%initialise('C32' ,'S3','Axial star aber. ',0.0_fp_kind,0.0_fp_kind,3,2)
call aberrations(6 )%initialise('C34' ,'A3','4-Fold astig. ',0.0_fp_kind,0.0_fp_kind,3,4)
call aberrations(7 )%initialise('C41' ,'B4','4th order coma ',0.0_fp_kind,0.0_fp_kind,4,1)
call aberrations(8 )%initialise('C43' ,'D4','3-Lobe aberr. ',0.0_fp_kind,0.0_fp_kind,4,3)
call aberrations(9 )%initialise('C45' ,'A4','5-Fold astig ',0.0_fp_kind,0.0_fp_kind,4,5)
call aberrations(10)%initialise('C50 = CS5','C5','5th order spher. ',0.0_fp_kind,0.0_fp_kind,5,0)
call aberrations(11)%initialise('C52' ,'S5','5th order star ',0.0_fp_kind,0.0_fp_kind,5,2)
call aberrations(12)%initialise('C54' ,'R5','5th order rosette',0.0_fp_kind,0.0_fp_kind,5,4)
call aberrations(13)%initialise('C56' ,'A5','6-Fold astig. ',0.0_fp_kind,0.0_fp_kind,5,6)
cutoff = set_cutoff(0.0_fp_kind)
write(*,*) 'Enter the defocus in Angstroms:'
call get_input('Defocus', set_defocus)
call read_sequence_string(set_defocus,120,ndf)
allocate(df(ndf))
call read_sequence_string(set_defocus,120,ndf,df)
nflag = -1
apodisation = -1
do while(nflag.ne.0)
write(6,11) atan(cutoff/ak1)*1000.0_fp_kind, char(143), cutoff, char(143),df(1)
do i=1,ndf-1
write(6,12) df(i+1)
enddo
do i=1,13
if(aberrations(i)%n==0) then
write(6,13) i+2,aberrations(i)%Krivanek,aberrations(i)%Haider,aberrations(i)%Description,aberrations(i)%amplitude
else
write(6,13) i+2,aberrations(i)%Krivanek,aberrations(i)%Haider,aberrations(i)%Description,aberrations(i)%amplitude,aberrations(i)%angle
endif
enddo
write(6,14)
11 format( ' Current simulation parameters:',/, &
&' -----------------------------------------------', /, &
&' < 1> Aperture cutoff (mrad) ', t40, g11.4,/, &
&' Aperture cutoff (', a1, '^-1) ',t40, g11.4,/, &
&' -----------------------------------------------', /, &
&' Symbol convention| | | ',/, &
&' Krivanek |Haider|Description | Size (',a1,') | Angle(rad)',/,&
&' < 2> C10 | C1 |Defocus |' g13.4,'|')
12 format( ' |' g13.4,'|')
13 format( 1x,'<',i2,'> ',a10, '| ',a2,3x,'|',a17, '|',g13.4, '|',g13.4)
14 format( ' <16> Output lens contrast transfer function ',t40,/,&
&' <17> Apodize probe (remove Airy tails) ',t40,/,&
&' -----------------------------------------------', /, &
&' Select option to change any parameter or <0> to continue')
call get_input('Change '//to_lower(trim(adjustl(string)))//' forming lens parameters', nflag)
write(*,*)
cs =aberrations(4)%amplitude
if (nflag.eq.1) cutoff = set_cutoff(cs)
if (nflag.eq.2) then
scherzer_df = -1.0_fp_kind*sign(1.0_fp_kind,Cs)*sqrt(4.0_fp_kind*abs(Cs)/(3.0_fp_kind*ak1))
write(*,*) 'Enter the defocus in Angstroms:'
if (abs(Cs).gt.1e-3) write(*,'(1x, a, f7.2, a)') '(The optimal Scherzer defocus for the specified Cs is ', scherzer_df, ' Angstroms)'
call get_input('Defocus', set_defocus)
call read_sequence_string(set_defocus,120,ndf)
if(allocated(df)) deallocate(df)
allocate(df(ndf))
call read_sequence_string(set_defocus,120,ndf,df)
endif
if (nflag.gt.2.and.nflag.lt.16) call aberrations(nflag-2)%set()
if(nflag.eq.16) then
xyposn = [0,0,0]
probe = make_ctf(xyposn,df(1),cutoff,aberrations,apodisation)
call binary_out_unwrap(nopiy,nopix,atan2(imag(probe),real(probe))*abs(probe)**2,&
&trim(adjustl(output_prefix)) //'_'//trim(adjustl(string))//'_forming_lens_ctf_phase')
call ifft2(nopiy,nopix,probe,nopiy,probe,nopiy)
call binary_out_unwrap(nopiy,nopix,abs(probe)**2,trim(adjustl(output_prefix))//'_'//trim(adjustl(string))&
&//'_forming_lens_ctf_real_space_intensity')
endif
if(nflag.eq.17) apodisation = set_probe_apodisation(cutoff)
enddo
if(to_lower(trim(adjustl(string)))=='image') then
imaging_ndf=ndf
if(allocated(imaging_df)) deallocate(imaging_df)
allocate(imaging_df(imaging_ndf))
call read_sequence_string(set_defocus,120,imaging_ndf,imaging_df)
imaging_apodisation = apodisation
else
if(allocated(probe_df)) deallocate(probe_df)
probe_ndf=ndf
allocate(probe_df(probe_ndf))
call read_sequence_string(set_defocus,120,probe_ndf,probe_df)
probe_apodisation = apodisation
endif
end subroutine
function set_probe_apodisation(cutoff)
use global_variables,only:pi
use m_user_input
real(fp_kind),intent(in)::cutoff
real(fp_kind)::set_probe_apodisation
20 format( ' This options allows the use of a real space aperture to remove the airy tails', /, &
&' of the probe.' /, &
&' Please input the radius of the aperture in Angstrom, for an aberration free,', /, &
&' a probe with cutoff of ',g11.4,1x, a1, '-1, the first, second and third radial minima', /, &
&' are located at ',g11.4,', ',g11.4,' and ',g11.4,1x, a1, '.',/,&
&' To disable probe apodisation input a negative number.')
write(6,20) cutoff,char(143),3.8317/(cutoff*2*pi),7.0156/(cutoff*2*pi),10.1735/(cutoff*2*pi),char(143)
call get_input('Probe real space cutoff',set_probe_apodisation)
end function
function set_cutoff(cstemp)
use global_variables, only: ak1
use m_user_input, only: get_input
implicit none
real(fp_kind) set_cutoff, cstemp, mrad_opt, mrad_cutoff
set_cutoff = 1.51_fp_kind*abs(cstemp)**(-0.25_fp_kind)*ak1**(0.75_fp_kind)
mrad_opt = atan(set_cutoff/ak1)*1000.0_fp_kind
if (mrad_opt .gt. 1500) mrad_opt = 1500
100 write(*,*) 'Enter the aperture cutoff in mrad:'
if (abs(cstemp).gt.1e-3) then
write(*,'(1x, a, f7.2, a)') '(The optimal cutoff for the specified Cs is ', mrad_opt, ' mrad)'
endif
call get_input('aperture cutoff', mrad_cutoff)
write(*,*)
if(mrad_cutoff < 0.0_fp_kind) then
goto 100
endif
set_cutoff = ak1*tan(mrad_cutoff/1000.0_fp_kind)
end function
function make_ctf(xyposn,df,cutoff,aberrations,apodisation) result(ctf)
use global_variables, only: nopiy, nopix, ifactory, ifactorx, pi, ss,a0
use m_multislice,only:make_detector
use m_crystallography, only: trimr,make_g_vec_array
use output
use CUFFT_wrapper
implicit none
complex(fp_kind),dimension(nopiy,nopix) :: ctf,real_space_aperture
real(fp_kind),intent(in) :: xyposn(3),df,cutoff,apodisation
real(fp_kind)::deltay,deltax
type(aberration_coefficient),intent(in)::aberrations(14)
optional::apodisation
integer(4) :: ny, nx
real(fp_kind) :: kr(3), akr, m1, m2,phi, g_vec_array(3,nopiy,nopix),x,y,r
call make_g_vec_array(g_vec_array,ifactory,ifactorx)
ctf=0.0_fp_kind
!$OMP PARALLEL DO PRIVATE(nx, m1, ny, m2, kr, akr,phi)
do nx = 1, nopix;do ny = 1, nopiy
kr = g_vec_array(:,ny,nx)
akr = trimr(kr,ss)
if (akr.le.cutoff) then
phi = atan2(kr(2),kr(1))
ctf(ny,nx) = exp(cmplx(0.0_fp_kind, -1*chi(aberrations,akr,phi,df), fp_kind))
endif
enddo;enddo
!$OMP END PARALLEL DO
if(present(apodisation)) then
if(apodisation>0) then
real_space_aperture = 0
do nx = 1, nopix;x = (nx-nopix/2-2)*a0(2)*ifactorx/nopix; do ny = 1, nopiy
y = (ny-nopiy/2-2)*a0(1)*ifactory/nopiy;r = sqrt(x**2+y**2)
if (r.le.apodisation) real_space_aperture(ny,nx) =1
enddo;enddo
real_space_aperture = quad_shift(real_space_aperture,nopiy,nopix)
call ifft2(nopiy,nopix,ctf,nopiy,ctf,nopiy)
ctf = ctf*real_space_aperture
call fft2(nopiy,nopix,ctf,nopiy,ctf,nopiy)
endif
endif
!$OMP PARALLEL DO PRIVATE(nx, m1, ny, m2, kr, akr,phi)
do nx = 1, nopix;do ny = 1, nopiy
ctf(ny,nx) = ctf(ny,nx) * exp(cmplx(0.0_fp_kind, -2*pi*dot_product(g_vec_array(:,ny,nx), xyposn), fp_kind))
enddo;enddo
!$OMP END PARALLEL DO
end function
subroutine setup_probe_scan(PACBED_only)
use global_variables, only: uvw1, uvw2,tiley,tilex, output_nopiy, output_nopix,interpolation
use m_string
implicit none
real(fp_kind) :: fract(2), origin(3)
logical,intent(in),optional::PACBED_only
logical::PACBED_only_
PACBED_only_ = .false.
if (present(PACBED_only)) PACBED_only_=PACBED_only
interpolation = .not.PACBED_only_
call command_line_title_box('Probe scan details')
write(*,*) 'Warning: changing the following parameters will '
write(*,*) 'disable interpolation of STEM images.',char(10)
call setup_scan_geometry(fract, origin,interpolation,PACBED_only_)
call calculate_probe_positions(uvw1, uvw2, origin)
if(interpolation) then
call setup_stem_image_interpolation
else
output_nopix = nxsample
output_nopiy = nysample
tiley = 1
tilex = 1
endif
end subroutine
subroutine reset_scan(origin,a1,a2,r1,r2,thetad2,fract,min_step,interpolation,PACBED_only)
use global_variables, only: a0, deg, ss, uvw1, uvw2, thetad, izone,fourdstem
use m_crystallography, only: zone, subuvw, angle, rsd
real(fp_kind),intent(out) :: fract(2), origin(3),a1, a2, r1(3), r2(3), thetad2,min_step
logical,intent(out)::interpolation
logical,intent(in)::PACBED_only
origin = 0.0_fp_kind
a1 = rsd(uvw1, a0, deg)
a2 = rsd(uvw2, a0, deg)
r1 = uvw1
r2 = uvw2
thetad2 = thetad
fract = 1.0
min_step = nyquist_step(probe_cutoff)
nysample = nyquist_sampling(probe_cutoff, fract(2)*a0(2),PACBED_only.and.(.not.fourDSTEM))
nxsample = nyquist_sampling(probe_cutoff, fract(1)*a0(1),PACBED_only.and.(.not.fourDSTEM))
interpolation = .not.PACBED_only
end subroutine
subroutine setup_scan_geometry(fract, origin,interpolation,PACBED_only)
use m_user_input, only: get_input
use global_variables, only: a0, deg, ss, uvw1, uvw2, thetad, izone,fourDSTEM
use m_crystallography, only: zone, subuvw, angle, rsd
implicit none
real(fp_kind),intent(out) :: fract(2), origin(3)
logical,intent(in)::PACBED_only
logical,intent(inout)::interpolation
integer(4) :: ich
integer(4) ig1a(3), ig2a(3),nysample_,nxsample_
real(fp_kind) a1, a2, r1(3), r2(3), thetad2,min_step
character(8)::able_string
character(7)::PACBED_or_STEM
integer :: i_scan_quarter
call reset_scan(origin,a1,a2,r1,r2,thetad2,fract,min_step,interpolation,PACBED_only)
nysample_ = nyquist_sampling(probe_cutoff, a0(2),PACBED_only.and.(.not.fourDSTEM))
nxsample_ = nyquist_sampling(probe_cutoff, a0(1),PACBED_only.and.(.not.fourDSTEM))
ich=-1
if(fourDSTEM.and.PACBED_only) then
PACBED_or_STEM = '4D-STEM'
elseif(PACBED_only) then
PACBED_or_STEM = 'PACBED'
else
PACBED_or_STEM = 'STEM'
endif
do while(ich.ne.1)
if(interpolation) able_string = 'enabled'
!DMH if(.not.interpolation) able_string = 'disabled'
if(.not.interpolation) then
able_string = 'disabled'
endif
write(6,103) r1, a1, char(143), r2, a2, char(143), thetad2, origin(1), origin(2), probe_cutoff
!DMH if(.not.PACBED_only) write(6,104)
if(.not.PACBED_only) then
write(6,104)
endif
write(6,105) PACBED_or_STEM,min_step,nxsample_, nysample_, ceiling(nxsample/fract(1)),ceiling(nysample/fract(2)),nxsample, nysample
!DMH if(.not.PACBED_only) write(6,106) able_string
if(.not.PACBED_only) then
write(6,106) able_string
endif
write(6,107)
103 format(/,' The probe scan vectors are: ', /, &
& ' x = ', 3g12.5, ' mag = ', g12.5, 1x, a1, /, &
& ' y = ', 3g12.5, ' mag = ', g12.5, 1x, a1, /, &
& ' The angle between these scan vectors is ', f12.2, ' degrees', /, &
& ' The inital (fractional) position is ', g12.5, ', ', g12.5, /,/, &
& ' The maximum spatial frequency allowed by the probe is ', f5.2, ' A-1.')
104 format( ' The STEM image has a bandwidth limit of twice that frequency. ')
105 format( ' This corresponds to minimum ',a7,' sampling of ', f6.2, ' positions per Angstrom:', /, &
& i4, ' x-positions and ', i4, ' y-positions per unit cell. Currently, sampling is',/,&
& i4, ' x-positions and ', i4, ' y-positions per unit cell for a total of' /, &
& i4, ' x-positions and ', i4, ' y-positions.')
106 format( ' Interpolation of STEM images is currently ',a)
107 format( ' <1> Accept', /, &
& ' <2> Change size of x and y (also adjusts sampling).', /, &
& ' <3> Change orientation of x and y.', /, &
& ' <4> Change the initial position.',/,&
& ' <5> Change the probe position sampling.',/,&
& ' <6> Reset.',/,&
& ' <7> Output probe positions.')
call get_input("Probe scan menu choice", ich)
write(*,*)
if(ich.eq.2) then !changing size of x and y vectors
write(6,111)
111 format(' Enter fractional increase in both x and y.',/, 'For example, to double the size of the scan enter 2 2')
call get_input("Enter fractional increase in x and y", fract(1),fract(2))
r1 = fract(1) * r1
r2 = fract(2) * r2
a1 = fract(1) * a1
a2 = fract(2) * a2
min_step = nyquist_step(probe_cutoff)
nxsample = nyquist_sampling(probe_cutoff, a1,PACBED_only.and.(.not.fourDSTEM))
nysample = nyquist_sampling(probe_cutoff, a2,PACBED_only.and.(.not.fourDSTEM))
interpolation=.false.
elseif(ich.eq.3) then
121 format( /, ' Please enter a new x-scan vector.' )
write(6,121)
call get_input("x-scan vector", ig1a, 3)
call zone(izone, ig1a, ig2a) !get an orthogonal vector to the zone axis and ig1
call angle(ig1a, ig2a, ss, thetad2) !calculate angle between scan vectors
call subuvw(ig1a, r1, a0, deg, ss) !calculate the real space scan vector from the 'ig1' given
call subuvw(ig2a, r2, a0, deg, ss) !calculate the real space scan length from the 'ig2' given
interpolation=.false.
elseif(ich.eq.4) then
call place_probe(origin)
interpolation=.false.
elseif(ich.eq.5) then
write(*,*) 'Enter the number of probe positions in the x direction.'
call get_input('nxsample', nxsample)
write(*,*) 'Enter the number of probe positions in the y direction.'
call get_input('nysample', nysample)
write(*,*)
interpolation = .false.
elseif(ich.eq.6) then
call reset_scan(origin,a1,a2,r1,r2,thetad2,fract,min_step,interpolation,PACBED_only)
elseif(ich.eq.7) then
call calculate_probe_positions(r1, r2, origin)
call plot_scan(probe_positions,nysample,nxsample)
endif
enddo
uvw1 = r1
uvw2 = r2
end subroutine
subroutine plot_scan(probe_positions,nysample,nxsample)
real(fp_kind),intent(in)::probe_positions(3,nysample,nxsample)
integer*4,intent(in)::nysample,nxsample
integer*4::ny,nx
write(*,*) 'Writing probe positions to file "probe_positions.txt"'
open(unit=52,file='probe_positions.txt')
467 format(3(f9.4))
do ny = 1, nysample;do nx = 1, nxsample
write(52,467) probe_positions(:,ny,nx)
enddo;enddo
close(52)
end subroutine
subroutine place_probe(xyposn)
use m_precision, only: fp_kind
use m_user_input, only: get_input
implicit none
real(fp_kind) :: xyposn(3)
write(*,*) 'Enter the co-ordinates "u v" at which to place the probe:'
write(*,*) '(as fractions of the unit cell side lengths)'
call get_input('Initial probe position', xyposn(1:2), 2)
write(*,*)
xyposn(3) = 0.0_fp_kind
end subroutine
integer function nyquist_sampling(qmax, L,PACBED) result(n)
implicit none
real(fp_kind) :: qmax, L
logical,intent(in),optional::PACBED
logical::PACBED_
PACBED_=.false.
if(present(PACBED)) PACBED_=PACBED
if(PACBED_) n = ceiling(2 * qmax * L)
!DMH if(.not.PACBED_) n = ceiling(4 * qmax * L)
if(.not.PACBED_) then
n = ceiling(4 * qmax * L)
endif
end function
real(fp_kind) function nyquist_step(qmax,PACBED) result(step)
implicit none
real(fp_kind) :: qmax
logical,intent(in),optional::PACBED
logical::PACBED_
PACBED_=.false.
if(present(PACBED)) PACBED_=PACBED
if(PACBED_) step = 2 * qmax
!DMH if(.not.PACBED_) step = 4 * qmax
if(.not.PACBED_) then
step = 4 * qmax
endif
end function
subroutine setup_stem_image_interpolation()
use m_user_input, only: get_input
use global_variables, only: tiley, tilex, output_nopiy, output_nopix,interpolation
implicit none
integer(4) :: out_max
if((nysample.gt.1).and.(nxsample.gt.1)) then
write(6,99)
99 format(' Enter the maximum number of pixels to interpolate the output image to.',/,&
&' Enter a negative number to disable interpolation.')
call get_input('output interpolation max pixels', out_max)
write(*,*)
if (out_max<0) then
write(*,*) 'Interpolation has been disabled.',char(10)
interpolation = .false.
output_nopix = nxsample
output_nopiy = nysample
tiley = 1
tilex = 1
return
endif
write(*,*) 'Enter the tiling in x and y for interpolation output'
call get_input('output interpolation tilex', tilex)
call get_input('output interpolation tiley', tiley)
write(*,*)
if(tilex.lt.1) tilex = 1
if(tiley.lt.1) tiley = 1
if(mod(out_max, 2).ne.0) out_max = out_max + 1
if(out_max.lt.max(nxsample*tilex, nysample*tiley)) then
write(6,105) out_max,max(nxsample*tilex, nysample*tiley)
105 format(' The choice of ',i4,' output pixels means that sampling of the output STEM image',/,&
& ' would fall below the Nyquist criterion for your choice of probe parameters.',/,&
&' The maximum number of output pixels has been increased to ',i4,' to avoid ',/,&
&' undersampling of the output.',/)
out_max = max(nxsample*tilex, nysample*tiley)
endif
if((nxsample*tilex).ge.(nysample*tiley)) then
output_nopix = out_max
output_nopiy = int( float(nysample*tiley)/float(nxsample*tilex)*output_nopix)
else
output_nopiy = out_max
output_nopix = int( float(nxsample*tilex)/float(nysample*tiley)*output_nopiy)
endif
endif
end subroutine
subroutine calculate_probe_positions(r1, r2, origin)
use global_variables, only: a0, deg
use m_crystallography, only: rsd
implicit none
real(fp_kind) :: r1(3), r2(3), origin(3)
integer :: ny, nx
real(fp_kind) :: sitey(3), sitex(3)
if(allocated(probe_positions)) deallocate(probe_positions)
allocate(probe_positions(3,nysample,nxsample))
do ny = 1, nysample
sitey = (ny-1) * r2 / nysample
do nx = 1, nxsample
sitex = (nx-1) * r1 / nxsample
probe_positions(:,ny,nx) = sitey + sitex + origin
enddo
enddo
delx = rsd(r1, a0, deg) / nxsample !get the step size in the x scan direction
dely = rsd(r2, a0, deg) / nysample !get the step size in the y scan direction
end subroutine
end module