-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathm_potential.f90
1006 lines (787 loc) · 36.7 KB
/
m_potential.f90
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
!--------------------------------------------------------------------------------
!
! 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_potential
use m_precision, only: fp_kind
implicit none
integer(4) :: num_ionizations
integer(4),allocatable:: atm_indices(:)
character(2),allocatable::ion_description(:)
logical:: EDX
complex(fp_kind), allocatable :: ionization_mu(:,:,:) !the ionization scattering factor array, calculated on the grid (supercell)
complex(fp_kind), allocatable :: fz_adf(:,:,:,:) !the adf scattering factor array, calculated on the grid (supercell)
real(fp_kind), allocatable :: adf_potential(:,:,:,:)
real(fp_kind), allocatable :: ionization_potential(:,:,:,:)
real(fp_kind), allocatable :: eels_correction_detector(:,:)
complex(fp_kind), allocatable :: inverse_sinc_new(:,:)
integer(4) :: n_qep_grates,n_qep_passes,nran ! Start of random number sequence
logical :: phase_ramp_shift
logical(4) :: quick_shift
!DMH
#ifdef LIN
character(len=1), parameter :: path_sep='/'
#elif WIN
character(len=1), parameter :: path_sep='\'
#else
#error "path_sep not defined, Set this constant for your system"
#endif
interface
subroutine make_site_factor_generic(site_factor, tau)
use m_precision, only: fp_kind
complex(fp_kind),intent(out) :: site_factor(:, :)
real(fp_kind),intent(in) :: tau(:,:)
end subroutine make_site_factor_generic
end interface
contains
subroutine prompt_high_accuracy
use m_user_input, only: get_input
use global_variables, only: high_accuracy
use m_string
implicit none
integer :: i
call command_line_title_box('Potential calculation method')
write(*,*) 'Two choices are available for the calculation of potentials.'
write(*,*) 'The reciprocal space method is accurate but may be slower.'
write(*,*) 'The hybrid method due to Van den Broek et al. is faster but'
write(*,*) 'is an approximate approach. Note that if "on-the-fly"'
write(*,*) 'scattering potentials are used the calculation defaults to the'
write(*,*) 'hybrid approach. '
write(*,*) '(Van den Broek et al., Ultramicroscopy 158 (2015) pp. 89-97)'
write(*,*)
write(*,*) 'Note: if there is insufficient GPU memory, this choice will be overridden.'
write(*,*)
10 write(*,*) 'Please choose a method:'
write(*,*) '<1> Reciprocal space (accuracy)'
write(*,*) '<2> Hybrid (speed)'
call get_input('Scattering factor accuracy', i)
write(*,*)
if (i.eq.1) then
high_accuracy = .true.
elseif (i.eq.2) then
high_accuracy = .false.
else
goto 10
endif
end subroutine prompt_high_accuracy
subroutine precalculate_scattering_factors
use m_crystallography
use m_precision, only: fp_kind
use global_variables
use m_electron, only: elsa_ext,peng_ionic_ff,element
use m_absorption!, only: complex_absorption, setup_absorptive_array, max_int, delta_kstep, tdsbr, fz_abs,calculate_absorption_mu,include_absorption
use m_numerical_tools, only: cubspl,ppvalu
use output
use m_string
implicit none
integer(4) :: i, j, k,Z
real(fp_kind) :: el_scat,ax,ay,g2,s2,sky,skx
real(fp_kind) :: xkstep, temp
real(fp_kind),allocatable :: xdata(:),tdsbrc(:,:,:)
real(fp_kind) :: factor, eps, g_vec_array(3,nopiy,nopix)
if(allocated(sinc)) deallocate(sinc)
if(allocated(inverse_sinc)) deallocate(inverse_sinc)
if(allocated(inverse_sinc_new)) deallocate(inverse_sinc_new)
if(allocated(fz)) deallocate(fz)
if(allocated(fz_DWF)) deallocate(fz_DWF)
allocate(fz(nopiy,nopix,nt))
allocate(sinc(nopiy,nopix))
allocate(inverse_sinc(nopiy,nopix))
allocate(inverse_sinc_new(nopiy,nopix))
allocate(fz_DWF(nopiy,nopix,nt))
ax = (a0(1)*float(ifactorx))/(float(nopix)*2.0_fp_kind)
ay = (a0(2)*float(ifactory))/(float(nopiy)*2.0_fp_kind)
factor = 1.0_fp_kind
eps = tiny(0.0_fp_kind)
call make_g_vec_array(g_vec_array,ifactory,ifactorx)
do i = 1, nopiy;do j = 1, nopix
sky = trimr([0.0_fp_kind,g_vec_array(2,i,j),0.0_fp_kind],ss)
skx = trimr([g_vec_array(1,i,j),0.0_fp_kind,0.0_fp_kind],ss)
g2 = trimr(g_vec_array(:,i,j),ss)**2
s2 = g2 / 4.0_fp_kind
do k = 1, nt
! Multiply by fractional occupancy
if (.not. ionic) el_scat = elsa_ext(nt,k,atomf,s2) * atf(2,k)
if(ionic) el_scat = Peng_ionic_FF(s2,nint(atf(1,k)),dZ(k)) * atf(2,k)
! Fill the potential matrix. Note: these are U(g)/2K
fz(i,j,k) = cmplx( el_scat, 0.0_fp_kind ,fp_kind)
fz_DWF(i,j,k) = cmplx( exp( -tp**2.0_fp_kind*g2*atf(3,k) / 2.0_fp_kind ), 0.0_fp_kind,fp_kind )
enddo
!Sinc
sinc(i,j) = cmplx((sin(tp*skx*ax)+eps)/(tp*skx*ax+eps)*((sin(tp*sky*ay)+eps)/(tp*sky*ay+eps)),0.0_fp_kind,fp_kind)
inverse_sinc(i,j) = cmplx((tp*skx*ax+eps)/(sin(tp*skx*ax)+eps)*(tp*sky*ay+eps)/(sin(tp*sky*ay)+eps),0.0_fp_kind,fp_kind)
inverse_sinc_new(i,j) = cmplx((tp*skx*ax+eps)/(sin(tp*skx*ax)+eps)*(tp*sky*ay+eps)/(sin(tp*sky*ay)+eps),0.0_fp_kind,fp_kind)
enddo; enddo
! Currently have U(g)/2K, so multiply by 2K
fz = 2*ak*fz
! Normalise the sinc functions
inverse_sinc = inverse_sinc*float(nopiy)*float(nopix)
sinc = sinc / (float(nopiy)*float(nopix))
end subroutine precalculate_scattering_factors
subroutine make_site_factor_matmul(site_factor, tau)
use m_precision, only: fp_kind
use global_variables, only: nopiy, nopix, tp
use m_crystallography
implicit none
!output
complex(fp_kind),intent(out) :: site_factor(:, :)
!input
real(fp_kind),intent(in) :: tau(:,:)
integer :: i, j
integer :: g_vec_array(3,nopiy,nopix)
call make_g_vec_array(g_vec_array)
!$OMP PARALLEL PRIVATE(i, j)
!$OMP DO
do i = 1, nopiy;do j = 1, nopix
site_factor(i,j) = sum(exp(cmplx(0.0_fp_kind, -tp*matmul(g_vec_array(:,i,j), tau), fp_kind)))
enddo;enddo
!$OMP END DO
!$OMP END PARALLEL
end subroutine make_site_factor_matmul
#ifdef GPU
subroutine make_site_factor_cuda(site_factor, tau)
use m_precision, only: fp_kind
use global_variables, only: nopiy, nopix, tp
use cuda_potential, only: cuda_site_factor
use cuda_array_library, only: blocks, threads
use m_crystallography,only:make_g_vec_array
implicit none
!output
complex(fp_kind),intent(out) :: site_factor(:, :)
!input
real(fp_kind),intent(in) :: tau(:,:)
integer :: g_vec_array(3,nopiy,nopix)
integer,device :: g_vec_array_d(3,nopiy,nopix)
real(fp_kind),device :: tau_d(3, size(tau,2))
complex(fp_kind),device :: site_factor_d(nopiy,nopix)
call make_g_vec_array(g_vec_array)
g_vec_array_d = g_vec_array
tau_d = tau
call cuda_site_factor<<<blocks,threads>>>(site_factor_d, tau_d, g_vec_array_d, nopiy, nopix)
site_factor = site_factor_d
end subroutine make_site_factor_cuda
#endif
subroutine make_site_factor_hybrid(site_factor, tau)
use m_precision, only: fp_kind
use global_variables, only: nopiy, nopix
use CUFFT_wrapper, only: fft2
implicit none
complex(fp_kind),intent(out) :: site_factor(:,:)
real(fp_kind),intent(in) :: tau(:,:)
integer :: j
integer :: xpixel, ypixel
real(fp_kind) :: xpos, ypos, fracx, fracy
site_factor = 0.0_fp_kind
!$OMP PARALLEL PRIVATE(xpos, ypos, j, xpixel,ypixel,fracx,fracy)
!$OMP DO
do j = 1, size(tau, 2)
xpos = tau(1,j)*nopix
ypos = tau(2,j)*nopiy
! Ensure that the pixel positions are in range
if (ceiling(xpos).gt.nopix) then
xpos = xpos - float(nopix)
elseif (floor(xpos).lt.1) then
xpos = xpos + float(nopix)
endif
if (ceiling(ypos).gt.nopiy) then
ypos = ypos - float(nopiy)
elseif (floor(ypos).lt.1) then
ypos = ypos + float(nopiy)
endif
!fraction of the pixel top right
xpixel = ceiling(xpos)
ypixel = ceiling(ypos)
fracx = mod(xpos, 1.0_fp_kind)
fracy = mod(ypos, 1.0_fp_kind)
call pixel_check(xpixel, ypixel)
site_factor(ypixel,xpixel) = site_factor(ypixel,xpixel) + fracx*fracy
!fraction of the pixel top left
xpixel = floor(xpos)
ypixel = ceiling(ypos)
fracx = 1.0_fp_kind - mod(xpos, 1.0_fp_kind)
fracy = mod(ypos, 1.0_fp_kind)
call pixel_check(xpixel, ypixel)
site_factor(ypixel,xpixel) = site_factor(ypixel,xpixel) + fracx*fracy
!fraction of the pixel bottom right
xpixel = ceiling(xpos)
ypixel = floor(ypos)
fracx = mod(xpos, 1.0_fp_kind)
fracy = 1.0_fp_kind - mod(ypos,1.0_fp_kind)
call pixel_check(xpixel, ypixel)
site_factor(ypixel,xpixel) = site_factor(ypixel,xpixel) + fracx*fracy
!fraction of the pixel bottom left
xpixel = floor(xpos)
ypixel = floor(ypos)
fracx = 1.0_fp_kind - mod(xpos, 1.0_fp_kind)
fracy = 1.0_fp_kind - mod(ypos, 1.0_fp_kind)
call pixel_check(xpixel, ypixel)
site_factor(ypixel,xpixel) = site_factor(ypixel,xpixel) + fracx*fracy
enddo
!$OMP end do
!$OMP end parallel
!fix pixel offset
site_factor = cshift(site_factor,SHIFT = -1,DIM=1)
site_factor = cshift(site_factor,SHIFT = -1,DIM=2)
call fft2(nopiy, nopix, site_factor, nopiy, site_factor, nopiy)
site_factor = site_factor * inverse_sinc_new * sqrt(float(nopiy)*float(nopix))
contains
subroutine pixel_check(x, y)
! Wrap pixel coordinates around so that they remain in range.
implicit none
integer(4) :: x,y
if(x.eq.0) x = nopix
if(x.eq.nopix+1) x = 1
if(y.eq.0) y = nopiy
if(y.eq.nopiy+1) y = 1
end subroutine pixel_check
end subroutine make_site_factor_hybrid
subroutine setup_inelastic_ionization_types()
use global_variables
use m_user_input
use m_string
implicit none
integer*4::i_eels
call command_line_title_box('Ionization')
i_eels = 0
do while(i_eels<1.or.i_eels>2)
write(*,*) char(10),' <1> EELS',char(10),' <2> EDX',char(10)
call get_input('Ionization choice', i_eels)
enddo
EDX = i_eels.eq.2
call local_potential(EDX)
end subroutine
function get_ionization_shell_line(shell,atno) result(lineno)
!Get the line for the given ionization shell and atom number,returns
!-1 if that shell is not contained in the parameterization
use m_string
character(2),intent(in)::shell
integer*4,intent(in)::atno
character*31::filename,line
character(len=:),allocatable ::string
integer*4::reason,lineno,l
!open the pertinent data files
!DMH filename = 'ionization_data\EELS_EDX_'//shell//'.dat'
filename = 'ionization_data'//path_sep//'EELS_EDX_'//shell//'.dat'
open(unit=35,file=filename,status='old',err=970)
l = len('Z = '//to_string(int(atno))//' ')
allocate(character(l)::string)
string = 'Z = '//to_string(int(atno))//' '
lineno = 1
DO
READ(35,960,IOSTAT=Reason) line
960 format(a31)
IF (Reason > 0) THEN
write(*,*) 'Problem reading ',filename
!If end of file is reach return -1 (shell is not in parametrization)
ELSE IF (Reason < 0) THEN
lineno = -1
close(35)
return
ELSE
!If the substring Z = atno, then return this line
if(index(line,string)>0) then
close(35)
return
endif
lineno = lineno+1
END IF
END DO
close(35)
return
970 write(*,*) 'Problem reading ',filename
end function
function get_ionization_parameters(shell,atno,DE,EDX) result (EELS_EDX_params)
!Read ionisation form factor parameters from ionization_data files
!shell should be a string describing the orbital ie, '1s', '2s', '2p' etc
!atno is the atomic number
!DE is the energy window for EELS and is ignored if the EDX parameterization is requested
!EDX is a boolean variable, pass .TRUE. for EDX parameterization and .FALSE. for EELS
use m_numerical_tools
use m_string
use global_variables,only: ekv,ak1,nt,atf,substance_atom_types
character(2),intent(in)::shell
integer*4,intent(in)::atno
real(fp_kind),intent(in)::DE
logical,intent(in):: EDX
real(fp_kind)::params(29,8,5),EELS_PARAM_SET2(5,29),xdata(8),bscoef_(4,8)
real(fp_kind) :: dedata(5),bscoef2_(4,5),p(29),EELS_EDX_params(29)
integer*4::iatom,atno_check,i,ii,m,ishell,iz,lineno,n,mm
character(10) junk
character(1) cjunk1,cjunk2,cjunk3
m = 5
if(EDX) m=1
n = str2int(shell(1:2))
lineno = get_ionization_shell_line(shell,atno)
!open the pertinent data files and read to relevant line
!DMH open(unit=16,file='ionization_data\EELS_EDX_'//shell//'.dat',status='old',err=970)
open(unit=16,file='ionization_data'//path_sep//'EELS_EDX_'//shell//'.dat',status='old',err=970)
do iz = 1,lineno
read(16,*) junk
enddo
p = 0
!Later parametrizations only contain 28 datapoints
mm=29;if (n>2) mm=28
!Read parameters
do i=1,8 !Loop over accelerating voltages
read(16,*) junk ! E=xx kev header
do ii=1,6 !Loop over energy loss above threshhold (EELS) and EDX
read(16,*) p(1:mm)
if((.not.EDX).and.(ii<6)) params(:,i,ii) = p(:) !EELS is the first 5 lines
if(EDX.and.(ii==6)) params(:,i,1) = p(:) !EDX is the last line
enddo
enddo
!Can close parameters file now
close(16)
!Interpolate to accelerating voltage used
!data in files is in steps of 50 keV with 8 points
!this is stored in xdata
xdata =(/(i*50, i=1,8,1)/)
do ii=1,m
do i=1,mm
bscoef_(1,:) = params(i,1:8,ii)
call cubspl ( xdata, bscoef_(:,:), 8, 0, 0 )
EELS_param_set2(ii,i) = ppvalu(xdata,bscoef_(:,:),7,4,ekv,0)
enddo
enddo
!If EDX then no energy window interpolation is needed
if (EDX) then
EELS_EDX_params = EELS_param_set2(1,:)
return
endif
! contained within EELS_param_set2(i,ii) is the 29 data points (first index) intepolated
! to the correct incident energy there are 5 rows Interpolate to energy window desired
dedata = real([1,10,25,50,100],kind=fp_kind)
!f(s)/DE is mostly flat and interpolates more simply
EELS_EDX_params=0
do i=1,mm
do ii=1,5
bscoef2_(1,ii) = EELS_param_set2(ii,i) / dedata(ii)
enddo
call cubspl ( dedata, bscoef2_(:,:), 5, 0, 0 )
EELS_EDX_params(i) = DE*ppvalu(dedata,bscoef2_(:,:),4,4,DE,0)
enddo
return
970 write(*,*) ' Cannot access data file EELS_EDX_'//shell//'.dat'
stop
end function
!********************************************************************************
! subroutine EELS_local_potential()
! reads in the scattering factors and performs the interpolation
! necessary to accommodate arbitrary geometries and energy windows
!********************************************************************************
subroutine local_potential(EDX)
use m_string
use m_numerical_tools, only: cubspl,ppvalu
use m_multislice
use global_variables
use m_user_input
implicit none
logical,intent(in)::EDX
integer(4) i,ii,iii,j,kval,m,nchoices,ZZ,nshells,norbitals,k
integer(4),allocatable::available_shells(:),available_atoms(:)
real(fp_kind),allocatable:: DE(:)
real(fp_kind) eels_inner,eels_outer
character(2) shell_name_EELS(9),orb
character(3) shells(9)!(9)
character(13):: contributions(4)
logical,allocatable::choices(:)
logical::k_shell,l_shell,EDXpresent(nt,4)
shell_name_EELS = ['1s','2s','2p','3s','3p','3d','4s','4p','4d']
shells = ['K','L1','L23','M1','M23','M45','N1','N23','N45']
contributions = ['1s','2s and 2p','3s, 3p and 3d','4s, 4p and 4d']
norbitals = size(shell_name_EELS)
nshells = size(shells)
!If EELS, setup detectors
if(.not.EDX) then
write(6,91)
91 format(1x,'The EELS calculations assume the local approximation, which', /, &
&1x,'may be inappropriate when the the EELS detector does not', /, &
&1x,'have a very large acceptance angle. To account for the', /, &
&1x,'finite detector size, a correction is applied.', /, &
&1x,'For more details see Y. Zhu et al. APL 103 (2013) 141908.', /)
eels_inner = 0.0_fp_kind
write(*,*) 'EELS detector outer angle (mrad):'
call get_input('Outer EELS angle', eels_outer)
write(*,*)
eels_inner = ak1*tan(eels_inner/1000.0_fp_kind)
eels_outer = ak1*tan(eels_outer/1000.0_fp_kind)
if(allocated(eels_correction_detector)) deallocate(eels_correction_detector)
allocate(eels_correction_detector(nopiy,nopix))
eels_correction_detector = make_detector(nopiy,nopix,ifactory,ifactorx,ss,eels_inner,eels_outer)
endif
!Count available orbitals by checking what is available for the given atoms in
!the parametrization files
ii=0
do i = 1, nt; ZZ=nint(ATF(1,i)); do j=1,norbitals
if(get_ionization_shell_line(shell_name_EELS(j),ZZ)>-1) ii=ii+1
enddo; enddo
!endif
nchoices = ii
allocate(choices(ii),DE(ii))
DE = 0
choices = .false.
kval = -1
write(*,*) char(10),' ',char(230),'STEM calculates EDX and EELS signals for ionization of electrons to the '
write(*,*) 'continuum, at this point bound->bound (white line) transitions are not taken'
write(*,*) 'into account.',char(10)
write(*,*) 'K, L, M and N shell ionizations are available though users should be aware '
write(*,*) 'that quantitative agreement between simulation and theory has only been '
write(*,*) 'demonstrated for K and L shells (see Y. Zhu and C. Dwyer, Microsc. Microanal.'
write(*,*) '20 (2014), 1070-1077)',char(10)
do while ((kval.ne.0).or.all(.not.choices))
100 format(/,' Ionization choices',/,/,'Index Atom| Z |',a,'| Included(y/n)'/&
&,'-----------------------------------------------------------')
if(EDX) write(*,100) ' Orbital | Shell '
110 format(1x,'<',i2,'>',2x,a2,2x,'|',1x,i2,1x,'|',2x,a2,5x,'|',1x,a3,3x,'|',1x,a1,6x)
!DMH changed to newline statement in if:
if(.not.EDX) then
write(*,100) ' Orbital | Shell | Window (eV)'
endif
111 format(1x,'<',i2,'>',2x,a2,2x,'|',1x,i2,1x,'|',2x,a2,5x,'|',1x,a3,3x,'|',1x,f5.1,6x,'|',1x,a1,6x)
120 format(' < 0> continue')
!Display choices for EDX and EELS ionizations
ii=1
do i = 1, nt;ZZ=nint(ATF(1,i)); do j=1,norbitals
if(get_ionization_shell_line(shell_name_EELS(j),ZZ)>-1) then
if(EDX) write(*,110) ii,trim(adjustl(substance_atom_types(i))),int(ZZ),shell_name_EELS(j),shells(j),logical_to_yn(choices(ii))
!DMH changed to newline statement in if:
if(.not.EDX) then
write(*,111) ii,trim(adjustl(substance_atom_types(i))),int(ZZ),shell_name_EELS(j),shells(j),DE(ii),logical_to_yn(choices(ii))
endif
ii=ii+1
endif
enddo;enddo
write(*,120)
call get_input('Shell choice <0> continue', kval)
!Update choice
if ((kval.gt.0).and.(kval.le.nchoices)) then
choices(kval) = .not.choices(kval)
!If EELS get energy window
if (.not.EDX) then
DE(kval) =-1
do while ((DE(kval).lt.0).or.(DE(kval).gt.100))
write(*,*) 'Enter EELS energy window above threshold in eV (between 1 and 100 ev):',char(10)
call get_input('Energy window', DE(kval))
enddo
end if
end if
enddo
num_ionizations = count(choices)
allocate(ionization_mu(nopiy,nopix,num_ionizations),atm_indices(num_ionizations),Ion_description(num_ionizations))
ionization_mu = 0
ii=1
iii=1
!Now read in EELS or EDX parameters
do i = 1, nt;ZZ=nint(ATF(1,i))
do j=1,norbitals
if(get_ionization_shell_line(shell_name_EELS(j),ZZ)>-1) then; if(choices(ii)) then
ionization_mu(:,:,iii) = make_fz_EELS_EDX(shell_name_EELS(j),zz,DE(ii),EDX)* atf(2,i)*fz_DWF(:,:,i)
atm_indices(iii) = i
Ion_description(iii) = shell_name_EELS(j)
iii=iii+1;endif; ii=ii+1; endif
enddo
enddo;
end subroutine
!Subrotuine to make the Fz_mu needs to have prefactors accounted for (volume fo the unit cell etc.)
!needs to be multiplied by the DWF for the pertinent atom type
function make_fz_EELS_EDX(orbital,zz,DE,EDX) result(fz_mu)
use m_precision
use global_variables
use m_numerical_tools, only: cubspl,ppvalu
use m_crystallography,only:trimr,make_g_vec_array
implicit none
character(2),intent(in)::orbital
integer*4,intent(in)::zz
real(fp_kind),intent(in)::DE
logical,intent(in)::EDX
real(fp_kind):: g_vec_array(3,nopiy,nopix)
complex(fp_kind):: fz_mu(nopiy,nopix)
!dummy variables
integer(4) i,j
real(fp_kind) sval
real(fp_kind) svals(29),EELS_EDX_bscoef(4,29)
!DATA POINTS USED FOR THE INTERPOLATION S-VALUES (q/2)
data svals / 0.0_fp_kind,0.025_fp_kind,0.05_fp_kind,0.1_fp_kind,0.2_fp_kind,0.3_fp_kind,0.4_fp_kind,0.5_fp_kind,0.625_fp_kind,&
& 0.75_fp_kind,0.875_fp_kind,1.0_fp_kind,1.5_fp_kind,2.0_fp_kind,2.5_fp_kind,3.0_fp_kind,3.5_fp_kind,4.0_fp_kind, &
& 5.0_fp_kind,6.0_fp_kind,7.0_fp_kind,8.0_fp_kind,9.0_fp_kind,10.0_fp_kind,12.0_fp_kind,14.0_fp_kind,16.0_fp_kind, &
& 18.0_fp_kind,20.0_fp_kind /
write(*,*) 'Making the ionization inelastic scattering factor grid, please wait...',char(10)
!pppack interpolation
EELS_EDX_bscoef(1,:)= get_ionization_parameters(orbital,zz,DE,EDX)
call cubspl(svals,EELS_EDX_bscoef(:,:), 29, 0, 0 )
fz_mu = 0.0_fp_kind
call make_g_vec_array(g_vec_array,ifactory,ifactorx)
!!$OMP PARALLEL PRIVATE(i, j, m2, m1, sky, skx, tempval, sval), SHARED(fz_mu)
!!$OMP DO
do i=1, nopiy;do j=1, nopix
sval = trimr(g_vec_array(:,i,j),ss) / 2.0_fp_kind
if (sval.le.20.0_fp_kind) fz_mu(i,j) = cmplx(ppvalu(svals,EELS_EDX_bscoef(:,:),28,4,sval,0),0.0_fp_kind ,fp_kind) / (tp * ak1)
enddo;enddo
!!$OMP END DO
!!$OMP END PARALLEL
return
end function
!--------------------------------------------------------------------------------------
! make_mu_matrix() makes the mu matrices for each HOLZ slice
! subroutine to take the unit cell input,
! and slice based on holz
subroutine make_local_inelastic_potentials(ionization)
use m_multislice
use global_variables!, only:adf,nopiy,nopix,high_accuracy,nt,ss,ndet,ig1,ig2,ifactory
use m_absorption
!use m_string
!use output
implicit none
logical,intent(in)::ionization
integer(4) i,j,k,nat_
real(fp_kind) :: potential_matrix_complex(nopiy,nopix),vol
real(8)::thmin,thmax,phmin,phmax
complex(fp_kind)::fz_adf(nopiy,nopix,nt,ndet)
write(6,134)
134 format(/,' Calculating effective inelastic potentials.',/)
if(allocated(adf_potential)) deallocate(adf_potential)
if(allocated(ionization_potential)) deallocate(ionization_potential)
allocate(adf_potential(nopiy,nopix,n_slices,ndet)) !the adf potential
adf_potential=0
if(ionization) allocate(ionization_potential(nopiy,nopix,num_ionizations,n_slices)) !the ionization potential
!if(adf) call make_fz_adf()
if(adf.and.complex_absorption) then
do k=1,ndet/nseg
thmin = atan(inner((k-1)/nseg+1)/ak)
thmax = atan(outer((k-1)/nseg+1)/ak)
!Note that the absorptive calculations do not take into account the directionality of inelastic scattering, the absorptive scattering
!factors are assumed isotropic and this is only an approximation for inelastic scattering to segmented detectors
fz_adf(:,:,:,(k-1)*nseg+1:k*nseg) = spread(absorptive_scattering_factors(ig1,ig2,ifactory,ifactorx,nopiy,nopix,nt,a0,ss,atf,nat, ak, relm, orthog,thmin,thmax),dim=4,ncopies=nseg)/nseg
enddo
endif
do j = 1, n_slices
vol = ss_slice(7,j)
!calculate the ionization potential
if(ionization) then
do i=1,num_ionizations
nat_ = nat_slice(atm_indices(i),j)
ionization_potential(:,:,i,j) = real(potential_from_scattering_factors(ionization_mu(:,:,i),tau_slice(:,atm_indices(i),:nat_,j),nat_,nopiy,nopix,high_accuracy)/vol)
enddo
endif
!calculate the ADF potential
if(adf.and.complex_absorption) then
do i=1,nt
nat_ = nat_slice(i,j)
do k=1,ndet
adf_potential(:,:,j,k)= adf_potential(:,:,j,k) + real(potential_from_scattering_factors(fz_adf(:,:,i,k),tau_slice(:,i,:nat_,j),nat_,nopiy,nopix,high_accuracy)/vol*ss(7)*4*pi)
enddo
enddo
endif
enddo !ends loop over the number of potential subslices
end subroutine
!--------------------------------------------------------------------------------------
function potential_from_scattering_factors(scattering_factor,atom_posn,nat_layer,nopiy,nopix,high_accuracy) result(slice_potential)
use m_precision
use cufft_wrapper
implicit none
integer(4),intent(in) :: nat_layer,nopiy,nopix
real(fp_kind),intent(in) :: atom_posn(3,nat_layer)
complex(fp_kind),intent(in)::scattering_factor(nopiy,nopix)
logical,intent(in),optional::high_accuracy
complex(fp_kind),dimension(nopiy,nopix) :: potential, site_term,slice_potential
logical::high_accuracy_
procedure(make_site_factor_generic),pointer :: make_site_factor
high_accuracy_ = .false.;if(present(high_accuracy)) high_accuracy_= high_accuracy
#ifdef GPU
make_site_factor => make_site_factor_cuda
#else
make_site_factor => make_site_factor_matmul
#endif
slice_potential = 0.0_fp_kind
if (nat_layer.ne.0) then
if (high_accuracy_) then
call make_site_factor(site_term, atom_posn)
else
call make_site_factor_hybrid(site_term, atom_posn)
endif
slice_potential = site_term*scattering_factor
! Get realspace potential
call ifft2(nopiy,nopix,slice_potential,nopiy,slice_potential,nopiy)
slice_potential = slice_potential*sqrt(float(nopiy*nopix))
endif
end function
function make_absorptive_grates(nopiy,nopix,n_slices) result(projected_potential)
use m_precision, only: fp_kind
use cufft_wrapper, only: fft2, ifft2
use global_variables, only: ig1,ig2,ifactory,ifactorx,nt, relm, tp, ak, atf, high_accuracy, ci, pi, bwl_mat,fz,fz_DWF,ss,a0,nat,orthog
use m_absorption!, only: transf_absorptive,fz_abs
use m_multislice, only: nat_slice, ss_slice, tau_slice
use m_string, only: to_string
use output
implicit none
integer(4),intent(in)::nopiy,nopix,n_slices
complex(fp_kind)::projected_potential(nopiy,nopix,n_slices)
integer(4) :: j, m, n,nat_layer
real(fp_kind) :: ccd_slice,V_corr
complex(fp_kind),dimension(nopiy,nopix) :: scattering_pot,temp,effective_scat_fact
complex(fp_kind)::fz_abs(nopiy,nopix,nt)
real(fp_kind) :: t1, delta,amplitude(nopiy,nopix),phase(nopiy,nopix)
procedure(make_site_factor_generic),pointer :: make_site_factor
projected_potential= 0
t1 = secnds(0.0_fp_kind)
fz_abs=0
if(include_absorption) fz_abs = 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
do j = 1, n_slices
write(*,'(1x, a, a, a, a, a)') 'Calculating transmission functions for slice ', to_string(j), '/', to_string(n_slices), '...'
198 write(6,199) to_string(sum(nat_slice(:,j)))
199 format(1x, 'Number of atoms in this slice: ', a, /)
ccd_slice = relm / (tp * ak * ss_slice(7,j))
V_corr = ss(7)/ss_slice(7,j)
do m=1,nt
nat_layer = nat_slice(m,j)
effective_scat_fact = CCD_slice*fz(:,:,m)*fz_DWF(:,:,m)+cmplx(0,1)*fz_abs(:,:,m)*V_corr
projected_potential(:,:,j) = projected_potential(:,:,j)+potential_from_scattering_factors(effective_scat_fact,tau_slice(:,m,:nat_layer,j),nat_layer,nopiy,nopix,high_accuracy)
enddo
enddo ! End loop over slices
delta = secnds(t1)
if(timing) then
write(*,*) 'The calculation of transmission functions for the absorptive model took ', delta, 'seconds.'
write(*,*)
open(unit=9834, file=trim(adjustl(output_prefix))//'_timing.txt', access='append')
write(9834, '(a, g, a, /)') 'The calculation of transmission functions for the absorptive model took ', delta, 'seconds.'
close(9834)
endif
end function make_absorptive_grates
integer function seed_rng() result(idum)
use m_numerical_tools, only: ran1
use m_precision, only: fp_kind
implicit none
integer :: i
real(fp_kind) :: random
idum = -1
do i = 1, nran
random = ran1(idum)
enddo
end function seed_rng
subroutine make_propagator(nopiy,nopix,prop,dz,ak1,ss,ig1,ig2,claue,ifactorx,ifactory)
use m_precision, only: fp_kind
use m_crystallography, only: trimr,make_g_vec_array
implicit none
integer(4) :: nopiy,nopix
complex(fp_kind) :: prop(nopiy,nopix)
real(fp_kind) :: ak1, ss(7), claue(3), dz, g_vec_array(3,nopiy,nopix)
integer(4) :: ifactorx, ifactory, ig1(3), ig2(3)
real(fp_kind),parameter :: pi = atan(1.0d0)*4.0d0
integer(4) :: ny, nx
call make_g_vec_array(g_vec_array,ifactory,ifactorx)
do ny = 1, nopiy;do nx = 1, nopix
prop(ny,nx) = exp(cmplx(0.0d0, -pi*dz*trimr(g_vec_array(:,ny,nx)-claue,ss)**2/ak1, fp_kind ))
enddo;enddo
end subroutine
function make_qep_grates(idum) result(projected_potential)
use m_precision, only: fp_kind
use cufft_wrapper, only: fft2, ifft2
use global_variables, only: nopiy, nopix, nt, relm, tp, ak, ak1, atf, high_accuracy, ci, pi, bwl_mat,fz
use m_multislice
use m_string, only: to_string
use output, only: output_prefix,timing,binary_in
use m_numerical_tools, only: displace
implicit none
integer(4),intent(inout) :: idum
complex(fp_kind) :: projected_potential(nopiy,nopix,n_qep_grates,n_slices),temp(nopiy,nopix),scattering_pot(nopiy,nopix,nt)
integer(4), allocatable :: handled(:,:)
integer(4):: save_list(2,nt),match_count, i, j, m, n,ii,jj,jjj,kk,iii
real(fp_kind) :: tau_holder(3),tau_holder2(3),ccd_slice,ums,amplitude(nopiy,nopix),phase(nopiy,nopix)
real(fp_kind) :: mod_tau(3,nt,maxnat_slice,n_slices,n_qep_grates),t1, delta
logical::fracocc
procedure(make_site_factor_generic),pointer :: make_site_factor
! Search for fractional occupancy
fracocc = any(atf(2,:).lt.0.99d0)
t1 = secnds(0.0_fp_kind)
do j = 1, n_slices
write(*,'(1x, a, a, a, a, a)') 'Calculating transmission functions for slice ', to_string(j), '/', to_string(n_slices), '...'
198 write(6,199) to_string(sum(nat_slice(:,j)))
199 format(1x, 'Number of atoms in this slice: ', a)
ccd_slice = relm / (tp * ak * ss_slice(7,j))
do i = 1, n_qep_grates
200 format(a1, 1x, i3, '/', i3)
write(6,200, advance='no') achar(13), i, n_qep_grates
!DMH
call flush(6)
! Randomly displace the atoms
if (.not.fracocc) then
do m = 1, nt
do n = 1, nat_slice(m,j)
call displace(tau_slice(1:3,m,n,j),mod_tau(1:3,m,n,j,i),sqrt(atf(3,m)),a0_slice,idum)
enddo
enddo
else
allocate( handled(nt,maxnat_slice) )
handled = 0
do ii=1, nt
do jj = 1, nat_slice(ii,j)
if (handled(ii,jj).eq.1) cycle
tau_holder(1:3) = tau_slice(1:3,ii,jj,j)
save_list = 0
match_count = 0
ums = atf(3,ii)
do iii=ii+1,nt
do jjj=1,nat_slice(iii,j)
if (same_site(tau_holder,tau_slice(1:3,iii,jjj,j))) then
match_count = match_count+1
save_list(1,match_count)=iii
save_list(2,match_count)=jjj
ums = ums + atf(3,iii)
cycle
endif
enddo
enddo
ums = ums / dfloat(match_count+1)
call displace(tau_holder(1:3),tau_holder2(1:3),sqrt(ums),a0_slice,idum)
mod_tau(1:3,ii,jj,j,i) = tau_holder2(1:3)
handled(ii,jj) = 1
do kk=1,match_count
mod_tau(1:3,save_list(1,kk),save_list(2,kk),j,i)&
&= tau_holder2(1:3)
handled(save_list(1,kk),save_list(2,kk)) = 1
enddo
enddo
enddo
deallocate( handled )
endif
projected_potential(:,:,i,j) = 0
do m = 1, nt
projected_potential(:,:,i,j) = projected_potential(:,:,i,j)+real(potential_from_scattering_factors(CCD_slice*fz(:,:,m)&
&,mod_tau(:,m,1:nat_slice(m,j),j,i),nat_slice(m,j),nopiy,nopix,high_accuracy))
enddo
enddo ! End loop over grates
write(*,*)
write(*,*)
enddo ! End loop over slices
delta = secnds(t1)
write(*,*) 'The calculation of transmission functions for the QEP model took ', delta, 'seconds.'
write(*,*)
if(timing) then
open(unit=9834, file=trim(adjustl(output_prefix))//'_timing.txt', access='append')
write(9834, '(a, g, a, /)') 'The calculation of transmission functions for the QEP model took ', delta, 'seconds.'
close(9834)
endif
end function make_qep_grates
logical(4) function same_site(site1,site2)
implicit none
real(fp_kind) site1(3),site2(3)
real(fp_kind) tol