-
Notifications
You must be signed in to change notification settings - Fork 3
/
cm5.f90
854 lines (739 loc) · 21 KB
/
cm5.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
! The MIT License (MIT)
!
! Copyright (c) 2016 Holger Kruse
!
! Permission is hereby granted, free of charge, to any person obtaining a copy
! of this software and associated documentation files (the "Software"), to deal
! in the Software without restriction, including without limitation the rights
! to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
! copies of the Software, and to permit persons to whom the Software is
! furnished to do so, subject to the following conditions:
!
! The above copyright notice and this permission notice shall be included in all
! copies or substantial portions of the Software.
!
! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
! IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
! FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
! AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
! LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
! OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
! SOFTWARE.
!
program cm5charge
implicit none
integer nat,i,j,k,l,ii,jj,kdelta
integer, allocatable :: iat(:)
real(8), allocatable :: xyz(:,:),qcm5(:),qh(:)
real(8) dx,dy,dz,rij,s,alpha,tkk,bkk,fscale,dipole(3)
character(120) infile,chrgfile
character(2) esym
real(kind=8) rvdw(94),rconv(94),bohr,quad(3,3)
real(8), parameter :: AMBER_ELECTROSTATIC = 18.2223d0
real(8), parameter :: INV_AMBER_ELECTROSTATIC = 1.0d0/AMBER_ELECTROSTATIC
! atomic radii from Mantina, Valero, Cramer, Truhlar "Atomic radii of elements"
! Copyed by hand, maybe contain typos...
! H He
data rvdw /1.10d0,1.40d0, &
! Li Be B C N O F Ne
1.82d0,1.53d0,1.92d0,1.70d0,1.54d0,1.52d0,1.47d0,1.54d0, &
! Na Mg Al Si P S Cl Ar
2.27d0,1.73d0,1.84d0,2.10d0,1.80d0,1.80d0,1.75d0,1.88d0, &
! K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
2.75d0,2.31d0,2.15d0,2.11d0,2.07d0,2.06d0,2.05d0,2.04d0,2.00d0,1.97d0,1.96d0,2.01d0,1.87d0,2.11d0,1.85d0,1.90d0,1.85d0,2.02d0, &
! Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
3.03d0,2.49d0,2.26d0,2.23d0,2.18d0,2.17d0,2.16d0,2.13d0,2.10d0,2.10d0,2.11d0,2.18d0,1.93d0,2.17d0,2.06d0,2.06d0,1.98d0,2.16d0, &
! Cs Ba
3.32d0,2.68d0, &
! La-Lu
2.43d0,2.42d0,2.40d0,2.46d0,2.38d0,2.36d0,2.35d0,2.34d0,2.33d0,2.31d0,2.30d0,2.29d0,2.27d0,2.26d0,2.24d0, &
! Hf Ta W Re Os Ir Pt Au Hg Ti Pb Bi Po At Rn
2.23d0,2.22d0,2.18d0,2.16d0,2.16d0,2.13d0,2.13d0,2.23d0,2.23d0,2.11d0,2.02d0,2.07d0,1.97d0,2.02d0,2.20d0, &
! Fr-Pu
3.48d0,2.83d0,2.47d0,2.45d0,2.43d0,2.41d0,2.39d0,2.43d0/
data rconv /0.32d0,0.37d0, &
! Li Be B C N O F Ne
1.30d0,0.99d0,0.84d0,0.75d0,0.71d0,0.64d0,0.60d0,0.62d0, &
! Na Mg Al Si P S Cl Ar
1.60d0,1.40d0,1.24d0,1.14d0,1.09d0,1.04d0,1.00d0,1.01d0, &
! K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
2.00d0,1.74d0,1.59d0,1.48d0,1.44d0,1.30d0,1.29d0,1.24d0,1.18d0,1.17d0,1.22d0,1.20d0,1.23d0,1.20d0,1.20d0,1.18d0,1.17d0,1.24d0, &
! Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
2.15d0,1.90d0,1.78d0,1.64d0,1.56d0,1.46d0,1.38d0,1.36d0,1.34d0,1.30d0,1.36d0,1.40d0,1.42d0,1.40d0,1.40d0,1.37d0,1.32d0,1.36d0, &
! Cs Ba
2.38d0,2.06d0, &
! La-Lu
1.94d0,1.84d0,1.90d0,1.73d0,1.86d0,1.85d0,1.83d0,1.82d0,1.81d0,1.80d0,1.79d0,1.77d0,1.77d0,1.78d0,1.74d0, &
! Hf Ta W Re Os Ir Pt Au Hg Ti Pb Bi Po At Rn
1.64d0,1.58d0,1.50d0,1.41d0,1.36d0,1.32d0,1.30d0,1.64d0,1.88d0,1.48d0,1.45d0,1.50d0,1.42d0,1.47d0,1.46d0, &
! Fr-Pu
2.42d0,2.11d0,2.01d0,1.90d0,1.84d0,1.83d0,1.80d0,1.80d0/
print*,'|-----------------------------------------|'
print*,'| CM5 charges calculator from |'
print*,'| ORCA Hirsheld charges |'
print*,'| set: "%output print[P_Hirshfeld] 1 end" |'
print*,'| v1.0 Holger Kruse |'
print*,'|-----------------------------------------|'
print*,''
bohr=0.52917726d0
alpha=2.474 ! angstrom
call getarg(1,infile)
call getarg(2,chrgfile)
if(chrgfile=='') then
fscale=1.20
else
read(chrgfile,*) fscale
endif
if(infile=='') then
print*,'USAGE: cm5 <orca output> [<scale factor]'
print*,''
stop
endif
write(*,*) ''
write(*,'(a,F4.2)'),'* scaling factor for CM5 *: ', fscale
write(*,*) ''
nat=1
call tmolrd(nat,xyz,iat,infile,.false.,.true.)
allocate(xyz(3,nat),iat(nat))
allocate(qh(nat),qcm5(nat))
call tmolrd(nat,xyz,iat,infile,.true.,.false.)
xyz=xyz*bohr ! angstrom
write(*,'(a)'),' data in electron/angstrom '
call read_hirsh(qh,nat,trim(infile))
!print*,' Hirshfeld charges '
!do i=1,nat
!write(*,'(I3,a,F5.2)') i,esym(iat(i)),qh(i)
!enddo
qcm5=0d0
do i=1,nat
ii=iat(i)
s=0
do j=1,nat
if(i==j) cycle
jj=iat(j)
dx=xyz(1,i)-xyz(1,j)
dy=xyz(2,i)-xyz(2,j)
dz=xyz(3,i)-xyz(3,j)
rij=sqrt(dx*dx+dy*dy+dz*dz)
bkk=exp(-alpha*(rij-rconv(ii)-rconv(jj))) ! eq.2
s=s+tkk(ii,jj)*bkk
! print*,s,tkk(ii,jj)*bkk,tkk(ii,jj),bkk,rij
enddo
qcm5(i)=qh(i)+s
enddo
print*,'CHARGES:'
print*,' CM5 CM5scale HPA X Y Z'
do i=1,nat
write(*,'(I3,2x,a2,2x,3(F9.5,x),3(F12.7,x))') i,esym(iat(i)),qcm5(i),qcm5(i)*fscale,qh(i),xyz(1:3,i)
enddo
write(*,*) ''
write(*,*) 'electrostatic moments'
write(*,*) ' ref. point: 0.0 0.0 0.0'
!CM5 dipole moment
dipole=0
do i=1,nat
do j=1,3
dipole(j)=dipole(j)+qcm5(i)*xyz(j,i)
enddo
enddo
dipole=dipole*4.802889778d0
dx= dipole(1)
dy= dipole(2)
dz= dipole(3)
s=sqrt(dipole(1)**2+dipole(2)**2+dipole(3)**2)
write(*,'(a,F10.6)' ) ' Total CM5 charge : ',sum(qcm5)
write(*,*) ' X Y Z TOTAL'
write(*,'(a,4(F10.6,x))') ' CM5 dipole [Debye] : ', dx,dy,dz,s
! scaled
! could have just scaled the dipole directly, oh well...
dipole=0
do i=1,nat
do j=1,3
dipole(j)=dipole(j)+qcm5(i)*xyz(j,i)*fscale
enddo
enddo
dipole=dipole*4.802889778d0
dx= dipole(1)
dy= dipole(2)
dz= dipole(3)
s=sqrt(dipole(1)**2+dipole(2)**2+dipole(3)**2)
write(*,'(a,4(F10.6,x))') ' CM5 scaled [Debye] : ', dx,dy,dz,s
! Quadrupole moment
quad=0
do k=1,nat
dx=xyz(1,k)/bohr
dy=xyz(2,k)/bohr
dz=xyz(3,k)/bohr
quad(1,1)=quad(1,1)+ dx*dx*qcm5(k)
quad(2,2)=quad(2,2)+ dy*dy*qcm5(k)
quad(3,3)=quad(3,3)+ dz*dz*qcm5(k)
quad(1,2)=quad(1,2)+ dx*dy*qcm5(k)
quad(1,3)=quad(1,3)+ dx*dz*qcm5(k)
quad(2,3)=quad(2,3)+ dy*dz*qcm5(k)
enddo
!quad=quad*4.802889778d0
print*, ' quadrupole moment (au):'
write(*,'(2x,3(a,F12.6,x))') 'XX= ',quad(1,1),'YY= ',quad(2,2),'ZZ= ',quad(3,3)
write(*,'(2x,3(a,F12.6,x))') 'XY= ',quad(1,2),'XZ= ',quad(1,3),'YZ= ',quad(2,3)
write(*,'(2x,a,F12.6)') ' 1/3 trace= ',(quad(1,1)+quad(2,2)+quad(3,3)/3d0)
! write data
print*,'writing: '//trim(infile)//'_cm5.dat with normal and scaled CM5 charges'
open(99,file=trim(infile)//'_cm5.dat')
do i=1,nat
write(99,'(2(F10.6,x))') qcm5(i),qcm5(i)*fscale
enddo
close(99)
! write topology file section
qcm5=qcm5*fscale/INV_AMBER_ELECTROSTATIC
print*,'writing: '//trim(infile)//'_cm5.top (amber topology) with scaled CM5 charges'
open(111,file=trim(infile)//'_cm5.top')
write(111,'(a)')'%FLAG CHARGE'
write(111,'(a)')'%FORMAT(5E16.8)'
write(111,'(5E16.8)') (qcm5(i),i = 1,nat)
close(111)
end program
! form Tkk' eq.3,4
real(kind=8) function tkk(i,j)
implicit none
integer i,j
real(8) dz(54)
real(8) dzz(6)
data dz /0.0056,-0.1543, &
0.0, 0.0333, -0.1030, -0.0446, -0.1072, -0.0802, -0.0629, -0.1088, & ! Li-Ne
0.0184, 0.0 ,-0.0726, -0.0790, -0.0756, -0.0565, -0.0444, -0.07676, & !Na-Ar
0.0130, 0.0,10*0.0,-0.0557,-0.0533,-0.0399, -0.0313,0.0,0.0, & !K-Kr
16*0.0, -0.0220,0.0/ !Rb - Xe
!H-C; H-N H-O C-N C-O N-O
data dzz /0.0502d0,0.1747d0,0.1671d0,0.0556d0, 0.0234d0,-0.0346d0/
tkk=dz(i)-dz(j)
! catch special cases
if(i==1.and.j==6) tkk=dzz(1)
if(i==1.and.j==7) tkk=dzz(2)
if(i==1.and.j==8) tkk=dzz(3)
if(i==6.and.j==7) tkk=dzz(4)
if(i==6.and.j==8) tkk=dzz(5)
if(i==7.and.j==8) tkk=dzz(6)
if(i==6.and.j==1) tkk=-dzz(1)
if(i==7.and.j==1) tkk=-dzz(2)
if(i==8.and.j==1) tkk=-dzz(3)
if(i==7.and.j==6) tkk=-dzz(4)
if(i==8.and.j==6) tkk=-dzz(5)
if(i==8.and.j==7) tkk=-dzz(6)
end function
subroutine read_hirsh(qh,nat,fname)
implicit none
integer nat,i
real(8) qh(nat)
character(*) fname
character(80) aa
real(8) xx,yy
write(*,*) 'reading ORCA file : ', trim(fname)
open(99,file=fname)
do
read(99,'(a)') aa
if(index(aa,'HIRSHFELD ANALYSIS').ne.0) then
! 6 dummy line, then read
read(99,'(a)') aa
read(99,'(a)') aa
read(99,'(a)') aa
read(99,'(a)') aa
read(99,'(a)') aa
read(99,'(a)') aa
do i=1,nat
read(99,*) yy,aa,qh(i),xx
enddo
exit
endif
enddo
! read charges file for testing
!open(99,file='charges')
!do i=1,nat
!read(99,*) qh(i)
!enddo
close(99)
end
!************************************************************
!* reads a turbomole (bohr) or xmol (angst)rom file. *
!* Tests if xmol starts with "number of atoms + blank" or *
!* directly with the coordinates. *
!************************************************************
subroutine tmolrd(nat,xyz,iat,infile,echo,c_nat)
!use parm
implicit none
integer i,j,k,l,nat
real(8) xyz(3,*),energy,s2r
integer ifrez(nat),iat(nat)
character*2 cc,ff
character(200) atmp
character*(*) infile
real(kind=8) txyz(3,nat),xx(10)
real(kind=8) bohr
integer tiat(nat),nn,tifrez(nat),istat,iff
logical da,c_nat,echo,doORCA
bohr=0.52917726d0
i=0
tifrez=0
iff=0
doORCA=.false.
inquire(file=infile,exist=da)
select case (da)
case (.true.)
if(echo) write(*,'('' reading...'',$)')
open(unit=33,file=infile)
! test for tmol or txyz file
! test for ORCA
do i=1,10
read(33,'(a)') atmp ! $coord
if(index(atmp,' O R C A ').ne.0) doORCA=.true.
enddo
rewind(33)
read(33,'(a)') atmp ! $coord
rewind(33)
if(index(atmp,'$coord').ne.0) then
! count number of atoms
do while (da)
read(33,'(a)',end=100) atmp ! $coord
if(index(atmp,'$coord').ne.0) cycle
if(index(atmp,'$').ne.0) exit
i=i+1
enddo
nat=i
100 continue
if(c_nat) then
close(33)
return ! just return number of atoms
endif
rewind(unit=33)
! read TMOL file
read(33,*) atmp ! $coord
do j=1,nat
read(33,'(a)') atmp ! $coord
backspace(33)
if(index(atmp,' f ').ne.0) then
read(33,*) txyz(1,j),txyz(2,j),txyz(3,j),cc,ff
tifrez(j)=1
iff=iff+1
else ! default
read(33,*) txyz(1,j),txyz(2,j),txyz(3,j),cc
endif
call elem(cc,tiat(j))
txyz(1:3,j)=txyz(1:3,j)
enddo
if(echo) write(*,*) ' Turbomole file [bohr] : ', trim(infile)
close(33)
!**********
! PDB FILE
!**********
elseif(index(atmp,'REMARK').ne.0.or.index(atmp,'ATOM').ne.0) then
rewind(33)
if(c_nat) then ! just count atoms
do
read (33,'(a)',end=777) atmp
if(index(atmp,'ATOM').ne.0) i=i+1
enddo
777 continue
nat=i
close(33)
return
endif
i=0
do
read (33,'(a)',end=778) atmp
if(index(atmp,'ATOM').ne.0) then
i=i+1
txyz(1,i)=s2r(atmp(31:38))
txyz(2,i)=s2r(atmp(39:46))
txyz(3,i)=s2r(atmp(47:54))
endif
enddo
txyz=0
778 continue
txyz=txyz*1d0/bohr
close(33)
if(echo) write(*,'(5x,'' PDB file [angst]: '',a)') trim(infile)
!******************
!* ORCA output file
!******************
elseif(doORCA) then
i=0
if(c_nat) then ! just count atoms
do
read(33,'(a)',end=801) atmp
if(index(atmp,'CARTESIAN COORDINATES (A.U.)').ne.0) then
read(33,'(a)') atmp
do
read(33,'(a)') atmp
i=i+1
if(index(atmp,'------').ne.0) goto 800
enddo
endif
enddo
800 continue
nat=i-3
close(33)
801 continue
if(nat<=0) stop 'no atoms found!'
return
endif
i=0
do
read(33,'(a)',end=779) atmp
if(index(atmp,'CARTESIAN COORDINATES (A.U.)').ne.0) then
read(33,'(a)') atmp ! dummy line
read(33,'(a)') atmp ! dummy line
do i=1,nat
read(33,'(a)') atmp ! dummy line
call readl(atmp,xx,nn)
call elem(atmp,tiat(i))
txyz(1:3,i)=xx(5:7)
enddo
endif
enddo
779 continue
close(33)
if(echo) write(*,'(5x,'' ORCA output file [A.U.]: '',a)') trim(infile)
!******************
!* TMOL output file
!******************
else ! txyz file
read(33,'(a)',end=101) atmp
! check for first two lines
call readl(atmp,xx,nn)
if(nn.gt.1) then ! more than one argument found, assuming they are coords
do
nat=nat+1
read(33,'(a)',end=123) atmp
enddo
if(c_nat) then
close(33)
return ! just return number of atoms
endif
else
nat=idint(xx(1))
if(c_nat) then
close(33)
return ! just return number of atoms
endif
read(33,'(a)',end=101) atmp !titel line
endif
123 if(nn.gt.1) rewind(3)
do i=1,nat
read(33,'(a)') atmp
call readl(atmp,xx,nn)
call elem(atmp,tiat(i))
txyz(1:3,i)=xx(1:3)*1d0/bohr
enddo
101 close(33)
if(echo) write(*,'(5x,'' XYZ file [angst]: '',a)') trim(infile)
endif
if(maxval(tifrez,nat).eq.1) then
if(echo) then
write(*,'(a,x,I4,x,a)') ' found ',iff,' frozen cart. coordinates'
if(iff.lt.50) then ! dont spam the output to much ...
write(*,'(a,$)') ' atom nr: '
do i=1,nat
if(tifrez(i)==1) write(*,'(x,I2,$)') i
enddo
print*,''
endif
endif
endif
case (.false.)
write(*,*) ' no input file <',trim(infile) ,'> found !! '
end select
do i=1,nat
xyz(1:3,i)=txyz(1:3,i)
iat(i)=tiat(i)
ifrez(i)=tifrez(i)
enddo
return
end subroutine
SUBROUTINE ELEM(KEY1, NAT)
IMPLICIT DOUBLE PRECISION (A-H,O-Z)
CHARACTER*(*) KEY1
CHARACTER*2 ELEMNT(94),E
DATA ELEMNT/'h ','he', &
'li','be','b ','c ','n ','o ','f ','ne', &
'na','mg','al','si','p ','s ','cl','ar', &
'k ','ca','sc','ti','v ','cr','mn','fe','co','ni','cu', &
'zn','ga','ge','as','se','br','kr', &
'rb','sr','y ','zr','nb','mo','tc','ru','rh','pd','ag', &
'cd','in','sn','sb','te','i ','xe', &
'cs','ba','la','ce','pr','nd','pm','sm','eu','gd','tb','dy',&
'ho','er','tm','yb','lu','hf','ta','w ','re','os','ir','pt',&
'au','hg','tl','pb','bi','po','at','rn', &
'fr','ra','ac','th','pa','u ','np','pu'/
nat=0
e=' '
k=1
DO J=1,len(key1)
if (k.gt.2)exit
N=ICHAR(key1(J:J))
if(n.ge.ichar('A') .and. n.le.ichar('Z') )then
e(k:k)=char(n+ICHAR('a')-ICHAR('A'))
k=k+1
endif
if(n.ge.ichar('a') .and. n.le.ichar('z') )then
e(k:k)=key1(j:j)
k=k+1
endif
enddo
DO I=1,107
if(e.eq.elemnt(i))then
NAT=I
RETURN
ENDIF
ENDDO
end
character*2 FUNCTION ESYM(I)
CHARACTER*2 ELEMNT(94)
DATA ELEMNT/'h ','he', &
'li','be','b ','c ','n ','o ','f ','ne', &
'na','mg','al','si','p ','s ','cl','ar', &
'k ','ca','sc','ti','v ','cr','mn','fe','co','ni','cu', &
'zn','ga','ge','as','se','br','kr', &
'rb','sr','y ','zr','nb','mo','tc','ru','rh','pd','ag', &
'cd','in','sn','sb','te','i ','xe', &
'cs','ba','la','ce','pr','nd','pm','sm','eu','gd','tb','dy', &
'ho','er','tm','yb','lu','hf','ta','w ','re','os','ir','pt', &
'au','hg','tl','pb','bi','po','at','rn', &
'fr','ra','ac','th','pa','u ','np','pu'/
ESYM=ELEMNT(I)
RETURN
END
SUBROUTINE READL(A1,X,N)
IMPLICIT REAL*8 (A-H,O-Z)
CHARACTER*(*) A1
DIMENSION X(*)
I=0
IS=1
10 I=I+1
X(I)=READAA(A1,IS,IB,IE)
IF(IB.GT.0 .AND. IE.GT.0) THEN
IS=IE
GOTO 10
ENDIF
N=I-1
RETURN
END
FUNCTION READAA(A,ISTART,IEND,IEND2)
IMPLICIT REAL*8 (A-H,O-Z)
REAL*8 READAA
CHARACTER*(*) A
NINE=ICHAR('9')
IZERO=ICHAR('0')
MINUS=ICHAR('-')
IDOT=ICHAR('.')
ND=ICHAR('D')
NE=ICHAR('E')
IBL=ICHAR(' ')
IEND=0
IEND2=0
IDIG=0
C1=0
C2=0
ONE=1.D0
X = 1.D0
NL=LEN(A)
DO 10 J=ISTART,NL-1
N=ICHAR(A(J:J))
M=ICHAR(A(J+1:J+1))
IF(N.LE.NINE.AND.N.GE.IZERO .OR.N.EQ.IDOT)GOTO 20
IF(N.EQ.MINUS.AND.(M.LE.NINE.AND.M.GE.IZERO.OR. M.EQ.IDOT)) GOTO 20
10 CONTINUE
READAA=0.D0
RETURN
20 CONTINUE
IEND=J
DO 30 I=J,NL
N=ICHAR(A(I:I))
IF(N.LE.NINE.AND.N.GE.IZERO) THEN
IDIG=IDIG+1
IF (IDIG.GT.10) GOTO 60
C1=C1*10+N-IZERO
ELSEIF(N.EQ.MINUS.AND.I.EQ.J) THEN
ONE=-1.D0
ELSEIF(N.EQ.IDOT) THEN
GOTO 40
ELSE
GOTO 60
ENDIF
30 CONTINUE
40 CONTINUE
IDIG=0
DO 50 II=I+1,NL
N=ICHAR(A(II:II))
IF(N.LE.NINE.AND.N.GE.IZERO) THEN
IDIG=IDIG+1
IF (IDIG.GT.10) GOTO 60
C2=C2*10+N-IZERO
X = X /10
ELSEIF(N.EQ.MINUS.AND.II.EQ.I) THEN
X=-X
ELSE
GOTO 60
ENDIF
50 CONTINUE
!C
!C PUT THE PIECES TOGETHER
!C
60 CONTINUE
READAA= ONE * ( C1 + C2 * X)
DO 55 J=IEND,NL
N=ICHAR(A(J:J))
IEND2=J
IF(N.EQ.IBL)RETURN
55 IF(N.EQ.ND .OR. N.EQ.NE)GOTO 57
RETURN
57 C1=0.0D0
ONE=1.0D0
DO 31 I=J+1,NL
N=ICHAR(A(I:I))
IEND2=I
IF(N.EQ.IBL)GOTO 70
IF(N.LE.NINE.AND.N.GE.IZERO) C1=C1*10.0D0+N-IZERO
IF(N.EQ.MINUS)ONE=-1.0D0
31 CONTINUE
61 CONTINUE
70 READAA=READAA*10**(ONE*C1)
RETURN
END
!********************************
!* convert a word to lower case *
!********************************
subroutine lower_case(word)
character (len=*) , intent(in out) :: word
integer :: i,ic,nlen
nlen = len(word)
do i=1,nlen
ic = ichar(word(i:i))
if (ic >= 65 .and. ic < 90) word(i:i) = char(ic+32)
end do
end subroutine lower_case
!********************************************
!* split a string s into n separate words w *
!********************************************
subroutine charsplit(s,n,w)
implicit none
integer i,n,k
character*80, intent(in) :: s
character*80, intent(out) :: w(n)
character*80 a,aa
aa=adjustl(s)
do i=1,n
a=aa
k=index(a,' ')
w(i)=trim(a(:(k-1)))
aa=adjustl(trim(a((k+1):)))
enddo
return
end subroutine
!***************************************************
!* split a string s iand the return the x'ths word *
!***************************************************
subroutine charXsplit(s,wx,x)
implicit none
integer i,n,k,x
character*80, intent(in) :: s
character*80, intent(out) ::wx
character*80 w(20)
character*80 a,aa
aa=adjustl(s)
i=0
do while (index(aa,' ').ne.1)
i=i+1
a=aa
k=index(a,' ')
w(i)=trim(a(:(k-1)))
aa=adjustl(trim(a((k+1):)))
! print*,'AA',trim(aa),index(aa,' ')
if(i.gt.50) stop '!* string split error: subroutine charXsplit *!'
enddo
wx=w(x)
!print*, trim(wx)
return
end subroutine
!***********************************
!* count words n in string s *
!***********************************
subroutine cstring(s,n)
implicit none
integer i,n,k,x
character(*), intent(in) :: s
character*80 a,aa
aa=adjustl(s)
i=0
do while (index(aa,' ').ne.1)
i=i+1
a=aa
k=index(a,' ')
! w(i)=trim(a(:(k-1)))
aa=adjustl(trim(a((k+1):)))
! print*,'AA',trim(aa),index(aa,' ')
if(i.gt.50) stop '!* string split error: subroutine charXsplit *!'
enddo
n=i
return
end subroutine
integer function nwords(s)
implicit none
integer i,k,x
character(*), intent(in) :: s
character*80 a,aa
aa=adjustl(s)
i=0
do while (index(aa,' ').ne.1)
i=i+1
a=aa
k=index(a,' ')
! w(i)=trim(a(:(k-1)))
aa=adjustl(trim(a((k+1):)))
! print*,'AA',trim(aa),index(aa,' ')
if(i.gt.50) stop '!* string split error: subroutine charXsplit *!'
enddo
nwords=i
return
end function
! String to integer
integer pure function s2i(a)
implicit none
character(*), intent(in):: a
read(a,*) s2i
return
end function
! String to real(8)
real(8) pure function s2r(a)
implicit none
character(*), intent(in):: a
read(a,*) s2r
return
end function
!******************
!* write xyz *
!******************
subroutine wrxyz(iat,nat,xyz,infile)
implicit none
integer i,j,k,l,nat,iat(nat)
real(8) xyz(3,*)
integer ierr
character(*) infile
character(2) esym
real(8) f
!f=0.5291770d0
f=1d0
open(unit=55,file=infile,iostat=ierr,status='replace')
if(ierr.ne.0) stop 'cannot write xopt.xyz'
write(55,'(I5)') nat
write(55,*)
!write(55,'(2F16.8)')energy,gnorm
do i=1,nat
write(55,'(a2,5x,3(F18.14,3x))') esym(iat(i)), xyz(1,i)*f,xyz(2,i)*f,xyz(3,i)*f
enddo
close(55)
end subroutine wrxyz
integer function kdelta(i,j)
implicit none
integer i,j
kdelta=0
if(i==j) kdelta=1
end function