root / utils / Xyz2Scan.f @ 2
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| 1 |
program Xyz2irc |
|---|---|
| 2 |
! This programs reads a XYZ file and converts it into distances, |
| 3 |
! valence angle and dihedral angles. |
| 4 |
! It prints them as a function of the irc distance... |
| 5 |
!----------------------------------------------- |
| 6 |
! Input: name of the ROOT file of PAW |
| 7 |
! it also needs a file call list which has the following structure: |
| 8 |
! the first line gives the time when you want to start your analysis |
| 9 |
! one line contains the type of the value you want to follow, it can be |
| 10 |
! b for a Bond distance |
| 11 |
! a for an angle |
| 12 |
! d for a dihedral |
| 13 |
! this descriptor is followed by the number of the atoms involved ! |
| 14 |
! a typical file can be: |
| 15 |
! 3. |
| 16 |
! b 1 2 |
| 17 |
! b 2 3 |
| 18 |
! a 1 2 3 |
| 19 |
!---------------------------------------------- |
| 20 |
! Ouput: A files call Scan.dat |
| 21 |
! wich contains in the first lines the input file (as a reminder) |
| 22 |
! and then for each step the wanted values |
| 23 |
!------------------------------------------------ |
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! Second version also reads the energy (as to be written after E= on |
| 25 |
! the comment line) |
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!------------------------------------------------ |
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! Third version contains a new command: c for Center of Mass |
| 28 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! v 3.1 the c command now creates the center of mass... and allows |
| 30 |
! people to do whatever they want with it... |
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! Syntax: c NbAt ListAt |
| 32 |
!! |
| 33 |
! v 3.2 |
| 34 |
! Added the p command that gives the oriented angle between two planes |
| 35 |
! Syntax: p At1 At2 At3 At4 At5 At6 |
| 36 |
! At1, At2, At3 define the first plane |
| 37 |
! At4, At5, At6 define the second plane |
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! How it works: gives the angles between the normal of the two planes, defined by |
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! the cross produc At2-At1 x At2-At3 etc. |
| 40 |
!!!! |
| 41 |
|
| 42 |
|
| 43 |
IMPLICIT NONE |
| 44 |
INTEGER*4 maxnat,MaxList |
| 45 |
Parameter (MaxNat=10000,MaxList=100) |
| 46 |
character*120 f1 |
| 47 |
REAL*8 geos(3,maxnat) |
| 48 |
character*33 fmt |
| 49 |
character*3 atoms(maxnat) |
| 50 |
character*5 Type |
| 51 |
Character*120 line |
| 52 |
INTEGER*4 NbPrint |
| 53 |
REAL*8 AU2PS,Pi |
| 54 |
! Mass is not used for now. |
| 55 |
! REAL*8 Mass(MaxNat) |
| 56 |
REAL*8 Ener, Conv |
| 57 |
INTEGER*4 At1,At2,At3,At4,At5,At6,IOOUT |
| 58 |
INTEGER*4 IArg, I, NNN, Ng, J |
| 59 |
|
| 60 |
INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbP,NbCOM |
| 61 |
INTEGER*4 At1B(MaxList),At2B(MaxList) |
| 62 |
INTEGER*4 At1A(MaxList),At2A(MaxList),At3A(MaxList) |
| 63 |
INTEGER*4 At1D(MaxList),At2D(MaxList),At3D(MaxList), |
| 64 |
$ At4D(MaxList) |
| 65 |
INTEGER*4 At1p(MaxList),At2p(MaxList),At3p(MaxList), |
| 66 |
$ At4p(MaxList),At5p(MaxList),At6p(MaxList) |
| 67 |
INTEGER*4 AtCom(0:MaxList,MaxList) |
| 68 |
REAL*8 VB(MaxList),VA(MaxList),VD(MaxList),VCOM(MaxList) |
| 69 |
REAL*8 Vp(MaxList) |
| 70 |
LOGICAL FExist |
| 71 |
|
| 72 |
c INTEGER*4 iargc |
| 73 |
c external iargc |
| 74 |
|
| 75 |
COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbP,NbCom, At1B,At2B, |
| 76 |
& At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom, |
| 77 |
& At1p,At2p,At3p,At4p,At5p,At6p |
| 78 |
COMMON /Values/VB,VA,VD,Vp,VCom |
| 79 |
COMMON /Const/AU2ps,Pi |
| 80 |
|
| 81 |
AU2PS=1./41341.37 |
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NbPrint=100 |
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Pi=dacos(-1.d0) |
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IOOUT=13 |
| 85 |
Conv=1. |
| 86 |
iarg=iargc() |
| 87 |
if (iarg.lt.1) then |
| 88 |
WRITE(*,*) "==============================================" |
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WRITE(*,*) "== ==" |
| 90 |
WRITE(*,*) "== Xyz2Scan: Xyz file to scan file ==" |
| 91 |
WRITE(*,*) "== ==" |
| 92 |
WRITE(*,*) "==============================================" |
| 93 |
WRITE(*,*) "Usage: xyz2scan XYZ_file " |
| 94 |
WRITE(*,*) "The XYZ file should follow the 'usual' format:" |
| 95 |
WRITE(*,*) "Number of atoms on the first line " |
| 96 |
WRITE(*,*) "Comment on the second line" |
| 97 |
WRITE(*,*) "The geometry is given in cartesian coordinates" |
| 98 |
WRITE(*,*) "with atom symbol and three coordinates:" |
| 99 |
WRITE(*,*) " C 0. 1. 0." |
| 100 |
WRITE(*,*) "" |
| 101 |
WRITE(*,*) " xyz2scan also needs a file called 'list' " |
| 102 |
WRITE(*,*) "which has the following structure:" |
| 103 |
WRITE(*,*) "Each line contains the type of the value you" |
| 104 |
WRITE(*,*) "want to follow, it can be:" |
| 105 |
WRITE(*,*) " - b for a Bond distance" |
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WRITE(*,*) " - a for an angle" |
| 107 |
WRITE(*,*) " - d for a dihedral" |
| 108 |
WRITE(*,*) " - p for the oriented angle between two planes" |
| 109 |
WRITE(*,*) "This descriptor is followed by the number of" |
| 110 |
WRITE(*,*) "the atoms involved" |
| 111 |
WRITE(*,*) "One can also create 'barycenter' atoms that" |
| 112 |
WRITE(*,*) "can then be used as normal atoms." |
| 113 |
WRITE(*,*) "the descriptor is 'c' followed by the number" |
| 114 |
WRITE(*,*) "of atoms and the list of atoms:" |
| 115 |
WRITE(*,*) " c 2 1 5" |
| 116 |
WRITE(*,*) "A typical file can be:" |
| 117 |
WRITE(*,*) " b 1 2" |
| 118 |
WRITE(*,*) " b 2 3" |
| 119 |
WRITE(*,*) " a 1 2 3" |
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WRITE(*,*) " " |
| 121 |
WRITE(*,*) "==============================================" |
| 122 |
write(*,*) 'XYZ filename:' |
| 123 |
read(*,'(a)') f1 |
| 124 |
else |
| 125 |
call getarg(1,f1) |
| 126 |
endif |
| 127 |
|
| 128 |
open(13,file='Scan.dat') |
| 129 |
|
| 130 |
INQUIRE(File='list',Exist=FExist) |
| 131 |
if (.NOT.FExist) THEN |
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WRITE(*,*) "File *list* is missing" |
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STOP |
| 134 |
END IF |
| 135 |
|
| 136 |
open(11,file=f1) |
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READ(11,*) nnn |
| 138 |
close(11) |
| 139 |
|
| 140 |
if (nnn.GT.MaxNat) THEN |
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WRITE(*,*) "Sorry but your system has too many atoms" |
| 142 |
WRITE(*,*) "Change the value of MaxNat in the source file" |
| 143 |
WRITE(*,*) "and then recompile." |
| 144 |
WRITE(*,*) "For information, now MaxNat=",MaxNat |
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WRITE(*,*) "and you have ",nnn," atoms." |
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STOP |
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END IF |
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|
| 149 |
open(14,file='list') |
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Type="d" |
| 151 |
DO WHILE (Type.ne."E") |
| 152 |
CALL READLINE(14,Type,Line) |
| 153 |
! WRITE(*,*) Line,Type |
| 154 |
if (Type.eq."b") THEN |
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NbDist=NbDist+1 |
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READ(Line,*) At1,At2 |
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At1B(NbDist)=At1 |
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At2B(NbDist)=At2 |
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END IF |
| 160 |
if (Type.eq."a") THEN |
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NbAngle=NbAngle+1 |
| 162 |
READ(Line,*) At1,At2,At3 |
| 163 |
At1A(NbAngle)=At1 |
| 164 |
At2A(NbAngle)=At2 |
| 165 |
At3A(NbAngle)=At3 |
| 166 |
END IF |
| 167 |
if (Type.eq."d") THEN |
| 168 |
NbDie=NbDie+1 |
| 169 |
READ(Line,*) At1,At2,At3,At4 |
| 170 |
At1D(NbDie)=At1 |
| 171 |
At2D(NbDie)=At2 |
| 172 |
At3D(NbDie)=At3 |
| 173 |
At4D(NbDie)=At4 |
| 174 |
! WRITE(13,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
| 175 |
! & Atoms(At3),At3,Atoms(At4),At4 |
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! WRITE(*,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
| 177 |
! & Atoms(At3),At3,Atoms(At4),At4 |
| 178 |
|
| 179 |
END IF |
| 180 |
if (Type.eq."p") THEN |
| 181 |
NbP=NbP+1 |
| 182 |
READ(Line,*) At1,At2,At3,At4,At5,At6 |
| 183 |
At1p(NbP)=At1 |
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At2p(NbP)=At2 |
| 185 |
At3p(NbP)=At3 |
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At4p(NbP)=At4 |
| 187 |
At5p(NbP)=At5 |
| 188 |
At6p(NbP)=At6 |
| 189 |
END IF |
| 190 |
|
| 191 |
if (Type.eq."c") THEN |
| 192 |
NbCOM=NbCOM+1 |
| 193 |
READ(Line,*) At1,(AtCom(j,NbCOM),j=1,At1) |
| 194 |
AtCom(0,NbCOM)=At1 |
| 195 |
Atoms(nat+NbCom)="G" |
| 196 |
END IF |
| 197 |
|
| 198 |
END DO |
| 199 |
|
| 200 |
CLOSE(14) |
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|
| 202 |
! We read one geoetry to get the atoms name |
| 203 |
open(11,file=f1) |
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call rtraitem(11,nnn,ener,geos,atoms) |
| 205 |
close(11) |
| 206 |
|
| 207 |
|
| 208 |
! We write things |
| 209 |
! First NbCom |
| 210 |
if (NbCom.GE.1) THEN |
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WRITE(*,*) "# Added center of mass" |
| 212 |
WRITE(IOOUT,*) "# Added center of mass" |
| 213 |
DO J=1,NbCom |
| 214 |
WRITE(IOOUT,'("# c ",I4,20(A3,I3))') AtCom(0,J),
|
| 215 |
& (Atoms(AtCom(i,J)),AtCom(i,J),i=1,At1) |
| 216 |
WRITE(*,'("# c ",I4,20(A3,I3))') AtCom(0,J),
|
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& (Atoms(AtCom(i,J)),AtCom(i,J),i=1,At1) |
| 218 |
END DO |
| 219 |
END IF |
| 220 |
|
| 221 |
! Distances |
| 222 |
if (NbDist.GE.1) THEN |
| 223 |
WRITE(*,*) "# Bonds" |
| 224 |
WRITE(IOOUT,*) "# Bonds" |
| 225 |
DO J=1,NbDist |
| 226 |
At1= At1B(J) |
| 227 |
At2=At2B(J) |
| 228 |
WRITE(IOOUT,'("# b ",2(A3,I3))') Atoms(At1),At1,
|
| 229 |
$ Atoms(At2),At2 |
| 230 |
WRITE(*,'("# b ",2(A3,I3))') Atoms(At1),At1,Atoms(At2),At2
|
| 231 |
END DO |
| 232 |
END IF |
| 233 |
|
| 234 |
! Angles |
| 235 |
if (NbAngle.GE.1) THEN |
| 236 |
WRITE(*,*) "# Angles" |
| 237 |
WRITE(IOOUT,*) "# Angles" |
| 238 |
DO J=1,NbAngle |
| 239 |
At1= At1A(J) |
| 240 |
At2= At2A(J) |
| 241 |
At3= At3A(J) |
| 242 |
WRITE(IOOUT,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),
|
| 243 |
& At2, Atoms(At3),At3 |
| 244 |
WRITE(*,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),
|
| 245 |
& At2, Atoms(At3),At3 |
| 246 |
|
| 247 |
END DO |
| 248 |
END IF |
| 249 |
|
| 250 |
|
| 251 |
! Dihedrals |
| 252 |
if (NbDie.GE.1) THEN |
| 253 |
WRITE(*,*) "# Dihedrals" |
| 254 |
WRITE(IOOUT,*) "# Dihedrals" |
| 255 |
DO J=1,NbDie |
| 256 |
At1= At1D(J) |
| 257 |
At2= At2D(J) |
| 258 |
At3= At3D(J) |
| 259 |
At4= At4D(J) |
| 260 |
WRITE(IOOUT,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2)
|
| 261 |
& ,At2,Atoms(At3),At3,Atoms(At4),At4 |
| 262 |
WRITE(*,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
| 263 |
& Atoms(At3),At3,Atoms(At4),At4 |
| 264 |
END DO |
| 265 |
END IF |
| 266 |
|
| 267 |
! Planar angles |
| 268 |
if (NbP.GE.1) THEN |
| 269 |
WRITE(*,*) "# Planes angles" |
| 270 |
WRITE(IOOUT,*) "# Planes angles" |
| 271 |
DO J=1,NbP |
| 272 |
At1= At1p(J) |
| 273 |
At2= At2p(J) |
| 274 |
At3= At3p(J) |
| 275 |
At4= At4p(J) |
| 276 |
At5= At5p(J) |
| 277 |
At6= At6p(J) |
| 278 |
WRITE(IOOUT,'("# p ",8(A3,I3))') Atoms(At1),At1,Atoms(At2)
|
| 279 |
& ,At2,Atoms(At3),At3,Atoms(At4),At4 |
| 280 |
& ,Atoms(At5),At5,Atoms(At6),At6 |
| 281 |
WRITE(*,'("# p ",8(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
| 282 |
& Atoms(At3),At3,Atoms(At4),At4 |
| 283 |
& ,Atoms(At5),At5,Atoms(At6),At6 |
| 284 |
END DO |
| 285 |
END IF |
| 286 |
|
| 287 |
|
| 288 |
fmt='( (1X,F12.5),1X,F15.6)' |
| 289 |
write(fmt(2:4),'(i3)') NbDist+NbAngle+NbDie+NbP |
| 290 |
! write(*,*) nat3 |
| 291 |
! write(*,*) 'fmt:',fmt |
| 292 |
|
| 293 |
ng=1 |
| 294 |
|
| 295 |
open(11,file=f1) |
| 296 |
|
| 297 |
10 call rtraitem(11,nnn,ener,geos,atoms) |
| 298 |
! WRITE(*,*) nnn |
| 299 |
|
| 300 |
if (nnn.gt.0) then |
| 301 |
! We convert coordinates in a0 into Angstroem |
| 302 |
! write(*,*) "Analyse !" |
| 303 |
Call Analyse(geos) |
| 304 |
|
| 305 |
write(IOOUT,fmt) (VB(j)/Conv,j=1,NbDist), |
| 306 |
& (VA(j),j=1,NbAngle), |
| 307 |
& (VD(j),j=1,NbDie),(Vp(j),j=1,NbP),ener |
| 308 |
write(*,fmt) (VB(j)/Conv,j=1,NbDist), |
| 309 |
& (VA(j),j=1,NbAngle), |
| 310 |
& (VD(j),j=1,NbDie),(Vp(j),j=1,NbP),ener |
| 311 |
|
| 312 |
ng=ng+1 |
| 313 |
goto 10 |
| 314 |
endif |
| 315 |
WRITE(*,*) 'Found ',ng-1,' geometries' |
| 316 |
close(11) |
| 317 |
end |
| 318 |
|
| 319 |
!-------------------------------------------------------------- |
| 320 |
subroutine rtraitem(ifil,nnn,E,tab,atoms) |
| 321 |
! implicit real*8 (a-h,o-z) |
| 322 |
IMPLICIT NONE |
| 323 |
character*120 line |
| 324 |
character*3 Atoms(*) |
| 325 |
integer*4 nnn, IFil, Idx, I, J |
| 326 |
REAL*8 Tab(3,*), E |
| 327 |
|
| 328 |
|
| 329 |
read(ifil,*,err=99,end=99) nnn |
| 330 |
read(ifil,'(A)') line |
| 331 |
idx=index(line,'E') |
| 332 |
! WRITE(*,*) 'idx,line',idx,line |
| 333 |
if (idx/=0) THEN |
| 334 |
line=line(idx+2:) |
| 335 |
idx=index(line,"=") |
| 336 |
if (idx/=0) line=line(idx+1:) |
| 337 |
idx=index(line,":") |
| 338 |
if (idx/=0) line=line(idx+1:) |
| 339 |
read(line,*) E |
| 340 |
ELSE |
| 341 |
E=0. |
| 342 |
END IF |
| 343 |
|
| 344 |
! write(*,*) 'coucou',line |
| 345 |
do i=1,nnn |
| 346 |
read(ifil,'(A)',err=99,end=99) Line |
| 347 |
do while (line(1:1)==' ') |
| 348 |
line=line(2:) |
| 349 |
end do |
| 350 |
atoms(i)=line(1:3) |
| 351 |
! write(*,*) 'coucou atoms',atoms(i) |
| 352 |
do while (line(1:1).ne.' ') |
| 353 |
line=line(2:) |
| 354 |
end do |
| 355 |
! WRITE(*,*) 'coucou2:',i,line |
| 356 |
read(line,*) (tab(j,i),j=1,3) |
| 357 |
end do |
| 358 |
! WRITE(*,*) 'coucou:',nnn,tab(1,1) |
| 359 |
return |
| 360 |
99 nnn=0 |
| 361 |
! WRITE(*,*) 'Erreur lecture',ifil,nnn |
| 362 |
return |
| 363 |
end |
| 364 |
|
| 365 |
!-------------------------------------------------------------- |
| 366 |
|
| 367 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 368 |
! READLINE |
| 369 |
! This subroutine reads a line for a file, and converts |
| 370 |
! the first field into a character variable, and the rest into 4 integers |
| 371 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 372 |
|
| 373 |
SUBROUTINE READLINE(IOIN,Type,Line) |
| 374 |
|
| 375 |
IMPLICIT NONE |
| 376 |
CHARACTER Type*5,LINE*120 |
| 377 |
INTEGER i,IOIN |
| 378 |
READ(IOIN,'(A120)',ERR=999,END=999) LINE |
| 379 |
! WRITE(*,*) Line |
| 380 |
DO WHILE (LINE(1:1).eq.' ') |
| 381 |
LINE=LINE(2:) |
| 382 |
END DO |
| 383 |
|
| 384 |
i=1 |
| 385 |
DO WHILE (LINE(i:i).ne.' ') |
| 386 |
i=i+1 |
| 387 |
END DO |
| 388 |
|
| 389 |
if (i.ge.6) THEN |
| 390 |
WRITE(*,*) 'Pb with READLINE:',LINE |
| 391 |
GOTO 999 |
| 392 |
END IF |
| 393 |
Type=LINE(1:i-1) |
| 394 |
LINE=LINE(i:120) // " 0 0 0 0" |
| 395 |
|
| 396 |
RETURN |
| 397 |
999 Type="E" |
| 398 |
END |
| 399 |
|
| 400 |
|
| 401 |
|
| 402 |
SUBROUTINE Analyse(geos) |
| 403 |
|
| 404 |
IMPLICIT NONE |
| 405 |
INTEGER*4 MaxNat,MaxList |
| 406 |
parameter (maxnat=10000,MaxList=100) |
| 407 |
REAL*8 geos(3,maxnat) |
| 408 |
REAL*8 AU2PS,Pi |
| 409 |
INTEGER*4 i,j,k |
| 410 |
REAL*8 V1x,V1y,V1z,V2x,V2y,V2z,V3x,V3y,V3z |
| 411 |
REAL*8 d1,d2,ca,sa |
| 412 |
REAL*8 V4x,v4y,v4z,v5x,v5y,v5z |
| 413 |
REAL*8 COG(3) |
| 414 |
|
| 415 |
INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbP,NbCOM |
| 416 |
INTEGER*4 At1B(MaxList),At2B(MaxList) |
| 417 |
INTEGER*4 At1A(MaxList),At2A(MaxList),At3A(MaxList) |
| 418 |
INTEGER*4 At1D(MaxList),At2D(MaxList),At3D(MaxList), |
| 419 |
$ At4D(MaxList) |
| 420 |
INTEGER*4 At1p(MaxList),At2p(MaxList),At3p(MaxList), |
| 421 |
$ At4p(MaxList),At5p(MaxList),At6p(MaxList) |
| 422 |
INTEGER*4 AtCom(0:MaxList,MaxList) |
| 423 |
REAL*8 VB(MaxList),VA(MaxList),VD(MaxList),VCOM(MaxList) |
| 424 |
REAL*8 Vp(MaxList) |
| 425 |
|
| 426 |
COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbP,NbCom, At1B,At2B, |
| 427 |
& At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom, |
| 428 |
& At1p,At2p,At3p,At4p,At5p,At6p |
| 429 |
COMMON /Values/VB,VA,VD,Vp,VCom |
| 430 |
COMMON /Const/AU2ps,Pi |
| 431 |
|
| 432 |
DO I=1,Nat |
| 433 |
WRITE(*,'(1X,I3,3(1X,F15.6))') i,(geos(j,i),j=1,3) |
| 434 |
END DO |
| 435 |
|
| 436 |
! First, we create the Centre of Mass atoms |
| 437 |
DO i=1,NbCOM |
| 438 |
COG(1)=0. |
| 439 |
COG(2)=0. |
| 440 |
COG(3)=0. |
| 441 |
DO j=1,AtCOm(0,i) |
| 442 |
DO k=1,3 |
| 443 |
COG(k)=COG(k)+geos(k,AtCom(j,i)) |
| 444 |
END DO |
| 445 |
END DO |
| 446 |
DO k=1,3 |
| 447 |
COG(k)=COG(k)/AtCOM(0,i) |
| 448 |
geos(k,Nat+i)=COG(k) |
| 449 |
END DO |
| 450 |
END DO |
| 451 |
|
| 452 |
|
| 453 |
DO i=1,NbDist |
| 454 |
VB(i)=sqrt((geos(1,At1B(i))-geos(1,At2B(i)))**2+ |
| 455 |
& (geos(2,At1B(i))-geos(2,At2B(i)))**2+ |
| 456 |
& (geos(3,At1B(i))-geos(3,At2B(i)))**2) |
| 457 |
END DO |
| 458 |
DO i=1,NbAngle |
| 459 |
v1x=geos(1,At1A(i))-geos(1,At2A(i)) |
| 460 |
v1y=geos(2,At1A(i))-geos(2,At2A(i)) |
| 461 |
v1z=geos(3,At1A(i))-geos(3,At2A(i)) |
| 462 |
d1=sqrt(v1x**2+v1y**2+v1z**2) |
| 463 |
v2x=geos(1,At3A(i))-geos(1,At2A(i)) |
| 464 |
v2y=geos(2,At3A(i))-geos(2,At2A(i)) |
| 465 |
v2z=geos(3,At3A(i))-geos(3,At2A(i)) |
| 466 |
d2=sqrt(v2x**2+v2y**2+v2z**2) |
| 467 |
VA(i)=acos((v1x*v2x+v1y*v2y+v1z*v2z)/(d1*d2))*180./Pi |
| 468 |
END DO |
| 469 |
DO i=1,NbDie |
| 470 |
! WRITE(*,*) At1D(i),At2D(i),At3D(i),At4D(i) |
| 471 |
! WRITE(*,*) geos(1,At1D(i)),geos(2,At1D(i)),geos(3,At1D(i)) |
| 472 |
! WRITE(*,*) geos(1,At2D(i)),geos(2,At2D(i)),geos(3,At2D(i)) |
| 473 |
v1x=geos(1,At1D(i))-geos(1,At2D(i)) |
| 474 |
v1y=geos(2,At1D(i))-geos(2,At2D(i)) |
| 475 |
v1z=geos(3,At1D(i))-geos(3,At2D(i)) |
| 476 |
v2x=geos(1,At3D(i))-geos(1,At2D(i)) |
| 477 |
v2y=geos(2,At3D(i))-geos(2,At2D(i)) |
| 478 |
v2z=geos(3,At3D(i))-geos(3,At2D(i)) |
| 479 |
v3x=geos(1,At4D(i))-geos(1,At3D(i)) |
| 480 |
v3y=geos(2,At4D(i))-geos(2,At3D(i)) |
| 481 |
v3z=geos(3,At4D(i))-geos(3,At3D(i)) |
| 482 |
|
| 483 |
v4x=v1y*v2z-v1z*v2y |
| 484 |
v4y=v1z*v2x-v1x*v2z |
| 485 |
v4z=v1x*v2y-v1y*v2x |
| 486 |
d1=sqrt(v4x**2+v4y**2+v4z**2) |
| 487 |
v5x=-v2y*v3z+v2z*v3y |
| 488 |
v5y=-v2z*v3x+v2x*v3z |
| 489 |
v5z=-v2x*v3y+v2y*v3x |
| 490 |
d2=sqrt(v5x**2+v5y**2+v5z**2) |
| 491 |
if (d1<=1e-12) THEN |
| 492 |
WRITE(*,*) "WARNING: Dihedral, d1=0" |
| 493 |
ca=-1. |
| 494 |
sa=0. |
| 495 |
END IF |
| 496 |
if (d2<=1e-12) THEN |
| 497 |
WRITE(*,*) "WARNING: Dihedral, d2=0" |
| 498 |
ca=-1. |
| 499 |
sa=0. |
| 500 |
END IF |
| 501 |
ca=(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2) |
| 502 |
sa=v1x*v5x+v1y*v5y+v1z*v5z |
| 503 |
if (abs(ca)>1.) ca=sign(1.d0,ca) |
| 504 |
VD(i)=acos(ca)*180./Pi |
| 505 |
if (sa<0.) VD(i)=-VD(i) |
| 506 |
! WRITE(*,*) "Dihe",v5x,v5y,v5z,v4x,v4y,v4z,d1,d2, |
| 507 |
! &(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2),pi |
| 508 |
! WRITE(*,*) "Dihe ca,sa,d1,d2",ca,sa,d1,d2,acos(ca) |
| 509 |
|
| 510 |
|
| 511 |
!!!!!!!!! Another solution, more elegant ? |
| 512 |
! norm2=sqrt(v2x**2+v2y**2+v2z**2) |
| 513 |
! sa=(v4x*(v5y*v2z-v5z*v2y) |
| 514 |
! * -v4y*(v5x*v2z-v5z*v2x) |
| 515 |
! * +v4z*(v5x*v2y-v5y*v2x)) |
| 516 |
! * /(d1*norm2*d2) |
| 517 |
! angle_d=datan2(sa,ca)*180./Pi |
| 518 |
! WRITE(*,*) sa,ca,angle_d,d1,d2,norm2 |
| 519 |
! WRITE(*,*) VD(i),angle_d |
| 520 |
END DO |
| 521 |
|
| 522 |
DO i=1,NbP |
| 523 |
! v1= At2-At1 |
| 524 |
v1x=geos(1,At1p(i))-geos(1,At2p(i)) |
| 525 |
v1y=geos(2,At1p(i))-geos(2,At2p(i)) |
| 526 |
v1z=geos(3,At1p(i))-geos(3,At2p(i)) |
| 527 |
! v2=At2-At3 |
| 528 |
v2x=geos(1,At3p(i))-geos(1,At2p(i)) |
| 529 |
v2y=geos(2,At3p(i))-geos(2,At2p(i)) |
| 530 |
v2z=geos(3,At3p(i))-geos(3,At2p(i)) |
| 531 |
! v4 = v1 x v2 |
| 532 |
v4x=v1y*v2z-v1z*v2y |
| 533 |
v4y=v1z*v2x-v1x*v2z |
| 534 |
v4z=v1x*v2y-v1y*v2x |
| 535 |
d1=sqrt(v4x**2+v4y**2+v4z**2) |
| 536 |
|
| 537 |
! v3= At5-At4 |
| 538 |
v3x=geos(1,At4p(i))-geos(1,At5p(i)) |
| 539 |
v3y=geos(2,At4p(i))-geos(2,At5p(i)) |
| 540 |
v3z=geos(3,At4p(i))-geos(3,At5p(i)) |
| 541 |
! v2=At5-At6 |
| 542 |
v2x=geos(1,At6p(i))-geos(1,At5p(i)) |
| 543 |
v2y=geos(2,At6p(i))-geos(2,At5p(i)) |
| 544 |
v2z=geos(3,At6p(i))-geos(3,At5p(i)) |
| 545 |
|
| 546 |
! v5 = v3 x v2 |
| 547 |
v5x=v3y*v2z-v3z*v2y |
| 548 |
v5y=v3z*v2x-v3x*v2z |
| 549 |
v5z=v3x*v2y-v3y*v2x |
| 550 |
d2=sqrt(v5x**2+v5y**2+v5z**2) |
| 551 |
|
| 552 |
ca=(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2) |
| 553 |
sa=v1x*v5x+v1y*v5y+v1z*v5z |
| 554 |
Vp(i)=acos(ca)*180./Pi |
| 555 |
if (sa<0.) Vp(i)=-Vp(i) |
| 556 |
! WRITE(*,*) "Dihe",v5x,v5y,v5z,v4x,v4y,v4z,d1,d2, |
| 557 |
! &(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2),pi |
| 558 |
!!!!!!!!! Another solution, more elegant ? |
| 559 |
! See Dihedral routine |
| 560 |
END DO |
| 561 |
|
| 562 |
|
| 563 |
END |