root / src / Calc_baker.f90
Historique | Voir | Annoter | Télécharger (42,05 ko)
| 1 |
SUBROUTINE Calc_baker(atome,r_cov,fact,frozen,IGeomRef) |
|---|---|
| 2 |
! |
| 3 |
! This subroutine analyses a geometry to construct the baker |
| 4 |
! delocalized internal coordinates |
| 5 |
! v1.0 |
| 6 |
! We use only one geometry |
| 7 |
! |
| 8 |
|
| 9 |
!---------------------------------------------------------------------- |
| 10 |
! Copyright 2003-2014 Ecole Normale Supérieure de Lyon, |
| 11 |
! Centre National de la Recherche Scientifique, |
| 12 |
! Université Claude Bernard Lyon 1. All rights reserved. |
| 13 |
! |
| 14 |
! This work is registered with the Agency for the Protection of Programs |
| 15 |
! as IDDN.FR.001.100009.000.S.P.2014.000.30625 |
| 16 |
! |
| 17 |
! Authors: P. Fleurat-Lessard, P. Dayal |
| 18 |
! Contact: optnpath@gmail.com |
| 19 |
! |
| 20 |
! This file is part of "Opt'n Path". |
| 21 |
! |
| 22 |
! "Opt'n Path" is free software: you can redistribute it and/or modify |
| 23 |
! it under the terms of the GNU Affero General Public License as |
| 24 |
! published by the Free Software Foundation, either version 3 of the License, |
| 25 |
! or (at your option) any later version. |
| 26 |
! |
| 27 |
! "Opt'n Path" is distributed in the hope that it will be useful, |
| 28 |
! but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 29 |
! |
| 30 |
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 31 |
! GNU Affero General Public License for more details. |
| 32 |
! |
| 33 |
! You should have received a copy of the GNU Affero General Public License |
| 34 |
! along with "Opt'n Path". If not, see <http://www.gnu.org/licenses/>. |
| 35 |
! |
| 36 |
! Contact The Office of Technology Licensing, valorisation@ens-lyon.fr, |
| 37 |
! for commercial licensing opportunities. |
| 38 |
!---------------------------------------------------------------------- |
| 39 |
Use Path_module, only : max_Z,NMaxL,Pi,Massat,BMat_BakerT, & |
| 40 |
Nat,NCoord,XyzGeomI,NGeomI,NGeomF,UMat,NPrim,BTransInv, & |
| 41 |
IntCoordI,Coordinate,CurrentCoord,ScanCoord,BprimT,BBT, & |
| 42 |
BBT_inv,Xprimitive,XPrimitiveF,UMat_local, & |
| 43 |
BTransInv_local, UMatF,BTransInvF, & |
| 44 |
indzmat, dzdc,renum,order,OrderInv |
| 45 |
! BMat_BakerT(3*Nat,NCoord), NCoord=3*Nat or NFree=3*Nat-6-Symmetry_elimination |
| 46 |
! depending upon the coordinate choice. IntCoordI(NGeomI,NCoord) where |
| 47 |
! UMat(NPrim,NCoord), NCoord number of vectors in UMat matrix, i.e. NCoord |
| 48 |
! Baker coordinates. NPrim is the number of primitive internal coordinates. |
| 49 |
|
| 50 |
Use Io_module |
| 51 |
IMPLICIT NONE |
| 52 |
|
| 53 |
! IGeom: Geometry index, IGeomRef: Reference Geometry. |
| 54 |
INTEGER(KINT), INTENT(IN) :: atome(Nat),IGeomRef |
| 55 |
REAL(KREAL), INTENT(IN) :: fact |
| 56 |
REAL(KREAL), INTENT(IN) :: r_cov(0:Max_Z) |
| 57 |
! Frozen contains the indices of frozen atoms |
| 58 |
INTEGER(KINT), INTENT(IN) :: Frozen(*) |
| 59 |
|
| 60 |
INTEGER(KINT), ALLOCATABLE :: LIAISONS(:,:) ! (Nat,0:NMaxL) |
| 61 |
REAL(KREAL), ALLOCATABLE :: Geom(:,:) !(3,Nat) |
| 62 |
! NPrim is the number of primitive coordinates and NCoord is the number |
| 63 |
! of internal coordinates. BMat is actually (NPrim,3*Nat). |
| 64 |
REAL(KREAL), ALLOCATABLE :: GMat(:,:) !(NPrim,NPrim) |
| 65 |
! EigVec(..) contains ALL eigevectors of BMat times BprimT, NOT only Baker Coordinate vectors. |
| 66 |
REAL(KREAL), ALLOCATABLE :: EigVec(:,:), EigVal(:) ! EigVec(NPrim,NPrim) |
| 67 |
REAL(KREAL), ALLOCATABLE :: x(:), y(:), z(:) |
| 68 |
REAL(KREAL), ALLOCATABLE :: x_refGeom(:), y_refGeom(:), z_refGeom(:) |
| 69 |
!REAL(KREAL), ALLOCATABLE :: V(:,:) ! (3*Nat,3*Nat) |
| 70 |
!REAL(KREAL), ALLOCATABLE :: P(:) ! Used in Baker Coordinates: Matrix Inversion |
| 71 |
REAL(KREAL), ALLOCATABLE :: UMat_tmp(:,:) |
| 72 |
INTEGER(KINT) :: NbBonds, NbAngles, NbDihedrals, IGeom |
| 73 |
|
| 74 |
real(KREAL) :: vx, vy, vz, Norm |
| 75 |
real(KREAL) :: vx1,vy1,vz1,norm1 |
| 76 |
real(KREAL) :: vx2,vy2,vz2,norm2 |
| 77 |
real(KREAL) :: vx3,vy3,vz3,norm3 |
| 78 |
real(KREAL) :: vx4,vy4,vz4,norm4 |
| 79 |
real(KREAL) :: vx5,vy5,vz5,norm5 |
| 80 |
|
| 81 |
INTEGER(KINT) :: I, J, IAt, K |
| 82 |
INTEGER(KINT) :: Kat, Lat, L |
| 83 |
|
| 84 |
REAL(KREAL) :: sAngleIatIKat, sAngleIIatLat |
| 85 |
|
| 86 |
LOGICAL :: debug, bond, AddPrimitiveCoord |
| 87 |
|
| 88 |
INTERFACE |
| 89 |
function valid(string) result (isValid) |
| 90 |
CHARACTER(*), intent(in) :: string |
| 91 |
logical :: isValid |
| 92 |
END function VALID |
| 93 |
|
| 94 |
|
| 95 |
FUNCTION angle(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2) |
| 96 |
use Path_module, only : Pi,KINT, KREAL |
| 97 |
real(KREAL) :: v1x,v1y,v1z,norm1 |
| 98 |
real(KREAL) :: v2x,v2y,v2z,norm2 |
| 99 |
real(KREAL) :: angle |
| 100 |
END FUNCTION ANGLE |
| 101 |
|
| 102 |
|
| 103 |
|
| 104 |
FUNCTION angle_d(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2,v3x,v3y,v3z,norm3) |
| 105 |
use Path_module, only : Pi,KINT, KREAL |
| 106 |
real(KREAL) :: v1x,v1y,v1z,norm1 |
| 107 |
real(KREAL) :: v2x,v2y,v2z,norm2 |
| 108 |
real(KREAL) :: v3x,v3y,v3z,norm3 |
| 109 |
real(KREAL) :: angle_d,ca,sa |
| 110 |
END FUNCTION ANGLE_D |
| 111 |
|
| 112 |
|
| 113 |
|
| 114 |
|
| 115 |
SUBROUTINE Calc_Xprim(nat,x,y,z,Coordinate,NPrim,XPrimitive,XPrimRef) |
| 116 |
! |
| 117 |
! This subroutine uses the description of a list of Coordinates |
| 118 |
! to compute the values of the coordinates for a given geometry. |
| 119 |
! |
| 120 |
!!!!!!!!!! |
| 121 |
! Input: |
| 122 |
! Na: INTEGER, Number of atoms |
| 123 |
! x,y,z(Na): REAL, cartesian coordinates of the considered geometry |
| 124 |
! Coordinate (Pointer(ListCoord)): description of the wanted coordiantes |
| 125 |
! NPrim, INTEGER: Number of coordinates to compute |
| 126 |
! |
| 127 |
! Optional: XPrimRef(NPrim) REAL: array that contains coordinates values for |
| 128 |
! a former geometry. Useful for Dihedral angles evolution... |
| 129 |
|
| 130 |
!!!!!!!!!!! |
| 131 |
! Output: |
| 132 |
! XPrimimite(NPrim) REAL: array that will contain the values of the coordinates |
| 133 |
! |
| 134 |
!!!!!!!!! |
| 135 |
|
| 136 |
Use VarTypes |
| 137 |
Use Io_module |
| 138 |
Use Path_module, only : pi |
| 139 |
|
| 140 |
IMPLICIT NONE |
| 141 |
|
| 142 |
Type (ListCoord), POINTER :: Coordinate |
| 143 |
INTEGER(KINT), INTENT(IN) :: Nat,NPrim |
| 144 |
REAL(KREAL), INTENT(IN) :: x(Nat), y(Nat), z(Nat) |
| 145 |
REAL(KREAL), INTENT(IN), OPTIONAL :: XPrimRef(NPrim) |
| 146 |
REAL(KREAL), INTENT(OUT) :: XPrimitive(NPrim) |
| 147 |
|
| 148 |
END SUBROUTINE CALC_XPRIM |
| 149 |
END INTERFACE |
| 150 |
|
| 151 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 152 |
! |
| 153 |
!!!!!!!! PFL Debug |
| 154 |
! |
| 155 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
| 156 |
INTEGER(KINT) :: I1,I2,I3,I4 |
| 157 |
LOGICAL :: debugPFL |
| 158 |
REAL(KREAL), ALLOCATABLE :: val_zmat(:,:) |
| 159 |
INTEGER(KINT), ALLOCATABLE :: indzmat0(:,:) |
| 160 |
|
| 161 |
|
| 162 |
debug=valid("Calc_baker")
|
| 163 |
debugPFL=valid("BakerPFL")
|
| 164 |
|
| 165 |
if (debug) Call Header(" Entering Cal_baker ")
|
| 166 |
|
| 167 |
IF (Nat.le.2) THEN |
| 168 |
WRITE(*,*) "I do not work for less than 2 atoms :-p" |
| 169 |
RETURN |
| 170 |
END IF |
| 171 |
|
| 172 |
IF (debug) THEN |
| 173 |
WRITE(*,*) "DBG Calc_baker, geom" |
| 174 |
DO I=1,Nat |
| 175 |
WRITE(*,'(1X,I5,":",I3,3(1X,F15.3))') I,atome(I),XyzGeomI(IGeomRef,1:3,I) |
| 176 |
END DO |
| 177 |
END IF |
| 178 |
|
| 179 |
|
| 180 |
|
| 181 |
|
| 182 |
! we construct the list of bonds, valence angles and dihedral angles using this connectivity |
| 183 |
ALLOCATE(Coordinate) |
| 184 |
NULLIFY(Coordinate%next) |
| 185 |
NbBonds=0 |
| 186 |
NbAngles=0 |
| 187 |
NbDihedrals=0 |
| 188 |
|
| 189 |
CurrentCoord => Coordinate |
| 190 |
|
| 191 |
ALLOCATE(Liaisons(Nat,0:NMaxL),Geom(3,Nat),x(Nat),y(Nat),z(Nat)) |
| 192 |
ALLOCATE(x_refGeom(Nat),y_refGeom(Nat),z_refGeom(Nat)) |
| 193 |
|
| 194 |
x_refGeom(1:Nat) = XyzGeomI(IGeomRef,1,1:Nat) |
| 195 |
y_refGeom(1:Nat) = XyzGeomI(IGeomRef,2,1:Nat) |
| 196 |
z_refGeom(1:Nat) = XyzGeomI(IGeomRef,3,1:Nat) |
| 197 |
|
| 198 |
!!!!!!!!!!!!!!!!!!!! |
| 199 |
! |
| 200 |
! PFL Debug |
| 201 |
! |
| 202 |
!!!!!!!!!!!!!!!!!!!! |
| 203 |
if (debugPFL) THEN |
| 204 |
WRITE(*,*) "DBG PFL Calc_BAKER - Calculating Zmat" |
| 205 |
if (.not.ALLOCATED(indzmat)) THEN |
| 206 |
ALLOCATE(indzmat(Nat,5)) |
| 207 |
END IF |
| 208 |
IF (.NOT.ALLOCATED(DzDc)) THEN |
| 209 |
ALLOCATE(DzDc(3,nat,3,Nat)) |
| 210 |
END IF |
| 211 |
IF (.NOT.ALLOCATED(Val_zmat)) THEN |
| 212 |
ALLOCATE(val_zmat(nat,3)) |
| 213 |
END IF |
| 214 |
IF (.NOT.ALLOCATED(indzmat0)) THEN |
| 215 |
ALLOCATE(indzmat0(nat,5)) |
| 216 |
END IF |
| 217 |
! We construct a Zmat |
| 218 |
IF (Frozen(1).NE.0) THEN |
| 219 |
Renum=.TRUE. |
| 220 |
!!! remplcaer indzmat par indzmat0 puis renumerotation |
| 221 |
call Calc_zmat_const_frag(Nat,atome,IndZmat0,val_zmat, & |
| 222 |
x_refGeom,y_refGeom,z_refGeom, & |
| 223 |
r_cov,fact,frozen) |
| 224 |
ELSE |
| 225 |
!no zmat... we create our own |
| 226 |
call Calc_zmat_frag(Nat,atome,IndZmat0,val_zmat, & |
| 227 |
x_refGeom,y_refGeom,z_refGeom, & |
| 228 |
r_cov,fact) |
| 229 |
END IF |
| 230 |
|
| 231 |
DO I=1,Nat |
| 232 |
Order(IndZmat0(I,1))=I |
| 233 |
OrderInv(I)=IndZmat0(I,1) |
| 234 |
END DO |
| 235 |
IndZmat(1,1)=Order(IndZmat0(1,1)) |
| 236 |
IndZmat(2,1)=Order(IndZmat0(2,1)) |
| 237 |
IndZmat(2,2)=Order(IndZmat0(2,2)) |
| 238 |
IndZmat(3,1)=Order(IndZmat0(3,1)) |
| 239 |
IndZmat(3,2)=Order(IndZmat0(3,2)) |
| 240 |
IndZmat(3,3)=Order(IndZmat0(3,3)) |
| 241 |
DO I=4,Nat |
| 242 |
DO J=1,4 |
| 243 |
IndZmat(I,J)=Order(IndZmat0(I,J)) |
| 244 |
END DO |
| 245 |
end do |
| 246 |
|
| 247 |
|
| 248 |
WRITE(*,*) "DBG PFL CalcBaker, IndZmat0" |
| 249 |
DO I=1,Nat |
| 250 |
WRITE(*,*) I, indZmat0(I,:) |
| 251 |
end do |
| 252 |
|
| 253 |
WRITE(*,*) "DBG PFL CalcBaker, IndZmat" |
| 254 |
DO I=1,Nat |
| 255 |
WRITE(*,*) I, indZmat(I,:) |
| 256 |
end do |
| 257 |
|
| 258 |
|
| 259 |
DO I=1,Nat |
| 260 |
I1=indzmat0(I,1) |
| 261 |
I2=indzmat0(I,2) |
| 262 |
I3=indzmat0(I,3) |
| 263 |
I4=indzmat0(I,4) |
| 264 |
! Adding BOND between at1 and at2 |
| 265 |
WRITE(*,*) "DBG Indzmat",I,I1,I2,I3,I4 |
| 266 |
if (I2.NE.0) THEN |
| 267 |
NbBonds=NbBonds+1 |
| 268 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 269 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) |
| 270 |
! are determined using all geometries. vecteur is defined in bib_oper.f |
| 271 |
Call vecteur(I1,I2,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 272 |
! CurrentCoord%value=Norm2 |
| 273 |
WRITE(*,'(1X,A,I5,A,2(1X,F12.6))') "Bond",NbBonds," Norm2,val_zmat",Norm2,val_zmat(I,1) |
| 274 |
CurrentCoord%value=val_zmat(I,1) |
| 275 |
CurrentCoord%SignDihedral = 0 |
| 276 |
CurrentCoord%At1=I1 |
| 277 |
CurrentCoord%At2=I2 |
| 278 |
CurrentCoord%Type="BOND" |
| 279 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 280 |
ALLOCATE(CurrentCoord%next) |
| 281 |
NULLIFY(CurrentCoord%next%next) |
| 282 |
END IF |
| 283 |
CurrentCoord => CurrentCoord%next |
| 284 |
END IF !IE.NE.0 |
| 285 |
if (I3.NE.0) THEN |
| 286 |
|
| 287 |
NbAngles=NbAngles+1 |
| 288 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 289 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
| 290 |
! determined using all geometries. |
| 291 |
Call vecteur(i2,I3,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 292 |
Call vecteur(i2,I1,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 293 |
! CurrentCoord%value=angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 294 |
WRITE(*,'(1X,A,I5,A,2(1X,F12.6))') "Angle",NbAngles," angle,val_zmat", & |
| 295 |
angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2),val_zmat(I,2) |
| 296 |
CurrentCoord%value=val_zmat(I,2)*Pi/180. |
| 297 |
CurrentCoord%SignDihedral = 0 |
| 298 |
CurrentCoord%At1=I1 |
| 299 |
CurrentCoord%At2=I2 |
| 300 |
CurrentCoord%At3=I3 |
| 301 |
CurrentCoord%Type="ANGLE" |
| 302 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 303 |
ALLOCATE(CurrentCoord%next) |
| 304 |
NULLIFY(CurrentCoord%next%next) |
| 305 |
END IF |
| 306 |
CurrentCoord => CurrentCoord%next |
| 307 |
END IF ! matches IF (I3.NE.0) |
| 308 |
if (I4.NE.0) THEN |
| 309 |
NbDihedrals=NbDihedrals+1 |
| 310 |
Call vecteur(I2,I1,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 311 |
Call vecteur(I2,I3,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 312 |
Call vecteur(I3,I4,x_refGeom,y_refGeom,z_refGeom,vx3,vy3,vz3,Norm3) |
| 313 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 314 |
vx4,vy4,vz4,norm4) |
| 315 |
CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, & |
| 316 |
vx5,vy5,vz5,norm5) |
| 317 |
! CurrentCoord%value=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 318 |
! vx2,vy2,vz2,norm2)*Pi/180. |
| 319 |
WRITE(*,'(1X,A,I5,A,2(1X,F12.6))') "Dihedral",NbDihedrals, & |
| 320 |
" angle_d,val_zmat", & |
| 321 |
angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 322 |
vx2,vy2,vz2,norm2) & |
| 323 |
,val_zmat(I,3) |
| 324 |
|
| 325 |
CurrentCoord%value = val_zmat(I,3)*Pi/180. |
| 326 |
CurrentCoord%SignDihedral = int(sign(1.D0,val_zmat(I,3))) |
| 327 |
CurrentCoord%At1=I1 |
| 328 |
CurrentCoord%At2=I2 |
| 329 |
CurrentCoord%At3=I3 |
| 330 |
CurrentCoord%At4=I4 |
| 331 |
CurrentCoord%Type="DIHEDRAL" |
| 332 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 333 |
ALLOCATE(CurrentCoord%next) |
| 334 |
NULLIFY(CurrentCoord%next%next) |
| 335 |
END IF |
| 336 |
CurrentCoord => CurrentCoord%next |
| 337 |
END IF ! matches IF (I4.NE.0) |
| 338 |
END DO ! matches DO I=1,Nat |
| 339 |
deallocate(indzmat0) |
| 340 |
|
| 341 |
ELSE !! if (debugPFL) |
| 342 |
|
| 343 |
DO IGeom=1, NGeomI |
| 344 |
!IGeom=1 ! need when using only first geometry. |
| 345 |
x(1:Nat) = XyzGeomI(IGeom,1,1:Nat) |
| 346 |
y(1:Nat) = XyzGeomI(IGeom,2,1:Nat) |
| 347 |
z(1:Nat) = XyzGeomI(IGeom,3,1:Nat) |
| 348 |
|
| 349 |
! First step: we calculate the connectivity |
| 350 |
Liaisons=0 |
| 351 |
|
| 352 |
Call CalcCnct(Nat,atome,x,y,z,LIAISONS,r_cov,fact) |
| 353 |
|
| 354 |
IF (debug) THEN |
| 355 |
WRITE(*,*) 'Connectivity done' |
| 356 |
DO I=1,Nat |
| 357 |
WRITE(*,'(1X,I5,":",I3,"=",15I4)') I,(Liaisons(I,J),J=0,NMaxL) |
| 358 |
WRITE(*,'(1X,I5,":",I3,"=",15I4)') I,(Liaisons(I,:)) |
| 359 |
END DO |
| 360 |
DO I=1,Nat |
| 361 |
WRITE(*,'(1X,I5,":",I3," r_cov=",F15.6)') I,atome(I),r_cov(atome(I)) |
| 362 |
END DO |
| 363 |
END IF |
| 364 |
|
| 365 |
DO I=1,Nat |
| 366 |
IF (Liaisons(I,0).NE.0) THEN |
| 367 |
DO J=1,Liaisons(I,0) |
| 368 |
! We add the bond |
| 369 |
Iat=Liaisons(I,J) |
| 370 |
IF (Iat.GT.I) THEN |
| 371 |
! Checking the uniqueness of bond. |
| 372 |
! Duplicate bonds should not be added. |
| 373 |
AddPrimitiveCoord=.True. |
| 374 |
ScanCoord=>Coordinate |
| 375 |
DO WHILE (Associated(ScanCoord%next)) |
| 376 |
IF (ScanCoord%Type .EQ. 'BOND') THEN |
| 377 |
IF (ScanCoord%At1 .EQ. Iat) THEN |
| 378 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 379 |
AddPrimitiveCoord=.False. |
| 380 |
END IF |
| 381 |
END IF |
| 382 |
END IF |
| 383 |
ScanCoord => ScanCoord%next |
| 384 |
END DO |
| 385 |
|
| 386 |
IF (AddPrimitiveCoord) THEN |
| 387 |
NbBonds=NbBonds+1 |
| 388 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 389 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) |
| 390 |
! are determined using all geometries. vecteur is defined in bib_oper.f |
| 391 |
Call vecteur(I,Iat,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 392 |
CurrentCoord%value=Norm2 |
| 393 |
CurrentCoord%SignDihedral = 0 |
| 394 |
CurrentCoord%At1=Iat |
| 395 |
CurrentCoord%At2=I |
| 396 |
CurrentCoord%Type="BOND" |
| 397 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 398 |
ALLOCATE(CurrentCoord%next) |
| 399 |
NULLIFY(CurrentCoord%next%next) |
| 400 |
END IF |
| 401 |
CurrentCoord => CurrentCoord%next |
| 402 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 403 |
END IF ! matches IF (Iat.GT.I) THEN |
| 404 |
|
| 405 |
! Call Annul(Liaisons,IAt,I,Nat,NMaxL) |
| 406 |
! Liaisons(Iat,0)=Liaisons(Iat,0)-1 |
| 407 |
|
| 408 |
! We add the valence angles |
| 409 |
DO K=J+1,Liaisons(I,0) |
| 410 |
Kat=Liaisons(I,K) |
| 411 |
IF (Kat.GT.I) THEN |
| 412 |
! Checking the uniqueness of valence angle. |
| 413 |
! Duplicate bonds should not be added. |
| 414 |
AddPrimitiveCoord=.True. |
| 415 |
ScanCoord=>Coordinate |
| 416 |
DO WHILE (Associated(ScanCoord%next)) |
| 417 |
IF (ScanCoord%Type .EQ. 'ANGLE') THEN |
| 418 |
IF (ScanCoord%At1 .EQ. Iat) THEN |
| 419 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 420 |
IF (ScanCoord%At3 .EQ. Kat) THEN |
| 421 |
AddPrimitiveCoord=.False. |
| 422 |
END IF |
| 423 |
END IF |
| 424 |
END IF |
| 425 |
END IF |
| 426 |
ScanCoord => ScanCoord%next |
| 427 |
END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 428 |
|
| 429 |
IF (AddPrimitiveCoord) THEN |
| 430 |
IF (debug) WRITE(*,*) "Adding angle:",Iat,I,Kat |
| 431 |
NbAngles=NbAngles+1 |
| 432 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 433 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
| 434 |
! determined using all geometries. |
| 435 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 436 |
Call vecteur(i,Iat,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 437 |
CurrentCoord%value=angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 438 |
CurrentCoord%SignDihedral = 0 |
| 439 |
sAngleIatIKat=abs(sin(angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180.)) |
| 440 |
CurrentCoord%At1=Iat |
| 441 |
CurrentCoord%At2=I |
| 442 |
CurrentCoord%At3=KAt |
| 443 |
CurrentCoord%Type="ANGLE" |
| 444 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 445 |
ALLOCATE(CurrentCoord%next) |
| 446 |
NULLIFY(CurrentCoord%next%next) |
| 447 |
END IF |
| 448 |
CurrentCoord => CurrentCoord%next |
| 449 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 450 |
ELSE ! matches IF (Kat.GT.I) THEN |
| 451 |
! Kat is less than I. If there is a bond between I and Kat, then this angle |
| 452 |
! has already been taken into account. |
| 453 |
if (debug) WRITE(*,*) "Testing angle:",Iat,I,Kat |
| 454 |
Bond=.FALSE. |
| 455 |
DO L=1,Liaisons(Iat,0) |
| 456 |
IF (Liaisons(Iat,L).EQ.Kat) Bond=.TRUE. |
| 457 |
END DO |
| 458 |
IF (.NOT.Bond) THEN |
| 459 |
IF (debug) WRITE(*,*) "Not Bond Adding angle:",Iat,I,Kat |
| 460 |
|
| 461 |
! Checking the uniqueness of valence angle. |
| 462 |
! Duplicate bonds should not be added. |
| 463 |
AddPrimitiveCoord=.True. |
| 464 |
ScanCoord=>Coordinate |
| 465 |
DO WHILE (Associated(ScanCoord%next)) |
| 466 |
IF (ScanCoord%Type .EQ. 'ANGLE') THEN |
| 467 |
IF (ScanCoord%At1 .EQ. Iat) THEN |
| 468 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 469 |
IF (ScanCoord%At3 .EQ. Kat) THEN |
| 470 |
AddPrimitiveCoord=.False. |
| 471 |
END IF |
| 472 |
END IF |
| 473 |
END IF |
| 474 |
END IF |
| 475 |
ScanCoord => ScanCoord%next |
| 476 |
END DO |
| 477 |
|
| 478 |
IF (AddPrimitiveCoord) THEN |
| 479 |
NbAngles=NbAngles+1 |
| 480 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 481 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) |
| 482 |
! are determined using all geometries. |
| 483 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 484 |
Call vecteur(i,Iat,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 485 |
CurrentCoord%value=angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 486 |
CurrentCoord%SignDihedral = 0 |
| 487 |
CurrentCoord%At1=Iat |
| 488 |
CurrentCoord%At2=I |
| 489 |
CurrentCoord%At3=KAt |
| 490 |
CurrentCoord%Type="ANGLE" |
| 491 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 492 |
ALLOCATE(CurrentCoord%next) |
| 493 |
NULLIFY(CurrentCoord%next%next) |
| 494 |
END IF |
| 495 |
CurrentCoord => CurrentCoord%next |
| 496 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 497 |
END IF ! matches IF (.NOT.Bond) THEN |
| 498 |
END IF ! matches IF (Kat.GT.I) THEN, after else |
| 499 |
END DO ! matches DO K=J+1,Liaisons(I,0) |
| 500 |
END DO ! matches DO J=1,Liaisons(I,0) |
| 501 |
END IF ! matches IF (Liaisons(I,0).NE.0) THEN |
| 502 |
|
| 503 |
! We add dihedral angles. We do not concentrate on necessary angles, ie those that are |
| 504 |
! needed to build the molecule. Instead we collect all of them, and the choice of the best |
| 505 |
! ones will be done when diagonalizing the Baker matrix. |
| 506 |
IF (Liaisons(I,0).GE.3) Then |
| 507 |
DO J=1,Liaisons(I,0) |
| 508 |
Iat=Liaisons(I,J) |
| 509 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 510 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
| 511 |
! determined using all geometries. |
| 512 |
Call vecteur(Iat,i,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 513 |
|
| 514 |
DO K=J+1,Liaisons(I,0) |
| 515 |
Kat=Liaisons(I,K) |
| 516 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 517 |
sAngleIatIKat=abs(sin(angle(vx1,vy1,vz1,Norm1,-vx2,-vy2,-vz2,Norm2)*Pi/180.)) |
| 518 |
|
| 519 |
DO L=K+1,Liaisons(I,0) |
| 520 |
Lat=Liaisons(I,L) |
| 521 |
if (debug) WRITE(*,*) "0-Dihe Kat,I,Iat:",Kat,I,Iat,angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2) |
| 522 |
Call vecteur(iat,lat,x_refGeom,y_refGeom,z_refGeom,vx3,vy3,vz3,Norm3) |
| 523 |
sAngleIIatLat=abs(sin(angle(vx3,vy3,vz3,Norm3,vx2,vy2,vz2,Norm2)*Pi/180.)) |
| 524 |
if (debug) WRITE(*,*) "0-Dihe I,Iat,Lat:",angle(vx3,vy3,vz3,Norm3,vx2,vy2,vz2,Norm2) |
| 525 |
IF ((sAngleIatIKat.ge.0.01d0).AND.(sAngleIIatLat.ge.0.01d0)) THEN |
| 526 |
if (debug) WRITE(*,*) "Adding dihedral:",Kat,I,Iat,Lat |
| 527 |
|
| 528 |
! Checking for the uniqueness of valence angle. |
| 529 |
! Duplicate bonds should not be added. |
| 530 |
AddPrimitiveCoord=.True. |
| 531 |
ScanCoord=>Coordinate |
| 532 |
DO WHILE (Associated(ScanCoord%next)) |
| 533 |
IF (ScanCoord%Type .EQ. 'DIHEDRAL') THEN |
| 534 |
IF (ScanCoord%At1 .EQ. Kat) THEN |
| 535 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 536 |
IF (ScanCoord%At3 .EQ. Iat) THEN |
| 537 |
IF (ScanCoord%At4 .EQ. Lat) THEN |
| 538 |
AddPrimitiveCoord=.False. |
| 539 |
END IF |
| 540 |
END IF |
| 541 |
END IF |
| 542 |
END IF |
| 543 |
END IF |
| 544 |
ScanCoord => ScanCoord%next |
| 545 |
END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 546 |
|
| 547 |
! IF (AddPrimitiveCoord) THEN |
| 548 |
! NbDihedrals=NbDihedrals+1 |
| 549 |
! CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, & |
| 550 |
! vx5,vy5,vz5,norm5) |
| 551 |
!CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 552 |
! vx4,vy4,vz4,norm4) |
| 553 |
! CurrentCoord%value=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 554 |
! vx2,vy2,vz2,norm2)*Pi/180. |
| 555 |
! CurrentCoord%SignDihedral = 0 |
| 556 |
! CurrentCoord%At1=Kat |
| 557 |
! CurrentCoord%At2=I |
| 558 |
! CurrentCoord%At3=IAt |
| 559 |
! CurrentCoord%At4=LAt |
| 560 |
!WRITE(*,'(1X,":(dihed 1)",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') & |
| 561 |
! ScanCoord%At1,ScanCoord%At2,ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 562 |
! CurrentCoord%Type="DIHEDRAL" |
| 563 |
! IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 564 |
! ALLOCATE(CurrentCoord%next) |
| 565 |
! NULLIFY(CurrentCoord%next%next) |
| 566 |
! END IF |
| 567 |
! CurrentCoord => CurrentCoord%next |
| 568 |
!END IF ! matches IF (AddPrimitiveCoord) THEN |
| 569 |
|
| 570 |
END IF ! matches IF ((sAngleIatIKat.ge.0.01d0).AND.(sAngleIIatLat.ge.0.01d0)) THEN |
| 571 |
END DO ! matches DO L=K+1,Liaisons(I,0) |
| 572 |
END DO ! matches DO K=J+1,Liaisons(I,0) |
| 573 |
END DO ! matches DO J=1,Liaisons(I,0) |
| 574 |
END IF !matches IF (Liaisons(I,0).GE.3) Then |
| 575 |
|
| 576 |
! we now add other dihedrals |
| 577 |
DO J=1,Liaisons(I,0) |
| 578 |
Iat=Liaisons(I,J) |
| 579 |
If (Iat.LE.I) Cycle |
| 580 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 581 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
| 582 |
! determined using all geometries. |
| 583 |
Call vecteur(Iat,i,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 584 |
|
| 585 |
DO K=1,Liaisons(I,0) |
| 586 |
IF (Liaisons(I,K).EQ.Iat) Cycle |
| 587 |
Kat=Liaisons(I,K) |
| 588 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 589 |
sAngleIatIKat=abs(sin(angle(vx1,vy1,vz1,Norm1,-vx2,-vy2,-vz2,Norm2)*Pi/180.)) |
| 590 |
|
| 591 |
DO L=1,Liaisons(Iat,0) |
| 592 |
Lat=Liaisons(Iat,L) |
| 593 |
IF (Lat.eq.I) Cycle |
| 594 |
|
| 595 |
if (debug) WRITE(*,*) "Dihe Kat,I,Iat:",angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2),sAngleIatIKat |
| 596 |
Call vecteur(iat,lat,x_refGeom,y_refGeom,z_refGeom,vx,vy,vz,Norm) |
| 597 |
|
| 598 |
sAngleIIatLat=abs(sin(angle(vx,vy,vz,Norm,vx2,vy2,vz2,Norm2)*Pi/180.)) |
| 599 |
if (debug) WRITE(*,*) "Dihe I,Iat,Lat:",angle(vx,vy,vz,Norm,vx2,vy2,vz2,Norm2) |
| 600 |
! we add the dihedral angle Kat-I-Iat-Lat |
| 601 |
if (debug) WRITE(*,*) "Trying dihedral:",Kat,I,Iat,Lat,sAngleIatIKat,sAngleIIatLat |
| 602 |
IF ((Lat.NE.Kat).AND.(Lat.Ne.I).AND.(sAngleIatIKat.ge.0.01d0) & |
| 603 |
.AND.(sAngleIIatLat.ge.0.01d0)) THEN |
| 604 |
if (debug) WRITE(*,*) "Adding dihedral:",Kat,I,Iat,Lat |
| 605 |
|
| 606 |
! Checking for the uniqueness of valence angle. |
| 607 |
! Duplicate bonds should not be added. |
| 608 |
AddPrimitiveCoord=.True. |
| 609 |
ScanCoord=>Coordinate |
| 610 |
DO WHILE (Associated(ScanCoord%next)) |
| 611 |
IF (ScanCoord%Type .EQ. 'DIHEDRAL') THEN |
| 612 |
IF (ScanCoord%At1 .EQ. Kat) THEN |
| 613 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 614 |
IF (ScanCoord%At3 .EQ. Iat) THEN |
| 615 |
IF (ScanCoord%At4 .EQ. Lat) THEN |
| 616 |
AddPrimitiveCoord=.False. |
| 617 |
END IF |
| 618 |
END IF |
| 619 |
END IF |
| 620 |
END IF |
| 621 |
END IF |
| 622 |
ScanCoord => ScanCoord%next |
| 623 |
END DO |
| 624 |
|
| 625 |
IF (AddPrimitiveCoord) THEN |
| 626 |
NbDihedrals=NbDihedrals+1 |
| 627 |
Call vecteur(iat,lat,x_refGeom,y_refGeom,z_refGeom,vx3,vy3,vz3,Norm3) |
| 628 |
CALL produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, & |
| 629 |
vx5,vy5,vz5,norm5) |
| 630 |
CALL produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 631 |
vx4,vy4,vz4,norm4) |
| 632 |
CurrentCoord%value=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 633 |
vx2,vy2,vz2,norm2)*Pi/180. |
| 634 |
CurrentCoord%At1=Kat |
| 635 |
CurrentCoord%At2=I |
| 636 |
CurrentCoord%At3=IAt |
| 637 |
CurrentCoord%At4=LAt |
| 638 |
CurrentCoord%Type="DIHEDRAL" |
| 639 |
CurrentCoord%SignDihedral=int(sign(1.d0,angle_d(vx4,vy4,vz4,norm4, & |
| 640 |
vx5,vy5,vz5,norm5, vx2,vy2,vz2,norm2))) |
| 641 |
WRITE(*,'(1X,":(dihed 2)",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') ScanCoord%At1,& |
| 642 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 643 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 644 |
ALLOCATE(CurrentCoord%next) |
| 645 |
NULLIFY(CurrentCoord%next%next) |
| 646 |
END IF |
| 647 |
CurrentCoord => CurrentCoord%next |
| 648 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 649 |
END IF ! matches IF ((Lat.NE.Kat).AND.(Lat.Ne.I).AND.(sAngleIatIKat.ge.0.01d0) ..... |
| 650 |
END DO ! matches DO L=1,Liaisons(Iat,0) |
| 651 |
END DO ! matches DO K=1,Liaisons(I,0) |
| 652 |
END DO ! matches DO J=1,Liaisons(I,0) |
| 653 |
END DO ! end of loop over all atoms, DO I=1, Nat |
| 654 |
END DO ! matches DO IGeom=1, NGeomI |
| 655 |
|
| 656 |
|
| 657 |
|
| 658 |
END IF ! if (debugPFL) |
| 659 |
DEALLOCATE(Liaisons) |
| 660 |
|
| 661 |
WRITE(*,*) "I have found" |
| 662 |
WRITE(*,*) NbBonds, " bonds" |
| 663 |
WRITE(*,*) NbAngles, " angles" |
| 664 |
WRITE(*,*) NbDihedrals, " dihedrals" |
| 665 |
|
| 666 |
WRITE(*,*) 'All in all...' |
| 667 |
ScanCoord=>Coordinate |
| 668 |
I=0 |
| 669 |
DO WHILE (Associated(ScanCoord%next)) |
| 670 |
I=I+1 |
| 671 |
SELECT CASE (ScanCoord%Type) |
| 672 |
CASE ('BOND')
|
| 673 |
!WRITE(IOOUT,'(1X,I3,":",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,ScanCoord%At2,ScanCoord%Value |
| 674 |
WRITE(*,'(1X,I3,":(bond )",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,ScanCoord%At2,ScanCoord%Value |
| 675 |
CASE ('ANGLE')
|
| 676 |
!WRITE(IOOUT,'(1X,I3,":",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1, & |
| 677 |
! ScanCoord%At2, ScanCoord%At3,ScanCoord%Value*180./Pi |
| 678 |
WRITE(*,'(1X,I3,":(angle)",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1, & |
| 679 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%Value*180./Pi |
| 680 |
CASE ('DIHEDRAL')
|
| 681 |
!WRITE(IOOUT,'(1X,I3,":",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,& |
| 682 |
! ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 683 |
WRITE(*,'(1X,I3,":(dihed)",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,& |
| 684 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 685 |
END SELECT |
| 686 |
ScanCoord => ScanCoord%next |
| 687 |
END DO |
| 688 |
|
| 689 |
! NPrim is the number of primitive coordinates. |
| 690 |
NPrim=NbBonds+NbAngles+NbDihedrals |
| 691 |
|
| 692 |
! Now calculating values of all primitive bonds for all geometries: |
| 693 |
ALLOCATE(Xprimitive(NgeomI,NPrim),XPrimitiveF(NGeomF,NPrim)) |
| 694 |
ALLOCATE(UMatF(NGeomF,NPrim,NCoord)) |
| 695 |
ALLOCATE(BTransInvF(NGeomF,NCoord,3*Nat)) |
| 696 |
|
| 697 |
! We calculate the Primitive values for the first geometry, this plays a special role |
| 698 |
! as it will serve as a reference for other geometries ! |
| 699 |
|
| 700 |
x(1:Nat) = XyzGeomI(1,1,1:Nat) |
| 701 |
y(1:Nat) = XyzGeomI(1,2,1:Nat) |
| 702 |
z(1:Nat) = XyzGeomI(1,3,1:Nat) |
| 703 |
|
| 704 |
Call Calc_Xprim(nat,x,y,z,Coordinate,NPrim,XPrimitive(1,:)) |
| 705 |
|
| 706 |
DO IGeom=2, NGeomI |
| 707 |
|
| 708 |
x(1:Nat) = XyzGeomI(IGeom,1,1:Nat) |
| 709 |
y(1:Nat) = XyzGeomI(IGeom,2,1:Nat) |
| 710 |
z(1:Nat) = XyzGeomI(IGeom,3,1:Nat) |
| 711 |
|
| 712 |
Call Calc_Xprim(nat,x,y,z,Coordinate,NPrim,XPrimitive(IGeom,:),Xprimitive(1,:)) |
| 713 |
|
| 714 |
! ScanCoord=>Coordinate |
| 715 |
! I=0 ! index for the NPrim (NPrim is the number of primitive coordinates). |
| 716 |
! DO WHILE (Associated(ScanCoord%next)) |
| 717 |
! I=I+1 |
| 718 |
! SELECT CASE (ScanCoord%Type) |
| 719 |
! CASE ('BOND')
|
| 720 |
! Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx2,vy2,vz2,Norm2) |
| 721 |
! Xprimitive(IGeom,I) = Norm2 |
| 722 |
! CASE ('ANGLE')
|
| 723 |
! Call vecteur(ScanCoord%At2,ScanCoord%At3,x,y,z,vx1,vy1,vz1,Norm1) |
| 724 |
! Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx2,vy2,vz2,Norm2) |
| 725 |
! Xprimitive(IGeom,I) = angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 726 |
! CASE ('DIHEDRAL')
|
| 727 |
|
| 728 |
|
| 729 |
! Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx1,vy1,vz1,Norm1) |
| 730 |
! Call vecteur(ScanCoord%At2,ScanCoord%At3,x,y,z,vx2,vy2,vz2,Norm2) |
| 731 |
! Call vecteur(ScanCoord%At3,ScanCoord%At4,x,y,z,vx3,vy3,vz3,Norm3) |
| 732 |
! Call produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, & |
| 733 |
! vx4,vy4,vz4,norm4) |
| 734 |
! Call produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, & |
| 735 |
! vx5,vy5,vz5,norm5) |
| 736 |
|
| 737 |
! DiheTmp= angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 738 |
! vx2,vy2,vz2,norm2) |
| 739 |
! Xprimitive(IGeom,I) = DiheTmp*Pi/180. |
| 740 |
! ! We treat large dihedral angles differently as +180=-180 mathematically and physically |
| 741 |
! ! but this causes lots of troubles when converting baker to cart. |
| 742 |
! ! So we ensure that large dihedral angles always have the same sign |
| 743 |
! if (abs(ScanCoord%SignDihedral).NE.1) THEN |
| 744 |
! ScanCoord%SignDihedral=Int(Sign(1.D0,DiheTmp)) |
| 745 |
! ELSE |
| 746 |
! If ((abs(DiheTmp).GE.170.D0).AND.(Sign(1.,DiheTmp)*ScanCoord%SignDihedral<0)) THEN |
| 747 |
! Xprimitive(IGeom,I) = DiheTmp*Pi/180.+ ScanCoord%SignDihedral*2.*Pi |
| 748 |
! END IF |
| 749 |
! END IF |
| 750 |
! ! Another test... will all this be consistent ??? |
| 751 |
! ! We want the shortest path, so we check that the change in dihedral angles is less than Pi: |
| 752 |
! IF (IGeom.GT.1) THEN |
| 753 |
! IF (abs(Xprimitive(IGeom,I)-XPrimitive(IGeom-1,I)).GE.Pi) THEN |
| 754 |
! if ((Xprimitive(IGeom,I)-XPrimitive(IGeom-1,I)).GE.Pi) THEN |
| 755 |
! Xprimitive(IGeom,I)=Xprimitive(IGeom,I)-2.d0*Pi |
| 756 |
! ELSE |
| 757 |
! Xprimitive(IGeom,I)=Xprimitive(IGeom,I)+2.d0*Pi |
| 758 |
! END IF |
| 759 |
! END IF |
| 760 |
! END IF |
| 761 |
! END SELECT |
| 762 |
! ScanCoord => ScanCoord%next |
| 763 |
! END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 764 |
END DO ! matches DO IGeom=1, NGeomI |
| 765 |
|
| 766 |
IF (debug) THEN |
| 767 |
WRITE(*,*) "DBG Calc_Baker Xprimitives for all geometries" |
| 768 |
DO IGeom=1, NGeomI |
| 769 |
WRITE(*,*) "Geometry ",IGeom |
| 770 |
ScanCoord=>Coordinate |
| 771 |
I=0 ! index for the NPrim (NPrim is the number of primitive coordinates). |
| 772 |
DO WHILE (Associated(ScanCoord%next)) |
| 773 |
I=I+1 |
| 774 |
SELECT CASE (ScanCoord%Type) |
| 775 |
CASE ('BOND')
|
| 776 |
WRITE(*,'(1X,I3,":",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,ScanCoord%At2,Xprimitive(IGeom,I) |
| 777 |
CASE ('ANGLE')
|
| 778 |
WRITE(*,'(1X,I3,":",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1, & |
| 779 |
ScanCoord%At2, ScanCoord%At3,Xprimitive(IGeom,I)*180./Pi |
| 780 |
CASE ('DIHEDRAL')
|
| 781 |
WRITE(*,'(1X,I3,":",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,& |
| 782 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,Xprimitive(IGeom,I)*180./Pi |
| 783 |
END SELECT |
| 784 |
ScanCoord => ScanCoord%next |
| 785 |
END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 786 |
END DO ! matches DO IGeom=1, NGeomI |
| 787 |
END IF |
| 788 |
! Here reference geometry is assigned to Geom. Earlier x,y,z(Nat) were assigned from XyzGeomI(...) |
| 789 |
! before the call of this (Calc_baker) subroutine and passed to this subroutine as arguments of the |
| 790 |
! subroutine. |
| 791 |
! PFL 19 Feb 2008 -> |
| 792 |
! In order to reproduce the B matrix in the Baker article, one has |
| 793 |
! to divide Geom by a0. |
| 794 |
! However, this is inconsitent with our way of storing geometries |
| 795 |
! so we do not do it ! |
| 796 |
|
| 797 |
Geom(1,:)=XyzGeomI(IGeomRef,1,1:Nat) ! XyzGeomI(NGeomI,3,Nat) |
| 798 |
Geom(2,:)=XyzGeomI(IGeomRef,2,1:Nat) |
| 799 |
Geom(3,:)=XyzGeomI(IGeomRef,3,1:Nat) |
| 800 |
|
| 801 |
! <- PFL 19 Feb 2008 |
| 802 |
|
| 803 |
! We now have to compute dq/dx... |
| 804 |
ALLOCATE(BprimT(3*Nat,NPrim)) |
| 805 |
BprimT=0.d0 |
| 806 |
|
| 807 |
ScanCoord=>Coordinate |
| 808 |
I=0 |
| 809 |
DO WHILE (Associated(ScanCoord%next)) |
| 810 |
I=I+1 |
| 811 |
SELECT CASE (ScanCoord%Type) |
| 812 |
CASE ('BOND')
|
| 813 |
CALL CONSTRAINTS_BONDLENGTH_DER(Nat,ScanCoord%at1,ScanCoord%AT2, & |
| 814 |
Geom,BprimT(1,I)) |
| 815 |
CASE ('ANGLE')
|
| 816 |
CALL CONSTRAINTS_BONDANGLE_DER(Nat,ScanCoord%At1,ScanCoord%AT2, & |
| 817 |
ScanCoord%At3,Geom,BprimT(1,I)) |
| 818 |
CASE ('DIHEDRAL')
|
| 819 |
CALL CONSTRAINTS_TORSION_DER2(Nat,ScanCoord%At1,ScanCoord%AT2, & |
| 820 |
ScanCoord%At3,ScanCoord%At4,Geom,BprimT(1,I)) |
| 821 |
! CALL CONSTRAINTS_TORSION_DER(Nat,ScanCoord%At1,ScanCoord%AT2, & |
| 822 |
! ScanCoord%At3,ScanCoord%At4,Geom,BprimT(1,I)) |
| 823 |
|
| 824 |
END SELECT |
| 825 |
ScanCoord => ScanCoord%next |
| 826 |
END DO |
| 827 |
|
| 828 |
|
| 829 |
!!!!!!!!!!!!!!!!!!!! |
| 830 |
! |
| 831 |
! PFL Debug |
| 832 |
! |
| 833 |
!!!!!!!!!!!!!!!!!!!! |
| 834 |
|
| 835 |
if (debugPFL) THEN |
| 836 |
WRITe(*,*) "DBG PFL Calc_Baker =====" |
| 837 |
DzDc=0.d0 |
| 838 |
WRITE(*,*) "PFL DBG, DzdC" |
| 839 |
do I=1,Nat |
| 840 |
Geom(1,i)=XyzGeomI(IGeomRef,1,orderInv(i)) ! XyzGeomI(NGeomI,3,Nat) |
| 841 |
Geom(2,i)=XyzGeomI(IGeomRef,2,OrderInv(i)) |
| 842 |
Geom(3,i)=XyzGeomI(IGeomRef,3,OrderInv(i)) |
| 843 |
WRITE(*,*) I,OrderInv(I),Geom(:,I) |
| 844 |
end do |
| 845 |
CALL CalcBMat_int (nat, Geom, indzmat, dzdc, massat,atome) |
| 846 |
|
| 847 |
WRITE(*,*) "PFL DBG, BPrimT" |
| 848 |
DO I=1,NPrim |
| 849 |
WRITE(*,'(50(1X,F12.6))') BPrimT(:,I) |
| 850 |
END DO |
| 851 |
WRITe(*,*) "DBG PFL Calc_Baker =====" |
| 852 |
END IF |
| 853 |
|
| 854 |
!!!!!!!!!!!!!!!!!!!! |
| 855 |
! |
| 856 |
! PFL Debug |
| 857 |
! |
| 858 |
!!!!!!!!!!!!!!!!!!!! |
| 859 |
|
| 860 |
DEALLOCATE(Geom) |
| 861 |
|
| 862 |
! BprimT(3*Nat,NPrim) |
| 863 |
! We now compute G=B(BT) matrix |
| 864 |
ALLOCATE(Gmat(NPrim,NPrim)) |
| 865 |
GMat=0.d0 |
| 866 |
DO I=1,NPrim |
| 867 |
DO J=1,3*Nat |
| 868 |
GMat(:,I)=Gmat(:,I)+BprimT(J,:)*BprimT(J,I) !*1.d0/mass(atome(int(K/3.d0))) |
| 869 |
END DO |
| 870 |
END DO |
| 871 |
|
| 872 |
!!!!!!!!!!!!!!!!!!!! |
| 873 |
! |
| 874 |
! PFL Debug ---> |
| 875 |
! |
| 876 |
!!!!!!!!!!!!!!!!!!!! |
| 877 |
if (debugPFL) THEN |
| 878 |
GMat=0.d0 |
| 879 |
DO I=1,NPrim |
| 880 |
GMat(I,I)=1. |
| 881 |
END DO |
| 882 |
END IF |
| 883 |
|
| 884 |
!!!!!!!!!!!!!!!!!!!! |
| 885 |
! |
| 886 |
! <--- PFL Debug |
| 887 |
! |
| 888 |
!!!!!!!!!!!!!!!!!!!! |
| 889 |
|
| 890 |
!DO I=1,NPrim |
| 891 |
! WRITE(*,'(20(1X,F6.3))') GMat(1:min(20,NPrim),I) |
| 892 |
!END DO |
| 893 |
|
| 894 |
! We diagonalize G |
| 895 |
ALLOCATE(EigVal(NPrim),EigVec(NPrim,NPrim)) |
| 896 |
Call Jacobi(GMat,NPrim,EigVal,EigVec,NPrim) |
| 897 |
Call Trie(NPrim,EigVal,EigVec,NPrim) |
| 898 |
DO I=1,NPrim |
| 899 |
WRITE(*,'(1X,"Vector ",I3,": e=",F8.3)') I,EigVal(i) |
| 900 |
WRITE(*,'(20(1X,F8.4))') EigVec(1:min(20,NPrim),I) |
| 901 |
END DO |
| 902 |
|
| 903 |
!DO I=1,NPrim |
| 904 |
! WRITE(*,'(1X,"Vector ",I3,(20(F8.3)))') I,EigVec(1:min(20,NPrim),I) |
| 905 |
! END DO |
| 906 |
|
| 907 |
!DO I=1,NPrim |
| 908 |
! WRITE(*,'(1X,"Vector ",I3,F8.3,F8.3,F8.3,F8.3,F8.3,F8.3,F8.3,F8.3,F8.3,F8.3,F8.3,F8.3,& |
| 909 |
! F8.3,F8.3,F8.3,F8.3,F8.3)') I,EigVec(1,I),EigVec(4,I),EigVec(6,I),EigVec(14,I),EigVec(16,I),& |
| 910 |
!EigVec(2,I),EigVec(3,I),EigVec(5,I),EigVec(12,I),EigVec(13,I),EigVec(15,I),EigVec(7,I),& |
| 911 |
!EigVec(8,I),EigVec(9,I),EigVec(10,I),EigVec(11,I),EigVec(17,I) |
| 912 |
!END DO |
| 913 |
|
| 914 |
! We construct the new DzDc(b=baker) matrix |
| 915 |
! UMat is nonredundant vector set, i.e. set of eigenvectors of BB^T corresponding |
| 916 |
! to eigenvalues > zero. |
| 917 |
ALLOCATE(UMat(NPrim,NCoord)) |
| 918 |
ALLOCATE(UMat_local(NPrim,NCoord)) |
| 919 |
ALLOCATE(UMat_tmp(NPrim,3*Nat-6)) |
| 920 |
! BMat_BakerT(3*Nat,NCoord), allocated in Path.f90, |
| 921 |
! NCoord=3*Nat-6 |
| 922 |
BMat_BakerT = 0.d0 |
| 923 |
J=0 |
| 924 |
UMat=0.d0 |
| 925 |
UMat_tmp=0.d0 |
| 926 |
DO I=1,NPrim |
| 927 |
IF (abs(eigval(I))>=1e-6) THEN |
| 928 |
J=J+1 |
| 929 |
DO K=1,NPrim |
| 930 |
!DzDcb(:,J)=DzDcb(:,J)+Eigvec(K,I)*BprimT(:,K) ! original |
| 931 |
! BprimT is transpose of B^prim. |
| 932 |
! B = UMat^T B^prim, B^T = (B^prim)^T UMat |
| 933 |
BMat_BakerT(:,J)=BMat_BakerT(:,J)+BprimT(:,K)*Eigvec(K,I) |
| 934 |
!Dzdcb(:,J)=DzDcb(:,J)+Eigvec(K,:)*BprimT(I,K) |
| 935 |
END DO |
| 936 |
IF(J .GT. 3*Nat-6) THEN |
| 937 |
WRITE(*,*) 'Number of vectors in Eigvec with eigval .GT. 1e-6(=UMat) (=' & |
| 938 |
,J,') exceeded 3*Nat-6=',3*Nat-6, & |
| 939 |
'Stopping the calculation.' |
| 940 |
STOP |
| 941 |
END IF |
| 942 |
UMat_tmp(:,J) = Eigvec(:,I) |
| 943 |
END IF |
| 944 |
END DO |
| 945 |
|
| 946 |
if (debug) THEN |
| 947 |
WRITE(*,*) "DBG Calc_Baker: UMat" |
| 948 |
DO I=1,3*Nat-6 |
| 949 |
WRITE(*,'(50(1X,F12.8))') UMat_tmp(:,I) |
| 950 |
END DO |
| 951 |
END IF |
| 952 |
|
| 953 |
! THIS IS TO BE CORRECTED: |
| 954 |
UMat = UMat_tmp |
| 955 |
!J=0 |
| 956 |
!DO I=1, 3*Nat-6 |
| 957 |
! IF ((I .NE. 6) .AND. (I .NE. 7) .AND. (I .NE. 9)) Then |
| 958 |
! J=J+1 |
| 959 |
! Print *, 'J=', J, ' I=', I |
| 960 |
! UMat(:,J) = UMat_tmp(:,I) |
| 961 |
!END IF |
| 962 |
!END DO |
| 963 |
! BMat_BakerT=0.d0 |
| 964 |
!DO I=1,NCoord |
| 965 |
! DO J=1,NPrim |
| 966 |
! B = UMat^T B^prim, B^T = (B^prim)^T UMat |
| 967 |
! BMat_BakerT(:,I)=BMat_BakerT(:,I)+BprimT(:,J)*UMat(J,I) |
| 968 |
! END DO |
| 969 |
!END DO |
| 970 |
! TO BE CORRECTED, ENDS HERE. |
| 971 |
|
| 972 |
IntCoordI=0.d0 |
| 973 |
DO IGeom=1, NGeomI |
| 974 |
DO I=1, NPrim |
| 975 |
! Transpose of UMat is needed below, that is why UMat(I,:). |
| 976 |
IntCoordI(IGeom,:) = IntCoordI(IGeom,:) + UMat(I,:)*Xprimitive(IGeom,I) |
| 977 |
END DO |
| 978 |
END DO |
| 979 |
|
| 980 |
if (debug) THEN |
| 981 |
WRITE(*,*) "DBG Calc_Baker IntCoordI" |
| 982 |
DO IGeom=1, NGeomI |
| 983 |
WRITE(*,'(1X,I5,":",30(1X,F10.6))') IGeom,IntCoordI(IGeom,:) |
| 984 |
END DO |
| 985 |
END IF |
| 986 |
|
| 987 |
|
| 988 |
! the following might be used to get rid of some coordinates that |
| 989 |
! do not respect the symmetry of the problem. |
| 990 |
|
| 991 |
! ! We look at the group symmetry of the molecule. Nothing complicate here |
| 992 |
! ! we just look for planar symmetry. |
| 993 |
! ! We first place it into the standard orientation |
| 994 |
! Call Std_ori(Nat,x,y,z,a,b,c,massat) |
| 995 |
|
| 996 |
! ! Is the molecule planar |
| 997 |
! DO I=1,Nat |
| 998 |
! WRITE(*,*) nom(atome(i)),x(i),y(i),z(i) |
| 999 |
! END DO |
| 1000 |
DEALLOCATE(BprimT,GMat,EigVal,EigVec) ! BprimT is B^prim^T |
| 1001 |
! Calculation of BTransInv starts here: |
| 1002 |
! Calculation of BBT(3*Nat-6,3*Nat-6)=BB^T: |
| 1003 |
! BMat_BakerT(3*Nat,NCoord) is Transpose of B = UMat^TB^prim |
| 1004 |
ALLOCATE(BBT(NCoord,NCoord)) |
| 1005 |
BBT = 0.d0 |
| 1006 |
DO I=1, NCoord |
| 1007 |
DO J=1, 3*Nat |
| 1008 |
! BBT(:,I) forms BB^T |
| 1009 |
BBT(:,I) = BBT(:,I) + BMat_BakerT(J,:)*BMat_BakerT(J,I) |
| 1010 |
END DO |
| 1011 |
END DO |
| 1012 |
|
| 1013 |
!ALLOCATE(V(3*Nat,3*Nat)) |
| 1014 |
!Call GINVSE(BBT,3*Nat,3*Nat,BBT_inv,3*Nat,3*Nat,3*Nat,1e-6,V,3*Nat,FAIL,NOUT) |
| 1015 |
!DEALLOCATE(V) |
| 1016 |
ALLOCATE(BBT_inv(NCoord,NCoord)) |
| 1017 |
! GenInv is in Mat_util.f90 |
| 1018 |
Call GenInv(NCoord,BBT,BBT_inv,NCoord) |
| 1019 |
|
| 1020 |
! Calculation of (B^T)^-1 = (BB^T)^-1B: |
| 1021 |
!ALLOCATE(BTransInv(3*Nat-6,3*Nat)) ! allocated in Path.f90 |
| 1022 |
BTransInv = 0.d0 |
| 1023 |
DO I=1, 3*Nat |
| 1024 |
DO J=1, NCoord |
| 1025 |
BTransInv(:,I) = BTransInv(:,I) + BBT_inv(:,J)*BMat_BakerT(I,J) |
| 1026 |
END DO |
| 1027 |
END DO |
| 1028 |
BTransInv_local = BTransInv |
| 1029 |
UMat_local = UMat |
| 1030 |
DEALLOCATE(BBT,BBT_inv,UMat_tmp) |
| 1031 |
DEALLOCATE(x_refGeom,y_refGeom,z_refGeom,x,y,z) |
| 1032 |
IF (debug) WRITE(*,*) "DBG Calc_baker over." |
| 1033 |
END SUBROUTINE Calc_baker |