root / src / Calc_baker.f90 @ 2
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SUBROUTINE Calc_baker(atome,r_cov,fact,frozen,IGeomRef) |
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! |
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! This subroutine analyses a geometry to construct the baker |
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! delocalized internal coordinates |
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! v1.0 |
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! We use only one geometry |
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! |
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Use Path_module, only : max_Z,NMaxL,Nom,MaxFroz,NFroz,Pi,Massat,a0,BMat_BakerT, & |
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Nat,NCoord,XyzGeomI,NGeomI,NGeomF,UMat,NPrim,BTransInv, & |
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IntCoordI,Coordinate,CurrentCoord,ScanCoord,BprimT,BBT, & |
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BBT_inv,Xprimitive,XPrimitiveF,Symmetry_elimination,UMat_local, & |
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BTransInv_local, UMatF,BTransInvF, & |
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indzmat, dzdc,renum,order,OrderInv |
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! BMat_BakerT(3*Nat,NCoord), NCoord=3*Nat or NFree=3*Nat-6-Symmetry_elimination |
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! depending upon the coordinate choice. IntCoordI(NGeomI,NCoord) where |
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! UMat(NPrim,NCoord), NCoord number of vectors in UMat matrix, i.e. NCoord |
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! Baker coordinates. NPrim is the number of primitive internal coordinates. |
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|
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Use Io_module |
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IMPLICIT NONE |
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|
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! IGeom: Geometry index, IGeomRef: Reference Geometry. |
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INTEGER(KINT), INTENT(IN) :: atome(Nat),IGeomRef |
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REAL(KREAL), INTENT(IN) :: fact |
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REAL(KREAL), INTENT(IN) :: r_cov(0:Max_Z) |
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! Frozen contains the indices of frozen atoms |
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INTEGER(KINT), INTENT(IN) :: Frozen(*) |
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|
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INTEGER(KINT), ALLOCATABLE :: LIAISONS(:,:) ! (Nat,0:NMaxL) |
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REAL(KREAL), ALLOCATABLE :: Geom(:,:) !(3,Nat) |
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! NPrim is the number of primitive coordinates and NCoord is the number |
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! of internal coordinates. BMat is actually (NPrim,3*Nat). |
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REAL(KREAL), ALLOCATABLE :: GMat(:,:) !(NPrim,NPrim) |
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! EigVec(..) contains ALL eigevectors of BMat times BprimT, NOT only Baker Coordinate vectors. |
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REAL(KREAL), ALLOCATABLE :: EigVec(:,:), EigVal(:) ! EigVec(NPrim,NPrim) |
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REAL(KREAL), ALLOCATABLE :: x(:), y(:), z(:) |
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REAL(KREAL), ALLOCATABLE :: x_refGeom(:), y_refGeom(:), z_refGeom(:) |
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!REAL(KREAL), ALLOCATABLE :: V(:,:) ! (3*Nat,3*Nat) |
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!REAL(KREAL), ALLOCATABLE :: P(:) ! Used in Baker Coordinates: Matrix Inversion |
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REAL(KREAL), ALLOCATABLE :: UMat_tmp(:,:) |
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INTEGER(KINT) :: NbBonds, NbAngles, NbDihedrals, IGeom |
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|
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real(KREAL) :: vx,vy,vz,dist, Norm |
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real(KREAL) :: vx1,vy1,vz1,norm1 |
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real(KREAL) :: vx2,vy2,vz2,norm2 |
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real(KREAL) :: vx3,vy3,vz3,norm3 |
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real(KREAL) :: vx4,vy4,vz4,norm4 |
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real(KREAL) :: vx5,vy5,vz5,norm5 |
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real(KREAL) :: val,val_d, Q, T |
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|
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INTEGER(KINT) :: I,J, n1,n2,n3,n4,IAt,IL,JL,IFrag,ITmp, K, KMax |
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INTEGER(KINT) :: I0, IOld, IAtTmp, Izm, JAt, Kat, Lat, L, NOUT |
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|
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REAL(KREAL) :: sAngleIatIKat, sAngleIIatLat |
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REAL(KREAL) :: DiheTmp |
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|
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LOGICAL :: debug, bond, AddPrimitiveCoord, FAIL |
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|
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INTERFACE |
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function valid(string) result (isValid) |
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CHARACTER(*), intent(in) :: string |
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logical :: isValid |
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END function VALID |
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|
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|
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FUNCTION angle(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2) |
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use Path_module, only : Pi,KINT, KREAL |
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real(KREAL) :: v1x,v1y,v1z,norm1 |
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real(KREAL) :: v2x,v2y,v2z,norm2 |
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real(KREAL) :: angle |
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END FUNCTION ANGLE |
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|
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|
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|
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FUNCTION angle_d(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2,v3x,v3y,v3z,norm3) |
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use Path_module, only : Pi,KINT, KREAL |
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real(KREAL) :: v1x,v1y,v1z,norm1 |
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real(KREAL) :: v2x,v2y,v2z,norm2 |
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real(KREAL) :: v3x,v3y,v3z,norm3 |
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real(KREAL) :: angle_d,ca,sa |
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END FUNCTION ANGLE_D |
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|
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|
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|
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|
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SUBROUTINE Calc_Xprim(nat,x,y,z,Coordinate,NPrim,XPrimitive,XPrimRef) |
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! |
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! This subroutine uses the description of a list of Coordinates |
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! to compute the values of the coordinates for a given geometry. |
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! |
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!!!!!!!!!! |
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! Input: |
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! Na: INTEGER, Number of atoms |
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! x,y,z(Na): REAL, cartesian coordinates of the considered geometry |
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! Coordinate (Pointer(ListCoord)): description of the wanted coordiantes |
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! NPrim, INTEGER: Number of coordinates to compute |
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! |
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! Optional: XPrimRef(NPrim) REAL: array that contains coordinates values for |
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! a former geometry. Useful for Dihedral angles evolution... |
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|
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!!!!!!!!!!! |
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! Output: |
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! XPrimimite(NPrim) REAL: array that will contain the values of the coordinates |
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! |
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!!!!!!!!! |
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|
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Use VarTypes |
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Use Io_module |
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Use Path_module, only : pi |
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|
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IMPLICIT NONE |
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|
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Type (ListCoord), POINTER :: Coordinate |
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INTEGER(KINT), INTENT(IN) :: Nat,NPrim |
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REAL(KREAL), INTENT(IN) :: x(Nat), y(Nat), z(Nat) |
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REAL(KREAL), INTENT(IN), OPTIONAL :: XPrimRef(NPrim) |
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REAL(KREAL), INTENT(OUT) :: XPrimitive(NPrim) |
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|
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END SUBROUTINE CALC_XPRIM |
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END INTERFACE |
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|
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! |
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!!!!!!!! PFL Debug |
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! |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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REAL(KREAL), ALLOCATABLE :: V(:,:) ! (NCoord,NCoord) |
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REAL(KREAL) :: tol |
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INTEGER(KINT) :: I1,I2,I3,I4 |
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LOGICAL :: FALOBBT,FALOBPrimt,FAloBBTInv |
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LOGICAL :: debugPFL |
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REAL(KREAL), ALLOCATABLE :: val_zmat(:,:) |
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INTEGER(KINT), ALLOCATABLE :: indzmat0(:,:) |
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|
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|
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debug=valid("Calc_baker")
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debugPFL=valid("BakerPFL")
|
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if (debug) WRITE(*,*) "============= Entering Cal_baker ==============" |
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|
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IF (Nat.le.2) THEN |
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WRITE(*,*) "I do not work for less than 2 atoms :-p" |
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RETURN |
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END IF |
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|
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IF (debug) THEN |
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WRITE(*,*) "DBG Calc_baker, geom" |
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DO I=1,Nat |
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WRITE(*,'(1X,I5,":",I3,3(1X,F15.3))') I,atome(I),XyzGeomI(IGeomRef,1:3,I) |
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END DO |
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END IF |
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|
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|
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|
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|
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! we construct the list of bonds, valence angles and dihedral angles using this connectivity |
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ALLOCATE(Coordinate) |
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NULLIFY(Coordinate%next) |
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NbBonds=0 |
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NbAngles=0 |
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NbDihedrals=0 |
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|
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CurrentCoord => Coordinate |
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|
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ALLOCATE(Liaisons(Nat,0:NMaxL),Geom(3,Nat),x(Nat),y(Nat),z(Nat)) |
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ALLOCATE(x_refGeom(Nat),y_refGeom(Nat),z_refGeom(Nat)) |
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|
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x_refGeom(1:Nat) = XyzGeomI(IGeomRef,1,1:Nat) |
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y_refGeom(1:Nat) = XyzGeomI(IGeomRef,2,1:Nat) |
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z_refGeom(1:Nat) = XyzGeomI(IGeomRef,3,1:Nat) |
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|
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!!!!!!!!!!!!!!!!!!!! |
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! |
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! PFL Debug |
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! |
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!!!!!!!!!!!!!!!!!!!! |
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if (debugPFL) THEN |
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WRITE(*,*) "DBG PFL Calc_BAKER - Calculating Zmat" |
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if (.not.ALLOCATED(indzmat)) THEN |
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ALLOCATE(indzmat(Nat,5)) |
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END IF |
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IF (.NOT.ALLOCATED(DzDc)) THEN |
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ALLOCATE(DzDc(3,nat,3,Nat)) |
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END IF |
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IF (.NOT.ALLOCATED(Val_zmat)) THEN |
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ALLOCATE(val_zmat(nat,3)) |
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END IF |
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IF (.NOT.ALLOCATED(indzmat0)) THEN |
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ALLOCATE(indzmat0(nat,5)) |
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END IF |
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! We construct a Zmat |
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IF (Frozen(1).NE.0) THEN |
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Renum=.TRUE. |
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!!! remplcaer indzmat par indzmat0 puis renumerotation |
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call Calc_zmat_const_frag(Nat,atome,IndZmat0,val_zmat, & |
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x_refGeom,y_refGeom,z_refGeom, & |
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r_cov,fact,frozen) |
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ELSE |
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!no zmat... we create our own |
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call Calc_zmat_frag(Nat,atome,IndZmat0,val_zmat, & |
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x_refGeom,y_refGeom,z_refGeom, & |
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r_cov,fact) |
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END IF |
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|
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DO I=1,Nat |
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Order(IndZmat0(I,1))=I |
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OrderInv(I)=IndZmat0(I,1) |
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END DO |
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IndZmat(1,1)=Order(IndZmat0(1,1)) |
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IndZmat(2,1)=Order(IndZmat0(2,1)) |
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IndZmat(2,2)=Order(IndZmat0(2,2)) |
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IndZmat(3,1)=Order(IndZmat0(3,1)) |
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IndZmat(3,2)=Order(IndZmat0(3,2)) |
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IndZmat(3,3)=Order(IndZmat0(3,3)) |
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DO I=4,Nat |
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DO J=1,4 |
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IndZmat(I,J)=Order(IndZmat0(I,J)) |
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END DO |
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end do |
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|
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|
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WRITE(*,*) "DBG PFL CalcBaker, IndZmat0" |
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DO I=1,Nat |
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WRITE(*,*) I, indZmat0(I,:) |
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end do |
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|
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WRITE(*,*) "DBG PFL CalcBaker, IndZmat" |
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DO I=1,Nat |
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WRITE(*,*) I, indZmat(I,:) |
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end do |
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|
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|
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DO I=1,Nat |
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I1=indzmat0(I,1) |
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I2=indzmat0(I,2) |
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I3=indzmat0(I,3) |
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I4=indzmat0(I,4) |
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! Adding BOND between at1 and at2 |
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WRITE(*,*) "DBG Indzmat",I,I1,I2,I3,I4 |
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if (I2.NE.0) THEN |
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NbBonds=NbBonds+1 |
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! values of the coordinate (bond) is calculated for the reference geometry |
| 242 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) |
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! are determined using all geometries. vecteur is defined in bib_oper.f |
| 244 |
Call vecteur(I1,I2,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
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! CurrentCoord%value=Norm2 |
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WRITE(*,'(1X,A,I5,A,2(1X,F12.6))') "Bond",NbBonds," Norm2,val_zmat",Norm2,val_zmat(I,1) |
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CurrentCoord%value=val_zmat(I,1) |
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CurrentCoord%SignDihedral = 0 |
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CurrentCoord%At1=I1 |
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CurrentCoord%At2=I2 |
| 251 |
CurrentCoord%Type="BOND" |
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IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
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ALLOCATE(CurrentCoord%next) |
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NULLIFY(CurrentCoord%next%next) |
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END IF |
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CurrentCoord => CurrentCoord%next |
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END IF !IE.NE.0 |
| 258 |
if (I3.NE.0) THEN |
| 259 |
|
| 260 |
NbAngles=NbAngles+1 |
| 261 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 262 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
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! determined using all geometries. |
| 264 |
Call vecteur(i2,I3,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 265 |
Call vecteur(i2,I1,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 266 |
! CurrentCoord%value=angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 267 |
WRITE(*,'(1X,A,I5,A,2(1X,F12.6))') "Angle",NbAngles," angle,val_zmat", & |
| 268 |
angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2),val_zmat(I,2) |
| 269 |
CurrentCoord%value=val_zmat(I,2)*Pi/180. |
| 270 |
CurrentCoord%SignDihedral = 0 |
| 271 |
CurrentCoord%At1=I1 |
| 272 |
CurrentCoord%At2=I2 |
| 273 |
CurrentCoord%At3=I3 |
| 274 |
CurrentCoord%Type="ANGLE" |
| 275 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 276 |
ALLOCATE(CurrentCoord%next) |
| 277 |
NULLIFY(CurrentCoord%next%next) |
| 278 |
END IF |
| 279 |
CurrentCoord => CurrentCoord%next |
| 280 |
END IF ! matches IF (I3.NE.0) |
| 281 |
if (I4.NE.0) THEN |
| 282 |
NbDihedrals=NbDihedrals+1 |
| 283 |
Call vecteur(I2,I1,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 284 |
Call vecteur(I2,I3,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 285 |
Call vecteur(I3,I4,x_refGeom,y_refGeom,z_refGeom,vx3,vy3,vz3,Norm3) |
| 286 |
CALL produit_vect(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2, & |
| 287 |
vx4,vy4,vz4,norm4) |
| 288 |
CALL produit_vect(vx3,vy3,vz3,norm3,vx2,vy2,vz2,norm2, & |
| 289 |
vx5,vy5,vz5,norm5) |
| 290 |
! CurrentCoord%value=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 291 |
! vx2,vy2,vz2,norm2)*Pi/180. |
| 292 |
WRITE(*,'(1X,A,I5,A,2(1X,F12.6))') "Dihedral",NbDihedrals, & |
| 293 |
" angle_d,val_zmat", & |
| 294 |
angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 295 |
vx2,vy2,vz2,norm2) & |
| 296 |
,val_zmat(I,3) |
| 297 |
|
| 298 |
CurrentCoord%value = val_zmat(I,3)*Pi/180. |
| 299 |
CurrentCoord%SignDihedral = int(sign(1.D0,val_zmat(I,3))) |
| 300 |
CurrentCoord%At1=I1 |
| 301 |
CurrentCoord%At2=I2 |
| 302 |
CurrentCoord%At3=I3 |
| 303 |
CurrentCoord%At4=I4 |
| 304 |
CurrentCoord%Type="DIHEDRAL" |
| 305 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 306 |
ALLOCATE(CurrentCoord%next) |
| 307 |
NULLIFY(CurrentCoord%next%next) |
| 308 |
END IF |
| 309 |
CurrentCoord => CurrentCoord%next |
| 310 |
END IF ! matches IF (I4.NE.0) |
| 311 |
END DO ! matches DO I=1,Nat |
| 312 |
deallocate(indzmat0) |
| 313 |
|
| 314 |
ELSE !! if (debugPFL) |
| 315 |
|
| 316 |
DO IGeom=1, NGeomI |
| 317 |
!IGeom=1 ! need when using only first geometry. |
| 318 |
x(1:Nat) = XyzGeomI(IGeom,1,1:Nat) |
| 319 |
y(1:Nat) = XyzGeomI(IGeom,2,1:Nat) |
| 320 |
z(1:Nat) = XyzGeomI(IGeom,3,1:Nat) |
| 321 |
|
| 322 |
! First step: we calculate the connectivity |
| 323 |
Liaisons=0 |
| 324 |
|
| 325 |
Call CalcCnct(Nat,atome,x,y,z,LIAISONS,r_cov,fact) |
| 326 |
|
| 327 |
IF (debug) THEN |
| 328 |
WRITE(*,*) 'Connectivity done' |
| 329 |
DO I=1,Nat |
| 330 |
WRITE(*,'(1X,I5,":",I3,"=",15I4)') I,(Liaisons(I,J),J=0,NMaxL) |
| 331 |
WRITE(*,'(1X,I5,":",I3,"=",15I4)') I,(Liaisons(I,:)) |
| 332 |
END DO |
| 333 |
DO I=1,Nat |
| 334 |
WRITE(*,'(1X,I5,":",I3," r_cov=",F15.6)') I,atome(I),r_cov(atome(I)) |
| 335 |
END DO |
| 336 |
END IF |
| 337 |
|
| 338 |
DO I=1,Nat |
| 339 |
IF (Liaisons(I,0).NE.0) THEN |
| 340 |
DO J=1,Liaisons(I,0) |
| 341 |
! We add the bond |
| 342 |
Iat=Liaisons(I,J) |
| 343 |
IF (Iat.GT.I) THEN |
| 344 |
! Checking the uniqueness of bond. |
| 345 |
! Duplicate bonds should not be added. |
| 346 |
AddPrimitiveCoord=.True. |
| 347 |
ScanCoord=>Coordinate |
| 348 |
DO WHILE (Associated(ScanCoord%next)) |
| 349 |
IF (ScanCoord%Type .EQ. 'BOND') THEN |
| 350 |
IF (ScanCoord%At1 .EQ. Iat) THEN |
| 351 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 352 |
AddPrimitiveCoord=.False. |
| 353 |
END IF |
| 354 |
END IF |
| 355 |
END IF |
| 356 |
ScanCoord => ScanCoord%next |
| 357 |
END DO |
| 358 |
|
| 359 |
IF (AddPrimitiveCoord) THEN |
| 360 |
NbBonds=NbBonds+1 |
| 361 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 362 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) |
| 363 |
! are determined using all geometries. vecteur is defined in bib_oper.f |
| 364 |
Call vecteur(I,Iat,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 365 |
CurrentCoord%value=Norm2 |
| 366 |
CurrentCoord%SignDihedral = 0 |
| 367 |
CurrentCoord%At1=Iat |
| 368 |
CurrentCoord%At2=I |
| 369 |
CurrentCoord%Type="BOND" |
| 370 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 371 |
ALLOCATE(CurrentCoord%next) |
| 372 |
NULLIFY(CurrentCoord%next%next) |
| 373 |
END IF |
| 374 |
CurrentCoord => CurrentCoord%next |
| 375 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 376 |
END IF ! matches IF (Iat.GT.I) THEN |
| 377 |
|
| 378 |
! Call Annul(Liaisons,IAt,I,Nat,NMaxL) |
| 379 |
! Liaisons(Iat,0)=Liaisons(Iat,0)-1 |
| 380 |
|
| 381 |
! We add the valence angles |
| 382 |
DO K=J+1,Liaisons(I,0) |
| 383 |
Kat=Liaisons(I,K) |
| 384 |
IF (Kat.GT.I) THEN |
| 385 |
! Checking the uniqueness of valence angle. |
| 386 |
! Duplicate bonds should not be added. |
| 387 |
AddPrimitiveCoord=.True. |
| 388 |
ScanCoord=>Coordinate |
| 389 |
DO WHILE (Associated(ScanCoord%next)) |
| 390 |
IF (ScanCoord%Type .EQ. 'ANGLE') THEN |
| 391 |
IF (ScanCoord%At1 .EQ. Iat) THEN |
| 392 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 393 |
IF (ScanCoord%At3 .EQ. Kat) THEN |
| 394 |
AddPrimitiveCoord=.False. |
| 395 |
END IF |
| 396 |
END IF |
| 397 |
END IF |
| 398 |
END IF |
| 399 |
ScanCoord => ScanCoord%next |
| 400 |
END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 401 |
|
| 402 |
IF (AddPrimitiveCoord) THEN |
| 403 |
IF (debug) WRITE(*,*) "Adding angle:",Iat,I,Kat |
| 404 |
NbAngles=NbAngles+1 |
| 405 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 406 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
| 407 |
! determined using all geometries. |
| 408 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 409 |
Call vecteur(i,Iat,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 410 |
CurrentCoord%value=angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 411 |
CurrentCoord%SignDihedral = 0 |
| 412 |
sAngleIatIKat=abs(sin(angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180.)) |
| 413 |
CurrentCoord%At1=Iat |
| 414 |
CurrentCoord%At2=I |
| 415 |
CurrentCoord%At3=KAt |
| 416 |
CurrentCoord%Type="ANGLE" |
| 417 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 418 |
ALLOCATE(CurrentCoord%next) |
| 419 |
NULLIFY(CurrentCoord%next%next) |
| 420 |
END IF |
| 421 |
CurrentCoord => CurrentCoord%next |
| 422 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 423 |
ELSE ! matches IF (Kat.GT.I) THEN |
| 424 |
! Kat is less than I. If there is a bond between I and Kat, then this angle |
| 425 |
! has already been taken into account. |
| 426 |
if (debug) WRITE(*,*) "Testing angle:",Iat,I,Kat |
| 427 |
Bond=.FALSE. |
| 428 |
DO L=1,Liaisons(Iat,0) |
| 429 |
IF (Liaisons(Iat,L).EQ.Kat) Bond=.TRUE. |
| 430 |
END DO |
| 431 |
IF (.NOT.Bond) THEN |
| 432 |
IF (debug) WRITE(*,*) "Not Bond Adding angle:",Iat,I,Kat |
| 433 |
|
| 434 |
! Checking the uniqueness of valence angle. |
| 435 |
! Duplicate bonds should not be added. |
| 436 |
AddPrimitiveCoord=.True. |
| 437 |
ScanCoord=>Coordinate |
| 438 |
DO WHILE (Associated(ScanCoord%next)) |
| 439 |
IF (ScanCoord%Type .EQ. 'ANGLE') THEN |
| 440 |
IF (ScanCoord%At1 .EQ. Iat) THEN |
| 441 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 442 |
IF (ScanCoord%At3 .EQ. Kat) THEN |
| 443 |
AddPrimitiveCoord=.False. |
| 444 |
END IF |
| 445 |
END IF |
| 446 |
END IF |
| 447 |
END IF |
| 448 |
ScanCoord => ScanCoord%next |
| 449 |
END DO |
| 450 |
|
| 451 |
IF (AddPrimitiveCoord) THEN |
| 452 |
NbAngles=NbAngles+1 |
| 453 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 454 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) |
| 455 |
! are determined using all geometries. |
| 456 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 457 |
Call vecteur(i,Iat,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 458 |
CurrentCoord%value=angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 459 |
CurrentCoord%SignDihedral = 0 |
| 460 |
CurrentCoord%At1=Iat |
| 461 |
CurrentCoord%At2=I |
| 462 |
CurrentCoord%At3=KAt |
| 463 |
CurrentCoord%Type="ANGLE" |
| 464 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 465 |
ALLOCATE(CurrentCoord%next) |
| 466 |
NULLIFY(CurrentCoord%next%next) |
| 467 |
END IF |
| 468 |
CurrentCoord => CurrentCoord%next |
| 469 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 470 |
END IF ! matches IF (.NOT.Bond) THEN |
| 471 |
END IF ! matches IF (Kat.GT.I) THEN, after else |
| 472 |
END DO ! matches DO K=J+1,Liaisons(I,0) |
| 473 |
END DO ! matches DO J=1,Liaisons(I,0) |
| 474 |
END IF ! matches IF (Liaisons(I,0).NE.0) THEN |
| 475 |
|
| 476 |
! We add dihedral angles. We do not concentrate on necessary angles, ie those that are |
| 477 |
! needed to build the molecule. Instead we collect all of them, and the choice of the best |
| 478 |
! ones will be done when diagonalizing the Baker matrix. |
| 479 |
IF (Liaisons(I,0).GE.3) Then |
| 480 |
DO J=1,Liaisons(I,0) |
| 481 |
Iat=Liaisons(I,J) |
| 482 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 483 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
| 484 |
! determined using all geometries. |
| 485 |
Call vecteur(Iat,i,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 486 |
|
| 487 |
DO K=J+1,Liaisons(I,0) |
| 488 |
Kat=Liaisons(I,K) |
| 489 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 490 |
sAngleIatIKat=abs(sin(angle(vx1,vy1,vz1,Norm1,-vx2,-vy2,-vz2,Norm2)*Pi/180.)) |
| 491 |
|
| 492 |
DO L=K+1,Liaisons(I,0) |
| 493 |
Lat=Liaisons(I,L) |
| 494 |
if (debug) WRITE(*,*) "0-Dihe Kat,I,Iat:",Kat,I,Iat,angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2) |
| 495 |
Call vecteur(iat,lat,x_refGeom,y_refGeom,z_refGeom,vx3,vy3,vz3,Norm3) |
| 496 |
sAngleIIatLat=abs(sin(angle(vx3,vy3,vz3,Norm3,vx2,vy2,vz2,Norm2)*Pi/180.)) |
| 497 |
if (debug) WRITE(*,*) "0-Dihe I,Iat,Lat:",angle(vx3,vy3,vz3,Norm3,vx2,vy2,vz2,Norm2) |
| 498 |
IF ((sAngleIatIKat.ge.0.01d0).AND.(sAngleIIatLat.ge.0.01d0)) THEN |
| 499 |
if (debug) WRITE(*,*) "Adding dihedral:",Kat,I,Iat,Lat |
| 500 |
|
| 501 |
! Checking for the uniqueness of valence angle. |
| 502 |
! Duplicate bonds should not be added. |
| 503 |
AddPrimitiveCoord=.True. |
| 504 |
ScanCoord=>Coordinate |
| 505 |
DO WHILE (Associated(ScanCoord%next)) |
| 506 |
IF (ScanCoord%Type .EQ. 'DIHEDRAL') THEN |
| 507 |
IF (ScanCoord%At1 .EQ. Kat) THEN |
| 508 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 509 |
IF (ScanCoord%At3 .EQ. Iat) THEN |
| 510 |
IF (ScanCoord%At4 .EQ. Lat) THEN |
| 511 |
AddPrimitiveCoord=.False. |
| 512 |
END IF |
| 513 |
END IF |
| 514 |
END IF |
| 515 |
END IF |
| 516 |
END IF |
| 517 |
ScanCoord => ScanCoord%next |
| 518 |
END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 519 |
|
| 520 |
! IF (AddPrimitiveCoord) THEN |
| 521 |
! NbDihedrals=NbDihedrals+1 |
| 522 |
! CALL produit_vect(vx3,vy3,vz3,norm3,vx2,vy2,vz2,norm2, & |
| 523 |
! vx5,vy5,vz5,norm5) |
| 524 |
!CALL produit_vect(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2, & |
| 525 |
! vx4,vy4,vz4,norm4) |
| 526 |
! CurrentCoord%value=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 527 |
! vx2,vy2,vz2,norm2)*Pi/180. |
| 528 |
! CurrentCoord%SignDihedral = 0 |
| 529 |
! CurrentCoord%At1=Kat |
| 530 |
! CurrentCoord%At2=I |
| 531 |
! CurrentCoord%At3=IAt |
| 532 |
! CurrentCoord%At4=LAt |
| 533 |
!WRITE(*,'(1X,":(dihed 1)",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') & |
| 534 |
! ScanCoord%At1,ScanCoord%At2,ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 535 |
! CurrentCoord%Type="DIHEDRAL" |
| 536 |
! IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 537 |
! ALLOCATE(CurrentCoord%next) |
| 538 |
! NULLIFY(CurrentCoord%next%next) |
| 539 |
! END IF |
| 540 |
! CurrentCoord => CurrentCoord%next |
| 541 |
!END IF ! matches IF (AddPrimitiveCoord) THEN |
| 542 |
|
| 543 |
END IF ! matches IF ((sAngleIatIKat.ge.0.01d0).AND.(sAngleIIatLat.ge.0.01d0)) THEN |
| 544 |
END DO ! matches DO L=K+1,Liaisons(I,0) |
| 545 |
END DO ! matches DO K=J+1,Liaisons(I,0) |
| 546 |
END DO ! matches DO J=1,Liaisons(I,0) |
| 547 |
END IF !matches IF (Liaisons(I,0).GE.3) Then |
| 548 |
|
| 549 |
! we now add other dihedrals |
| 550 |
DO J=1,Liaisons(I,0) |
| 551 |
Iat=Liaisons(I,J) |
| 552 |
If (Iat.LE.I) Cycle |
| 553 |
! values of the coordinate (bond) is calculated for the reference geometry |
| 554 |
! whereas the coordinates (bonds) (CurrentCoord%At1, CurrentCoord%At2, etc.) are |
| 555 |
! determined using all geometries. |
| 556 |
Call vecteur(Iat,i,x_refGeom,y_refGeom,z_refGeom,vx2,vy2,vz2,Norm2) |
| 557 |
|
| 558 |
DO K=1,Liaisons(I,0) |
| 559 |
IF (Liaisons(I,K).EQ.Iat) Cycle |
| 560 |
Kat=Liaisons(I,K) |
| 561 |
Call vecteur(i,kat,x_refGeom,y_refGeom,z_refGeom,vx1,vy1,vz1,Norm1) |
| 562 |
sAngleIatIKat=abs(sin(angle(vx1,vy1,vz1,Norm1,-vx2,-vy2,-vz2,Norm2)*Pi/180.)) |
| 563 |
|
| 564 |
DO L=1,Liaisons(Iat,0) |
| 565 |
Lat=Liaisons(Iat,L) |
| 566 |
IF (Lat.eq.I) Cycle |
| 567 |
|
| 568 |
if (debug) WRITE(*,*) "Dihe Kat,I,Iat:",angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2),sAngleIatIKat |
| 569 |
Call vecteur(iat,lat,x_refGeom,y_refGeom,z_refGeom,vx,vy,vz,Norm) |
| 570 |
|
| 571 |
sAngleIIatLat=abs(sin(angle(vx,vy,vz,Norm,vx2,vy2,vz2,Norm2)*Pi/180.)) |
| 572 |
if (debug) WRITE(*,*) "Dihe I,Iat,Lat:",angle(vx,vy,vz,Norm,vx2,vy2,vz2,Norm2) |
| 573 |
! we add the dihedral angle Kat-I-Iat-Lat |
| 574 |
if (debug) WRITE(*,*) "Trying dihedral:",Kat,I,Iat,Lat,sAngleIatIKat,sAngleIIatLat |
| 575 |
IF ((Lat.NE.Kat).AND.(Lat.Ne.I).AND.(sAngleIatIKat.ge.0.01d0) & |
| 576 |
.AND.(sAngleIIatLat.ge.0.01d0)) THEN |
| 577 |
if (debug) WRITE(*,*) "Adding dihedral:",Kat,I,Iat,Lat |
| 578 |
|
| 579 |
! Checking for the uniqueness of valence angle. |
| 580 |
! Duplicate bonds should not be added. |
| 581 |
AddPrimitiveCoord=.True. |
| 582 |
ScanCoord=>Coordinate |
| 583 |
DO WHILE (Associated(ScanCoord%next)) |
| 584 |
IF (ScanCoord%Type .EQ. 'DIHEDRAL') THEN |
| 585 |
IF (ScanCoord%At1 .EQ. Kat) THEN |
| 586 |
IF (ScanCoord%At2 .EQ. I) THEN |
| 587 |
IF (ScanCoord%At3 .EQ. Iat) THEN |
| 588 |
IF (ScanCoord%At4 .EQ. Lat) THEN |
| 589 |
AddPrimitiveCoord=.False. |
| 590 |
END IF |
| 591 |
END IF |
| 592 |
END IF |
| 593 |
END IF |
| 594 |
END IF |
| 595 |
ScanCoord => ScanCoord%next |
| 596 |
END DO |
| 597 |
|
| 598 |
IF (AddPrimitiveCoord) THEN |
| 599 |
NbDihedrals=NbDihedrals+1 |
| 600 |
Call vecteur(iat,lat,x_refGeom,y_refGeom,z_refGeom,vx3,vy3,vz3,Norm3) |
| 601 |
CALL produit_vect(vx3,vy3,vz3,norm3,vx2,vy2,vz2,norm2, & |
| 602 |
vx5,vy5,vz5,norm5) |
| 603 |
CALL produit_vect(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2, & |
| 604 |
vx4,vy4,vz4,norm4) |
| 605 |
CurrentCoord%value=angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 606 |
vx2,vy2,vz2,norm2)*Pi/180. |
| 607 |
CurrentCoord%At1=Kat |
| 608 |
CurrentCoord%At2=I |
| 609 |
CurrentCoord%At3=IAt |
| 610 |
CurrentCoord%At4=LAt |
| 611 |
CurrentCoord%Type="DIHEDRAL" |
| 612 |
CurrentCoord%SignDihedral=int(sign(1.d0,angle_d(vx4,vy4,vz4,norm4, & |
| 613 |
vx5,vy5,vz5,norm5, vx2,vy2,vz2,norm2))) |
| 614 |
WRITE(*,'(1X,":(dihed 2)",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') ScanCoord%At1,& |
| 615 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 616 |
IF (.NOT.ASSOCIATED(CurrentCoord%next)) THEN |
| 617 |
ALLOCATE(CurrentCoord%next) |
| 618 |
NULLIFY(CurrentCoord%next%next) |
| 619 |
END IF |
| 620 |
CurrentCoord => CurrentCoord%next |
| 621 |
END IF ! matches IF (AddPrimitiveCoord) THEN |
| 622 |
END IF ! matches IF ((Lat.NE.Kat).AND.(Lat.Ne.I).AND.(sAngleIatIKat.ge.0.01d0) ..... |
| 623 |
END DO ! matches DO L=1,Liaisons(Iat,0) |
| 624 |
END DO ! matches DO K=1,Liaisons(I,0) |
| 625 |
END DO ! matches DO J=1,Liaisons(I,0) |
| 626 |
END DO ! end of loop over all atoms, DO I=1, Nat |
| 627 |
END DO ! matches DO IGeom=1, NGeomI |
| 628 |
|
| 629 |
|
| 630 |
|
| 631 |
END IF ! if (debugPFL) |
| 632 |
DEALLOCATE(Liaisons) |
| 633 |
|
| 634 |
WRITE(*,*) "I have found" |
| 635 |
WRITE(*,*) NbBonds, " bonds" |
| 636 |
WRITE(*,*) NbAngles, " angles" |
| 637 |
WRITE(*,*) NbDihedrals, " dihedrals" |
| 638 |
|
| 639 |
WRITE(*,*) 'All in all...' |
| 640 |
ScanCoord=>Coordinate |
| 641 |
I=0 |
| 642 |
DO WHILE (Associated(ScanCoord%next)) |
| 643 |
I=I+1 |
| 644 |
SELECT CASE (ScanCoord%Type) |
| 645 |
CASE ('BOND')
|
| 646 |
!WRITE(IOOUT,'(1X,I3,":",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,ScanCoord%At2,ScanCoord%Value |
| 647 |
WRITE(*,'(1X,I3,":(bond )",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,ScanCoord%At2,ScanCoord%Value |
| 648 |
CASE ('ANGLE')
|
| 649 |
!WRITE(IOOUT,'(1X,I3,":",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1, & |
| 650 |
! ScanCoord%At2, ScanCoord%At3,ScanCoord%Value*180./Pi |
| 651 |
WRITE(*,'(1X,I3,":(angle)",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1, & |
| 652 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%Value*180./Pi |
| 653 |
CASE ('DIHEDRAL')
|
| 654 |
!WRITE(IOOUT,'(1X,I3,":",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,& |
| 655 |
! ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 656 |
WRITE(*,'(1X,I3,":(dihed)",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,& |
| 657 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,ScanCoord%Value*180./Pi |
| 658 |
END SELECT |
| 659 |
ScanCoord => ScanCoord%next |
| 660 |
END DO |
| 661 |
|
| 662 |
! NPrim is the number of primitive coordinates. |
| 663 |
NPrim=NbBonds+NbAngles+NbDihedrals |
| 664 |
|
| 665 |
! Now calculating values of all primitive bonds for all geometries: |
| 666 |
ALLOCATE(Xprimitive(NgeomI,NPrim),XPrimitiveF(NGeomF,NPrim)) |
| 667 |
ALLOCATE(UMatF(NGeomF,NPrim,NCoord)) |
| 668 |
ALLOCATE(BTransInvF(NGeomF,NCoord,3*Nat)) |
| 669 |
|
| 670 |
! We calculate the Primitive values for the first geometry, this plays a special role |
| 671 |
! as it will serve as a reference for other geometries ! |
| 672 |
|
| 673 |
x(1:Nat) = XyzGeomI(1,1,1:Nat) |
| 674 |
y(1:Nat) = XyzGeomI(1,2,1:Nat) |
| 675 |
z(1:Nat) = XyzGeomI(1,3,1:Nat) |
| 676 |
|
| 677 |
Call Calc_Xprim(nat,x,y,z,Coordinate,NPrim,XPrimitive(1,:)) |
| 678 |
|
| 679 |
DO IGeom=2, NGeomI |
| 680 |
|
| 681 |
x(1:Nat) = XyzGeomI(IGeom,1,1:Nat) |
| 682 |
y(1:Nat) = XyzGeomI(IGeom,2,1:Nat) |
| 683 |
z(1:Nat) = XyzGeomI(IGeom,3,1:Nat) |
| 684 |
|
| 685 |
Call Calc_Xprim(nat,x,y,z,Coordinate,NPrim,XPrimitive(IGeom,:),Xprimitive(1,:)) |
| 686 |
|
| 687 |
! ScanCoord=>Coordinate |
| 688 |
! I=0 ! index for the NPrim (NPrim is the number of primitive coordinates). |
| 689 |
! DO WHILE (Associated(ScanCoord%next)) |
| 690 |
! I=I+1 |
| 691 |
! SELECT CASE (ScanCoord%Type) |
| 692 |
! CASE ('BOND')
|
| 693 |
! Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx2,vy2,vz2,Norm2) |
| 694 |
! Xprimitive(IGeom,I) = Norm2 |
| 695 |
! CASE ('ANGLE')
|
| 696 |
! Call vecteur(ScanCoord%At2,ScanCoord%At3,x,y,z,vx1,vy1,vz1,Norm1) |
| 697 |
! Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx2,vy2,vz2,Norm2) |
| 698 |
! Xprimitive(IGeom,I) = angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180. |
| 699 |
! CASE ('DIHEDRAL')
|
| 700 |
|
| 701 |
|
| 702 |
! Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx1,vy1,vz1,Norm1) |
| 703 |
! Call vecteur(ScanCoord%At2,ScanCoord%At3,x,y,z,vx2,vy2,vz2,Norm2) |
| 704 |
! Call vecteur(ScanCoord%At3,ScanCoord%At4,x,y,z,vx3,vy3,vz3,Norm3) |
| 705 |
! Call produit_vect(vx1,vy1,vz1,norm1,vx2,vy2,vz2,norm2, & |
| 706 |
! vx4,vy4,vz4,norm4) |
| 707 |
! Call produit_vect(vx3,vy3,vz3,norm3,vx2,vy2,vz2,norm2, & |
| 708 |
! vx5,vy5,vz5,norm5) |
| 709 |
|
| 710 |
! DiheTmp= angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, & |
| 711 |
! vx2,vy2,vz2,norm2) |
| 712 |
! Xprimitive(IGeom,I) = DiheTmp*Pi/180. |
| 713 |
! ! We treat large dihedral angles differently as +180=-180 mathematically and physically |
| 714 |
! ! but this causes lots of troubles when converting baker to cart. |
| 715 |
! ! So we ensure that large dihedral angles always have the same sign |
| 716 |
! if (abs(ScanCoord%SignDihedral).NE.1) THEN |
| 717 |
! ScanCoord%SignDihedral=Int(Sign(1.D0,DiheTmp)) |
| 718 |
! ELSE |
| 719 |
! If ((abs(DiheTmp).GE.170.D0).AND.(Sign(1.,DiheTmp)*ScanCoord%SignDihedral<0)) THEN |
| 720 |
! Xprimitive(IGeom,I) = DiheTmp*Pi/180.+ ScanCoord%SignDihedral*2.*Pi |
| 721 |
! END IF |
| 722 |
! END IF |
| 723 |
! ! Another test... will all this be consistent ??? |
| 724 |
! ! We want the shortest path, so we check that the change in dihedral angles is less than Pi: |
| 725 |
! IF (IGeom.GT.1) THEN |
| 726 |
! IF (abs(Xprimitive(IGeom,I)-XPrimitive(IGeom-1,I)).GE.Pi) THEN |
| 727 |
! if ((Xprimitive(IGeom,I)-XPrimitive(IGeom-1,I)).GE.Pi) THEN |
| 728 |
! Xprimitive(IGeom,I)=Xprimitive(IGeom,I)-2.d0*Pi |
| 729 |
! ELSE |
| 730 |
! Xprimitive(IGeom,I)=Xprimitive(IGeom,I)+2.d0*Pi |
| 731 |
! END IF |
| 732 |
! END IF |
| 733 |
! END IF |
| 734 |
! END SELECT |
| 735 |
! ScanCoord => ScanCoord%next |
| 736 |
! END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 737 |
END DO ! matches DO IGeom=1, NGeomI |
| 738 |
|
| 739 |
IF (debug) THEN |
| 740 |
WRITE(*,*) "DBG Calc_Baker Xprimitives for all geometries" |
| 741 |
DO IGeom=1, NGeomI |
| 742 |
WRITE(*,*) "Geometry ",IGeom |
| 743 |
ScanCoord=>Coordinate |
| 744 |
I=0 ! index for the NPrim (NPrim is the number of primitive coordinates). |
| 745 |
DO WHILE (Associated(ScanCoord%next)) |
| 746 |
I=I+1 |
| 747 |
SELECT CASE (ScanCoord%Type) |
| 748 |
CASE ('BOND')
|
| 749 |
WRITE(*,'(1X,I3,":",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,ScanCoord%At2,Xprimitive(IGeom,I) |
| 750 |
CASE ('ANGLE')
|
| 751 |
WRITE(*,'(1X,I3,":",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1, & |
| 752 |
ScanCoord%At2, ScanCoord%At3,Xprimitive(IGeom,I)*180./Pi |
| 753 |
CASE ('DIHEDRAL')
|
| 754 |
WRITE(*,'(1X,I3,":",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,& |
| 755 |
ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,Xprimitive(IGeom,I)*180./Pi |
| 756 |
END SELECT |
| 757 |
ScanCoord => ScanCoord%next |
| 758 |
END DO ! matches DO WHILE (Associated(ScanCoord%next)) |
| 759 |
END DO ! matches DO IGeom=1, NGeomI |
| 760 |
END IF |
| 761 |
! Here reference geometry is assigned to Geom. Earlier x,y,z(Nat) were assigned from XyzGeomI(...) |
| 762 |
! before the call of this (Calc_baker) subroutine and passed to this subroutine as arguments of the |
| 763 |
! subroutine. |
| 764 |
! PFL 19 Feb 2008 -> |
| 765 |
! In order to reproduce the B matrix in the Baker article, one has |
| 766 |
! to divide Geom by a0. |
| 767 |
! However, this is inconsitent with our way of storing geometries |
| 768 |
! so we do not do it ! |
| 769 |
|
| 770 |
Geom(1,:)=XyzGeomI(IGeomRef,1,1:Nat) ! XyzGeomI(NGeomI,3,Nat) |
| 771 |
Geom(2,:)=XyzGeomI(IGeomRef,2,1:Nat) |
| 772 |
Geom(3,:)=XyzGeomI(IGeomRef,3,1:Nat) |
| 773 |
|
| 774 |
! <- PFL 19 Feb 2008 |
| 775 |
|
| 776 |
! We now have to compute dq/dx... |
| 777 |
ALLOCATE(BprimT(3*Nat,NPrim)) |
| 778 |
BprimT=0.d0 |
| 779 |
|
| 780 |
ScanCoord=>Coordinate |
| 781 |
I=0 |
| 782 |
DO WHILE (Associated(ScanCoord%next)) |
| 783 |
I=I+1 |
| 784 |
SELECT CASE (ScanCoord%Type) |
| 785 |
CASE ('BOND')
|
| 786 |
CALL CONSTRAINTS_BONDLENGTH_DER(Nat,ScanCoord%at1,ScanCoord%AT2, & |
| 787 |
Geom,BprimT(1,I)) |
| 788 |
CASE ('ANGLE')
|
| 789 |
CALL CONSTRAINTS_BONDANGLE_DER(Nat,ScanCoord%At1,ScanCoord%AT2, & |
| 790 |
ScanCoord%At3,Geom,BprimT(1,I)) |
| 791 |
CASE ('DIHEDRAL')
|
| 792 |
CALL CONSTRAINTS_TORSION_DER2(Nat,ScanCoord%At1,ScanCoord%AT2, & |
| 793 |
ScanCoord%At3,ScanCoord%At4,Geom,BprimT(1,I)) |
| 794 |
! CALL CONSTRAINTS_TORSION_DER(Nat,ScanCoord%At1,ScanCoord%AT2, & |
| 795 |
! ScanCoord%At3,ScanCoord%At4,Geom,BprimT(1,I)) |
| 796 |
|
| 797 |
END SELECT |
| 798 |
ScanCoord => ScanCoord%next |
| 799 |
END DO |
| 800 |
|
| 801 |
|
| 802 |
!!!!!!!!!!!!!!!!!!!! |
| 803 |
! |
| 804 |
! PFL Debug |
| 805 |
! |
| 806 |
!!!!!!!!!!!!!!!!!!!! |
| 807 |
|
| 808 |
if (debugPFL) THEN |
| 809 |
WRITe(*,*) "DBG PFL Calc_Baker =====" |
| 810 |
DzDc=0.d0 |
| 811 |
WRITE(*,*) "PFL DBG, DzdC" |
| 812 |
do I=1,Nat |
| 813 |
Geom(1,i)=XyzGeomI(IGeomRef,1,orderInv(i)) ! XyzGeomI(NGeomI,3,Nat) |
| 814 |
Geom(2,i)=XyzGeomI(IGeomRef,2,OrderInv(i)) |
| 815 |
Geom(3,i)=XyzGeomI(IGeomRef,3,OrderInv(i)) |
| 816 |
WRITE(*,*) I,OrderInv(I),Geom(:,I) |
| 817 |
end do |
| 818 |
CALL CalcBMat_int (nat, Geom, indzmat, dzdc, massat,atome) |
| 819 |
|
| 820 |
WRITE(*,*) "PFL DBG, BPrimT" |
| 821 |
DO I=1,NPrim |
| 822 |
WRITE(*,'(50(1X,F12.6))') BPrimT(:,I) |
| 823 |
END DO |
| 824 |
WRITe(*,*) "DBG PFL Calc_Baker =====" |
| 825 |
END IF |
| 826 |
|
| 827 |
!!!!!!!!!!!!!!!!!!!! |
| 828 |
! |
| 829 |
! PFL Debug |
| 830 |
! |
| 831 |
!!!!!!!!!!!!!!!!!!!! |
| 832 |
|
| 833 |
DEALLOCATE(Geom) |
| 834 |
|
| 835 |
! BprimT(3*Nat,NPrim) |
| 836 |
! We now compute G=B(BT) matrix |
| 837 |
ALLOCATE(Gmat(NPrim,NPrim)) |
| 838 |
GMat=0.d0 |
| 839 |
DO I=1,NPrim |
| 840 |
DO J=1,3*Nat |
| 841 |
GMat(:,I)=Gmat(:,I)+BprimT(J,:)*BprimT(J,I) !*1.d0/mass(atome(int(K/3.d0))) |
| 842 |
END DO |
| 843 |
END DO |
| 844 |
|
| 845 |
!!!!!!!!!!!!!!!!!!!! |
| 846 |
! |
| 847 |
! PFL Debug ---> |
| 848 |
! |
| 849 |
!!!!!!!!!!!!!!!!!!!! |
| 850 |
if (debugPFL) THEN |
| 851 |
GMat=0.d0 |
| 852 |
DO I=1,NPrim |
| 853 |
GMat(I,I)=1. |
| 854 |
END DO |
| 855 |
END IF |
| 856 |
|
| 857 |
!!!!!!!!!!!!!!!!!!!! |
| 858 |
! |
| 859 |
! <--- PFL Debug |
| 860 |
! |
| 861 |
!!!!!!!!!!!!!!!!!!!! |
| 862 |
|
| 863 |
!DO I=1,NPrim |
| 864 |
! WRITE(*,'(20(1X,F6.3))') GMat(1:min(20,NPrim),I) |
| 865 |
!END DO |
| 866 |
|
| 867 |
! We diagonalize G |
| 868 |
ALLOCATE(EigVal(NPrim),EigVec(NPrim,NPrim)) |
| 869 |
Call Jacobi(GMat,NPrim,EigVal,EigVec,NPrim) |
| 870 |
Call Trie(NPrim,EigVal,EigVec,NPrim) |
| 871 |
DO I=1,NPrim |
| 872 |
WRITE(*,'(1X,"Vector ",I3,": e=",F8.3)') I,EigVal(i) |
| 873 |
WRITE(*,'(20(1X,F8.4))') EigVec(1:min(20,NPrim),I) |
| 874 |
END DO |
| 875 |
|
| 876 |
!DO I=1,NPrim |
| 877 |
! WRITE(*,'(1X,"Vector ",I3,(20(F8.3)))') I,EigVec(1:min(20,NPrim),I) |
| 878 |
! END DO |
| 879 |
|
| 880 |
!DO I=1,NPrim |
| 881 |
! 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,& |
| 882 |
! 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),& |
| 883 |
!EigVec(2,I),EigVec(3,I),EigVec(5,I),EigVec(12,I),EigVec(13,I),EigVec(15,I),EigVec(7,I),& |
| 884 |
!EigVec(8,I),EigVec(9,I),EigVec(10,I),EigVec(11,I),EigVec(17,I) |
| 885 |
!END DO |
| 886 |
|
| 887 |
! We construct the new DzDc(b=baker) matrix |
| 888 |
! UMat is nonredundant vector set, i.e. set of eigenvectors of BB^T corresponding |
| 889 |
! to eigenvalues > zero. |
| 890 |
ALLOCATE(UMat(NPrim,NCoord)) |
| 891 |
ALLOCATE(UMat_local(NPrim,NCoord)) |
| 892 |
ALLOCATE(UMat_tmp(NPrim,3*Nat-6)) |
| 893 |
! BMat_BakerT(3*Nat,NCoord), allocated in Path.f90, |
| 894 |
! NCoord=3*Nat-6 |
| 895 |
BMat_BakerT = 0.d0 |
| 896 |
J=0 |
| 897 |
UMat=0.d0 |
| 898 |
UMat_tmp=0.d0 |
| 899 |
DO I=1,NPrim |
| 900 |
IF (abs(eigval(I))>=1e-6) THEN |
| 901 |
J=J+1 |
| 902 |
DO K=1,NPrim |
| 903 |
!DzDcb(:,J)=DzDcb(:,J)+Eigvec(K,I)*BprimT(:,K) ! original |
| 904 |
! BprimT is transpose of B^prim. |
| 905 |
! B = UMat^T B^prim, B^T = (B^prim)^T UMat |
| 906 |
BMat_BakerT(:,J)=BMat_BakerT(:,J)+BprimT(:,K)*Eigvec(K,I) |
| 907 |
!Dzdcb(:,J)=DzDcb(:,J)+Eigvec(K,:)*BprimT(I,K) |
| 908 |
END DO |
| 909 |
IF(J .GT. 3*Nat-6) THEN |
| 910 |
WRITE(*,*) 'Number of vectors in Eigvec with eigval .GT. 1e-6(=UMat) (=' & |
| 911 |
,J,') exceeded 3*Nat-6=',3*Nat-6, & |
| 912 |
'Stopping the calculation.' |
| 913 |
STOP |
| 914 |
END IF |
| 915 |
UMat_tmp(:,J) = Eigvec(:,I) |
| 916 |
END IF |
| 917 |
END DO |
| 918 |
|
| 919 |
if (debug) THEN |
| 920 |
WRITE(*,*) "DBG Calc_Baker: UMat" |
| 921 |
DO I=1,3*Nat-6 |
| 922 |
WRITE(*,'(50(1X,F12.8))') UMat_tmp(:,I) |
| 923 |
END DO |
| 924 |
END IF |
| 925 |
|
| 926 |
! THIS IS TO BE CORRECTED: |
| 927 |
UMat = UMat_tmp |
| 928 |
!J=0 |
| 929 |
!DO I=1, 3*Nat-6 |
| 930 |
! IF ((I .NE. 6) .AND. (I .NE. 7) .AND. (I .NE. 9)) Then |
| 931 |
! J=J+1 |
| 932 |
! Print *, 'J=', J, ' I=', I |
| 933 |
! UMat(:,J) = UMat_tmp(:,I) |
| 934 |
!END IF |
| 935 |
!END DO |
| 936 |
! BMat_BakerT=0.d0 |
| 937 |
!DO I=1,NCoord |
| 938 |
! DO J=1,NPrim |
| 939 |
! B = UMat^T B^prim, B^T = (B^prim)^T UMat |
| 940 |
! BMat_BakerT(:,I)=BMat_BakerT(:,I)+BprimT(:,J)*UMat(J,I) |
| 941 |
! END DO |
| 942 |
!END DO |
| 943 |
! TO BE CORRECTED, ENDS HERE. |
| 944 |
|
| 945 |
IntCoordI=0.d0 |
| 946 |
DO IGeom=1, NGeomI |
| 947 |
DO I=1, NPrim |
| 948 |
! Transpose of UMat is needed below, that is why UMat(I,:). |
| 949 |
IntCoordI(IGeom,:) = IntCoordI(IGeom,:) + UMat(I,:)*Xprimitive(IGeom,I) |
| 950 |
END DO |
| 951 |
END DO |
| 952 |
|
| 953 |
if (debug) THEN |
| 954 |
WRITE(*,*) "DBG Calc_Baker IntCoordI" |
| 955 |
DO IGeom=1, NGeomI |
| 956 |
WRITE(*,'(1X,I5,":",30(1X,F10.6))') IGeom,IntCoordI(IGeom,:) |
| 957 |
END DO |
| 958 |
END IF |
| 959 |
|
| 960 |
|
| 961 |
! the following might be used to get rid of some coordinates that |
| 962 |
! do not respect the symmetry of the problem. |
| 963 |
|
| 964 |
! ! We look at the group symmetry of the molecule. Nothing complicate here |
| 965 |
! ! we just look for planar symmetry. |
| 966 |
! ! We first place it into the standard orientation |
| 967 |
! Call Std_ori(Nat,x,y,z,a,b,c,massat) |
| 968 |
|
| 969 |
! ! Is the molecule planar |
| 970 |
! DO I=1,Nat |
| 971 |
! WRITE(*,*) nom(atome(i)),x(i),y(i),z(i) |
| 972 |
! END DO |
| 973 |
DEALLOCATE(BprimT,GMat,EigVal,EigVec) ! BprimT is B^prim^T |
| 974 |
! Calculation of BTransInv starts here: |
| 975 |
! Calculation of BBT(3*Nat-6,3*Nat-6)=BB^T: |
| 976 |
! BMat_BakerT(3*Nat,NCoord) is Transpose of B = UMat^TB^prim |
| 977 |
ALLOCATE(BBT(NCoord,NCoord)) |
| 978 |
BBT = 0.d0 |
| 979 |
DO I=1, NCoord |
| 980 |
DO J=1, 3*Nat |
| 981 |
! BBT(:,I) forms BB^T |
| 982 |
BBT(:,I) = BBT(:,I) + BMat_BakerT(J,:)*BMat_BakerT(J,I) |
| 983 |
END DO |
| 984 |
END DO |
| 985 |
|
| 986 |
!ALLOCATE(V(3*Nat,3*Nat)) |
| 987 |
!Call GINVSE(BBT,3*Nat,3*Nat,BBT_inv,3*Nat,3*Nat,3*Nat,1e-6,V,3*Nat,FAIL,NOUT) |
| 988 |
!DEALLOCATE(V) |
| 989 |
ALLOCATE(BBT_inv(NCoord,NCoord)) |
| 990 |
! GenInv is in Mat_util.f90 |
| 991 |
Call GenInv(NCoord,BBT,BBT_inv,NCoord) |
| 992 |
|
| 993 |
! Calculation of (B^T)^-1 = (BB^T)^-1B: |
| 994 |
!ALLOCATE(BTransInv(3*Nat-6,3*Nat)) ! allocated in Path.f90 |
| 995 |
BTransInv = 0.d0 |
| 996 |
DO I=1, 3*Nat |
| 997 |
DO J=1, NCoord |
| 998 |
BTransInv(:,I) = BTransInv(:,I) + BBT_inv(:,J)*BMat_BakerT(I,J) |
| 999 |
END DO |
| 1000 |
END DO |
| 1001 |
BTransInv_local = BTransInv |
| 1002 |
UMat_local = UMat |
| 1003 |
DEALLOCATE(BBT,BBT_inv,UMat_tmp) |
| 1004 |
DEALLOCATE(x_refGeom,y_refGeom,z_refGeom,x,y,z) |
| 1005 |
IF (debug) WRITE(*,*) "DBG Calc_baker over." |
| 1006 |
END SUBROUTINE Calc_baker |