Chimie Théorique » Opt'n Path

SUBROUTINE Calc_Xprim(nat,x,y,z,Coordinate,NPrim,XPrimitive,XPrimRef)

!     

! This subroutine uses the description of a list of Coordinates

! to compute the values of the coordinates for a given geometry.

!

!!!!!!!!!!

! Input:

!   Na: INTEGER, Number of atoms

!  x,y,z(Na): REAL, cartesian coordinates of the considered geometry

! Coordinate (Pointer(ListCoord)): description of the wanted coordiantes

! NPrim, INTEGER: Number of coordinates to compute

!

! Optional: XPrimRef(NPrim) REAL: array that contains coordinates values for

! a former geometry. Useful for Dihedral angles evolution...

!!!!!!!!!!!

! Output:

! XPrimimite(NPrim) REAL: array that will contain the values of the coordinates

!

!!!!!!!!!

!----------------------------------------------------------------------

!  Copyright 2003-2014 Ecole Normale Supérieure de Lyon, 

!  Centre National de la Recherche Scientifique,

!  Université Claude Bernard Lyon 1. All rights reserved.

!

!  This work is registered with the Agency for the Protection of Programs 

!  as IDDN.FR.001.100009.000.S.P.2014.000.30625

!

!  Authors: P. Fleurat-Lessard, P. Dayal

!  Contact: optnpath@gmail.com

!

! This file is part of "Opt'n Path".

!

!  "Opt'n Path" is free software: you can redistribute it and/or modify

!  it under the terms of the GNU Affero General Public License as

!  published by the Free Software Foundation, either version 3 of the License,

!  or (at your option) any later version.

!

!  "Opt'n Path" is distributed in the hope that it will be useful,

!  but WITHOUT ANY WARRANTY; without even the implied warranty of

!

!  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

!  GNU Affero General Public License for more details.

!

!  You should have received a copy of the GNU Affero General Public License

!  along with "Opt'n Path". If not, see <http://www.gnu.org/licenses/>.

!

! Contact The Office of Technology Licensing, valorisation@ens-lyon.fr,

! for commercial licensing opportunities.

!----------------------------------------------------------------------

  Use VarTypes

  Use Io_module

  Use Path_module, only : pi

  IMPLICIT NONE

  Type (ListCoord), POINTER :: Coordinate

  INTEGER(KINT), INTENT(IN) :: Nat,NPrim

  REAL(KREAL), INTENT(IN) :: x(Nat), y(Nat), z(Nat)

  REAL(KREAL), INTENT(IN), OPTIONAL :: XPrimRef(NPrim) 

  REAL(KREAL), INTENT(OUT) :: XPrimitive(NPrim)

  Type (ListCoord), POINTER :: ScanCoord

  real(KREAL) :: vx1,vy1,vz1,norm1

  real(KREAL) :: vx2,vy2,vz2,norm2

  real(KREAL) :: vx3,vy3,vz3,norm3

  real(KREAL) :: vx4,vy4,vz4,norm4

  real(KREAL) :: vx5,vy5,vz5,norm5

  INTEGER(KINT) :: I

  REAL(KREAL) :: DiheTmp

  LOGICAL :: debug, debugPFL

  INTERFACE

     function valid(string) result (isValid)

       CHARACTER(*), intent(in) :: string

       logical                  :: isValid

     END function VALID

     FUNCTION angle(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2)

        use Path_module, only :  Pi,KINT, KREAL

       real(KREAL) ::  v1x,v1y,v1z,norm1

       real(KREAL) ::  v2x,v2y,v2z,norm2

       real(KREAL) ::  angle

     END FUNCTION ANGLE

     FUNCTION SinAngle(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2)

        use Path_module, only :  Pi,KINT, KREAL

       real(KREAL) ::  v1x,v1y,v1z,norm1

       real(KREAL) ::  v2x,v2y,v2z,norm2

       real(KREAL) ::  SinAngle

     END FUNCTION SINANGLE

     FUNCTION angle_d(v1x,v1y,v1z,norm1,v2x,v2y,v2z,norm2,v3x,v3y,v3z,norm3)

        use Path_module, only :  Pi,KINT, KREAL

       real(KREAL) ::  v1x,v1y,v1z,norm1

       real(KREAL) ::  v2x,v2y,v2z,norm2

       real(KREAL) ::  v3x,v3y,v3z,norm3

       real(KREAL) ::  angle_d,ca,sa

     END FUNCTION ANGLE_D

  END INTERFACE

  debug=valid("Calc_Xprim")

  debugPFL=valid("BakerPFL")

  if (debug) Call Header("Entering Cal_XPrim")

  IF (debug) THEN

     WRITE(*,*) "DBG Calc_Xprim, geom"

     DO I=1,Nat

        WRITE(*,'(1X,I5,3(1X,F15.3))') I,X(I),y(i),z(i)

     END DO

     IF (Present(XPrimRef)) THEN

        WRITE(*,*) "XPrimRef"

        WRITE(*,'(15(1X,F10.6))') XPrimRef

     END IF

     WRITE(*,*) "NPrim:",NPrim

  END IF

!  WRITE(*,*) "Coordinate:",associated(Coordinate),coordinate%Type

     ScanCoord => Coordinate

!  WRITE(*,*) "ScanCoord:",associated(ScanCoord),ScanCoord%Type

!     WRITE(*,*) "coucou"

     I=0 ! index for the NPrim (NPrim is the number of primitive coordinates).

     DO WHILE (Associated(ScanCoord%next))

        I=I+1

!        WRITE(*,*) i

        SELECT CASE (ScanCoord%Type)

        CASE ('BOND')

           Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx2,vy2,vz2,Norm2)

           Xprimitive(I) = Norm2  

        CASE ('ANGLE')

           Call vecteur(ScanCoord%At2,ScanCoord%At3,x,y,z,vx1,vy1,vz1,Norm1)

           Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx2,vy2,vz2,Norm2)

           Xprimitive(I) = angle(vx1,vy1,vz1,Norm1,vx2,vy2,vz2,Norm2)*Pi/180.

        CASE ('DIHEDRAL')

           Call vecteur(ScanCoord%At2,ScanCoord%At1,x,y,z,vx1,vy1,vz1,Norm1)

           Call vecteur(ScanCoord%At2,ScanCoord%At3,x,y,z,vx2,vy2,vz2,Norm2)

           Call vecteur(ScanCoord%At3,ScanCoord%At4,x,y,z,vx3,vy3,vz3,Norm3)

           Call produit_vect(vx1,vy1,vz1,vx2,vy2,vz2, &

                vx4,vy4,vz4,norm4)

           Call produit_vect(vx3,vy3,vz3,vx2,vy2,vz2, &

                vx5,vy5,vz5,norm5)

           DiheTmp= angle_d(vx4,vy4,vz4,norm4,vx5,vy5,vz5,norm5, &

                vx2,vy2,vz2,norm2)

           Xprimitive(I) = DiheTmp*Pi/180.

! PFL 15th March 2008 ->

! I think that the test on changes less than Pi should be enough

!! We treat large dihedral angles differently as +180=-180 mathematically and physically

!! but this causes lots of troubles when converting baker to cart.

!! So we ensure that large dihedral angles always have the same sign

!                    if (abs(ScanCoord%SignDihedral).NE.1) THEN

!                        ScanCoord%SignDihedral=Int(Sign(1.D0,DiheTmp))

!                    ELSE

!                        If ((abs(DiheTmp).GE.170.D0).AND.(Sign(1.,DiheTmp)*ScanCoord%SignDihedral<0)) THEN

!                          Xprimitive(I) = DiheTmp*Pi/180.+ ScanCoord%SignDihedral*2.*Pi

!                       END IF

!                  END IF

!!!! <- PFL 15th March 2008

! Another test... will all this be consistent ??? 

! We want the shortest path, so we check that the change in dihedral angles is less than Pi:

           IF (Present(XPrimRef)) THEN

              IF (abs(Xprimitive(I)-XPrimRef(I)).GE.Pi) THEN

                 if (debug) THEN 

                    WRITE(*,*) "Pb dihedral, i,Xprimivite,XPrimref=",i,XPrimitive(I),XPrimRef(I)

                    WRITE(*,*) "In deg Xprimivite,XPrimref=",XPrimitive(I)*180./Pi,XPrimRef(I)*180/Pi

                 END IF

                 if ((Xprimitive(I)-XPrimRef(I)).GE.Pi) THEN

                    Xprimitive(I)=Xprimitive(I)-2.d0*Pi

                 ELSE

                    Xprimitive(I)=Xprimitive(I)+2.d0*Pi

                 END IF

              END IF

              if (debug) WRITE(*,*) " New Xprimivite",XPrimitive(I),XPrimitive(I)*180./Pi

           END IF

        CASE DEFAULT

           WRITE(*,*) "Scancoord%type unknown for I",I,scancoord%type

      END SELECT

        ScanCoord => ScanCoord%next

     END DO ! matches DO WHILE (Associated(ScanCoord%next))

  IF (debug) THEN

     WRITE(*,*) "DBG Calc_Xprim Values"

     WRITE(*,*) "Found ",I," primitives"

     ScanCoord=>Coordinate

     I=0 ! index for the NPrim (NPrim is the number of primitive coordinates).

     DO WHILE (Associated(ScanCoord%next))

        I=I+1

        SELECT CASE (ScanCoord%Type)

        CASE ('BOND')

           WRITE(*,'(1X,I3,":",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,ScanCoord%At2,Xprimitive(I)

        CASE ('ANGLE')

           WRITE(*,'(1X,I3,":",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1, &

            ScanCoord%At2, ScanCoord%At3,Xprimitive(I)*180./Pi

        CASE ('DIHEDRAL')

           WRITE(*,'(1X,I3,":",I5," - ",I5," - ",I5," - ",I5," = ",F15.6)') I,ScanCoord%At1,&

           ScanCoord%At2, ScanCoord%At3,ScanCoord%At4,Xprimitive(I)*180./Pi

        END SELECT

        ScanCoord => ScanCoord%next

     END DO ! matches DO WHILE (Associated(ScanCoord%next))

  END IF

  if (debug) Call Header(" Cal_XPrim OVER ")

END SUBROUTINE Calc_Xprim