Chimie Théorique » OpenPath

          program Xyz2Path

! This programs reads a XYZ file and converts it into distances,

! valence angle and dihedral angles.

! It prints them as a function of the irc distance...

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

! Input: name of the XYZ File

! it also needs a file call list which has the following structure:

! one line contains the type of the value you want to follow, it can be

! b  for a Bond distance

! a for an angle

! d for a dihedral

! this descriptor is followed by the number of the atoms involved !

! a typical file can be:

! b  1  2

! b 2  3

! a 1 2 3

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

! Ouput: A files call Scan.dat

! wich contains in the first lines the input file (as a reminder)

! and then for each step the wanted values

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

! Second version also reads the energy (as to be written after E= on

! the comment line)

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

! Third version contains a new command: c for Center of Mass

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

! v 3.1 the c command now creates the center of mass... and allows

! people to do whatever they want with it...

! Syntax: c NbAt ListAt

          IMPLICIT NONE

          INCLUDE "Xyz2Path.param"

          character*40 f1

          REAL*8   geos(3,maxnat), geos1(3,maxnat)

          character*33 fmt

          character*3 atoms(maxnat)

          character*5 Type

          Character*120 line

          INTEGER*4 NbPrint

          REAL*8   AU2PS,Pi

          REAL*8  Mass(MaxNat), Ener, Conv, Ds, s

          REAL*8  MassAt(0:86)

          INTEGER*4 At1,At2,At3,At4,IOOUT,Iat

          INTEGER*4  IArg, I, NNN, Ng, J

          INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbCOM

          INTEGER*4 At1B(MaxNat),At2B(MaxNat)

          INTEGER*4 At1A(MaxNat),At2A(MaxNat),At3A(MaxNat)

          INTEGER*4 At1D(MaxNat),At2D(MaxNat),At3D(MaxNat),At4D(MaxNat)

          INTEGER*4 AtCom(0:MaxNat,MaxNat)

          REAL*8    VB(MaxNat),VA(MaxNat),VD(MaxNat),VCOM(MaxNat)

          REAL*8 MRot(3,3), Rmsd

          LOGICAL FExist,FRot,FAlign,Debug

          INTEGER*4 ConvertNumAt

          external ConvertNumAt

          COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbCom, At1B,At2B,

     &         At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom

          COMMON /Values/VB,VA,VD,VCom

          COMMON /Const/AU2ps,Pi

          DATA MassAt/0.0D0,

     $           1.0078D0,                      4.0026D0,

     $            7.0160D0, 9.0122D0,11.0093D0,

     $           12.0000D0,14.0031D0,15.9949D0,18.9984D0,19.9924D0,

     $           22.9898D0,23.9850D0,26.9815D0,

     $           27.9769D0,30.9738D0,31.9721D0,34.9688D0,39.9624D0,

     $           39.0983D0,40.08D0,

     $             44.9559D0, 47.88D0, 50.9415D0, 51.996D0, 54.9380D0,

     $             55.847D0, 58.9332D0, 58.69D0, 63.546D0, 65.39D0,

     $           69.72D0,72.59D0,74.9216D0,78.96D0,79.904D0,83.80D0,

     $           85.4678D0,87.62D0,88.9059D0,91.224D0,92.9064D0,

     $   95.94D0,98D0,101.07D0,102.906D0,106.42D0,107.868D0,112.41D0,

     $   114.82D0,118.71D0,121.75D0,127.60D0,126.905D0,131.29D0,

!     6           'CS','BA',

     $           132.905,137.34,

!     6       'LA',

!               'CE','PR','ND','PM','SM','EU','GD',

!               'TB','DY','HO', 'ER','TM','YB','LU',

     $      138.91,

     $       140.12, 130.91, 144.24,147.,150.35, 151.96,157.25,

     $       158.924, 162.50, 164.93, 167.26,168.93,173.04,174.97,

!     6                'HF','TA',' W','RE','OS','IR','PT',

!                      'AU','HG',

!     6                                 'TL','PB','BI','PO','AT','RN'/

     $       178.49, 180.95, 183.85, 186.2, 190.2, 192.2, 195.09,

     $       196.97, 200.59,

     $       204.37, 207.19,208.98,210.,210.,222. /

          AU2PS=1./41341.37

          NbPrint=100

          Pi=dacos(-1.d0)

          IOOUT=13

          Conv=1.

          FRot=.TRUE.

          FAlign=.TRUE.

          Debug=.FALSE.

          NbDist=0

          NbAngle=0

          NbDie=0

          iarg=command_argument_count()

          if (iarg.lt.1) then

                 write(*,*) 'XYZ filename:'

              read(*,'(a)') f1

            else

              call getarg(1,f1)

          endif

          open(13,file='Scan.dat')

          INQUIRE(File='list',Exist=FExist)

          if (.NOT.FExist) THEN

             WRITE(*,*) "No file 'list', just printing Energy"

          END IF

          open(11,file=f1)

          call rtraitem(11,nnn,ener,geos1,atoms)

          close(11)

         DO I=1,nnn

            Iat=ConvertNumAt(atoms(I))

            Mass(I)=MassAt(Iat)

!           write(*,*) I,Atoms(I),Mass(I),geos1(:,I)

         END DO

         if (FExist) THEN

         open(14,file='list')

         Type="d"

         DO WHILE (Type.ne."E")

          CALL READLINE(14,Type,Line)

!          WRITE(*,*) Line,Type

          if (Type.eq."b") THEN

             NbDist=NbDist+1

             READ(Line,*) At1,At2

             At1B(NbDist)=At1

             At2B(NbDist)=At2

             WRITE(13,'("# b ",2(A3,I3))') Atoms(At1),At1,Atoms(At2),At2

             WRITE(*,'("# b ",2(A3,I3))') Atoms(At1),At1,Atoms(At2),At2

          END IF

          if (Type.eq."a") THEN

             NbAngle=NbAngle+1

             READ(Line,*) At1,At2,At3

             At1A(NbAngle)=At1

             At2A(NbAngle)=At2

             At3A(NbAngle)=At3

            WRITE(13,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),

     &            At2, Atoms(At3),At3

            WRITE(*,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),

     &           At2, Atoms(At3),At3

          END IF

          if (Type.eq."d") THEN

             NbDie=NbDie+1

             READ(Line,*) At1,At2,At3,At4

             At1D(NbDie)=At1

             At2D(NbDie)=At2

             At3D(NbDie)=At3

             At4D(NbDie)=At4

            WRITE(13,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,

     &          Atoms(At3),At3,Atoms(At4),At4

            WRITE(*,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,

     &          Atoms(At3),At3,Atoms(At4),At4

          END IF

          if (Type.eq."c") THEN

            NbCOM=NbCOM+1

            READ(Line,*) At1,(AtCom(j,NbCOM),j=1,At1)

            AtCom(0,NbCOM)=At1

            Atoms(nat+NbCom)="G"

            WRITE(13,'("# c ",I4,20(A3,I3))') At1,

     &          (Atoms(AtCom(i,NbCoM)),AtCom(i,NbCOM),i=1,At1)

            WRITE(*,'("# c ",I4,20(A3,I3))') At1,

     &          (Atoms(AtCom(i,NbCoM)),AtCom(i,NbCOM),i=1,At1)

          END IF

         END DO

         END IF

          fmt='(   (1X,F12.5),1X,F15.6)'

          write(fmt(2:4),'(i3)') NbDist+NbAngle+NbDie+1

!           write(*,*) nat3

!          write(*,*) 'fmt:',fmt

          ng=1

         s=0.

          open(11,file=f1)

10           call rtraitem(11,nnn,ener,geos,atoms)

!           WRITE(*,*) nnn

           if (nnn.gt.0) then

          call CalcRmsd(nnn, geos1, geos,MRot,rmsd,FRot,FAlign,debug)

         ds=0.

           DO I=1,nnn

             DO J=1,3

             ds=ds+mass(I)*(geos(J,I)-geos1(J,I))**2

!            write(*,*) I,J,geos(J,I),Geos1(J,I),ds

             geos1(J,I)=Geos(J,I)

              END DO

            END DO

           s=s+sqrt(ds)

! We convert coordinates in a0 into Angstroem

!              write(*,*) "Analyse !"

            if (FExist) THEN

            Call Analyse(geos)

             write(IOOUT,fmt) s,(VB(j)/Conv,j=1,NbDist),

     &            (VA(j),j=1,NbAngle),

     &            (VD(j),j=1,NbDie),ener

             write(*,fmt) s,(VB(j)/Conv,j=1,NbDist),

     &            (VA(j),j=1,NbAngle),

     &            (VD(j),j=1,NbDie),ener

             ELSE

                        write(IOOUT,fmt) s,ener

             write(*,fmt) s,ener

            END IF

           ng=ng+1

            goto 10

           endif

           WRITE(*,*) 'Found ',ng-1,' geometries'

           close(11)

         end

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

          subroutine rtraitem(ifil,nnn,E,tab,atoms)

!           implicit real*8 (a-h,o-z)

            IMPLICIT NONE

           character*120 line

           character*3 Atoms(*)

           integer*4 nnn, IFil, Idx, I, J

           REAL*8  Tab(3,*), E

           read(ifil,*,err=99,end=99) nnn

           read(ifil,'(A)') line

           idx=index(line,'E')

!           WRITE(*,*) 'idx,line',idx,line

           if (idx/=0) THEN

             line=line(idx+2:)

              idx=index(line,"=")

              if (idx/=0) line=line(idx+1:)

              idx=index(line,":")

              if (idx/=0) line=line(idx+1:)

              read(line,*) E

           ELSE

             E=0.

           END IF

!           write(*,*) 'coucou',line

           do i=1,nnn

              read(ifil,'(A)',err=99,end=99) Line

              do while (line(1:1)==' ')

                 line=line(2:)

              end do

              atoms(i)=line(1:3)

!            write(*,*) 'coucou atoms',atoms(i)

              do while (line(1:1).ne.' ')

                 line=line(2:)

              end do

!              WRITE(*,*) 'coucou2:',i,line

              read(line,*) (tab(j,i),j=1,3)

           end do

!           WRITE(*,*) 'coucou:',nnn,tab(1,1)

           return

99           nnn=0

!             WRITE(*,*) 'Erreur lecture',ifil,nnn

             return

          end

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

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

! READLINE

! This subroutine reads a line for a file, and converts

! the first field into a character variable, and the rest into 4 integers

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

      SUBROUTINE READLINE(IOIN,Type,Line)

       IMPLICIT NONE

      CHARACTER Type*5,LINE*120

      INTEGER i,IOIN

      READ(IOIN,'(A120)',ERR=999,END=999) LINE

!      WRITE(*,*) Line

      DO WHILE (LINE(1:1).eq.' ')

         LINE=LINE(2:)

      END DO

      i=1

      DO WHILE (LINE(i:i).ne.' ')

         i=i+1

      END DO

      if (i.ge.6) THEN

         WRITE(*,*) 'Pb with READLINE:',LINE

         GOTO 999

      END IF

      Type=LINE(1:i-1)

      LINE=LINE(i:120) // " 0 0 0 0"

      RETURN

 999  Type="E"

      END

      SUBROUTINE Analyse(geos)

      IMPLICIT NONE

          INCLUDE "Xyz2Path.param"

      REAL*8 geos(3,maxnat)

      REAL*8 AU2PS,Pi

      INTEGER*4 i,j,k

      REAL*8 V1x,V1y,V1z,V2x,V2y,V2z,V3x,V3y,V3z

      REAL*8 d1,d2,ca,sa

      REAL*8 V4x,v4y,v4z,v5x,v5y,v5z

      REAL*8 COG(3)

      INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbCOM

      INTEGER*4 At1B(MaxNat),At2B(MaxNat)

      INTEGER*4 At1A(MaxNat),At2A(MaxNat),At3A(MaxNat)

      INTEGER*4 At1D(MaxNat),At2D(MaxNat),At3D(MaxNat),At4D(MaxNat)

      INTEGER*4 AtCom(0:MaxNat,MaxNat)

      REAL*8    VB(MaxNat),VA(MaxNat),VD(MaxNat),VCOM(MaxNat)

      COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbCom,

     &      At1B,At2B,At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom

      COMMON /Values/VB,VA,VD,VCom

      COMMON /Const/AU2ps,Pi

          DO I=1,Nat

             WRITE(*,'(1X,I3,3(1X,F15.6))') i,(geos(j,i),j=1,3)

          END DO

! First, we create the Centre of Mass atoms

            DO i=1,NbCOM

              COG(1)=0.

              COG(2)=0.

              COG(3)=0.

              DO j=1,AtCOm(0,i)

                 DO k=1,3

                    COG(k)=COG(k)+geos(k,AtCom(j,i))

                 END DO

              END DO

              DO k=1,3

                 COG(k)=COG(k)/AtCOM(0,i)

                 geos(k,Nat+i)=COG(k)

              END DO

            END DO

            DO i=1,NbDist

               VB(i)=sqrt((geos(1,At1B(i))-geos(1,At2B(i)))**2+

     &      (geos(2,At1B(i))-geos(2,At2B(i)))**2+

     &      (geos(3,At1B(i))-geos(3,At2B(i)))**2)

            END DO

            DO i=1,NbAngle

               v1x=geos(1,At1A(i))-geos(1,At2A(i))

               v1y=geos(2,At1A(i))-geos(2,At2A(i))

               v1z=geos(3,At1A(i))-geos(3,At2A(i))

               d1=sqrt(v1x**2+v1y**2+v1z**2)

               v2x=geos(1,At3A(i))-geos(1,At2A(i))

               v2y=geos(2,At3A(i))-geos(2,At2A(i))

               v2z=geos(3,At3A(i))-geos(3,At2A(i))

               d2=sqrt(v2x**2+v2y**2+v2z**2)

               VA(i)=acos((v1x*v2x+v1y*v2y+v1z*v2z)/(d1*d2))*180./Pi

            END DO

            DO i=1,NbDie

!               WRITE(*,*) At1D(i),At2D(i),At3D(i),At4D(i)

!              WRITE(*,*) geos(1,At1D(i)),geos(2,At1D(i)),geos(3,At1D(i))

!              WRITE(*,*) geos(1,At2D(i)),geos(2,At2D(i)),geos(3,At2D(i))

               v1x=geos(1,At1D(i))-geos(1,At2D(i))

               v1y=geos(2,At1D(i))-geos(2,At2D(i))

               v1z=geos(3,At1D(i))-geos(3,At2D(i))

               v2x=geos(1,At3D(i))-geos(1,At2D(i))

               v2y=geos(2,At3D(i))-geos(2,At2D(i))

               v2z=geos(3,At3D(i))-geos(3,At2D(i))

               v3x=geos(1,At4D(i))-geos(1,At3D(i))

               v3y=geos(2,At4D(i))-geos(2,At3D(i))

               v3z=geos(3,At4D(i))-geos(3,At3D(i))

               v4x=v1y*v2z-v1z*v2y

               v4y=v1z*v2x-v1x*v2z

               v4z=v1x*v2y-v1y*v2x

               d1=sqrt(v4x**2+v4y**2+v4z**2)

               v5x=-v2y*v3z+v2z*v3y

               v5y=-v2z*v3x+v2x*v3z

               v5z=-v2x*v3y+v2y*v3x

               d2=sqrt(v5x**2+v5y**2+v5z**2)

               ca=(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2)

               sa=v1x*v5x+v1y*v5y+v1z*v5z

               VD(i)=acos(ca)*180./Pi

               if (sa<0.) VD(i)=-VD(i)

!               WRITE(*,*) "Dihe",v5x,v5y,v5z,v4x,v4y,v4z,d1,d2,

!     &(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2),pi

!!!!!!!!! Another solution, more elegant ?

!               norm2=sqrt(v2x**2+v2y**2+v2z**2)

!               sa=(v4x*(v5y*v2z-v5z*v2y)

!     *            -v4y*(v5x*v2z-v5z*v2x)

!     *            +v4z*(v5x*v2y-v5y*v2x))

!     *       /(d1*norm2*d2)

!               angle_d=datan2(sa,ca)*180./Pi

!               WRITE(*,*) sa,ca,angle_d,d1,d2,norm2

!               WRITE(*,*) VD(i),angle_d

            END DO

        END

C================================================================

C    Convertit un nom d'atome (2 lettres) en nombre de masse (entier)

C cette fonction a ete modifiee pour pouvoir convertir un nom

C d'atome avec un numero a la fin...

C================================================================

        FUNCTION ConvertNumAt(ATOM)

        IMPLICIT NONE

        INTEGER*4 I,Long,ConvertNumAt,IC

        character*2 ATOM*2,ATOME*3,L_Atom*2

        INTEGER*4  Max_Z

        PARAMETER (Max_Z=86)

        CHARACTER*2  Nom(0:Max_Z)

       DATA NOM/ ' X',' H',                                    'HE',

     $          'LI','BE',            ' B',' C',' N',' O',' F','NE',

     $          'NA','MG',            'AL','SI',' P',' S','CL','AR',

     $          ' K','CA',

     $      'SC','TI',' V','CR','MN','FE','CO','NI','CU','ZN',

     $                                'GA','GE','AS','SE','BR','KR',

     $          'RB','SR',

     $      ' Y','ZR','NB','MO','TC','RU','RH','PD','AG','CD',

     $                                'IN','SN','SB','TE',' I','XE',

     $          'CS','BA',

     $      'LA',

     $        'CE','PR','ND','PM','SM','EU','GD','TB','DY','HO',

     $        'ER','TM','YB','LU',

     $               'HF','TA',' W','RE','OS','IR','PT','AU','HG',

     $                                'TL','PB','BI','PO','AT','RN'/

C Verifie qu'il n'y a que des lettres et des espaces dans ATOM

!        WRITE(*,*) 'DBG CNVNUMAT, ATOM:',ATOM

        L_atom=Atom

        IF (ATOM(1:1).LT.'A') L_ATOM(1:1)=' '

        IC=Ichar(ATOM(1:1))

        IF ((ic.le.123).AND.(ic.ge.97)) L_ATOM(1:1)=CHAr(IC-32)

        IF (ATOM(2:2).LT.'A') L_ATOM(2:2)=' '

        IC=Ichar(ATOM(2:2))

        IF ((ic.le.123).AND.(ic.ge.97)) L_ATOM(2:2)=CHAr(IC-32)

C Justifie le nom sur la droite (et non sur la gauche comme souvent...)

         Long=INDEX(L_ATOM,' ')-1

         ATOME=' ' // L_ATOM

        IF (Long.EQ.1) L_ATOM=ATOME(1:2)

!        WRITE(*,*) 'DBG CNVNUMAT, L_ATOM:',L_ATOM

        I=max_Z

        DO WHILE ((nom(I).NE.L_ATOM) .AND. (I.GT.0))

         I=I-1

        END DO

        ConvertNumAT=I

        END

! This subroutine calculates RMSD using quaternions.

! It is based on the F90 routine bu E. Coutsias

! http://www.math.unm.edu/~vageli/homepage.html

! I (PFL) have just translated it, and I have changed the diagonalization

! subroutine.

! I also made some changes to make it suitable for Cart package.

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

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

! Copyright (C) 2004, 2005 Chaok Seok, Evangelos Coutsias and Ken Dill

!      UCSF, Univeristy of New Mexico, Seoul National University

! Witten by Chaok Seok and Evangelos Coutsias 2004.

! This library is free software; you can redistribute it and/or

! modify it under the terms of the GNU Lesser General Public

! License as published by the Free Software Foundation; either

! version 2.1 of the License, or (at your option) any later version.

!

! This library 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

! Lesser General Public License for more details.

!

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

! License along with this library; if not, write to the Free Software

! Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA

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

      subroutine CalcRmsd(na, geom,geom2,U,rmsd,FRot,FAlign,debug)

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

!  This subroutine calculates the least square rmsd of two coordinate

!  sets coord1(3,n) and coord2(3,n) using a method based on quaternion.

!  It then calculate the  rotation matrix U and the centers of coord, and uses

! them to align the two molecules.

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

      IMPLICIT NONE

      INCLUDE "Xyz2Path.param"

      INTEGER*4 IOIN, IOOUT, IOSCRN, IOPRNT, IOTAMP

      COMMON/IODEFS/IOIN,IOOUT,IOSCRN,IOPRNT,IOTAMP

      integer*4 na

      real*8  geom(3,MaxNAt), Geom2(3,MaxNAt)

      real*8  U(3,3), rmsd

      LOGICAL  FRot,FAlign,Debug

      REAL*8 Coord1(3,MaxNAt), Coord2(3,MaxNAt)

      real*8  xc1,yc1,zc1, xc2,yc2,zc2

      integer*4 i, j,  ia

      real*8 x_norm, y_norm, lambda

      real*8 Rmatrix(3,3)

      real*8 S(4,4)

      real*8 EigVec(4,4), EigVal(4)

  ! calculate the barycenters, centroidal coordinates, and the norms

      x_norm = 0.0d0

      y_norm = 0.0d0

      xc1=0.

      yc1=0.

      zc1=0.

      xc2=0.

      yc2=0.

      zc2=0.

      do ia=1,na

         xc1=xc1+geom(1,ia)

         xc2=xc2+geom2(1,ia)

         yc1=yc1+geom(2,ia)

         yc2=yc2+geom2(2,ia)

         zc1=zc1+geom(3,ia)

         zc2=zc2+geom2(3,ia)

!         if (debug) WRITE(*,'(A,I5,4(1X,F10.4))') 'ia...',ia,x(ia),

!     &                        x2(ia),xc1,xc2

      END DO

      xc1=xc1/dble(na)

      yc1=yc1/dble(na)

      zc1=zc1/dble(na)

      xc2=xc2/dble(na)

      yc2=yc2/dble(na)

      zc2=zc2/dble(na)

      IF (debug) WRITE(*,'(1X,A,3(1X,F10.4))') 'Center1',xc1,yc1,zc1

      IF (debug) WRITE(*,'(1X,A,3(1X,F10.4))') 'Center2',xc2,yc2,zc2

      do i=1,na

         Coord1(1,i)=geom(1,i)-xc1

         Coord1(2,i)=geom(2,i)-yc1

         Coord1(3,i)=geom(3,i)-zc1

         Coord2(1,i)=geom2(1,i)-xc2

         Coord2(2,i)=geom2(2,i)-yc2

         Coord2(3,i)=geom2(3,i)-zc2

         x_norm=x_norm+Coord1(1,i)**2+Coord1(2,i)**2+Coord1(3,i)**2

         y_norm=y_norm+Coord2(1,i)**2+Coord2(2,i)**2+Coord2(3,i)**2

      end do

      IF (debug) THEN

         WRITE(*,*) "R matrix"

         DO I=1,3

            WRITE(*,*) (RMatrix(I,j),j=1,3)

         END DO

      END IF

  ! calculate the R matrix

      do i = 1, 3

         do j = 1, 3

            Rmatrix(i,j)=0.

            do ia=1,na

               Rmatrix(i,j) = Rmatrix(i,j)+Coord1(i,ia)*Coord2(j,ia)

            END DO

         end do

      end do

      IF (debug) THEN

         WRITE(*,*) "R matrix"

         DO I=1,3

            WRITE(*,*) (RMatrix(I,j),j=1,3)

         END DO

      END IF

  ! S matrix

      S(1, 1) = Rmatrix(1, 1) + Rmatrix(2, 2) + Rmatrix(3, 3)

      S(2, 1) = Rmatrix(2, 3) - Rmatrix(3, 2)

      S(3, 1) = Rmatrix(3, 1) - Rmatrix(1, 3)

      S(4, 1) = Rmatrix(1, 2) - Rmatrix(2, 1)

      S(1, 2) = S(2, 1)

      S(2, 2) = Rmatrix(1, 1) - Rmatrix(2, 2) - Rmatrix(3, 3)

      S(3, 2) = Rmatrix(1, 2) + Rmatrix(2, 1)

      S(4, 2) = Rmatrix(1, 3) + Rmatrix(3, 1)

      S(1, 3) = S(3, 1)

      S(2, 3) = S(3, 2)

      S(3, 3) =-Rmatrix(1, 1) + Rmatrix(2, 2) - Rmatrix(3, 3)

      S(4, 3) = Rmatrix(2, 3) + Rmatrix(3, 2)

      S(1, 4) = S(4, 1)

      S(2, 4) = S(4, 2)

      S(3, 4) = S(4, 3)

      S(4, 4) =-Rmatrix(1, 1) - Rmatrix(2, 2) + Rmatrix(3, 3)

! PFL : I use my usual Jacobi diagonalisation

  ! Calculate eigenvalues and eigenvectors, and

  ! take the maximum eigenvalue lambda and the corresponding eigenvector q.

      IF (debug) THEN

         WRITE(*,*) "S matrix"

         DO I=1,4

            WRITE(*,*) (S(I,j),j=1,4)

         END DO

      END IF

      Call Jacobi(S,4,EigVal,EigVec,4)

      Call Trie(4,EigVal,EigVec,4)

      Lambda=EigVal(4)

! RMS Deviation

       rmsd=sqrt(max(0.0d0,((x_norm+y_norm)-2.0d0*lambda))/dble(na))

      if (FRot.OR.FAlign) Call rotation_matrix(EigVec(1,4),U)

      IF (FAlign) THEN

         DO I=1,na

            geom2(1,i)=Coord2(1,i)*U(1,1)+Coord2(2,i)*U(2,1)

     &           +Coord2(3,i)*U(3,1) +xc1

            geom2(2,i)=Coord2(1,i)*U(1,2)+Coord2(2,i)*U(2,2)

     &           +Coord2(3,i)*U(3,2) +yc1

            geom2(3,i)=Coord2(1,i)*U(1,3)+Coord2(2,i)*U(2,3)

     &           +Coord2(3,i)*U(3,3) +zc1

         END DO

      END IF

      END

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

      subroutine rotation_matrix(q, U)

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

! This subroutine constructs rotation matrix U from quaternion q.

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

! This subroutine calculates RMSD using quaternions.

! It is based on the F90 routine bu E. Coutsias

! http://www.math.unm.edu/~vageli/homepage.html

! I (PFL) have just translated it, and I have changed the diagonalization

! subroutine.

! I also made some changes to make it suitable for Cart package.

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

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

! Copyright (C) 2004, 2005 Chaok Seok, Evangelos Coutsias and Ken Dill

!      UCSF, Univeristy of New Mexico, Seoul National University

! Witten by Chaok Seok and Evangelos Coutsias 2004.

! This library is free software; you can redistribute it and/or

! modify it under the terms of the GNU Lesser General Public

! License as published by the Free Software Foundation; either

! version 2.1 of the License, or (at your option) any later version.

!

! This library 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

! Lesser General Public License for more details.

!

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

! License along with this library; if not, write to the Free Software

! Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA

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

      real*8 q(4)

      real*8 U(3,3)

      real*8 q0,q1,q2,q3,b0,b1,b2,b3,q00,q01,q02,q03

      REAL*8 q11,q12,q13,q22,q23,q33

      q0 = q(1)

      q1 = q(2)

      q2 = q(3)

      q3 = q(4)

      b0 = 2.0d0*q0

      b1 = 2.0d0*q1

      b2 = 2.0d0*q2

      b3 = 2.0d0*q3

      q00 = b0*q0-1.0d0

      q01 = b0*q1

      q02 = b0*q2

      q03 = b0*q3

      q11 = b1*q1

      q12 = b1*q2

      q13 = b1*q3

      q22 = b2*q2

      q23 = b2*q3

      q33 = b3*q3

      U(1,1) = q00+q11

      U(1,2) = q12-q03

      U(1,3) = q13+q02

      U(2,1) = q12+q03

      U(2,2) = q00+q22

      U(2,3) = q23-q01

      U(3,1) = q13-q02

      U(3,2) = q23+q01

      U(3,3) = q00+q33

      end

c============================================================

c

c ++  diagonalisation par jacobi

c     vecteur propre i : V(i,i)

c     valeur propre i : D(i)

c

c============================================================

c

      SUBROUTINE JACOBI(A,N,D,V,max_N)

      IMPLICIT REAL*8 (A-H,O-Z)

      parameter (max_it=500)

      DIMENSION A(max_N,max_N),B(max_N),Z(max_N)

      DIMENSION V(max_N,max_N),D(max_N)

      DO 12 IP=1,N

        DO 11 IQ=1,N

          V(IP,IQ)=0.

11      CONTINUE

        V(IP,IP)=1.

12    CONTINUE

      DO 13 IP=1,N

        B(IP)=A(IP,IP)

        D(IP)=B(IP)

        Z(IP)=0.

13    CONTINUE

      NROT=0

      DO 24 I=1,max_it

        SM=0.

        DO 15 IP=1,N-1

          DO 14 IQ=IP+1,N

            SM=SM+ABS(A(IP,IQ))

14        CONTINUE

15      CONTINUE

        IF(SM.EQ.0.)RETURN

        IF(I.LT.4)THEN

          TRESH=0.2*SM/N**2

        ELSE

          TRESH=0.

        ENDIF

        DO 22 IP=1,N-1

          DO 21 IQ=IP+1,N

            G=100.*ABS(A(IP,IQ))

            IF((I.GT.4).AND.(ABS(D(IP))+G.EQ.ABS(D(IP)))

     *         .AND.(ABS(D(IQ))+G.EQ.ABS(D(IQ))))THEN

              A(IP,IQ)=0.

            ELSE IF(ABS(A(IP,IQ)).GT.TRESH)THEN

              H=D(IQ)-D(IP)

              IF(ABS(H)+G.EQ.ABS(H))THEN

                T=A(IP,IQ)/H

              ELSE

                THETA=0.5*H/A(IP,IQ)

                T=1./(ABS(THETA)+SQRT(1.+THETA**2))

                IF(THETA.LT.0.)T=-T

              ENDIF

              C=1./SQRT(1+T**2)

              S=T*C

              TAU=S/(1.+C)

              H=T*A(IP,IQ)

              Z(IP)=Z(IP)-H

              Z(IQ)=Z(IQ)+H

              D(IP)=D(IP)-H

              D(IQ)=D(IQ)+H

              A(IP,IQ)=0.

              DO 16 J=1,IP-1

                G=A(J,IP)

                H=A(J,IQ)

                A(J,IP)=G-S*(H+G*TAU)

                A(J,IQ)=H+S*(G-H*TAU)

16            CONTINUE

              DO 17 J=IP+1,IQ-1

                G=A(IP,J)

                H=A(J,IQ)

                A(IP,J)=G-S*(H+G*TAU)

                A(J,IQ)=H+S*(G-H*TAU)

17            CONTINUE

              DO 18 J=IQ+1,N

                G=A(IP,J)

                H=A(IQ,J)

                A(IP,J)=G-S*(H+G*TAU)

                A(IQ,J)=H+S*(G-H*TAU)

18            CONTINUE

              DO 19 J=1,N

                G=V(J,IP)

                H=V(J,IQ)

                V(J,IP)=G-S*(H+G*TAU)

                V(J,IQ)=H+S*(G-H*TAU)

19            CONTINUE

              NROT=NROT+1

            ENDIF

21        CONTINUE

22      CONTINUE

        DO 23 IP=1,N

          B(IP)=B(IP)+Z(IP)

          D(IP)=B(IP)

          Z(IP)=0.

23      CONTINUE

24    CONTINUE

      write(6,*) max_it,' iterations should never happen'

      STOP

      RETURN

      END

c

c============================================================

c

c ++  trie des vecteur dans l'ordre croissant

c

c============================================================

c

        SUBROUTINE trie(nb_niv,ene,psi,max_niv)

        integer i,j,k,nb_niv,max_niv

        real*8 ene(max_niv),psi(max_niv,max_niv)

        real*8 a

        DO i=1,nb_niv

          DO j=i+1,nb_niv

            IF (ene(i) .GT. ene(j)) THEN

c              permutation

              a=ene(i)

              ene(i)=ene(j)

              ene(j)=a

              DO k=1,nb_niv

                 a=psi(k,i)

                 psi(k,i)=psi(k,j)

                 psi(k,j)=a

              END DO

            END IF

          END DO

        END DO

        END