Chimie Théorique » OpenPath

          program Xyz2irc

! 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 ROOT file of PAW

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

! the first line gives the time when you want to start your analysis

! 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:

! 3.

! 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

!!

! v 3.2

! Added the p command that gives the oriented angle between two planes

! Syntax: p At1 At2 At3 At4 At5 At6

! At1, At2, At3 define the first plane

! At4, At5, At6 define the second plane

! How it works: gives the angles between the normal of the two planes, defined by

! the cross produc At2-At1 x At2-At3 etc.

!!!!

          IMPLICIT NONE

          INTEGER*4 maxnat,MaxList

          Parameter (MaxNat=10000,MaxList=100)

          character*120 f1

          REAL*8   geos(3,maxnat)

          character*33 fmt

          character*3 atoms(maxnat)

          character*5 Type

          Character*120 line

          INTEGER*4 NbPrint

          REAL*8   AU2PS,Pi

! Mass is not used for now.

!          REAL*8  Mass(MaxNat)

          REAL*8 Ener, Conv

          INTEGER*4 At1,At2,At3,At4,At5,At6,IOOUT

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

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

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

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

          INTEGER*4 At1D(MaxList),At2D(MaxList),At3D(MaxList),

     $              At4D(MaxList)

          INTEGER*4 At1p(MaxList),At2p(MaxList),At3p(MaxList),

     $              At4p(MaxList),At5p(MaxList),At6p(MaxList)

          INTEGER*4 AtCom(0:MaxList,MaxList)

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

          REAL*8    Vp(MaxList)

          LOGICAL FExist

c          INTEGER*4 iargc

c          external iargc

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

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

     &         At1p,At2p,At3p,At4p,At5p,At6p

          COMMON /Values/VB,VA,VD,Vp,VCom

          COMMON /Const/AU2ps,Pi

          AU2PS=1./41341.37

          NbPrint=100

          Pi=dacos(-1.d0)

          IOOUT=13

          Conv=1.

          iarg=iargc()

          if (iarg.lt.1) then

             WRITE(*,*) "=============================================="

             WRITE(*,*) "==                                          =="

             WRITE(*,*) "==   Xyz2Scan: Xyz file to scan file        =="

             WRITE(*,*) "==                                          =="

             WRITE(*,*) "=============================================="

             WRITE(*,*) "Usage: xyz2scan XYZ_file "

             WRITE(*,*) "The XYZ file should follow the 'usual' format:"

             WRITE(*,*) "Number of atoms on the first line "

             WRITE(*,*) "Comment on the second line"

             WRITE(*,*) "The geometry is given in cartesian coordinates"

             WRITE(*,*) "with atom symbol and three coordinates:"

             WRITE(*,*) " C   0. 1. 0."

             WRITE(*,*) ""

             WRITE(*,*) " xyz2scan also needs a file called 'list' "

             WRITE(*,*) "which has the following structure:"

             WRITE(*,*) "Each line contains the type of the value you"

             WRITE(*,*) "want to follow, it can be:"

             WRITE(*,*) " - b  for a Bond distance"

             WRITE(*,*) " - a for an angle"

             WRITE(*,*) " - d for a dihedral"

             WRITE(*,*) " - p for the oriented angle between two planes"

             WRITE(*,*) "This descriptor is followed by the number of"

             WRITE(*,*) "the atoms involved"

             WRITE(*,*) "One can also create 'barycenter' atoms that"

             WRITE(*,*) "can then be used as normal atoms."

             WRITE(*,*) "the descriptor is 'c' followed by the number"

             WRITE(*,*) "of atoms and the list of atoms:"

             WRITE(*,*) " c 2  1 5"

             WRITE(*,*) "A typical file can be:"

             WRITE(*,*) " b  1  2"

             WRITE(*,*) " b 2  3"

             WRITE(*,*) " a 1 2 3"

             WRITE(*,*) "     "

             WRITE(*,*) "=============================================="

             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(*,*) "File *list* is missing"

             STOP

          END IF

          open(11,file=f1)

          READ(11,*) nnn

          close(11)

          if (nnn.GT.MaxNat) THEN

             WRITE(*,*) "Sorry but your system has too many atoms"

             WRITE(*,*) "Change the value of MaxNat in the source file"

             WRITE(*,*) "and then recompile."

             WRITE(*,*) "For information, now MaxNat=",MaxNat

             WRITE(*,*) "and you have ",nnn," atoms."

             STOP

          END IF

         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

          END IF

          if (Type.eq."a") THEN

             NbAngle=NbAngle+1

             READ(Line,*) At1,At2,At3

             At1A(NbAngle)=At1

             At2A(NbAngle)=At2

             At3A(NbAngle)=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."p") THEN

             NbP=NbP+1

             READ(Line,*) At1,At2,At3,At4,At5,At6

             At1p(NbP)=At1

             At2p(NbP)=At2

             At3p(NbP)=At3

             At4p(NbP)=At4

             At5p(NbP)=At5

             At6p(NbP)=At6

          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"

          END IF

         END DO

         CLOSE(14)

! We read one geoetry to get the atoms name

         open(11,file=f1)

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

         close(11)

! We write things

! First NbCom

         if (NbCom.GE.1) THEN

            WRITE(*,*) "# Added center of mass"

            WRITE(IOOUT,*) "# Added center of mass"

            DO J=1,NbCom

            WRITE(IOOUT,'("# c ",I4,20(A3,I3))') AtCom(0,J),

     &          (Atoms(AtCom(i,J)),AtCom(i,J),i=1,At1)

            WRITE(*,'("# c ",I4,20(A3,I3))') AtCom(0,J),

     &          (Atoms(AtCom(i,J)),AtCom(i,J),i=1,At1)

            END DO

         END IF

! Distances

         if (NbDist.GE.1) THEN

            WRITE(*,*) "# Bonds"

            WRITE(IOOUT,*) "# Bonds"

            DO J=1,NbDist

               At1= At1B(J)

               At2=At2B(J)

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

     $              Atoms(At2),At2

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

            END DO

         END IF

! Angles

         if (NbAngle.GE.1) THEN

            WRITE(*,*) "# Angles"

            WRITE(IOOUT,*) "# Angles"

            DO J=1,NbAngle

            At1= At1A(J)

            At2= At2A(J)

            At3= At3A(J)

            WRITE(IOOUT,'("# 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 DO

         END IF

! Dihedrals

         if (NbDie.GE.1) THEN

            WRITE(*,*) "# Dihedrals"

            WRITE(IOOUT,*) "# Dihedrals"

            DO J=1,NbDie

            At1= At1D(J)

            At2= At2D(J)

            At3= At3D(J)

            At4= At4D(J)

            WRITE(IOOUT,'("# 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 DO

         END IF

! Planar angles

         if (NbP.GE.1) THEN

            WRITE(*,*) "# Planes angles"

            WRITE(IOOUT,*) "# Planes angles"

            DO J=1,NbP

            At1= At1p(J)

            At2= At2p(J)

            At3= At3p(J)

            At4= At4p(J)

            At5= At5p(J)

            At6= At6p(J)

            WRITE(IOOUT,'("# p ",8(A3,I3))') Atoms(At1),At1,Atoms(At2)

     &          ,At2,Atoms(At3),At3,Atoms(At4),At4

     &          ,Atoms(At5),At5,Atoms(At6),At6

            WRITE(*,'("# p ",8(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,

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

     &          ,Atoms(At5),At5,Atoms(At6),At6

            END DO

         END IF

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

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

!           write(*,*) nat3

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

          ng=1

          open(11,file=f1)

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

!           WRITE(*,*) nnn

           if (nnn.gt.0) then

! We convert coordinates in a0 into Angstroem

!              write(*,*) "Analyse !"

            Call Analyse(geos)

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

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

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

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

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

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

           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

      INTEGER*4 MaxNat,MaxList

      parameter (maxnat=10000,MaxList=100)

      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,NbP,NbCOM

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

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

          INTEGER*4 At1D(MaxList),At2D(MaxList),At3D(MaxList),

     $              At4D(MaxList)

          INTEGER*4 At1p(MaxList),At2p(MaxList),At3p(MaxList),

     $              At4p(MaxList),At5p(MaxList),At6p(MaxList)

          INTEGER*4 AtCom(0:MaxList,MaxList)

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

          REAL*8    Vp(MaxList)

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

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

     &         At1p,At2p,At3p,At4p,At5p,At6p

          COMMON /Values/VB,VA,VD,Vp,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)

               if (d1<=1e-12) THEN

                  WRITE(*,*) "WARNING: Dihedral, d1=0"

                  ca=-1.

                  sa=0.

               END IF

               if (d2<=1e-12) THEN

                  WRITE(*,*) "WARNING: Dihedral, d2=0"

                  ca=-1.

                  sa=0.

               END IF

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

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

               if (abs(ca)>1.) ca=sign(1.d0,ca)

               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

!                WRITE(*,*) "Dihe ca,sa,d1,d2",ca,sa,d1,d2,acos(ca)

!!!!!!!!! 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

            DO i=1,NbP

! v1= At2-At1

               v1x=geos(1,At1p(i))-geos(1,At2p(i))

               v1y=geos(2,At1p(i))-geos(2,At2p(i))

               v1z=geos(3,At1p(i))-geos(3,At2p(i))

! v2=At2-At3

               v2x=geos(1,At3p(i))-geos(1,At2p(i))

               v2y=geos(2,At3p(i))-geos(2,At2p(i))

               v2z=geos(3,At3p(i))-geos(3,At2p(i))

! v4 = v1 x v2

               v4x=v1y*v2z-v1z*v2y

               v4y=v1z*v2x-v1x*v2z

               v4z=v1x*v2y-v1y*v2x

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

! v3= At5-At4

               v3x=geos(1,At4p(i))-geos(1,At5p(i))

               v3y=geos(2,At4p(i))-geos(2,At5p(i))

               v3z=geos(3,At4p(i))-geos(3,At5p(i))

! v2=At5-At6

               v2x=geos(1,At6p(i))-geos(1,At5p(i))

               v2y=geos(2,At6p(i))-geos(2,At5p(i))

               v2z=geos(3,At6p(i))-geos(3,At5p(i))

! v5 = v3 x v2

               v5x=v3y*v2z-v3z*v2y

               v5y=v3z*v2x-v3x*v2z

               v5z=v3x*v2y-v3y*v2x

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

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

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

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

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

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

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

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

! See Dihedral routine

            END DO

        END