Revision 6
| utils/Xyz2Path.f (revision 6) | ||
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program Xyz2Path |
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! This programs reads a XYZ file and converts it into distances, |
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! valence angle and dihedral angles. |
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! It prints them as a function of the irc distance... |
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!----------------------------------------------- |
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! Input: name of the XYZ File |
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! it also needs a file call list which has the following structure: |
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! one line contains the type of the value you want to follow, it can be |
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! b for a Bond distance |
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! a for an angle |
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! d for a dihedral |
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! this descriptor is followed by the number of the atoms involved ! |
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! a typical file can be: |
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! b 1 2 |
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! b 2 3 |
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! a 1 2 3 |
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!---------------------------------------------- |
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! Ouput: A files call Scan.dat |
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! wich contains in the first lines the input file (as a reminder) |
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! and then for each step the wanted values |
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!------------------------------------------------ |
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! Second version also reads the energy (as to be written after E= on |
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! the comment line) |
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!------------------------------------------------ |
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! Third version contains a new command: c for Center of Mass |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! v 3.1 the c command now creates the center of mass... and allows |
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! people to do whatever they want with it... |
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! Syntax: c NbAt ListAt |
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IMPLICIT NONE |
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INCLUDE "Xyz2Path.param" |
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character*40 f1 |
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REAL*8 geos(3,maxnat), geos1(3,maxnat) |
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character*33 fmt |
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character*3 atoms(maxnat) |
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character*5 Type |
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Character*120 line |
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INTEGER*4 NbPrint |
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REAL*8 AU2PS,Pi |
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REAL*8 Mass(MaxNat), Ener, Conv, Ds, s |
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REAL*8 MassAt(0:86) |
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INTEGER*4 At1,At2,At3,At4,IOOUT,Iat |
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INTEGER*4 IArg, I, NNN, Ng, J |
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INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbCOM |
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INTEGER*4 At1B(MaxNat),At2B(MaxNat) |
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INTEGER*4 At1A(MaxNat),At2A(MaxNat),At3A(MaxNat) |
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INTEGER*4 At1D(MaxNat),At2D(MaxNat),At3D(MaxNat),At4D(MaxNat) |
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INTEGER*4 AtCom(0:MaxNat,MaxNat) |
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REAL*8 VB(MaxNat),VA(MaxNat),VD(MaxNat),VCOM(MaxNat) |
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REAL*8 MRot(3,3), Rmsd |
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LOGICAL FExist,FRot,FAlign,Debug |
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INTEGER*4 ConvertNumAt |
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external ConvertNumAt |
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COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbCom, At1B,At2B, |
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& At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom |
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COMMON /Values/VB,VA,VD,VCom |
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COMMON /Const/AU2ps,Pi |
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DATA MassAt/0.0D0, |
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$ 1.0078D0, 4.0026D0, |
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$ 7.0160D0, 9.0122D0,11.0093D0, |
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$ 12.0000D0,14.0031D0,15.9949D0,18.9984D0,19.9924D0, |
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$ 22.9898D0,23.9850D0,26.9815D0, |
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$ 27.9769D0,30.9738D0,31.9721D0,34.9688D0,39.9624D0, |
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$ 39.0983D0,40.08D0, |
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$ 44.9559D0, 47.88D0, 50.9415D0, 51.996D0, 54.9380D0, |
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$ 55.847D0, 58.9332D0, 58.69D0, 63.546D0, 65.39D0, |
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$ 69.72D0,72.59D0,74.9216D0,78.96D0,79.904D0,83.80D0, |
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$ 85.4678D0,87.62D0,88.9059D0,91.224D0,92.9064D0, |
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$ 95.94D0,98D0,101.07D0,102.906D0,106.42D0,107.868D0,112.41D0, |
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$ 114.82D0,118.71D0,121.75D0,127.60D0,126.905D0,131.29D0, |
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! 6 'CS','BA', |
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$ 132.905,137.34, |
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! 6 'LA', |
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! 'CE','PR','ND','PM','SM','EU','GD', |
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! 'TB','DY','HO', 'ER','TM','YB','LU', |
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$ 138.91, |
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$ 140.12, 130.91, 144.24,147.,150.35, 151.96,157.25, |
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$ 158.924, 162.50, 164.93, 167.26,168.93,173.04,174.97, |
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! 6 'HF','TA',' W','RE','OS','IR','PT', |
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! 'AU','HG', |
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! 6 'TL','PB','BI','PO','AT','RN'/ |
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$ 178.49, 180.95, 183.85, 186.2, 190.2, 192.2, 195.09, |
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$ 196.97, 200.59, |
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$ 204.37, 207.19,208.98,210.,210.,222. / |
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AU2PS=1./41341.37 |
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NbPrint=100 |
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Pi=dacos(-1.d0) |
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IOOUT=13 |
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Conv=1. |
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FRot=.TRUE. |
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FAlign=.TRUE. |
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Debug=.FALSE. |
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NbDist=0 |
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NbAngle=0 |
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NbDie=0 |
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iarg=command_argument_count() |
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if (iarg.lt.1) then |
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write(*,*) 'XYZ filename:' |
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read(*,'(a)') f1 |
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else |
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call getarg(1,f1) |
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endif |
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open(13,file='Scan.dat') |
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INQUIRE(File='list',Exist=FExist) |
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if (.NOT.FExist) THEN |
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WRITE(*,*) "No file 'list', just printing Energy" |
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END IF |
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open(11,file=f1) |
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call rtraitem(11,nnn,ener,geos1,atoms) |
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close(11) |
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DO I=1,nnn |
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Iat=ConvertNumAt(atoms(I)) |
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Mass(I)=MassAt(Iat) |
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! write(*,*) I,Atoms(I),Mass(I),geos1(:,I) |
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END DO |
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Nat=nnn |
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if (FExist) THEN |
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open(14,file='list') |
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Type="d" |
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DO WHILE (Type.ne."E") |
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CALL READLINE(14,Type,Line) |
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! WRITE(*,*) Line,Type |
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if (Type.eq."b") THEN |
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NbDist=NbDist+1 |
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READ(Line,*) At1,At2 |
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At1B(NbDist)=At1 |
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At2B(NbDist)=At2 |
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WRITE(13,'("# b ",2(A3,I3))') Atoms(At1),At1,Atoms(At2),At2
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WRITE(*,'("# b ",2(A3,I3))') Atoms(At1),At1,Atoms(At2),At2
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END IF |
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if (Type.eq."a") THEN |
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NbAngle=NbAngle+1 |
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READ(Line,*) At1,At2,At3 |
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At1A(NbAngle)=At1 |
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At2A(NbAngle)=At2 |
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At3A(NbAngle)=At3 |
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WRITE(13,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),
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& At2, Atoms(At3),At3 |
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WRITE(*,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),
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& At2, Atoms(At3),At3 |
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END IF |
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if (Type.eq."d") THEN |
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NbDie=NbDie+1 |
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READ(Line,*) At1,At2,At3,At4 |
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At1D(NbDie)=At1 |
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At2D(NbDie)=At2 |
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At3D(NbDie)=At3 |
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At4D(NbDie)=At4 |
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WRITE(13,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
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& Atoms(At3),At3,Atoms(At4),At4 |
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WRITE(*,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
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& Atoms(At3),At3,Atoms(At4),At4 |
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END IF |
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if (Type.eq."c") THEN |
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NbCOM=NbCOM+1 |
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READ(Line,*) At1,(AtCom(j,NbCOM),j=1,At1) |
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AtCom(0,NbCOM)=At1 |
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Atoms(nat+NbCom)="G" |
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WRITE(13,'("# c ",I4,20(A3,I3))') At1,
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& (Atoms(AtCom(i,NbCoM)),AtCom(i,NbCOM),i=1,At1) |
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WRITE(*,'("# c ",I4,20(A3,I3))') At1,
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& (Atoms(AtCom(i,NbCoM)),AtCom(i,NbCOM),i=1,At1) |
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END IF |
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END DO |
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END IF |
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fmt='( (1X,F12.5),1X,F15.6)' |
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write(fmt(2:4),'(i3)') NbDist+NbAngle+NbDie+1 |
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! write(*,*) nat3 |
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! write(*,*) 'fmt:',fmt |
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ng=1 |
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s=0. |
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open(11,file=f1) |
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10 call rtraitem(11,nnn,ener,geos,atoms) |
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! WRITE(*,*) nnn |
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if (nnn.gt.0) then |
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call CalcRmsd(nnn, geos1, geos,MRot,rmsd,FRot,FAlign,debug) |
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ds=0. |
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DO I=1,nnn |
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DO J=1,3 |
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ds=ds+mass(I)*(geos(J,I)-geos1(J,I))**2 |
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! write(*,*) I,J,geos(J,I),Geos1(J,I),ds |
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geos1(J,I)=Geos(J,I) |
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END DO |
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END DO |
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s=s+sqrt(ds) |
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! We convert coordinates in a0 into Angstroem |
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! write(*,*) "Analyse !" |
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if (FExist) THEN |
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Call Analyse(geos) |
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write(IOOUT,fmt) s,(VB(j)/Conv,j=1,NbDist), |
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& (VA(j),j=1,NbAngle), |
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& (VD(j),j=1,NbDie),ener |
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write(*,fmt) s,(VB(j)/Conv,j=1,NbDist), |
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& (VA(j),j=1,NbAngle), |
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& (VD(j),j=1,NbDie),ener |
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ELSE |
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write(IOOUT,fmt) s,ener |
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write(*,fmt) s,ener |
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END IF |
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ng=ng+1 |
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goto 10 |
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endif |
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WRITE(*,*) 'Found ',ng-1,' geometries' |
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close(11) |
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end |
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!-------------------------------------------------------------- |
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subroutine rtraitem(ifil,nnn,E,tab,atoms) |
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! implicit real*8 (a-h,o-z) |
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IMPLICIT NONE |
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character*120 line |
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character*3 Atoms(*) |
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integer*4 nnn, IFil, Idx, I, J |
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REAL*8 Tab(3,*), E |
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read(ifil,*,err=99,end=99) nnn |
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read(ifil,'(A)') line |
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idx=index(line,'E') |
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! WRITE(*,*) 'idx,line',idx,line |
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if (idx/=0) THEN |
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line=line(idx+2:) |
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idx=index(line,"=") |
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if (idx/=0) line=line(idx+1:) |
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idx=index(line,":") |
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if (idx/=0) line=line(idx+1:) |
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read(line,*) E |
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ELSE |
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E=0. |
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END IF |
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|
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! write(*,*) 'coucou',line |
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do i=1,nnn |
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read(ifil,'(A)',err=99,end=99) Line |
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do while (line(1:1)==' ') |
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line=line(2:) |
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end do |
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atoms(i)=line(1:3) |
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! write(*,*) 'coucou atoms',atoms(i) |
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do while (line(1:1).ne.' ') |
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line=line(2:) |
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end do |
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! WRITE(*,*) 'coucou2:',i,line |
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read(line,*) (tab(j,i),j=1,3) |
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end do |
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! WRITE(*,*) 'coucou:',nnn,tab(1,1) |
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return |
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99 nnn=0 |
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! WRITE(*,*) 'Erreur lecture',ifil,nnn |
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return |
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end |
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|
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!-------------------------------------------------------------- |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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! READLINE |
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! This subroutine reads a line for a file, and converts |
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! the first field into a character variable, and the rest into 4 integers |
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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SUBROUTINE READLINE(IOIN,Type,Line) |
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IMPLICIT NONE |
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CHARACTER Type*5,LINE*120 |
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INTEGER i,IOIN |
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READ(IOIN,'(A120)',ERR=999,END=999) LINE |
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! WRITE(*,*) Line |
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DO WHILE (LINE(1:1).eq.' ') |
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LINE=LINE(2:) |
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END DO |
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i=1 |
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DO WHILE (LINE(i:i).ne.' ') |
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i=i+1 |
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END DO |
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|
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if (i.ge.6) THEN |
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WRITE(*,*) 'Pb with READLINE:',LINE |
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GOTO 999 |
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END IF |
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Type=LINE(1:i-1) |
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LINE=LINE(i:120) // " 0 0 0 0" |
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RETURN |
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999 Type="E" |
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END |
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SUBROUTINE Analyse(geos) |
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IMPLICIT NONE |
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INCLUDE "Xyz2Path.param" |
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| 324 |
|
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REAL*8 geos(3,maxnat) |
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REAL*8 AU2PS,Pi |
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INTEGER*4 i,j,k |
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REAL*8 V1x,V1y,V1z,V2x,V2y,V2z,V3x,V3y,V3z |
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REAL*8 d1,d2,ca,sa |
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REAL*8 V4x,v4y,v4z,v5x,v5y,v5z |
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REAL*8 COG(3) |
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| 332 |
|
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INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbCOM |
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INTEGER*4 At1B(MaxNat),At2B(MaxNat) |
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INTEGER*4 At1A(MaxNat),At2A(MaxNat),At3A(MaxNat) |
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INTEGER*4 At1D(MaxNat),At2D(MaxNat),At3D(MaxNat),At4D(MaxNat) |
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INTEGER*4 AtCom(0:MaxNat,MaxNat) |
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| 338 |
REAL*8 VB(MaxNat),VA(MaxNat),VD(MaxNat),VCOM(MaxNat) |
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| 339 |
|
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COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbCom, |
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& At1B,At2B,At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom |
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COMMON /Values/VB,VA,VD,VCom |
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COMMON /Const/AU2ps,Pi |
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| 344 |
|
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| 345 |
DO I=1,Nat |
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WRITE(*,'(1X,I3,3(1X,F15.6))') i,(geos(j,i),j=1,3) |
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END DO |
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| 348 |
|
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! First, we create the Centre of Mass atoms |
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DO i=1,NbCOM |
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COG(1)=0. |
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COG(2)=0. |
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COG(3)=0. |
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DO j=1,AtCOm(0,i) |
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DO k=1,3 |
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COG(k)=COG(k)+geos(k,AtCom(j,i)) |
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END DO |
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END DO |
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DO k=1,3 |
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COG(k)=COG(k)/AtCOM(0,i) |
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geos(k,Nat+i)=COG(k) |
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END DO |
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| 363 |
END DO |
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| 364 |
|
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| 365 |
|
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| 366 |
DO i=1,NbDist |
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VB(i)=sqrt((geos(1,At1B(i))-geos(1,At2B(i)))**2+ |
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& (geos(2,At1B(i))-geos(2,At2B(i)))**2+ |
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& (geos(3,At1B(i))-geos(3,At2B(i)))**2) |
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END DO |
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| 371 |
DO i=1,NbAngle |
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| 372 |
v1x=geos(1,At1A(i))-geos(1,At2A(i)) |
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| 373 |
v1y=geos(2,At1A(i))-geos(2,At2A(i)) |
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| 374 |
v1z=geos(3,At1A(i))-geos(3,At2A(i)) |
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| 375 |
d1=sqrt(v1x**2+v1y**2+v1z**2) |
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| 376 |
v2x=geos(1,At3A(i))-geos(1,At2A(i)) |
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| 377 |
v2y=geos(2,At3A(i))-geos(2,At2A(i)) |
|
| 378 |
v2z=geos(3,At3A(i))-geos(3,At2A(i)) |
|
| 379 |
d2=sqrt(v2x**2+v2y**2+v2z**2) |
|
| 380 |
VA(i)=acos((v1x*v2x+v1y*v2y+v1z*v2z)/(d1*d2))*180./Pi |
|
| 381 |
END DO |
|
| 382 |
DO i=1,NbDie |
|
| 383 |
! WRITE(*,*) At1D(i),At2D(i),At3D(i),At4D(i) |
|
| 384 |
! WRITE(*,*) geos(1,At1D(i)),geos(2,At1D(i)),geos(3,At1D(i)) |
|
| 385 |
! WRITE(*,*) geos(1,At2D(i)),geos(2,At2D(i)),geos(3,At2D(i)) |
|
| 386 |
v1x=geos(1,At1D(i))-geos(1,At2D(i)) |
|
| 387 |
v1y=geos(2,At1D(i))-geos(2,At2D(i)) |
|
| 388 |
v1z=geos(3,At1D(i))-geos(3,At2D(i)) |
|
| 389 |
v2x=geos(1,At3D(i))-geos(1,At2D(i)) |
|
| 390 |
v2y=geos(2,At3D(i))-geos(2,At2D(i)) |
|
| 391 |
v2z=geos(3,At3D(i))-geos(3,At2D(i)) |
|
| 392 |
v3x=geos(1,At4D(i))-geos(1,At3D(i)) |
|
| 393 |
v3y=geos(2,At4D(i))-geos(2,At3D(i)) |
|
| 394 |
v3z=geos(3,At4D(i))-geos(3,At3D(i)) |
|
| 395 |
|
|
| 396 |
v4x=v1y*v2z-v1z*v2y |
|
| 397 |
v4y=v1z*v2x-v1x*v2z |
|
| 398 |
v4z=v1x*v2y-v1y*v2x |
|
| 399 |
d1=sqrt(v4x**2+v4y**2+v4z**2) |
|
| 400 |
v5x=-v2y*v3z+v2z*v3y |
|
| 401 |
v5y=-v2z*v3x+v2x*v3z |
|
| 402 |
v5z=-v2x*v3y+v2y*v3x |
|
| 403 |
d2=sqrt(v5x**2+v5y**2+v5z**2) |
|
| 404 |
ca=(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2) |
|
| 405 |
sa=v1x*v5x+v1y*v5y+v1z*v5z |
|
| 406 |
VD(i)=acos(ca)*180./Pi |
|
| 407 |
if (sa<0.) VD(i)=-VD(i) |
|
| 408 |
! WRITE(*,*) "Dihe",v5x,v5y,v5z,v4x,v4y,v4z,d1,d2, |
|
| 409 |
! &(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2),pi |
|
| 410 |
!!!!!!!!! Another solution, more elegant ? |
|
| 411 |
! norm2=sqrt(v2x**2+v2y**2+v2z**2) |
|
| 412 |
! sa=(v4x*(v5y*v2z-v5z*v2y) |
|
| 413 |
! * -v4y*(v5x*v2z-v5z*v2x) |
|
| 414 |
! * +v4z*(v5x*v2y-v5y*v2x)) |
|
| 415 |
! * /(d1*norm2*d2) |
|
| 416 |
! angle_d=datan2(sa,ca)*180./Pi |
|
| 417 |
! WRITE(*,*) sa,ca,angle_d,d1,d2,norm2 |
|
| 418 |
! WRITE(*,*) VD(i),angle_d |
|
| 419 |
END DO |
|
| 420 |
|
|
| 421 |
END |
|
| 422 |
|
|
| 423 |
C================================================================ |
|
| 424 |
C Convertit un nom d'atome (2 lettres) en nombre de masse (entier) |
|
| 425 |
C cette fonction a ete modifiee pour pouvoir convertir un nom |
|
| 426 |
C d'atome avec un numero a la fin... |
|
| 427 |
C================================================================ |
|
| 428 |
|
|
| 429 |
FUNCTION ConvertNumAt(ATOM) |
|
| 430 |
|
|
| 431 |
|
|
| 432 |
IMPLICIT NONE |
|
| 433 |
|
|
| 434 |
INTEGER*4 I,Long,ConvertNumAt,IC |
|
| 435 |
character*2 ATOM*2,ATOME*3,L_Atom*2 |
|
| 436 |
INTEGER*4 Max_Z |
|
| 437 |
PARAMETER (Max_Z=86) |
|
| 438 |
CHARACTER*2 Nom(0:Max_Z) |
|
| 439 |
|
|
| 440 |
DATA NOM/ ' X',' H', 'HE', |
|
| 441 |
$ 'LI','BE', ' B',' C',' N',' O',' F','NE', |
|
| 442 |
$ 'NA','MG', 'AL','SI',' P',' S','CL','AR', |
|
| 443 |
$ ' K','CA', |
|
| 444 |
$ 'SC','TI',' V','CR','MN','FE','CO','NI','CU','ZN', |
|
| 445 |
$ 'GA','GE','AS','SE','BR','KR', |
|
| 446 |
$ 'RB','SR', |
|
| 447 |
$ ' Y','ZR','NB','MO','TC','RU','RH','PD','AG','CD', |
|
| 448 |
$ 'IN','SN','SB','TE',' I','XE', |
|
| 449 |
$ 'CS','BA', |
|
| 450 |
$ 'LA', |
|
| 451 |
$ 'CE','PR','ND','PM','SM','EU','GD','TB','DY','HO', |
|
| 452 |
$ 'ER','TM','YB','LU', |
|
| 453 |
$ 'HF','TA',' W','RE','OS','IR','PT','AU','HG', |
|
| 454 |
$ 'TL','PB','BI','PO','AT','RN'/ |
|
| 455 |
|
|
| 456 |
|
|
| 457 |
C Verifie qu'il n'y a que des lettres et des espaces dans ATOM |
|
| 458 |
! WRITE(*,*) 'DBG CNVNUMAT, ATOM:',ATOM |
|
| 459 |
|
|
| 460 |
L_atom=Atom |
|
| 461 |
IF (ATOM(1:1).LT.'A') L_ATOM(1:1)=' ' |
|
| 462 |
IC=Ichar(ATOM(1:1)) |
|
| 463 |
IF ((ic.le.123).AND.(ic.ge.97)) L_ATOM(1:1)=CHAr(IC-32) |
|
| 464 |
IF (ATOM(2:2).LT.'A') L_ATOM(2:2)=' ' |
|
| 465 |
IC=Ichar(ATOM(2:2)) |
|
| 466 |
IF ((ic.le.123).AND.(ic.ge.97)) L_ATOM(2:2)=CHAr(IC-32) |
|
| 467 |
C Justifie le nom sur la droite (et non sur la gauche comme souvent...) |
|
| 468 |
Long=INDEX(L_ATOM,' ')-1 |
|
| 469 |
ATOME=' ' // L_ATOM |
|
| 470 |
IF (Long.EQ.1) L_ATOM=ATOME(1:2) |
|
| 471 |
! WRITE(*,*) 'DBG CNVNUMAT, L_ATOM:',L_ATOM |
|
| 472 |
I=max_Z |
|
| 473 |
DO WHILE ((nom(I).NE.L_ATOM) .AND. (I.GT.0)) |
|
| 474 |
I=I-1 |
|
| 475 |
END DO |
|
| 476 |
ConvertNumAT=I |
|
| 477 |
END |
|
| 478 |
! This subroutine calculates RMSD using quaternions. |
|
| 479 |
! It is based on the F90 routine bu E. Coutsias |
|
| 480 |
! http://www.math.unm.edu/~vageli/homepage.html |
|
| 481 |
! I (PFL) have just translated it, and I have changed the diagonalization |
|
| 482 |
! subroutine. |
|
| 483 |
! I also made some changes to make it suitable for Cart package. |
|
| 484 |
!---------------------------------------------------------------------- |
|
| 485 |
!---------------------------------------------------------------------- |
|
| 486 |
! Copyright (C) 2004, 2005 Chaok Seok, Evangelos Coutsias and Ken Dill |
|
| 487 |
! UCSF, Univeristy of New Mexico, Seoul National University |
|
| 488 |
! Witten by Chaok Seok and Evangelos Coutsias 2004. |
|
| 489 |
|
|
| 490 |
! This library is free software; you can redistribute it and/or |
|
| 491 |
! modify it under the terms of the GNU Lesser General Public |
|
| 492 |
! License as published by the Free Software Foundation; either |
|
| 493 |
! version 2.1 of the License, or (at your option) any later version. |
|
| 494 |
! |
|
| 495 |
|
|
| 496 |
! This library is distributed in the hope that it will be useful, |
|
| 497 |
! but WITHOUT ANY WARRANTY; without even the implied warranty of |
|
| 498 |
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
|
| 499 |
! Lesser General Public License for more details. |
|
| 500 |
! |
|
| 501 |
|
|
| 502 |
! You should have received a copy of the GNU Lesser General Public |
|
| 503 |
! License along with this library; if not, write to the Free Software |
|
| 504 |
! Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
|
| 505 |
!---------------------------------------------------------------------------- |
|
| 506 |
|
|
| 507 |
subroutine CalcRmsd(na, geom,geom2,U,rmsd,FRot,FAlign,debug) |
|
| 508 |
!----------------------------------------------------------------------- |
|
| 509 |
! This subroutine calculates the least square rmsd of two coordinate |
|
| 510 |
! sets coord1(3,n) and coord2(3,n) using a method based on quaternion. |
|
| 511 |
! It then calculate the rotation matrix U and the centers of coord, and uses |
|
| 512 |
! them to align the two molecules. |
|
| 513 |
!----------------------------------------------------------------------- |
|
| 514 |
|
|
| 515 |
|
|
| 516 |
IMPLICIT NONE |
|
| 517 |
|
|
| 518 |
INCLUDE "Xyz2Path.param" |
|
| 519 |
|
|
| 520 |
INTEGER*4 IOIN, IOOUT, IOSCRN, IOPRNT, IOTAMP |
|
| 521 |
COMMON/IODEFS/IOIN,IOOUT,IOSCRN,IOPRNT,IOTAMP |
|
| 522 |
|
|
| 523 |
integer*4 na |
|
| 524 |
real*8 geom(3,MaxNAt), Geom2(3,MaxNAt) |
|
| 525 |
real*8 U(3,3), rmsd |
|
| 526 |
LOGICAL FRot,FAlign,Debug |
|
| 527 |
|
|
| 528 |
REAL*8 Coord1(3,MaxNAt), Coord2(3,MaxNAt) |
|
| 529 |
real*8 xc1,yc1,zc1, xc2,yc2,zc2 |
|
| 530 |
|
|
| 531 |
|
|
| 532 |
integer*4 i, j, ia |
|
| 533 |
real*8 x_norm, y_norm, lambda |
|
| 534 |
real*8 Rmatrix(3,3) |
|
| 535 |
real*8 S(4,4) |
|
| 536 |
real*8 EigVec(4,4), EigVal(4) |
|
| 537 |
|
|
| 538 |
|
|
| 539 |
|
|
| 540 |
! calculate the barycenters, centroidal coordinates, and the norms |
|
| 541 |
x_norm = 0.0d0 |
|
| 542 |
y_norm = 0.0d0 |
|
| 543 |
xc1=0. |
|
| 544 |
yc1=0. |
|
| 545 |
zc1=0. |
|
| 546 |
xc2=0. |
|
| 547 |
yc2=0. |
|
| 548 |
zc2=0. |
|
| 549 |
do ia=1,na |
|
| 550 |
xc1=xc1+geom(1,ia) |
|
| 551 |
xc2=xc2+geom2(1,ia) |
|
| 552 |
yc1=yc1+geom(2,ia) |
|
| 553 |
yc2=yc2+geom2(2,ia) |
|
| 554 |
zc1=zc1+geom(3,ia) |
|
| 555 |
zc2=zc2+geom2(3,ia) |
|
| 556 |
! if (debug) WRITE(*,'(A,I5,4(1X,F10.4))') 'ia...',ia,x(ia), |
|
| 557 |
! & x2(ia),xc1,xc2 |
|
| 558 |
END DO |
|
| 559 |
xc1=xc1/dble(na) |
|
| 560 |
yc1=yc1/dble(na) |
|
| 561 |
zc1=zc1/dble(na) |
|
| 562 |
xc2=xc2/dble(na) |
|
| 563 |
yc2=yc2/dble(na) |
|
| 564 |
zc2=zc2/dble(na) |
|
| 565 |
|
|
| 566 |
IF (debug) WRITE(*,'(1X,A,3(1X,F10.4))') 'Center1',xc1,yc1,zc1 |
|
| 567 |
IF (debug) WRITE(*,'(1X,A,3(1X,F10.4))') 'Center2',xc2,yc2,zc2 |
|
| 568 |
do i=1,na |
|
| 569 |
Coord1(1,i)=geom(1,i)-xc1 |
|
| 570 |
Coord1(2,i)=geom(2,i)-yc1 |
|
| 571 |
Coord1(3,i)=geom(3,i)-zc1 |
|
| 572 |
Coord2(1,i)=geom2(1,i)-xc2 |
|
| 573 |
Coord2(2,i)=geom2(2,i)-yc2 |
|
| 574 |
Coord2(3,i)=geom2(3,i)-zc2 |
|
| 575 |
x_norm=x_norm+Coord1(1,i)**2+Coord1(2,i)**2+Coord1(3,i)**2 |
|
| 576 |
y_norm=y_norm+Coord2(1,i)**2+Coord2(2,i)**2+Coord2(3,i)**2 |
|
| 577 |
end do |
|
| 578 |
|
|
| 579 |
IF (debug) THEN |
|
| 580 |
WRITE(*,*) "R matrix" |
|
| 581 |
DO I=1,3 |
|
| 582 |
WRITE(*,*) (RMatrix(I,j),j=1,3) |
|
| 583 |
END DO |
|
| 584 |
END IF |
|
| 585 |
|
|
| 586 |
! calculate the R matrix |
|
| 587 |
do i = 1, 3 |
|
| 588 |
do j = 1, 3 |
|
| 589 |
Rmatrix(i,j)=0. |
|
| 590 |
do ia=1,na |
|
| 591 |
Rmatrix(i,j) = Rmatrix(i,j)+Coord1(i,ia)*Coord2(j,ia) |
|
| 592 |
END DO |
|
| 593 |
end do |
|
| 594 |
end do |
|
| 595 |
|
|
| 596 |
IF (debug) THEN |
|
| 597 |
WRITE(*,*) "R matrix" |
|
| 598 |
DO I=1,3 |
|
| 599 |
WRITE(*,*) (RMatrix(I,j),j=1,3) |
|
| 600 |
END DO |
|
| 601 |
END IF |
|
| 602 |
|
|
| 603 |
|
|
| 604 |
! S matrix |
|
| 605 |
S(1, 1) = Rmatrix(1, 1) + Rmatrix(2, 2) + Rmatrix(3, 3) |
|
| 606 |
S(2, 1) = Rmatrix(2, 3) - Rmatrix(3, 2) |
|
| 607 |
S(3, 1) = Rmatrix(3, 1) - Rmatrix(1, 3) |
|
| 608 |
S(4, 1) = Rmatrix(1, 2) - Rmatrix(2, 1) |
|
| 609 |
|
|
| 610 |
S(1, 2) = S(2, 1) |
|
| 611 |
S(2, 2) = Rmatrix(1, 1) - Rmatrix(2, 2) - Rmatrix(3, 3) |
|
| 612 |
S(3, 2) = Rmatrix(1, 2) + Rmatrix(2, 1) |
|
| 613 |
S(4, 2) = Rmatrix(1, 3) + Rmatrix(3, 1) |
|
| 614 |
|
|
| 615 |
S(1, 3) = S(3, 1) |
|
| 616 |
S(2, 3) = S(3, 2) |
|
| 617 |
S(3, 3) =-Rmatrix(1, 1) + Rmatrix(2, 2) - Rmatrix(3, 3) |
|
| 618 |
S(4, 3) = Rmatrix(2, 3) + Rmatrix(3, 2) |
|
| 619 |
|
|
| 620 |
S(1, 4) = S(4, 1) |
|
| 621 |
S(2, 4) = S(4, 2) |
|
| 622 |
S(3, 4) = S(4, 3) |
|
| 623 |
S(4, 4) =-Rmatrix(1, 1) - Rmatrix(2, 2) + Rmatrix(3, 3) |
|
| 624 |
|
|
| 625 |
|
|
| 626 |
! PFL : I use my usual Jacobi diagonalisation |
|
| 627 |
! Calculate eigenvalues and eigenvectors, and |
|
| 628 |
! take the maximum eigenvalue lambda and the corresponding eigenvector q. |
|
| 629 |
|
|
| 630 |
IF (debug) THEN |
|
| 631 |
WRITE(*,*) "S matrix" |
|
| 632 |
DO I=1,4 |
|
| 633 |
WRITE(*,*) (S(I,j),j=1,4) |
|
| 634 |
END DO |
|
| 635 |
END IF |
|
| 636 |
|
|
| 637 |
Call Jacobi(S,4,EigVal,EigVec,4) |
|
| 638 |
|
|
| 639 |
Call Trie(4,EigVal,EigVec,4) |
|
| 640 |
|
|
| 641 |
Lambda=EigVal(4) |
|
| 642 |
|
|
| 643 |
! RMS Deviation |
|
| 644 |
rmsd=sqrt(max(0.0d0,((x_norm+y_norm)-2.0d0*lambda))/dble(na)) |
|
| 645 |
|
|
| 646 |
if (FRot.OR.FAlign) Call rotation_matrix(EigVec(1,4),U) |
|
| 647 |
IF (FAlign) THEN |
|
| 648 |
DO I=1,na |
|
| 649 |
geom2(1,i)=Coord2(1,i)*U(1,1)+Coord2(2,i)*U(2,1) |
|
| 650 |
& +Coord2(3,i)*U(3,1) +xc1 |
|
| 651 |
geom2(2,i)=Coord2(1,i)*U(1,2)+Coord2(2,i)*U(2,2) |
|
| 652 |
& +Coord2(3,i)*U(3,2) +yc1 |
|
| 653 |
geom2(3,i)=Coord2(1,i)*U(1,3)+Coord2(2,i)*U(2,3) |
|
| 654 |
& +Coord2(3,i)*U(3,3) +zc1 |
|
| 655 |
END DO |
|
| 656 |
END IF |
|
| 657 |
|
|
| 658 |
END |
|
| 659 |
|
|
| 660 |
|
|
| 661 |
!----------------------------------------------------------------------- |
|
| 662 |
subroutine rotation_matrix(q, U) |
|
| 663 |
!----------------------------------------------------------------------- |
|
| 664 |
! This subroutine constructs rotation matrix U from quaternion q. |
|
| 665 |
!----------------------------------------------------------------------- |
|
| 666 |
! This subroutine calculates RMSD using quaternions. |
|
| 667 |
! It is based on the F90 routine bu E. Coutsias |
|
| 668 |
! http://www.math.unm.edu/~vageli/homepage.html |
|
| 669 |
! I (PFL) have just translated it, and I have changed the diagonalization |
|
| 670 |
! subroutine. |
|
| 671 |
! I also made some changes to make it suitable for Cart package. |
|
| 672 |
!---------------------------------------------------------------------- |
|
| 673 |
!---------------------------------------------------------------------- |
|
| 674 |
! Copyright (C) 2004, 2005 Chaok Seok, Evangelos Coutsias and Ken Dill |
|
| 675 |
! UCSF, Univeristy of New Mexico, Seoul National University |
|
| 676 |
! Witten by Chaok Seok and Evangelos Coutsias 2004. |
|
| 677 |
|
|
| 678 |
! This library is free software; you can redistribute it and/or |
|
| 679 |
! modify it under the terms of the GNU Lesser General Public |
|
| 680 |
! License as published by the Free Software Foundation; either |
|
| 681 |
! version 2.1 of the License, or (at your option) any later version. |
|
| 682 |
! |
|
| 683 |
|
|
| 684 |
! This library is distributed in the hope that it will be useful, |
|
| 685 |
! but WITHOUT ANY WARRANTY; without even the implied warranty of |
|
| 686 |
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
|
| 687 |
! Lesser General Public License for more details. |
|
| 688 |
! |
|
| 689 |
|
|
| 690 |
! You should have received a copy of the GNU Lesser General Public |
|
| 691 |
! License along with this library; if not, write to the Free Software |
|
| 692 |
! Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
|
| 693 |
!---------------------------------------------------------------------------- |
|
| 694 |
|
|
| 695 |
real*8 q(4) |
|
| 696 |
real*8 U(3,3) |
|
| 697 |
real*8 q0,q1,q2,q3,b0,b1,b2,b3,q00,q01,q02,q03 |
|
| 698 |
REAL*8 q11,q12,q13,q22,q23,q33 |
|
| 699 |
|
|
| 700 |
q0 = q(1) |
|
| 701 |
q1 = q(2) |
|
| 702 |
q2 = q(3) |
|
| 703 |
q3 = q(4) |
|
| 704 |
|
|
| 705 |
b0 = 2.0d0*q0 |
|
| 706 |
b1 = 2.0d0*q1 |
|
| 707 |
b2 = 2.0d0*q2 |
|
| 708 |
b3 = 2.0d0*q3 |
|
| 709 |
|
|
| 710 |
q00 = b0*q0-1.0d0 |
|
| 711 |
q01 = b0*q1 |
|
| 712 |
q02 = b0*q2 |
|
| 713 |
q03 = b0*q3 |
|
| 714 |
|
|
| 715 |
q11 = b1*q1 |
|
| 716 |
q12 = b1*q2 |
|
| 717 |
q13 = b1*q3 |
|
| 718 |
|
|
| 719 |
q22 = b2*q2 |
|
| 720 |
q23 = b2*q3 |
|
| 721 |
|
|
| 722 |
q33 = b3*q3 |
|
| 723 |
|
|
| 724 |
U(1,1) = q00+q11 |
|
| 725 |
U(1,2) = q12-q03 |
|
| 726 |
U(1,3) = q13+q02 |
|
| 727 |
|
|
| 728 |
U(2,1) = q12+q03 |
|
| 729 |
U(2,2) = q00+q22 |
|
| 730 |
U(2,3) = q23-q01 |
|
| 731 |
|
|
| 732 |
U(3,1) = q13-q02 |
|
| 733 |
U(3,2) = q23+q01 |
|
| 734 |
U(3,3) = q00+q33 |
|
| 735 |
|
|
| 736 |
end |
|
| 737 |
|
|
| 738 |
c============================================================ |
|
| 739 |
c |
|
| 740 |
c ++ diagonalisation par jacobi |
|
| 741 |
c vecteur propre i : V(i,i) |
|
| 742 |
c valeur propre i : D(i) |
|
| 743 |
c |
|
| 744 |
c============================================================ |
|
| 745 |
c |
|
| 746 |
SUBROUTINE JACOBI(A,N,D,V,max_N) |
|
| 747 |
IMPLICIT REAL*8 (A-H,O-Z) |
|
| 748 |
parameter (max_it=500) |
|
| 749 |
DIMENSION A(max_N,max_N),B(max_N),Z(max_N) |
|
| 750 |
DIMENSION V(max_N,max_N),D(max_N) |
|
| 751 |
|
|
| 752 |
|
|
| 753 |
DO 12 IP=1,N |
|
| 754 |
DO 11 IQ=1,N |
|
| 755 |
V(IP,IQ)=0. |
|
| 756 |
11 CONTINUE |
|
| 757 |
V(IP,IP)=1. |
|
| 758 |
12 CONTINUE |
|
| 759 |
DO 13 IP=1,N |
|
| 760 |
B(IP)=A(IP,IP) |
|
| 761 |
D(IP)=B(IP) |
|
| 762 |
Z(IP)=0. |
|
| 763 |
13 CONTINUE |
|
| 764 |
NROT=0 |
|
| 765 |
DO 24 I=1,max_it |
|
| 766 |
SM=0. |
|
| 767 |
DO 15 IP=1,N-1 |
|
| 768 |
DO 14 IQ=IP+1,N |
|
| 769 |
SM=SM+ABS(A(IP,IQ)) |
|
| 770 |
14 CONTINUE |
|
| 771 |
15 CONTINUE |
|
| 772 |
IF(SM.EQ.0.)RETURN |
|
| 773 |
IF(I.LT.4)THEN |
|
| 774 |
TRESH=0.2*SM/N**2 |
|
| 775 |
ELSE |
|
| 776 |
TRESH=0. |
|
| 777 |
ENDIF |
|
| 778 |
DO 22 IP=1,N-1 |
|
| 779 |
DO 21 IQ=IP+1,N |
|
| 780 |
G=100.*ABS(A(IP,IQ)) |
|
| 781 |
IF((I.GT.4).AND.(ABS(D(IP))+G.EQ.ABS(D(IP))) |
|
| 782 |
* .AND.(ABS(D(IQ))+G.EQ.ABS(D(IQ))))THEN |
|
| 783 |
A(IP,IQ)=0. |
|
| 784 |
ELSE IF(ABS(A(IP,IQ)).GT.TRESH)THEN |
|
| 785 |
H=D(IQ)-D(IP) |
|
| 786 |
IF(ABS(H)+G.EQ.ABS(H))THEN |
|
| 787 |
T=A(IP,IQ)/H |
|
| 788 |
ELSE |
|
| 789 |
THETA=0.5*H/A(IP,IQ) |
|
| 790 |
T=1./(ABS(THETA)+SQRT(1.+THETA**2)) |
|
| 791 |
IF(THETA.LT.0.)T=-T |
|
| 792 |
ENDIF |
|
| 793 |
C=1./SQRT(1+T**2) |
|
| 794 |
S=T*C |
|
| 795 |
TAU=S/(1.+C) |
|
| 796 |
H=T*A(IP,IQ) |
|
| 797 |
Z(IP)=Z(IP)-H |
|
| 798 |
Z(IQ)=Z(IQ)+H |
|
| 799 |
D(IP)=D(IP)-H |
|
| 800 |
D(IQ)=D(IQ)+H |
|
| 801 |
A(IP,IQ)=0. |
|
| 802 |
DO 16 J=1,IP-1 |
|
| 803 |
G=A(J,IP) |
|
| 804 |
H=A(J,IQ) |
|
| 805 |
A(J,IP)=G-S*(H+G*TAU) |
|
| 806 |
A(J,IQ)=H+S*(G-H*TAU) |
|
| 807 |
16 CONTINUE |
|
| 808 |
DO 17 J=IP+1,IQ-1 |
|
| 809 |
G=A(IP,J) |
|
| 810 |
H=A(J,IQ) |
|
| 811 |
A(IP,J)=G-S*(H+G*TAU) |
|
| 812 |
A(J,IQ)=H+S*(G-H*TAU) |
|
| 813 |
17 CONTINUE |
|
| 814 |
DO 18 J=IQ+1,N |
|
| 815 |
G=A(IP,J) |
|
| 816 |
H=A(IQ,J) |
|
| 817 |
A(IP,J)=G-S*(H+G*TAU) |
|
| 818 |
A(IQ,J)=H+S*(G-H*TAU) |
|
| 819 |
18 CONTINUE |
|
| 820 |
DO 19 J=1,N |
|
| 821 |
G=V(J,IP) |
|
| 822 |
H=V(J,IQ) |
|
| 823 |
V(J,IP)=G-S*(H+G*TAU) |
|
| 824 |
V(J,IQ)=H+S*(G-H*TAU) |
|
| 825 |
19 CONTINUE |
|
| 826 |
NROT=NROT+1 |
|
| 827 |
ENDIF |
|
| 828 |
21 CONTINUE |
|
| 829 |
22 CONTINUE |
|
| 830 |
DO 23 IP=1,N |
|
| 831 |
B(IP)=B(IP)+Z(IP) |
|
| 832 |
D(IP)=B(IP) |
|
| 833 |
Z(IP)=0. |
|
| 834 |
23 CONTINUE |
|
| 835 |
24 CONTINUE |
|
| 836 |
write(6,*) max_it,' iterations should never happen' |
|
| 837 |
STOP |
|
| 838 |
RETURN |
|
| 839 |
END |
|
| 840 |
c |
|
| 841 |
c============================================================ |
|
| 842 |
c |
|
| 843 |
c ++ trie des vecteur dans l'ordre croissant |
|
| 844 |
c |
|
| 845 |
c============================================================ |
|
| 846 |
c |
|
| 847 |
SUBROUTINE trie(nb_niv,ene,psi,max_niv) |
|
| 848 |
integer i,j,k,nb_niv,max_niv |
|
| 849 |
real*8 ene(max_niv),psi(max_niv,max_niv) |
|
| 850 |
real*8 a |
|
| 851 |
|
|
| 852 |
DO i=1,nb_niv |
|
| 853 |
DO j=i+1,nb_niv |
|
| 854 |
IF (ene(i) .GT. ene(j)) THEN |
|
| 855 |
c permutation |
|
| 856 |
a=ene(i) |
|
| 857 |
ene(i)=ene(j) |
|
| 858 |
ene(j)=a |
|
| 859 |
DO k=1,nb_niv |
|
| 860 |
a=psi(k,i) |
|
| 861 |
psi(k,i)=psi(k,j) |
|
| 862 |
psi(k,j)=a |
|
| 863 |
END DO |
|
| 864 |
END IF |
|
| 865 |
END DO |
|
| 866 |
END DO |
|
| 867 |
|
|
| 868 |
END |
|
| 869 |
|
|
| utils/Xyz2Scan.f (revision 6) | ||
|---|---|---|
| 1 |
program Xyz2irc |
|
| 2 |
! This programs reads a XYZ file and converts it into distances, |
|
| 3 |
! valence angle and dihedral angles. |
|
| 4 |
! It prints them as a function of the irc distance... |
|
| 5 |
!----------------------------------------------- |
|
| 6 |
! Input: name of the ROOT file of PAW |
|
| 7 |
! it also needs a file call list which has the following structure: |
|
| 8 |
! the first line gives the time when you want to start your analysis |
|
| 9 |
! one line contains the type of the value you want to follow, it can be |
|
| 10 |
! b for a Bond distance |
|
| 11 |
! a for an angle |
|
| 12 |
! d for a dihedral |
|
| 13 |
! this descriptor is followed by the number of the atoms involved ! |
|
| 14 |
! a typical file can be: |
|
| 15 |
! 3. |
|
| 16 |
! b 1 2 |
|
| 17 |
! b 2 3 |
|
| 18 |
! a 1 2 3 |
|
| 19 |
!---------------------------------------------- |
|
| 20 |
! Ouput: A files call Scan.dat |
|
| 21 |
! wich contains in the first lines the input file (as a reminder) |
|
| 22 |
! and then for each step the wanted values |
|
| 23 |
!------------------------------------------------ |
|
| 24 |
! Second version also reads the energy (as to be written after E= on |
|
| 25 |
! the comment line) |
|
| 26 |
!------------------------------------------------ |
|
| 27 |
! Third version contains a new command: c for Center of Mass |
|
| 28 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
|
| 29 |
! v 3.1 the c command now creates the center of mass... and allows |
|
| 30 |
! people to do whatever they want with it... |
|
| 31 |
! Syntax: c NbAt ListAt |
|
| 32 |
!! |
|
| 33 |
! v 3.2 |
|
| 34 |
! Added the p command that gives the oriented angle between two planes |
|
| 35 |
! Syntax: p At1 At2 At3 At4 At5 At6 |
|
| 36 |
! At1, At2, At3 define the first plane |
|
| 37 |
! At4, At5, At6 define the second plane |
|
| 38 |
! How it works: gives the angles between the normal of the two planes, defined by |
|
| 39 |
! the cross produc At2-At1 x At2-At3 etc. |
|
| 40 |
!!!! |
|
| 41 |
|
|
| 42 |
|
|
| 43 |
IMPLICIT NONE |
|
| 44 |
INTEGER*4 maxnat,MaxList |
|
| 45 |
Parameter (MaxNat=10000,MaxList=100) |
|
| 46 |
character*120 f1 |
|
| 47 |
REAL*8 geos(3,maxnat) |
|
| 48 |
character*33 fmt |
|
| 49 |
character*3 atoms(maxnat) |
|
| 50 |
character*5 Type |
|
| 51 |
Character*120 line |
|
| 52 |
INTEGER*4 NbPrint |
|
| 53 |
REAL*8 AU2PS,Pi |
|
| 54 |
! Mass is not used for now. |
|
| 55 |
! REAL*8 Mass(MaxNat) |
|
| 56 |
REAL*8 Ener, Conv |
|
| 57 |
INTEGER*4 At1,At2,At3,At4,At5,At6,IOOUT |
|
| 58 |
INTEGER*4 IArg, I, NNN, Ng, J |
|
| 59 |
|
|
| 60 |
INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbP,NbCOM |
|
| 61 |
INTEGER*4 At1B(MaxList),At2B(MaxList) |
|
| 62 |
INTEGER*4 At1A(MaxList),At2A(MaxList),At3A(MaxList) |
|
| 63 |
INTEGER*4 At1D(MaxList),At2D(MaxList),At3D(MaxList), |
|
| 64 |
$ At4D(MaxList) |
|
| 65 |
INTEGER*4 At1p(MaxList),At2p(MaxList),At3p(MaxList), |
|
| 66 |
$ At4p(MaxList),At5p(MaxList),At6p(MaxList) |
|
| 67 |
INTEGER*4 AtCom(0:MaxList,MaxList) |
|
| 68 |
REAL*8 VB(MaxList),VA(MaxList),VD(MaxList),VCOM(MaxList) |
|
| 69 |
REAL*8 Vp(MaxList) |
|
| 70 |
LOGICAL FExist |
|
| 71 |
|
|
| 72 |
c INTEGER*4 iargc |
|
| 73 |
c external iargc |
|
| 74 |
|
|
| 75 |
COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbP,NbCom, At1B,At2B, |
|
| 76 |
& At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom, |
|
| 77 |
& At1p,At2p,At3p,At4p,At5p,At6p |
|
| 78 |
COMMON /Values/VB,VA,VD,Vp,VCom |
|
| 79 |
COMMON /Const/AU2ps,Pi |
|
| 80 |
|
|
| 81 |
AU2PS=1./41341.37 |
|
| 82 |
NbPrint=100 |
|
| 83 |
Pi=dacos(-1.d0) |
|
| 84 |
IOOUT=13 |
|
| 85 |
Conv=1. |
|
| 86 |
iarg=iargc() |
|
| 87 |
if (iarg.lt.1) then |
|
| 88 |
WRITE(*,*) "==============================================" |
|
| 89 |
WRITE(*,*) "== ==" |
|
| 90 |
WRITE(*,*) "== Xyz2Scan: Xyz file to scan file ==" |
|
| 91 |
WRITE(*,*) "== ==" |
|
| 92 |
WRITE(*,*) "==============================================" |
|
| 93 |
WRITE(*,*) "Usage: xyz2scan XYZ_file " |
|
| 94 |
WRITE(*,*) "The XYZ file should follow the 'usual' format:" |
|
| 95 |
WRITE(*,*) "Number of atoms on the first line " |
|
| 96 |
WRITE(*,*) "Comment on the second line" |
|
| 97 |
WRITE(*,*) "The geometry is given in cartesian coordinates" |
|
| 98 |
WRITE(*,*) "with atom symbol and three coordinates:" |
|
| 99 |
WRITE(*,*) " C 0. 1. 0." |
|
| 100 |
WRITE(*,*) "" |
|
| 101 |
WRITE(*,*) " xyz2scan also needs a file called 'list' " |
|
| 102 |
WRITE(*,*) "which has the following structure:" |
|
| 103 |
WRITE(*,*) "Each line contains the type of the value you" |
|
| 104 |
WRITE(*,*) "want to follow, it can be:" |
|
| 105 |
WRITE(*,*) " - b for a Bond distance" |
|
| 106 |
WRITE(*,*) " - a for an angle" |
|
| 107 |
WRITE(*,*) " - d for a dihedral" |
|
| 108 |
WRITE(*,*) " - p for the oriented angle between two planes" |
|
| 109 |
WRITE(*,*) "This descriptor is followed by the number of" |
|
| 110 |
WRITE(*,*) "the atoms involved" |
|
| 111 |
WRITE(*,*) "One can also create 'barycenter' atoms that" |
|
| 112 |
WRITE(*,*) "can then be used as normal atoms." |
|
| 113 |
WRITE(*,*) "the descriptor is 'c' followed by the number" |
|
| 114 |
WRITE(*,*) "of atoms and the list of atoms:" |
|
| 115 |
WRITE(*,*) " c 2 1 5" |
|
| 116 |
WRITE(*,*) "A typical file can be:" |
|
| 117 |
WRITE(*,*) " b 1 2" |
|
| 118 |
WRITE(*,*) " b 2 3" |
|
| 119 |
WRITE(*,*) " a 1 2 3" |
|
| 120 |
WRITE(*,*) " " |
|
| 121 |
WRITE(*,*) "==============================================" |
|
| 122 |
write(*,*) 'XYZ filename:' |
|
| 123 |
read(*,'(a)') f1 |
|
| 124 |
else |
|
| 125 |
call getarg(1,f1) |
|
| 126 |
endif |
|
| 127 |
|
|
| 128 |
open(13,file='Scan.dat') |
|
| 129 |
|
|
| 130 |
INQUIRE(File='list',Exist=FExist) |
|
| 131 |
if (.NOT.FExist) THEN |
|
| 132 |
WRITE(*,*) "File *list* is missing" |
|
| 133 |
STOP |
|
| 134 |
END IF |
|
| 135 |
|
|
| 136 |
open(11,file=f1) |
|
| 137 |
READ(11,*) nnn |
|
| 138 |
close(11) |
|
| 139 |
|
|
| 140 |
|
|
| 141 |
if (nnn.GT.MaxNat) THEN |
|
| 142 |
WRITE(*,*) "Sorry but your system has too many atoms" |
|
| 143 |
WRITE(*,*) "Change the value of MaxNat in the source file" |
|
| 144 |
WRITE(*,*) "and then recompile." |
|
| 145 |
WRITE(*,*) "For information, now MaxNat=",MaxNat |
|
| 146 |
WRITE(*,*) "and you have ",nnn," atoms." |
|
| 147 |
STOP |
|
| 148 |
END IF |
|
| 149 |
|
|
| 150 |
Nat=nnn |
|
| 151 |
|
|
| 152 |
open(14,file='list') |
|
| 153 |
Type="d" |
|
| 154 |
DO WHILE (Type.ne."E") |
|
| 155 |
CALL READLINE(14,Type,Line) |
|
| 156 |
! WRITE(*,*) Line,Type |
|
| 157 |
if (Type.eq."b") THEN |
|
| 158 |
NbDist=NbDist+1 |
|
| 159 |
READ(Line,*) At1,At2 |
|
| 160 |
At1B(NbDist)=At1 |
|
| 161 |
At2B(NbDist)=At2 |
|
| 162 |
END IF |
|
| 163 |
if (Type.eq."a") THEN |
|
| 164 |
NbAngle=NbAngle+1 |
|
| 165 |
READ(Line,*) At1,At2,At3 |
|
| 166 |
At1A(NbAngle)=At1 |
|
| 167 |
At2A(NbAngle)=At2 |
|
| 168 |
At3A(NbAngle)=At3 |
|
| 169 |
END IF |
|
| 170 |
if (Type.eq."d") THEN |
|
| 171 |
NbDie=NbDie+1 |
|
| 172 |
READ(Line,*) At1,At2,At3,At4 |
|
| 173 |
At1D(NbDie)=At1 |
|
| 174 |
At2D(NbDie)=At2 |
|
| 175 |
At3D(NbDie)=At3 |
|
| 176 |
At4D(NbDie)=At4 |
|
| 177 |
! WRITE(13,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
|
| 178 |
! & Atoms(At3),At3,Atoms(At4),At4 |
|
| 179 |
! WRITE(*,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
|
| 180 |
! & Atoms(At3),At3,Atoms(At4),At4 |
|
| 181 |
|
|
| 182 |
END IF |
|
| 183 |
if (Type.eq."p") THEN |
|
| 184 |
NbP=NbP+1 |
|
| 185 |
READ(Line,*) At1,At2,At3,At4,At5,At6 |
|
| 186 |
At1p(NbP)=At1 |
|
| 187 |
At2p(NbP)=At2 |
|
| 188 |
At3p(NbP)=At3 |
|
| 189 |
At4p(NbP)=At4 |
|
| 190 |
At5p(NbP)=At5 |
|
| 191 |
At6p(NbP)=At6 |
|
| 192 |
END IF |
|
| 193 |
|
|
| 194 |
if (Type.eq."c") THEN |
|
| 195 |
NbCOM=NbCOM+1 |
|
| 196 |
READ(Line,*) At1,(AtCom(j,NbCOM),j=1,At1) |
|
| 197 |
AtCom(0,NbCOM)=At1 |
|
| 198 |
Atoms(nat+NbCom)="G" |
|
| 199 |
END IF |
|
| 200 |
|
|
| 201 |
END DO |
|
| 202 |
|
|
| 203 |
CLOSE(14) |
|
| 204 |
|
|
| 205 |
! We read one geoetry to get the atoms name |
|
| 206 |
open(11,file=f1) |
|
| 207 |
call rtraitem(11,nnn,ener,geos,atoms) |
|
| 208 |
close(11) |
|
| 209 |
|
|
| 210 |
|
|
| 211 |
! We write things |
|
| 212 |
! First NbCom |
|
| 213 |
if (NbCom.GE.1) THEN |
|
| 214 |
WRITE(*,*) "# Added center of mass" |
|
| 215 |
WRITE(IOOUT,*) "# Added center of mass" |
|
| 216 |
DO J=1,NbCom |
|
| 217 |
WRITE(IOOUT,'("# c ",I4,20(A3,I3))') AtCom(0,J),
|
|
| 218 |
& (Atoms(AtCom(i,J)),AtCom(i,J),i=1,At1) |
|
| 219 |
WRITE(*,'("# c ",I4,20(A3,I3))') AtCom(0,J),
|
|
| 220 |
& (Atoms(AtCom(i,J)),AtCom(i,J),i=1,At1) |
|
| 221 |
END DO |
|
| 222 |
END IF |
|
| 223 |
|
|
| 224 |
! Distances |
|
| 225 |
if (NbDist.GE.1) THEN |
|
| 226 |
WRITE(*,*) "# Bonds" |
|
| 227 |
WRITE(IOOUT,*) "# Bonds" |
|
| 228 |
DO J=1,NbDist |
|
| 229 |
At1= At1B(J) |
|
| 230 |
At2=At2B(J) |
|
| 231 |
WRITE(IOOUT,'("# b ",2(A3,I3))') Atoms(At1),At1,
|
|
| 232 |
$ Atoms(At2),At2 |
|
| 233 |
WRITE(*,'("# b ",2(A3,I3))') Atoms(At1),At1,Atoms(At2),At2
|
|
| 234 |
END DO |
|
| 235 |
END IF |
|
| 236 |
|
|
| 237 |
! Angles |
|
| 238 |
if (NbAngle.GE.1) THEN |
|
| 239 |
WRITE(*,*) "# Angles" |
|
| 240 |
WRITE(IOOUT,*) "# Angles" |
|
| 241 |
DO J=1,NbAngle |
|
| 242 |
At1= At1A(J) |
|
| 243 |
At2= At2A(J) |
|
| 244 |
At3= At3A(J) |
|
| 245 |
WRITE(IOOUT,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),
|
|
| 246 |
& At2, Atoms(At3),At3 |
|
| 247 |
WRITE(*,'("# a ",3(A3,I3))') Atoms(At1),At1,Atoms(At2),
|
|
| 248 |
& At2, Atoms(At3),At3 |
|
| 249 |
|
|
| 250 |
END DO |
|
| 251 |
END IF |
|
| 252 |
|
|
| 253 |
|
|
| 254 |
! Dihedrals |
|
| 255 |
if (NbDie.GE.1) THEN |
|
| 256 |
WRITE(*,*) "# Dihedrals" |
|
| 257 |
WRITE(IOOUT,*) "# Dihedrals" |
|
| 258 |
DO J=1,NbDie |
|
| 259 |
At1= At1D(J) |
|
| 260 |
At2= At2D(J) |
|
| 261 |
At3= At3D(J) |
|
| 262 |
At4= At4D(J) |
|
| 263 |
WRITE(IOOUT,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2)
|
|
| 264 |
& ,At2,Atoms(At3),At3,Atoms(At4),At4 |
|
| 265 |
WRITE(*,'("# d ",4(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
|
| 266 |
& Atoms(At3),At3,Atoms(At4),At4 |
|
| 267 |
END DO |
|
| 268 |
END IF |
|
| 269 |
|
|
| 270 |
! Planar angles |
|
| 271 |
if (NbP.GE.1) THEN |
|
| 272 |
WRITE(*,*) "# Planes angles" |
|
| 273 |
WRITE(IOOUT,*) "# Planes angles" |
|
| 274 |
DO J=1,NbP |
|
| 275 |
At1= At1p(J) |
|
| 276 |
At2= At2p(J) |
|
| 277 |
At3= At3p(J) |
|
| 278 |
At4= At4p(J) |
|
| 279 |
At5= At5p(J) |
|
| 280 |
At6= At6p(J) |
|
| 281 |
WRITE(IOOUT,'("# p ",8(A3,I3))') Atoms(At1),At1,Atoms(At2)
|
|
| 282 |
& ,At2,Atoms(At3),At3,Atoms(At4),At4 |
|
| 283 |
& ,Atoms(At5),At5,Atoms(At6),At6 |
|
| 284 |
WRITE(*,'("# p ",8(A3,I3))') Atoms(At1),At1,Atoms(At2),At2,
|
|
| 285 |
& Atoms(At3),At3,Atoms(At4),At4 |
|
| 286 |
& ,Atoms(At5),At5,Atoms(At6),At6 |
|
| 287 |
END DO |
|
| 288 |
END IF |
|
| 289 |
|
|
| 290 |
|
|
| 291 |
fmt='( (1X,F12.5),1X,F15.6)' |
|
| 292 |
write(fmt(2:4),'(i3)') NbDist+NbAngle+NbDie+NbP |
|
| 293 |
! write(*,*) nat3 |
|
| 294 |
! write(*,*) 'fmt:',fmt |
|
| 295 |
|
|
| 296 |
ng=1 |
|
| 297 |
|
|
| 298 |
open(11,file=f1) |
|
| 299 |
|
|
| 300 |
10 call rtraitem(11,nnn,ener,geos,atoms) |
|
| 301 |
! WRITE(*,*) nnn |
|
| 302 |
|
|
| 303 |
if (nnn.gt.0) then |
|
| 304 |
! We convert coordinates in a0 into Angstroem |
|
| 305 |
! write(*,*) "Analyse !" |
|
| 306 |
Call Analyse(geos) |
|
| 307 |
|
|
| 308 |
write(IOOUT,fmt) (VB(j)/Conv,j=1,NbDist), |
|
| 309 |
& (VA(j),j=1,NbAngle), |
|
| 310 |
& (VD(j),j=1,NbDie),(Vp(j),j=1,NbP),ener |
|
| 311 |
write(*,fmt) (VB(j)/Conv,j=1,NbDist), |
|
| 312 |
& (VA(j),j=1,NbAngle), |
|
| 313 |
& (VD(j),j=1,NbDie),(Vp(j),j=1,NbP),ener |
|
| 314 |
|
|
| 315 |
ng=ng+1 |
|
| 316 |
goto 10 |
|
| 317 |
endif |
|
| 318 |
WRITE(*,*) 'Found ',ng-1,' geometries' |
|
| 319 |
close(11) |
|
| 320 |
end |
|
| 321 |
|
|
| 322 |
!-------------------------------------------------------------- |
|
| 323 |
subroutine rtraitem(ifil,nnn,E,tab,atoms) |
|
| 324 |
! implicit real*8 (a-h,o-z) |
|
| 325 |
IMPLICIT NONE |
|
| 326 |
character*120 line |
|
| 327 |
character*3 Atoms(*) |
|
| 328 |
integer*4 nnn, IFil, Idx, I, J |
|
| 329 |
REAL*8 Tab(3,*), E |
|
| 330 |
|
|
| 331 |
|
|
| 332 |
read(ifil,*,err=99,end=99) nnn |
|
| 333 |
read(ifil,'(A)') line |
|
| 334 |
idx=index(line,'E') |
|
| 335 |
! WRITE(*,*) 'idx,line',idx,line |
|
| 336 |
if (idx/=0) THEN |
|
| 337 |
line=line(idx+2:) |
|
| 338 |
idx=index(line,"=") |
|
| 339 |
if (idx/=0) line=line(idx+1:) |
|
| 340 |
idx=index(line,":") |
|
| 341 |
if (idx/=0) line=line(idx+1:) |
|
| 342 |
read(line,*) E |
|
| 343 |
ELSE |
|
| 344 |
E=0. |
|
| 345 |
END IF |
|
| 346 |
|
|
| 347 |
! write(*,*) 'coucou',line |
|
| 348 |
do i=1,nnn |
|
| 349 |
read(ifil,'(A)',err=99,end=99) Line |
|
| 350 |
do while (line(1:1)==' ') |
|
| 351 |
line=line(2:) |
|
| 352 |
end do |
|
| 353 |
atoms(i)=line(1:3) |
|
| 354 |
! write(*,*) 'coucou atoms',atoms(i) |
|
| 355 |
do while (line(1:1).ne.' ') |
|
| 356 |
line=line(2:) |
|
| 357 |
end do |
|
| 358 |
! WRITE(*,*) 'coucou2:',i,line |
|
| 359 |
read(line,*) (tab(j,i),j=1,3) |
|
| 360 |
end do |
|
| 361 |
! WRITE(*,*) 'coucou:',nnn,tab(1,1) |
|
| 362 |
return |
|
| 363 |
99 nnn=0 |
|
| 364 |
! WRITE(*,*) 'Erreur lecture',ifil,nnn |
|
| 365 |
return |
|
| 366 |
end |
|
| 367 |
|
|
| 368 |
!-------------------------------------------------------------- |
|
| 369 |
|
|
| 370 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
|
| 371 |
! READLINE |
|
| 372 |
! This subroutine reads a line for a file, and converts |
|
| 373 |
! the first field into a character variable, and the rest into 4 integers |
|
| 374 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
|
| 375 |
|
|
| 376 |
SUBROUTINE READLINE(IOIN,Type,Line) |
|
| 377 |
|
|
| 378 |
IMPLICIT NONE |
|
| 379 |
CHARACTER Type*5,LINE*120 |
|
| 380 |
INTEGER i,IOIN |
|
| 381 |
READ(IOIN,'(A120)',ERR=999,END=999) LINE |
|
| 382 |
! WRITE(*,*) Line |
|
| 383 |
DO WHILE (LINE(1:1).eq.' ') |
|
| 384 |
LINE=LINE(2:) |
|
| 385 |
END DO |
|
| 386 |
|
|
| 387 |
i=1 |
|
| 388 |
DO WHILE (LINE(i:i).ne.' ') |
|
| 389 |
i=i+1 |
|
| 390 |
END DO |
|
| 391 |
|
|
| 392 |
if (i.ge.6) THEN |
|
| 393 |
WRITE(*,*) 'Pb with READLINE:',LINE |
|
| 394 |
GOTO 999 |
|
| 395 |
END IF |
|
| 396 |
Type=LINE(1:i-1) |
|
| 397 |
LINE=LINE(i:120) // " 0 0 0 0" |
|
| 398 |
|
|
| 399 |
RETURN |
|
| 400 |
999 Type="E" |
|
| 401 |
END |
|
| 402 |
|
|
| 403 |
|
|
| 404 |
|
|
| 405 |
SUBROUTINE Analyse(geos) |
|
| 406 |
|
|
| 407 |
IMPLICIT NONE |
|
| 408 |
INTEGER*4 MaxNat,MaxList |
|
| 409 |
parameter (maxnat=10000,MaxList=100) |
|
| 410 |
REAL*8 geos(3,maxnat) |
|
| 411 |
REAL*8 AU2PS,Pi |
|
| 412 |
INTEGER*4 i,j,k |
|
| 413 |
REAL*8 V1x,V1y,V1z,V2x,V2y,V2z,V3x,V3y,V3z |
|
| 414 |
REAL*8 d1,d2,ca,sa |
|
| 415 |
REAL*8 V4x,v4y,v4z,v5x,v5y,v5z |
|
| 416 |
REAL*8 COG(3) |
|
| 417 |
|
|
| 418 |
INTEGER*4 Nat,NbDist, NbAngle, NbDie,NbP,NbCOM |
|
| 419 |
INTEGER*4 At1B(MaxList),At2B(MaxList) |
|
| 420 |
INTEGER*4 At1A(MaxList),At2A(MaxList),At3A(MaxList) |
|
| 421 |
INTEGER*4 At1D(MaxList),At2D(MaxList),At3D(MaxList), |
|
| 422 |
$ At4D(MaxList) |
|
| 423 |
INTEGER*4 At1p(MaxList),At2p(MaxList),At3p(MaxList), |
|
| 424 |
$ At4p(MaxList),At5p(MaxList),At6p(MaxList) |
|
| 425 |
INTEGER*4 AtCom(0:MaxList,MaxList) |
|
| 426 |
REAL*8 VB(MaxList),VA(MaxList),VD(MaxList),VCOM(MaxList) |
|
| 427 |
REAL*8 Vp(MaxList) |
|
| 428 |
|
|
| 429 |
COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbP,NbCom, At1B,At2B, |
|
| 430 |
& At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom, |
|
| 431 |
& At1p,At2p,At3p,At4p,At5p,At6p |
|
| 432 |
COMMON /Values/VB,VA,VD,Vp,VCom |
|
| 433 |
COMMON /Const/AU2ps,Pi |
|
| 434 |
|
|
| 435 |
DO I=1,Nat |
|
| 436 |
WRITE(*,'(1X,I3,3(1X,F15.6))') i,(geos(j,i),j=1,3) |
|
| 437 |
END DO |
|
| 438 |
|
|
| 439 |
! First, we create the Centre of Mass atoms |
|
| 440 |
DO i=1,NbCOM |
|
| 441 |
COG(1)=0. |
|
| 442 |
COG(2)=0. |
|
| 443 |
COG(3)=0. |
|
| 444 |
DO j=1,AtCOm(0,i) |
|
| 445 |
DO k=1,3 |
|
| 446 |
COG(k)=COG(k)+geos(k,AtCom(j,i)) |
|
| 447 |
END DO |
|
| 448 |
END DO |
|
| 449 |
DO k=1,3 |
|
| 450 |
COG(k)=COG(k)/AtCOM(0,i) |
|
| 451 |
geos(k,Nat+i)=COG(k) |
|
| 452 |
END DO |
|
| 453 |
END DO |
|
| 454 |
|
|
| 455 |
|
|
| 456 |
DO i=1,NbDist |
|
| 457 |
VB(i)=sqrt((geos(1,At1B(i))-geos(1,At2B(i)))**2+ |
|
| 458 |
& (geos(2,At1B(i))-geos(2,At2B(i)))**2+ |
|
| 459 |
& (geos(3,At1B(i))-geos(3,At2B(i)))**2) |
|
| 460 |
END DO |
|
| 461 |
DO i=1,NbAngle |
|
| 462 |
v1x=geos(1,At1A(i))-geos(1,At2A(i)) |
|
| 463 |
v1y=geos(2,At1A(i))-geos(2,At2A(i)) |
|
| 464 |
v1z=geos(3,At1A(i))-geos(3,At2A(i)) |
|
| 465 |
d1=sqrt(v1x**2+v1y**2+v1z**2) |
|
| 466 |
v2x=geos(1,At3A(i))-geos(1,At2A(i)) |
|
| 467 |
v2y=geos(2,At3A(i))-geos(2,At2A(i)) |
|
| 468 |
v2z=geos(3,At3A(i))-geos(3,At2A(i)) |
|
| 469 |
d2=sqrt(v2x**2+v2y**2+v2z**2) |
|
| 470 |
VA(i)=acos((v1x*v2x+v1y*v2y+v1z*v2z)/(d1*d2))*180./Pi |
|
| 471 |
END DO |
|
| 472 |
DO i=1,NbDie |
|
| 473 |
! WRITE(*,*) At1D(i),At2D(i),At3D(i),At4D(i) |
|
| 474 |
! WRITE(*,*) geos(1,At1D(i)),geos(2,At1D(i)),geos(3,At1D(i)) |
|
| 475 |
! WRITE(*,*) geos(1,At2D(i)),geos(2,At2D(i)),geos(3,At2D(i)) |
|
| 476 |
v1x=geos(1,At1D(i))-geos(1,At2D(i)) |
|
| 477 |
v1y=geos(2,At1D(i))-geos(2,At2D(i)) |
|
| 478 |
v1z=geos(3,At1D(i))-geos(3,At2D(i)) |
|
| 479 |
v2x=geos(1,At3D(i))-geos(1,At2D(i)) |
|
| 480 |
v2y=geos(2,At3D(i))-geos(2,At2D(i)) |
|
| 481 |
v2z=geos(3,At3D(i))-geos(3,At2D(i)) |
|
| 482 |
v3x=geos(1,At4D(i))-geos(1,At3D(i)) |
|
| 483 |
v3y=geos(2,At4D(i))-geos(2,At3D(i)) |
|
| 484 |
v3z=geos(3,At4D(i))-geos(3,At3D(i)) |
|
| 485 |
|
|
| 486 |
v4x=v1y*v2z-v1z*v2y |
|
| 487 |
v4y=v1z*v2x-v1x*v2z |
|
| 488 |
v4z=v1x*v2y-v1y*v2x |
|
| 489 |
d1=sqrt(v4x**2+v4y**2+v4z**2) |
|
| 490 |
v5x=-v2y*v3z+v2z*v3y |
|
| 491 |
v5y=-v2z*v3x+v2x*v3z |
|
| 492 |
v5z=-v2x*v3y+v2y*v3x |
|
| 493 |
d2=sqrt(v5x**2+v5y**2+v5z**2) |
|
| 494 |
if (d1<=1e-12) THEN |
|
| 495 |
WRITE(*,*) "WARNING: Dihedral, d1=0" |
|
| 496 |
ca=-1. |
|
| 497 |
sa=0. |
|
| 498 |
END IF |
|
| 499 |
if (d2<=1e-12) THEN |
|
| 500 |
WRITE(*,*) "WARNING: Dihedral, d2=0" |
|
| 501 |
ca=-1. |
|
| 502 |
sa=0. |
|
| 503 |
END IF |
|
| 504 |
ca=(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2) |
|
| 505 |
sa=v1x*v5x+v1y*v5y+v1z*v5z |
|
| 506 |
if (abs(ca)>1.) ca=sign(1.d0,ca) |
|
| 507 |
VD(i)=acos(ca)*180./Pi |
|
| 508 |
if (sa<0.) VD(i)=-VD(i) |
|
| 509 |
! WRITE(*,*) "Dihe",v5x,v5y,v5z,v4x,v4y,v4z,d1,d2, |
|
| 510 |
! &(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2),pi |
|
| 511 |
! WRITE(*,*) "Dihe ca,sa,d1,d2",ca,sa,d1,d2,acos(ca) |
|
| 512 |
|
|
| 513 |
|
|
| 514 |
!!!!!!!!! Another solution, more elegant ? |
|
| 515 |
! norm2=sqrt(v2x**2+v2y**2+v2z**2) |
|
| 516 |
! sa=(v4x*(v5y*v2z-v5z*v2y) |
|
| 517 |
! * -v4y*(v5x*v2z-v5z*v2x) |
|
| 518 |
! * +v4z*(v5x*v2y-v5y*v2x)) |
|
| 519 |
! * /(d1*norm2*d2) |
|
| 520 |
! angle_d=datan2(sa,ca)*180./Pi |
|
| 521 |
! WRITE(*,*) sa,ca,angle_d,d1,d2,norm2 |
|
| 522 |
! WRITE(*,*) VD(i),angle_d |
|
| 523 |
END DO |
|
| 524 |
|
|
| 525 |
DO i=1,NbP |
|
| 526 |
! v1= At2-At1 |
|
| 527 |
v1x=geos(1,At1p(i))-geos(1,At2p(i)) |
|
| 528 |
v1y=geos(2,At1p(i))-geos(2,At2p(i)) |
|
| 529 |
v1z=geos(3,At1p(i))-geos(3,At2p(i)) |
|
| 530 |
! v2=At2-At3 |
|
| 531 |
v2x=geos(1,At3p(i))-geos(1,At2p(i)) |
|
| 532 |
v2y=geos(2,At3p(i))-geos(2,At2p(i)) |
|
| 533 |
v2z=geos(3,At3p(i))-geos(3,At2p(i)) |
|
| 534 |
! v4 = v1 x v2 |
|
| 535 |
v4x=v1y*v2z-v1z*v2y |
|
| 536 |
v4y=v1z*v2x-v1x*v2z |
|
| 537 |
v4z=v1x*v2y-v1y*v2x |
|
| 538 |
d1=sqrt(v4x**2+v4y**2+v4z**2) |
|
| 539 |
|
|
| 540 |
! v3= At5-At4 |
|
| 541 |
v3x=geos(1,At4p(i))-geos(1,At5p(i)) |
|
| 542 |
v3y=geos(2,At4p(i))-geos(2,At5p(i)) |
|
| 543 |
v3z=geos(3,At4p(i))-geos(3,At5p(i)) |
|
| 544 |
! v2=At5-At6 |
|
| 545 |
v2x=geos(1,At6p(i))-geos(1,At5p(i)) |
|
| 546 |
v2y=geos(2,At6p(i))-geos(2,At5p(i)) |
|
| 547 |
v2z=geos(3,At6p(i))-geos(3,At5p(i)) |
|
| 548 |
|
|
| 549 |
! v5 = v3 x v2 |
|
| 550 |
v5x=v3y*v2z-v3z*v2y |
|
| 551 |
v5y=v3z*v2x-v3x*v2z |
|
| 552 |
v5z=v3x*v2y-v3y*v2x |
|
| 553 |
d2=sqrt(v5x**2+v5y**2+v5z**2) |
|
| 554 |
|
|
| 555 |
ca=(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2) |
|
| 556 |
sa=v1x*v5x+v1y*v5y+v1z*v5z |
|
| 557 |
Vp(i)=acos(ca)*180./Pi |
|
| 558 |
if (sa<0.) Vp(i)=-Vp(i) |
|
| 559 |
! WRITE(*,*) "Dihe",v5x,v5y,v5z,v4x,v4y,v4z,d1,d2, |
|
| 560 |
! &(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2),pi |
|
| 561 |
!!!!!!!!! Another solution, more elegant ? |
|
| 562 |
! See Dihedral routine |
|
| 563 |
END DO |
|
| 564 |
|
|
| 565 |
|
|
| 566 |
END |
|
| utils/Xyz2Scan.f90 (revision 6) | ||
|---|---|---|
| 1 |
program Xyz2irc |
|
| 2 |
! This programs reads a XYZ file and converts it into distances, |
|
| 3 |
! valence angle and dihedral angles. |
|
| 4 |
! It prints them as a function of the irc distance... |
|
| 5 |
!----------------------------------------------- |
|
| 6 |
! Input: name of the ROOT file of PAW |
|
| 7 |
! it also needs a file call list which has the following structure: |
|
| 8 |
! the first line gives the time when you want to start your analysis |
|
| 9 |
! one line contains the type of the value you want to follow, it can be |
|
| 10 |
! b for a Bond distance |
|
| 11 |
! a for an angle |
|
| 12 |
! d for a dihedral |
|
| 13 |
! this descriptor is followed by the number of the atoms involved ! |
|
| 14 |
! a typical file can be: |
|
| 15 |
! 3. |
|
| 16 |
! b 1 2 |
|
| 17 |
! b 2 3 |
|
| 18 |
! a 1 2 3 |
|
| 19 |
!---------------------------------------------- |
|
| 20 |
! Ouput: A files call Scan.dat |
|
| 21 |
! wich contains in the first lines the input file (as a reminder) |
|
| 22 |
! and then for each step the wanted values |
|
| 23 |
!------------------------------------------------ |
|
| 24 |
! Second version also reads the energy (as to be written after E= on |
|
| 25 |
! the comment line) |
|
| 26 |
!------------------------------------------------ |
|
| 27 |
! Third version contains a new command: c for Center of Mass |
|
| 28 |
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
|
| 29 |
! v 3.1 the c command now creates the center of mass... and allows |
|
| 30 |
! people to do whatever they want with it... |
|
| 31 |
! Syntax: c NbAt ListAt |
|
| 32 |
!! |
|
| 33 |
! v 3.2 |
|
| 34 |
! Added the p command that gives the oriented angle between two planes |
|
| 35 |
! Syntax: p At1 At2 At3 At4 At5 At6 |
|
| 36 |
! At1, At2, At3 define the first plane |
|
| 37 |
! At4, At5, At6 define the second plane |
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! How it works: gives the angles between the normal of the two planes, defined by |
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! the cross produc At2-At1 x At2-At3 etc. |
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!!!! |
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IMPLICIT NONE |
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INTEGER(4), PARAMETER :: maxnat=10000,MaxList=100 |
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CHARACTER(120) :: f1 |
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REAL(8) :: geos(3,maxnat) |
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CHARACTER(33) :: fmt |
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CHARACTER(3) :: atoms(maxnat) |
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character(5) :: Type |
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CHARACTER(120) :: line |
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Also available in: Unified diff