root / utils / Xyz2Path.f90 @ 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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|
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|
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IMPLICIT NONE |
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|
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INCLUDE "Xyz2Path.param" |
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|
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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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INTEGER(4) :: At1,At2,At3,At4,IOOUT,Iat |
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INTEGER(4) :: IArg, I, NNN, Ng, J |
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|
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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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|
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REAL(8) :: MRot(3,3), Rmsd |
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LOGICAL FExist,FRot,FAlign,Debug |
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|
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INTEGER(4) :: ConvertNumAt |
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external ConvertNumAt |
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|
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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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|
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|
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|
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REAL(8) :: MassAt(0:86)=(/0.0D0,1.0078D0, 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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132.905D0,137.34D0, & |
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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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138.91D0, & |
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140.12D0, 130.91D0, 144.24D0,147.D0,150.35D0, 151.96D0,157.25D0, & |
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158.924D0, 162.50D0, 164.93D0, 167.26D0,168.93D0,173.04D0,174.97D0, & |
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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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178.49D0, 180.95D0, 183.85D0, 186.2D0, 190.2D0, 192.2D0, 195.09D0, & |
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196.97D0, 200.59D0, & |
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204.37D0, 207.19D0,208.98D0,210.D0,210.D0,222.D0 /) |
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|
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|
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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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|
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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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|
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open(13,file='Scan.dat') |
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|
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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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|
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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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|
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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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|
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Nat=nnn |
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|
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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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|
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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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|
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END DO |
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END IF |
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|
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|
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|
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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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|
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ng=1 |
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|
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s=0. |
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|
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open(11,file=f1) |
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|
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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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|
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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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|
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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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|
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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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!-------------------------------------------------------------- |
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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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|
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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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|
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|
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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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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
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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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|
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SUBROUTINE READLINE(IOIN,Type,Line) |
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|
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IMPLICIT NONE |
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CHARACTER(5) :: Type |
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CHARACTER(120) :: LINE |
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INTEGER(4) :: 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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|
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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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|
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RETURN |
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999 Type="E" |
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END |
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|
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|
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|
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SUBROUTINE Analyse(geos) |
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|
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IMPLICIT NONE |
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INCLUDE "Xyz2Path.param" |
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|
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REAL(8) :: geos(3,maxnat) |
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REAL(8) :: AU2PS,Pi |
| 329 |
INTEGER(4) :: i,j,k |
| 330 |
REAL(8) :: V1x,V1y,V1z,V2x,V2y,V2z,V3x,V3y,V3z |
| 331 |
REAL(8) :: d1,d2,ca,sa |
| 332 |
REAL(8) :: V4x,v4y,v4z,v5x,v5y,v5z |
| 333 |
REAL(8) :: COG(3) |
| 334 |
LOGICAL :: Debug=.FALSE. |
| 335 |
INTEGER(4) :: Nat,NbDist, NbAngle, NbDie,NbCOM |
| 336 |
INTEGER(4) :: At1B(MaxNat),At2B(MaxNat) |
| 337 |
INTEGER(4) :: At1A(MaxNat),At2A(MaxNat),At3A(MaxNat) |
| 338 |
INTEGER(4) :: At1D(MaxNat),At2D(MaxNat),At3D(MaxNat),At4D(MaxNat) |
| 339 |
INTEGER(4) :: AtCom(0:MaxNat,MaxNat) |
| 340 |
REAL(8) :: VB(MaxNat),VA(MaxNat),VD(MaxNat),VCOM(MaxNat) |
| 341 |
|
| 342 |
COMMON /Indices/Nat,NbDist,NbAngle,NbDie,NbCom, & |
| 343 |
At1B,At2B,At1A,At2A,At3A,At1D,At2D,At3D,At4D,AtCom |
| 344 |
COMMON /Values/VB,VA,VD,VCom |
| 345 |
COMMON /Const/AU2ps,Pi |
| 346 |
|
| 347 |
if (debug) THEN |
| 348 |
DO I=1,Nat |
| 349 |
WRITE(*,'(1X,I3,3(1X,F15.6))') i,(geos(j,i),j=1,3) |
| 350 |
END DO |
| 351 |
END IF |
| 352 |
|
| 353 |
! First, we create the Centre of Mass atoms |
| 354 |
DO i=1,NbCOM |
| 355 |
COG(1)=0. |
| 356 |
COG(2)=0. |
| 357 |
COG(3)=0. |
| 358 |
DO j=1,AtCOm(0,i) |
| 359 |
DO k=1,3 |
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COG(k)=COG(k)+geos(k,AtCom(j,i)) |
| 361 |
END DO |
| 362 |
END DO |
| 363 |
DO k=1,3 |
| 364 |
COG(k)=COG(k)/AtCOM(0,i) |
| 365 |
geos(k,Nat+i)=COG(k) |
| 366 |
END DO |
| 367 |
END DO |
| 368 |
|
| 369 |
|
| 370 |
DO i=1,NbDist |
| 371 |
VB(i)=sqrt((geos(1,At1B(i))-geos(1,At2B(i)))**2+ & |
| 372 |
(geos(2,At1B(i))-geos(2,At2B(i)))**2+ & |
| 373 |
(geos(3,At1B(i))-geos(3,At2B(i)))**2) |
| 374 |
END DO |
| 375 |
DO i=1,NbAngle |
| 376 |
v1x=geos(1,At1A(i))-geos(1,At2A(i)) |
| 377 |
v1y=geos(2,At1A(i))-geos(2,At2A(i)) |
| 378 |
v1z=geos(3,At1A(i))-geos(3,At2A(i)) |
| 379 |
d1=sqrt(v1x**2+v1y**2+v1z**2) |
| 380 |
v2x=geos(1,At3A(i))-geos(1,At2A(i)) |
| 381 |
v2y=geos(2,At3A(i))-geos(2,At2A(i)) |
| 382 |
v2z=geos(3,At3A(i))-geos(3,At2A(i)) |
| 383 |
d2=sqrt(v2x**2+v2y**2+v2z**2) |
| 384 |
VA(i)=acos((v1x*v2x+v1y*v2y+v1z*v2z)/(d1*d2))*180./Pi |
| 385 |
END DO |
| 386 |
DO i=1,NbDie |
| 387 |
! WRITE(*,*) At1D(i),At2D(i),At3D(i),At4D(i) |
| 388 |
! WRITE(*,*) geos(1,At1D(i)),geos(2,At1D(i)),geos(3,At1D(i)) |
| 389 |
! WRITE(*,*) geos(1,At2D(i)),geos(2,At2D(i)),geos(3,At2D(i)) |
| 390 |
v1x=geos(1,At1D(i))-geos(1,At2D(i)) |
| 391 |
v1y=geos(2,At1D(i))-geos(2,At2D(i)) |
| 392 |
v1z=geos(3,At1D(i))-geos(3,At2D(i)) |
| 393 |
v2x=geos(1,At3D(i))-geos(1,At2D(i)) |
| 394 |
v2y=geos(2,At3D(i))-geos(2,At2D(i)) |
| 395 |
v2z=geos(3,At3D(i))-geos(3,At2D(i)) |
| 396 |
v3x=geos(1,At4D(i))-geos(1,At3D(i)) |
| 397 |
v3y=geos(2,At4D(i))-geos(2,At3D(i)) |
| 398 |
v3z=geos(3,At4D(i))-geos(3,At3D(i)) |
| 399 |
|
| 400 |
v4x=v1y*v2z-v1z*v2y |
| 401 |
v4y=v1z*v2x-v1x*v2z |
| 402 |
v4z=v1x*v2y-v1y*v2x |
| 403 |
d1=sqrt(v4x**2+v4y**2+v4z**2) |
| 404 |
v5x=-v2y*v3z+v2z*v3y |
| 405 |
v5y=-v2z*v3x+v2x*v3z |
| 406 |
v5z=-v2x*v3y+v2y*v3x |
| 407 |
d2=sqrt(v5x**2+v5y**2+v5z**2) |
| 408 |
ca=(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2) |
| 409 |
sa=v1x*v5x+v1y*v5y+v1z*v5z |
| 410 |
VD(i)=acos(ca)*180./Pi |
| 411 |
if (sa<0.) VD(i)=-VD(i) |
| 412 |
! WRITE(*,*) "Dihe",v5x,v5y,v5z,v4x,v4y,v4z,d1,d2, |
| 413 |
! &(v4x*v5x+v4y*v5y+v4z*v5z)/(d1*d2),pi |
| 414 |
!!!!!!!!! Another solution, more elegant ? |
| 415 |
! norm2=sqrt(v2x**2+v2y**2+v2z**2) |
| 416 |
! sa=(v4x*(v5y*v2z-v5z*v2y) |
| 417 |
! * -v4y*(v5x*v2z-v5z*v2x) |
| 418 |
! * +v4z*(v5x*v2y-v5y*v2x)) |
| 419 |
! * /(d1*norm2*d2) |
| 420 |
! angle_d=datan2(sa,ca)*180./Pi |
| 421 |
! WRITE(*,*) sa,ca,angle_d,d1,d2,norm2 |
| 422 |
! WRITE(*,*) VD(i),angle_d |
| 423 |
END DO |
| 424 |
|
| 425 |
END SUBROUTINE Analyse |
| 426 |
|
| 427 |
!C================================================================ |
| 428 |
!C Convertit un nom d'atome (2 lettres) en nombre de masse (entier) |
| 429 |
!C cette fonction a ete modifiee pour pouvoir convertir un nom |
| 430 |
!C d'atome avec un numero a la fin... |
| 431 |
!C================================================================ |
| 432 |
|
| 433 |
FUNCTION ConvertNumAt(ATOM) |
| 434 |
|
| 435 |
|
| 436 |
IMPLICIT NONE |
| 437 |
|
| 438 |
INTEGER(4) :: I,Long,ConvertNumAt,IC |
| 439 |
character(2) :: ATOM,L_Atom |
| 440 |
character(3) :: ATOME |
| 441 |
INTEGER(4), PARAMETER :: Max_Z=86 |
| 442 |
|
| 443 |
|
| 444 |
CHARACTER(2) :: Nom(0:max_Z)=(/ ' X',' H', 'HE', & |
| 445 |
'LI','BE', ' B',' C',' N',' O',' F','NE', & |
| 446 |
'NA','MG', 'AL','SI',' P',' S','CL','AR', & |
| 447 |
' K','CA', & |
| 448 |
'SC','TI',' V','CR','MN','FE','CO','NI','CU','ZN', & |
| 449 |
'GA','GE','AS','SE','BR','KR', & |
| 450 |
'RB','SR', & |
| 451 |
' Y','ZR','NB','MO','TC','RU','RH','PD','AG','CD', & |
| 452 |
'IN','SN','SB','TE',' I','XE', & |
| 453 |
'CS','BA', & |
| 454 |
'LA', & |
| 455 |
'CE','PR','ND','PM','SM','EU','GD','TB','DY','HO', & |
| 456 |
'ER','TM','YB','LU', & |
| 457 |
'HF','TA',' W','RE','OS','IR','PT','AU','HG', & |
| 458 |
'TL','PB','BI','PO','AT','RN'/) |
| 459 |
|
| 460 |
|
| 461 |
!C Verifie qu'il n'y a que des lettres et des espaces dans ATOM |
| 462 |
! WRITE(*,*) 'DBG CNVNUMAT, ATOM:',ATOM |
| 463 |
|
| 464 |
L_atom=Atom |
| 465 |
IF (ATOM(1:1).LT.'A') L_ATOM(1:1)=' ' |
| 466 |
IC=Ichar(ATOM(1:1)) |
| 467 |
IF ((ic.le.123).AND.(ic.ge.97)) L_ATOM(1:1)=CHAr(IC-32) |
| 468 |
IF (ATOM(2:2).LT.'A') L_ATOM(2:2)=' ' |
| 469 |
IC=Ichar(ATOM(2:2)) |
| 470 |
IF ((ic.le.123).AND.(ic.ge.97)) L_ATOM(2:2)=CHAr(IC-32) |
| 471 |
!C Justifie le nom sur la droite (et non sur la gauche comme souvent...) |
| 472 |
Long=INDEX(L_ATOM,' ')-1 |
| 473 |
ATOME=' ' // L_ATOM |
| 474 |
IF (Long.EQ.1) L_ATOM=ATOME(1:2) |
| 475 |
! WRITE(*,*) 'DBG CNVNUMAT, L_ATOM:',L_ATOM |
| 476 |
I=max_Z |
| 477 |
DO WHILE ((nom(I).NE.L_ATOM) .AND. (I.GT.0)) |
| 478 |
I=I-1 |
| 479 |
END DO |
| 480 |
ConvertNumAT=I |
| 481 |
END |
| 482 |
! This subroutine calculates RMSD using quaternions. |
| 483 |
! It is based on the F90 routine bu E. Coutsias |
| 484 |
! http://www.math.unm.edu/~vageli/homepage.html |
| 485 |
! I (PFL) have just translated it, and I have changed the diagonalization |
| 486 |
! subroutine. |
| 487 |
! I also made some changes to make it suitable for Cart package. |
| 488 |
!---------------------------------------------------------------------- |
| 489 |
!---------------------------------------------------------------------- |
| 490 |
! Copyright (C) 2004, 2005 Chaok Seok, Evangelos Coutsias and Ken Dill |
| 491 |
! UCSF, Univeristy of New Mexico, Seoul National University |
| 492 |
! Witten by Chaok Seok and Evangelos Coutsias 2004. |
| 493 |
|
| 494 |
! This library is free software; you can redistribute it and/or |
| 495 |
! modify it under the terms of the GNU Lesser General Public |
| 496 |
! License as published by the Free Software Foundation; either |
| 497 |
! version 2.1 of the License, or (at your option) any later version. |
| 498 |
! |
| 499 |
|
| 500 |
! This library is distributed in the hope that it will be useful, |
| 501 |
! but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 502 |
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| 503 |
! Lesser General Public License for more details. |
| 504 |
! |
| 505 |
|
| 506 |
! You should have received a copy of the GNU Lesser General Public |
| 507 |
! License along with this library; if not, write to the Free Software |
| 508 |
! Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
| 509 |
!---------------------------------------------------------------------------- |
| 510 |
|
| 511 |
subroutine CalcRmsd(na, geom,geom2,U,rmsd,FRot,FAlign,debug) |
| 512 |
!----------------------------------------------------------------------- |
| 513 |
! This subroutine calculates the least square rmsd of two coordinate |
| 514 |
! sets coord1(3,n) and coord2(3,n) using a method based on quaternion. |
| 515 |
! It then calculate the rotation matrix U and the centers of coord, and uses |
| 516 |
! them to align the two molecules. |
| 517 |
!----------------------------------------------------------------------- |
| 518 |
|
| 519 |
|
| 520 |
IMPLICIT NONE |
| 521 |
|
| 522 |
INCLUDE "Xyz2Path.param" |
| 523 |
|
| 524 |
INTEGER(4) :: IOIN, IOOUT, IOSCRN, IOPRNT, IOTAMP |
| 525 |
COMMON/IODEFS/IOIN,IOOUT,IOSCRN,IOPRNT,IOTAMP |
| 526 |
|
| 527 |
INTEGER(4) :: na |
| 528 |
REAL(8) :: geom(3,MaxNAt), Geom2(3,MaxNAt) |
| 529 |
REAL(8) :: U(3,3), rmsd |
| 530 |
LOGICAL FRot,FAlign,Debug |
| 531 |
|
| 532 |
REAL(8) :: Coord1(3,MaxNAt), Coord2(3,MaxNAt) |
| 533 |
REAL(8) :: xc1,yc1,zc1, xc2,yc2,zc2 |
| 534 |
|
| 535 |
|
| 536 |
INTEGER(4) :: i, j, ia |
| 537 |
REAL(8) :: x_norm, y_norm, lambda |
| 538 |
REAL(8) :: Rmatrix(3,3) |
| 539 |
REAL(8) :: S(4,4) |
| 540 |
REAL(8) :: EigVec(4,4), EigVal(4) |
| 541 |
|
| 542 |
|
| 543 |
|
| 544 |
! calculate the barycenters, centroidal coordinates, and the norms |
| 545 |
x_norm = 0.0d0 |
| 546 |
y_norm = 0.0d0 |
| 547 |
xc1=0. |
| 548 |
yc1=0. |
| 549 |
zc1=0. |
| 550 |
xc2=0. |
| 551 |
yc2=0. |
| 552 |
zc2=0. |
| 553 |
do ia=1,na |
| 554 |
xc1=xc1+geom(1,ia) |
| 555 |
xc2=xc2+geom2(1,ia) |
| 556 |
yc1=yc1+geom(2,ia) |
| 557 |
yc2=yc2+geom2(2,ia) |
| 558 |
zc1=zc1+geom(3,ia) |
| 559 |
zc2=zc2+geom2(3,ia) |
| 560 |
! if (debug) WRITE(*,'(A,I5,4(1X,F10.4))') 'ia...',ia,x(ia), |
| 561 |
! & x2(ia),xc1,xc2 |
| 562 |
END DO |
| 563 |
xc1=xc1/dble(na) |
| 564 |
yc1=yc1/dble(na) |
| 565 |
zc1=zc1/dble(na) |
| 566 |
xc2=xc2/dble(na) |
| 567 |
yc2=yc2/dble(na) |
| 568 |
zc2=zc2/dble(na) |
| 569 |
|
| 570 |
IF (debug) WRITE(*,'(1X,A,3(1X,F10.4))') 'Center1',xc1,yc1,zc1 |
| 571 |
IF (debug) WRITE(*,'(1X,A,3(1X,F10.4))') 'Center2',xc2,yc2,zc2 |
| 572 |
do i=1,na |
| 573 |
Coord1(1,i)=geom(1,i)-xc1 |
| 574 |
Coord1(2,i)=geom(2,i)-yc1 |
| 575 |
Coord1(3,i)=geom(3,i)-zc1 |
| 576 |
Coord2(1,i)=geom2(1,i)-xc2 |
| 577 |
Coord2(2,i)=geom2(2,i)-yc2 |
| 578 |
Coord2(3,i)=geom2(3,i)-zc2 |
| 579 |
x_norm=x_norm+Coord1(1,i)**2+Coord1(2,i)**2+Coord1(3,i)**2 |
| 580 |
y_norm=y_norm+Coord2(1,i)**2+Coord2(2,i)**2+Coord2(3,i)**2 |
| 581 |
end do |
| 582 |
|
| 583 |
IF (debug) THEN |
| 584 |
WRITE(*,*) "R matrix" |
| 585 |
DO I=1,3 |
| 586 |
WRITE(*,*) (RMatrix(I,j),j=1,3) |
| 587 |
END DO |
| 588 |
END IF |
| 589 |
|
| 590 |
! calculate the R matrix |
| 591 |
do i = 1, 3 |
| 592 |
do j = 1, 3 |
| 593 |
Rmatrix(i,j)=0. |
| 594 |
do ia=1,na |
| 595 |
Rmatrix(i,j) = Rmatrix(i,j)+Coord1(i,ia)*Coord2(j,ia) |
| 596 |
END DO |
| 597 |
end do |
| 598 |
end do |
| 599 |
|
| 600 |
IF (debug) THEN |
| 601 |
WRITE(*,*) "R matrix" |
| 602 |
DO I=1,3 |
| 603 |
WRITE(*,*) (RMatrix(I,j),j=1,3) |
| 604 |
END DO |
| 605 |
END IF |
| 606 |
|
| 607 |
|
| 608 |
! S matrix |
| 609 |
S(1, 1) = Rmatrix(1, 1) + Rmatrix(2, 2) + Rmatrix(3, 3) |
| 610 |
S(2, 1) = Rmatrix(2, 3) - Rmatrix(3, 2) |
| 611 |
S(3, 1) = Rmatrix(3, 1) - Rmatrix(1, 3) |
| 612 |
S(4, 1) = Rmatrix(1, 2) - Rmatrix(2, 1) |
| 613 |
|
| 614 |
S(1, 2) = S(2, 1) |
| 615 |
S(2, 2) = Rmatrix(1, 1) - Rmatrix(2, 2) - Rmatrix(3, 3) |
| 616 |
S(3, 2) = Rmatrix(1, 2) + Rmatrix(2, 1) |
| 617 |
S(4, 2) = Rmatrix(1, 3) + Rmatrix(3, 1) |
| 618 |
|
| 619 |
S(1, 3) = S(3, 1) |
| 620 |
S(2, 3) = S(3, 2) |
| 621 |
S(3, 3) =-Rmatrix(1, 1) + Rmatrix(2, 2) - Rmatrix(3, 3) |
| 622 |
S(4, 3) = Rmatrix(2, 3) + Rmatrix(3, 2) |
| 623 |
|
| 624 |
S(1, 4) = S(4, 1) |
| 625 |
S(2, 4) = S(4, 2) |
| 626 |
S(3, 4) = S(4, 3) |
| 627 |
S(4, 4) =-Rmatrix(1, 1) - Rmatrix(2, 2) + Rmatrix(3, 3) |
| 628 |
|
| 629 |
|
| 630 |
! PFL : I use my usual Jacobi diagonalisation |
| 631 |
! Calculate eigenvalues and eigenvectors, and |
| 632 |
! take the maximum eigenvalue lambda and the corresponding eigenvector q. |
| 633 |
|
| 634 |
IF (debug) THEN |
| 635 |
WRITE(*,*) "S matrix" |
| 636 |
DO I=1,4 |
| 637 |
WRITE(*,*) (S(I,j),j=1,4) |
| 638 |
END DO |
| 639 |
END IF |
| 640 |
|
| 641 |
Call Jacobi(S,4,EigVal,EigVec,4) |
| 642 |
|
| 643 |
Call Trie(4,EigVal,EigVec,4) |
| 644 |
|
| 645 |
Lambda=EigVal(4) |
| 646 |
|
| 647 |
! RMS Deviation |
| 648 |
rmsd=sqrt(max(0.0d0,((x_norm+y_norm)-2.0d0*lambda))/dble(na)) |
| 649 |
|
| 650 |
if (FRot.OR.FAlign) Call rotation_matrix(EigVec(1,4),U) |
| 651 |
IF (FAlign) THEN |
| 652 |
DO I=1,na |
| 653 |
geom2(1,i)=Coord2(1,i)*U(1,1)+Coord2(2,i)*U(2,1)+Coord2(3,i)*U(3,1) +xc1 |
| 654 |
geom2(2,i)=Coord2(1,i)*U(1,2)+Coord2(2,i)*U(2,2)+Coord2(3,i)*U(3,2) +yc1 |
| 655 |
geom2(3,i)=Coord2(1,i)*U(1,3)+Coord2(2,i)*U(2,3)+Coord2(3,i)*U(3,3) +zc1 |
| 656 |
END DO |
| 657 |
END IF |
| 658 |
|
| 659 |
END |
| 660 |
|
| 661 |
|
| 662 |
!----------------------------------------------------------------------- |
| 663 |
subroutine rotation_matrix(q, U) |
| 664 |
!----------------------------------------------------------------------- |
| 665 |
! This subroutine constructs rotation matrix U from quaternion q. |
| 666 |
!----------------------------------------------------------------------- |
| 667 |
! This subroutine calculates RMSD using quaternions. |
| 668 |
! It is based on the F90 routine bu E. Coutsias |
| 669 |
! http://www.math.unm.edu/~vageli/homepage.html |
| 670 |
! I (PFL) have just translated it, and I have changed the diagonalization |
| 671 |
! subroutine. |
| 672 |
! I also made some changes to make it suitable for Cart package. |
| 673 |
!---------------------------------------------------------------------- |
| 674 |
!---------------------------------------------------------------------- |
| 675 |
! Copyright (C) 2004, 2005 Chaok Seok, Evangelos Coutsias and Ken Dill |
| 676 |
! UCSF, Univeristy of New Mexico, Seoul National University |
| 677 |
! Witten by Chaok Seok and Evangelos Coutsias 2004. |
| 678 |
|
| 679 |
! This library is free software; you can redistribute it and/or |
| 680 |
! modify it under the terms of the GNU Lesser General Public |
| 681 |
! License as published by the Free Software Foundation; either |
| 682 |
! version 2.1 of the License, or (at your option) any later version. |
| 683 |
! |
| 684 |
|
| 685 |
! This library is distributed in the hope that it will be useful, |
| 686 |
! but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 687 |
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| 688 |
! Lesser General Public License for more details. |
| 689 |
! |
| 690 |
|
| 691 |
! You should have received a copy of the GNU Lesser General Public |
| 692 |
! License along with this library; if not, write to the Free Software |
| 693 |
! Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
| 694 |
!---------------------------------------------------------------------------- |
| 695 |
|
| 696 |
REAL(8) :: q(4) |
| 697 |
REAL(8) :: U(3,3) |
| 698 |
REAL(8) :: q0,q1,q2,q3,b0,b1,b2,b3,q00,q01,q02,q03 |
| 699 |
REAL(8) :: q11,q12,q13,q22,q23,q33 |
| 700 |
|
| 701 |
q0 = q(1) |
| 702 |
q1 = q(2) |
| 703 |
q2 = q(3) |
| 704 |
q3 = q(4) |
| 705 |
|
| 706 |
b0 = 2.0d0*q0 |
| 707 |
b1 = 2.0d0*q1 |
| 708 |
b2 = 2.0d0*q2 |
| 709 |
b3 = 2.0d0*q3 |
| 710 |
|
| 711 |
q00 = b0*q0-1.0d0 |
| 712 |
q01 = b0*q1 |
| 713 |
q02 = b0*q2 |
| 714 |
q03 = b0*q3 |
| 715 |
|
| 716 |
q11 = b1*q1 |
| 717 |
q12 = b1*q2 |
| 718 |
q13 = b1*q3 |
| 719 |
|
| 720 |
q22 = b2*q2 |
| 721 |
q23 = b2*q3 |
| 722 |
|
| 723 |
q33 = b3*q3 |
| 724 |
|
| 725 |
U(1,1) = q00+q11 |
| 726 |
U(1,2) = q12-q03 |
| 727 |
U(1,3) = q13+q02 |
| 728 |
|
| 729 |
U(2,1) = q12+q03 |
| 730 |
U(2,2) = q00+q22 |
| 731 |
U(2,3) = q23-q01 |
| 732 |
|
| 733 |
U(3,1) = q13-q02 |
| 734 |
U(3,2) = q23+q01 |
| 735 |
U(3,3) = q00+q33 |
| 736 |
|
| 737 |
end |
| 738 |
|
| 739 |
!c============================================================ |
| 740 |
!c |
| 741 |
!c ++ diagonalisation par jacobi |
| 742 |
!c vecteur propre i : V(i,i) |
| 743 |
!c valeur propre i : D(i) |
| 744 |
!c |
| 745 |
!c============================================================ |
| 746 |
!c |
| 747 |
SUBROUTINE JACOBI(A,N,D,V,max_N) |
| 748 |
IMPLICIT REAL(8) (A-H,O-Z) |
| 749 |
parameter (max_it=500) |
| 750 |
DIMENSION A(max_N,max_N),B(max_N),Z(max_N) |
| 751 |
DIMENSION V(max_N,max_N),D(max_N) |
| 752 |
|
| 753 |
|
| 754 |
DO 12 IP=1,N |
| 755 |
DO 11 IQ=1,N |
| 756 |
V(IP,IQ)=0. |
| 757 |
11 CONTINUE |
| 758 |
V(IP,IP)=1. |
| 759 |
12 CONTINUE |
| 760 |
DO 13 IP=1,N |
| 761 |
B(IP)=A(IP,IP) |
| 762 |
D(IP)=B(IP) |
| 763 |
Z(IP)=0. |
| 764 |
13 CONTINUE |
| 765 |
NROT=0 |
| 766 |
DO 24 I=1,max_it |
| 767 |
SM=0. |
| 768 |
DO 15 IP=1,N-1 |
| 769 |
DO 14 IQ=IP+1,N |
| 770 |
SM=SM+ABS(A(IP,IQ)) |
| 771 |
14 CONTINUE |
| 772 |
15 CONTINUE |
| 773 |
IF(SM.EQ.0.)RETURN |
| 774 |
IF(I.LT.4)THEN |
| 775 |
TRESH=0.2*SM/N**2 |
| 776 |
ELSE |
| 777 |
TRESH=0. |
| 778 |
ENDIF |
| 779 |
DO 22 IP=1,N-1 |
| 780 |
DO 21 IQ=IP+1,N |
| 781 |
G=100.*ABS(A(IP,IQ)) |
| 782 |
IF((I.GT.4).AND.(ABS(D(IP))+G.EQ.ABS(D(IP))) & |
| 783 |
.AND.(ABS(D(IQ))+G.EQ.ABS(D(IQ))))THEN |
| 784 |
A(IP,IQ)=0. |
| 785 |
ELSE IF(ABS(A(IP,IQ)).GT.TRESH)THEN |
| 786 |
H=D(IQ)-D(IP) |
| 787 |
IF(ABS(H)+G.EQ.ABS(H))THEN |
| 788 |
T=A(IP,IQ)/H |
| 789 |
ELSE |
| 790 |
THETA=0.5*H/A(IP,IQ) |
| 791 |
T=1./(ABS(THETA)+SQRT(1.+THETA**2)) |
| 792 |
IF(THETA.LT.0.)T=-T |
| 793 |
ENDIF |
| 794 |
C=1./SQRT(1+T**2) |
| 795 |
S=T*C |
| 796 |
TAU=S/(1.+C) |
| 797 |
H=T*A(IP,IQ) |
| 798 |
Z(IP)=Z(IP)-H |
| 799 |
Z(IQ)=Z(IQ)+H |
| 800 |
D(IP)=D(IP)-H |
| 801 |
D(IQ)=D(IQ)+H |
| 802 |
A(IP,IQ)=0. |
| 803 |
DO 16 J=1,IP-1 |
| 804 |
G=A(J,IP) |
| 805 |
H=A(J,IQ) |
| 806 |
A(J,IP)=G-S*(H+G*TAU) |
| 807 |
A(J,IQ)=H+S*(G-H*TAU) |
| 808 |
16 CONTINUE |
| 809 |
DO 17 J=IP+1,IQ-1 |
| 810 |
G=A(IP,J) |
| 811 |
H=A(J,IQ) |
| 812 |
A(IP,J)=G-S*(H+G*TAU) |
| 813 |
A(J,IQ)=H+S*(G-H*TAU) |
| 814 |
17 CONTINUE |
| 815 |
DO 18 J=IQ+1,N |
| 816 |
G=A(IP,J) |
| 817 |
H=A(IQ,J) |
| 818 |
A(IP,J)=G-S*(H+G*TAU) |
| 819 |
A(IQ,J)=H+S*(G-H*TAU) |
| 820 |
18 CONTINUE |
| 821 |
DO 19 J=1,N |
| 822 |
G=V(J,IP) |
| 823 |
H=V(J,IQ) |
| 824 |
V(J,IP)=G-S*(H+G*TAU) |
| 825 |
V(J,IQ)=H+S*(G-H*TAU) |
| 826 |
19 CONTINUE |
| 827 |
NROT=NROT+1 |
| 828 |
ENDIF |
| 829 |
21 CONTINUE |
| 830 |
22 CONTINUE |
| 831 |
DO 23 IP=1,N |
| 832 |
B(IP)=B(IP)+Z(IP) |
| 833 |
D(IP)=B(IP) |
| 834 |
Z(IP)=0. |
| 835 |
23 CONTINUE |
| 836 |
24 CONTINUE |
| 837 |
write(6,*) max_it,' iterations should never happen' |
| 838 |
STOP |
| 839 |
RETURN |
| 840 |
END |
| 841 |
! |
| 842 |
!============================================================ |
| 843 |
!c |
| 844 |
!c ++ trie des vecteur dans l'ordre croissant |
| 845 |
!c |
| 846 |
!c============================================================ |
| 847 |
!c |
| 848 |
SUBROUTINE trie(nb_niv,ene,psi,max_niv) |
| 849 |
integer(4) :: i,j,k,nb_niv,max_niv |
| 850 |
REAL(8) :: ene(max_niv),psi(max_niv,max_niv) |
| 851 |
REAL(8) :: a |
| 852 |
|
| 853 |
DO i=1,nb_niv |
| 854 |
DO j=i+1,nb_niv |
| 855 |
IF (ene(i) .GT. ene(j)) THEN |
| 856 |
!c permutation |
| 857 |
a=ene(i) |
| 858 |
ene(i)=ene(j) |
| 859 |
ene(j)=a |
| 860 |
DO k=1,nb_niv |
| 861 |
a=psi(k,i) |
| 862 |
psi(k,i)=psi(k,j) |
| 863 |
psi(k,j)=a |
| 864 |
END DO |
| 865 |
END IF |
| 866 |
END DO |
| 867 |
END DO |
| 868 |
|
| 869 |
END SUBROUTINE trie |
| 870 |
|