mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1741 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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@ -40,6 +40,7 @@ You need to create a user input file. In the examples folder you will find
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an example input script, LAMMPS dump file, and the correct .cfg output.
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The input script reads like this:
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2898 #total number of atoms in system (may be more than in dump)
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7 #number of atom types in your LAMMPS file
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'dump.atom' #name of the LAMMPS dump file, you need the ' '
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1 #first frame
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@ -1,7 +1,7 @@
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Number of particles = 2898
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#
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A = 1.5 Angstrom
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A = 1.0 Angstrom
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#
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H0(1,1) = 26.05200 A
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@ -1,7 +1,7 @@
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Number of particles = 2898
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#
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A = 1.5 Angstrom
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A = 1.0 Angstrom
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#
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H0(1,1) = 26.05200 A
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@ -1,3 +1,4 @@
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2898
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7
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'dump.atom'
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1
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@ -1,184 +1,164 @@
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*23456789|123456789|123456789|123456789|123456789|123456789|123456789|12
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c----------------------------------------------------------------------
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program lammps to cfg
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c----------------------------------------------------------------------
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*Programming by Jeff Greathouse and Ara Kooser
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*Version 1.0 9/1/04
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*Sandia National Labs
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*Converts LAMMPS atom dump to .cfg files for AtomEye
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*This program is provided as is. Please see the README file.
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c----------------------------------------------------------------------
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implicit real*8 (a-h,o-z)
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character*12 inhist,snapshot
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character*4 fftype(100),name,ciframe
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integer natom,iatom,itype(50000),q
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integer atype(99),itycon,ntype,mass(99)
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dimension x(50000),y(50000),z(50000)
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dimension amass(99)
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c-------Reads in the user input file-------------------------------
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read(*,*) ntype
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read(*,*) inhist
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read(*,*) iframe1
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read(*,*) iframe2
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c write(*,*) ntype
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c write(*,*) inhist
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do 1, i=1, ntype
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read(*,*) atype(i)
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read(*,*) amass(i)
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mass(i)=anint(amass(i))
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read(*,*) fftype(i)
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c write(*,*) atype(i)
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c write(*,*) amass(i)
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c write(*,*) fftype(i)
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1 continue
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c-------Lammps output file is 9, reads in lmps header--------------
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name=inhist(1:4)
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open(9,file=inhist,status='old',form='formatted')
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c open(2,status='new',form='formatted')
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iatom=0
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iframe=0
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jframe=0
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c---------------------------------------------------------------------
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c----------This begins the frame by frame reading section-------------
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9999 continue
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read(9,*,end=999)
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read(9,*,end=999)
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read(9,*,end=999)
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read(9,*,end=999) natom
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read(9,*,end=999)
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read(9,*,end=999) xlower,xupper
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read(9,*,end=999) ylower,yupper
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read(9,*,end=999) zlower,zupper
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read(9,*,end=999)
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50 format(2f12.5)
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xcell=xupper-xlower
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ycell=yupper-ylower
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zcell=zupper-zlower
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1000 format(1x,i5,1x,i2,3f9.5)
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do 440 j=1,natom
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420 read(9,*,end=999)iatom,itype(iatom),x(iatom),y(iatom),z(iatom)
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*23456789|123456789|123456789|123456789|123456789|123456789|123456789|12
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440 continue
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jframe=jframe+1
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if(jframe.lt.iframe1)goto 9999
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iframe=iframe+1
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if(iframe.ge.iframe2) goto 999
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c--------------------------------------------------------------------
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c-------This section writes each ts to a seperate .cfg file----------
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c ciframe=char(iframe)
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c snapshot(iframe)=name//ciframe//'.cfg'
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c write(*,*)ciframe
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c write(snapshot,'("Cfgs/",i7.7,".cfg")') iframe
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ciframe='.cfg'
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c write(*,*)ciframe
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write(snapshot,'(i5.5,a4)')iframe,ciframe
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c write(*,*)snapshot
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open(unit=iframe+20,file=snapshot,status='new',
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* form='formatted')
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write((iframe+20),'(a22,i7)')'Number of particles = ',natom
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a16)')'A = 1.0 Angstrom'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),435)'H0(1,1) = ',xcell,' A'
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write((iframe+20),'(a14)')'H0(1,2) = 0 A'
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write((iframe+20),'(a14)')'H0(1,3) = 0 A'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a14)')'H0(2,1) = 0 A'
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write((iframe+20),435)'H0(2,2) = ',ycell,' A'
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write((iframe+20),'(a14)')'H0(2,3) = 0 A'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a14)')'H0(3,1) = 0 A'
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write((iframe+20),'(a14)')'H0(3,2) = 0 A'
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write((iframe+20),435)'H0(3,3) = ',zcell,' A'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a12)')'eta(1,1) = 0'
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write((iframe+20),'(a12)')'eta(1,2) = 0'
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write((iframe+20),'(a12)')'eta(1,3) = 0'
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write((iframe+20),'(a12)')'eta(2,2) = 0'
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write((iframe+20),'(a12)')'eta(2,3) = 0'
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write((iframe+20),'(a12)')'eta(3,3) = 0'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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435 format(a11,f10.5,a2)
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do 460, j=1,natom
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do 450,i=1,ntype
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c write(*,*)i,amass(i),fftype(i)
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c write(*,*)ntype
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if(itype(j).eq.atype(i))
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* write((iframe+20),445)mass(i),fftype(i),x(j),
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* y(j),z(j),' 0',' 0',' 0'
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c---445 is the format for writing atom data to .cfg file------------
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445 format(i3.3,1x,a2,1x,3f9.6,3a2)
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450 continue
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460 continue
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go to 9999
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999 continue
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close(9)
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end
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*23456789|123456789|123456789|123456789|123456789|123456789|123456789|12
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c----------------------------------------------------------------------
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program lammps to cfg
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c----------------------------------------------------------------------
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*Programming by Jeff Greathouse and Ara Kooser
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*Version 1.0 9/1/04
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*Version 1.1 4/10/08 by Axel Kohlmeyer
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*Sandia National Labs
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*Converts LAMMPS atom dump to .cfg files for AtomEye
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*This program is provided as is. Please see the README file.
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c----------------------------------------------------------------------
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implicit none
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character*12 inhist,snapshot
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character*4 fftype(100),name,ciframe
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integer maxatom,maxtype
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parameter(maxatom=50000,maxtype=99)
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integer i,j,iframe,iframe1,iframe2,jframe
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integer natom,iatom,allatom,itype(maxatom)
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integer atype(maxtype),ntype,mass(maxtype)
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real*8 x(maxatom),y(maxatom),z(maxatom),amass(maxtype)
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real*8 xcell,ycell,zcell,upper,lower
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c-------Reads in the user input file-------------------------------
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read(*,*) allatom
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if(allatom.gt.maxatom) then
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write(*,*) 'number of total atoms larger than:',maxatom
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write(*,*) 'change maxatom and recompile'
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STOP
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endif
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read(*,*) ntype
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if(ntype.gt.maxtype) then
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write(*,*) 'number of total types larger than:',maxtype
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write(*,*) 'change maxtype and recompile'
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STOP
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endif
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read(*,*) inhist
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read(*,*) iframe1
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read(*,*) iframe2
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do 1, i=1, ntype
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read(*,*) atype(i)
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read(*,*) amass(i)
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mass(i)=anint(amass(i))
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read(*,*) fftype(i)
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1 continue
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c-------Lammps output file is 9, reads in lmps header--------------
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name=inhist(1:4)
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open(9,file=inhist,status='old',form='formatted')
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iatom=0
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iframe=0
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jframe=0
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c---------------------------------------------------------------------
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c----------This begins the frame by frame reading section-------------
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9999 continue
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read(9,*,end=999)
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read(9,*,end=999)
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read(9,*,end=999)
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read(9,*,end=999) natom
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read(9,*,end=999)
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read(9,*,end=999) lower,upper
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xcell=upper-lower
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read(9,*,end=999) lower,upper
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ycell=upper-lower
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read(9,*,end=999) lower,upper
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zcell=upper-lower
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read(9,*,end=999)
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C clear data array.
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do 400 j=1,allatom
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itype(j)=0
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x(j)=0.0d0
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y(j)=0.0d0
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z(j)=0.0d0
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400 continue
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do 440 j=1,natom
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read(9,*,end=999)iatom,itype(iatom),x(iatom),y(iatom),z(iatom)
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440 continue
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jframe=jframe+1
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if(jframe.lt.iframe1)goto 9999
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iframe=iframe+1
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if(iframe.ge.iframe2) goto 999
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c--------------------------------------------------------------------
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c-------This section writes each ts to a seperate .cfg file----------
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ciframe='.cfg'
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write(snapshot,'(i5.5,a4)')iframe,ciframe
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open(unit=iframe+20,file=snapshot,status='new',
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* form='formatted')
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write((iframe+20),'(a22,i7)')'Number of particles = ',natom
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a16)')'A = 1.0 Angstrom'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),435)'H0(1,1) = ',xcell,' A'
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write((iframe+20),'(a14)')'H0(1,2) = 0 A'
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write((iframe+20),'(a14)')'H0(1,3) = 0 A'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a14)')'H0(2,1) = 0 A'
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write((iframe+20),435)'H0(2,2) = ',ycell,' A'
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write((iframe+20),'(a14)')'H0(2,3) = 0 A'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a14)')'H0(3,1) = 0 A'
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write((iframe+20),'(a14)')'H0(3,2) = 0 A'
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write((iframe+20),435)'H0(3,3) = ',zcell,' A'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a12)')'eta(1,1) = 0'
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write((iframe+20),'(a12)')'eta(1,2) = 0'
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write((iframe+20),'(a12)')'eta(1,3) = 0'
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write((iframe+20),'(a12)')'eta(2,2) = 0'
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write((iframe+20),'(a12)')'eta(2,3) = 0'
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write((iframe+20),'(a12)')'eta(3,3) = 0'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),*)
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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write((iframe+20),'(a1)')'#'
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435 format(a11,f10.5,a2)
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do 460, j=1,allatom
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do 450,i=1,ntype
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if(itype(j).eq.atype(i))
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* write((iframe+20),445)mass(i),fftype(i),x(j),
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* y(j),z(j),' 0',' 0',' 0'
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c---445 is the format for writing atom data to .cfg file------------
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445 format(i3.3,1x,a2,1x,3f9.6,3a2)
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450 continue
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460 continue
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go to 9999
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999 continue
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close(9)
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end
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