remove obsolete tools and files
This commit is contained in:
Axel Kohlmeyer
@ -1,366 +0,0 @@
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/* data2xmovie tool
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read LAMMPS data file as input
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write a snapshot in XMOVIE format
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Syntax: data2xmovie [options] < infile > outfile
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Options:
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-style atom_style
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use the LAMMPS atom style that corresponds to this file
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e.g. atomic or bond or angle or full or eam or granular
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will be used for reading and writing files
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if not specified, atom_style = full
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-unmap
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unmap all input atom positions using input image flags
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image flags must be specified in infile
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default is to leave atoms mapped to periodic box
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-inbox xlo xhi ylo yhi zlo zhi
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use these values for the output bounding box of the system
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useful if are unmapping atoms into a larger domain
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if not specified use the box bounds read in from infile
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*/
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#include <string.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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struct box {
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double xlo,xhi,xsize;
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double ylo,yhi,ysize;
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double zlo,zhi,zsize;
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};
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#define MAXLINE 1000
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#define ATOMIC 1
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#define BOND 2
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#define ANGLE 3
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#define FULL 4
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#define EAM 5
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#define GRANULAR 6
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main(int argc, char *argv[])
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{
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char line[1000]; /* strings for reading/parsing input file */
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char linetoken[1000];
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char *token;
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/* numbers of various quantities as read in */
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int natoms,nbonds,nangles,ndihedrals,nimpropers;
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int ntypes,nbondtypes,nangletypes,ndihedtypes,nimprotypes;
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int nmolecules; /* total # of mols specified by mol tags */
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int atomstyle; /* atomstyle for read/write of Atoms */
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int unmap; /* 0 = no unmapping, 1 = unmap from input box */
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int outbox; /* flag for whether out box is explicitly set */
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struct box in,out; /* input/output bounding box */
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char *gettoken(char *, int); /* function defs */
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void skipline(int);
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/* default input values */
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atomstyle = 0;
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unmap = 0;
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outbox = 0;
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/* read input options from command line
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should do more error checking for missing args */
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int i = 1;
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while (i < argc) {
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if (!strcmp(argv[i],"-style")) {
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if (strcmp(argv[i+1],"atomic") == 0) atomstyle = ATOMIC;
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else if (strcmp(argv[i+1],"bond") == 0) atomstyle = BOND;
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else if (strcmp(argv[i+1],"angle") == 0) atomstyle = ANGLE;
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else if (strcmp(argv[i+1],"full") == 0) atomstyle = FULL;
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else if (strcmp(argv[i+1],"eam") == 0) atomstyle = EAM;
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else if (strcmp(argv[i+1],"granular") == 0) atomstyle = GRANULAR;
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else {
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fprintf(stderr,"Error with command-line arg style\n");
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exit(1);
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}
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i += 2;
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} else if (!strcmp(argv[i],"-unmap")) {
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unmap = 1;
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i += 1;
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} else if (!strcmp(argv[i],"-inbox")) {
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outbox = 1;
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sscanf(argv[i+1],"%lg",&out.xlo);
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sscanf(argv[i+2],"%lg",&out.xhi);
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sscanf(argv[i+3],"%lg",&out.ylo);
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sscanf(argv[i+4],"%lg",&out.yhi);
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sscanf(argv[i+5],"%lg",&out.zlo);
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sscanf(argv[i+6],"%lg",&out.zhi);
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i += 7;
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} else {
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fprintf(stderr,"Syntax error: data2xmovie [options] < infile > outfile\n");
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exit(1);
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}
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}
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/* error checks */
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if (atomstyle == 0) {
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fprintf(stderr,"ERROR: must use -style to set atom style\n");
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exit(1);
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}
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/* defaults */
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natoms = nbonds = nangles = ndihedrals = nimpropers = 0;
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ntypes = nbondtypes = nangletypes = ndihedtypes = nimprotypes = 0;
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/* read header */
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fgets(line,MAXLINE,stdin);
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while (1) {
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fgets(line,MAXLINE,stdin);
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if (strspn(line," \t\n\r") == strlen(line)) continue;
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else if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
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else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
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else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
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else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
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else if (strstr(line,"impropers")) sscanf(line,"%d",&nimpropers);
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else if (strstr(line,"atom types")) sscanf(line,"%d",&ntypes);
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else if (strstr(line,"bond types")) sscanf(line,"%d",&nbondtypes);
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else if (strstr(line,"angle types")) sscanf(line,"%d",&nangletypes);
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else if (strstr(line,"dihedral types")) sscanf(line,"%d",&ndihedtypes);
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else if (strstr(line,"improper types")) sscanf(line,"%d",&nimprotypes);
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else if (strstr(line,"xlo xhi")) sscanf(line,"%lg %lg",&in.xlo,&in.xhi);
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else if (strstr(line,"ylo yhi")) sscanf(line,"%lg %lg",&in.ylo,&in.yhi);
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else if (strstr(line,"zlo zhi")) sscanf(line,"%lg %lg",&in.zlo,&in.zhi);
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else break;
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}
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/* compute input box size */
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in.xsize = in.xhi - in.xlo;
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in.ysize = in.yhi - in.ylo;
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in.zsize = in.zhi - in.zlo;
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/* write XMOVIE header */
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printf("ITEM: TIMESTEP\n");
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printf("%d\n",0);
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printf("ITEM: NUMBER OF ATOMS\n");
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printf("%d\n",natoms);
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printf("ITEM: BOX BOUNDS\n");
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if (outbox) {
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printf("%g %g\n",out.xlo,out.xhi);
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printf("%g %g\n",out.ylo,out.yhi);
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printf("%g %g\n",out.zlo,out.zhi);
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} else {
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printf("%g %g\n",in.xlo,in.xhi);
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printf("%g %g\n",in.ylo,in.yhi);
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printf("%g %g\n",in.zlo,in.zhi);
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}
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/* read identifier strings one by one in free-form part of data file */
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token = gettoken(line,1);
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while (token) {
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/* read atoms */
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if (!strcmp(token,"Atoms")) {
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printf("ITEM: ATOMS\n");
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int tag,type,molecule,imagex,imagey,imagez;
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double x,y,z,radius,density,q;
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for (i = 0; i < natoms; i++) {
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fgets(line,MAXLINE,stdin);
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if (unmap) {
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if (atomstyle == ATOMIC)
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sscanf(line,"%d %d %lg %lg %lg %d %d %d",
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&tag,&type,&x,&y,&z,
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&imagex,&imagey,&imagez);
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else if (atomstyle == BOND)
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sscanf(line,"%d %d %d %lg %lg %lg %d %d %d",
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&tag,&molecule,&type,&x,&y,&z,
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&imagex,&imagey,&imagez);
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else if (atomstyle == ANGLE)
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sscanf(line,"%d %d %d %lg %lg %lg %d %d %d",
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&tag,&molecule,&type,&x,&y,&z,
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&imagex,&imagey,&imagez);
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else if (atomstyle == FULL)
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sscanf(line,"%d %d %d %lg %lg %lg %lg %d %d %d",
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&tag,&molecule,&type,&q,&x,&y,&z,
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&imagex,&imagey,&imagez);
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else if (atomstyle == EAM)
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sscanf(line,"%d %d %lg %lg %lg %d %d %d",
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&tag,&type,&x,&y,&z,
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&imagex,&imagey,&imagez);
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else if (atomstyle == GRANULAR)
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sscanf(line,"%d %d %lg %lg %lg %lg %lg %d %d %d",
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&tag,&type,&radius,&density,&x,&y,&z,
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&imagex,&imagey,&imagez);
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} else {
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if (atomstyle == ATOMIC)
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sscanf(line,"%d %d %lg %lg %lg",
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&tag,&type,&x,&y,&z);
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else if (atomstyle == BOND)
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sscanf(line,"%d %d %d %lg %lg %lg",
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&tag,&molecule,&type,&x,&y,&z);
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else if (atomstyle == ANGLE)
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sscanf(line,"%d %d %d %lg %lg %lg",
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&tag,&molecule,&type,&x,&y,&z);
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else if (atomstyle == FULL)
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sscanf(line,"%d %d %d %lg %lg %lg %lg",
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&tag,&molecule,&type,&q,&x,&y,&z);
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else if (atomstyle == EAM)
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sscanf(line,"%d %d %lg %lg %lg",
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&tag,&type,&x,&y,&z);
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else if (atomstyle == GRANULAR)
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sscanf(line,"%d %d %lg %lg %lg %lg %lg",
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&tag,&type,&radius,&density,&x,&y,&z);
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imagez = imagey = imagex = 0;
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}
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/* unmap atom position if requested */
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if (unmap) {
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x = x + imagex*in.xsize;
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y = y + imagey*in.ysize;
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z = z + imagez*in.zsize;
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}
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printf("%d %d %g %g %g\n",tag,type,x,y,z);
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}
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}
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/* read bonds and replicate */
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else if (!strcmp(token,"Bonds")) {
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printf("ITEM: BONDS\n");
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int n,btype,bond1,bond2;
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for (i = 0; i < nbonds; i++) {
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fgets(line,MAXLINE,stdin);
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sscanf(line,"%d %d %d %d",&n,&btype,&bond1,&bond2);
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printf("%d %d %d\n",btype,bond1,bond2);
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}
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}
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/* non-replicated sections - just skip lines */
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else if (!strcmp(token,"Velocities"))
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skipline(natoms);
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else if (!strcmp(token,"Angles"))
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skipline(nangles);
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else if (!strcmp(token,"Dihedrals"))
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skipline(ndihedrals);
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else if (!strcmp(token,"Impropers"))
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skipline(nimpropers);
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else if (!strcmp(token,"Masses"))
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skipline(ntypes);
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else if (!strcmp(token,"Dipoles"))
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skipline(ntypes);
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else if (!strcmp(token,"Pair Coeffs"))
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skipline(ntypes);
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else if (!strcmp(token,"Bond Coeffs"))
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skipline(nbondtypes);
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else if (!strcmp(token,"Angle Coeffs"))
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skipline(nangletypes);
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else if (!strcmp(token,"Dihedral Coeffs"))
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skipline(ndihedtypes);
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else if (!strcmp(token,"Improper Coeffs"))
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skipline(nimprotypes);
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else if (!strcmp(token,"BondBond Coeffs"))
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skipline(nangletypes);
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else if (!strcmp(token,"BondAngle Coeffs"))
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skipline(nangletypes);
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else if (!strcmp(token,"MiddleBondTorsion Coeffs"))
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skipline(ndihedtypes);
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else if (!strcmp(token,"EndBondTorsion Coeffs"))
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skipline(ndihedtypes);
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else if (!strcmp(token,"AngleTorsion Coeffs"))
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skipline(ndihedtypes);
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else if (!strcmp(token,"AngleAngleTorsion Coeffs"))
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skipline(ndihedtypes);
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else if (!strcmp(token,"BondBond13 Coeffs"))
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skipline(ndihedtypes);
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else if (!strcmp(token,"AngleAngle Coeffs"))
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skipline(nimprotypes);
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else {
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fprintf(stderr,
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"Error in input data file - unknown identifier %s\n",token);
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exit(1);
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}
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token = gettoken(line,0);
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}
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}
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/* ------------------------------------------------------------------- */
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/* return a LAMMPS keyword from data file
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if first is 1, non-blank line with token is in line
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else read until find a non-blank line
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keyword is all text on line w/out leading & trailing white space
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read one additional line after non-blank line (assumed blank)
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return ptr to keyword
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return NULL if end of file */
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char *gettoken(char *line, int first)
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{
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char buffer[MAXLINE];
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/* read upto non-blank line plus 1 following line
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eof is set to 1 if any read hits end-of-file */
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int eof = 0;
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if (!first) if (fgets(line,MAXLINE,stdin) == NULL) eof = 1;
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while (eof == 0 && strspn(line," \t\n\r") == strlen(line))
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if (fgets(line,MAXLINE,stdin) == NULL) eof = 1;
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if (fgets(buffer,MAXLINE,stdin) == NULL) eof = 1;
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/* if eof, return NULL */
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if (eof) return NULL;
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/* bracket non-whitespace portion of line */
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int start = strspn(line," \t\n\r");
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int stop = strlen(line) - 1;
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while (line[stop] == ' ' || line[stop] == '\t'
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|| line[stop] == '\n' || line[stop] == '\r') stop--;
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line[stop+1] = '\0';
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/* return ptr to keyword */
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return &line[start];
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}
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/* read n lines and ignore */
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void skipline(int n)
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{
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char line[1000];
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while (n) {
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fgets(line,MAXLINE,stdin);
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n--;
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}
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}
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@ -1,80 +0,0 @@
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This directory used to contain utility scripts for using VMD to
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visualize and analyze LAMMPS trajectories. As of April 2010 all of the
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scripts and many additional features have been merged into the topotools
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plugin that is bundled with VMD. Updates between VMD releases are here:
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http://sites.google.com/site/akohlmey/software/topotools
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This page also contains detailed documentation and some tutorials.
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These scripts within VMD and the plugin for native LAMMPS dump files are
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are maintained by Axel Kohlmeyer <akohlmey@gmail.com>; please contact
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him through the LAMMPS mailing list in case of problems.
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Below are a few comments on support for LAMMPS in VMD.
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-------------------------
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1. File formats and VMD limitations
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VMD currently supports reading several but not all file formats
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that LAMMPS can generate. Supported are: atom (text mode), custom
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(text mode, only some fields are directly supported, please see
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below for more details), dcd, xyz and xtc. Cfg and binary native
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dump files are not supported (06/2012). The new molfile dump style
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in addition allows to use VMD molfile plugins to write dumps in
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any format that is supported by VMD.
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However VMD requires all frames of a file to have the same number of
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atoms. If the number of atoms changes between two frames, the file
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reader will stop. The topotools plugin has a special scripted file
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reader for .xyz files that can generate the necessary padding so that
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the file can still be read into VMD. Whether an atom is real or
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"invisible" is then flagged in the "user" field. For efficiency
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reasons this script will not preserve atom identity between frames.
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2. Topology files, a.k.a. as "data" files
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The topotools plugin also contains a read and write option for LAMMPS
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data files. This reader will try to preserve as much information as
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possible and will also store useful information as comments upon
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writing. It does not store or read coefficient data. In combination
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with other functionality in topotools complete topologies for rather
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complicated systems for LAMMPS can be build with VMD scripting.
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3. Reading custom data fields into VMD
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At this moment VMD only supports reading coordinates and velocities
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(if present) as per timestep data. Everthing else is just taken
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from the first frame or whatever file was used to generate this
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structure information. Through setting the environment variable
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LAMMPSREMAPFIELDS, custom properties can be mapped to the x, y, z,
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vx, vy, vz data fields and then accessed from within VMD. For
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example to store radius and charge of a particle in the vx and vy
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fields, respectively set this variable to "vx=radius,vy=q". Future
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versions of VMD will allow more flexibility.
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4. Recovering information about elements
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Colorization in VMD is by default based on atom names, yet LAMMPS
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requires identification of atoms by consecutive numbers starting at
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1. With the option of reading a LAMMPS data file, additional
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information is provided that can help to recover some of this
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data. 'topo guessatom element mass' will guess the atom's element
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name from it mass (with fuzz, where possible).
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5. Reading files from the command line
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Converting a LAMMPS data file to a .psf file can be very convenient
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for loading trajectories from the command line. This conversion is
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done with
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topo readlammpsdata data.rhodo full
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animate write psf rhodo.psf
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In the future you can now load this PSF file first and then the
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LAMMPS dump file(s) (or a more compact and faster loading DCD or
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XTC file) with:
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vmd micelle.psf -lammpstrj dump.micelle
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Note how the -lammpstrj flag will tell VMD that dump.micelle is a
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lammps trajectory file.
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Reference in New Issue
Block a user