diff --git a/tools/data2xmovie.c b/tools/data2xmovie.c
deleted file mode 100644
index 85cb2f7a2af39c3edd3751fb4f6bc573dfd5578d..0000000000000000000000000000000000000000
--- a/tools/data2xmovie.c
+++ /dev/null
@@ -1,366 +0,0 @@
-/* data2xmovie tool
-
- read LAMMPS data file as input
- write a snapshot in XMOVIE format
-
- Syntax: data2xmovie [options] < infile > outfile
-
- Options:
-
- -style atom_style
-
- use the LAMMPS atom style that corresponds to this file
- e.g. atomic or bond or angle or full or eam or granular
- will be used for reading and writing files
- if not specified, atom_style = full
-
- -unmap
-
- unmap all input atom positions using input image flags
- image flags must be specified in infile
- default is to leave atoms mapped to periodic box
-
- -inbox xlo xhi ylo yhi zlo zhi
-
- use these values for the output bounding box of the system
- useful if are unmapping atoms into a larger domain
- if not specified use the box bounds read in from infile
-*/
-
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-
-struct box {
- double xlo,xhi,xsize;
- double ylo,yhi,ysize;
- double zlo,zhi,zsize;
-};
-
-#define MAXLINE 1000
-
-#define ATOMIC 1
-#define BOND 2
-#define ANGLE 3
-#define FULL 4
-#define EAM 5
-#define GRANULAR 6
-
-main(int argc, char *argv[])
-
-{
- char line[1000]; /* strings for reading/parsing input file */
- char linetoken[1000];
- char *token;
- /* numbers of various quantities as read in */
-
- int natoms,nbonds,nangles,ndihedrals,nimpropers;
- int ntypes,nbondtypes,nangletypes,ndihedtypes,nimprotypes;
-
- int nmolecules; /* total # of mols specified by mol tags */
-
- int atomstyle; /* atomstyle for read/write of Atoms */
- int unmap; /* 0 = no unmapping, 1 = unmap from input box */
- int outbox; /* flag for whether out box is explicitly set */
-
- struct box in,out; /* input/output bounding box */
-
- char *gettoken(char *, int); /* function defs */
- void skipline(int);
-
- /* default input values */
-
- atomstyle = 0;
- unmap = 0;
- outbox = 0;
-
- /* read input options from command line
- should do more error checking for missing args */
-
- int i = 1;
- while (i < argc) {
-
- if (!strcmp(argv[i],"-style")) {
- if (strcmp(argv[i+1],"atomic") == 0) atomstyle = ATOMIC;
- else if (strcmp(argv[i+1],"bond") == 0) atomstyle = BOND;
- else if (strcmp(argv[i+1],"angle") == 0) atomstyle = ANGLE;
- else if (strcmp(argv[i+1],"full") == 0) atomstyle = FULL;
- else if (strcmp(argv[i+1],"eam") == 0) atomstyle = EAM;
- else if (strcmp(argv[i+1],"granular") == 0) atomstyle = GRANULAR;
- else {
- fprintf(stderr,"Error with command-line arg style\n");
- exit(1);
- }
- i += 2;
- } else if (!strcmp(argv[i],"-unmap")) {
- unmap = 1;
- i += 1;
- } else if (!strcmp(argv[i],"-inbox")) {
- outbox = 1;
- sscanf(argv[i+1],"%lg",&out.xlo);
- sscanf(argv[i+2],"%lg",&out.xhi);
- sscanf(argv[i+3],"%lg",&out.ylo);
- sscanf(argv[i+4],"%lg",&out.yhi);
- sscanf(argv[i+5],"%lg",&out.zlo);
- sscanf(argv[i+6],"%lg",&out.zhi);
- i += 7;
- } else {
- fprintf(stderr,"Syntax error: data2xmovie [options] < infile > outfile\n");
- exit(1);
- }
- }
-
- /* error checks */
-
- if (atomstyle == 0) {
- fprintf(stderr,"ERROR: must use -style to set atom style\n");
- exit(1);
- }
-
- /* defaults */
-
- natoms = nbonds = nangles = ndihedrals = nimpropers = 0;
- ntypes = nbondtypes = nangletypes = ndihedtypes = nimprotypes = 0;
-
- /* read header */
-
- fgets(line,MAXLINE,stdin);
-
- while (1) {
- fgets(line,MAXLINE,stdin);
-
- if (strspn(line," \t\n\r") == strlen(line)) continue;
- else if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
- else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
- else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
- else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
- else if (strstr(line,"impropers")) sscanf(line,"%d",&nimpropers);
- else if (strstr(line,"atom types")) sscanf(line,"%d",&ntypes);
- else if (strstr(line,"bond types")) sscanf(line,"%d",&nbondtypes);
- else if (strstr(line,"angle types")) sscanf(line,"%d",&nangletypes);
- else if (strstr(line,"dihedral types")) sscanf(line,"%d",&ndihedtypes);
- else if (strstr(line,"improper types")) sscanf(line,"%d",&nimprotypes);
- else if (strstr(line,"xlo xhi")) sscanf(line,"%lg %lg",&in.xlo,&in.xhi);
- else if (strstr(line,"ylo yhi")) sscanf(line,"%lg %lg",&in.ylo,&in.yhi);
- else if (strstr(line,"zlo zhi")) sscanf(line,"%lg %lg",&in.zlo,&in.zhi);
- else break;
- }
-
- /* compute input box size */
-
- in.xsize = in.xhi - in.xlo;
- in.ysize = in.yhi - in.ylo;
- in.zsize = in.zhi - in.zlo;
-
- /* write XMOVIE header */
-
- printf("ITEM: TIMESTEP\n");
- printf("%d\n",0);
- printf("ITEM: NUMBER OF ATOMS\n");
- printf("%d\n",natoms);
- printf("ITEM: BOX BOUNDS\n");
- if (outbox) {
- printf("%g %g\n",out.xlo,out.xhi);
- printf("%g %g\n",out.ylo,out.yhi);
- printf("%g %g\n",out.zlo,out.zhi);
- } else {
- printf("%g %g\n",in.xlo,in.xhi);
- printf("%g %g\n",in.ylo,in.yhi);
- printf("%g %g\n",in.zlo,in.zhi);
- }
-
- /* read identifier strings one by one in free-form part of data file */
-
- token = gettoken(line,1);
-
- while (token) {
-
- /* read atoms */
-
- if (!strcmp(token,"Atoms")) {
-
- printf("ITEM: ATOMS\n");
-
- int tag,type,molecule,imagex,imagey,imagez;
- double x,y,z,radius,density,q;
-
- for (i = 0; i < natoms; i++) {
- fgets(line,MAXLINE,stdin);
- if (unmap) {
- if (atomstyle == ATOMIC)
- sscanf(line,"%d %d %lg %lg %lg %d %d %d",
- &tag,&type,&x,&y,&z,
- &imagex,&imagey,&imagez);
- else if (atomstyle == BOND)
- sscanf(line,"%d %d %d %lg %lg %lg %d %d %d",
- &tag,&molecule,&type,&x,&y,&z,
- &imagex,&imagey,&imagez);
- else if (atomstyle == ANGLE)
- sscanf(line,"%d %d %d %lg %lg %lg %d %d %d",
- &tag,&molecule,&type,&x,&y,&z,
- &imagex,&imagey,&imagez);
- else if (atomstyle == FULL)
- sscanf(line,"%d %d %d %lg %lg %lg %lg %d %d %d",
- &tag,&molecule,&type,&q,&x,&y,&z,
- &imagex,&imagey,&imagez);
- else if (atomstyle == EAM)
- sscanf(line,"%d %d %lg %lg %lg %d %d %d",
- &tag,&type,&x,&y,&z,
- &imagex,&imagey,&imagez);
- else if (atomstyle == GRANULAR)
- sscanf(line,"%d %d %lg %lg %lg %lg %lg %d %d %d",
- &tag,&type,&radius,&density,&x,&y,&z,
- &imagex,&imagey,&imagez);
- } else {
- if (atomstyle == ATOMIC)
- sscanf(line,"%d %d %lg %lg %lg",
- &tag,&type,&x,&y,&z);
- else if (atomstyle == BOND)
- sscanf(line,"%d %d %d %lg %lg %lg",
- &tag,&molecule,&type,&x,&y,&z);
- else if (atomstyle == ANGLE)
- sscanf(line,"%d %d %d %lg %lg %lg",
- &tag,&molecule,&type,&x,&y,&z);
- else if (atomstyle == FULL)
- sscanf(line,"%d %d %d %lg %lg %lg %lg",
- &tag,&molecule,&type,&q,&x,&y,&z);
- else if (atomstyle == EAM)
- sscanf(line,"%d %d %lg %lg %lg",
- &tag,&type,&x,&y,&z);
- else if (atomstyle == GRANULAR)
- sscanf(line,"%d %d %lg %lg %lg %lg %lg",
- &tag,&type,&radius,&density,&x,&y,&z);
- imagez = imagey = imagex = 0;
- }
-
- /* unmap atom position if requested */
-
- if (unmap) {
- x = x + imagex*in.xsize;
- y = y + imagey*in.ysize;
- z = z + imagez*in.zsize;
- }
-
- printf("%d %d %g %g %g\n",tag,type,x,y,z);
- }
- }
-
- /* read bonds and replicate */
-
- else if (!strcmp(token,"Bonds")) {
-
- printf("ITEM: BONDS\n");
-
- int n,btype,bond1,bond2;
-
- for (i = 0; i < nbonds; i++) {
- fgets(line,MAXLINE,stdin);
- sscanf(line,"%d %d %d %d",&n,&btype,&bond1,&bond2);
- printf("%d %d %d\n",btype,bond1,bond2);
- }
- }
-
- /* non-replicated sections - just skip lines */
-
- else if (!strcmp(token,"Velocities"))
- skipline(natoms);
- else if (!strcmp(token,"Angles"))
- skipline(nangles);
- else if (!strcmp(token,"Dihedrals"))
- skipline(ndihedrals);
- else if (!strcmp(token,"Impropers"))
- skipline(nimpropers);
- else if (!strcmp(token,"Masses"))
- skipline(ntypes);
- else if (!strcmp(token,"Dipoles"))
- skipline(ntypes);
- else if (!strcmp(token,"Pair Coeffs"))
- skipline(ntypes);
- else if (!strcmp(token,"Bond Coeffs"))
- skipline(nbondtypes);
- else if (!strcmp(token,"Angle Coeffs"))
- skipline(nangletypes);
- else if (!strcmp(token,"Dihedral Coeffs"))
- skipline(ndihedtypes);
- else if (!strcmp(token,"Improper Coeffs"))
- skipline(nimprotypes);
- else if (!strcmp(token,"BondBond Coeffs"))
- skipline(nangletypes);
- else if (!strcmp(token,"BondAngle Coeffs"))
- skipline(nangletypes);
- else if (!strcmp(token,"MiddleBondTorsion Coeffs"))
- skipline(ndihedtypes);
- else if (!strcmp(token,"EndBondTorsion Coeffs"))
- skipline(ndihedtypes);
- else if (!strcmp(token,"AngleTorsion Coeffs"))
- skipline(ndihedtypes);
- else if (!strcmp(token,"AngleAngleTorsion Coeffs"))
- skipline(ndihedtypes);
- else if (!strcmp(token,"BondBond13 Coeffs"))
- skipline(ndihedtypes);
- else if (!strcmp(token,"AngleAngle Coeffs"))
- skipline(nimprotypes);
- else {
- fprintf(stderr,
- "Error in input data file - unknown identifier %s\n",token);
- exit(1);
- }
-
- token = gettoken(line,0);
- }
-
-}
-
-/* ------------------------------------------------------------------- */
-
-/* return a LAMMPS keyword from data file
- if first is 1, non-blank line with token is in line
- else read until find a non-blank line
- keyword is all text on line w/out leading & trailing white space
- read one additional line after non-blank line (assumed blank)
- return ptr to keyword
- return NULL if end of file */
-
-char *gettoken(char *line, int first)
-{
- char buffer[MAXLINE];
-
- /* read upto non-blank line plus 1 following line
- eof is set to 1 if any read hits end-of-file */
-
- int eof = 0;
-
- if (!first) if (fgets(line,MAXLINE,stdin) == NULL) eof = 1;
- while (eof == 0 && strspn(line," \t\n\r") == strlen(line))
- if (fgets(line,MAXLINE,stdin) == NULL) eof = 1;
- if (fgets(buffer,MAXLINE,stdin) == NULL) eof = 1;
-
- /* if eof, return NULL */
-
- if (eof) return NULL;
-
- /* bracket non-whitespace portion of line */
-
- int start = strspn(line," \t\n\r");
- int stop = strlen(line) - 1;
- while (line[stop] == ' ' || line[stop] == '\t'
- || line[stop] == '\n' || line[stop] == '\r') stop--;
- line[stop+1] = '\0';
-
- /* return ptr to keyword */
-
- return &line[start];
-}
-
-/* read n lines and ignore */
-
-void skipline(int n)
-{
- char line[1000];
-
- while (n) {
- fgets(line,MAXLINE,stdin);
- n--;
- }
-}
diff --git a/tools/lmp2vmd/README.txt b/tools/lmp2vmd/README.txt
deleted file mode 100644
index 10b9497f4a0d3b69532c631427d14ec7c7839cc5..0000000000000000000000000000000000000000
--- a/tools/lmp2vmd/README.txt
+++ /dev/null
@@ -1,80 +0,0 @@
-This directory used to contain utility scripts for using VMD to
-visualize and analyze LAMMPS trajectories. As of April 2010 all of the
-scripts and many additional features have been merged into the topotools
-plugin that is bundled with VMD. Updates between VMD releases are here:
-http://sites.google.com/site/akohlmey/software/topotools
-This page also contains detailed documentation and some tutorials.
-
-These scripts within VMD and the plugin for native LAMMPS dump files are
-are maintained by Axel Kohlmeyer <akohlmey@gmail.com>; please contact
-him through the LAMMPS mailing list in case of problems.
-
-Below are a few comments on support for LAMMPS in VMD.
-
--------------------------
-
-1. File formats and VMD limitations
-
- VMD currently supports reading several but not all file formats
- that LAMMPS can generate. Supported are: atom (text mode), custom
- (text mode, only some fields are directly supported, please see
- below for more details), dcd, xyz and xtc. Cfg and binary native
- dump files are not supported (06/2012). The new molfile dump style
- in addition allows to use VMD molfile plugins to write dumps in
- any format that is supported by VMD.
-
- However VMD requires all frames of a file to have the same number of
- atoms. If the number of atoms changes between two frames, the file
- reader will stop. The topotools plugin has a special scripted file
- reader for .xyz files that can generate the necessary padding so that
- the file can still be read into VMD. Whether an atom is real or
- "invisible" is then flagged in the "user" field. For efficiency
- reasons this script will not preserve atom identity between frames.
-
-2. Topology files, a.k.a. as "data" files
-
- The topotools plugin also contains a read and write option for LAMMPS
- data files. This reader will try to preserve as much information as
- possible and will also store useful information as comments upon
- writing. It does not store or read coefficient data. In combination
- with other functionality in topotools complete topologies for rather
- complicated systems for LAMMPS can be build with VMD scripting.
-
-3. Reading custom data fields into VMD
-
- At this moment VMD only supports reading coordinates and velocities
- (if present) as per timestep data. Everthing else is just taken
- from the first frame or whatever file was used to generate this
- structure information. Through setting the environment variable
- LAMMPSREMAPFIELDS, custom properties can be mapped to the x, y, z,
- vx, vy, vz data fields and then accessed from within VMD. For
- example to store radius and charge of a particle in the vx and vy
- fields, respectively set this variable to "vx=radius,vy=q". Future
- versions of VMD will allow more flexibility.
-
-4. Recovering information about elements
-
- Colorization in VMD is by default based on atom names, yet LAMMPS
- requires identification of atoms by consecutive numbers starting at
- 1. With the option of reading a LAMMPS data file, additional
- information is provided that can help to recover some of this
- data. 'topo guessatom element mass' will guess the atom's element
- name from it mass (with fuzz, where possible).
-
-5. Reading files from the command line
-
- Converting a LAMMPS data file to a .psf file can be very convenient
- for loading trajectories from the command line. This conversion is
- done with
-
- topo readlammpsdata data.rhodo full
- animate write psf rhodo.psf
-
- In the future you can now load this PSF file first and then the
- LAMMPS dump file(s) (or a more compact and faster loading DCD or
- XTC file) with:
-
- vmd micelle.psf -lammpstrj dump.micelle
-
- Note how the -lammpstrj flag will tell VMD that dump.micelle is a
- lammps trajectory file.