diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index c0f4bc06c..0ae2b707e 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -1,366 +1,366 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
- Axel Kohlmeyer (Temple U), support for groups
-------------------------------------------------------------------------- */
-
-#include "math.h"
-#include "inttypes.h"
-#include "stdio.h"
-#include "time.h"
-#include "string.h"
-#include "dump_dcd.h"
-#include "domain.h"
-#include "atom.h"
-#include "update.h"
-#include "output.h"
-#include "group.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-#define NFILE_POS 8L
-#define NSTEP_POS 20L
-
-// necessary to set SEEK params b/c MPI-2 messes with these settings
-
-#ifndef SEEK_SET
-#define SEEK_SET 0
-#define SEEK_CUR 1
-#define SEEK_END 2
-#endif
-
-/* ---------------------------------------------------------------------- */
-
-static inline void fwrite_int32(FILE* fd, uint32_t i)
-{
- fwrite(&i,sizeof(uint32_t),1,fd);
-}
-
-/* ---------------------------------------------------------------------- */
-
-DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
-{
- if (narg != 5) error->all("Illegal dump dcd command");
- if (binary || compressed || multifile || multiproc)
- error->all("Invalid dump dcd filename");
-
- size_one = 3;
- sort_flag = 1;
- sortcol = 0;
-
- unwrap_flag = 0;
- format_default = NULL;
-
- // allocate global array for atom coords
-
- if (igroup == 0) natoms = static_cast<int> (atom->natoms);
- else natoms = static_cast<int> (group->count(igroup));
- if (natoms <= 0) error->all("Invalid natoms for dump dcd");
-
- coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
- xf = &coords[0*natoms];
- yf = &coords[1*natoms];
- zf = &coords[2*natoms];
-
- openfile();
- headerflag = 0;
- nevery_save = 0;
- ntotal = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-DumpDCD::~DumpDCD()
-{
- memory->sfree(coords);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpDCD::init_style()
-{
- if (sort_flag == 0 || sortcol != 0)
- error->all("Dump dcd requires sorting by atom ID");
-
- // check that dump frequency has not changed and is not a variable
-
- int idump;
- for (idump = 0; idump < output->ndump; idump++)
- if (strcmp(id,output->dump[idump]->id) == 0) break;
- if (output->every_dump[idump] == 0)
- error->all("Cannot use variable every setting for dump dcd");
-
- if (nevery_save == 0) nevery_save = output->every_dump[idump];
- else if (nevery_save != output->every_dump[idump])
- error->all("Cannot change dump_modify every for dump dcd");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpDCD::openfile()
-{
- if (me == 0) {
- fp = fopen(filename,"wb");
- if (fp == NULL) error->one("Cannot open dump file");
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpDCD::write_header(int n)
-{
- if (n != natoms) error->all("Dump dcd of non-matching # of atoms");
-
- // first time, write header for entire file
-
- if (headerflag == 0) {
- if (me == 0) write_dcd_header("Written by LAMMPS");
- headerflag = 1;
- nframes = 0;
- }
-
- // dim[] = size and angle cosines of orthogonal or triclinic box
- // dim[0] = a = length of unit cell vector along x-axis
- // dim[1] = alpha = cosine of angle between b and c
- // dim[2] = b = length of unit cell vector in xy-plane
- // dim[3] = beta = cosine of angle between a and c
- // dim[4] = gamma = cosine of angle between a and b
- // dim[5] = c = length of final unit cell vector
- // 48 = 6 doubles
-
- double dim[6];
- if (domain->triclinic) {
- double *h = domain->h;
- double alen = h[0];
- double blen = sqrt(h[5]*h[5] + h[1]*h[1]);
- double clen = sqrt(h[4]*h[4] + h[3]*h[3] + h[2]*h[2]);
- dim[0] = alen;
- dim[2] = blen;
- dim[5] = clen;
- dim[1] = (h[5]*h[4] + h[1]*h[3]) / blen/clen;
- dim[3] = (h[0]*h[4]) / alen/clen;
- dim[4] = (h[0]*h[5]) / alen/blen;
- } else {
- dim[0] = domain->xprd;
- dim[2] = domain->yprd;
- dim[5] = domain->zprd;
- dim[1] = dim[3] = dim[4] = 0.0;
- }
-
- if (me == 0) {
- uint32_t out_integer = 48;
- fwrite_int32(fp,out_integer);
- fwrite(dim,out_integer,1,fp);
- fwrite_int32(fp,out_integer);
- if (flush_flag) fflush(fp);
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-int DumpDCD::count()
-{
- if (igroup == 0) return atom->nlocal;
-
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- int m = 0;
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) m++;
- return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpDCD::pack(int *ids)
-{
- int m,n;
-
- int *tag = atom->tag;
- double **x = atom->x;
- int *image = atom->image;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
-
- m = n = 0;
- if (unwrap_flag) {
- double xprd = domain->xprd;
- double yprd = domain->yprd;
- double zprd = domain->zprd;
- double xy = domain->xy;
- double xz = domain->xz;
- double yz = domain->yz;
-
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- int ix = (image[i] & 1023) - 512;
- int iy = (image[i] >> 10 & 1023) - 512;
- int iz = (image[i] >> 20) - 512;
-
- if (domain->triclinic) {
- buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
- buf[m++] = x[i][1] + iy * yprd + iz * yz;
- buf[m++] = x[i][2] + iz * zprd;
- } else {
- buf[m++] = x[i][0] + ix * xprd;
- buf[m++] = x[i][1] + iy * yprd;
- buf[m++] = x[i][2] + iz * zprd;
- }
- ids[n++] = tag[i];
- }
- }
-
- } else {
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) {
- buf[m++] = x[i][0];
- buf[m++] = x[i][1];
- buf[m++] = x[i][2];
- ids[n++] = tag[i];
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpDCD::write_data(int n, double *mybuf)
-{
- // copy buf atom coords into 3 global arrays
-
- int m = 0;
- for (int i = 0; i < n; i++) {
- xf[ntotal] = mybuf[m++];
- yf[ntotal] = mybuf[m++];
- zf[ntotal] = mybuf[m++];
- ntotal++;
- }
-
- // if last chunk of atoms in this snapshot, write global arrays to file
-
- if (ntotal == natoms) {
- write_frame();
- ntotal = 0;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-int DumpDCD::modify_param(int narg, char **arg)
-{
- if (strcmp(arg[0],"unwrap") == 0) {
- if (narg < 2) error->all("Illegal dump_modify command");
- if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
- else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
- else error->all("Illegal dump_modify command");
- return 2;
- }
- return 0;
-}
-
-/* ----------------------------------------------------------------------
- return # of bytes of allocated memory in buf and global coords array
-------------------------------------------------------------------------- */
-
-double DumpDCD::memory_usage()
-{
- double bytes = Dump::memory_usage();
- bytes += 3*natoms * sizeof(float);
- return bytes;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpDCD::write_frame()
-{
- // write coords
-
- uint32_t out_integer = natoms*sizeof(float);
- fwrite_int32(fp,out_integer);
- fwrite(xf,out_integer,1,fp);
- fwrite_int32(fp,out_integer);
- fwrite_int32(fp,out_integer);
- fwrite(yf,out_integer,1,fp);
- fwrite_int32(fp,out_integer);
- fwrite_int32(fp,out_integer);
- fwrite(zf,out_integer,1,fp);
- fwrite_int32(fp,out_integer);
-
- // update NFILE and NSTEP fields in DCD header
-
- nframes++;
- out_integer = nframes;
- fseek(fp,NFILE_POS,SEEK_SET);
- fwrite_int32(fp,out_integer);
- out_integer = update->ntimestep;
- fseek(fp,NSTEP_POS,SEEK_SET);
- fwrite_int32(fp,out_integer);
- fseek(fp,0,SEEK_END);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpDCD::write_dcd_header(const char *remarks)
-{
- uint32_t out_integer;
- float out_float;
- char title_string[200];
- time_t cur_time;
- struct tm *tmbuf;
-
- out_integer = 84;
- fwrite_int32(fp,out_integer);
- strcpy(title_string,"CORD");
- fwrite(title_string,4,1,fp);
- fwrite_int32(fp,0); // NFILE = # of snapshots in file
- fwrite_int32(fp,update->ntimestep); // START = timestep of first snapshot
- fwrite_int32(fp,nevery_save); // SKIP = interval between snapshots
- fwrite_int32(fp,update->ntimestep); // NSTEP = timestep of last snapshot
- fwrite_int32(fp,0); // NAMD writes NSTEP or ISTART
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- out_float = update->dt;
- fwrite(&out_float,sizeof(float),1,fp);
- fwrite_int32(fp,1);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,0);
- fwrite_int32(fp,24); // pretend to be Charmm version 24
- fwrite_int32(fp,84);
- fwrite_int32(fp,164);
- fwrite_int32(fp,2);
- strncpy(title_string,remarks,80);
- title_string[79] = '\0';
- fwrite(title_string,80,1,fp);
- cur_time=time(NULL);
- tmbuf=localtime(&cur_time);
- memset(title_string,' ',81);
- strftime(title_string,80,"REMARKS Created %d %B,%Y at %R",tmbuf);
- fwrite(title_string,80,1,fp);
- fwrite_int32(fp,164);
- fwrite_int32(fp,4);
- fwrite_int32(fp,natoms); // number of atoms in each snapshot
- fwrite_int32(fp,4);
- if (flush_flag) fflush(fp);
-}
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
+ Axel Kohlmeyer (Temple U), support for groups
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "inttypes.h"
+#include "stdio.h"
+#include "time.h"
+#include "string.h"
+#include "dump_dcd.h"
+#include "domain.h"
+#include "atom.h"
+#include "update.h"
+#include "output.h"
+#include "group.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define NFILE_POS 8L
+#define NSTEP_POS 20L
+
+// necessary to set SEEK params b/c MPI-2 messes with these settings
+
+#ifndef SEEK_SET
+#define SEEK_SET 0
+#define SEEK_CUR 1
+#define SEEK_END 2
+#endif
+
+/* ---------------------------------------------------------------------- */
+
+static inline void fwrite_int32(FILE* fd, uint32_t i)
+{
+ fwrite(&i,sizeof(uint32_t),1,fd);
+}
+
+/* ---------------------------------------------------------------------- */
+
+DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
+{
+ if (narg != 5) error->all("Illegal dump dcd command");
+ if (binary || compressed || multifile || multiproc)
+ error->all("Invalid dump dcd filename");
+
+ size_one = 3;
+ sort_flag = 1;
+ sortcol = 0;
+
+ unwrap_flag = 0;
+ format_default = NULL;
+
+ // allocate global array for atom coords
+
+ if (igroup == 0) natoms = static_cast<int> (atom->natoms);
+ else natoms = static_cast<int> (group->count(igroup));
+ if (natoms <= 0) error->all("Invalid natoms for dump dcd");
+
+ coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
+ xf = &coords[0*natoms];
+ yf = &coords[1*natoms];
+ zf = &coords[2*natoms];
+
+ openfile();
+ headerflag = 0;
+ nevery_save = 0;
+ ntotal = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+DumpDCD::~DumpDCD()
+{
+ memory->sfree(coords);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpDCD::init_style()
+{
+ if (sort_flag == 0 || sortcol != 0)
+ error->all("Dump dcd requires sorting by atom ID");
+
+ // check that dump frequency has not changed and is not a variable
+
+ int idump;
+ for (idump = 0; idump < output->ndump; idump++)
+ if (strcmp(id,output->dump[idump]->id) == 0) break;
+ if (output->every_dump[idump] == 0)
+ error->all("Cannot use variable every setting for dump dcd");
+
+ if (nevery_save == 0) nevery_save = output->every_dump[idump];
+ else if (nevery_save != output->every_dump[idump])
+ error->all("Cannot change dump_modify every for dump dcd");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpDCD::openfile()
+{
+ if (me == 0) {
+ fp = fopen(filename,"wb");
+ if (fp == NULL) error->one("Cannot open dump file");
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpDCD::write_header(int n)
+{
+ if (n != natoms) error->all("Dump dcd of non-matching # of atoms");
+
+ // first time, write header for entire file
+
+ if (headerflag == 0) {
+ if (me == 0) write_dcd_header("Written by LAMMPS");
+ headerflag = 1;
+ nframes = 0;
+ }
+
+ // dim[] = size and angle cosines of orthogonal or triclinic box
+ // dim[0] = a = length of unit cell vector along x-axis
+ // dim[1] = gamma = cosine of angle between a and b
+ // dim[2] = b = length of unit cell vector in xy-plane
+ // dim[3] = beta = cosine of angle between a and c
+ // dim[4] = alpha = cosine of angle between b and c
+ // dim[5] = c = length of final unit cell vector
+ // 48 = 6 doubles
+
+ double dim[6];
+ if (domain->triclinic) {
+ double *h = domain->h;
+ double alen = h[0];
+ double blen = sqrt(h[5]*h[5] + h[1]*h[1]);
+ double clen = sqrt(h[4]*h[4] + h[3]*h[3] + h[2]*h[2]);
+ dim[0] = alen;
+ dim[2] = blen;
+ dim[5] = clen;
+ dim[4] = (h[5]*h[4] + h[1]*h[3]) / blen/clen; // alpha
+ dim[3] = (h[0]*h[4]) / alen/clen; // beta
+ dim[1] = (h[0]*h[5]) / alen/blen; // gamma
+ } else {
+ dim[0] = domain->xprd;
+ dim[2] = domain->yprd;
+ dim[5] = domain->zprd;
+ dim[1] = dim[3] = dim[4] = 0.0;
+ }
+
+ if (me == 0) {
+ uint32_t out_integer = 48;
+ fwrite_int32(fp,out_integer);
+ fwrite(dim,out_integer,1,fp);
+ fwrite_int32(fp,out_integer);
+ if (flush_flag) fflush(fp);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int DumpDCD::count()
+{
+ if (igroup == 0) return atom->nlocal;
+
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ int m = 0;
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) m++;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpDCD::pack(int *ids)
+{
+ int m,n;
+
+ int *tag = atom->tag;
+ double **x = atom->x;
+ int *image = atom->image;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ m = n = 0;
+ if (unwrap_flag) {
+ double xprd = domain->xprd;
+ double yprd = domain->yprd;
+ double zprd = domain->zprd;
+ double xy = domain->xy;
+ double xz = domain->xz;
+ double yz = domain->yz;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ int ix = (image[i] & 1023) - 512;
+ int iy = (image[i] >> 10 & 1023) - 512;
+ int iz = (image[i] >> 20) - 512;
+
+ if (domain->triclinic) {
+ buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
+ buf[m++] = x[i][1] + iy * yprd + iz * yz;
+ buf[m++] = x[i][2] + iz * zprd;
+ } else {
+ buf[m++] = x[i][0] + ix * xprd;
+ buf[m++] = x[i][1] + iy * yprd;
+ buf[m++] = x[i][2] + iz * zprd;
+ }
+ ids[n++] = tag[i];
+ }
+ }
+
+ } else {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) {
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2];
+ ids[n++] = tag[i];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpDCD::write_data(int n, double *mybuf)
+{
+ // copy buf atom coords into 3 global arrays
+
+ int m = 0;
+ for (int i = 0; i < n; i++) {
+ xf[ntotal] = mybuf[m++];
+ yf[ntotal] = mybuf[m++];
+ zf[ntotal] = mybuf[m++];
+ ntotal++;
+ }
+
+ // if last chunk of atoms in this snapshot, write global arrays to file
+
+ if (ntotal == natoms) {
+ write_frame();
+ ntotal = 0;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int DumpDCD::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"unwrap") == 0) {
+ if (narg < 2) error->all("Illegal dump_modify command");
+ if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
+ else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
+ else error->all("Illegal dump_modify command");
+ return 2;
+ }
+ return 0;
+}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory in buf and global coords array
+------------------------------------------------------------------------- */
+
+double DumpDCD::memory_usage()
+{
+ double bytes = Dump::memory_usage();
+ bytes += 3*natoms * sizeof(float);
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpDCD::write_frame()
+{
+ // write coords
+
+ uint32_t out_integer = natoms*sizeof(float);
+ fwrite_int32(fp,out_integer);
+ fwrite(xf,out_integer,1,fp);
+ fwrite_int32(fp,out_integer);
+ fwrite_int32(fp,out_integer);
+ fwrite(yf,out_integer,1,fp);
+ fwrite_int32(fp,out_integer);
+ fwrite_int32(fp,out_integer);
+ fwrite(zf,out_integer,1,fp);
+ fwrite_int32(fp,out_integer);
+
+ // update NFILE and NSTEP fields in DCD header
+
+ nframes++;
+ out_integer = nframes;
+ fseek(fp,NFILE_POS,SEEK_SET);
+ fwrite_int32(fp,out_integer);
+ out_integer = update->ntimestep;
+ fseek(fp,NSTEP_POS,SEEK_SET);
+ fwrite_int32(fp,out_integer);
+ fseek(fp,0,SEEK_END);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DumpDCD::write_dcd_header(const char *remarks)
+{
+ uint32_t out_integer;
+ float out_float;
+ char title_string[200];
+ time_t cur_time;
+ struct tm *tmbuf;
+
+ out_integer = 84;
+ fwrite_int32(fp,out_integer);
+ strcpy(title_string,"CORD");
+ fwrite(title_string,4,1,fp);
+ fwrite_int32(fp,0); // NFILE = # of snapshots in file
+ fwrite_int32(fp,update->ntimestep); // START = timestep of first snapshot
+ fwrite_int32(fp,nevery_save); // SKIP = interval between snapshots
+ fwrite_int32(fp,update->ntimestep); // NSTEP = timestep of last snapshot
+ fwrite_int32(fp,0); // NAMD writes NSTEP or ISTART
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ out_float = update->dt;
+ fwrite(&out_float,sizeof(float),1,fp);
+ fwrite_int32(fp,1);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,0);
+ fwrite_int32(fp,24); // pretend to be Charmm version 24
+ fwrite_int32(fp,84);
+ fwrite_int32(fp,164);
+ fwrite_int32(fp,2);
+ strncpy(title_string,remarks,80);
+ title_string[79] = '\0';
+ fwrite(title_string,80,1,fp);
+ cur_time=time(NULL);
+ tmbuf=localtime(&cur_time);
+ memset(title_string,' ',81);
+ strftime(title_string,80,"REMARKS Created %d %B,%Y at %R",tmbuf);
+ fwrite(title_string,80,1,fp);
+ fwrite_int32(fp,164);
+ fwrite_int32(fp,4);
+ fwrite_int32(fp,natoms); // number of atoms in each snapshot
+ fwrite_int32(fp,4);
+ if (flush_flag) fflush(fp);
+}