Unverified Commit d4dbc32b authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1672 from akohlmey/dump-with-unit 

Add ITEM: UNITS line to native text format dumps
parents eab66f27 c37d0011

doc/src/dump.txt

+2 −1
Original line number Diff line number Diff line
@@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre 


ID = user-assigned name for the dump :ulb,l

group-ID = ID of the group of atoms to be dumped :l

style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l

style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or

{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l

N = dump every this many timesteps :l

file = name of file to write dump info to :l

args = list of arguments for a particular style :l

doc/src/dump_modify.txt

+17 −0
Original line number Diff line number Diff line
@@ -50,6 +50,7 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi 
  {sfactor} arg = coordinate scaling factor (> 0.0)

  {thermo} arg = {yes} or {no}

  {tfactor} arg = time scaling factor (> 0.0)

  {units} arg = {yes} or {no}

  {sort} arg = {off} or {id} or N or -N

     off = no sorting of per-atom lines within a snapshot

     id = sort per-atom lines by atom ID
@@ -620,6 +621,21 @@ threshold criterion is met. Otherwise it is not met. 


:line



The {units} keyword only applies to the dump {atom}, {custom}, and

{local} styles (and their COMPRESS package versions {atom/gz},

{custom/gz} and {local/gz}). If set to {yes}, each individual dump

file will contain two extra lines at the very beginning with:



ITEM: UNITS

\<units style\> :pre



This will output the current selected "units"_units.html style

to the dump file and thus allows visualization and post-processing

tools to determine the choice of units of the data in the dump file.

The default setting is {no}.



:line



The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.

If set to {yes}, coordinates will be written "unwrapped" by the image

flags for each atom.  Unwrapped means that if the atom has passed through
@@ -924,6 +940,7 @@ scale = yes 
sort = off for dump styles {atom}, {custom}, {cfg}, and {local}

sort = id for dump styles {dcd}, {xtc}, and {xyz}

thresh = none

units = no

unwrap = no :ul



acolor = * red/green/blue/yellow/aqua/cyan

src/COMPRESS/dump_atom_gz.cpp

+9 −10
Original line number Diff line number Diff line
@@ -108,27 +108,26 @@ void DumpAtomGZ::openfile() 
void DumpAtomGZ::write_header(bigint ndump)

{

  if ((multiproc) || (!multiproc && me == 0)) {

    if (domain->triclinic == 0) {

    if (unit_flag && !unit_count) {

      ++unit_count;

      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);

    }

    gzprintf(gzFp,"ITEM: TIMESTEP\n");

    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);

    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");

    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);

    if (domain->triclinic == 0) {

      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);

      gzprintf(gzFp,"%g %g\n",boxxlo,boxxhi);

      gzprintf(gzFp,"%g %g\n",boxylo,boxyhi);

      gzprintf(gzFp,"%g %g\n",boxzlo,boxzhi);

      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);

    } else {

      gzprintf(gzFp,"ITEM: TIMESTEP\n");

      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);

      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");

      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);

      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);

      gzprintf(gzFp,"%g %g %g\n",boxxlo,boxxhi,boxxy);

      gzprintf(gzFp,"%g %g %g\n",boxylo,boxyhi,boxxz);

      gzprintf(gzFp,"%g %g %g\n",boxzlo,boxzhi,boxyz);

      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);

    }

    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);

  }

}

src/COMPRESS/dump_custom_gz.cpp

+9 −10
Original line number Diff line number Diff line
@@ -108,27 +108,26 @@ void DumpCustomGZ::openfile() 
void DumpCustomGZ::write_header(bigint ndump)

{

  if ((multiproc) || (!multiproc && me == 0)) {

    if (domain->triclinic == 0) {

    if (unit_flag && !unit_count) {

      ++unit_count;

      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);

    }

    gzprintf(gzFp,"ITEM: TIMESTEP\n");

    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);

    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");

    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);

    if (domain->triclinic == 0) {

      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);

      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);

      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);

      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);

      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);

    } else {

      gzprintf(gzFp,"ITEM: TIMESTEP\n");

      gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);

      gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");

      gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);

      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);

      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);

      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);

      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);

      gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);

    }

    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);

  }

}

src/COMPRESS/dump_local_gz.cpp

0 → 100644
+171 −0
Original line number Diff line number Diff line 
/* ----------------------------------------------------------------------

   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.

------------------------------------------------------------------------- */



#include "dump_local_gz.h"

#include "domain.h"

#include "error.h"

#include "update.h"



#include <cstring>



using namespace LAMMPS_NS;



DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :

  DumpLocal(lmp, narg, arg)

{

  gzFp = NULL;



  if (!compressed)

    error->all(FLERR,"Dump local/gz only writes compressed files");

}





/* ---------------------------------------------------------------------- */



DumpLocalGZ::~DumpLocalGZ()

{

  if (gzFp) gzclose(gzFp);

  gzFp = NULL;

  fp = NULL;

}





/* ----------------------------------------------------------------------

   generic opening of a dump file

   ASCII or binary or gzipped

   some derived classes override this function

------------------------------------------------------------------------- */



void DumpLocalGZ::openfile()

{

  // single file, already opened, so just return



  if (singlefile_opened) return;

  if (multifile == 0) singlefile_opened = 1;



  // if one file per timestep, replace '*' with current timestep



  char *filecurrent = filename;

  if (multiproc) filecurrent = multiname;



  if (multifile) {

    char *filestar = filecurrent;

    filecurrent = new char[strlen(filestar) + 16];

    char *ptr = strchr(filestar,'*');

    *ptr = '\0';

    if (padflag == 0)

      sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",

              filestar,update->ntimestep,ptr+1);

    else {

      char bif[8],pad[16];

      strcpy(bif,BIGINT_FORMAT);

      sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]);

      sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);

    }

    *ptr = '*';

    if (maxfiles > 0) {

      if (numfiles < maxfiles) {

        nameslist[numfiles] = new char[strlen(filecurrent)+1];

        strcpy(nameslist[numfiles],filecurrent);

        ++numfiles;

      } else {

        remove(nameslist[fileidx]);

        delete[] nameslist[fileidx];

        nameslist[fileidx] = new char[strlen(filecurrent)+1];

        strcpy(nameslist[fileidx],filecurrent);

        fileidx = (fileidx + 1) % maxfiles;

      }

    }

  }



  // each proc with filewriter = 1 opens a file



  if (filewriter) {

    if (append_flag) {

      gzFp = gzopen(filecurrent,"ab9");

    } else {

      gzFp = gzopen(filecurrent,"wb9");

    }



    if (gzFp == NULL) error->one(FLERR,"Cannot open dump file");

  } else gzFp = NULL;



  // delete string with timestep replaced



  if (multifile) delete [] filecurrent;

}



void DumpLocalGZ::write_header(bigint ndump)

{

  if ((multiproc) || (!multiproc && me == 0)) {

    if (unit_flag && !unit_count) {

      ++unit_count;

      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);

    }

    gzprintf(gzFp,"ITEM: TIMESTEP\n");

    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);

    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");

    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);

    if (domain->triclinic == 0) {

      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);

      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxxlo,boxxhi);

      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxylo,boxyhi);

      gzprintf(gzFp,"%-1.16g %-1.16g\n",boxzlo,boxzhi);

    } else {

      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);

      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxxlo,boxxhi,boxxy);

      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxylo,boxyhi,boxxz);

      gzprintf(gzFp,"%-1.16g %-1.16g %-1.16g\n",boxzlo,boxzhi,boxyz);

    }

    gzprintf(gzFp,"ITEM: %s %s\n",label,columns);

  }

}



/* ---------------------------------------------------------------------- */



void DumpLocalGZ::write_data(int n, double *mybuf)

{

  if (buffer_flag == 1) {

    gzwrite(gzFp,mybuf,sizeof(char)*n);



  } else {

    int i,j;

    int m = 0;

    for (i = 0; i < n; i++) {

      for (j = 0; j < size_one; j++) {

        if (vtype[j] == INT)

          gzprintf(gzFp,vformat[j],static_cast<int> (mybuf[m]));

        else gzprintf(gzFp,vformat[j],mybuf[m]);

        m++;

      }

      gzprintf(gzFp,"\n");

    }

  }

}



/* ---------------------------------------------------------------------- */



void DumpLocalGZ::write()

{

  DumpLocal::write();

  if (filewriter) {

    if (multifile) {

      gzclose(gzFp);

      gzFp = NULL;

    } else {

      if (flush_flag)

        gzflush(gzFp,Z_SYNC_FLUSH);

    }

  }

}

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