Merge pull request #4193 from akohlmey/extra-command-package

Create new EXTRA-COMMAND package

cmake/CMakeLists.txt

@@ -256,6 +256,7 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX

cmake/presets/all_off.cmake

@@ -28,6 +28,7 @@ set(ALL_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX

cmake/presets/all_on.cmake

@@ -30,6 +30,7 @@ set(ALL_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX

cmake/presets/mingw-cross.cmake

@@ -24,6 +24,7 @@ set(WIN_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX

cmake/presets/most.cmake

@@ -26,6 +26,7 @@ set(ALL_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX

cmake/presets/windows.cmake

@@ -22,6 +22,7 @@ set(WIN_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX

doc/src/Packages_details.rst

@@ -52,6 +52,7 @@ page gives those details.
    * :ref:`DRUDE <PKG-DRUDE>`
    * :ref:`EFF <PKG-EFF>`
    * :ref:`ELECTRODE <PKG-ELECTRODE>`
+   * :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
    * :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
    * :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
    * :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
@@ -893,6 +894,22 @@ This package has :ref:`specific installation instructions <electrode>` on the
 
 ----------
 
+.. _PKG-EXTRA-COMMAND:
+
+EXTRA-COMMAND package
+---------------------
+
+**Contents:**
+
+Additional command styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-COMMAND: filenames -> commands
+* :doc:`general commands <Commands_all>`
+
+----------
+
 .. _PKG-EXTRA-COMPUTE:
 
 EXTRA-COMPUTE package

doc/src/Packages_list.rst

@@ -158,6 +158,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`fix electrode/conp <fix_electrode>`
      - PACKAGES/electrode
      - no
+   * - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
+     - additional command styles
+     - :doc:`general commands <Commands_all>`
+     - n/a
+     - no
    * - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
      - additional compute styles
      - :doc:`compute <compute>`

doc/src/group2ndx.rst

@@ -34,32 +34,66 @@ Description
 Write or read a Gromacs style index file in text format that associates
 atom IDs with the corresponding group definitions. This index file can be
 used with in combination with Gromacs analysis tools or to import group
-definitions into the :doc:`fix colvars <fix_colvars>` input file. It can
+definitions into the :doc:`fix colvars <fix_colvars>` input file.
-also be used to save and restore group definitions for static groups.
+
+It can also be used to save and restore group definitions for static groups
+using the individual atom IDs. This may be important if the original
+group definition depends on a region or otherwise on the geometry and thus
+cannot be easily recreated.
+
+Another application would be to import atom groups defined for Gromacs
+simulation into LAMMPS.  When translating Gromacs topology and geometry
+data to LAMMPS.
 
 The *group2ndx* command will write group definitions to an index file.
-Without specifying any group IDs, all groups will be written to the index
+Without specifying any group IDs, all groups will be written to the
-file. When specifying group IDs, only those groups will be written to the
+index file.  When specifying group IDs, only those groups will be
-index file. In order to follow the Gromacs conventions, the group *all*
+written to the index file.  In order to follow the Gromacs conventions,
-will be renamed to *System* in the index file.
+the group *all* will be renamed to *System* in the index file.
 
-The *ndx2group* command will create of update group definitions from those
+The *ndx2group* command will create of update group definitions from
-stored in an index file. Without specifying any group IDs, all groups except
+those stored in an index file.  Without specifying any group IDs, all
-*System* will be read from the index file and the corresponding groups
+groups except *System* will be read from the index file and the
-recreated. If a group of the same name already exists, it will be completely
+corresponding groups recreated.  If a group of the same name already
-reset. When specifying group IDs, those groups, if present, will be read
+exists, it will be completely reset.  When specifying group IDs, those
-from the index file and restored.
+groups, if present, will be read from the index file and restored.
+
+File Format
+"""""""""""
+
+The file format is equivalent and compatible with what is produced by
+the `Gromacs make_ndx command <https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_.
+and follows the `Gromacs definition of an ndx file <https://manual.gromacs.org/current/reference-manual/file-formats.html#ndx>`_
+
+Each group definition begins with the group name in square brackets with
+blanks, e.g. \[ water \] and is then followed by the list of atom
+indices, which may be spread over multiple lines.  Here is a small
+example file:
+
+.. code-block:: ini
+
+   [ Oxygen ]
+   1  4  7
+   [ Hydrogen ]
+   2  3  5  6
+   8  9
+   [ Water ]
+   1 2 3 4 5 6 7 8 9
+
+The index file defines 3 groups: Oxygen, Hydrogen, and Water and the
+latter happens to be the union of the first two.
 
 ----------
 
 Restrictions
 """"""""""""
 
-This command requires that atoms have atom IDs, since this is the
+These commands require that atoms have atom IDs, since this is the
 information that is written to the index file.
 
-These commands are part of the COLVARS package.  They are only
+These commands are part of the EXTRA-COMMAND package.  They are only
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+enabled if LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

src/COLVARS/ndx_group.cpp

@@ -1,199 +0,0 @@
-// clang-format off
-// -*- c++ -*-
-
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
-
-   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:  Axel Kohlmeyer (Temple U)
-------------------------------------------------------------------------- */
-
-#include "ndx_group.h"
-
-#include "atom.h"
-#include "comm.h"
-#include "error.h"
-#include "group.h"
-#include "tokenizer.h"
-
-using namespace LAMMPS_NS;
-static constexpr int BUFLEN = 4096;
-
-// read file until next section "name" or any next section if name == ""
-
-static std::string find_section(FILE *fp, const std::string &name)
-{
-  char linebuf[BUFLEN];
-
-  std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$";
-  if (!name.empty())
-    pattern = fmt::format("^\\s*\\[\\s+{}\\s+\\]\\s*$",name);
-
-  fgets(linebuf,BUFLEN,fp);
-  while (!feof(fp)) {
-    if (utils::strmatch(linebuf,pattern))
-      return Tokenizer(linebuf).as_vector()[1];
-    fgets(linebuf,BUFLEN,fp);
-  }
-  return "";
-}
-
-static std::vector<tagint> read_section(FILE *fp, std::string &name)
-{
-  char linebuf[BUFLEN];
-  std::vector<tagint> tagbuf;
-  std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$";
-
-  while (fgets(linebuf,BUFLEN,fp)) {
-    // start of new section. we are done, update "name"
-    if (utils::strmatch(linebuf,pattern)) {
-      name = Tokenizer(linebuf).as_vector()[1];
-      return tagbuf;
-    }
-    ValueTokenizer values(linebuf);
-    while (values.has_next())
-      tagbuf.push_back(values.next_tagint());
-  }
-  // set empty name to indicate end of file
-  name = "";
-  return tagbuf;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Ndx2Group::command(int narg, char **arg)
-{
-  int len;
-  bigint num;
-  FILE *fp;
-  std::string name, next;
-
-  if (narg < 1) error->all(FLERR,"Illegal ndx2group command");
-  if (atom->tag_enable == 0)
-    error->all(FLERR,"Must have atom IDs for ndx2group command");
-  if (atom->map_style == Atom::MAP_NONE)
-    error->all(FLERR,"Must have an atom map for ndx2group command");
-  if (comm->me == 0) {
-    fp = fopen(arg[0], "r");
-    if (fp == nullptr)
-      error->one(FLERR,"Cannot open index file for reading: {}",
-                                   utils::getsyserror());
-    utils::logmesg(lmp,"Reading groups from index file {}:\n",arg[0]);
-  }
-
-  if (narg == 1) {              // restore all groups
-
-    if (comm->me == 0) {
-      name = find_section(fp,"");
-      while (!name.empty()) {
-
-        // skip over group "all", which is called "System" in gromacs
-        if (name == "System") {
-          name = find_section(fp,"");
-          continue;
-        }
-
-        utils::logmesg(lmp," Processing group '{}'\n",name);
-        len = name.size()+1;
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len > 1) {
-          MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
-
-          // read tags for atoms in group and broadcast
-          std::vector<tagint> tags = read_section(fp,next);
-          num = tags.size();
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
-          create(name,tags);
-          name = next;
-        }
-      }
-      len = -1;
-      MPI_Bcast(&len,1,MPI_INT,0,world);
-
-    } else {
-
-      while (true) {
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len < 0) break;
-        if (len > 1) {
-          char *buf = new char[len];
-          MPI_Bcast(buf,len,MPI_CHAR,0,world);
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          tagint *tbuf = new tagint[num];
-          MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world);
-          create(buf,std::vector<tagint>(tbuf,tbuf+num));
-          delete[] buf;
-          delete[] tbuf;
-        }
-      }
-    }
-
-  } else {            // restore selected groups
-
-    for (int idx=1; idx < narg; ++idx) {
-      if (comm->me == 0) {
-
-        // find named section, search from beginning of file
-        rewind(fp);
-        name = find_section(fp,arg[idx]);
-        utils::logmesg(lmp," {} group '{}'\n", name.size()
-                       ? "Processing" : "Skipping",arg[idx]);
-        len = name.size()+1;
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len > 1) {
-          MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
-
-          // read tags for atoms in group and broadcast
-          std::vector<tagint> tags = read_section(fp,next);
-          num = tags.size();
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
-          create(name,tags);
-          name = next;
-        }
-      } else {
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len > 1) {
-          char *buf = new char[len];
-          MPI_Bcast(buf,len,MPI_CHAR,0,world);
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          tagint *tbuf = new tagint[num];
-          MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world);
-          create(buf,std::vector<tagint>(tbuf,tbuf+num));
-          delete[] buf;
-          delete[] tbuf;
-        }
-      }
-    }
-  }
-  if (comm->me == 0) fclose(fp);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Ndx2Group::create(const std::string &name, const std::vector<tagint> &tags)
-{
-  // wipe out all members if the group exists. gid==0 is group "all"
-  int gid = group->find(name);
-  if (gid > 0) group->assign(name + " clear");
-
-  // map from global to local
-  const int nlocal = atom->nlocal;
-  int *flags = (int *)calloc(nlocal,sizeof(int));
-  for (bigint i=0; i < (int)tags.size(); ++i) {
-    const int id = atom->map(tags[i]);
-    if (id < nlocal && id >= 0) flags[id] = 1;
-  }
-  group->create(name,flags);
-  free(flags);
-}

src/EXTRA-COMMAND/group_ndx.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 // -*- c++ -*-
 
 /* ----------------------------------------------------------------------
@@ -34,12 +33,15 @@ using namespace LAMMPS_NS;
 
 static int cmptagint(const void *p1, const void *p2)
 {
-  const tagint i1 = * static_cast<const tagint *>(p1);
+  const tagint i1 = *static_cast<const tagint *>(p1);
-  const tagint i2 = * static_cast<const tagint *>(p2);
+  const tagint i2 = *static_cast<const tagint *>(p2);
-  if (i1 == i2) return 0;
+  if (i1 == i2)
+    return 0;
   else {
-    if (i1 < i2) return -1;
+    if (i1 < i2)
-    else return 1;
+      return -1;
+    else
+      return 1;
   }
 }
 
@@ -49,27 +51,24 @@ void Group2Ndx::command(int narg, char **arg)
 {
   FILE *fp = nullptr;
 
-  if (narg < 1) error->all(FLERR,"Illegal group2ndx command");
+  if (narg < 1) utils::missing_cmd_args(FLERR, "group2ndx", error);
 
-  if (atom->tag_enable == 0)
+  if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for group2ndx command");
-      error->all(FLERR,"Must have atom IDs for group2ndx command");
 
   if (comm->me == 0) {
     fp = fopen(arg[0], "w");
     if (fp == nullptr)
-      error->one(FLERR,"Cannot open index file for writing: {}", utils::getsyserror());
+      error->one(FLERR, "Cannot open index file for writing: {}", utils::getsyserror());
-    utils::logmesg(lmp,"Writing groups to index file {}:\n",arg[0]);
+    utils::logmesg(lmp, "Writing groups to index file {}:\n", arg[0]);
   }
 
   if (narg == 1) {    // write out all groups
-    for (int i=0; i < group->ngroup; ++i) {
+    for (int i = 0; i < group->ngroup; ++i) { write_group(fp, i); }
-      write_group(fp,i);
-    }
   } else {    // write only selected groups
-    for (int i=1; i < narg; ++i) {
+    for (int i = 1; i < narg; ++i) {
       int gid = group->find(arg[i]);
       if (gid < 0) error->all(FLERR, "Non-existing group requested");
-      write_group(fp,gid);
+      write_group(fp, gid);
     }
   }
 
@@ -85,22 +84,26 @@ void Group2Ndx::write_group(FILE *fp, int gid)
   bigint gcount = group->count(gid);
   int lnum, width, cols;
 
+  if (utils::strmatch(group->names[gid], "\\s+")) {
+    if (fp) utils::logmesg(lmp, " skipping group {}...done", group->names[gid]);
+    return;
+  }
   if (fp) {
-    utils::logmesg(lmp," writing group {}...",group->names[gid]);
+    utils::logmesg(lmp, " writing group {}...", group->names[gid]);
 
     // the "all" group in LAMMPS is called "System" in Gromacs
     if (gid == 0) {
       fputs("[ System ]\n", fp);
     } else {
-      fmt::print(fp,"[ {} ]\n", group->names[gid]);
+      fmt::print(fp, "[ {} ]\n", group->names[gid]);
     }
-    width = log10((double) atom->natoms)+2;
+    width = log10((double) atom->natoms) + 2;
     cols = 80 / width;
   }
 
   if (gcount > 0) {
-    const int * const mask = atom->mask;
+    const int *const mask = atom->mask;
-    const tagint * const tag = atom->tag;
+    const tagint *const tag = atom->tag;
     const int groupbit = group->bitmask[gid];
     const int nlocal = atom->nlocal;
     int i;
@@ -111,45 +114,45 @@ void Group2Ndx::write_group(FILE *fp, int gid)
     for (i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) sendlist[lnum++] = tag[i];
 
-    int nrecv=0;
+    int nrecv = 0;
     bigint allrecv;
     if (comm->me == 0) {
       MPI_Status status;
       MPI_Request request;
 
-      for (i=0; i < lnum; i++)
+      for (i = 0; i < lnum; i++) recvlist[i] = sendlist[i];
-        recvlist[i] = sendlist[i];
 
       allrecv = lnum;
-      for (i=1; i < comm->nprocs; ++i) {
+      for (i = 1; i < comm->nprocs; ++i) {
-        MPI_Irecv(recvlist+allrecv,gcount-allrecv,MPI_LMP_TAGINT,i,0, world,&request);
+        MPI_Irecv(recvlist + allrecv, gcount - allrecv, MPI_LMP_TAGINT, i, 0, world, &request);
-        MPI_Send(&nrecv,0,MPI_INT,i,0,world); // block rank "i" until we are ready to receive
+        // block rank "i" until we are ready to receive
-        MPI_Wait(&request,&status);
+        MPI_Send(&nrecv, 0, MPI_INT, i, 0, world);
-        MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv);
+        MPI_Wait(&request, &status);
+        MPI_Get_count(&status, MPI_LMP_TAGINT, &nrecv);
         allrecv += nrecv;
       }
 
       // sort received list
-      qsort((void *)recvlist, allrecv, sizeof(tagint), cmptagint);
+      qsort((void *) recvlist, allrecv, sizeof(tagint), cmptagint);
     } else {
-      MPI_Recv(&nrecv,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
+      MPI_Recv(&nrecv, 0, MPI_INT, 0, 0, world, MPI_STATUS_IGNORE);
-      MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world);
+      MPI_Rsend(sendlist, lnum, MPI_LMP_TAGINT, 0, 0, world);
     }
-    delete [] sendlist;
+    delete[] sendlist;
   }
 
   if (fp) {
     int i, j;
-    for (i=0, j=0; i < gcount; ++i) {
+    for (i = 0, j = 0; i < gcount; ++i) {
-      fmt::print(fp,"{:>{}}",recvlist[i],width);
+      fmt::print(fp, "{:>{}}", recvlist[i], width);
       ++j;
       if (j == cols) {
-        fputs("\n",fp);
+        fputs("\n", fp);
         j = 0;
       }
     }
-    if (j > 0) fputs("\n",fp);
+    if (j > 0) fputs("\n", fp);
-    utils::logmesg(lmp,"done\n");
+    utils::logmesg(lmp, "done\n");
   }
   if (gcount > 0) delete[] recvlist;
 }

src/EXTRA-COMMAND/ndx_group.cpp

@@ -0,0 +1,220 @@
+// -*- c++ -*-
+
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   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:  Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#include "ndx_group.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "group.h"
+#include "tokenizer.h"
+
+using namespace LAMMPS_NS;
+static constexpr int BUFLEN = 4096;
+
+// read file until next section "name" or any next section if name == ""
+
+static std::string find_section(FILE *fp, const std::string &name)
+{
+  char linebuf[BUFLEN];
+
+  fgets(linebuf, BUFLEN, fp);
+  while (!feof(fp)) {
+    if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
+      auto words = Tokenizer(linebuf).as_vector();
+      if (words.size() != 3)
+        throw TokenizerException("Invalid group name in index file",
+                                 utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+")));
+      if (name.empty() || (name == words[1])) return words[1];
+    }
+    fgets(linebuf, BUFLEN, fp);
+  }
+  return "";
+}
+
+static std::vector<tagint> read_section(FILE *fp, std::string &name)
+{
+  char linebuf[BUFLEN];
+  std::vector<tagint> tagbuf;
+
+  while (fgets(linebuf, BUFLEN, fp)) {
+    // start of new section. we are done, update "name"
+    if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
+      auto words = Tokenizer(linebuf).as_vector();
+      if (words.size() != 3)
+        throw TokenizerException("Invalid group name in index file",
+                                 utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+")));
+      name = words[1];
+      return tagbuf;
+    }
+    ValueTokenizer values(linebuf);
+    while (values.has_next()) tagbuf.push_back(values.next_tagint());
+  }
+  // set empty name to indicate end of file
+  name = "";
+  return tagbuf;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Ndx2Group::command(int narg, char **arg)
+{
+  int len;
+  bigint num;
+  FILE *fp;
+  std::string name, next;
+
+  if (narg < 1) utils::missing_cmd_args(FLERR, "ndx2group", error);
+  if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for ndx2group command");
+  if (atom->map_style == Atom::MAP_NONE)
+    error->all(FLERR, "Must have an atom map for ndx2group command");
+  if (comm->me == 0) {
+    fp = fopen(arg[0], "r");
+    if (fp == nullptr)
+      error->one(FLERR, "Cannot open index file for reading: {}", utils::getsyserror());
+    utils::logmesg(lmp, "Reading groups from index file {}:\n", arg[0]);
+  }
+
+  if (narg == 1) {    // restore all groups
+
+    if (comm->me == 0) {
+      try {
+        name = find_section(fp, "");
+      } catch (std::exception &e) {
+        error->one(FLERR, e.what());
+      }
+
+      while (!name.empty()) {
+        // skip over group "all", which is called "System" in gromacs
+        if (name == "System") {
+          try {
+            name = find_section(fp, "");
+          } catch (std::exception &e) {
+            error->one(FLERR, e.what());
+          }
+          continue;
+        }
+
+        utils::logmesg(lmp, " Processing group '{}'\n", name);
+        len = name.size() + 1;
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len > 1) {
+          MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world);
+
+          // read tags for atoms in group and broadcast
+          std::vector<tagint> tags;
+          try {
+            tags = read_section(fp, next);
+          } catch (std::exception &e) {
+            error->one(FLERR, e.what());
+          }
+          num = tags.size();
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world);
+          create(name, tags);
+          name = next;
+        }
+      }
+      len = -1;
+      MPI_Bcast(&len, 1, MPI_INT, 0, world);
+
+    } else {
+
+      while (true) {
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len < 0) break;
+        if (len > 1) {
+          char *buf = new char[len];
+          MPI_Bcast(buf, len, MPI_CHAR, 0, world);
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          tagint *tbuf = new tagint[num];
+          MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world);
+          create(buf, std::vector<tagint>(tbuf, tbuf + num));
+          delete[] buf;
+          delete[] tbuf;
+        }
+      }
+    }
+
+  } else {    // restore selected groups
+
+    for (int idx = 1; idx < narg; ++idx) {
+      if (comm->me == 0) {
+
+        // find named section, search from beginning of file
+        rewind(fp);
+        try {
+          name = find_section(fp, arg[idx]);
+        } catch (std::exception &e) {
+          error->one(FLERR, e.what());
+        }
+        utils::logmesg(lmp, " {} group '{}'\n", name.size() ? "Processing" : "Skipping", arg[idx]);
+        len = name.size() + 1;
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len > 1) {
+          MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world);
+
+          // read tags for atoms in group and broadcast
+          std::vector<tagint> tags;
+          try {
+            tags = read_section(fp, next);
+          } catch (std::exception &e) {
+            error->one(FLERR, e.what());
+          }
+          num = tags.size();
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world);
+          create(name, tags);
+          name = next;
+        }
+      } else {
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len > 1) {
+          char *buf = new char[len];
+          MPI_Bcast(buf, len, MPI_CHAR, 0, world);
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          tagint *tbuf = new tagint[num];
+          MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world);
+          create(buf, std::vector<tagint>(tbuf, tbuf + num));
+          delete[] buf;
+          delete[] tbuf;
+        }
+      }
+    }
+  }
+  if (comm->me == 0) fclose(fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Ndx2Group::create(const std::string &name, const std::vector<tagint> &tags)
+{
+  // wipe out all members if the group exists. gid==0 is group "all"
+  int gid = group->find(name);
+  if (gid > 0) group->assign(name + " clear");
+
+  // map from global to local
+  const int nlocal = atom->nlocal;
+  int *flags = (int *) calloc(nlocal, sizeof(int));
+  for (bigint i = 0; i < (int) tags.size(); ++i) {
+    const int id = atom->map(tags[i]);
+    if (id < nlocal && id >= 0) flags[id] = 1;
+  }
+  group->create(name, flags);
+  free(flags);
+}

src/Makefile

@@ -74,6 +74,7 @@ PACKAGE = \
 	dpd-smooth \
 	drude \
 	eff \
+	extra-command \
 	extra-compute \
 	extra-dump \
 	extra-fix \
@@ -168,6 +169,7 @@ PACKMOST = \
 	dpd-smooth \
 	drude \
 	eff \
+	extra-command \
 	extra-compute \
 	extra-dump \
 	extra-fix \