Introduce ComputeChunk class with shared functionality of all /chunk computes

src/EXTRA-COMPUTE/compute_dipole_tip4p_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -22,11 +21,9 @@
 #include "domain.h"
 #include "error.h"
 #include "force.h"
-#include "pair.h"
 #include "math_special.h"
 #include "memory.h"
-#include "modify.h"
+#include "pair.h"
-#include "update.h"
 
 #include <cmath>
 #include <cstring>
@@ -39,13 +36,10 @@ enum { MASSCENTER, GEOMCENTER };
 /* ---------------------------------------------------------------------- */
 
 ComputeDipoleTIP4PChunk::ComputeDipoleTIP4PChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), chrgproc(nullptr),
-  idchunk(nullptr), massproc(nullptr), masstotal(nullptr), chrgproc(nullptr),
+    chrgtotal(nullptr), com(nullptr), comall(nullptr), dipole(nullptr), dipoleall(nullptr)
-  chrgtotal(nullptr), com(nullptr),
-  comall(nullptr), dipole(nullptr), dipoleall(nullptr)
 {
-  if ((narg != 4) && (narg != 5))
+  if ((narg != 4) && (narg != 5)) error->all(FLERR, "Illegal compute dipole/tip4p/chunk command");
-    error->all(FLERR,"Illegal compute dipole/tip4p/chunk command");
 
   array_flag = 1;
   size_array_cols = 4;
@@ -53,32 +47,25 @@ ComputeDipoleTIP4PChunk::ComputeDipoleTIP4PChunk(LAMMPS *lmp, int narg, char **a
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   usecenter = MASSCENTER;
 
   if (narg == 5) {
-    if (strncmp(arg[4],"geom",4) == 0) usecenter = GEOMCENTER;
+    if (strncmp(arg[4], "geom", 4) == 0)
-    else if (strcmp(arg[4],"mass") == 0) usecenter = MASSCENTER;
+      usecenter = GEOMCENTER;
-    else error->all(FLERR,"Illegal compute dipole/tip4p/chunk command");
+    else if (strcmp(arg[4], "mass") == 0)
+      usecenter = MASSCENTER;
+    else
+      error->all(FLERR, "Illegal compute dipole/tip4p/chunk command");
   }
 
   ComputeDipoleTIP4PChunk::init();
-
+  ComputeDipoleTIP4PChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeDipoleTIP4PChunk::~ComputeDipoleTIP4PChunk()
 {
-  delete[] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(chrgproc);
@@ -93,14 +80,10 @@ ComputeDipoleTIP4PChunk::~ComputeDipoleTIP4PChunk()
 
 void ComputeDipoleTIP4PChunk::init()
 {
-  int icompute = modify->find_compute(idchunk);
+  ComputeChunk::init();
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for compute dipole/tip4p/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute dipole/tip4p/chunk does not use chunk/atom compute");
 
-  if (!force->pair) error->all(FLERR, "Pair style must be defined for compute dipole/tip4p/chunk");
+  if (!force->pair)
+    error->all(FLERR, "A pair style must be defined for compute dipole/tip4p/chunk");
 
   int itmp;
   double *p_qdist = (double *) force->pair->extract("qdist", itmp);
@@ -134,19 +117,9 @@ void ComputeDipoleTIP4PChunk::compute_array()
   double massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
-
   // zero local per-chunk values
 
   for (i = 0; i < nchunk; i++) {
@@ -175,9 +148,12 @@ void ComputeDipoleTIP4PChunk::compute_array()
       index = ichunk[i] - 1;
       if (index < 0) continue;
       if (usecenter == MASSCENTER) {
-        if (rmass) massone = rmass[i];
+        if (rmass)
-        else massone = mass[type[i]];
+          massone = rmass[i];
-      } else massone = 1.0;     // usecenter == GEOMCENTER
+        else
+          massone = mass[type[i]];
+      } else
+        massone = 1.0;    // usecenter == GEOMCENTER
       domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       if (atom->q_flag) chrgproc[index] += q[i];
@@ -233,74 +209,18 @@ void ComputeDipoleTIP4PChunk::compute_array()
     dipoleall[i][1] -= chrgtotal[i] * comall[i][1];
     dipoleall[i][2] -= chrgtotal[i] * comall[i][2];
     // compute total dipole moment
-    dipoleall[i][3] = sqrt(square(dipoleall[i][0])
+    dipoleall[i][3] =
-                           + square(dipoleall[i][1])
+        sqrt(square(dipoleall[i][0]) + square(dipoleall[i][1]) + square(dipoleall[i][2]));
-                           + square(dipoleall[i][2]));
   }
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeDipoleTIP4PChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeDipoleTIP4PChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeDipoleTIP4PChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeDipoleTIP4PChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeDipoleTIP4PChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeDipoleTIP4PChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(chrgproc);
@@ -327,7 +247,7 @@ void ComputeDipoleTIP4PChunk::allocate()
 
 double ComputeDipoleTIP4PChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = (double) maxchunk * 2 * sizeof(double) + ComputeChunk::memory_usage();
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   bytes += (double) maxchunk * 2 * 4 * sizeof(double);
   return bytes;

src/EXTRA-COMPUTE/compute_dipole_tip4p_chunk.h

@@ -20,31 +20,21 @@ ComputeStyle(dipole/tip4p/chunk,ComputeDipoleTIP4PChunk);
 #ifndef LMP_COMPUTE_DIPOLE_TIP4P_CHUNK_H
 #define LMP_COMPUTE_DIPOLE_TIP4P_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 class Fix;
 
-class ComputeDipoleTIP4PChunk : public Compute {
+class ComputeDipoleTIP4PChunk : public ComputeChunk {
  public:
   ComputeDipoleTIP4PChunk(class LAMMPS *, int, char **);
   ~ComputeDipoleTIP4PChunk() override;
   void init() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(Fix *, bigint, bigint) override;
-  void unlock(Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc, *masstotal;
   double *chrgproc, *chrgtotal;
   double **com, **comall;
@@ -55,10 +45,8 @@ class ComputeDipoleTIP4PChunk : public Compute {
   double alpha;
   void find_M(int i, double *xM);
 
-  void allocate();
+  void allocate() override;
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -67,22 +66,22 @@ ComputeGyrationShapeChunk::~ComputeGyrationShapeChunk()
 void ComputeGyrationShapeChunk::init()
 {
   // check that the compute gyration command exist
-  int icompute = modify->find_compute(id_gyration_chunk);
+
-  if (icompute < 0)
+  c_gyration_chunk = modify->get_compute_by_id(id_gyration_chunk);
-    error->all(FLERR,"Compute gyration/chunk ID does not exist for "
+  if (!c_gyration_chunk)
-               "compute gyration/shape/chunk");
+    error->all(FLERR,
+               "Compute gyration/chunk ID {} does not exist for compute gyration/shape/chunk",
+               id_gyration_chunk);
 
   // check the id_gyration_chunk corresponds really to a compute gyration/chunk command
-  c_gyration_chunk = (Compute *) modify->compute[icompute];
+
   if (strcmp(c_gyration_chunk->style, "gyration/chunk") != 0)
-    error->all(FLERR,"Compute gyration/shape/chunk does not point to "
+    error->all(FLERR, "Compute {} is not of style gyration/chunk", id_gyration_chunk);
-               "gyration compute/chunk");
 
   // check the compute gyration/chunk command computes the whole gyration tensor
   if (c_gyration_chunk->array_flag == 0)
-    error->all(FLERR,"Compute gyration/chunk where gyration/shape/chunk points to "
+    error->all(FLERR, "Compute gyration/chunk {} does not calculate the gyration tensor",
-               "does not calculate the gyration tensor");
+               id_gyration_chunk);
-
 }
 
 /* ---------------------------------------------------------------------- */
@@ -108,7 +107,7 @@ void ComputeGyrationShapeChunk::compute_array()
   invoked_array = update->ntimestep;
   c_gyration_chunk->compute_array();
 
-  current_nchunks = c_gyration_chunk->size_array_rows; // how to check for the number of chunks in the gyration/chunk?
+  current_nchunks = c_gyration_chunk->size_array_rows;
   if (former_nchunks != current_nchunks) allocate();
 
   double **gyration_tensor = c_gyration_chunk->array;
@@ -126,7 +125,9 @@ void ComputeGyrationShapeChunk::compute_array()
     ione[1][2] = ione[2][1] = gyration_tensor[ichunk][5];
 
     int ierror = MathEigen::jacobi3(ione, evalues, evectors);
-    if (ierror) error->all(FLERR, "Insufficient Jacobi rotations "
+    if (ierror)
+      error->all(FLERR,
+                 "Insufficient Jacobi rotations "
                  "for gyration/shape");
 
     // sort the eigenvalues according to their size with bubble sort

src/compute_angmom_chunk.cpp

@@ -18,17 +18,13 @@
 #include "domain.h"
 #include "error.h"
 #include "memory.h"
-#include "modify.h"
-#include "update.h"
-
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) :
-    Compute(lmp, narg, arg), idchunk(nullptr), massproc(nullptr), masstotal(nullptr), com(nullptr),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), com(nullptr),
     comall(nullptr), angmom(nullptr), angmomall(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute angmom/chunk command");
@@ -39,24 +35,14 @@ ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   ComputeAngmomChunk::init();
-
+  ComputeAngmomChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeAngmomChunk::~ComputeAngmomChunk()
 {
-  delete[] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -67,35 +53,15 @@ ComputeAngmomChunk::~ComputeAngmomChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeAngmomChunk::init()
-{
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->get_compute_by_id(idchunk));
-  if (!cchunk) error->all(FLERR, "Chunk/atom compute does not exist for compute angmom/chunk");
-  if (strcmp(cchunk->style, "chunk/atom") != 0)
-    error->all(FLERR, "Compute angmom/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeAngmomChunk::compute_array()
 {
+  ComputeChunk::compute_array();
+
   int i, index;
   double dx, dy, dz, massone;
   double unwrap[3];
-
-  invoked_array = update->ntimestep;
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
-
   // zero local per-chunk values
 
   for (i = 0; i < nchunk; i++) {
@@ -164,59 +130,6 @@ void ComputeAngmomChunk::compute_array()
   MPI_Allreduce(&angmom[0][0], &angmomall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeAngmomChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeAngmomChunk::lock_disable()
-{
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->get_compute_by_id(idchunk));
-  if (cchunk) cchunk->lockcount--;
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeAngmomChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeAngmomChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr, startstep, stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeAngmomChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
@@ -245,7 +158,8 @@ void ComputeAngmomChunk::allocate()
 
 double ComputeAngmomChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   return bytes;

src/compute_angmom_chunk.h

@@ -20,39 +20,25 @@ ComputeStyle(angmom/chunk,ComputeAngmomChunk);
 #ifndef LMP_COMPUTE_ANGMOM_CHUNK_H
 #define LMP_COMPUTE_ANGMOM_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
-  class Fix;
 
-class ComputeAngmomChunk : public Compute {
+class ComputeAngmomChunk : public ComputeChunk {
  public:
   ComputeAngmomChunk(class LAMMPS *, int, char **);
   ~ComputeAngmomChunk() override;
-  void init() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(Fix *, bigint, bigint) override;
-  void unlock(Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc, *masstotal;
   double **com, **comall;
   double **angmom, **angmomall;
 
-  void allocate();
+  void allocate() override;
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

src/compute_chunk.cpp

@@ -0,0 +1,156 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#include "compute_chunk.h"
+
+#include "compute_chunk_atom.h"
+#include "error.h"
+#include "modify.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+/* ---------------------------------------------------------------------- */
+
+ComputeChunk::ComputeChunk(LAMMPS *lmp, int narg, char **arg) :
+    Compute(lmp, narg, arg), idchunk(nullptr), cchunk(nullptr)
+{
+  if (narg < 4) utils::missing_cmd_args(FLERR, std::string("compute ") + style, error);
+
+  // ID of compute chunk/atom
+
+  idchunk = utils::strdup(arg[3]);
+
+  ComputeChunk::init();
+
+  // chunk-based data
+
+  nchunk = 1;
+  maxchunk = 0;
+  firstflag = 1;
+  massneed = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeChunk::~ComputeChunk()
+{
+  delete[] idchunk;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeChunk::init()
+{
+  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->get_compute_by_id(idchunk));
+  if (!cchunk)
+    error->all(FLERR, "Chunk/atom compute {} does not exist or is incorrect style for compute {}",
+               idchunk, style);
+}
+
+/* ----------------------------------------------------------------------
+   common code used by all /chunk computes
+------------------------------------------------------------------------- */
+
+void ComputeChunk::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  // compute chunk/atom assigns atoms to chunk IDs
+  // extract ichunk index vector from compute
+  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
+
+  nchunk = cchunk->setup_chunks();
+  cchunk->compute_ichunk();
+
+  if (nchunk > maxchunk) allocate();
+  size_vector = nchunk;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeChunk::compute_array()
+{
+  invoked_array = update->ntimestep;
+
+  // compute chunk/atom assigns atoms to chunk IDs
+  // extract ichunk index vector from compute
+  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
+
+  nchunk = cchunk->setup_chunks();
+  cchunk->compute_ichunk();
+
+  if (nchunk > maxchunk) allocate();
+  size_array_rows = nchunk;
+}
+
+/* ----------------------------------------------------------------------
+   lock methods: called by fix ave/time
+   these methods ensure vector/array size is locked for Nfreq epoch
+     by passing lock info along to compute chunk/atom
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   increment lock counter
+------------------------------------------------------------------------- */
+
+void ComputeChunk::lock_enable()
+{
+  cchunk->lockcount++;
+}
+
+/* ----------------------------------------------------------------------
+   decrement lock counter in compute chunk/atom, it if still exists
+------------------------------------------------------------------------- */
+
+void ComputeChunk::lock_disable()
+{
+  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->get_compute_by_id(idchunk));
+  if (!cchunk) cchunk->lockcount--;
+}
+
+/* ----------------------------------------------------------------------
+   calculate and return # of chunks = length of vector/array
+------------------------------------------------------------------------- */
+
+int ComputeChunk::lock_length()
+{
+  nchunk = cchunk->setup_chunks();
+  return nchunk;
+}
+
+/* ----------------------------------------------------------------------
+   set the lock from startstep to stopstep
+------------------------------------------------------------------------- */
+
+void ComputeChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
+{
+  cchunk->lock(fixptr, startstep, stopstep);
+}
+
+/* ----------------------------------------------------------------------
+   unset the lock
+------------------------------------------------------------------------- */
+
+void ComputeChunk::unlock(Fix *fixptr)
+{
+  cchunk->unlock(fixptr);
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local data
+------------------------------------------------------------------------- */
+
+double ComputeChunk::memory_usage()
+{
+  return sizeof(ComputeChunk) + sizeof(ComputeChunkAtom);
+}

src/compute_chunk.h

@@ -0,0 +1,49 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_COMPUTE_CHUNK_H
+#define LMP_COMPUTE_CHUNK_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+class ComputeChunkAtom;
+class Fix;
+
+class ComputeChunk : public Compute {
+ public:
+  char *idchunk;    // fields accessed by other classes
+
+  ComputeChunk(class LAMMPS *, int, char **);
+  ~ComputeChunk() override;
+  void init() override;
+  void compute_vector() override;
+  void compute_array() override;
+
+  void lock_enable() override;
+  void lock_disable() override;
+  int lock_length() override;
+  void lock(Fix *, bigint, bigint) override;
+  void unlock(Fix *) override;
+
+  double memory_usage() override;
+
+ protected:
+  int nchunk, maxchunk;
+  int firstflag, massneed;
+  ComputeChunkAtom *cchunk;
+
+  virtual void allocate(){};
+};
+}    // namespace LAMMPS_NS
+#endif

src/compute_com_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,10 +18,6 @@
 #include "domain.h"
 #include "error.h"
 #include "memory.h"
-#include "modify.h"
-#include "update.h"
-
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -31,8 +26,8 @@ enum{ONCE,NFREQ,EVERY};
 /* ---------------------------------------------------------------------- */
 
 ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), masstotal(nullptr), massproc(nullptr), com(nullptr),
-  idchunk(nullptr), masstotal(nullptr), massproc(nullptr), com(nullptr), comall(nullptr)
+    comall(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute com/chunk command");
 
@@ -42,26 +37,14 @@ ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   ComputeCOMChunk::init();
-
+  ComputeCOMChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
-
-  firstflag = massneed = 1;
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeCOMChunk::~ComputeCOMChunk()
 {
-  delete [] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -70,18 +53,6 @@ ComputeCOMChunk::~ComputeCOMChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeCOMChunk::init()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for compute com/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute com/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeCOMChunk::setup()
 {
   // one-time calculation of per-chunk mass
@@ -101,23 +72,12 @@ void ComputeCOMChunk::compute_array()
   double massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
-
   // zero local per-chunk values
 
-  for (int i = 0; i < nchunk; i++)
+  for (int i = 0; i < nchunk; i++) com[i][0] = com[i][1] = com[i][2] = 0.0;
-    com[i][0] = com[i][1] = com[i][2] = 0.0;
   if (massneed)
     for (int i = 0; i < nchunk; i++) massproc[i] = 0.0;
 
@@ -135,8 +95,10 @@ void ComputeCOMChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       com[index][0] += unwrap[0] * massone;
       com[index][1] += unwrap[1] * massone;
@@ -145,74 +107,18 @@ void ComputeCOMChunk::compute_array()
     }
 
   MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-  if (massneed)
+  if (massneed) MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-    MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
 
   for (int i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
       comall[i][0] /= masstotal[i];
       comall[i][1] /= masstotal[i];
       comall[i][2] /= masstotal[i];
-    } else comall[i][0] = comall[i][1] = comall[i][2] = 0.0;
+    } else
+      comall[i][0] = comall[i][1] = comall[i][2] = 0.0;
   }
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeCOMChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeCOMChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeCOMChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeCOMChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeCOMChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
@@ -237,7 +143,8 @@ void ComputeCOMChunk::allocate()
 
 double ComputeCOMChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   return bytes;
 }

src/compute_com_chunk.h

@@ -20,42 +20,26 @@ ComputeStyle(com/chunk,ComputeCOMChunk);
 #ifndef LMP_COMPUTE_COM_CHUNK_H
 #define LMP_COMPUTE_COM_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
-class Fix;
+class ComputeCOMChunk : public ComputeChunk {
-
-class ComputeCOMChunk : public Compute {
  public:
-  char *idchunk;    // fields accessed by other classes
   double *masstotal;
 
   ComputeCOMChunk(class LAMMPS *, int, char **);
   ~ComputeCOMChunk() override;
-  void init() override;
   void setup() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(Fix *, bigint, bigint) override;
-  void unlock(Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  int firstflag, massneed;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc;
   double **com, **comall;
 
-  void allocate();
+  void allocate() override;
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

src/compute_dipole_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -22,8 +21,6 @@
 #include "force.h"
 #include "math_special.h"
 #include "memory.h"
-#include "modify.h"
-#include "update.h"
 
 #include <cmath>
 #include <cstring>
@@ -36,13 +33,10 @@ enum { MASSCENTER, GEOMCENTER };
 /* ---------------------------------------------------------------------- */
 
 ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), chrgproc(nullptr),
-  idchunk(nullptr), massproc(nullptr), masstotal(nullptr), chrgproc(nullptr),
+    chrgtotal(nullptr), com(nullptr), comall(nullptr), dipole(nullptr), dipoleall(nullptr)
-  chrgtotal(nullptr), com(nullptr),
-  comall(nullptr), dipole(nullptr), dipoleall(nullptr)
 {
-  if ((narg != 4) && (narg != 5))
+  if ((narg != 4) && (narg != 5)) error->all(FLERR, "Illegal compute dipole/chunk command");
-    error->all(FLERR,"Illegal compute dipole/chunk command");
 
   array_flag = 1;
   size_array_cols = 4;
@@ -50,32 +44,25 @@ ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   usecenter = MASSCENTER;
 
   if (narg == 5) {
-    if (strncmp(arg[4],"geom",4) == 0) usecenter = GEOMCENTER;
+    if (strncmp(arg[4], "geom", 4) == 0)
-    else if (strcmp(arg[4],"mass") == 0) usecenter = MASSCENTER;
+      usecenter = GEOMCENTER;
-    else error->all(FLERR,"Illegal compute dipole/chunk command");
+    else if (strcmp(arg[4], "mass") == 0)
+      usecenter = MASSCENTER;
+    else
+      error->all(FLERR, "Illegal compute dipole/chunk command");
   }
 
   ComputeDipoleChunk::init();
-
+  ComputeDipoleChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeDipoleChunk::~ComputeDipoleChunk()
 {
-  delete [] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(chrgproc);
@@ -90,17 +77,10 @@ ComputeDipoleChunk::~ComputeDipoleChunk()
 
 void ComputeDipoleChunk::init()
 {
-  int icompute = modify->find_compute(idchunk);
+  ComputeChunk::init();
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for "
-               "compute dipole/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute dipole/chunk does not use chunk/atom compute");
 
-  if ((force->pair_match("/tip4p/",0) != nullptr) && (comm->me == 0))
+  if ((force->pair_match("tip4p/", 0) != nullptr) && (comm->me == 0))
-    error->warning(FLERR,"Computed dipole moments may be incorrect when "
+    error->warning(FLERR, "Dipole moments may be incorrect when sing a TIP4P pair style");
-                   "using a tip4p pair style");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -111,19 +91,9 @@ void ComputeDipoleChunk::compute_array()
   double massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
-
   // zero local per-chunk values
 
   for (i = 0; i < nchunk; i++) {
@@ -150,9 +120,12 @@ void ComputeDipoleChunk::compute_array()
       index = ichunk[i] - 1;
       if (index < 0) continue;
       if (usecenter == MASSCENTER) {
-        if (rmass) massone = rmass[i];
+        if (rmass)
-        else massone = mass[type[i]];
+          massone = rmass[i];
-      } else massone = 1.0;     // usecenter == GEOMCENTER
+        else
+          massone = mass[type[i]];
+      } else
+        massone = 1.0;    // usecenter == GEOMCENTER
 
       domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
@@ -194,8 +167,7 @@ void ComputeDipoleChunk::compute_array()
     }
   }
 
-  MPI_Allreduce(&dipole[0][0],&dipoleall[0][0],4*nchunk,
+  MPI_Allreduce(&dipole[0][0], &dipoleall[0][0], 4 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-                MPI_DOUBLE,MPI_SUM,world);
 
   for (i = 0; i < nchunk; i++) {
     // correct for position dependence with charged chunks
@@ -203,74 +175,17 @@ void ComputeDipoleChunk::compute_array()
     dipoleall[i][1] -= chrgtotal[i] * comall[i][1];
     dipoleall[i][2] -= chrgtotal[i] * comall[i][2];
     // compute total dipole moment
-    dipoleall[i][3] = sqrt(square(dipoleall[i][0])
+    dipoleall[i][3] =
-                           + square(dipoleall[i][1])
+        sqrt(square(dipoleall[i][0]) + square(dipoleall[i][1]) + square(dipoleall[i][2]));
-                           + square(dipoleall[i][2]));
   }
 }
-
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeDipoleChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeDipoleChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeDipoleChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeDipoleChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeDipoleChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeDipoleChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(chrgproc);
@@ -297,7 +212,8 @@ void ComputeDipoleChunk::allocate()
 
 double ComputeDipoleChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   bytes += (double) maxchunk * 2 * 4 * sizeof(double);
   return bytes;

src/compute_dipole_chunk.h

@@ -20,38 +20,28 @@ ComputeStyle(dipole/chunk,ComputeDipoleChunk);
 #ifndef LMP_COMPUTE_DIPOLE_CHUNK_H
 #define LMP_COMPUTE_DIPOLE_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 class Fix;
 
-class ComputeDipoleChunk : public Compute {
+class ComputeDipoleChunk : public ComputeChunk {
  public:
   ComputeDipoleChunk(class LAMMPS *, int, char **);
   ~ComputeDipoleChunk() override;
   void init() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(Fix *, bigint, bigint) override;
-  void unlock(Fix *) override;
-
   double memory_usage() override;
 
- private:
+ protected:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc, *masstotal;
   double *chrgproc, *chrgtotal;
   double **com, **comall;
   double **dipole, **dipoleall;
   int usecenter;
 
-  void allocate();
+  void allocate() override;
 };
 
 }    // namespace LAMMPS_NS

src/compute_gyration_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,31 +13,23 @@
 
 #include "compute_gyration_chunk.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "compute_chunk_atom.h"
 #include "domain.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), com(nullptr),
-  idchunk(nullptr), massproc(nullptr), masstotal(nullptr), com(nullptr), comall(nullptr),
+    comall(nullptr), rg(nullptr), rgall(nullptr), rgt(nullptr), rgtall(nullptr)
-  rg(nullptr), rgall(nullptr), rgt(nullptr), rgtall(nullptr)
 {
-  if (narg < 4) error->all(FLERR,"Illegal compute gyration/chunk command");
-
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   ComputeGyrationChunk::init();
 
   // optional args
@@ -49,7 +40,8 @@ ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
     if (strcmp(arg[iarg], "tensor") == 0) {
       tensor = 1;
       iarg++;
-    } else error->all(FLERR,"Illegal compute gyration/chunk command");
+    } else
+      error->all(FLERR, "Illegal compute gyration/chunk command");
   }
 
   if (tensor) {
@@ -65,18 +57,13 @@ ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
     extvector = 0;
   }
 
-  // chunk-based data
+  ComputeGyrationChunk::allocate();
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeGyrationChunk::~ComputeGyrationChunk()
 {
-  delete [] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -89,26 +76,13 @@ ComputeGyrationChunk::~ComputeGyrationChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeGyrationChunk::init()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for "
-               "compute gyration/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute gyration/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeGyrationChunk::compute_vector()
 {
   int i, index;
   double dx, dy, dz, massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_vector();
 
   com_chunk();
   int *ichunk = cchunk->ichunk;
@@ -133,16 +107,17 @@ void ComputeGyrationChunk::compute_vector()
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
       dz = unwrap[2] - comall[index][2];
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       rg[index] += (dx * dx + dy * dy + dz * dz) * massone;
     }
 
   MPI_Allreduce(rg, rgall, nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++)
-    if (masstotal[i] > 0.0)
+    if (masstotal[i] > 0.0) rgall[i] = sqrt(rgall[i] / masstotal[i]);
-      rgall[i] = sqrt(rgall[i]/masstotal[i]);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -153,7 +128,7 @@ void ComputeGyrationChunk::compute_array()
   double dx, dy, dz, massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
 
   com_chunk();
   int *ichunk = cchunk->ichunk;
@@ -177,8 +152,10 @@ void ComputeGyrationChunk::compute_array()
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
       dz = unwrap[2] - comall[index][2];
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       rgt[index][0] += dx * dx * massone;
       rgt[index][1] += dy * dy * massone;
       rgt[index][2] += dz * dz * massone;
@@ -187,18 +164,15 @@ void ComputeGyrationChunk::compute_array()
       rgt[index][5] += dy * dz * massone;
     }
 
-  if (nchunk)
+  if (nchunk) MPI_Allreduce(&rgt[0][0], &rgtall[0][0], nchunk * 6, MPI_DOUBLE, MPI_SUM, world);
-    MPI_Allreduce(&rgt[0][0],&rgtall[0][0],nchunk*6,MPI_DOUBLE,MPI_SUM,world);
 
   for (i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
-      for (j = 0; j < 6; j++)
+      for (j = 0; j < 6; j++) rgtall[i][j] = rgtall[i][j] / masstotal[i];
-        rgtall[i][j] = rgtall[i][j]/masstotal[i];
     }
   }
 }
 
-
 /* ----------------------------------------------------------------------
    calculate per-chunk COM, used by both scalar and tensor
 ------------------------------------------------------------------------- */
@@ -209,18 +183,8 @@ void ComputeGyrationChunk::com_chunk()
   double massone;
   double unwrap[3];
 
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  if (tensor) size_array_rows = nchunk;
-  else size_vector = nchunk;
-
   // zero local per-chunk values
 
   for (int i = 0; i < nchunk; i++) {
@@ -242,8 +206,10 @@ void ComputeGyrationChunk::com_chunk()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
@@ -263,68 +229,13 @@ void ComputeGyrationChunk::com_chunk()
   }
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeGyrationChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeGyrationChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeGyrationChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeGyrationChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeGyrationChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeGyrationChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -355,9 +266,12 @@ void ComputeGyrationChunk::allocate()
 
 double ComputeGyrationChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
-  if (tensor) bytes += (double) maxchunk * 2*6 * sizeof(double);
+  if (tensor)
-  else bytes += (double) maxchunk * 2 * sizeof(double);
+    bytes += (double) maxchunk * 2 * 6 * sizeof(double);
+  else
+    bytes += (double) maxchunk * 2 * sizeof(double);
   return bytes;
 }

src/compute_gyration_chunk.h

@@ -20,31 +20,21 @@ ComputeStyle(gyration/chunk,ComputeGyrationChunk);
 #ifndef LMP_COMPUTE_GYRATION_CHUNK_H
 #define LMP_COMPUTE_GYRATION_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeGyrationChunk : public Compute {
+class ComputeGyrationChunk : public ComputeChunk {
  public:
   ComputeGyrationChunk(class LAMMPS *, int, char **);
   ~ComputeGyrationChunk() override;
-  void init() override;
+
   void compute_vector() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   int tensor;
 
   double *massproc, *masstotal;
@@ -53,7 +43,7 @@ class ComputeGyrationChunk : public Compute {
   double **rgt, **rgtall;
 
   void com_chunk();
-  void allocate();
+  void allocate() override;
 };
 
 }    // namespace LAMMPS_NS

src/compute_inertia_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,23 +13,19 @@
 
 #include "compute_inertia_chunk.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "compute_chunk_atom.h"
 #include "domain.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), com(nullptr),
-  idchunk(nullptr), massproc(nullptr), masstotal(nullptr), com(nullptr), comall(nullptr),
+    comall(nullptr), inertia(nullptr), inertiaall(nullptr)
-  inertia(nullptr), inertiaall(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute inertia/chunk command");
 
@@ -40,24 +35,14 @@ ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   ComputeInertiaChunk::init();
-
+  ComputeInertiaChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeInertiaChunk::~ComputeInertiaChunk()
 {
-  delete [] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -68,38 +53,15 @@ ComputeInertiaChunk::~ComputeInertiaChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeInertiaChunk::init()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for "
-               "compute inertia/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute inertia/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeInertiaChunk::compute_array()
 {
   int i, j, index;
   double dx, dy, dz, massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
-
   // zero local per-chunk values
 
   for (i = 0; i < nchunk; i++) {
@@ -122,8 +84,10 @@ void ComputeInertiaChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
@@ -148,8 +112,10 @@ void ComputeInertiaChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
@@ -162,67 +128,8 @@ void ComputeInertiaChunk::compute_array()
       inertia[index][5] -= massone * dx * dz;
     }
 
-  MPI_Allreduce(&inertia[0][0],&inertiaall[0][0],6*nchunk,
+  MPI_Allreduce(&inertia[0][0], &inertiaall[0][0], 6 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-                MPI_DOUBLE,MPI_SUM,world);
 }
-
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeInertiaChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeInertiaChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeInertiaChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeInertiaChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeInertiaChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
@@ -251,7 +158,8 @@ void ComputeInertiaChunk::allocate()
 
 double ComputeInertiaChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   bytes += (double) maxchunk * 2 * 6 * sizeof(double);
   return bytes;

src/compute_inertia_chunk.h

@@ -20,38 +20,25 @@ ComputeStyle(inertia/chunk,ComputeInertiaChunk);
 #ifndef LMP_COMPUTE_INERTIA_CHUNK_H
 #define LMP_COMPUTE_INERTIA_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeInertiaChunk : public Compute {
+class ComputeInertiaChunk : public ComputeChunk {
  public:
   ComputeInertiaChunk(class LAMMPS *, int, char **);
   ~ComputeInertiaChunk() override;
-  void init() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc, *masstotal;
   double **com, **comall;
   double **inertia, **inertiaall;
 
-  void allocate();
+  void allocate() override;
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

src/compute_msd_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -22,17 +21,14 @@
 #include "group.h"
 #include "memory.h"
 #include "modify.h"
-#include "update.h"
-
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg), idchunk(nullptr), id_fix(nullptr), massproc(nullptr),
+    ComputeChunk(lmp, narg, arg), id_fix(nullptr), massproc(nullptr), masstotal(nullptr),
-  masstotal(nullptr), com(nullptr), comall(nullptr), msd(nullptr)
+    com(nullptr), comall(nullptr), msd(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute msd/chunk command");
 
@@ -42,11 +38,6 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
-  firstflag = 1;
   ComputeMSDChunk::init();
 
   // create a new fix STORE style for reference positions
@@ -70,7 +61,6 @@ ComputeMSDChunk::~ComputeMSDChunk()
   if (modify->nfix) modify->delete_fix(id_fix);
 
   delete[] id_fix;
-  delete[] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -82,12 +72,7 @@ ComputeMSDChunk::~ComputeMSDChunk()
 
 void ComputeMSDChunk::init()
 {
-  int icompute = modify->find_compute(idchunk);
+  ComputeChunk::init();
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for compute msd/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute msd/chunk does not use chunk/atom compute");
 
   // set fix which stores reference atom coords
   // if firstflag, will be created in setup()
@@ -132,24 +117,14 @@ void ComputeMSDChunk::compute_array()
   double massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  int oldnchunk = nchunk;
-
+  ComputeChunk::compute_array();
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  int n = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
   // first time call, allocate per-chunk arrays
   // thereafter, require nchunk remain the same
 
-  if (firstflag) {
+  if (!firstflag && (oldnchunk != nchunk))
-    nchunk = n;
-    allocate();
-    size_array_rows = nchunk;
-  } else if (n != nchunk)
     error->all(FLERR, "Compute msd/chunk nchunk is not static");
 
   // zero local per-chunk values
@@ -173,8 +148,10 @@ void ComputeMSDChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
@@ -212,68 +189,13 @@ void ComputeMSDChunk::compute_array()
   }
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeMSDChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeMSDChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeMSDChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeMSDChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeMSDChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    one-time allocate of per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeMSDChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->create(massproc, nchunk, "msd/chunk:massproc");
   memory->create(masstotal, nchunk, "msd/chunk:masstotal");
   memory->create(com, nchunk, 3, "msd/chunk:com");
@@ -288,7 +210,8 @@ void ComputeMSDChunk::allocate()
 
 double ComputeMSDChunk::memory_usage()
 {
-  double bytes = (bigint) nchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) nchunk * 2 * sizeof(double);
   bytes += (double) nchunk * 2 * 3 * sizeof(double);
   bytes += (double) nchunk * 4 * sizeof(double);
   return bytes;

src/compute_msd_chunk.h

@@ -20,11 +20,11 @@ ComputeStyle(msd/chunk,ComputeMSDChunk);
 #ifndef LMP_COMPUTE_MSD_CHUNK_H
 #define LMP_COMPUTE_MSD_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeMSDChunk : public Compute {
+class ComputeMSDChunk : public ComputeChunk {
  public:
   ComputeMSDChunk(class LAMMPS *, int, char **);
   ~ComputeMSDChunk() override;
@@ -32,27 +32,17 @@ class ComputeMSDChunk : public Compute {
   void setup() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
   char *id_fix;
   class FixStoreGlobal *fix;
-  int firstflag;
 
   double *massproc, *masstotal;
   double **com, **comall;
   double **msd;
 
-  void allocate();
+  void allocate() override;
 };
 }    // namespace LAMMPS_NS
 #endif

src/compute_omega_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,16 +13,13 @@
 
 #include "compute_omega_chunk.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "compute_chunk_atom.h"
 #include "domain.h"
-#include "math_extra.h"
-#include "math_eigen.h"
-#include "memory.h"
 #include "error.h"
+#include "math_eigen.h"
+#include "math_extra.h"
+#include "memory.h"
 
 using namespace LAMMPS_NS;
 
@@ -32,9 +28,9 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), com(nullptr),
-  idchunk(nullptr),massproc(nullptr),masstotal(nullptr),com(nullptr),comall(nullptr),
+    comall(nullptr), inertia(nullptr), inertiaall(nullptr), angmom(nullptr), angmomall(nullptr),
-  inertia(nullptr),inertiaall(nullptr),angmom(nullptr),angmomall(nullptr),omega(nullptr)
+    omega(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute omega/chunk command");
 
@@ -44,24 +40,14 @@ ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   ComputeOmegaChunk::init();
-
+  ComputeOmegaChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeOmegaChunk::~ComputeOmegaChunk()
 {
-  delete [] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -75,33 +61,13 @@ ComputeOmegaChunk::~ComputeOmegaChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeOmegaChunk::init()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for "
-               "compute omega/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute omega/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeOmegaChunk::compute_array()
 {
   int i, j, m, index;
   double dx, dy, dz, massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
   if (nchunk > maxchunk) allocate();
@@ -131,8 +97,10 @@ void ComputeOmegaChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
@@ -157,8 +125,10 @@ void ComputeOmegaChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
@@ -171,8 +141,7 @@ void ComputeOmegaChunk::compute_array()
       inertia[index][5] -= massone * dx * dz;
     }
 
-  MPI_Allreduce(&inertia[0][0],&inertiaall[0][0],6*nchunk,
+  MPI_Allreduce(&inertia[0][0], &inertiaall[0][0], 6 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-                MPI_DOUBLE,MPI_SUM,world);
 
   // compute angmom for each chunk
 
@@ -186,15 +155,16 @@ void ComputeOmegaChunk::compute_array()
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
       dz = unwrap[2] - comall[index][2];
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       angmom[index][0] += massone * (dy * v[i][2] - dz * v[i][1]);
       angmom[index][1] += massone * (dz * v[i][0] - dx * v[i][2]);
       angmom[index][2] += massone * (dx * v[i][1] - dy * v[i][0]);
     }
 
-  MPI_Allreduce(&angmom[0][0],&angmomall[0][0],3*nchunk,
+  MPI_Allreduce(&angmom[0][0], &angmomall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-                MPI_DOUBLE,MPI_SUM,world);
 
   // compute omega for each chunk
 
@@ -237,16 +207,12 @@ void ComputeOmegaChunk::compute_array()
 
       invdeterminant = 1.0 / determinant;
       for (i = 0; i < 3; i++)
-        for (j = 0; j < 3; j++)
+        for (j = 0; j < 3; j++) inverse[i][j] *= invdeterminant;
-          inverse[i][j] *= invdeterminant;
 
       mall = &angmomall[m][0];
-      omega[m][0] = inverse[0][0]*mall[0] + inverse[0][1]*mall[1] +
+      omega[m][0] = inverse[0][0] * mall[0] + inverse[0][1] * mall[1] + inverse[0][2] * mall[2];
-        inverse[0][2]*mall[2];
+      omega[m][1] = inverse[1][0] * mall[0] + inverse[1][1] * mall[1] + inverse[1][2] * mall[2];
-      omega[m][1] = inverse[1][0]*mall[0] + inverse[1][1]*mall[1] +
+      omega[m][2] = inverse[2][0] * mall[0] + inverse[2][1] * mall[1] + inverse[2][2] * mall[2];
-        inverse[1][2]*mall[2];
-      omega[m][2] = inverse[2][0]*mall[0] + inverse[2][1]*mall[1] +
-        inverse[2][2]*mall[2];
 
       // handle each (nearly) singular I matrix
       // due to 2-atom chunk or linear molecule
@@ -254,8 +220,7 @@ void ComputeOmegaChunk::compute_array()
 
     } else {
       int ierror = MathEigen::jacobi3(ione, idiag, evectors);
-      if (ierror) error->all(FLERR,
+      if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for omega/chunk");
-                             "Insufficient Jacobi rotations for omega/chunk");
 
       ex[0] = evectors[0][0];
       ex[1] = evectors[1][0];
@@ -289,69 +254,13 @@ void ComputeOmegaChunk::compute_array()
     }
   }
 }
-
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeOmegaChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeOmegaChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeOmegaChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeOmegaChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeOmegaChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeOmegaChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -380,7 +289,8 @@ void ComputeOmegaChunk::allocate()
 
 double ComputeOmegaChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   bytes += (double) maxchunk * 2 * 6 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);

src/compute_omega_chunk.h

@@ -20,40 +20,28 @@ ComputeStyle(omega/chunk,ComputeOmegaChunk);
 #ifndef LMP_COMPUTE_OMEGA_CHUNK_H
 #define LMP_COMPUTE_OMEGA_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeOmegaChunk : public Compute {
+class ComputeOmegaChunk : public ComputeChunk {
  public:
   ComputeOmegaChunk(class LAMMPS *, int, char **);
   ~ComputeOmegaChunk() override;
-  void init() override;
-  void compute_array() override;
 
-  void lock_enable() override;
+  void compute_array() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
 
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc, *masstotal;
   double **com, **comall;
   double **inertia, **inertiaall;
   double **angmom, **angmomall;
   double **omega;
 
-  void allocate();
+  void allocate() override;
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

src/compute_property_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,27 +13,21 @@
 
 #include "compute_property_chunk.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "compute_chunk_atom.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), count_one(nullptr), count_all(nullptr)
-  idchunk(nullptr), count_one(nullptr), count_all(nullptr)
 {
-  if (narg < 5) error->all(FLERR,"Illegal compute property/chunk command");
+  if (narg < 5) utils::missing_cmd_args(FLERR, "compute property/chunk", error);
-
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
 
   ComputePropertyChunk::init();
 
@@ -53,33 +46,25 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
       countflag = 1;
     } else if (strcmp(arg[iarg], "id") == 0) {
       if (!cchunk->compress)
-        error->all(FLERR,"Compute chunk/atom stores no IDs for "
+        error->all(FLERR, "Compute chunk/atom stores no IDs for compute property/chunk");
-                   "compute property/chunk");
       pack_choice[i] = &ComputePropertyChunk::pack_id;
     } else if (strcmp(arg[iarg], "coord1") == 0) {
       if (cchunk->ncoord < 1)
-        error->all(FLERR,"Compute chunk/atom stores no coord1 for "
+        error->all(FLERR, "Compute chunk/atom stores no coord1 for compute property/chunk");
-                   "compute property/chunk");
       pack_choice[i] = &ComputePropertyChunk::pack_coord1;
     } else if (strcmp(arg[iarg], "coord2") == 0) {
       if (cchunk->ncoord < 2)
-        error->all(FLERR,"Compute chunk/atom stores no coord2 for "
+        error->all(FLERR, "Compute chunk/atom stores no coord2 for compute property/chunk");
-                   "compute property/chunk");
       pack_choice[i] = &ComputePropertyChunk::pack_coord2;
     } else if (strcmp(arg[iarg], "coord3") == 0) {
       if (cchunk->ncoord < 3)
-        error->all(FLERR,"Compute chunk/atom stores no coord3 for "
+        error->all(FLERR, "Compute chunk/atom stores no coord3 for compute property/chunk");
-                   "compute property/chunk");
       pack_choice[i] = &ComputePropertyChunk::pack_coord3;
-    } else error->all(FLERR,
+    } else
-                    "Invalid keyword in compute property/chunk command");
+      error->all(FLERR, "Unkown keyword {} in compute property/chunk command", arg[iarg]);
   }
 
-  // initialization
+  ComputePropertyChunk::allocate();
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 
   if (nvalues == 1) {
     vector_flag = 1;
@@ -99,7 +84,6 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
 
 ComputePropertyChunk::~ComputePropertyChunk()
 {
-  delete [] idchunk;
   delete[] pack_choice;
   memory->destroy(vector);
   memory->destroy(array);
@@ -109,36 +93,11 @@ ComputePropertyChunk::~ComputePropertyChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputePropertyChunk::init()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for "
-               "compute property/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute property/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputePropertyChunk::compute_vector()
 {
-  invoked_vector = update->ntimestep;
+  ComputeChunk::compute_vector();
 
-  // compute chunk/atom assigns atoms to chunk IDs
+  if (countflag) ichunk = cchunk->ichunk;
-  // if need count, extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  if (nchunk > maxchunk) allocate();
-  if (nvalues == 1) size_vector = nchunk;
-  else size_array_rows = nchunk;
-
-  if (countflag) {
-    cchunk->compute_ichunk();
-    ichunk = cchunk->ichunk;
-  }
 
   // fill vector
 
@@ -150,98 +109,31 @@ void ComputePropertyChunk::compute_vector()
 
 void ComputePropertyChunk::compute_array()
 {
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
 
-  // compute chunk/atom assigns atoms to chunk IDs
+  if (countflag) ichunk = cchunk->ichunk;
-  // if need count, extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  if (nchunk > maxchunk) allocate();
-  if (nvalues == 1) size_vector = nchunk;
-  else size_array_rows = nchunk;
-
-  if (countflag) {
-    cchunk->compute_ichunk();
-    ichunk = cchunk->ichunk;
-  }
 
   // fill array
 
   if (array) buf = &array[0][0];
-  for (int n = 0; n < nvalues; n++)
+  for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n);
-    (this->*pack_choice[n])(n);
 }
-
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputePropertyChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputePropertyChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputePropertyChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputePropertyChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputePropertyChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputePropertyChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(vector);
   memory->destroy(array);
   memory->destroy(count_one);
   memory->destroy(count_all);
   maxchunk = nchunk;
-  if (nvalues == 1) memory->create(vector,maxchunk,"property/chunk:vector");
+  if (nvalues == 1)
-  else memory->create(array,maxchunk,nvalues,"property/chunk:array");
+    memory->create(vector, maxchunk, "property/chunk:vector");
+  else
+    memory->create(array, maxchunk, nvalues, "property/chunk:array");
   if (countflag) {
     memory->create(count_one, maxchunk, "property/chunk:count_one");
     memory->create(count_all, maxchunk, "property/chunk:count_all");
@@ -254,7 +146,8 @@ void ComputePropertyChunk::allocate()
 
 double ComputePropertyChunk::memory_usage()
 {
-  double bytes = (bigint) nchunk * nvalues * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) nchunk * nvalues * sizeof(double);
   if (countflag) bytes += (double) nchunk * 2 * sizeof(int);
   return bytes;
 }

src/compute_property_chunk.h

@@ -20,37 +20,27 @@ ComputeStyle(property/chunk,ComputePropertyChunk);
 #ifndef LMP_COMPUTE_CHUNK_MOLECULE_H
 #define LMP_COMPUTE_CHUNK_MOLECULE_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputePropertyChunk : public Compute {
+class ComputePropertyChunk : public ComputeChunk {
  public:
   ComputePropertyChunk(class LAMMPS *, int, char **);
   ~ComputePropertyChunk() override;
-  void init() override;
+
   void compute_vector() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
   int *ichunk;
-
   int nvalues, countflag;
   double *buf;
   int *count_one, *count_all;
 
-  void allocate();
+  void allocate() override;
 
   typedef void (ComputePropertyChunk::*FnPtrPack)(int);
   FnPtrPack *pack_choice;    // ptrs to pack functions
@@ -61,8 +51,6 @@ class ComputePropertyChunk : public Compute {
   void pack_coord2(int);
   void pack_coord3(int);
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

src/compute_reduce_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -37,22 +36,23 @@ enum{ SUM, MINN, MAXX };
 /* ---------------------------------------------------------------------- */
 
 ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg), idchunk(nullptr), vlocal(nullptr), vglobal(nullptr),
+    ComputeChunk(lmp, narg, arg), vlocal(nullptr), vglobal(nullptr), alocal(nullptr),
-  alocal(nullptr), aglobal(nullptr), varatom(nullptr), cchunk(nullptr), ichunk(nullptr)
+    aglobal(nullptr), varatom(nullptr), ichunk(nullptr)
 {
   if (narg < 6) utils::missing_cmd_args(FLERR, "compute reduce/chunk", error);
 
-  // ID of compute chunk/atom
+  ComputeChunk::init();
-
-  idchunk = utils::strdup(arg[3]);
-  init_chunk();
 
   // mode
 
-  if (strcmp(arg[4],"sum") == 0) mode = SUM;
+  if (strcmp(arg[4], "sum") == 0)
-  else if (strcmp(arg[4],"min") == 0) mode = MINN;
+    mode = SUM;
-  else if (strcmp(arg[4],"max") == 0) mode = MAXX;
+  else if (strcmp(arg[4], "min") == 0)
-  else error->all(FLERR,"Unknown compute reduce/chunk mode: {}", arg[4]);
+    mode = MINN;
+  else if (strcmp(arg[4], "max") == 0)
+    mode = MAXX;
+  else
+    error->all(FLERR, "Unknown compute reduce/chunk mode: {}", arg[4]);
 
   int iarg = 5;
 
@@ -116,9 +116,11 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
       if (!val.val.f->peratom_flag)
         error->all(FLERR, "Compute reduce/chunk fix {} does not calculate per-atom values", val.id);
       if ((val.argindex == 0) && (val.val.f->size_peratom_cols != 0))
-        error->all(FLERR,"Compute reduce/chunk fix {} does not calculate a per-atom vector", val.id);
+        error->all(FLERR, "Compute reduce/chunk fix {} does not calculate a per-atom vector",
+                   val.id);
       if (val.argindex && (val.val.f->size_peratom_cols == 0))
-        error->all(FLERR,"Compute reduce/chunk fix {} does not calculate a per-atom array", val.id);
+        error->all(FLERR, "Compute reduce/chunk fix {} does not calculate a per-atom array",
+                   val.id);
       if (val.argindex && (val.argindex > val.val.f->size_peratom_cols))
         error->all(FLERR, "Compute reduce/chunk fix {} array is accessed out-of-range", val.id);
 
@@ -146,11 +148,13 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
 
   // setup
 
-  if (mode == SUM) initvalue = 0.0;
+  if (mode == SUM)
-  else if (mode == MINN) initvalue = BIG;
+    initvalue = 0.0;
-  else if (mode == MAXX) initvalue = -BIG;
+  else if (mode == MINN)
+    initvalue = BIG;
+  else if (mode == MAXX)
+    initvalue = -BIG;
 
-  maxchunk = 0;
   vlocal = vglobal = nullptr;
   alocal = aglobal = nullptr;
 
@@ -162,8 +166,6 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeReduceChunk::~ComputeReduceChunk()
 {
-  delete[] idchunk;
-
   memory->destroy(vlocal);
   memory->destroy(vglobal);
   memory->destroy(alocal);
@@ -176,7 +178,7 @@ ComputeReduceChunk::~ComputeReduceChunk()
 
 void ComputeReduceChunk::init()
 {
-  init_chunk();
+  ComputeChunk::init();
 
   // set indices of all computes,fixes,variables
 
@@ -201,31 +203,12 @@ void ComputeReduceChunk::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeReduceChunk::init_chunk()
-{
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->get_compute_by_id(idchunk));
-  if (!cchunk)
-    error->all(FLERR,"Compute chunk/atom {} does not exist or is incorrect style for "
-               "compute reduce/chunk", idchunk);
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeReduceChunk::compute_vector()
 {
-  invoked_vector = update->ntimestep;
+  ComputeChunk::compute_vector();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   ichunk = cchunk->ichunk;
   if (!nchunk) return;
 
-  size_vector = nchunk;
-
   if (nchunk > maxchunk) {
     memory->destroy(vlocal);
     memory->destroy(vglobal);
@@ -253,19 +236,10 @@ void ComputeReduceChunk::compute_vector()
 
 void ComputeReduceChunk::compute_array()
 {
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   ichunk = cchunk->ichunk;
   if (!nchunk) return;
 
-  size_array_rows = nchunk;
-
   if (nchunk > maxchunk) {
     memory->destroy(alocal);
     memory->destroy(aglobal);
@@ -282,11 +256,14 @@ void ComputeReduceChunk::compute_array()
   // reduce the per-chunk values across all procs
 
   if (mode == SUM)
-    MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*values.size(),MPI_DOUBLE,MPI_SUM,world);
+    MPI_Allreduce(&alocal[0][0], &aglobal[0][0], nchunk * values.size(), MPI_DOUBLE, MPI_SUM,
+                  world);
   else if (mode == MINN)
-    MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*values.size(),MPI_DOUBLE,MPI_MIN,world);
+    MPI_Allreduce(&alocal[0][0], &aglobal[0][0], nchunk * values.size(), MPI_DOUBLE, MPI_MIN,
+                  world);
   else if (mode == MAXX)
-    MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*values.size(),MPI_DOUBLE,MPI_MAX,world);
+    MPI_Allreduce(&alocal[0][0], &aglobal[0][0], nchunk * values.size(), MPI_DOUBLE, MPI_MAX,
+                  world);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -386,7 +363,8 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
 
 void ComputeReduceChunk::combine(double &one, double two)
 {
-  if (mode == SUM) one += two;
+  if (mode == SUM)
+    one += two;
   else if (mode == MINN) {
     if (two < one) one = two;
   } else if (mode == MAXX) {
@@ -394,67 +372,16 @@ void ComputeReduceChunk::combine(double &one, double two)
   }
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeReduceChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, if it still exists
-------------------------------------------------------------------------- */
-
-void ComputeReduceChunk::lock_disable()
-{
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->get_compute_by_id(idchunk));
-  if (cchunk) cchunk->lockcount--;
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeReduceChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeReduceChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeReduceChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    memory usage of local data
 ------------------------------------------------------------------------- */
 
 double ComputeReduceChunk::memory_usage()
 {
-  double bytes = (bigint) maxatom * sizeof(double);
+  double bytes = (double) maxatom * sizeof(double) + ComputeChunk::memory_usage();
-  if (values.size() == 1) bytes += (double) maxchunk * 2 * sizeof(double);
+  if (values.size() == 1)
-  else bytes += (double) maxchunk * values.size() * 2 * sizeof(double);
+    bytes += (double) maxchunk * 2 * sizeof(double);
+  else
+    bytes += (double) maxchunk * values.size() * 2 * sizeof(double);
   return bytes;
 }

src/compute_reduce_chunk.h

@@ -20,11 +20,11 @@ ComputeStyle(reduce/chunk,ComputeReduceChunk);
 #ifndef LMP_COMPUTE_REDUCE_CHUNK_H
 #define LMP_COMPUTE_REDUCE_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeReduceChunk : public Compute {
+class ComputeReduceChunk : public ComputeChunk {
  public:
   ComputeReduceChunk(class LAMMPS *, int, char **);
   ~ComputeReduceChunk() override;
@@ -32,12 +32,6 @@ class ComputeReduceChunk : public Compute {
   void compute_vector() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
@@ -53,19 +47,14 @@ class ComputeReduceChunk : public Compute {
   };
   std::vector<value_t> values;
 
-  char *idchunk;
+  int mode, maxatom;
-
-  int mode, nchunk;
-  int maxchunk, maxatom;
   double initvalue;
   double *vlocal, *vglobal;
   double **alocal, **aglobal;
   double *varatom;
 
-  class ComputeChunkAtom *cchunk;
   int *ichunk;
 
-  void init_chunk();
   void compute_one(int, double *, int);
   void combine(double &, double);
 };

src/compute_temp_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -32,22 +31,16 @@ enum{TEMP,KECOM,INTERNAL};
 /* ---------------------------------------------------------------------- */
 
 ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), which(nullptr), id_bias(nullptr), sum(nullptr), sumall(nullptr),
-  which(nullptr), idchunk(nullptr), id_bias(nullptr), sum(nullptr), sumall(nullptr), count(nullptr),
+    count(nullptr), countall(nullptr), massproc(nullptr), masstotal(nullptr), vcm(nullptr),
-  countall(nullptr), massproc(nullptr), masstotal(nullptr), vcm(nullptr), vcmall(nullptr)
+    vcmall(nullptr)
 {
-  if (narg < 4) error->all(FLERR,"Illegal compute temp/chunk command");
-
   scalar_flag = vector_flag = 1;
   size_vector = 6;
   extscalar = 0;
   extvector = 1;
   tempflag = 1;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   biasflag = 0;
   ComputeTempChunk::init();
 
@@ -59,10 +52,14 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
 
   int iarg = 4;
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"temp") == 0) which[nvalues] = TEMP;
+    if (strcmp(arg[iarg], "temp") == 0)
-    else if (strcmp(arg[iarg],"kecom") == 0) which[nvalues] = KECOM;
+      which[nvalues] = TEMP;
-    else if (strcmp(arg[iarg],"internal") == 0) which[nvalues] = INTERNAL;
+    else if (strcmp(arg[iarg], "kecom") == 0)
-    else break;
+      which[nvalues] = KECOM;
+    else if (strcmp(arg[iarg], "internal") == 0)
+      which[nvalues] = INTERNAL;
+    else
+      break;
     iarg++;
     nvalues++;
   }
@@ -93,20 +90,18 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
       if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
       cdof = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
       iarg += 2;
-    } else error->all(FLERR,"Illegal compute temp/chunk command");
+    } else
+      error->all(FLERR, "Illegal compute temp/chunk command");
   }
 
   // error check on bias compute
 
   if (biasflag) {
-    int i = modify->find_compute(id_bias);
+    tbias = modify->get_compute_by_id(id_bias);
-    if (i < 0)
+    if (!tbias) error->all(FLERR, "Could not find compute {} for temperature bias", id_bias);
-      error->all(FLERR,"Could not find compute ID for temperature bias");
+
-    tbias = modify->compute[i];
+    if (tbias->tempflag == 0) error->all(FLERR, "Bias compute does not calculate temperature");
-    if (tbias->tempflag == 0)
+    if (tbias->tempbias == 0) error->all(FLERR, "Bias compute does not calculate a velocity bias");
-      error->all(FLERR,"Bias compute does not calculate temperature");
-    if (tbias->tempbias == 0)
-      error->all(FLERR,"Bias compute does not calculate a velocity bias");
   }
 
   // this compute only calculates a bias, if comflag is set
@@ -120,11 +115,6 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
 
   vector = new double[size_vector];
 
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-
   if (nvalues) {
     array_flag = 1;
     size_array_cols = nvalues;
@@ -133,7 +123,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
     extarray = 0;
   }
 
-  allocate();
+  ComputeTempChunk::allocate();
   comstep = -1;
 }
 
@@ -141,7 +131,6 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeTempChunk::~ComputeTempChunk()
 {
-  delete [] idchunk;
   delete[] which;
   delete[] id_bias;
   delete[] vector;
@@ -160,19 +149,11 @@ ComputeTempChunk::~ComputeTempChunk()
 
 void ComputeTempChunk::init()
 {
-  int icompute = modify->find_compute(idchunk);
+  ComputeChunk::init();
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for "
-               "compute temp/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute temp/chunk does not use chunk/atom compute");
 
   if (biasflag) {
-    int i = modify->find_compute(id_bias);
+    tbias = modify->get_compute_by_id(id_bias);
-    if (i < 0)
+    if (!tbias) error->all(FLERR, "Could not find compute ID {} for temperature bias", id_bias);
-      error->all(FLERR,"Could not find compute ID for temperature bias");
-    tbias = modify->compute[i];
   }
 }
 
@@ -226,8 +207,7 @@ double ComputeTempChunk::compute_scalar()
         if (mask[i] & groupbit) {
           index = ichunk[i] - 1;
           if (index < 0) continue;
-          t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+          t += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * rmass[i];
-            rmass[i];
           mycount++;
         }
     } else {
@@ -235,8 +215,7 @@ double ComputeTempChunk::compute_scalar()
         if (mask[i] & groupbit) {
           index = ichunk[i] - 1;
           if (index < 0) continue;
-          t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+          t += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * mass[type[i]];
-            mass[type[i]];
           mycount++;
         }
     }
@@ -282,8 +261,7 @@ double ComputeTempChunk::compute_scalar()
   double dof = nchunk * cdof + adof * allcount;
   double tfactor = 0.0;
   if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
-  if (dof < 0.0 && allcount > 0.0)
+  if (dof < 0.0 && allcount > 0.0) error->all(FLERR, "Temperature compute degrees of freedom < 0");
-    error->all(FLERR,"Temperature compute degrees of freedom < 0");
   scalar *= tfactor;
   return scalar;
 }
@@ -294,20 +272,9 @@ void ComputeTempChunk::compute_vector()
 {
   int i, index;
 
-  invoked_vector = update->ntimestep;
+  ComputeChunk::compute_vector();
-
-  // calculate chunk assignments,
-  //   since only atoms in chunks contribute to global temperature
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-
   // remove velocity bias
 
   if (biasflag) {
@@ -337,8 +304,10 @@ void ComputeTempChunk::compute_vector()
       if (mask[i] & groupbit) {
         index = ichunk[i] - 1;
         if (index < 0) continue;
-        if (rmass) massone = rmass[i];
+        if (rmass)
-        else massone = mass[type[i]];
+          massone = rmass[i];
+        else
+          massone = mass[type[i]];
         t[0] += massone * v[i][0] * v[i][0];
         t[1] += massone * v[i][1] * v[i][1];
         t[2] += massone * v[i][2] * v[i][2];
@@ -352,8 +321,10 @@ void ComputeTempChunk::compute_vector()
       if (mask[i] & groupbit) {
         index = ichunk[i] - 1;
         if (index < 0) continue;
-        if (rmass) massone = rmass[i];
+        if (rmass)
-        else massone = mass[type[i]];
+          massone = rmass[i];
+        else
+          massone = mass[type[i]];
         vx = v[i][0] - vcmall[index][0];
         vy = v[i][1] - vcmall[index][1];
         vz = v[i][2] - vcmall[index][2];
@@ -380,17 +351,7 @@ void ComputeTempChunk::compute_vector()
 
 void ComputeTempChunk::compute_array()
 {
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
-
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
 
   // remove velocity bias
 
@@ -409,9 +370,12 @@ void ComputeTempChunk::compute_array()
   // compute each value
 
   for (int i = 0; i < nvalues; i++) {
-    if (which[i] == TEMP) temperature(i);
+    if (which[i] == TEMP)
-    else if (which[i] == KECOM) kecom(i);
+      temperature(i);
-    else if (which[i] == INTERNAL) internal(i);
+    else if (which[i] == KECOM)
+      kecom(i);
+    else if (which[i] == INTERNAL)
+      internal(i);
   }
 
   // restore velocity bias
@@ -450,8 +414,10 @@ void ComputeTempChunk::vcm_compute()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       vcm[index][0] += v[i][0] * massone;
       vcm[index][1] += v[i][1] * massone;
       vcm[index][2] += v[i][2] * massone;
@@ -503,8 +469,7 @@ void ComputeTempChunk::temperature(int icol)
         if (mask[i] & groupbit) {
           index = ichunk[i] - 1;
           if (index < 0) continue;
-          sum[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+          sum[index] += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * rmass[i];
-            rmass[i];
           count[index]++;
         }
     } else {
@@ -512,8 +477,7 @@ void ComputeTempChunk::temperature(int icol)
         if (mask[i] & groupbit) {
           index = ichunk[i] - 1;
           if (index < 0) continue;
-          sum[index] += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
+          sum[index] += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * mass[type[i]];
-            mass[type[i]];
           count[index]++;
         }
     }
@@ -558,8 +522,10 @@ void ComputeTempChunk::temperature(int icol)
 
   for (i = 0; i < nchunk; i++) {
     dof = cdof + adof * countall[i];
-    if (dof > 0.0) tfactor = mvv2e / (dof * boltz);
+    if (dof > 0.0)
-    else tfactor = 0.0;
+      tfactor = mvv2e / (dof * boltz);
+    else
+      tfactor = 0.0;
     array[i][icol] = tfactor * sumall[i];
   }
 }
@@ -613,9 +579,7 @@ void ComputeTempChunk::kecom(int icol)
   MPI_Allreduce(sum, sumall, nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   double mvv2e = force->mvv2e;
-  for (int i = 0; i < nchunk; i++)
+  for (int i = 0; i < nchunk; i++) array[i][icol] = 0.5 * mvv2e * sumall[i];
-    array[i][icol] = 0.5 * mvv2e * sumall[i];
-
 }
 
 /* ----------------------------------------------------------------------
@@ -669,8 +633,7 @@ void ComputeTempChunk::internal(int icol)
   MPI_Allreduce(sum, sumall, nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   double mvv2e = force->mvv2e;
-  for (int i = 0; i < nchunk; i++)
+  for (int i = 0; i < nchunk; i++) array[i][icol] = 0.5 * mvv2e * sumall[i];
-    array[i][icol] = 0.5 * mvv2e * sumall[i];
 }
 
 /* ----------------------------------------------------------------------
@@ -751,68 +714,13 @@ void ComputeTempChunk::restore_bias_all()
     }
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeTempChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeTempChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeTempChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeTempChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeTempChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeTempChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(sum);
   memory->destroy(sumall);
   memory->destroy(count);
@@ -843,7 +751,7 @@ void ComputeTempChunk::allocate()
 
 double ComputeTempChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = (double) maxchunk * 2 * sizeof(double) + ComputeChunk::memory_usage();
   bytes += (double) maxchunk * 2 * sizeof(int);
   bytes += (double) maxchunk * nvalues * sizeof(double);
   if (comflag || nvalues) {

src/compute_temp_chunk.h

@@ -20,11 +20,11 @@ ComputeStyle(temp/chunk,ComputeTempChunk);
 #ifndef LMP_COMPUTE_TEMP_CHUNK_H
 #define LMP_COMPUTE_TEMP_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeTempChunk : public Compute {
+class ComputeTempChunk : public ComputeChunk {
  public:
   ComputeTempChunk(class LAMMPS *, int, char **);
   ~ComputeTempChunk() override;
@@ -38,20 +38,12 @@ class ComputeTempChunk : public Compute {
   void restore_bias(int, double *) override;
   void restore_bias_all() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk, comflag, biasflag;
+  int comflag, biasflag;
   int nvalues;
   int *which;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
   double adof, cdof;
   char *id_bias;
   class Compute *tbias;    // ptr to additional bias compute
@@ -66,10 +58,8 @@ class ComputeTempChunk : public Compute {
   void temperature(int);
   void kecom(int);
   void internal(int);
-  void allocate();
+  void allocate() override;
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif

src/compute_torque_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,22 +13,19 @@
 
 #include "compute_torque_chunk.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "compute_chunk_atom.h"
 #include "domain.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), com(nullptr),
-  idchunk(nullptr), massproc(nullptr), masstotal(nullptr), com(nullptr), comall(nullptr), torque(nullptr), torqueall(nullptr)
+    comall(nullptr), torque(nullptr), torqueall(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute torque/chunk command");
 
@@ -39,24 +35,14 @@ ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   ComputeTorqueChunk::init();
-
+  ComputeTorqueChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeTorqueChunk::~ComputeTorqueChunk()
 {
-  delete [] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -67,38 +53,15 @@ ComputeTorqueChunk::~ComputeTorqueChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeTorqueChunk::init()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for "
-               "compute torque/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute torque/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeTorqueChunk::compute_array()
 {
   int i, index;
   double dx, dy, dz, massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
-
   // zero local per-chunk values
 
   for (i = 0; i < nchunk; i++) {
@@ -121,8 +84,10 @@ void ComputeTorqueChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
@@ -158,72 +123,15 @@ void ComputeTorqueChunk::compute_array()
       torque[index][2] += dx * f[i][1] - dy * f[i][0];
     }
 
-  MPI_Allreduce(&torque[0][0],&torqueall[0][0],3*nchunk,
+  MPI_Allreduce(&torque[0][0], &torqueall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-                MPI_DOUBLE,MPI_SUM,world);
 }
-
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeTorqueChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeTorqueChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeTorqueChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeTorqueChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeTorqueChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeTorqueChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(com);
@@ -246,7 +154,7 @@ void ComputeTorqueChunk::allocate()
 
 double ComputeTorqueChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = (double) maxchunk * 2 * sizeof(double) + ComputeChunk::memory_usage();
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   return bytes;

src/compute_torque_chunk.h

@@ -20,35 +20,24 @@ ComputeStyle(torque/chunk,ComputeTorqueChunk);
 #ifndef LMP_COMPUTE_TORQUE_CHUNK_H
 #define LMP_COMPUTE_TORQUE_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeTorqueChunk : public Compute {
+class ComputeTorqueChunk : public ComputeChunk {
  public:
   ComputeTorqueChunk(class LAMMPS *, int, char **);
   ~ComputeTorqueChunk() override;
-  void init() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc, *masstotal;
   double **com, **comall;
   double **torque, **torqueall;
 
-  void allocate();
+  void allocate() override;
 };
 
 }    // namespace LAMMPS_NS

src/compute_vcm_chunk.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,13 +13,10 @@
 
 #include "compute_vcm_chunk.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "compute_chunk_atom.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
 
 using namespace LAMMPS_NS;
 
@@ -29,8 +25,8 @@ enum{ONCE,NFREQ,EVERY};
 /* ---------------------------------------------------------------------- */
 
 ComputeVCMChunk::ComputeVCMChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    ComputeChunk(lmp, narg, arg), massproc(nullptr), masstotal(nullptr), vcm(nullptr),
-  idchunk(nullptr), massproc(nullptr), masstotal(nullptr), vcm(nullptr), vcmall(nullptr)
+    vcmall(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute vcm/chunk command");
 
@@ -40,26 +36,14 @@ ComputeVCMChunk::ComputeVCMChunk(LAMMPS *lmp, int narg, char **arg) :
   size_array_rows_variable = 1;
   extarray = 0;
 
-  // ID of compute chunk/atom
-
-  idchunk = utils::strdup(arg[3]);
-
   ComputeVCMChunk::init();
-
+  ComputeVCMChunk::allocate();
-  // chunk-based data
-
-  nchunk = 1;
-  maxchunk = 0;
-  allocate();
-
-  firstflag = massneed = 1;
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeVCMChunk::~ComputeVCMChunk()
 {
-  delete [] idchunk;
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(vcm);
@@ -68,18 +52,6 @@ ComputeVCMChunk::~ComputeVCMChunk()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeVCMChunk::init()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute < 0)
-    error->all(FLERR,"Chunk/atom compute does not exist for compute vcm/chunk");
-  cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-  if (strcmp(cchunk->style,"chunk/atom") != 0)
-    error->all(FLERR,"Compute vcm/chunk does not use chunk/atom compute");
-}
-
-/* ---------------------------------------------------------------------- */
-
 void ComputeVCMChunk::setup()
 {
   // one-time calculation of per-chunk mass
@@ -98,23 +70,12 @@ void ComputeVCMChunk::compute_array()
   int index;
   double massone;
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
-
-  // compute chunk/atom assigns atoms to chunk IDs
-  // extract ichunk index vector from compute
-  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
-
-  nchunk = cchunk->setup_chunks();
-  cchunk->compute_ichunk();
   int *ichunk = cchunk->ichunk;
 
-  if (nchunk > maxchunk) allocate();
-  size_array_rows = nchunk;
-
   // zero local per-chunk values
 
-  for (int i = 0; i < nchunk; i++)
+  for (int i = 0; i < nchunk; i++) vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
-    vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
   if (massneed)
     for (int i = 0; i < nchunk; i++) massproc[i] = 0.0;
 
@@ -131,8 +92,10 @@ void ComputeVCMChunk::compute_array()
     if (mask[i] & groupbit) {
       index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
       vcm[index][0] += v[i][0] * massone;
       vcm[index][1] += v[i][1] * massone;
       vcm[index][2] += v[i][2] * massone;
@@ -140,80 +103,25 @@ void ComputeVCMChunk::compute_array()
     }
 
   MPI_Allreduce(&vcm[0][0], &vcmall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-  if (massneed)
+  if (massneed) MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-    MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
 
   for (int i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
       vcmall[i][0] /= masstotal[i];
       vcmall[i][1] /= masstotal[i];
       vcmall[i][2] /= masstotal[i];
-    } else vcmall[i][0] = vcmall[i][1] = vcmall[i][2] = 0.0;
+    } else
+      vcmall[i][0] = vcmall[i][1] = vcmall[i][2] = 0.0;
   }
 }
 
-/* ----------------------------------------------------------------------
-   lock methods: called by fix ave/time
-   these methods ensure vector/array size is locked for Nfreq epoch
-     by passing lock info along to compute chunk/atom
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
-   increment lock counter
-------------------------------------------------------------------------- */
-
-void ComputeVCMChunk::lock_enable()
-{
-  cchunk->lockcount++;
-}
-
-/* ----------------------------------------------------------------------
-   decrement lock counter in compute chunk/atom, it if still exists
-------------------------------------------------------------------------- */
-
-void ComputeVCMChunk::lock_disable()
-{
-  int icompute = modify->find_compute(idchunk);
-  if (icompute >= 0) {
-    cchunk = dynamic_cast<ComputeChunkAtom *>(modify->compute[icompute]);
-    cchunk->lockcount--;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   calculate and return # of chunks = length of vector/array
-------------------------------------------------------------------------- */
-
-int ComputeVCMChunk::lock_length()
-{
-  nchunk = cchunk->setup_chunks();
-  return nchunk;
-}
-
-/* ----------------------------------------------------------------------
-   set the lock from startstep to stopstep
-------------------------------------------------------------------------- */
-
-void ComputeVCMChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
-{
-  cchunk->lock(fixptr,startstep,stopstep);
-}
-
-/* ----------------------------------------------------------------------
-   unset the lock
-------------------------------------------------------------------------- */
-
-void ComputeVCMChunk::unlock(Fix *fixptr)
-{
-  cchunk->unlock(fixptr);
-}
-
 /* ----------------------------------------------------------------------
    free and reallocate per-chunk arrays
 ------------------------------------------------------------------------- */
 
 void ComputeVCMChunk::allocate()
 {
+  ComputeChunk::allocate();
   memory->destroy(massproc);
   memory->destroy(masstotal);
   memory->destroy(vcm);
@@ -232,7 +140,7 @@ void ComputeVCMChunk::allocate()
 
 double ComputeVCMChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = (double) maxchunk * 2 * sizeof(double) + ComputeChunk::memory_usage();
   bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   return bytes;
 }

src/compute_vcm_chunk.h

@@ -20,39 +20,26 @@ ComputeStyle(vcm/chunk,ComputeVCMChunk);
 #ifndef LMP_COMPUTE_VCM_CHUNK_H
 #define LMP_COMPUTE_VCM_CHUNK_H
 
-#include "compute.h"
+#include "compute_chunk.h"
 
 namespace LAMMPS_NS {
 
-class ComputeVCMChunk : public Compute {
+class ComputeVCMChunk : public ComputeChunk {
  public:
   ComputeVCMChunk(class LAMMPS *, int, char **);
   ~ComputeVCMChunk() override;
-  void init() override;
+
   void setup() override;
   void compute_array() override;
 
-  void lock_enable() override;
-  void lock_disable() override;
-  int lock_length() override;
-  void lock(class Fix *, bigint, bigint) override;
-  void unlock(class Fix *) override;
-
   double memory_usage() override;
 
  private:
-  int nchunk, maxchunk;
-  int firstflag, massneed;
-  char *idchunk;
-  class ComputeChunkAtom *cchunk;
-
   double *massproc, *masstotal;
   double **vcm, **vcmall;
 
-  void allocate();
+  void allocate() override;
 };
-
 }    // namespace LAMMPS_NS
-
 #endif
 #endif