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);
@@ -130,23 +113,13 @@ void ComputeDipoleTIP4PChunk::init()
 
 void ComputeDipoleTIP4PChunk::compute_array()
 {
-  int i,index;
+  int i, index;
   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++) {
@@ -172,13 +145,16 @@ void ComputeDipoleTIP4PChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      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
-      domain->unmap(x[i],image[i],unwrap);
+          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];
       com[index][0] += unwrap[0] * massone;
@@ -186,9 +162,9 @@ void ComputeDipoleTIP4PChunk::compute_array()
       com[index][2] += unwrap[2] * massone;
     }
 
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(chrgproc,chrgtotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(chrgproc, chrgtotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -202,20 +178,20 @@ void ComputeDipoleTIP4PChunk::compute_array()
 
   for (i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
 
       if (type[i] == typeO) {
-        find_M(i,xM);
+        find_M(i, xM);
         xi = xM;
       } else {
         xi = x[i];
       }
-      domain->unmap(xi,image[i],unwrap);
+      domain->unmap(xi, image[i], unwrap);
       if (atom->q_flag) {
-        dipole[index][0] += q[i]*unwrap[0];
+        dipole[index][0] += q[i] * unwrap[0];
-        dipole[index][1] += q[i]*unwrap[1];
+        dipole[index][1] += q[i] * unwrap[1];
-        dipole[index][2] += q[i]*unwrap[2];
+        dipole[index][2] += q[i] * unwrap[2];
       }
       if (atom->mu_flag) {
         dipole[index][0] += mu[i][0];
@@ -225,82 +201,26 @@ void ComputeDipoleTIP4PChunk::compute_array()
     }
   }
 
-  MPI_Allreduce(&dipole[0][0],&dipoleall[0][0],4*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&dipole[0][0], &dipoleall[0][0], 4 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++) {
     // correct for position dependence with charged chunks
-    dipoleall[i][0] -= chrgtotal[i]*comall[i][0];
+    dipoleall[i][0] -= chrgtotal[i] * comall[i][0];
-    dipoleall[i][1] -= chrgtotal[i]*comall[i][1];
+    dipoleall[i][1] -= chrgtotal[i] * comall[i][1];
-    dipoleall[i][2] -= chrgtotal[i]*comall[i][2];
+    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);
@@ -310,14 +230,14 @@ void ComputeDipoleTIP4PChunk::allocate()
   memory->destroy(dipole);
   memory->destroy(dipoleall);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"dipole/tip4p/chunk:massproc");
+  memory->create(massproc, maxchunk, "dipole/tip4p/chunk:massproc");
-  memory->create(masstotal,maxchunk,"dipole/tip4p/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "dipole/tip4p/chunk:masstotal");
-  memory->create(chrgproc,maxchunk,"dipole/tip4p/chunk:chrgproc");
+  memory->create(chrgproc, maxchunk, "dipole/tip4p/chunk:chrgproc");
-  memory->create(chrgtotal,maxchunk,"dipole/tip4p/chunk:chrgtotal");
+  memory->create(chrgtotal, maxchunk, "dipole/tip4p/chunk:chrgtotal");
-  memory->create(com,maxchunk,3,"dipole/tip4p/chunk:com");
+  memory->create(com, maxchunk, 3, "dipole/tip4p/chunk:com");
-  memory->create(comall,maxchunk,3,"dipole/tip4p/chunk:comall");
+  memory->create(comall, maxchunk, 3, "dipole/tip4p/chunk:comall");
-  memory->create(dipole,maxchunk,4,"dipole/tip4p/chunk:dipole");
+  memory->create(dipole, maxchunk, 4, "dipole/tip4p/chunk:dipole");
-  memory->create(dipoleall,maxchunk,4,"dipole/tip4p/chunk:dipoleall");
+  memory->create(dipoleall, maxchunk, 4, "dipole/tip4p/chunk:dipoleall");
   array = dipoleall;
 }
 
@@ -327,9 +247,9 @@ 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 * 3 * sizeof(double);
-  bytes += (double)maxchunk * 2*4 * sizeof(double);
+  bytes += (double) maxchunk * 2 * 4 * sizeof(double);
   return bytes;
 }
 
@@ -342,14 +262,14 @@ void ComputeDipoleTIP4PChunk::find_M(int i, double *xM)
   int iH1 = atom->map(atom->tag[i] + 1);
   int iH2 = atom->map(atom->tag[i] + 2);
 
-  if ((iH1 == -1) || (iH2 == -1)) error->one(FLERR,"TIP4P hydrogen is missing");
+  if ((iH1 == -1) || (iH2 == -1)) error->one(FLERR, "TIP4P hydrogen is missing");
   if ((atom->type[iH1] != typeH) || (atom->type[iH2] != typeH))
-    error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
+    error->one(FLERR, "TIP4P hydrogen has incorrect atom type");
 
   // set iH1,iH2 to index of closest image to O
 
-  iH1 = domain->closest_image(i,iH1);
+  iH1 = domain->closest_image(i, iH1);
-  iH2 = domain->closest_image(i,iH2);
+  iH2 = domain->closest_image(i, iH2);
 
   double delx1 = x[iH1][0] - x[i][0];
   double dely1 = x[iH1][1] - x[i][1];

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
@@ -33,9 +32,9 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg), id_gyration_chunk(nullptr), shape_parameters(nullptr)
+    Compute(lmp, narg, arg), id_gyration_chunk(nullptr), shape_parameters(nullptr)
 {
-  if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape/chunk command");
+  if (narg != 4) error->all(FLERR, "Illegal compute gyration/shape/chunk command");
 
   // ID of compute gyration
   id_gyration_chunk = utils::strdup(arg[3]);
@@ -58,7 +57,7 @@ ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char
 
 ComputeGyrationShapeChunk::~ComputeGyrationShapeChunk()
 {
-  delete [] id_gyration_chunk;
+  delete[] id_gyration_chunk;
   memory->destroy(shape_parameters);
 }
 
@@ -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)
+  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;
@@ -125,18 +124,20 @@ void ComputeGyrationShapeChunk::compute_array()
     ione[0][2] = ione[2][0] = gyration_tensor[ichunk][4];
     ione[1][2] = ione[2][1] = gyration_tensor[ichunk][5];
 
-    int ierror = MathEigen::jacobi3(ione,evalues,evectors);
+    int ierror = MathEigen::jacobi3(ione, evalues, evectors);
-    if (ierror) error->all(FLERR, "Insufficient Jacobi rotations "
+    if (ierror)
-                         "for gyration/shape");
+      error->all(FLERR,
+                 "Insufficient Jacobi rotations "
+                 "for gyration/shape");
 
     // sort the eigenvalues according to their size with bubble sort
     double t;
     for (int i = 0; i < 3; i++) {
-      for (int j = 0; j < 2-i; j++) {
+      for (int j = 0; j < 2 - i; j++) {
-        if (fabs(evalues[j]) < fabs(evalues[j+1])) {
+        if (fabs(evalues[j]) < fabs(evalues[j + 1])) {
           t = evalues[j];
-          evalues[j] = evalues[j+1];
+          evalues[j] = evalues[j + 1];
-          evalues[j+1] = t;
+          evalues[j + 1] = t;
         }
       }
     }
@@ -147,14 +148,14 @@ void ComputeGyrationShapeChunk::compute_array()
     double sq_eigen_z = MathSpecial::square(evalues[2]);
 
     double nominator = sq_eigen_x + sq_eigen_y + sq_eigen_z;
-    double denominator = MathSpecial::square(evalues[0]+evalues[1]+evalues[2]);
+    double denominator = MathSpecial::square(evalues[0] + evalues[1] + evalues[2]);
 
     shape_parameters[ichunk][0] = evalues[0];
     shape_parameters[ichunk][1] = evalues[1];
     shape_parameters[ichunk][2] = evalues[2];
-    shape_parameters[ichunk][3] = evalues[0] - 0.5*(evalues[1] + evalues[2]);
+    shape_parameters[ichunk][3] = evalues[0] - 0.5 * (evalues[1] + evalues[2]);
     shape_parameters[ichunk][4] = evalues[1] - evalues[2];
-    shape_parameters[ichunk][5] = 1.5*nominator/denominator - 0.5;
+    shape_parameters[ichunk][5] = 1.5 * nominator / denominator - 0.5;
   }
 }
 
@@ -176,7 +177,7 @@ void ComputeGyrationShapeChunk::allocate()
 {
   memory->destroy(shape_parameters);
   former_nchunks = current_nchunks;
-  memory->create(shape_parameters,current_nchunks,6,"gyration/shape/chunk:shape_parameters");
+  memory->create(shape_parameters, current_nchunks, 6, "gyration/shape/chunk:shape_parameters");
   array = shape_parameters;
   size_array_rows = current_nchunks;
 }

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
@@ -19,22 +18,18 @@
 #include "domain.h"
 #include "error.h"
 #include "memory.h"
-#include "modify.h"
-#include "update.h"
-
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
-enum{ONCE,NFREQ,EVERY};
+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");
+  if (narg != 4) error->all(FLERR, "Illegal compute com/chunk command");
 
   array_flag = 1;
   size_array_cols = 3;
@@ -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;
 
@@ -133,86 +93,32 @@ void ComputeCOMChunk::compute_array()
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       com[index][0] += unwrap[0] * massone;
       com[index][1] += unwrap[1] * massone;
       com[index][2] += unwrap[2] * massone;
       if (massneed) massproc[index] += massone;
     }
 
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  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
 ------------------------------------------------------------------------- */
@@ -224,10 +130,10 @@ void ComputeCOMChunk::allocate()
   memory->destroy(com);
   memory->destroy(comall);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"com/chunk:massproc");
+  memory->create(massproc, maxchunk, "com/chunk:massproc");
-  memory->create(masstotal,maxchunk,"com/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "com/chunk:masstotal");
-  memory->create(com,maxchunk,3,"com/chunk:com");
+  memory->create(com, maxchunk, 3, "com/chunk:com");
-  memory->create(comall,maxchunk,3,"com/chunk:comall");
+  memory->create(comall, maxchunk, 3, "com/chunk:comall");
   array = comall;
 }
 
@@ -237,7 +143,8 @@ void ComputeCOMChunk::allocate()
 
 double ComputeCOMChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
-  bytes += (double) maxchunk * 2*3 * sizeof(double);
+  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);
@@ -90,40 +77,23 @@ 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");
 }
 
 /* ---------------------------------------------------------------------- */
 
 void ComputeDipoleChunk::compute_array()
 {
-  int i,index;
+  int i, index;
   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++) {
@@ -147,14 +117,17 @@ void ComputeDipoleChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      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);
+      domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       if (atom->q_flag) chrgproc[index] += atom->q[i];
       com[index][0] += unwrap[0] * massone;
@@ -162,9 +135,9 @@ void ComputeDipoleChunk::compute_array()
       com[index][2] += unwrap[2] * massone;
     }
 
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(chrgproc,chrgtotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(chrgproc, chrgtotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -178,13 +151,13 @@ void ComputeDipoleChunk::compute_array()
 
   for (i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      domain->unmap(x[i],image[i],unwrap);
+      domain->unmap(x[i], image[i], unwrap);
       if (atom->q_flag) {
-        dipole[index][0] += q[i]*unwrap[0];
+        dipole[index][0] += q[i] * unwrap[0];
-        dipole[index][1] += q[i]*unwrap[1];
+        dipole[index][1] += q[i] * unwrap[1];
-        dipole[index][2] += q[i]*unwrap[2];
+        dipole[index][2] += q[i] * unwrap[2];
       }
       if (atom->mu_flag) {
         dipole[index][0] += mu[i][0];
@@ -194,83 +167,25 @@ 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
-    dipoleall[i][0] -= chrgtotal[i]*comall[i][0];
+    dipoleall[i][0] -= chrgtotal[i] * comall[i][0];
-    dipoleall[i][1] -= chrgtotal[i]*comall[i][1];
+    dipoleall[i][1] -= chrgtotal[i] * comall[i][1];
-    dipoleall[i][2] -= chrgtotal[i]*comall[i][2];
+    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);
@@ -280,14 +195,14 @@ void ComputeDipoleChunk::allocate()
   memory->destroy(dipole);
   memory->destroy(dipoleall);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"dipole/chunk:massproc");
+  memory->create(massproc, maxchunk, "dipole/chunk:massproc");
-  memory->create(masstotal,maxchunk,"dipole/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "dipole/chunk:masstotal");
-  memory->create(chrgproc,maxchunk,"dipole/chunk:chrgproc");
+  memory->create(chrgproc, maxchunk, "dipole/chunk:chrgproc");
-  memory->create(chrgtotal,maxchunk,"dipole/chunk:chrgtotal");
+  memory->create(chrgtotal, maxchunk, "dipole/chunk:chrgtotal");
-  memory->create(com,maxchunk,3,"dipole/chunk:com");
+  memory->create(com, maxchunk, 3, "dipole/chunk:com");
-  memory->create(comall,maxchunk,3,"dipole/chunk:comall");
+  memory->create(comall, maxchunk, 3, "dipole/chunk:comall");
-  memory->create(dipole,maxchunk,4,"dipole/chunk:dipole");
+  memory->create(dipole, maxchunk, 4, "dipole/chunk:dipole");
-  memory->create(dipoleall,maxchunk,4,"dipole/chunk:dipoleall");
+  memory->create(dipoleall, maxchunk, 4, "dipole/chunk:dipoleall");
   array = dipoleall;
 }
 
@@ -297,8 +212,9 @@ void ComputeDipoleChunk::allocate()
 
 double ComputeDipoleChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
-  bytes += (double)maxchunk * 2*3 * sizeof(double);
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
-  bytes += (double)maxchunk * 2*4 * 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
@@ -46,10 +37,11 @@ ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
   tensor = 0;
   int iarg = 4;
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"tensor") == 0) {
+    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;
+  int i, index;
-  double dx,dy,dz,massone;
+  double dx, dy, dz, massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_vector();
 
   com_chunk();
   int *ichunk = cchunk->ichunk;
@@ -127,33 +101,34 @@ void ComputeGyrationChunk::compute_vector()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      domain->unmap(x[i],image[i],unwrap);
+      domain->unmap(x[i], image[i], unwrap);
       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];
-      rg[index] += (dx*dx + dy*dy + dz*dz) * massone;
+      else
+        massone = mass[type[i]];
+      rg[index] += (dx * dx + dy * dy + dz * dz) * massone;
     }
 
-  MPI_Allreduce(rg,rgall,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  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]);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void ComputeGyrationChunk::compute_array()
 {
-  int i,j,index;
+  int i, j, index;
-  double dx,dy,dz,massone;
+  double dx, dy, dz, massone;
   double unwrap[3];
 
-  invoked_array = update->ntimestep;
+  ComputeChunk::compute_array();
 
   com_chunk();
   int *ichunk = cchunk->ichunk;
@@ -171,34 +146,33 @@ void ComputeGyrationChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      domain->unmap(x[i],image[i],unwrap);
+      domain->unmap(x[i], image[i], unwrap);
       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];
-      rgt[index][0] += dx*dx * massone;
+      else
-      rgt[index][1] += dy*dy * massone;
+        massone = mass[type[i]];
-      rgt[index][2] += dz*dz * massone;
+      rgt[index][0] += dx * dx * massone;
-      rgt[index][3] += dx*dy * massone;
+      rgt[index][1] += dy * dy * massone;
-      rgt[index][4] += dx*dz * massone;
+      rgt[index][2] += dz * dz * massone;
-      rgt[index][5] += dy*dz * massone;
+      rgt[index][3] += dx * dy * massone;
+      rgt[index][4] += dx * dz * massone;
+      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++) {
@@ -240,19 +204,21 @@ void ComputeGyrationChunk::com_chunk()
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
       com[index][1] += unwrap[1] * massone;
       com[index][2] += unwrap[2] * massone;
     }
 
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (int i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -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);
@@ -334,17 +245,17 @@ void ComputeGyrationChunk::allocate()
   memory->destroy(rgt);
   memory->destroy(rgtall);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"gyration/chunk:massproc");
+  memory->create(massproc, maxchunk, "gyration/chunk:massproc");
-  memory->create(masstotal,maxchunk,"gyration/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "gyration/chunk:masstotal");
-  memory->create(com,maxchunk,3,"gyration/chunk:com");
+  memory->create(com, maxchunk, 3, "gyration/chunk:com");
-  memory->create(comall,maxchunk,3,"gyration/chunk:comall");
+  memory->create(comall, maxchunk, 3, "gyration/chunk:comall");
   if (tensor) {
-    memory->create(rgt,maxchunk,6,"gyration/chunk:rgt");
+    memory->create(rgt, maxchunk, 6, "gyration/chunk:rgt");
-    memory->create(rgtall,maxchunk,6,"gyration/chunk:rgtall");
+    memory->create(rgtall, maxchunk, 6, "gyration/chunk:rgtall");
     array = rgtall;
   } else {
-    memory->create(rg,maxchunk,"gyration/chunk:rg");
+    memory->create(rg, maxchunk, "gyration/chunk:rg");
-    memory->create(rgall,maxchunk,"gyration/chunk:rgall");
+    memory->create(rgall, maxchunk, "gyration/chunk:rgall");
     vector = rgall;
   }
 }
@@ -355,9 +266,12 @@ void ComputeGyrationChunk::allocate()
 
 double ComputeGyrationChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
-  bytes += (double) maxchunk * 2*3 * sizeof(double);
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
-  if (tensor) bytes += (double) maxchunk * 2*6 * sizeof(double);
+  bytes += (double) maxchunk * 2 * 3 * sizeof(double);
-  else bytes += (double) maxchunk * 2 * sizeof(double);
+  if (tensor)
+    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
@@ -14,25 +13,21 @@
 
 #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");
+  if (narg != 4) error->all(FLERR, "Illegal compute inertia/chunk command");
 
   array_flag = 1;
   size_array_cols = 6;
@@ -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;
+  int i, j, index;
-  double dx,dy,dz,massone;
+  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++) {
@@ -120,19 +82,21 @@ void ComputeInertiaChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
       com[index][1] += unwrap[1] * massone;
       com[index][2] += unwrap[2] * massone;
     }
 
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -146,83 +110,26 @@ void ComputeInertiaChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
       dz = unwrap[2] - comall[index][2];
-      inertia[index][0] += massone * (dy*dy + dz*dz);
+      inertia[index][0] += massone * (dy * dy + dz * dz);
-      inertia[index][1] += massone * (dx*dx + dz*dz);
+      inertia[index][1] += massone * (dx * dx + dz * dz);
-      inertia[index][2] += massone * (dx*dx + dy*dy);
+      inertia[index][2] += massone * (dx * dx + dy * dy);
-      inertia[index][3] -= massone * dx*dy;
+      inertia[index][3] -= massone * dx * dy;
-      inertia[index][4] -= massone * dy*dz;
+      inertia[index][4] -= massone * dy * dz;
-      inertia[index][5] -= massone * dx*dz;
+      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
 ------------------------------------------------------------------------- */
@@ -236,12 +143,12 @@ void ComputeInertiaChunk::allocate()
   memory->destroy(inertia);
   memory->destroy(inertiaall);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"inertia/chunk:massproc");
+  memory->create(massproc, maxchunk, "inertia/chunk:massproc");
-  memory->create(masstotal,maxchunk,"inertia/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "inertia/chunk:masstotal");
-  memory->create(com,maxchunk,3,"inertia/chunk:com");
+  memory->create(com, maxchunk, 3, "inertia/chunk:com");
-  memory->create(comall,maxchunk,3,"inertia/chunk:comall");
+  memory->create(comall, maxchunk, 3, "inertia/chunk:comall");
-  memory->create(inertia,maxchunk,6,"inertia/chunk:inertia");
+  memory->create(inertia, maxchunk, 6, "inertia/chunk:inertia");
-  memory->create(inertiaall,maxchunk,6,"inertia/chunk:inertiaall");
+  memory->create(inertiaall, maxchunk, 6, "inertia/chunk:inertiaall");
   array = inertiaall;
 }
 
@@ -251,8 +158,9 @@ void ComputeInertiaChunk::allocate()
 
 double ComputeInertiaChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
-  bytes += (double) maxchunk * 2*3 * sizeof(double);
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
-  bytes += (double) maxchunk * 2*6 * 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
@@ -22,19 +21,16 @@
 #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");
+  if (narg != 4) error->all(FLERR, "Illegal compute msd/chunk command");
 
   array_flag = 1;
   size_array_cols = 4;
@@ -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
@@ -58,7 +49,7 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
 
   id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
   fix = dynamic_cast<FixStoreGlobal *>(
-    modify->add_fix(fmt::format("{} {} STORE/GLOBAL 1 1", id_fix,group->names[igroup])));
+      modify->add_fix(fmt::format("{} {} STORE/GLOBAL 1 1", id_fix, group->names[igroup])));
 }
 
 /* ---------------------------------------------------------------------- */
@@ -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);
@@ -82,19 +72,14 @@ 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()
 
   if (!firstflag) {
     fix = dynamic_cast<FixStoreGlobal *>(modify->get_fix_by_id(id_fix));
-    if (!fix) error->all(FLERR,"Could not find compute msd/chunk fix with ID {}", id_fix);
+    if (!fix) error->all(FLERR, "Could not find compute msd/chunk fix with ID {}", id_fix);
   }
 }
 
@@ -113,7 +98,7 @@ void ComputeMSDChunk::setup()
   // otherwise reset its size now and initialize to current COM
 
   if (fix->nrow == nchunk && fix->ncol == 3) return;
-  fix->reset_global(nchunk,3);
+  fix->reset_global(nchunk, 3);
 
   double **cominit = fix->astore;
   for (int i = 0; i < nchunk; i++) {
@@ -132,25 +117,15 @@ 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;
+    error->all(FLERR, "Compute msd/chunk nchunk is not static");
-    allocate();
-    size_array_rows = nchunk;
-  } else if (n != nchunk)
-    error->all(FLERR,"Compute msd/chunk nchunk is not static");
 
   // zero local per-chunk values
 
@@ -171,19 +146,21 @@ void ComputeMSDChunk::compute_array()
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
       com[index][1] += unwrap[1] * massone;
       com[index][2] += unwrap[2] * massone;
     }
 
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (int i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -198,87 +175,32 @@ void ComputeMSDChunk::compute_array()
 
   if (firstflag) return;
 
-  double dx,dy,dz;
+  double dx, dy, dz;
   double **cominit = fix->astore;
 
   for (int i = 0; i < nchunk; i++) {
     dx = comall[i][0] - cominit[i][0];
     dy = comall[i][1] - cominit[i][1];
     dz = comall[i][2] - cominit[i][2];
-    msd[i][0] = dx*dx;
+    msd[i][0] = dx * dx;
-    msd[i][1] = dy*dy;
+    msd[i][1] = dy * dy;
-    msd[i][2] = dz*dz;
+    msd[i][2] = dz * dz;
-    msd[i][3] = dx*dx + dy*dy + dz*dz;
+    msd[i][3] = dx * dx + dy * dy + dz * dz;
   }
 }
 
-/* ----------------------------------------------------------------------
-   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()
 {
-  memory->create(massproc,nchunk,"msd/chunk:massproc");
+  ComputeChunk::allocate();
-  memory->create(masstotal,nchunk,"msd/chunk:masstotal");
+  memory->create(massproc, nchunk, "msd/chunk:massproc");
-  memory->create(com,nchunk,3,"msd/chunk:com");
+  memory->create(masstotal, nchunk, "msd/chunk:masstotal");
-  memory->create(comall,nchunk,3,"msd/chunk:comall");
+  memory->create(com, nchunk, 3, "msd/chunk:com");
-  memory->create(msd,nchunk,4,"msd/chunk:msd");
+  memory->create(comall, nchunk, 3, "msd/chunk:comall");
+  memory->create(msd, nchunk, 4, "msd/chunk:msd");
   array = msd;
 }
 
@@ -288,8 +210,9 @@ void ComputeMSDChunk::allocate()
 
 double ComputeMSDChunk::memory_usage()
 {
-  double bytes = (bigint) nchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
-  bytes += (double) nchunk * 2*3 * sizeof(double);
+  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;
 
@@ -32,11 +28,11 @@ 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");
+  if (narg != 4) error->all(FLERR, "Illegal compute omega/chunk command");
 
   array_flag = 1;
   size_array_cols = 3;
@@ -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;
+  int i, j, m, index;
-  double dx,dy,dz,massone;
+  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();
@@ -129,19 +95,21 @@ void ComputeOmegaChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
       com[index][1] += unwrap[1] * massone;
       com[index][2] += unwrap[2] * massone;
     }
 
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -155,24 +123,25 @@ void ComputeOmegaChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
       dz = unwrap[2] - comall[index][2];
-      inertia[index][0] += massone * (dy*dy + dz*dz);
+      inertia[index][0] += massone * (dy * dy + dz * dz);
-      inertia[index][1] += massone * (dx*dx + dz*dz);
+      inertia[index][1] += massone * (dx * dx + dz * dz);
-      inertia[index][2] += massone * (dx*dx + dy*dy);
+      inertia[index][2] += massone * (dx * dx + dy * dy);
-      inertia[index][3] -= massone * dx*dy;
+      inertia[index][3] -= massone * dx * dy;
-      inertia[index][4] -= massone * dy*dz;
+      inertia[index][4] -= massone * dy * dz;
-      inertia[index][5] -= massone * dx*dz;
+      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
 
@@ -180,37 +149,38 @@ void ComputeOmegaChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      domain->unmap(x[i],image[i],unwrap);
+      domain->unmap(x[i], image[i], unwrap);
       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];
-      angmom[index][0] += massone * (dy*v[i][2] - dz*v[i][1]);
+      else
-      angmom[index][1] += massone * (dz*v[i][0] - dx*v[i][2]);
+        massone = mass[type[i]];
-      angmom[index][2] += massone * (dx*v[i][1] - dy*v[i][0]);
+      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
 
-  double determinant,invdeterminant;
+  double determinant, invdeterminant;
-  double idiag[3],ex[3],ey[3],ez[3],cross[3];
+  double idiag[3], ex[3], ey[3], ez[3], cross[3];
-  double ione[3][3],inverse[3][3],evectors[3][3];
+  double ione[3][3], inverse[3][3], evectors[3][3];
-  double *iall,*mall;
+  double *iall, *mall;
 
   for (m = 0; m < nchunk; m++) {
 
     // determinant = triple product of rows of inertia matrix
 
     iall = &inertiaall[m][0];
-    determinant = iall[0] * (iall[1]*iall[2] - iall[4]*iall[4]) +
+    determinant = iall[0] * (iall[1] * iall[2] - iall[4] * iall[4]) +
-      iall[3] * (iall[4]*iall[5] - iall[3]*iall[2]) +
+        iall[3] * (iall[4] * iall[5] - iall[3] * iall[2]) +
-      iall[5] * (iall[3]*iall[4] - iall[1]*iall[5]);
+        iall[5] * (iall[3] * iall[4] - iall[1] * iall[5]);
 
     ione[0][0] = iall[0];
     ione[1][1] = iall[1];
@@ -223,39 +193,34 @@ void ComputeOmegaChunk::compute_array()
     // use L = Iw, inverting I to solve for w
 
     if (determinant > EPSILON) {
-      inverse[0][0] = ione[1][1]*ione[2][2] - ione[1][2]*ione[2][1];
+      inverse[0][0] = ione[1][1] * ione[2][2] - ione[1][2] * ione[2][1];
-      inverse[0][1] = -(ione[0][1]*ione[2][2] - ione[0][2]*ione[2][1]);
+      inverse[0][1] = -(ione[0][1] * ione[2][2] - ione[0][2] * ione[2][1]);
-      inverse[0][2] = ione[0][1]*ione[1][2] - ione[0][2]*ione[1][1];
+      inverse[0][2] = ione[0][1] * ione[1][2] - ione[0][2] * ione[1][1];
 
-      inverse[1][0] = -(ione[1][0]*ione[2][2] - ione[1][2]*ione[2][0]);
+      inverse[1][0] = -(ione[1][0] * ione[2][2] - ione[1][2] * ione[2][0]);
-      inverse[1][1] = ione[0][0]*ione[2][2] - ione[0][2]*ione[2][0];
+      inverse[1][1] = ione[0][0] * ione[2][2] - ione[0][2] * ione[2][0];
-      inverse[1][2] = -(ione[0][0]*ione[1][2] - ione[0][2]*ione[1][0]);
+      inverse[1][2] = -(ione[0][0] * ione[1][2] - ione[0][2] * ione[1][0]);
 
-      inverse[2][0] = ione[1][0]*ione[2][1] - ione[1][1]*ione[2][0];
+      inverse[2][0] = ione[1][0] * ione[2][1] - ione[1][1] * ione[2][0];
-      inverse[2][1] = -(ione[0][0]*ione[2][1] - ione[0][1]*ione[2][0]);
+      inverse[2][1] = -(ione[0][0] * ione[2][1] - ione[0][1] * ione[2][0]);
-      inverse[2][2] = ione[0][0]*ione[1][1] - ione[0][1]*ione[1][0];
+      inverse[2][2] = ione[0][0] * ione[1][1] - ione[0][1] * ione[1][0];
 
-      invdeterminant = 1.0/determinant;
+      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
+      // handle each (nearly) singular I matrix
-    // due to 2-atom chunk or linear molecule
+      // due to 2-atom chunk or linear molecule
-    // use jacobi3() and angmom_to_omega() to calculate valid omega
+      // use jacobi3() and angmom_to_omega() to calculate valid omega
 
     } else {
-      int ierror = MathEigen::jacobi3(ione,idiag,evectors);
+      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];
@@ -270,88 +235,32 @@ void ComputeOmegaChunk::compute_array()
       // enforce 3 evectors as a right-handed coordinate system
       // flip 3rd vector if needed
 
-      MathExtra::cross3(ex,ey,cross);
+      MathExtra::cross3(ex, ey, cross);
-      if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
+      if (MathExtra::dot3(cross, ez) < 0.0) MathExtra::negate3(ez);
 
       // if any principal moment < scaled EPSILON, set to 0.0
 
       double max;
-      max = MAX(idiag[0],idiag[1]);
+      max = MAX(idiag[0], idiag[1]);
-      max = MAX(max,idiag[2]);
+      max = MAX(max, idiag[2]);
 
-      if (idiag[0] < EPSILON*max) idiag[0] = 0.0;
+      if (idiag[0] < EPSILON * max) idiag[0] = 0.0;
-      if (idiag[1] < EPSILON*max) idiag[1] = 0.0;
+      if (idiag[1] < EPSILON * max) idiag[1] = 0.0;
-      if (idiag[2] < EPSILON*max) idiag[2] = 0.0;
+      if (idiag[2] < EPSILON * max) idiag[2] = 0.0;
 
       // calculate omega using diagonalized inertia matrix
 
-      MathExtra::angmom_to_omega(&angmomall[m][0],ex,ey,ez,idiag,&omega[m][0]);
+      MathExtra::angmom_to_omega(&angmomall[m][0], ex, ey, ez, idiag, &omega[m][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 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);
@@ -362,15 +271,15 @@ void ComputeOmegaChunk::allocate()
   memory->destroy(angmomall);
   memory->destroy(omega);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"omega/chunk:massproc");
+  memory->create(massproc, maxchunk, "omega/chunk:massproc");
-  memory->create(masstotal,maxchunk,"omega/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "omega/chunk:masstotal");
-  memory->create(com,maxchunk,3,"omega/chunk:com");
+  memory->create(com, maxchunk, 3, "omega/chunk:com");
-  memory->create(comall,maxchunk,3,"omega/chunk:comall");
+  memory->create(comall, maxchunk, 3, "omega/chunk:comall");
-  memory->create(inertia,maxchunk,6,"omega/chunk:inertia");
+  memory->create(inertia, maxchunk, 6, "omega/chunk:inertia");
-  memory->create(inertiaall,maxchunk,6,"omega/chunk:inertiaall");
+  memory->create(inertiaall, maxchunk, 6, "omega/chunk:inertiaall");
-  memory->create(angmom,maxchunk,3,"omega/chunk:angmom");
+  memory->create(angmom, maxchunk, 3, "omega/chunk:angmom");
-  memory->create(angmomall,maxchunk,3,"omega/chunk:angmomall");
+  memory->create(angmomall, maxchunk, 3, "omega/chunk:angmomall");
-  memory->create(omega,maxchunk,3,"omega/chunk:omega");
+  memory->create(omega, maxchunk, 3, "omega/chunk:omega");
   array = omega;
 }
 
@@ -380,10 +289,11 @@ void ComputeOmegaChunk::allocate()
 
 double ComputeOmegaChunk::memory_usage()
 {
-  double bytes = (bigint) maxchunk * 2 * sizeof(double);
+  double bytes = ComputeChunk::memory_usage();
-  bytes += (double) maxchunk * 2*3 * sizeof(double);
+  bytes += (bigint) maxchunk * 2 * sizeof(double);
-  bytes += (double) maxchunk * 2*6 * sizeof(double);
+  bytes += (double) maxchunk * 2 * 3 * sizeof(double);
-  bytes += (double) maxchunk * 2*3 * sizeof(double);
+  bytes += (double) maxchunk * 2 * 6 * sizeof(double);
+  bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   bytes += (double) maxchunk * 3 * sizeof(double);
   return bytes;
 }

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();
 
@@ -46,40 +39,32 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
 
   int i;
   for (int iarg = 4; iarg < narg; iarg++) {
-    i = iarg-4;
+    i = iarg - 4;
 
-    if (strcmp(arg[iarg],"count") == 0) {
+    if (strcmp(arg[iarg], "count") == 0) {
       pack_choice[i] = &ComputePropertyChunk::pack_count;
       countflag = 1;
-    } else if (strcmp(arg[iarg],"id") == 0) {
+    } 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) {
+    } 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) {
+    } 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) {
+    } 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;
@@ -99,8 +84,7 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) :
 
 ComputePropertyChunk::~ComputePropertyChunk()
 {
-  delete [] idchunk;
+  delete[] pack_choice;
-  delete [] pack_choice;
   memory->destroy(vector);
   memory->destroy(array);
   memory->destroy(count_one);
@@ -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
 
@@ -150,101 +109,34 @@ 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_one, maxchunk, "property/chunk:count_one");
-    memory->create(count_all,maxchunk,"property/chunk:count_all");
+    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;
 }
@@ -277,13 +170,13 @@ void ComputePropertyChunk::pack_count(int n)
   int nlocal = atom->nlocal;
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
       count_one[index]++;
     }
   }
 
-  MPI_Allreduce(count_one,count_all,nchunk,MPI_INT,MPI_SUM,world);
+  MPI_Allreduce(count_one, count_all, nchunk, MPI_INT, MPI_SUM, world);
 
   for (int m = 0; m < nchunk; m++) {
     buf[n] = count_all[m];

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
@@ -30,29 +29,30 @@
 
 using namespace LAMMPS_NS;
 
-enum{ SUM, MINN, MAXX };
+enum { SUM, MINN, MAXX };
 
 #define BIG 1.0e20
 
 /* ---------------------------------------------------------------------- */
 
 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);
+  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;
 
@@ -60,7 +60,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
 
   int expand = 0;
   char **earg;
-  int nargnew = utils::expand_args(FLERR,narg-iarg,&arg[iarg],1,earg,lmp);
+  int nargnew = utils::expand_args(FLERR, narg - iarg, &arg[iarg], 1, earg, lmp);
 
   if (earg != &arg[iarg]) expand = 1;
   arg = earg;
@@ -78,7 +78,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
     val.val.c = nullptr;
 
     if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1))
-      error->all(FLERR,"Illegal compute reduce/chunk argument: {}", arg[iarg]);
+      error->all(FLERR, "Illegal compute reduce/chunk argument: {}", arg[iarg]);
 
     values.push_back(val);
   }
@@ -86,7 +86,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
   // if wildcard expansion occurred, free earg memory from expand_args()
 
   if (expand) {
-    for (int i = 0; i < nargnew; i++) delete [] earg[i];
+    for (int i = 0; i < nargnew; i++) delete[] earg[i];
     memory->sfree(earg);
   }
 
@@ -96,15 +96,15 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
     if (val.which == ArgInfo::COMPUTE) {
       val.val.c = modify->get_compute_by_id(val.id);
       if (!val.val.c)
-        error->all(FLERR,"Compute ID {} for compute reduce/chunk does not exist", val.id);
+        error->all(FLERR, "Compute ID {} for compute reduce/chunk does not exist", val.id);
       if (!val.val.c->peratom_flag)
-        error->all(FLERR,"Compute reduce/chunk compute {} does not calculate per-atom values",
+        error->all(FLERR, "Compute reduce/chunk compute {} does not calculate per-atom values",
                    val.id);
       if ((val.argindex == 0) && (val.val.c->size_peratom_cols != 0))
-        error->all(FLERR,"Compute reduce/chunk compute {} does not calculate a per-atom vector",
+        error->all(FLERR, "Compute reduce/chunk compute {} does not calculate a per-atom vector",
                    val.id);
       if (val.argindex && (val.val.c->size_peratom_cols == 0))
-        error->all(FLERR,"Compute reduce/chunk compute {} does not calculate a per-atom array",
+        error->all(FLERR, "Compute reduce/chunk compute {} does not calculate a per-atom array",
                    val.id);
       if (val.argindex && (val.argindex > val.val.c->size_peratom_cols))
         error->all(FLERR, "Compute reduce/chunk compute array {} is accessed out-of-range", val.id);
@@ -112,22 +112,24 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) :
     } else if (val.which == ArgInfo::FIX) {
       val.val.f = modify->get_fix_by_id(val.id);
       if (!val.val.f)
-        error->all(FLERR,"Fix ID {} for compute reduce/chunk does not exist", val.id);
+        error->all(FLERR, "Fix ID {} for compute reduce/chunk does not exist", val.id);
       if (!val.val.f->peratom_flag)
-        error->all(FLERR,"Compute reduce/chunk fix {} does not calculate per-atom values", val.id);
+        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);
+        error->all(FLERR, "Compute reduce/chunk fix {} array is accessed out-of-range", val.id);
 
     } else if (val.which == ArgInfo::VARIABLE) {
       val.val.v = input->variable->find(val.id.c_str());
       if (val.val.v < 0)
-        error->all(FLERR,"Variable name {} for compute reduce/chunk does not exist", val.id);
+        error->all(FLERR, "Variable name {} for compute reduce/chunk does not exist", val.id);
       if (input->variable->atomstyle(val.val.v) == 0)
-        error->all(FLERR,"Compute reduce/chunk variable is not atom-style variable");
+        error->all(FLERR, "Compute reduce/chunk variable is not atom-style variable");
     }
   }
 
@@ -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
 
@@ -184,109 +186,84 @@ void ComputeReduceChunk::init()
     if (val.which == ArgInfo::COMPUTE) {
       val.val.c = modify->get_compute_by_id(val.id);
       if (!val.val.c)
-        error->all(FLERR,"Compute ID {} for compute reduce/chunk does not exist", val.id);
+        error->all(FLERR, "Compute ID {} for compute reduce/chunk does not exist", val.id);
 
     } else if (val.which == ArgInfo::FIX) {
       val.val.f = modify->get_fix_by_id(val.id);
       if (!val.val.f)
-        error->all(FLERR,"Fix ID {} for compute reduce/chunk does not exist", val.id);
+        error->all(FLERR, "Fix ID {} for compute reduce/chunk does not exist", val.id);
 
     } else if (val.which == ArgInfo::VARIABLE) {
       val.val.v = input->variable->find(val.id.c_str());
       if (val.val.v < 0)
-        error->all(FLERR,"Variable name {} for compute reduce/chunk does not exist", val.id);
+        error->all(FLERR, "Variable name {} for compute reduce/chunk does not exist", val.id);
     }
   }
 }
 
 /* ---------------------------------------------------------------------- */
 
-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);
     maxchunk = nchunk;
-    memory->create(vlocal,maxchunk,"reduce/chunk:vlocal");
+    memory->create(vlocal, maxchunk, "reduce/chunk:vlocal");
-    memory->create(vglobal,maxchunk,"reduce/chunk:vglobal");
+    memory->create(vglobal, maxchunk, "reduce/chunk:vglobal");
     vector = vglobal;
   }
 
   // perform local reduction of single peratom value
 
-  compute_one(0,vlocal,1);
+  compute_one(0, vlocal, 1);
 
   // reduce the per-chunk values across all procs
 
   if (mode == SUM)
-    MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+    MPI_Allreduce(vlocal, vglobal, nchunk, MPI_DOUBLE, MPI_SUM, world);
   else if (mode == MINN)
-    MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MIN,world);
+    MPI_Allreduce(vlocal, vglobal, nchunk, MPI_DOUBLE, MPI_MIN, world);
   else if (mode == MAXX)
-    MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MAX,world);
+    MPI_Allreduce(vlocal, vglobal, nchunk, MPI_DOUBLE, MPI_MAX, world);
 }
 
 /* ---------------------------------------------------------------------- */
 
 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);
     maxchunk = nchunk;
-    memory->create(alocal,maxchunk,values.size(),"reduce/chunk:alocal");
+    memory->create(alocal, maxchunk, values.size(), "reduce/chunk:alocal");
-    memory->create(aglobal,maxchunk,values.size(),"reduce/chunk:aglobal");
+    memory->create(aglobal, maxchunk, values.size(), "reduce/chunk:aglobal");
     array = aglobal;
   }
 
   // perform local reduction of all peratom values
 
-  for (std::size_t m = 0; m < values.size(); m++) compute_one(m,&alocal[0][m],values.size());
+  for (std::size_t m = 0; m < values.size(); m++) compute_one(m, &alocal[0][m], values.size());
 
   // 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);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -295,7 +272,7 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
 {
   // initialize per-chunk values in accumulation vector
 
-  for (std::size_t i = 0; i < values.size()*nchunk; i += nstride) vchunk[i] = initvalue;
+  for (std::size_t i = 0; i < values.size() * nchunk; i += nstride) vchunk[i] = initvalue;
 
   // loop over my atoms
   // use peratom input and chunk ID of each atom to update vector
@@ -321,61 +298,61 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride)
       double *vcompute = val.val.c->vector_atom;
       for (int i = 0; i < nlocal; i++) {
         if (!(mask[i] & groupbit)) continue;
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
-        combine(vchunk[index*nstride],vcompute[i]);
+        combine(vchunk[index * nstride], vcompute[i]);
       }
     } else {
       double **acompute = val.val.c->array_atom;
       int argindexm1 = val.argindex - 1;
       for (int i = 0; i < nlocal; i++) {
         if (!(mask[i] & groupbit)) continue;
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
-        combine(vchunk[index*nstride],acompute[i][argindexm1]);
+        combine(vchunk[index * nstride], acompute[i][argindexm1]);
       }
     }
 
-  // access fix fields, check if fix frequency is a match
+    // access fix fields, check if fix frequency is a match
 
   } else if (val.which == ArgInfo::FIX) {
     if (update->ntimestep % val.val.f->peratom_freq)
-      error->all(FLERR,"Fix used in compute reduce/chunk not computed at compatible time");
+      error->all(FLERR, "Fix used in compute reduce/chunk not computed at compatible time");
 
     if (val.argindex == 0) {
       double *vfix = val.val.f->vector_atom;
       for (int i = 0; i < nlocal; i++) {
         if (!(mask[i] & groupbit)) continue;
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
-        combine(vchunk[index*nstride],vfix[i]);
+        combine(vchunk[index * nstride], vfix[i]);
       }
     } else {
       double **afix = val.val.f->array_atom;
       int argindexm1 = val.argindex - 1;
       for (int i = 0; i < nlocal; i++) {
         if (!(mask[i] & groupbit)) continue;
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
-        combine(vchunk[index*nstride],afix[i][argindexm1]);
+        combine(vchunk[index * nstride], afix[i][argindexm1]);
       }
     }
 
-  // evaluate atom-style variable
+    // evaluate atom-style variable
 
   } else if (val.which == ArgInfo::VARIABLE) {
     if (atom->nmax > maxatom) {
       memory->destroy(varatom);
       maxatom = atom->nmax;
-      memory->create(varatom,maxatom,"reduce/chunk:varatom");
+      memory->create(varatom, maxatom, "reduce/chunk:varatom");
     }
 
-    input->variable->compute_atom(val.val.v,igroup,varatom,1,0);
+    input->variable->compute_atom(val.val.v, igroup, varatom, 1, 0);
     for (int i = 0; i < nlocal; i++) {
       if (!(mask[i] & groupbit)) continue;
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      combine(vchunk[index*nstride],varatom[i]);
+      combine(vchunk[index * nstride], varatom[i]);
     }
   }
 }
@@ -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
@@ -27,42 +26,40 @@
 
 using namespace LAMMPS_NS;
 
-enum{TEMP,KECOM,INTERNAL};
+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();
 
   // optional per-chunk values
 
-  nvalues = narg-4;
+  nvalues = narg - 4;
   which = new int[nvalues];
   nvalues = 0;
 
   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++;
   }
@@ -76,56 +73,49 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
   cdof = 0.0;
 
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"com") == 0) {
+    if (strcmp(arg[iarg], "com") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
+      if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
-      comflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
+      comflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       iarg += 2;
-    } else if (strcmp(arg[iarg],"bias") == 0) {
+    } else if (strcmp(arg[iarg], "bias") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
+      if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
       biasflag = 1;
-      id_bias = utils::strdup(arg[iarg+1]);
+      id_bias = utils::strdup(arg[iarg + 1]);
       iarg += 2;
-    } else if (strcmp(arg[iarg],"adof") == 0) {
+    } else if (strcmp(arg[iarg], "adof") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
+      if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
-      adof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
+      adof = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
       iarg += 2;
-    } else if (strcmp(arg[iarg],"cdof") == 0) {
+    } else if (strcmp(arg[iarg], "cdof") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/chunk command");
+      if (iarg + 2 > narg) error->all(FLERR, "Illegal compute temp/chunk command");
-      cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
+      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
   // won't be two biases since comflag and biasflag cannot both be set
 
   if (comflag && biasflag)
-    error->all(FLERR,"Cannot use both com and bias with compute temp/chunk");
+    error->all(FLERR, "Cannot use both com and bias with compute temp/chunk");
   if (comflag) tempbias = 1;
 
   // vector data
 
   vector = new double[size_vector];
 
-  // chunk-based data
+  if (nvalues) {
-
-  nchunk = 1;
-  maxchunk = 0;
-
-  if (nvalues)  {
     array_flag = 1;
     size_array_cols = nvalues;
     size_array_rows = 0;
@@ -133,7 +123,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
     extarray = 0;
   }
 
-  allocate();
+  ComputeTempChunk::allocate();
   comstep = -1;
 }
 
@@ -141,10 +131,9 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeTempChunk::~ComputeTempChunk()
 {
-  delete [] idchunk;
+  delete[] which;
-  delete [] which;
+  delete[] id_bias;
-  delete [] id_bias;
+  delete[] vector;
-  delete [] vector;
   memory->destroy(sum);
   memory->destroy(sumall);
   memory->destroy(count);
@@ -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];
   }
 }
 
@@ -180,7 +161,7 @@ void ComputeTempChunk::init()
 
 double ComputeTempChunk::compute_scalar()
 {
-  int i,index;
+  int i, index;
 
   invoked_scalar = update->ntimestep;
 
@@ -224,47 +205,45 @@ double ComputeTempChunk::compute_scalar()
     if (rmass) {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          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 {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          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++;
-      }
+        }
     }
 
   } else {
-    double vx,vy,vz;
+    double vx, vy, vz;
     if (rmass) {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          index = ichunk[i] - 1;
           if (index < 0) continue;
           vx = v[i][0] - vcmall[index][0];
           vy = v[i][1] - vcmall[index][1];
           vz = v[i][2] - vcmall[index][2];
-          t += (vx*vx + vy*vy + vz*vz) * rmass[i];
+          t += (vx * vx + vy * vy + vz * vz) * rmass[i];
           mycount++;
         }
     } else {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          index = ichunk[i] - 1;
           if (index < 0) continue;
           vx = v[i][0] - vcmall[index][0];
           vy = v[i][1] - vcmall[index][1];
           vz = v[i][2] - vcmall[index][2];
-          t += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
+          t += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
           mycount++;
-      }
+        }
     }
   }
 
@@ -274,16 +253,15 @@ double ComputeTempChunk::compute_scalar()
 
   // final temperature
 
-  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&t, &scalar, 1, MPI_DOUBLE, MPI_SUM, world);
   double rcount = mycount;
   double allcount;
-  MPI_Allreduce(&rcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&rcount, &allcount, 1, MPI_DOUBLE, MPI_SUM, world);
 
-  double dof = nchunk*cdof + adof*allcount;
+  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;
 }
@@ -292,22 +270,11 @@ double ComputeTempChunk::compute_scalar()
 
 void ComputeTempChunk::compute_vector()
 {
-  int i,index;
+  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) {
@@ -329,40 +296,44 @@ void ComputeTempChunk::compute_vector()
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
-  double massone,t[6];
+  double massone, t[6];
   for (i = 0; i < 6; i++) t[i] = 0.0;
 
   if (!comflag) {
     for (i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
-        if (rmass) massone = rmass[i];
+        if (rmass)
-        else massone = mass[type[i]];
+          massone = rmass[i];
-        t[0] += massone * v[i][0]*v[i][0];
+        else
-        t[1] += massone * v[i][1]*v[i][1];
+          massone = mass[type[i]];
-        t[2] += massone * v[i][2]*v[i][2];
+        t[0] += massone * v[i][0] * v[i][0];
-        t[3] += massone * v[i][0]*v[i][1];
+        t[1] += massone * v[i][1] * v[i][1];
-        t[4] += massone * v[i][0]*v[i][2];
+        t[2] += massone * v[i][2] * v[i][2];
-        t[5] += massone * v[i][1]*v[i][2];
+        t[3] += massone * v[i][0] * v[i][1];
+        t[4] += massone * v[i][0] * v[i][2];
+        t[5] += massone * v[i][1] * v[i][2];
       }
   } else {
-    double vx,vy,vz;
+    double vx, vy, vz;
     for (i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        index = ichunk[i]-1;
+        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];
-        t[0] += massone * vx*vx;
+        t[0] += massone * vx * vx;
-        t[1] += massone * vy*vy;
+        t[1] += massone * vy * vy;
-        t[2] += massone * vz*vz;
+        t[2] += massone * vz * vz;
-        t[3] += massone * vx*vy;
+        t[3] += massone * vx * vy;
-        t[4] += massone * vx*vz;
+        t[4] += massone * vx * vz;
-        t[5] += massone * vy*vz;
+        t[5] += massone * vy * vz;
       }
   }
 
@@ -372,7 +343,7 @@ void ComputeTempChunk::compute_vector()
 
   // final KE
 
-  MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(t, vector, 6, MPI_DOUBLE, MPI_SUM, world);
   for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
 }
 
@@ -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
@@ -425,7 +389,7 @@ void ComputeTempChunk::compute_array()
 
 void ComputeTempChunk::vcm_compute()
 {
-  int i,index;
+  int i, index;
   double massone;
 
   // avoid re-computing VCM more than once per step
@@ -448,18 +412,20 @@ void ComputeTempChunk::vcm_compute()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      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;
       massproc[index] += massone;
     }
 
-  MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&vcm[0][0], &vcmall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -478,7 +444,7 @@ void ComputeTempChunk::vcm_compute()
 
 void ComputeTempChunk::temperature(int icol)
 {
-  int i,index;
+  int i, index;
   int *ichunk = cchunk->ichunk;
 
   // zero local per-chunk values
@@ -501,65 +467,65 @@ void ComputeTempChunk::temperature(int icol)
     if (rmass) {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          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 {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          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]++;
-      }
+        }
     }
 
   } else {
-    double vx,vy,vz;
+    double vx, vy, vz;
     if (rmass) {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          index = ichunk[i] - 1;
           if (index < 0) continue;
           vx = v[i][0] - vcmall[index][0];
           vy = v[i][1] - vcmall[index][1];
           vz = v[i][2] - vcmall[index][2];
-          sum[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
+          sum[index] += (vx * vx + vy * vy + vz * vz) * rmass[i];
           count[index]++;
         }
     } else {
       for (i = 0; i < nlocal; i++)
         if (mask[i] & groupbit) {
-          index = ichunk[i]-1;
+          index = ichunk[i] - 1;
           if (index < 0) continue;
           vx = v[i][0] - vcmall[index][0];
           vy = v[i][1] - vcmall[index][1];
           vz = v[i][2] - vcmall[index][2];
-          sum[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
+          sum[index] += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
           count[index]++;
-      }
+        }
     }
   }
 
   // sum across procs
 
-  MPI_Allreduce(sum,sumall,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(sum, sumall, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(count,countall,nchunk,MPI_INT,MPI_SUM,world);
+  MPI_Allreduce(count, countall, nchunk, MPI_INT, MPI_SUM, world);
 
   // normalize temperatures by per-chunk DOF
 
-  double dof,tfactor;
+  double dof, tfactor;
   double mvv2e = force->mvv2e;
   double boltz = force->boltz;
 
   for (i = 0; i < nchunk; i++) {
-    dof = cdof + adof*countall[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];
   }
 }
@@ -585,37 +551,35 @@ void ComputeTempChunk::kecom(int icol)
   int *type = atom->type;
   int nlocal = atom->nlocal;
 
-  double vx,vy,vz;
+  double vx, vy, vz;
   if (rmass) {
     for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
         vx = vcmall[index][0];
         vy = vcmall[index][1];
         vz = vcmall[index][2];
-        sum[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
+        sum[index] += (vx * vx + vy * vy + vz * vz) * rmass[i];
       }
   } else {
     for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
         vx = vcmall[index][0];
         vy = vcmall[index][1];
         vz = vcmall[index][2];
-        sum[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
+        sum[index] += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
       }
   }
 
   // sum across procs
 
-  MPI_Allreduce(sum,sumall,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  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];
-
 }
 
 /* ----------------------------------------------------------------------
@@ -641,36 +605,35 @@ void ComputeTempChunk::internal(int icol)
   int *type = atom->type;
   int nlocal = atom->nlocal;
 
-  double vx,vy,vz;
+  double vx, vy, vz;
   if (rmass) {
     for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
         vx = v[i][0] - vcmall[index][0];
         vy = v[i][1] - vcmall[index][1];
         vz = v[i][2] - vcmall[index][2];
-        sum[index] += (vx*vx + vy*vy + vz*vz) * rmass[i];
+        sum[index] += (vx * vx + vy * vy + vz * vz) * rmass[i];
       }
   } else {
     for (int i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) {
-        index = ichunk[i]-1;
+        index = ichunk[i] - 1;
         if (index < 0) continue;
         vx = v[i][0] - vcmall[index][0];
         vy = v[i][1] - vcmall[index][1];
         vz = v[i][2] - vcmall[index][2];
-        sum[index] += (vx*vx + vy*vy + vz*vz) * mass[type[i]];
+        sum[index] += (vx * vx + vy * vy + vz * vz) * mass[type[i]];
       }
   }
 
   // sum across procs
 
-  MPI_Allreduce(sum,sumall,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  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];
 }
 
 /* ----------------------------------------------------------------------
@@ -683,7 +646,7 @@ void ComputeTempChunk::internal(int icol)
 
 void ComputeTempChunk::remove_bias(int i, double *v)
 {
-  int index = cchunk->ichunk[i]-1;
+  int index = cchunk->ichunk[i] - 1;
   if (index < 0) return;
   v[0] -= vcmall[index][0];
   v[1] -= vcmall[index][1];
@@ -705,7 +668,7 @@ void ComputeTempChunk::remove_bias_all()
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
       v[i][0] -= vcmall[index][0];
       v[i][1] -= vcmall[index][1];
@@ -720,7 +683,7 @@ void ComputeTempChunk::remove_bias_all()
 
 void ComputeTempChunk::restore_bias(int i, double *v)
 {
-  int index = cchunk->ichunk[i]-1;
+  int index = cchunk->ichunk[i] - 1;
   if (index < 0) return;
   v[0] += vcmall[index][0];
   v[1] += vcmall[index][1];
@@ -743,7 +706,7 @@ void ComputeTempChunk::restore_bias_all()
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
       v[i][0] += vcmall[index][0];
       v[i][1] += vcmall[index][1];
@@ -751,89 +714,34 @@ 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);
   memory->destroy(countall);
   memory->destroy(array);
   maxchunk = nchunk;
-  memory->create(sum,maxchunk,"temp/chunk:sum");
+  memory->create(sum, maxchunk, "temp/chunk:sum");
-  memory->create(sumall,maxchunk,"temp/chunk:sumall");
+  memory->create(sumall, maxchunk, "temp/chunk:sumall");
-  memory->create(count,maxchunk,"temp/chunk:count");
+  memory->create(count, maxchunk, "temp/chunk:count");
-  memory->create(countall,maxchunk,"temp/chunk:countall");
+  memory->create(countall, maxchunk, "temp/chunk:countall");
-  memory->create(array,maxchunk,nvalues,"temp/chunk:array");
+  memory->create(array, maxchunk, nvalues, "temp/chunk:array");
 
   if (comflag || nvalues) {
     memory->destroy(massproc);
     memory->destroy(masstotal);
     memory->destroy(vcm);
     memory->destroy(vcmall);
-    memory->create(massproc,maxchunk,"vcm/chunk:massproc");
+    memory->create(massproc, maxchunk, "vcm/chunk:massproc");
-    memory->create(masstotal,maxchunk,"vcm/chunk:masstotal");
+    memory->create(masstotal, maxchunk, "vcm/chunk:masstotal");
-    memory->create(vcm,maxchunk,3,"vcm/chunk:vcm");
+    memory->create(vcm, maxchunk, 3, "vcm/chunk:vcm");
-    memory->create(vcmall,maxchunk,3,"vcm/chunk:vcmall");
+    memory->create(vcmall, maxchunk, 3, "vcm/chunk:vcmall");
   }
 }
 
@@ -843,12 +751,12 @@ 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) {
     bytes += (double) maxchunk * 2 * sizeof(double);
-    bytes += (double) maxchunk * 2*3 * sizeof(double);
+    bytes += (double) maxchunk * 2 * 3 * sizeof(double);
   }
   return bytes;
 }

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
@@ -14,24 +13,21 @@
 
 #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");
+  if (narg != 4) error->all(FLERR, "Illegal compute torque/chunk command");
 
   array_flag = 1;
   size_array_cols = 3;
@@ -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;
+  int i, index;
-  double dx,dy,dz,massone;
+  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++) {
@@ -119,19 +82,21 @@ void ComputeTorqueChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      if (rmass) massone = rmass[i];
+      if (rmass)
-      else massone = mass[type[i]];
+        massone = rmass[i];
-      domain->unmap(x[i],image[i],unwrap);
+      else
+        massone = mass[type[i]];
+      domain->unmap(x[i], image[i], unwrap);
       massproc[index] += massone;
       com[index][0] += unwrap[0] * massone;
       com[index][1] += unwrap[1] * massone;
       com[index][2] += unwrap[2] * massone;
     }
 
-  MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
-  MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&com[0][0], &comall[0][0], 3 * nchunk, MPI_DOUBLE, MPI_SUM, world);
 
   for (i = 0; i < nchunk; i++) {
     if (masstotal[i] > 0.0) {
@@ -147,83 +112,26 @@ void ComputeTorqueChunk::compute_array()
 
   for (i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      index = ichunk[i] - 1;
       if (index < 0) continue;
-      domain->unmap(x[i],image[i],unwrap);
+      domain->unmap(x[i], image[i], unwrap);
       dx = unwrap[0] - comall[index][0];
       dy = unwrap[1] - comall[index][1];
       dz = unwrap[2] - comall[index][2];
-      torque[index][0] += dy*f[i][2] - dz*f[i][1];
+      torque[index][0] += dy * f[i][2] - dz * f[i][1];
-      torque[index][1] += dz*f[i][0] - dx*f[i][2];
+      torque[index][1] += dz * f[i][0] - dx * f[i][2];
-      torque[index][2] += dx*f[i][1] - dy*f[i][0];
+      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);
@@ -231,12 +139,12 @@ void ComputeTorqueChunk::allocate()
   memory->destroy(torque);
   memory->destroy(torqueall);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"torque/chunk:massproc");
+  memory->create(massproc, maxchunk, "torque/chunk:massproc");
-  memory->create(masstotal,maxchunk,"torque/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "torque/chunk:masstotal");
-  memory->create(com,maxchunk,3,"torque/chunk:com");
+  memory->create(com, maxchunk, 3, "torque/chunk:com");
-  memory->create(comall,maxchunk,3,"torque/chunk:comall");
+  memory->create(comall, maxchunk, 3, "torque/chunk:comall");
-  memory->create(torque,maxchunk,3,"torque/chunk:torque");
+  memory->create(torque, maxchunk, 3, "torque/chunk:torque");
-  memory->create(torqueall,maxchunk,3,"torque/chunk:torqueall");
+  memory->create(torqueall, maxchunk, 3, "torque/chunk:torqueall");
   array = torqueall;
 }
 
@@ -246,8 +154,8 @@ 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);
-  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
@@ -14,25 +13,22 @@
 
 #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;
 
-enum{ONCE,NFREQ,EVERY};
+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");
+  if (narg != 4) error->all(FLERR, "Illegal compute vcm/chunk command");
 
   array_flag = 1;
   size_array_cols = 3;
@@ -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;
 
@@ -129,100 +90,47 @@ void ComputeVCMChunk::compute_array()
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      index = ichunk[i]-1;
+      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;
       if (massneed) massproc[index] += massone;
     }
 
-  MPI_Allreduce(&vcm[0][0],&vcmall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
+  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);
   memory->destroy(vcmall);
   maxchunk = nchunk;
-  memory->create(massproc,maxchunk,"vcm/chunk:massproc");
+  memory->create(massproc, maxchunk, "vcm/chunk:massproc");
-  memory->create(masstotal,maxchunk,"vcm/chunk:masstotal");
+  memory->create(masstotal, maxchunk, "vcm/chunk:masstotal");
-  memory->create(vcm,maxchunk,3,"vcm/chunk:vcm");
+  memory->create(vcm, maxchunk, 3, "vcm/chunk:vcm");
-  memory->create(vcmall,maxchunk,3,"vcm/chunk:vcmall");
+  memory->create(vcmall, maxchunk, 3, "vcm/chunk:vcmall");
   array = vcmall;
 }
 
@@ -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);
+  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