add compute vacf/chunk command

doc/src/Commands_compute.rst

@@ -178,6 +178,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ti <compute_ti>`
    * :doc:`torque/chunk <compute_torque_chunk>`
    * :doc:`vacf <compute_vacf>`
+   * :doc:`vacf/chunk <compute_vacf_chunk>`
    * :doc:`vcm/chunk <compute_vcm_chunk>`
    * :doc:`viscosity/cos <compute_viscosity_cos>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`

doc/src/compute.rst

@@ -356,6 +356,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`ti <compute_ti>` - thermodynamic integration free energy values
 * :doc:`torque/chunk <compute_torque_chunk>` - torque applied on each chunk
 * :doc:`vacf <compute_vacf>` - velocity auto-correlation function of group of atoms
+* :doc:`vacf/chunk <compute_vacf_chunk>` - velocity auto-correlation for the center of mass velocities of chunks of atoms
 * :doc:`vcm/chunk <compute_vcm_chunk>` - velocity of center-of-mass for each chunk
 * :doc:`viscosity/cos <compute_viscosity_cos>` - velocity profile under cosine-shaped acceleration
 * :doc:`voronoi/atom <compute_voronoi_atom>` - Voronoi volume and neighbors for each atom

doc/src/compute_msd.rst

@@ -116,7 +116,9 @@ Compute *msd* cannot be used with a dynamic group.
 Related commands
 """"""""""""""""
 
-:doc:`compute msd/nongauss <compute_msd_nongauss>`, :doc:`compute displace_atom <compute_displace_atom>`, :doc:`fix store/state <fix_store_state>`, :doc:`compute msd/chunk <compute_msd_chunk>`
+:doc:`compute msd/nongauss <compute_msd_nongauss>`,
+:doc:`compute displace_atom <compute_displace_atom>`, :doc:`fix store/state <fix_store_state>`,
+:doc:`compute msd/chunk <compute_msd_chunk>`
 
 Default
 """""""

doc/src/compute_msd_chunk.rst

@@ -131,7 +131,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute msd <compute_msd>`
+:doc:`compute msd <compute_msd>`, :doc:`compute vacf/chunk <compute_vacf_chunk>`
 
 Default
 """""""

doc/src/compute_vacf.rst

@@ -76,7 +76,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute msd <compute_msd>`
+:doc:`compute msd <compute_msd>`, :doc:`compute vacf/chunk <compute_vacf_chunk>`
 
 Default
 """""""

doc/src/compute_vacf_chunk.rst

@@ -0,0 +1,122 @@
+.. index:: compute vacf/chunk
+
+compute vacf/chunk command
+==========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID vacf/chunk chunkID
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* vacf/chunk = style name of this compute command
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all vacf/chunk molchunk
+
+Description
+"""""""""""
+
+Define a computation that calculates the velocity auto-correlation
+function (VACF) for multiple chunks of atoms.
+
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
+chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
+single chunk (or no chunk).  The ID for this command is specified as
+chunkID.  For example, a single chunk could be the atoms in a molecule
+or atoms in a spatial bin.  See the :doc:`compute chunk/atom
+<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
+details of how chunks can be defined and examples of how they can be
+used to measure properties of a system.
+
+Four quantities are calculated by this compute for each chunk.  The
+first 3 quantities are the product of the initial center of mass
+velocity (VCM) for each chunk in *x*, *y*, and *z* direction with the
+current center of mass velocity in the same direction.  The fourth
+component is the total VACF, i.e. the sum of the three components.
+
+Note that only atoms in the specified group contribute to the
+calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
+defines its own group; atoms will have a chunk ID = 0 if they are not in
+that group, signifying they are not assigned to a chunk, and will thus
+also not contribute to this calculation.  You can specify the "all"
+group for this command if you simply want to include atoms with non-zero
+chunk IDs.
+
+The integral of the VACF versus time is proportional to the diffusion
+coefficient of the diffusing chunks.
+
+.. note::
+
+   The number of chunks *Nchunk* calculated by the
+   :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant
+   each time this compute is invoked, so that the dot product for each chunk
+   from its original position can be computed consistently.  If *Nchunk*
+   does not remain constant, an error will be generated.  If needed, you
+   can enforce a constant *Nchunk* by using the *nchunk once* or *ids once*
+   options when specifying the :doc:`compute chunk/atom <compute_chunk_atom>`
+   command.
+
+.. note::
+
+   This compute stores the original center-of-mass velocities of each
+   chunk.  When a VACF is calculated on a later timestep, it is assumed
+   that the same atoms are assigned to the same chunk ID.  However
+   LAMMPS has no simple way to ensure this is the case, though you can
+   use the *ids once* option when specifying the :doc:`compute
+   chunk/atom <compute_chunk_atom>` command.  Note that if this is not
+   the case, the VACF calculation does not have a sensible meaning.
+
+.. note::
+
+   If you want the quantities calculated by this compute to be
+   continuous when running from a :doc:`restart file <read_restart>`, then
+   you should use the same ID for this compute, as in the original run.
+   This is so that the fix this compute creates to store per-chunk
+   quantities will also have the same ID, and thus be initialized
+   correctly with chunk reference positions from the restart file.
+
+The simplest way to output the results of the compute vacf/chunk
+calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
+command, for example:
+
+.. code-block:: LAMMPS
+
+   compute cc1 all chunk/atom molecule
+   compute myChunk all vacf/chunk cc1
+   fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+
+Output info
+"""""""""""
+
+This compute calculates a global array where the number of rows = the
+number of chunks *Nchunk* as calculated by the specified :doc:`compute
+chunk/atom <compute_chunk_atom>` command.  The number of columns = 4 for
+the *x*, *y*, *z*, component and the total VACF.  These values can be
+accessed by any command that uses global array values from a compute as
+input.  See the :doc:`Howto output <Howto_output>` page for an overview
+of LAMMPS output options.
+
+The array values are "intensive".  The array values will be in
+distance\ :math:`^2` divided by time\ :math:`^2` :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`compute vacf <compute_vacf>`, :doc:`compute msd/chunk <compute_msd_chunk>`
+
+Default
+"""""""
+
+none

src/compute_msd_chunk.cpp

@@ -21,6 +21,7 @@
 #include "group.h"
 #include "memory.h"
 #include "modify.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -30,7 +31,7 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
     ComputeChunk(lmp, narg, arg), id_fix(nullptr), fix(nullptr), massproc(nullptr),
     masstotal(nullptr), com(nullptr), comall(nullptr), msd(nullptr)
 {
-  if (narg != 4) error->all(FLERR, "Illegal compute msd/chunk command");
+  if (narg != 4) error->all(FLERR, "Incorrect number of arguments for compute msd/chunk");
 
   msdnchunk = 0;
   array_flag = 1;
@@ -114,6 +115,8 @@ void ComputeMSDChunk::setup()
 
 void ComputeMSDChunk::compute_array()
 {
+  invoked_array = update->ntimestep;
+
   int index;
   double massone;
   double unwrap[3];
@@ -127,7 +130,7 @@ void ComputeMSDChunk::compute_array()
   if (firstflag)
     msdnchunk = nchunk;
   else if (msdnchunk != nchunk)
-    error->all(FLERR, "Compute msd/chunk nchunk is not static");
+    error->all(FLERR, Error::NOLASTLINE, "Compute msd/chunk nchunk is not static");
 
   // zero local per-chunk values
 

src/compute_vacf_chunk.cpp

@@ -0,0 +1,225 @@
+/* ----------------------------------------------------------------------
+   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_vacf_chunk.h"
+
+#include "atom.h"
+#include "compute_chunk_atom.h"
+#include "error.h"
+#include "fix_store_global.h"
+#include "group.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVACFChunk::ComputeVACFChunk(LAMMPS *lmp, int narg, char **arg) :
+    ComputeChunk(lmp, narg, arg), id_fix(nullptr), fix(nullptr), massproc(nullptr),
+    masstotal(nullptr), vcm(nullptr), vcmall(nullptr), vacf(nullptr)
+{
+  if (narg != 4) error->all(FLERR, "Incorrect number of arguments for compute vacf/chunk");
+
+  vacfnchunk = 0;
+  array_flag = 1;
+  size_array_cols = 4;
+  size_array_rows = 0;
+  size_array_rows_variable = 1;
+  extarray = 0;
+
+  ComputeVACFChunk::init();
+
+  // create a new fix STORE style for reference velocities
+  // id = compute-ID + COMPUTE_STORE, fix group = compute group
+  // do not know size of array at this point, just allocate 1x1 array
+  // fix creation must be done now so that a restart run can
+  //   potentially re-populate the fix array (and change it to correct size)
+  // otherwise size reset and init will be done in setup()
+
+  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])));
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVACFChunk::~ComputeVACFChunk()
+{
+  // check nfix in case all fixes have already been deleted
+
+  if (modify->nfix) modify->delete_fix(id_fix);
+
+  delete[] id_fix;
+  memory->destroy(massproc);
+  memory->destroy(masstotal);
+  memory->destroy(vcm);
+  memory->destroy(vcmall);
+  memory->destroy(vacf);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeVACFChunk::init()
+{
+  ComputeChunk::init();
+
+  // 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 vacf/chunk fix with ID {}", id_fix);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   compute initial VCM for each chunk
+   only once on timestep compute is defined, when firstflag = 1
+------------------------------------------------------------------------- */
+
+void ComputeVACFChunk::setup()
+{
+  if (!firstflag) return;
+  compute_array();
+  firstflag = 0;
+
+  // if fix->astore is already correct size, restart file set it up
+  // otherwise reset its size now and initialize to current VCM
+
+  if (fix->nrow == nchunk && fix->ncol == 3) return;
+  fix->reset_global(nchunk, 3);
+
+  double **vcminit = fix->astore;
+  for (int i = 0; i < nchunk; i++) {
+    vcminit[i][0] = vcmall[i][0];
+    vcminit[i][1] = vcmall[i][1];
+    vcminit[i][2] = vcmall[i][2];
+    vacf[i][0] = vacf[i][1] = vacf[i][2] = vacf[i][3] = 1.0;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeVACFChunk::compute_array()
+{
+  invoked_array = update->ntimestep;
+
+  int index;
+  double massone;
+
+  ComputeChunk::compute_array();
+  int *ichunk = cchunk->ichunk;
+
+  // first time call, allocate per-chunk arrays
+  // thereafter, require nchunk remain the same
+
+  if (firstflag)
+    vacfnchunk = nchunk;
+  else if (vacfnchunk != nchunk)
+    error->all(FLERR, Error::NOLASTLINE, "Compute vacf/chunk nchunk is not static");
+
+  // zero local per-chunk values
+
+  for (int i = 0; i < nchunk; i++) {
+    massproc[i] = 0.0;
+    vcm[i][0] = vcm[i][1] = vcm[i][2] = 0.0;
+  }
+
+  // compute current VCM for each chunk
+
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int *type = atom->type;
+  double *mass = atom->mass;
+  double *rmass = atom->rmass;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      index = ichunk[i] - 1;
+      if (index < 0) continue;
+      if (rmass)
+        massone = rmass[i];
+      else
+        massone = mass[type[i]];
+      massproc[index] += massone;
+      vcm[index][0] += v[i][0] * massone;
+      vcm[index][1] += v[i][1] * massone;
+      vcm[index][2] += v[i][2] * massone;
+    }
+
+  MPI_Allreduce(massproc, masstotal, nchunk, MPI_DOUBLE, MPI_SUM, world);
+  MPI_Allreduce(&vcm[0][0], &vcmall[0][0], 3 * 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];
+    }
+  }
+
+  // VACF is dot product between current and initial VCM
+  // vcminit is initilialized by setup() when firstflag is set
+
+  if (firstflag) return;
+
+  double vxsq, vysq, vzsq;
+  double **vcminit = fix->astore;
+
+  for (int i = 0; i < nchunk; i++) {
+    vxsq = vcmall[i][0] * vcminit[i][0];
+    vysq = vcmall[i][1] * vcminit[i][1];
+    vzsq = vcmall[i][2] * vcminit[i][2];
+    vacf[i][0] = vxsq;
+    vacf[i][1] = vysq;
+    vacf[i][2] = vzsq;
+    vacf[i][3] = vxsq + vysq + vzsq;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   one-time allocate of per-chunk arrays
+------------------------------------------------------------------------- */
+
+void ComputeVACFChunk::allocate()
+{
+  ComputeChunk::allocate();
+  memory->destroy(massproc);
+  memory->destroy(masstotal);
+  memory->destroy(vcm);
+  memory->destroy(vcmall);
+  memory->destroy(vacf);
+
+  memory->create(massproc, nchunk, "vacf/chunk:massproc");
+  memory->create(masstotal, nchunk, "vacf/chunk:masstotal");
+  memory->create(vcm, nchunk, 3, "vacf/chunk:vcm");
+  memory->create(vcmall, nchunk, 3, "vacf/chunk:vcmall");
+  memory->create(vacf, nchunk, 4, "vacf/chunk:vacf");
+  array = vacf;
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local data
+------------------------------------------------------------------------- */
+
+double ComputeVACFChunk::memory_usage()
+{
+  double bytes = ComputeChunk::memory_usage();
+  bytes += (bigint) nchunk * 2 * sizeof(double);
+  bytes += (double) nchunk * 2 * 3 * sizeof(double);
+  bytes += (double) nchunk * 4 * sizeof(double);
+  return bytes;
+}

src/compute_vacf_chunk.h

@@ -0,0 +1,52 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+// clang-format off
+ComputeStyle(vacf/chunk,ComputeVACFChunk);
+// clang-format on
+#else
+
+#ifndef LMP_COMPUTE_VACF_CHUNK_H
+#define LMP_COMPUTE_VACF_CHUNK_H
+
+#include "compute_chunk.h"
+
+namespace LAMMPS_NS {
+
+class ComputeVACFChunk : public ComputeChunk {
+ public:
+  ComputeVACFChunk(class LAMMPS *, int, char **);
+  ~ComputeVACFChunk() override;
+  void init() override;
+  void setup() override;
+
+  void compute_array() override;
+
+  double memory_usage() override;
+
+ protected:
+  bigint vacfnchunk;
+
+  char *id_fix;
+  class FixStoreGlobal *fix;
+
+  double *massproc, *masstotal;
+  double **vcm, **vcmall;
+  double **vacf;
+
+  void allocate() override;
+};
+}    // namespace LAMMPS_NS
+#endif
+#endif