rename fix STORE/PERATOM to STORE/ATOM

doc/src/Developer_notes.rst

@@ -11,6 +11,7 @@ Available topics are:
 
 - `Reading and parsing of text and text files`_
 - `Requesting and accessing neighbor lists`_
+- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
 - `Fix contributions to instantaneous energy, virial, and cumulative energy`_
 - `KSpace PPPM FFT grids`_
 
@@ -216,6 +217,30 @@ command:
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 
+Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are multiple ways to manage per-atom data within LAMMPS.  Often
+the per-atom storage is only used locally and managed by the class that
+uses it.  If the data has to persist between multiple time steps and
+migrate with atoms when they move from sub-domain to sub-domain or
+across periodic boundaries, then using a custom atom style, or :doc:`fix
+property/atom <fix_property_atom>`, or the internal fix STORE/ATOM are
+possible options.
+
+- Using the atom style is usually the most programming effort and mostly
+  needed when the per-atom data is an integral part of the model like a
+  per-atom charge or diameter and thus should be part of the Atoms
+  section of a :doc:`data file <read_data>`.
+
+- Fix property/atom is useful if the data is optional or should be
+  entered by the user, or accessed as a (named) custom property. In this
+  case the fix should be entered as part of the input (and not
+  internally) which allows to enter and store its content with data files.
+
+- Fix STORE/ATOM should be used when the data should be accessed internally
+  only and thus the fix can be created internally.
+
 Fix contributions to instantaneous energy, virial, and cumulative energy
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_updating.rst

@@ -24,6 +24,7 @@ Available topics in mostly chronological order are:
 - `Use of "override" instead of "virtual"`_
 - `Simplified and more compact neighbor list requests`_
 - `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
+- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
 - `Use Output::get_dump_by_id() instead of Output::find_dump()`_
 - `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
 
@@ -385,6 +386,34 @@ New:
 
 This change is **required** or else the code will not compile.
 
+Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: TBD
+
+The available functionality of the internal fix to store per-atom
+properties was expanded to enable storing data with ghost atoms and to
+support binary restart files.  With those changes, the fix was renamed
+to fix STORE/ATOM and the number and order of (required) arguments has
+changed.
+
+Old syntax: ``ID group-ID STORE/PERATOM rflag n1 n2 [n3]``
+
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+- :math:`n1 = 1, n2 = 1, \mathrm{no}\;n3 \to` per-atom vector, single value per atom
+- :math:`n1 = 1, n2 > 1, \mathrm{no}\;n3 \to` per-atom array, *n2* values per atom
+- :math:`n1 = 1, n2 > 0, n3 > 0 \to` per-atom tensor, *n2* x *n3* values per atom
+
+New syntax:  ``ID group-ID STORE/ATOM n1 n2 gflag rflag``
+
+- :math:`n1 = 1, n2 = 0 \to` per-atom vector, single value per atom
+- :math:`n1 > 1, n2 = 0 \to` per-atom array, *n1* values per atom
+- :math:`n1 > 0, n2 > 0 \to` per-atom tensor, *n1* x *n2* values per atom
+- *gflag* = 0/1, *no*/*yes* communicate per-atom values with ghost atoms
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+
+Since this is an internal fix, there is no user visible change.
+
 Use Output::get_dump_by_id() instead of Output::find_dump()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

src/AMOEBA/amoeba_induce.cpp

@@ -19,7 +19,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "my_page.h"

src/AMOEBA/amoeba_utils.cpp

@@ -17,7 +17,7 @@
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "neigh_list.h"
 
 #include <cmath>

src/AMOEBA/pair_amoeba.cpp

@@ -20,7 +20,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "math_special.h"
@@ -861,8 +861,8 @@ void PairAmoeba::init_style()
   Fix *myfix;
   if (first_flag) {
     id_pole = utils::strdup("AMOEBA_pole");
-    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 13 0 0 1",id_pole,group->names[0]));
+    myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM 13 0 0 1",id_pole,group->names[0]));
-    fixpole = dynamic_cast<FixStorePeratom *>(myfix);
+    fixpole = dynamic_cast<FixStoreAtom *>(myfix);
   }
 
   // creation of per-atom storage
@@ -873,14 +873,14 @@ void PairAmoeba::init_style()
 
   if (first_flag && use_pred) {
     id_udalt = utils::strdup("AMOEBA_udalt");
-    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM {} 3 0 1",
+    myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
                                         id_udalt, group->names[0], maxualt));
-    fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
 
     id_upalt = utils::strdup("AMOEBA_upalt");
-    myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM {} 3 0 1",
+    myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
                                         id_upalt, group->names[0], maxualt));
-    fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
   }
 
   // create pages for storing pairwise data:
@@ -995,21 +995,21 @@ void PairAmoeba::init_style()
   if (id_pole) {
     myfix = modify->get_fix_by_id(id_pole);
     if (!myfix)
-      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_pole);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_pole);
-    fixpole = dynamic_cast<FixStorePeratom *>(myfix);
+    fixpole = dynamic_cast<FixStoreAtom *>(myfix);
 
   }
 
   if (id_udalt) {
     myfix = modify->get_fix_by_id(id_udalt);
     if (!myfix)
-      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_udalt);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_udalt);
-    fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
 
     myfix = modify->get_fix_by_id(id_upalt);
     if (!myfix)
-      error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_upalt);
+      error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_upalt);
-    fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
+    fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
   }
 
   // assign hydrogen neighbors (redID) to each owned atom

src/AMOEBA/pair_amoeba.h

@@ -166,9 +166,9 @@ class PairAmoeba : public Pair {
   int *amgroup;    // AMOEBA polarization group, 1 to Ngroup
 
   char *id_pole, *id_udalt, *id_upalt;
-  class FixStorePeratom *fixpole;     // stores pole = multipole components
+  class FixStoreAtom *fixpole;     // stores pole = multipole components
-  class FixStorePeratom *fixudalt;    // stores udalt = induced dipole history
+  class FixStoreAtom *fixudalt;    // stores udalt = induced dipole history
-  class FixStorePeratom *fixupalt;    // stores upalt = induced dipole history
+  class FixStoreAtom *fixupalt;    // stores upalt = induced dipole history
 
   // static per-type properties defined in force-field file
 

src/CORESHELL/compute_temp_cs.cpp

@@ -24,7 +24,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "memory.h"
@@ -67,8 +67,8 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
   // id = compute-ID + COMPUTE_STORE, fix group = compute group
 
   id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
-  fix = dynamic_cast<FixStorePeratom *>(
+  fix = dynamic_cast<FixStoreAtom *>(
-    modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 0", id_fix, group->names[igroup])));
+    modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 0", id_fix, group->names[igroup])));
 
   // set fix store values = 0 for now
   // fill them in via setup() once Comm::borders() has been called

src/CORESHELL/compute_temp_cs.h

@@ -54,7 +54,7 @@ class ComputeTempCS : public Compute {
   double **vint;
 
   char *id_fix;
-  class FixStorePeratom *fix;
+  class FixStoreAtom *fix;
 
   void dof_compute();
   void vcm_pairs();

src/EXTRA-COMPUTE/compute_hma.cpp

@@ -54,7 +54,7 @@ https://doi.org/10.1103/PhysRevE.92.043303
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "improper.h"
@@ -90,8 +90,8 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
   // our new fix's group = same as compute group
 
   id_fix = utils::strdup(std::string(id)+"_COMPUTE_STORE");
-  fix = dynamic_cast<FixStorePeratom *>(
+  fix = dynamic_cast<FixStoreAtom *>(
-    modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
+    modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
 
   // calculate xu,yu,zu for fix store array
   // skip if reset from restart file
@@ -196,7 +196,7 @@ void ComputeHMA::setup()
 
   // set fix which stores original atom coords
 
-  fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
+  fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
   if (!fix) error->all(FLERR,"Could not find hma per-atom store fix ID {}", id_fix);
 }
 

src/EXTRA-COMPUTE/compute_hma.h

@@ -43,7 +43,7 @@ class ComputeHMA : public Compute {
   char *id_fix;
   char *id_temp;
   double finaltemp;
-  class FixStorePeratom *fix;
+  class FixStoreAtom *fix;
   double boltz, nktv2p, inv_volume;
   double deltaPcap;
   double virial_compute(int);

src/EXTRA-COMPUTE/compute_msd_nongauss.cpp

@@ -19,7 +19,7 @@
 
 #include "atom.h"
 #include "domain.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "group.h"
 #include "update.h"
 

src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp

@@ -17,7 +17,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "memory.h"
 #include "modify.h"
@@ -162,8 +162,8 @@ void BondHarmonicRestrain::init_style()
   if (natoms < 0) {
 
     // create internal fix to store initial positions
-    initial = dynamic_cast<FixStorePeratom *>(
+    initial = dynamic_cast<FixStoreAtom *>(
-      modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
+      modify->add_fix("BOND_RESTRAIN_X0 all STORE/ATOM 3 0 1 1"));
     if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
 
     natoms = atom->natoms;
@@ -178,8 +178,8 @@ void BondHarmonicRestrain::init_style()
     // we add the fix, but do not initialize it.  It will pull the data from the restart.
 
     if (!initial) {
-      initial = dynamic_cast<FixStorePeratom *>(
+      initial = dynamic_cast<FixStoreAtom *>(
-        modify->add_fix("BOND_RESTRAIN_X0 all STORE/PERATOM 3 0 1 1"));
+        modify->add_fix("BOND_RESTRAIN_X0 all STORE/ATOM 3 0 1 1"));
       if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
     }
   }

src/EXTRA-MOLECULE/bond_harmonic_restrain.h

@@ -41,7 +41,7 @@ class BondHarmonicRestrain : public Bond {
  protected:
   double *k;
   bigint natoms;
-  class FixStorePeratom *initial;
+  class FixStoreAtom *initial;
 
   virtual void allocate();
 };

src/FEP/fix_adapt_fep.cpp

@@ -20,7 +20,7 @@
 
 #include "atom.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "input.h"
@@ -211,8 +211,8 @@ void FixAdaptFEP::post_constructor()
 
   if (diamflag) {
     id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
-    fix_diam = dynamic_cast<FixStorePeratom *>(
+    fix_diam = dynamic_cast<FixStoreAtom *>(
-      modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
+      modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
     if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
     else {
       double *vec = fix_diam->vstore;
@@ -229,8 +229,8 @@ void FixAdaptFEP::post_constructor()
 
   if (chgflag) {
     id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG"));
-    fix_chg = dynamic_cast<FixStorePeratom *>(
+    fix_chg = dynamic_cast<FixStoreAtom *>(
-      modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
+      modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
     if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
     else {
       double *vec = fix_chg->vstore;
@@ -333,11 +333,11 @@ void FixAdaptFEP::init()
   // fixes that store initial per-atom values
 
   if (id_fix_diam) {
-    fix_diam = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_diam));
+    fix_diam = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_diam));
     if (!fix_diam) error->all(FLERR,"Could not find fix adapt/fep storage fix ID {}", id_fix_diam);
   }
   if (id_fix_chg) {
-    fix_chg = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_chg));
+    fix_chg = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_chg));
     if (!fix_chg) error->all(FLERR,"Could not find fix adapt/fep storage fix ID {}", id_fix_chg);
   }
 

src/FEP/fix_adapt_fep.h

@@ -46,7 +46,7 @@ class FixAdaptFEP : public Fix {
   int anypair;
   int nlevels_respa;
   char *id_fix_diam, *id_fix_chg;
-  class FixStorePeratom *fix_diam, *fix_chg;
+  class FixStoreAtom *fix_diam, *fix_chg;
 
   struct Adapt {
     int which, ivar;

src/GPU/pair_amoeba_gpu.cpp

@@ -23,7 +23,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "gpu_extra.h"
 #include "info.h"

src/GPU/pair_hippo_gpu.cpp

@@ -23,7 +23,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "gpu_extra.h"
 #include "info.h"

src/REPLICA/tad.cpp

@@ -24,7 +24,7 @@
 #include "error.h"
 #include "finish.h"
 #include "fix_event_tad.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "integrate.h"
 #include "memory.h"
@@ -133,9 +133,9 @@ void TAD::command(int narg, char **arg)
 
   fix_event = dynamic_cast<FixEventTAD *>(modify->add_fix("tad_event all EVENT/TAD"));
 
-  // create FixStorePeratom object to store revert state
+  // create FixStoreAtom object to store revert state
 
-  fix_revert = dynamic_cast<FixStorePeratom *>(modify->add_fix("tad_revert all STORE/PERATOM 7 0 0 0"));
+  fix_revert = dynamic_cast<FixStoreAtom *>(modify->add_fix("tad_revert all STORE/ATOM 7 0 0 0"));
 
   // create Finish for timing output
 

src/REPLICA/tad.h

@@ -48,15 +48,15 @@ class TAD : public Command {
   double time_dynamics, time_quench, time_neb, time_comm, time_output;
   double time_start;
 
-  class NEB *neb;                       // NEB object
+  class NEB *neb;                    // NEB object
-  class Fix *fix_neb;                   // FixNEB object
+  class Fix *fix_neb;                // FixNEB object
-  class Compute *compute_event;         // compute to detect event
+  class Compute *compute_event;      // compute to detect event
-  class FixEventTAD *fix_event;         // current event/state
+  class FixEventTAD *fix_event;      // current event/state
-  class FixStorePeratom *fix_revert;    // revert state
+  class FixStoreAtom *fix_revert;    // revert state
-  FixEventTAD **fix_event_list;         // list of possible events
+  FixEventTAD **fix_event_list;      // list of possible events
-  int n_event_list;                     // number of events
+  int n_event_list;                  // number of events
-  int nmax_event_list;                  // allocated events
+  int nmax_event_list;               // allocated events
-  int nmin_event_list;                  // minimum allocation
+  int nmin_event_list;               // minimum allocation
 
   char *neb_logfilename;    // filename for ulogfile_neb
   FILE *uscreen_neb;        // neb universe screen output

src/VTK/dump_vtk.cpp

@@ -31,7 +31,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "input.h"
@@ -2357,16 +2357,16 @@ int DumpVTK::modify_param(int narg, char **arg)
       thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
       thresh_last[nthresh] = -1;
     } else {
-      thresh_fix = (FixStorePeratom **)
+      thresh_fix = (FixStoreAtom **)
-        memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStorePeratom *),"dump:thresh_fix");
+        memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStoreAtom *),"dump:thresh_fix");
       thresh_fixID = (char **)
         memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID");
       memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
 
       std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
       thresh_fixID[nthreshlast] = utils::strdup(threshid);
-      threshid += fmt::format(" {} STORE/PERATOM 1 0 0 1", group->names[igroup]);
+      threshid += fmt::format(" {} STORE/ATOM 1 0 0 1", group->names[igroup]);
-      thresh_fix[nthreshlast] = dynamic_cast<FixStorePeratom *>(modify->add_fix(threshid));
+      thresh_fix[nthreshlast] = dynamic_cast<FixStoreAtom *>(modify->add_fix(threshid));
 
       thresh_last[nthreshlast] = nthreshlast;
       thresh_first[nthreshlast] = 1;

src/balance.cpp

@@ -26,7 +26,7 @@
 #include "neighbor.h"
 #include "comm.h"
 #include "domain.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "imbalance.h"
 #include "imbalance_group.h"
@@ -513,9 +513,9 @@ void Balance::weight_storage(char *prefix)
   if (prefix) cmd = prefix;
   cmd += "IMBALANCE_WEIGHTS";
 
-  fixstore = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(cmd));
+  fixstore = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(cmd));
   if (!fixstore)
-    fixstore = dynamic_cast<FixStorePeratom *>(modify->add_fix(cmd + " all STORE/PERATOM 1 0 0 0"));
+    fixstore = dynamic_cast<FixStoreAtom *>(modify->add_fix(cmd + " all STORE/ATOM 1 0 0 0"));
 
   // do not carry weights with atoms during normal atom migration
 

src/balance.h

@@ -27,11 +27,11 @@ namespace LAMMPS_NS {
 class Balance : public Command {
  public:
   class RCB *rcb;
-  class FixStorePeratom *fixstore;    // per-atom weights stored in FixStorePeratom
+  class FixStoreAtom *fixstore;    // per-atom weights stored in FixStorePeratom
-  int wtflag;                         // 1 if particle weighting is used
+  int wtflag;                      // 1 if particle weighting is used
-  int varflag;                        // 1 if weight style var(iable) is used
+  int varflag;                     // 1 if weight style var(iable) is used
-  int sortflag;                       // 1 if sorting of comm messages is done
+  int sortflag;                    // 1 if sorting of comm messages is done
-  int outflag;                        // 1 for output of balance results to file
+  int outflag;                     // 1 for output of balance results to file
 
   Balance(class LAMMPS *);
   ~Balance() override;

src/compute_chunk_atom.cpp

@@ -21,7 +21,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "group.h"
 #include "input.h"
 #include "lattice.h"
@@ -571,8 +571,8 @@ void ComputeChunkAtom::init()
 
   if ((idsflag == ONCE || lockcount) && !fixstore) {
     id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
-    fixstore = dynamic_cast<FixStorePeratom *>(
+    fixstore = dynamic_cast<FixStoreAtom *>(
-        modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix, group->names[igroup])));
+        modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix, group->names[igroup])));
   }
 
   if ((idsflag != ONCE && !lockcount) && fixstore) {

src/compute_chunk_atom.h

@@ -93,7 +93,7 @@ class ComputeChunkAtom : public Compute {
   double *varatom;
 
   char *id_fix;
-  class FixStorePeratom *fixstore;
+  class FixStoreAtom *fixstore;
 
   class Fix *lockfix;            // ptr to FixAveChunk that is locking out setups
                                  // null pointer if no lock currently in place

src/compute_displace_atom.cpp

@@ -17,7 +17,7 @@
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "group.h"
 #include "input.h"
 #include "memory.h"
@@ -74,8 +74,8 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
   // id = compute-ID + COMPUTE_STORE, fix group = compute group
 
   id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
-  fix = dynamic_cast<FixStorePeratom *>(
+  fix = dynamic_cast<FixStoreAtom *>(
-    modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
+    modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
 
   // calculate xu,yu,zu for fix store array
   // skip if reset from restart file
@@ -120,7 +120,7 @@ void ComputeDisplaceAtom::init()
 {
   // set fix which stores original atom coords
 
-  fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
+  fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
   if (!fix) error->all(FLERR,"Could not find compute displace/atom fix with ID {}", id_fix);
 
   if (refreshflag) {

src/compute_displace_atom.h

@@ -38,7 +38,7 @@ class ComputeDisplaceAtom : public Compute {
   int nmax;
   double **displace;
   char *id_fix;
-  class FixStorePeratom *fix;
+  class FixStoreAtom *fix;
 
   int refreshflag, ivar, nvmax;    // refresh option is enabled
   char *rvar;                      // for incremental dumps

src/compute_msd.cpp

@@ -16,7 +16,7 @@
 #include "atom.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "group.h"
 #include "modify.h"
 #include "update.h"
@@ -63,8 +63,8 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, a
   // id = compute-ID + COMPUTE_STORE, fix group = compute group
 
   id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
-  fix = dynamic_cast<FixStorePeratom *>(
+  fix = dynamic_cast<FixStoreAtom *>(
-      modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
+      modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
 
   // calculate xu,yu,zu for fix store array
   // skip if reset from restart file
@@ -127,7 +127,7 @@ void ComputeMSD::init()
 {
   // set fix which stores reference atom coords
 
-  fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
+  fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
   if (!fix) error->all(FLERR, "Could not find compute msd fix with ID {}", id_fix);
 
   // nmsd = # of atoms in group

src/compute_msd.h

@@ -39,7 +39,7 @@ class ComputeMSD : public Compute {
   bigint nmsd;
   double masstotal;
   char *id_fix;
-  class FixStorePeratom *fix;
+  class FixStoreAtom *fix;
 };
 
 }    // namespace LAMMPS_NS

src/compute_vacf.cpp

@@ -18,7 +18,7 @@
 #include "update.h"
 #include "group.h"
 #include "modify.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -39,8 +39,8 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
   // id = compute-ID + COMPUTE_STORE, fix group = compute group
 
   id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
-  fix = dynamic_cast<FixStorePeratom *>(
+  fix = dynamic_cast<FixStoreAtom *>(
-    modify->add_fix(fmt::format("{} {} STORE/PERATOM 3 0 0 1", id_fix, group->names[igroup])));
+    modify->add_fix(fmt::format("{} {} STORE/ATOM 3 0 0 1", id_fix, group->names[igroup])));
 
   // store current velocities in fix store array
   // skip if reset from restart file
@@ -84,7 +84,7 @@ void ComputeVACF::init()
 {
   // set fix which stores original atom velocities
 
-  fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
+  fix = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix));
   if (!fix) error->all(FLERR,"Could not find compute vacf fix ID {}", id_fix);
 
   // nvacf = # of atoms in group

src/compute_vacf.h

@@ -35,7 +35,7 @@ class ComputeVACF : public Compute {
  protected:
   bigint nvacf;
   char *id_fix;
-  class FixStorePeratom *fix;
+  class FixStoreAtom *fix;
 };
 
 }    // namespace LAMMPS_NS

src/dump_custom.cpp

@@ -20,7 +20,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "group.h"
 #include "input.h"
 #include "memory.h"
@@ -2005,16 +2005,16 @@ int DumpCustom::modify_param(int narg, char **arg)
       thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
       thresh_last[nthresh] = -1;
     } else {
-      thresh_fix = (FixStorePeratom **)
+      thresh_fix = (FixStoreAtom **)
-        memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStorePeratom *),"dump:thresh_fix");
+        memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStoreAtom *),"dump:thresh_fix");
       thresh_fixID = (char **)
         memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),"dump:thresh_fixID");
       memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
 
       std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
       thresh_fixID[nthreshlast] = utils::strdup(threshid);
-      threshid += fmt::format(" {} STORE/PERATOM 1 0 0 1", group->names[igroup]);
+      threshid += fmt::format(" {} STORE/ATOM 1 0 0 1", group->names[igroup]);
-      thresh_fix[nthreshlast] = dynamic_cast<FixStorePeratom *>(modify->add_fix(threshid));
+      thresh_fix[nthreshlast] = dynamic_cast<FixStoreAtom *>(modify->add_fix(threshid));
 
       thresh_last[nthreshlast] = nthreshlast;
       thresh_first[nthreshlast] = 1;

src/dump_custom.h

@@ -37,19 +37,19 @@ class DumpCustom : public Dump {
   int nevery;        // dump frequency for output
   char *idregion;    // region ID, nullptr if no region
 
-  int nthresh;                           // # of defined thresholds
+  int nthresh;                        // # of defined thresholds
-  int nthreshlast;                       // # of defined thresholds with value = LAST
+  int nthreshlast;                    // # of defined thresholds with value = LAST
-                                         //
+                                      //
-  int *thresh_array;                     // array to threshold on for each nthresh
+  int *thresh_array;                  // array to threshold on for each nthresh
-  int *thresh_op;                        // threshold operation for each nthresh
+  int *thresh_op;                     // threshold operation for each nthresh
-  double *thresh_value;                  // threshold value for each nthresh
+  double *thresh_value;               // threshold value for each nthresh
-  int *thresh_last;                      // for threshold value = LAST,
+  int *thresh_last;                   // for threshold value = LAST,
-                                         // index into thresh_fix
+                                      // index into thresh_fix
-                                         // -1 if not LAST, value is numeric
+                                      // -1 if not LAST, value is numeric
-                                         //
+                                      //
-  class FixStorePeratom **thresh_fix;    // stores values for each threshold LAST
+  class FixStoreAtom **thresh_fix;    // stores values for each threshold LAST
-  char **thresh_fixID;                   // IDs of thresh_fixes
+  char **thresh_fixID;                // IDs of thresh_fixes
-  int *thresh_first;                     // 1 the first time a FixStore values accessed
+  int *thresh_first;                  // 1 the first time a FixStore values accessed
 
   int expand;        // flag for whether field args were expanded
   char **earg;       // field names with wildcard expansion

src/fix_adapt.cpp

@@ -19,7 +19,7 @@
 #include "bond.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "group.h"
 #include "input.h"
@@ -278,8 +278,8 @@ void FixAdapt::post_constructor()
 
   if (diamflag && atom->radius_flag) {
     id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
-    fix_diam = dynamic_cast<FixStorePeratom *>(
+    fix_diam = dynamic_cast<FixStoreAtom *>(
-      modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
+      modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
     if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
     else {
       double *vec = fix_diam->vstore;
@@ -296,8 +296,8 @@ void FixAdapt::post_constructor()
 
   if (chgflag && atom->q_flag) {
     id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG"));
-    fix_chg = dynamic_cast<FixStorePeratom *>(
+    fix_chg = dynamic_cast<FixStoreAtom *>(
-      modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
+      modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
     if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
     else {
       double *vec = fix_chg->vstore;
@@ -494,11 +494,11 @@ void FixAdapt::init()
   // fixes that store initial per-atom values
 
   if (id_fix_diam) {
-    fix_diam = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_diam));
+    fix_diam = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_diam));
     if (!fix_diam) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_diam);
   }
   if (id_fix_chg) {
-    fix_chg = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix_chg));
+    fix_chg = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_chg));
     if (!fix_chg) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_chg);
   }
 

src/fix_adapt.h

@@ -48,7 +48,7 @@ class FixAdapt : public Fix {
   int anypair, anybond, anyangle;
   int nlevels_respa;
   char *id_fix_diam, *id_fix_chg;
-  class FixStorePeratom *fix_diam, *fix_chg;
+  class FixStoreAtom *fix_diam, *fix_chg;
   double previous_diam_scale, previous_chg_scale;
   int discflag;
 

src/fix_balance.cpp

@@ -19,7 +19,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "force.h"
 #include "irregular.h"
 #include "kspace.h"

src/fix_store_atom.cpp

@@ -11,7 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 
 #include "atom.h"
 #include "error.h"
@@ -32,10 +32,10 @@ using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
+FixStoreAtom::FixStoreAtom(LAMMPS *lmp, int narg, char **arg) :
     Fix(lmp, narg, arg), vstore(nullptr), astore(nullptr)
 {
-  if (narg != 7) error->all(FLERR, "Illegal fix STORE/PERATOM command: number of args");
+  if (narg != 7) error->all(FLERR, "Illegal fix STORE/ATOM command: number of args");
 
   disable = 0;
 
@@ -52,7 +52,7 @@ FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
   else if (n1 > 0 && n2 > 0)
     tensorflag = 1;
   else
-    error->all(FLERR, "Illegal fix STORE/PERATOM dimension args: {} {}", n1, n2);
+    error->all(FLERR, "Illegal fix STORE/ATOM dimension args: {} {}", n1, n2);
 
   if (vecflag || arrayflag)
     nvalues = n1;
@@ -71,7 +71,7 @@ FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
   astore = nullptr;
   tstore = nullptr;
 
-  FixStorePeratom::grow_arrays(atom->nmax);
+  FixStoreAtom::grow_arrays(atom->nmax);
   atom->add_callback(Atom::GROW);
   if (restartflag) atom->add_callback(Atom::RESTART);
   if (ghostflag) atom->add_callback(Atom::BORDER);
@@ -93,7 +93,7 @@ FixStorePeratom::FixStorePeratom(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-FixStorePeratom::~FixStorePeratom()
+FixStoreAtom::~FixStoreAtom()
 {
   // unregister callbacks to this fix from Atom class
 
@@ -108,7 +108,7 @@ FixStorePeratom::~FixStorePeratom()
 
 /* ---------------------------------------------------------------------- */
 
-int FixStorePeratom::setmask()
+int FixStoreAtom::setmask()
 {
   int mask = 0;
   return mask;
@@ -118,7 +118,7 @@ int FixStorePeratom::setmask()
    allocate atom-based array
 ------------------------------------------------------------------------- */
 
-void FixStorePeratom::grow_arrays(int nmax)
+void FixStoreAtom::grow_arrays(int nmax)
 {
   if (vecflag)
     memory->grow(vstore, nmax, "store:vstore");
@@ -132,7 +132,7 @@ void FixStorePeratom::grow_arrays(int nmax)
    copy values within local atom-based array
 ------------------------------------------------------------------------- */
 
-void FixStorePeratom::copy_arrays(int i, int j, int /*delflag*/)
+void FixStoreAtom::copy_arrays(int i, int j, int /*delflag*/)
 {
   if (disable) return;
 
@@ -149,7 +149,7 @@ void FixStorePeratom::copy_arrays(int i, int j, int /*delflag*/)
    pack values for border communication at re-neighboring
 ------------------------------------------------------------------------- */
 
-int FixStorePeratom::pack_border(int n, int *list, double *buf)
+int FixStoreAtom::pack_border(int n, int *list, double *buf)
 {
   int i, j, k;
 
@@ -179,7 +179,7 @@ int FixStorePeratom::pack_border(int n, int *list, double *buf)
    unpack values for border communication at re-neighboring
 ------------------------------------------------------------------------- */
 
-int FixStorePeratom::unpack_border(int n, int first, double *buf)
+int FixStoreAtom::unpack_border(int n, int first, double *buf)
 {
   int i, k, last;
 
@@ -203,7 +203,7 @@ int FixStorePeratom::unpack_border(int n, int first, double *buf)
    pack values in local atom-based array for exchange with another proc
 ------------------------------------------------------------------------- */
 
-int FixStorePeratom::pack_exchange(int i, double *buf)
+int FixStoreAtom::pack_exchange(int i, double *buf)
 {
   if (disable) return 0;
 
@@ -222,7 +222,7 @@ int FixStorePeratom::pack_exchange(int i, double *buf)
    unpack values in local atom-based array from exchange with another proc
 ------------------------------------------------------------------------- */
 
-int FixStorePeratom::unpack_exchange(int nlocal, double *buf)
+int FixStoreAtom::unpack_exchange(int nlocal, double *buf)
 {
   if (disable) return 0;
 
@@ -241,7 +241,7 @@ int FixStorePeratom::unpack_exchange(int nlocal, double *buf)
    pack values in local atom-based arrays for restart file
 ------------------------------------------------------------------------- */
 
-int FixStorePeratom::pack_restart(int i, double *buf)
+int FixStoreAtom::pack_restart(int i, double *buf)
 {
   if (disable) {
     buf[0] = 0;
@@ -266,7 +266,7 @@ int FixStorePeratom::pack_restart(int i, double *buf)
    unpack values from atom->extra array to restart the fix
 ------------------------------------------------------------------------- */
 
-void FixStorePeratom::unpack_restart(int nlocal, int nth)
+void FixStoreAtom::unpack_restart(int nlocal, int nth)
 {
   if (disable) return;
 
@@ -292,7 +292,7 @@ void FixStorePeratom::unpack_restart(int nlocal, int nth)
    maxsize of any atom's restart data
 ------------------------------------------------------------------------- */
 
-int FixStorePeratom::maxsize_restart()
+int FixStoreAtom::maxsize_restart()
 {
   if (disable) return 1;
   return nvalues + 1;
@@ -302,17 +302,17 @@ int FixStorePeratom::maxsize_restart()
    size of atom nlocal's restart data
 ------------------------------------------------------------------------- */
 
-int FixStorePeratom::size_restart(int /*nlocal*/)
+int FixStoreAtom::size_restart(int /*nlocal*/)
 {
   if (disable) return 1;
   return nvalues + 1;
 }
 
 /* ----------------------------------------------------------------------
-   memory usage of global or peratom atom-based array
+   memory usage of per-atom atom-based array
 ------------------------------------------------------------------------- */
 
-double FixStorePeratom::memory_usage()
+double FixStoreAtom::memory_usage()
 {
   return (double) atom->nmax * nvalues * sizeof(double);
 }

src/fix_store_atom.h

@@ -13,26 +13,26 @@
 
 #ifdef FIX_CLASS
 // clang-format off
-FixStyle(STORE/PERATOM,FixStorePeratom);
+FixStyle(STORE/ATOM,FixStoreAtom);
 // clang-format on
 #else
 
-#ifndef LMP_FIX_STORE_PERATOM_H
+#ifndef LMP_FIX_STORE_ATOM_H
-#define LMP_FIX_STORE_PERATOM_H
+#define LMP_FIX_STORE_ATOM_H
 
 #include "fix.h"
 
 namespace LAMMPS_NS {
 
-class FixStorePeratom : public Fix {
+class FixStoreAtom : public Fix {
  public:
   double *vstore;      // vector storage
   double **astore;     // array storage
   double ***tstore;    // tensor (3d array) storage
   int disable;         // 1 if operations (except grow) are currently disabled
 
-  FixStorePeratom(class LAMMPS *, int, char **);
+  FixStoreAtom(class LAMMPS *, int, char **);
-  ~FixStorePeratom() override;
+  ~FixStoreAtom() override;
   int setmask() override;
 
   void grow_arrays(int) override;

src/fix_store_global.cpp

@@ -182,7 +182,7 @@ void FixStoreGlobal::restart(char *buf)
 }
 
 /* ----------------------------------------------------------------------
-   memory usage of global or peratom atom-based array
+   memory usage of global data
 ------------------------------------------------------------------------- */
 
 double FixStoreGlobal::memory_usage()

src/variable.cpp

@@ -20,7 +20,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix.h"
-#include "fix_store_peratom.h"
+#include "fix_store_atom.h"
 #include "group.h"
 #include "info.h"
 #include "input.h"
@@ -5027,8 +5027,8 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
       error->all(FLERR,"Cannot use atomfile-style variable unless an atom map exists");
 
     id_fix = utils::strdup(std::string(name) + "_VARIABLE_STORE");
-    fixstore = dynamic_cast<FixStorePeratom *>(
+    fixstore = dynamic_cast<FixStoreAtom *>(
-      modify->add_fix(std::string(id_fix) + " all STORE/PERATOM 1 0 0 0"));
+      modify->add_fix(std::string(id_fix) + " all STORE/ATOM 1 0 0 0"));
     buffer = new char[CHUNK*MAXLINE];
   }
 }

src/variable.h

@@ -152,7 +152,7 @@ class Variable : protected Pointers {
 
 class VarReader : protected Pointers {
  public:
-  class FixStorePeratom *fixstore;
+  class FixStoreAtom *fixstore;
   char *id_fix;
 
   VarReader(class LAMMPS *, char *, char *, int);