modernize access for fixes and computes

src/atom.cpp

@@ -1818,17 +1818,16 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
 
 void Atom::data_fix_compute_variable(int nprev, int nnew)
 {
-  for (const auto &fix : modify->get_fix_list()) {
+  for (const auto &ifix : modify->get_fix_list()) {
-    if (fix->create_attribute)
+    if (ifix->create_attribute)
       for (int i = nprev; i < nnew; i++)
-        fix->set_arrays(i);
+        ifix->set_arrays(i);
   }
 
-  for (int m = 0; m < modify->ncompute; m++) {
+  for (const auto &icompute : modify->get_compute_list()) {
-    Compute *compute = modify->compute[m];
+    if (icompute->create_attribute)
-    if (compute->create_attribute)
       for (int i = nprev; i < nnew; i++)
-        compute->set_arrays(i);
+        icompute->set_arrays(i);
   }
 
   for (int i = nprev; i < nnew; i++)

src/atom_vec_sphere.cpp

@@ -17,6 +17,7 @@
 #include "error.h"
 #include "fix.h"
 #include "fix_adapt.h"
+#include "fix_adapt_fep.h"
 #include "math_const.h"
 #include "modify.h"
 
@@ -88,12 +89,18 @@ void AtomVecSphere::init()
 
   // check if optional radvary setting should have been set to 1
 
-  for (int i = 0; i < modify->nfix; i++)
+  for (auto &ifix : modify->get_fix_by_style("^adapt")) {
-    if (strcmp(modify->fix[i]->style, "adapt") == 0) {
+    if (utils::strmatch(ifix->style, "^adapt$")) {
-      auto fix = dynamic_cast<FixAdapt *>(modify->fix[i]);
+      auto fix = dynamic_cast<FixAdapt *>(ifix);
-      if (fix->diamflag && radvary == 0)
+      if (fix && fix->diamflag && radvary == 0)
         error->all(FLERR, "Fix adapt changes particle radii but atom_style sphere is not dynamic");
     }
+    if (utils::strmatch(ifix->style, "^adapt/fep$")) {
+      auto fix = dynamic_cast<FixAdaptFEP *>(ifix);
+      if (fix && fix->diamflag && radvary == 0)
+        error->all(FLERR, "Fix adapt/fep changes particle radii but atom_style sphere is not dynamic");
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------

src/compute_aggregate_atom.cpp

@@ -82,10 +82,8 @@ void ComputeAggregateAtom::init()
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
 
-  int count = 0;
+  if (modify->get_compute_by_style(style).size() > 1)
-  for (int i = 0; i < modify->ncompute; i++)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
-    if (strcmp(modify->compute[i]->style, "aggregate/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute aggregate/atom");
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_centro_atom.cpp

@@ -93,14 +93,12 @@ void ComputeCentroAtom::init()
   if (force->pair == nullptr)
     error->all(FLERR, "Compute centro/atom requires a pair style be defined");
 
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style, "centro/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute centro/atom");
-
   // need an occasional full neighbor list
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
+
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_cluster_atom.cpp

@@ -69,10 +69,8 @@ void ComputeClusterAtom::init()
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
 
-  int count = 0;
+  if (modify->get_compute_by_style(style).size() > 1)
-  for (int i = 0; i < modify->ncompute; i++)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
-    if (strcmp(modify->compute[i]->style, "cluster/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute cluster/atom");
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_cna_atom.cpp

@@ -76,19 +76,15 @@ void ComputeCNAAtom::init()
 
   // cannot use neighbor->cutneighmax b/c neighbor has not yet been init
 
-  if (2.0 * sqrt(cutsq) > force->pair->cutforce + neighbor->skin && comm->me == 0)
+  if ((2.0 * sqrt(cutsq)) > (force->pair->cutforce + neighbor->skin) && (comm->me == 0))
-    error->warning(FLERR,
+    error->warning(FLERR, "Compute cna/atom cutoff may be too large to find ghost atom neighbors");
-                   "Compute cna/atom cutoff may be too large to find "
-                   "ghost atom neighbors");
-
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style, "cna/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute cna/atom defined");
 
   // need an occasional full neighbor list
 
   neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
+
+  if (modify->get_compute_by_style(style).size() > 1)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_coord_atom.cpp

@@ -82,10 +82,11 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
 
     id_orientorder = utils::strdup(arg[4]);
 
-    int iorientorder = modify->find_compute(id_orientorder);
+    auto iorientorder = modify->get_compute_by_id(id_orientorder);
-    if (iorientorder < 0) error->all(FLERR, "Could not find compute coord/atom compute ID");
+    if (!iorientorder)
-    if (!utils::strmatch(modify->compute[iorientorder]->style, "^orientorder/atom"))
+      error->all(FLERR, "Could not find compute coord/atom compute ID {}", id_orientorder);
-      error->all(FLERR, "Compute coord/atom compute ID is not orientorder/atom");
+    if (!utils::strmatch(iorientorder->style, "^orientorder/atom"))
+      error->all(FLERR, "Compute coord/atom compute ID {} is not orientorder/atom", id_orientorder);
 
     threshold = utils::numeric(FLERR, arg[5], false, lmp);
     if (threshold <= -1.0 || threshold >= 1.0)
@@ -128,8 +129,11 @@ ComputeCoordAtom::~ComputeCoordAtom()
 void ComputeCoordAtom::init()
 {
   if (cstyle == ORIENT) {
-    int iorientorder = modify->find_compute(id_orientorder);
+    c_orientorder =
-    c_orientorder = dynamic_cast<ComputeOrientOrderAtom *>(modify->compute[iorientorder]);
+        dynamic_cast<ComputeOrientOrderAtom *>(modify->get_compute_by_id(id_orientorder));
+    if (!c_orientorder)
+      error->all(FLERR, "Could not find compute coord/atom compute ID {}", id_orientorder);
+
     cutsq = c_orientorder->cutsq;
     l = c_orientorder->qlcomp;
     //  communicate real and imaginary 2*l+1 components of the normalized vector

src/compute_erotate_sphere_atom.cpp

@@ -57,11 +57,8 @@ ComputeErotateSphereAtom::~ComputeErotateSphereAtom()
 
 void ComputeErotateSphereAtom::init()
 {
-  int count = 0;
+  if (modify->get_compute_by_style(style).size() > 1)
-  for (int i = 0; i < modify->ncompute; i++)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
-    if (strcmp(modify->compute[i]->style,"erotate/sphere/atom") == 0) count++;
-  if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute erotate/sphere/atom");
 
   pfactor = 0.5 * force->mvv2e * INERTIA;
 }

src/compute_fragment_atom.cpp

@@ -84,11 +84,8 @@ void ComputeFragmentAtom::init()
   if (atom->molecular != Atom::MOLECULAR)
     error->all(FLERR,"Compute fragment/atom requires a molecular system");
 
-  int count = 0;
+  if (modify->get_compute_by_style(style).size() > 1)
-  for (int i = 0; i < modify->ncompute; i++)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
-    if (strcmp(modify->compute[i]->style,"fragment/atom") == 0) count++;
-  if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute fragment/atom");
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_ke_atom.cpp

@@ -47,10 +47,8 @@ ComputeKEAtom::~ComputeKEAtom()
 
 void ComputeKEAtom::init()
 {
-  int count = 0;
+  if (modify->get_compute_by_style(style).size() > 1)
-  for (int i = 0; i < modify->ncompute; i++)
+    if (comm->me == 0) error->warning(FLERR, "More than one compute {}", style);
-    if (strcmp(modify->compute[i]->style, "ke/atom") == 0) count++;
-  if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute ke/atom");
 }
 
 /* ---------------------------------------------------------------------- */