simplify using new APIs

src/comm.cpp

@@ -201,8 +201,9 @@ void Comm::init()
   if (ghost_velocity) size_forward += atom->avec->size_velocity;
   if (ghost_velocity) size_border += atom->avec->size_velocity;
 
-  for (int i = 0; i < modify->nfix; i++)
+  const auto &fix_list = modify->get_fix_list();
-    size_border += modify->fix[i]->comm_border;
+  for (auto fix : fix_list)
+    size_border += fix->comm_border;
 
   // per-atom limits for communication
   // maxexchange = max # of datums in exchange comm, set in exchange()
@@ -217,9 +218,9 @@ void Comm::init()
   if (force->pair) maxforward = MAX(maxforward,force->pair->comm_forward);
   if (force->pair) maxreverse = MAX(maxreverse,force->pair->comm_reverse);
 
-  for (int i = 0; i < modify->nfix; i++) {
+  for (auto fix : fix_list) {
-    maxforward = MAX(maxforward,modify->fix[i]->comm_forward);
+    maxforward = MAX(maxforward,fix->comm_forward);
-    maxreverse = MAX(maxreverse,modify->fix[i]->comm_reverse);
+    maxreverse = MAX(maxreverse,fix->comm_reverse);
   }
 
   for (int i = 0; i < modify->ncompute; i++) {
@@ -241,12 +242,9 @@ void Comm::init()
 
   maxexchange_atom = atom->avec->maxexchange;
 
-  int nfix = modify->nfix;
-  Fix **fix = modify->fix;
-
   maxexchange_fix_dynamic = 0;
-  for (int i = 0; i < nfix; i++)
+  for (auto fix : fix_list)
-    if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
+    if (fix->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
 
   if ((mode == Comm::MULTI) && (neighbor->style != Neighbor::MULTI))
     error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists");
@@ -267,12 +265,9 @@ void Comm::init()
 
 void Comm::init_exchange()
 {
-  int nfix = modify->nfix;
-  Fix **fix = modify->fix;
-
   maxexchange_fix = 0;
-  for (int i = 0; i < nfix; i++)
+  for (auto fix : modify->get_fix_list())
-    maxexchange_fix += fix[i]->maxexchange;
+    maxexchange_fix += fix->maxexchange;
 
   maxexchange = maxexchange_atom + maxexchange_fix;
   bufextra = maxexchange + BUFEXTRA;

src/group.cpp

@@ -105,8 +105,8 @@ void Group::assign(int narg, char **arg)
     int igroup = find(arg[0]);
     if (igroup == -1) error->all(FLERR,"Could not find group delete group ID");
     if (igroup == 0) error->all(FLERR,"Cannot delete group all");
-    for (i = 0; i < modify->nfix; i++)
+    for (auto fix : modify->get_fix_list())
-      if (modify->fix[i]->igroup == igroup)
+      if (fix->igroup == igroup)
         error->all(FLERR,"Cannot delete group currently used by a fix");
     for (i = 0; i < modify->ncompute; i++)
       if (modify->compute[i]->igroup == igroup)

src/info.cpp

@@ -906,10 +906,8 @@ bool Info::is_defined(const char *category, const char *name)
         return true;
     }
   } else if (strcmp(category,"fix") == 0) {
-    int nfix = modify->nfix;
+    for (auto fix : modify->get_fix_list()) {
-    Fix **fix = modify->fix;
+      if (strcmp(fix->id,name) == 0)
-    for (int i=0; i < nfix; ++i) {
-      if (strcmp(fix[i]->id,name) == 0)
         return true;
     }
   } else if (strcmp(category,"group") == 0) {

src/write_data.cpp

@@ -213,9 +213,9 @@ void WriteData::write(const std::string &file)
   // extra sections managed by fixes
 
   if (fixflag)
-    for (int i = 0; i < modify->nfix; i++)
+    for (auto ifix : modify->get_fix_list())
-      if (modify->fix[i]->wd_section)
+      if (ifix->wd_section)
-        for (int m = 0; m < modify->fix[i]->wd_section; m++) fix(i,m);
+        for (int m = 0; m < ifix->wd_section; m++) fix(ifix,m);
 
   // close data file
 
@@ -267,22 +267,19 @@ void WriteData::header()
   // fix info
 
   if (fixflag)
-    for (int i = 0; i < modify->nfix; i++)
+    for (auto ifix : modify->get_fix_list())
-      if (modify->fix[i]->wd_header)
+      if (ifix->wd_header)
-        for (int m = 0; m < modify->fix[i]->wd_header; m++)
+        for (int m = 0; m < ifix->wd_header; m++)
-          modify->fix[i]->write_data_header(fp,m);
+          ifix->write_data_header(fp,m);
 
   // box info
 
-  auto box = fmt::format("\n{} {} xlo xhi"
+  auto box = fmt::format("\n{} {} xlo xhi\n{} {} ylo yhi\n{} {} zlo zhi\n",
-                         "\n{} {} ylo yhi"
-                         "\n{} {} zlo zhi\n",
                          domain->boxlo[0],domain->boxhi[0],
                          domain->boxlo[1],domain->boxhi[1],
                          domain->boxlo[2],domain->boxhi[2]);
   if (domain->triclinic)
-    box += fmt::format("{} {} {} xy xz yz\n",
+    box += fmt::format("{} {} {} xy xz yz\n",domain->xy,domain->xz,domain->yz);
-                       domain->xy,domain->xz,domain->yz);
   fputs(box.c_str(),fp);
 }
 
@@ -722,13 +719,13 @@ void WriteData::bonus(int flag)
    write out Mth section of data file owned by Fix ifix
 ------------------------------------------------------------------------- */
 
-void WriteData::fix(int ifix, int mth)
+void WriteData::fix(Fix *ifix, int mth)
 {
   // communication buffer for Fix info
   // maxrow X ncol = largest buffer needed by any proc
 
   int sendrow,ncol;
-  modify->fix[ifix]->write_data_section_size(mth,sendrow,ncol);
+  ifix->write_data_section_size(mth,sendrow,ncol);
   int maxrow;
   MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
 
@@ -738,7 +735,7 @@ void WriteData::fix(int ifix, int mth)
 
   // pack my fix data into buf
 
-  modify->fix[ifix]->write_data_section_pack(mth,buf);
+  ifix->write_data_section_pack(mth,buf);
 
   // write one chunk of info per proc to file
   // proc 0 pings each proc, receives its chunk, writes to file
@@ -751,7 +748,7 @@ void WriteData::fix(int ifix, int mth)
     MPI_Status status;
     MPI_Request request;
 
-    modify->fix[ifix]->write_data_section_keyword(mth,fp);
+    ifix->write_data_section_keyword(mth,fp);
     for (int iproc = 0; iproc < nprocs; iproc++) {
       if (iproc) {
         MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_DOUBLE,iproc,0,world,&request);
@@ -761,7 +758,7 @@ void WriteData::fix(int ifix, int mth)
         recvrow /= ncol;
       } else recvrow = sendrow;
 
-      modify->fix[ifix]->write_data_section(mth,fp,recvrow,buf,index);
+      ifix->write_data_section(mth,fp,recvrow,buf,index);
       index += recvrow;
     }
 

src/write_data.h

@@ -51,7 +51,7 @@ class WriteData : public Command {
   void dihedrals();
   void impropers();
   void bonus(int);
-  void fix(int, int);
+  void fix(class Fix *, int);
 };
 
 }    // namespace LAMMPS_NS

src/write_restart.cpp

@@ -413,9 +413,9 @@ void WriteRestart::write(const std::string &file)
 
   // invoke any fixes that write their own restart file
 
-  for (int ifix = 0; ifix < modify->nfix; ifix++)
+  for (auto fix : modify->get_fix_list())
-    if (modify->fix[ifix]->restart_file)
+    if (fix->restart_file)
-      modify->fix[ifix]->write_restart_file(file.c_str());
+      fix->write_restart_file(file.c_str());
 }
 
 /* ----------------------------------------------------------------------