Merge pull request #3855 from akohlmey/collected-small-changes

Collected small changes and fixes

doc/src/dynamical_matrix.rst

@@ -4,7 +4,7 @@
 dynamical_matrix command
 ========================
 
-Accelerator Variants: dynamical_matrix/kk
+Accelerator Variant: dynamical_matrix/kk
 
 Syntax
 """"""

doc/src/minimize.rst

@@ -1,10 +1,10 @@
 .. index:: minimize
+.. index:: minimize/kk
 
 minimize command
 ================
 
-minimize/kk command
+Accelerator Variant: minimize/kk
-===================
 
 Syntax
 """"""

doc/src/third_order.rst

@@ -4,7 +4,7 @@
 third_order command
 ===================
 
-Accelerator Variants: third_order/kk
+Accelerator Variant: third_order/kk
 
 Syntax
 """"""

src/REPLICA/temper.cpp

@@ -37,7 +37,7 @@
 
 using namespace LAMMPS_NS;
 
-// #define TEMPER_DEBUG 1
+#define TEMPER_DEBUG 0
 
 /* ---------------------------------------------------------------------- */
 
@@ -63,11 +63,10 @@ Temper::~Temper()
 void Temper::command(int narg, char **arg)
 {
   if (universe->nworlds == 1)
-    error->all(FLERR,"Must have more than one processor partition to temper");
+    error->universe_all(FLERR,"More than one processor partition required for temper command");
   if (domain->box_exist == 0)
-    error->all(FLERR,"Temper command before simulation box is defined");
+    error->universe_all(FLERR,"Temper command before simulation box is defined");
-  if (narg != 6 && narg != 7)
+  if (narg != 6 && narg != 7) error->universe_all(FLERR,"Illegal temper command");
-    error->universe_all(FLERR,"Illegal temper command");
 
   int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
   nevery = utils::inumeric(FLERR,arg[1],false,lmp);
@@ -77,10 +76,9 @@ void Temper::command(int narg, char **arg)
 
   if (timer->is_timeout()) return;
 
-  for (whichfix = 0; whichfix < modify->nfix; whichfix++)
+  whichfix = modify->get_fix_by_id(arg[3]);
-    if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
+  if (!whichfix)
-  if (whichfix == modify->nfix)
+    error->universe_all(FLERR,fmt::format("Tempering fix ID {} is not defined", arg[3]));
-    error->universe_all(FLERR,"Tempering fix ID is not defined");
 
   seed_swap = utils::inumeric(FLERR,arg[4],false,lmp);
   seed_boltz = utils::inumeric(FLERR,arg[5],false,lmp);
@@ -88,7 +86,7 @@ void Temper::command(int narg, char **arg)
   my_set_temp = universe->iworld;
   if (narg == 7) my_set_temp = utils::inumeric(FLERR,arg[6],false,lmp);
   if ((my_set_temp < 0) || (my_set_temp >= universe->nworlds))
-    error->universe_one(FLERR,"Illegal temperature index");
+    error->universe_one(FLERR,"Invalid temperature index value");
 
   // swap frequency must evenly divide total # of timesteps
 
@@ -101,11 +99,11 @@ void Temper::command(int narg, char **arg)
   // fix style must be appropriate for temperature control, i.e. it needs
   // to provide a working Fix::reset_target() and must not change the volume.
 
-  if ((!utils::strmatch(modify->fix[whichfix]->style,"^nvt")) &&
+  if ((!utils::strmatch(whichfix->style,"^nvt")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) &&
+      (!utils::strmatch(whichfix->style,"^langevin")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) &&
+      (!utils::strmatch(whichfix->style,"^gl[de]$")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) &&
+      (!utils::strmatch(whichfix->style,"^rigid/nvt")) &&
-      (!utils::strmatch(modify->fix[whichfix]->style,"^temp/")))
+      (!utils::strmatch(whichfix->style,"^temp/")))
     error->universe_all(FLERR,"Tempering temperature fix is not supported");
 
   // setup for long tempering run
@@ -116,8 +114,7 @@ void Temper::command(int narg, char **arg)
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
-  if (update->laststep < 0)
+  if (update->laststep < 0) error->all(FLERR,"Too many timesteps");
-    error->all(FLERR,"Too many timesteps");
 
   lmp->init();
 
@@ -132,9 +129,9 @@ void Temper::command(int narg, char **arg)
   // pe_compute = ptr to thermo_pe compute
   // notify compute it will be called at first swap
 
-  int id = modify->find_compute("thermo_pe");
+  Compute *pe_compute = modify->get_compute_by_id("thermo_pe");
-  if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute");
+  if (!pe_compute) error->all(FLERR,"Tempering could not find thermo_pe compute");
-  Compute *pe_compute = modify->compute[id];
+
   pe_compute->addstep(update->ntimestep + nevery);
 
   // create MPI communicator for root proc from each world
@@ -183,7 +180,7 @@ void Temper::command(int narg, char **arg)
 
   if (narg == 7) {
     double new_temp = set_temp[my_set_temp];
-    modify->fix[whichfix]->reset_target(new_temp);
+    whichfix->reset_target(new_temp);
   }
 
   // setup tempering runs
@@ -289,13 +286,12 @@ void Temper::command(int narg, char **arg)
       else
         MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE);
 
-#ifdef TEMPER_DEBUG
+#if TEMPER_DEBUG
       if (me_universe < partner)
-        printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
+        fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
                 me_universe,partner,swap,my_set_temp,partner_set_temp,
                 pe,pe_partner,boltz_factor,exp(boltz_factor));
 #endif
-
     }
 
     // bcast swap result to other procs in my world
@@ -310,7 +306,7 @@ void Temper::command(int narg, char **arg)
 
     if (swap) {
       new_temp = set_temp[partner_set_temp];
-      modify->fix[whichfix]->reset_target(new_temp);
+      whichfix->reset_target(new_temp);
     }
 
     // update my_set_temp and temp2world on every proc

src/REPLICA/temper.h

@@ -40,8 +40,7 @@ class Temper : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  int whichfix;                         // index of temperature fix to use
+  class Fix *whichfix;                  // temperature fix to use
-  int fixstyle;                         // what kind of temperature fix is used
 
   int my_set_temp;     // which set temp I am simulating
   double *set_temp;    // static list of replica set temperatures

src/REPLICA/temper_grem.cpp

@@ -24,6 +24,7 @@
 #include "finish.h"
 #include "fix.h"
 #include "fix_grem.h"
+#include "fix_nh.h"
 #include "force.h"
 #include "integrate.h"
 #include "modify.h"
@@ -37,7 +38,7 @@
 
 using namespace LAMMPS_NS;
 
-//#define TEMPER_DEBUG 1
+#define TEMPER_DEBUG 0
 
 /* ---------------------------------------------------------------------- */
 
@@ -54,7 +55,6 @@ TemperGrem::~TemperGrem()
   delete[] lambda2world;
   delete[] world2lambda;
   delete[] world2root;
-  delete [] id_nh;
 }
 
 /* ----------------------------------------------------------------------
@@ -64,46 +64,50 @@ TemperGrem::~TemperGrem()
 void TemperGrem::command(int narg, char **arg)
 {
   if (universe->nworlds == 1)
-    error->all(FLERR,"Must have more than one processor partition to temper");
+    error->universe_all(FLERR,"More than one processor partition required for temper/grem command");
   if (domain->box_exist == 0)
-    error->all(FLERR,"Temper/gREM command before simulation box is defined");
+    error->universe_all(FLERR,"Temper/grem command before simulation box is defined");
-  if (narg != 7 && narg != 8)
+  if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/grem command");
-    error->universe_all(FLERR,"Illegal temper command");
 
   int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
   nevery = utils::inumeric(FLERR,arg[1],false,lmp);
   double lambda = utils::numeric(FLERR,arg[2],false,lmp);
 
   // ignore temper command, if walltime limit was already reached
+
   if (timer->is_timeout()) return;
 
-  // Get and check if gREM fix exists
+  // Get and check if gREM fix exists and is correct style
-  for (whichfix = 0; whichfix < modify->nfix; whichfix++)
+
-    if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
+  auto ifix = modify->get_fix_by_id(arg[3]);
-  if (whichfix == modify->nfix)
+  if (!ifix) error->universe_all(FLERR,fmt::format("Tempering fix ID {} is not defined", arg[3]));
-    error->universe_all(FLERR,"Tempering fix ID is not defined");
+
-  fix_grem = dynamic_cast<FixGrem*>(modify->fix[whichfix]);
+  fix_grem = dynamic_cast<FixGrem*>(ifix);
+  if (!fix_grem || (strcmp(ifix->style,"grem") != 0))
+    error->universe_all(FLERR,"Tempering temperature fix is of incorrect style");
 
   // Check input values lambdas should be equal, assign other gREM values
   if (lambda != fix_grem->lambda)
-    error->universe_all(FLERR,"Lambda from tempering and fix in the same world"
+    error->universe_all(FLERR,"Lambda from tempering and fix in the same world must be the same");
-        " must be the same");
   double eta = fix_grem->eta;
   double h0 = fix_grem->h0;
   double pressref = 0;
 
   // Get and check for nh fix
-  id_nh = utils::strdup(arg[4]);
+
-  int ifix = modify->find_fix(id_nh);
+  FixNH *nh = dynamic_cast<FixNH *>(modify->get_fix_by_id(arg[4]));
-  if (ifix < 0)
+  if (!nh)
-    error->all(FLERR,"Fix id for nvt or npt fix does not exist");
+    error->all(FLERR,fmt::format("Fix {} for Nose-Hoover fix does not exist", arg[4]));
-  Fix *nh = modify->fix[ifix];
 
   // get result from nvt vs npt check from fix_grem
+
   int pressflag = fix_grem->pressflag;
+
   // fix_grem does all the checking...
+
   if (pressflag) {
-    auto p_start = (double *) nh->extract("p_start",ifix);
+    int dummy;
+    auto p_start = (double *) nh->extract("p_start",dummy);
     pressref = p_start[0];
   }
 
@@ -123,11 +127,6 @@ void TemperGrem::command(int narg, char **arg)
   if (nswaps*nevery != nsteps)
     error->universe_all(FLERR,"Non integer # of swaps in temper command");
 
-  // Must be used with fix_grem
-
-  if (strcmp(modify->fix[whichfix]->style,"grem") != 0)
-    error->universe_all(FLERR,"Tempering temperature fix is not supported");
-
   // setup for long tempering run
 
   update->whichflag = 1;
@@ -136,8 +135,7 @@ void TemperGrem::command(int narg, char **arg)
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
-  if (update->laststep < 0)
+  if (update->laststep < 0) error->all(FLERR,"Too many timesteps");
-    error->all(FLERR,"Too many timesteps");
 
   lmp->init();
 
@@ -152,9 +150,9 @@ void TemperGrem::command(int narg, char **arg)
   // pe_compute = ptr to thermo_pe compute
   // notify compute it will be called at first swap
 
-  int id = modify->find_compute("thermo_pe");
+  Compute *pe_compute = modify->get_compute_by_id("thermo_pe");
-  if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute");
+  if (!pe_compute) error->all(FLERR,"Tempering could not find thermo_pe compute");
-  Compute *pe_compute = modify->compute[id];
+
   pe_compute->addstep(update->ntimestep + nevery);
 
   // create MPI communicator for root proc from each world
@@ -319,13 +317,12 @@ void TemperGrem::command(int narg, char **arg)
       else
         MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE);
 
-#ifdef TEMPER_DEBUG
+#if TEMPER_DEBUG
       if (me_universe < partner)
-        printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
+        fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
                 me_universe,partner,swap,my_set_lambda,partner_set_lambda,
                 weight,weight_partner,boltz_factor,exp(boltz_factor));
 #endif
-
     }
 
     // bcast swap result to other procs in my world

src/REPLICA/temper_grem.h

@@ -40,8 +40,7 @@ class TemperGrem : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  int whichfix;                         // index of temperature fix to use
+  class Fix *whichfix;                  // temperature fix to use
-  int fixstyle;                         // what kind of temperature fix is used
 
   int my_set_lambda;     // which set lambda I am simulating
   double *set_lambda;    // static list of replica set lambdas
@@ -54,7 +53,6 @@ class TemperGrem : public Command {
   class FixGrem *fix_grem;
 
  protected:
-  char *id_nh;
   int pressflag;
 };
 

src/REPLICA/temper_npt.cpp

@@ -65,11 +65,10 @@ TemperNPT::~TemperNPT()
 void TemperNPT::command(int narg, char **arg)
 {
   if (universe->nworlds == 1)
-    error->all(FLERR,"Must have more than one processor partition to temper");
+    error->universe_all(FLERR,"More than one processor partition required for temper/npt command");
   if (domain->box_exist == 0)
-    error->all(FLERR,"temper/npt command before simulation box is defined");
+    error->universe_all(FLERR,"Temper/npt command before simulation box is defined");
-  if (narg != 7 && narg != 8)
+  if (narg != 7 && narg != 8) error->universe_all(FLERR,"Illegal temper/npt command");
-    error->universe_all(FLERR,"Illegal temper/npt command");
 
   int nsteps = utils::inumeric(FLERR,arg[0],false,lmp);
   nevery = utils::inumeric(FLERR,arg[1],false,lmp);
@@ -80,16 +79,17 @@ void TemperNPT::command(int narg, char **arg)
 
   if (timer->is_timeout()) return;
 
-  for (whichfix = 0; whichfix < modify->nfix; whichfix++)
+  whichfix = modify->get_fix_by_id(arg[3]);
-    if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
+  if (!whichfix)
-  if (whichfix == modify->nfix)
+    error->universe_all(FLERR,fmt::format("Tempering fix ID {} is not defined", arg[3]));
-    error->universe_all(FLERR,"Tempering fix ID is not defined");
 
   seed_swap = utils::inumeric(FLERR,arg[4],false,lmp);
   seed_boltz = utils::inumeric(FLERR,arg[5],false,lmp);
 
   my_set_temp = universe->iworld;
-  if (narg == 8) my_set_temp = utils::inumeric(FLERR,arg[6],false,lmp);
+  if (narg == 8) my_set_temp = utils::inumeric(FLERR,arg[7],false,lmp);
+  if ((my_set_temp < 0) || (my_set_temp >= universe->nworlds))
+    error->universe_one(FLERR,"Invalid temperature index value");
 
   // swap frequency must evenly divide total # of timesteps
 
@@ -104,8 +104,8 @@ void TemperNPT::command(int narg, char **arg)
   // change the volume. This currently only applies to fix npt and
   // fix rigid/npt variants
 
-  if ( (!utils::strmatch(modify->fix[whichfix]->style,"^npt")) &&
+  if ( (!utils::strmatch(whichfix->style,"^npt")) &&
-       (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/npt")) )
+       (!utils::strmatch(whichfix->style,"^rigid/npt")) )
     error->universe_all(FLERR,"Tempering temperature and pressure fix is not supported");
 
   // setup for long tempering run
@@ -116,8 +116,7 @@ void TemperNPT::command(int narg, char **arg)
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
-  if (update->laststep < 0)
+  if (update->laststep < 0) error->all(FLERR,"Too many timesteps");
-    error->all(FLERR,"Too many timesteps");
 
   lmp->init();
 
@@ -133,9 +132,9 @@ void TemperNPT::command(int narg, char **arg)
   // pe_compute = ptr to thermo_pe compute
   // notify compute it will be called at first swap
 
-  int id = modify->find_compute("thermo_pe");
+  Compute *pe_compute = modify->get_compute_by_id("thermo_pe");
-  if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute");
+  if (!pe_compute) error->all(FLERR,"Tempering could not find thermo_pe compute");
-  Compute *pe_compute = modify->compute[id];
+
   pe_compute->addstep(update->ntimestep + nevery);
 
   // create MPI communicator for root proc from each world
@@ -184,7 +183,7 @@ void TemperNPT::command(int narg, char **arg)
 
   if (narg == 8) {
     double new_temp = set_temp[my_set_temp];
-    modify->fix[whichfix]->reset_target(new_temp);
+    whichfix->reset_target(new_temp);
   }
 
   // setup tempering runs
@@ -279,22 +278,23 @@ void TemperNPT::command(int narg, char **arg)
 
     swap = 0;
     if (partner != -1) {
-      if (me_universe > partner) {
+      if (me_universe > partner)
         MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
-        }
+      else
-      else {
         MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
-        }
+
-      if (me_universe > partner) {
+      if (me_universe > partner)
         MPI_Send(&vol,1, MPI_DOUBLE,partner,0,universe->uworld);
-        }
+      else
-      else {
         MPI_Recv(&vol_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE);
-        }
+
-    // Acceptance criteria changed for NPT ensemble
+    // Acceptance criteria changed versus temper command for NPT ensemble
       if (me_universe < partner) {
         press_units = press_set/nktv2p;
-        delr = (pe_partner - pe)*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp])) + press_units*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp]))*(vol_partner - vol);
+        delr = (pe_partner - pe)*(1.0/(boltz*set_temp[my_set_temp])
+                                  - 1.0/(boltz*set_temp[partner_set_temp]))
+          + press_units*(1.0/(boltz*set_temp[my_set_temp])
+                         - 1.0/(boltz*set_temp[partner_set_temp]))*(vol_partner - vol);
         boltz_factor = -delr;
         if (boltz_factor >= 0.0) swap = 1;
         else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
@@ -304,13 +304,13 @@ void TemperNPT::command(int narg, char **arg)
         MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
       else
         MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE);
-#ifdef TEMPER_DEBUG
+
+#if TEMPER_DEBUG
       if (me_universe < partner)
         fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g, vol = %g %g\n",
                me_universe,partner,swap,my_set_temp,partner_set_temp,
                pe,pe_partner,boltz_factor,exp(boltz_factor), vol, vol_partner);
 #endif
-
     }
 
     // bcast swap result to other procs in my world
@@ -325,7 +325,7 @@ void TemperNPT::command(int narg, char **arg)
 
     if (swap) {
       new_temp = set_temp[partner_set_temp];
-      modify->fix[whichfix]->reset_target(new_temp);
+      whichfix->reset_target(new_temp);
     }
 
     // update my_set_temp and temp2world on every proc

src/REPLICA/temper_npt.h

@@ -42,8 +42,7 @@ class TemperNPT : public Command {
   int nswaps;                           // # of tempering swaps to perform
   int seed_swap;                        // 0 = toggle swaps, n = RNG for swap direction
   int seed_boltz;                       // seed for Boltz factor comparison
-  int whichfix;                         // index of temperature fix to use
+  class Fix *whichfix;                  // temperature fix to use
-  int fixstyle;                         // what kind of temperature fix is used
 
   int my_set_temp;     // which set temp I am simulating
   double *set_temp;    // static list of replica set temperatures

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_count_type.cpp

@@ -159,6 +159,8 @@ void ComputeCountType::compute_vector()
     nvec = count_dihedrals();
   else if (mode == IMPROPER)
     nvec = count_impropers();
+  else
+    nvec = 0;
 
   // sum across procs as bigint, then convert to double
   // correct for multiple counting if newton_bond off

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");
 }
 
 /* ---------------------------------------------------------------------- */

src/fix_wall_reflect.cpp

@@ -176,12 +176,11 @@ void FixWallReflect::init()
   }
 
   int nrigid = 0;
-  for (int i = 0; i < modify->nfix; i++)
+  for (const auto &ifix : modify->get_fix_list())
-    if (modify->fix[i]->rigid_flag) nrigid++;
+    if (ifix->rigid_flag) nrigid++;
 
-  if (nrigid && comm->me == 0)
+  if (nrigid && (comm->me == 0))
-    error->warning(FLERR,"Should not allow rigid bodies to bounce off "
+    error->warning(FLERR,"Should not use reflecting walls with rigid bodies");
-                   "relecting walls");
 }
 
 /* ---------------------------------------------------------------------- */

src/reset_atoms_id.cpp

@@ -55,9 +55,9 @@ void ResetAtomsID::command(int narg, char **arg)
     error->all(FLERR, "Reset_atoms id command before simulation box is defined");
   if (atom->tag_enable == 0) error->all(FLERR, "Cannot use reset_atoms id unless atoms have IDs");
 
-  for (int i = 0; i < modify->nfix; i++)
+  for (const auto &ifix : modify->get_fix_list())
-    if (modify->fix[i]->stores_ids)
+    if (ifix->stores_ids)
-      error->all(FLERR, "Cannot use reset_atoms id when a fix exists that stores atom IDs");
+      error->all(FLERR, "Cannot use reset_atoms id with a fix {} storing atom IDs", ifix->style);
 
   if (comm->me == 0) utils::logmesg(lmp, "Resetting atom IDs ...\n");
 

tools/vim/lammps.vim

@@ -2,22 +2,26 @@
 " Language:          Lammps Simulation Script File
 " Maintainer:        Gerolf Ziegenhain <gerolf@ziegenhain.com>
 " Updates:           Axel Kohlmeyer <akohlmey@gmail.com>, Sam Bateman <sam.bateman@nrlssc.navy.mil>, Daniel Möller Montull <d.moller.m@gmail.com>, Eryk Skalinski <eskalinski@protonmail.com>
-" Latest Revision:   2022-08-17
+" Latest Revision:   2023-07-15
 
 syn clear
 
-syn keyword     lammpsOutput    log write_data write_dump info shell write_restart restart dump undump thermo thermo_modify thermo_style print timer
+" Add '/' to list of valid keyword characters
+set iskeyword+=/
+
+syn keyword     lammpsOutput    log write_data write_dump write_coeff info shell write_restart restart dump undump thermo thermo_modify
+syn keyword     lammpsOutput    thermo_style print timer
 syn keyword     lammpsRead      include read_restart read_data read_dump molecule
 syn keyword     lammpsLattice   boundary units atom_style lattice region create_box create_atoms dielectric
 syn keyword     lammpsLattice   delete_atoms displace_atoms change_box dimension replicate
-syn keyword     lammpsParticle  pair_coeff pair_style pair_modify pair_write mass velocity angle_coeff angle_style
+syn keyword     lammpsParticle  pair_coeff pair_style pair_modify pair_write mass velocity angle_coeff angle_style angle_write
 syn keyword     lammpsParticle  atom_modify atom_style bond_coeff bond_style bond_write create_bonds delete_bonds kspace_style
-syn keyword     lammpsParticle  kspace_modify dihedral_style dihedral_coeff improper_style improper_coeff
+syn keyword     lammpsParticle  kspace_modify dihedral_style dihedral_coeff dihedral_write improper_style improper_coeff labelmap
-syn keyword     lammpsSetup     min_style fix_modify run_style timestep neighbor neigh_modify fix unfix suffix special_bonds
+syn keyword     lammpsSetup     min_style min_modify fix_modify run_style timestep neighbor neigh_modify fix unfix suffix special_bonds
-syn keyword     lammpsSetup     balance box clear comm_modify comm_style newton package processors reset_ids reset_timestep
+syn keyword     lammpsSetup     balance box clear comm_modify comm_style newton package processors reset_atoms reset_ids reset_timestep
-syn keyword     lammpsRun       minimize run rerun tad neb prd quit server temper temper/grem temper/npt
+syn keyword     lammpsRun       minimize minimize/kk run rerun tad neb neb/spin prd quit server temper/npt temper/grem temper
-syn keyword     lammpsRun       min/spin message hyper dynamical_matrix
+syn keyword     lammpsRun       message hyper dynamical_matrix dynamical_matrix/kk third_order third_order/kk fitpod
-syn keyword     lammpsDefine    variable group compute python set uncompute kim_query
+syn keyword     lammpsDefine    variable group compute python set uncompute kim_query kim group2ndx ndx2group mdi
 
 syn keyword     lammpsRepeat    jump next loop