modernize lookup of fixes

src/COLVARS/fix_colvars.cpp

@@ -324,7 +324,7 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
   if (!out_name) out_name = utils::strdup("out");
 
   /* initialize various state variables. */
-  tstat_id = -1;
+  tstat_fix = nullptr;
   energy = 0.0;
   nlevels_respa = 0;
   init_flag = 0;
@@ -432,12 +432,13 @@ void FixColvars::one_time_init()
     double t_target = 0.0;
     if (tmp_name) {
       if (strcmp(tmp_name,"NULL") == 0) {
-        tstat_id = -1;
+        tstat_fix = nullptr;
       } else {
-        tstat_id = modify->find_fix(tmp_name);
+        tstat_fix = modify->get_fix_by_id(tmp_name);
-        if (tstat_id < 0) error->one(FLERR,"Could not find tstat fix ID");
+        if (!tstat_fix) error->one(FLERR, "Could not find thermostat fix ID {}", tmp_name);
-        double *tt = (double*)modify->fix[tstat_id]->extract("t_target",tmp);
+        double *tt = (double*) tstat_fix->extract("t_target", tmp);
         if (tt) t_target = *tt;
+        else error->one(FLERR, "Fix ID {} is not a thermostat fix", tmp_name);
       }
     }
 
@@ -675,13 +676,13 @@ void FixColvars::post_force(int /*vflag*/)
     if (proxy->want_exit())
       error->one(FLERR,"Run aborted on request from colvars module.\n");
 
-    if (tstat_id < 0) {
+    if (!tstat_fix) {
       proxy->set_temperature(0.0);
     } else {
       int tmp;
       // get thermostat target temperature from corresponding fix,
       // if the fix supports extraction.
-      double *tt = (double *) modify->fix[tstat_id]->extract("t_target",tmp);
+      double *tt = (double *) tstat_fix->extract("t_target", tmp);
       if (tt)
         proxy->set_temperature(*tt);
       else

src/COLVARS/fix_colvars.h

@@ -68,7 +68,7 @@ class FixColvars : public Fix {
   char *out_name;               // prefix string for all output files
   char *tmp_name;               // name of thermostat fix.
   int rng_seed;                 // seed to initialize random number generator
-  int tstat_id;                 // id of the thermostat fix
+  Fix *tstat_fix;               // pointer to thermostat fix
   double energy;                // biasing energy of the fix
 
   int me;             // my MPI rank in this "world".

src/EXTRA-COMPUTE/compute_hma.cpp

@@ -188,11 +188,11 @@ void ComputeHMA::init_list(int /* id */, NeighList *ptr)
 void ComputeHMA::setup()
 {
   int dummy=0;
-  int ifix = modify->find_fix(id_temp);
+  Fix *ifix = modify->get_fix_by_id(id_temp);
-  if (ifix < 0) error->all(FLERR,"Could not find compute hma temperature ID");
+  if (!ifix) error->all(FLERR,"Could not find compute hma temperature fix ID {}", id_temp);
-  auto  temperat = (double *) modify->fix[ifix]->extract("t_target",dummy);
+  auto  temperat = (double *) ifix->extract("t_target",dummy);
-  if (temperat==nullptr) error->all(FLERR,"Could not find compute hma temperature ID");
+  if (temperat == nullptr) error->all(FLERR,"Fix ID {} is not a thermostat {}", id_temp);
-  finaltemp = * temperat;
+  finaltemp = *temperat;
 
   // set fix which stores original atom coords
 

src/EXTRA-FIX/fix_controller.cpp

@@ -71,28 +71,22 @@ FixController::FixController(LAMMPS *lmp, int narg, char **arg) :
   // error check
 
   if (pvwhich == ArgInfo::COMPUTE) {
-    int icompute = modify->find_compute(pvID);
+    Compute *c = modify->get_compute_by_id(pvID);
-    if (icompute < 0)
+    if (!c) error->all(FLERR,"Compute ID {} for fix controller does not exist", pvID);
-      error->all(FLERR,"Compute ID for fix controller does not exist");
-    Compute *c = modify->compute[icompute];
     int flag = 0;
     if (c->scalar_flag && pvindex == 0) flag = 1;
     else if (c->vector_flag && pvindex > 0) flag = 1;
-    if (!flag) error->all(FLERR,"Fix controller compute does not "
+    if (!flag)
-                          "calculate a global scalar or vector");
+      error->all(FLERR,"Fix controller compute does not calculate a global scalar or vector");
     if (pvindex && pvindex > c->size_vector)
-      error->all(FLERR,"Fix controller compute vector is "
+      error->all(FLERR,"Fix controller compute vector is accessed out-of-range");
-                 "accessed out-of-range");
   } else if (pvwhich == ArgInfo::FIX) {
-    int ifix = modify->find_fix(pvID);
+    Fix *f = modify->get_fix_by_id(pvID);
-    if (ifix < 0)
+    if (!f) error->all(FLERR,"Fix ID {} for fix controller does not exist", pvID);
-      error->all(FLERR,"Fix ID for fix controller does not exist");
-    Fix *f = modify->fix[ifix];
     int flag = 0;
     if (f->scalar_flag && pvindex == 0) flag = 1;
     else if (f->vector_flag && pvindex > 0) flag = 1;
-    if (!flag) error->all(FLERR,"Fix controller fix does not "
+    if (!flag) error->all(FLERR,"Fix controller fix does not calculate a global scalar or vector");
-                          "calculate a global scalar or vector");
     if (pvindex && pvindex > f->size_vector)
       error->all(FLERR,"Fix controller fix vector is accessed out-of-range");
   } else if (pvwhich == ArgInfo::VARIABLE) {
@@ -135,25 +129,20 @@ int FixController::setmask()
 void FixController::init()
 {
   if (pvwhich == ArgInfo::COMPUTE) {
-    int icompute = modify->find_compute(pvID);
+    pcompute = modify->get_compute_by_id(pvID);
-    if (icompute < 0)
+    if (!pcompute) error->all(FLERR,"Compute ID {} for fix controller does not exist", pvID);
-      error->all(FLERR,"Compute ID for fix controller does not exist");
-    pcompute = modify->compute[icompute];
 
   } else if (pvwhich == ArgInfo::FIX) {
-    int ifix = modify->find_fix(pvID);
+    pfix = modify->get_fix_by_id(pvID);
-    if (ifix < 0) error->all(FLERR,"Fix ID for fix controller does not exist");
+    if (!pfix) error->all(FLERR,"Fix ID {} for fix controller does not exist", pvID);
-    pfix = modify->fix[ifix];
 
   } else if (pvwhich == ArgInfo::VARIABLE) {
     pvar = input->variable->find(pvID);
-    if (pvar < 0)
+    if (pvar < 0) error->all(FLERR,"Variable name for fix controller does not exist");
-      error->all(FLERR,"Variable name for fix controller does not exist");
   }
 
   cvar = input->variable->find(cvID);
-  if (cvar < 0)
+  if (cvar < 0) error->all(FLERR,"Variable name for fix controller does not exist");
-    error->all(FLERR,"Variable name for fix controller does not exist");
 
   // set sampling time
 

src/MC/fix_charge_regulation.cpp

@@ -1294,16 +1294,13 @@ void FixChargeRegulation::restart(char *buf)
 /* ---------------------------------------------------------------------- */
 
 void FixChargeRegulation::setThermoTemperaturePointer() {
-  int ifix = -1;
+  Fix *ifix = modify->get_fix_by_id(idftemp);
-  ifix = modify->find_fix(idftemp);
+  if (!ifix)
-  if (ifix == -1) {
+    error->all(FLERR, "fix charge/regulation could not find thermostat fix id {}", idftemp);
-    error->all(FLERR, "fix charge/regulation regulation could not find "
-               "a temperature fix id provided by tempfixid\n");
-  }
-  Fix *temperature_fix = modify->fix[ifix];
-  int dim;
-  target_temperature_tcp = (double *) temperature_fix->extract("t_target", dim);
 
+  int dim;
+  target_temperature_tcp = (double *) ifix->extract("t_target", dim);
+  if (!target_temperature_tcp) error->all(FLERR, "Fix id {} does not control temperature", idftemp);
 }
 
 /* ---------------------------------------------------------------------- */

src/MC/fix_gcmc.cpp

@@ -565,9 +565,8 @@ void FixGCMC::init()
 
   fixrigid = nullptr;
   if (rigidflag) {
-    int ifix = modify->find_fix(idrigid);
+    fixrigid = modify->get_fix_by_id(idrigid);
-    if (ifix < 0) error->all(FLERR,"Fix gcmc rigid fix does not exist");
+    if (!fixrigid) error->all(FLERR,"Fix gcmc rigid fix ID {} does not exist", idrigid);
-    fixrigid = modify->fix[ifix];
     int tmp;
     if (&onemols[imol] != (Molecule **) fixrigid->extract("onemol",tmp))
       error->all(FLERR, "Fix gcmc and fix rigid/small not using same molecule template ID");
@@ -578,9 +577,8 @@ void FixGCMC::init()
 
   fixshake = nullptr;
   if (shakeflag) {
-    int ifix = modify->find_fix(idshake);
+    fixshake = modify->get_fix_by_id(idshake);
-    if (ifix < 0) error->all(FLERR,"Fix gcmc shake fix does not exist");
+    if (!fixshake) error->all(FLERR,"Fix gcmc shake fix ID {} does not exist", idshake);
-    fixshake = modify->fix[ifix];
     int tmp;
     if (&onemols[imol] != (Molecule **) fixshake->extract("onemol",tmp))
       error->all(FLERR,"Fix gcmc and fix shake not using same molecule template ID");

src/OPENMP/thr_omp.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* -------------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -17,42 +16,37 @@
    OpenMP based threading support for LAMMPS
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-
-#include "atom.h"
-#include "comm.h"
-#include "error.h"
-#include "force.h"
-#include "modify.h"
-#include "neighbor.h"
-
-
 #include "thr_omp.h"
 
-#include "pair.h"
-#include "bond.h"
 #include "angle.h"
-#include "dihedral.h"
+#include "atom.h"
-#include "improper.h"
+#include "bond.h"
+#include "comm.h"
 #include "compute.h"
-
+#include "dihedral.h"
+#include "error.h"
+#include "force.h"
+#include "improper.h"
 #include "math_const.h"
+#include "modify.h"
+#include "neighbor.h"
+#include "pair.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
-using namespace MathConst;
+using MathConst::THIRD;
 
 /* ---------------------------------------------------------------------- */
 
-ThrOMP::ThrOMP(LAMMPS *ptr, int style)
+ThrOMP::ThrOMP(LAMMPS *ptr, int style) : lmp(ptr), fix(nullptr), thr_style(style), thr_error(0)
-  : lmp(ptr), fix(nullptr), thr_style(style), thr_error(0)
 {
   // register fix omp with this class
-  int ifix = lmp->modify->find_fix("package_omp");
+  fix = static_cast<FixOMP *>(lmp->modify->get_fix_by_id("package_omp"));
-  if (ifix < 0)
+  if (!fix) lmp->error->all(FLERR, "The 'package omp' command is required for /omp styles");
-    lmp->error->all(FLERR,"The 'package omp' command is required for /omp styles");
-  fix = static_cast<FixOMP *>(lmp->modify->fix[ifix]);
 }
 
+// clang-format off
 /* ----------------------------------------------------------------------
    Hook up per thread per atom arrays into the tally infrastructure
    ---------------------------------------------------------------------- */
@@ -154,7 +148,6 @@ void ThrOMP::ev_setup_thr(int eflag, int vflag, int nall, double *eatom,
         memset(&(thr->cvatom_imprp[0][0]),0,nall*9*sizeof(double));
     }
   }
-
   // nothing to do for THR_KSPACE
 }
 
@@ -1312,7 +1305,6 @@ void ThrOMP::ev_tally_thr(Dihedral * const dihed, const int i1, const int i2,
       if (i4 < nlocal) v_tally9(thr->cvatom_dihed[i4],v4);
     }
   }
-
 }
 
 /* ----------------------------------------------------------------------