Merge pull request lammps#4250 from akohlmey/collected-small-fixes

Collected small changes and fixes

cmake/CMakeLists.txt

@@ -887,7 +887,7 @@ endif()
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
-find_package(ClangFormat 8.0)
+find_package(ClangFormat 11.0)
 
 if(ClangFormat_FOUND)
   add_custom_target(format-src

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,8 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-20.0
+                                          clang-format-19.0
+                                          clang-format-18.0
                                           clang-format-17.0
                                           clang-format-16.0
                                           clang-format-15.0

doc/utils/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx >= 5.3.0, <8.0
+Sphinx >= 5.3.0, <7.5
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 sphinx-design

src/AMOEBA/amoeba_convolution.h

@@ -14,8 +14,8 @@
 #ifndef LMP_AMOEBA_CONVOLUTION_H
 #define LMP_AMOEBA_CONVOLUTION_H
 
-#include "pointers.h"
 #include "lmpfftsettings.h"
+#include "pointers.h"
 
 namespace LAMMPS_NS {
 
@@ -27,7 +27,7 @@ class AmoebaConvolution : protected Pointers {
   int nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in;
   int nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out;
   int nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft, nzlo_fft, nzhi_fft;
-  bigint nfft_global;          // nx * ny * nz
+  bigint nfft_global;              // nx * ny * nz
   FFT_SCALAR *grid_brick_start;    // lower left corner of (c)grid_brick data
 
   AmoebaConvolution(class LAMMPS *, class Pair *, int, int, int, int, int);
@@ -40,11 +40,11 @@ class AmoebaConvolution : protected Pointers {
   double time_fft;
 
  protected:
-  int which;                   // caller name for convolution being performed
-  int flag3d;                  // 1 if using 3d grid_brick, 0 for 4d cgrid_brick
-  int nbrick_owned;            // owned grid points in brick decomp
-  int nbrick_ghosts;           // owned + ghost brick grid points
-  int ngrid_either;            // max of nbrick_owned or nfft_owned
+  int which;            // caller name for convolution being performed
+  int flag3d;           // 1 if using 3d grid_brick, 0 for 4d cgrid_brick
+  int nbrick_owned;     // owned grid points in brick decomp
+  int nbrick_ghosts;    // owned + ghost brick grid points
+  int ngrid_either;     // max of nbrick_owned or nfft_owned
 
   class Pair *amoeba;
   class FFT3d *fft1, *fft2;

src/DPD-REACT/fix_eos_table.cpp

@@ -307,8 +307,8 @@ void FixEOStable::param_extract(Table *tb, Table *tb2, char *line)
   while (word) {
     if (strcmp(word,"N") == 0) {
       word = strtok(nullptr," \t\n\r\f");
-      tb->ninput = atoi(word);
-      tb2->ninput = atoi(word);
+      tb->ninput = std::stoi(word);
+      tb2->ninput = std::stoi(word);
     } else {
       error->one(FLERR,"Invalid keyword in fix eos/table parameters");
     }

src/DPD-REACT/fix_eos_table_rx.cpp

@@ -134,11 +134,11 @@ FixEOStableRX::FixEOStableRX(LAMMPS *lmp, int narg, char **arg) :
   }
 
   if (rx_flag) read_file(arg[7]);
-  else dHf[0] = atof(arg[7]);
+  else dHf[0] = std::stod(arg[7]);
 
   if (narg==10) {
-    energyCorr[0] = atof(arg[8]);
-    tempCorrCoeff[0] = atof(arg[9]);
+    energyCorr[0] = std::stod(arg[8]);
+    tempCorrCoeff[0] = std::stod(arg[9]);
   }
 
   comm_forward = 3;
@@ -373,11 +373,11 @@ void FixEOStableRX::read_file(char *file)
       if (strcmp(words[0],&atom->dvname[ispecies][0]) == 0) break;
 
     if (ispecies < nspecies) {
-      dHf[ispecies] = atof(words[1]);
+      dHf[ispecies] = std::stod(words[1]);
       if (nwords > min_params_per_line+1) {
-        energyCorr[ispecies] = atof(words[2]);
-        tempCorrCoeff[ispecies] = atof(words[3]);
-        moleculeCorrCoeff[ispecies] = atof(words[4]);
+        energyCorr[ispecies] = std::stod(words[2]);
+        tempCorrCoeff[ispecies] = std::stod(words[3]);
+        moleculeCorrCoeff[ispecies] = std::stod(words[4]);
       }
     }
   }
@@ -482,7 +482,7 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
 
     word = strtok(line," \t\n\r\f");
     word = strtok(nullptr," \t\n\r\f");
-    rtmp = atof(word);
+    rtmp = std::stod(word);
 
     for (int icolumn=0; icolumn < ncolumn; icolumn++) {
       ispecies = eosSpecies[icolumn];
@@ -491,7 +491,7 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
       Table *tbl2 = &tables2[ispecies];
 
       word = strtok(nullptr," \t\n\r\f");
-      tmpE = atof(word);
+      tmpE = std::stod(word);
 
       tbl->rfile[i] = rtmp;
       tbl->efile[i] = tmpE;
@@ -574,7 +574,7 @@ void FixEOStableRX::param_extract(Table *tb, char *line)
   char *word = strtok(line," \t\n\r\f");
   if (strcmp(word,"N") == 0) {
     word = strtok(nullptr," \t\n\r\f");
-    tb->ninput = atoi(word);
+    tb->ninput = std::stoi(word);
   } else
     error->one(FLERR,"Invalid keyword in fix eos/table/rx parameters");
   word = strtok(nullptr," \t\n\r\f");

src/DPD-REACT/fix_rx.cpp

@@ -863,7 +863,7 @@ void FixRX::read_file(char *file)
 
     word = strtok(line," \t\n\r\f");
     while (word != nullptr) {
-      tmpStoich = atof(word);
+      tmpStoich = std::stod(word);
       word = strtok(nullptr, " \t\n\r\f");
       for (ispecies = 0; ispecies < nspecies; ispecies++) {
         if (strcmp(word,&atom->dvname[ispecies][0]) == 0) {
@@ -886,13 +886,13 @@ void FixRX::read_file(char *file)
       if (strcmp(word,"=") == 0) sign = 1.0;
       if (strcmp(word,"+") != 0 && strcmp(word,"=") != 0) {
         if (word==nullptr) error->all(FLERR,"Missing parameters in reaction kinetic equation");
-        Arr[nreactions] = atof(word);
+        Arr[nreactions] = std::stod(word);
         word = strtok(nullptr, " \t\n\r\f");
         if (word==nullptr) error->all(FLERR,"Missing parameters in reaction kinetic equation");
-        nArr[nreactions]  = atof(word);
+        nArr[nreactions]  = std::stod(word);
         word = strtok(nullptr, " \t\n\r\f");
         if (word==nullptr) error->all(FLERR,"Missing parameters in reaction kinetic equation");
-        Ea[nreactions]  = atof(word);
+        Ea[nreactions]  = std::stod(word);
         sign = -1.0;
         break;
       }

src/DPD-REACT/pair_exp6_rx.cpp

@@ -889,15 +889,15 @@ void PairExp6rx::read_file2(char *file)
 
     if (strcmp(words[0],"alpha") == 0) {
       for (int ii=1; ii<params_per_line; ii++)
-        coeffAlpha[ii-1] = atof(words[ii]);
+        coeffAlpha[ii-1] = std::stod(words[ii]);
     }
     if (strcmp(words[0],"epsilon") == 0) {
       for (int ii=1; ii<params_per_line; ii++)
-        coeffEps[ii-1] = atof(words[ii]);
+        coeffEps[ii-1] = std::stod(words[ii]);
     }
     if (strcmp(words[0],"rm") == 0) {
       for (int ii=1; ii<params_per_line; ii++)
-        coeffRm[ii-1] = atof(words[ii]);
+        coeffRm[ii-1] = std::stod(words[ii]);
     }
   }
 

src/DPD-REACT/pair_multi_lucy.cpp

@@ -481,20 +481,20 @@ void PairMultiLucy::param_extract(Table *tb, char *line)
   while (word) {
     if (strcmp(word,"N") == 0) {
       word = strtok(nullptr," \t\n\r\f");
-      tb->ninput = atoi(word);
+      tb->ninput = std::stoi(word);
     } else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0) {
       if (strcmp(word,"R") == 0) tb->rflag = RLINEAR;
       else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ;
       word = strtok(nullptr," \t\n\r\f");
-      tb->rlo = atof(word);
+      tb->rlo = std::stod(word);
       word = strtok(nullptr," \t\n\r\f");
-      tb->rhi = atof(word);
+      tb->rhi = std::stod(word);
     } else if (strcmp(word,"FP") == 0) {
       tb->fpflag = 1;
       word = strtok(nullptr," \t\n\r\f");
-      tb->fplo = atof(word);
+      tb->fplo = std::stod(word);
       word = strtok(nullptr," \t\n\r\f");
-      tb->fphi = atof(word);
+      tb->fphi = std::stod(word);
     } else {
       printf("WORD: %s\n",word);
       error->one(FLERR,"Invalid keyword in pair table parameters");

src/DPD-REACT/pair_multi_lucy_rx.cpp

@@ -612,20 +612,20 @@ void PairMultiLucyRX::param_extract(Table *tb, char *line)
   while (word) {
     if (strcmp(word,"N") == 0) {
       word = strtok(nullptr," \t\n\r\f");
-      tb->ninput = atoi(word);
+      tb->ninput = std::stoi(word);
     } else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0) {
       if (strcmp(word,"R") == 0) tb->rflag = RLINEAR;
       else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ;
       word = strtok(nullptr," \t\n\r\f");
-      tb->rlo = atof(word);
+      tb->rlo = std::stod(word);
       word = strtok(nullptr," \t\n\r\f");
-      tb->rhi = atof(word);
+      tb->rhi = std::stod(word);
     } else if (strcmp(word,"FP") == 0) {
       tb->fpflag = 1;
       word = strtok(nullptr," \t\n\r\f");
-      tb->fplo = atof(word);
+      tb->fplo = std::stod(word);
       word = strtok(nullptr," \t\n\r\f");
-      tb->fphi = atof(word);
+      tb->fphi = std::stod(word);
     } else {
       printf("WORD: %s\n",word);
       error->one(FLERR,"Invalid keyword in pair table parameters");

src/ELECTRODE/electrode_vector.cpp

@@ -37,8 +37,7 @@ using namespace LAMMPS_NS;
 using namespace MathConst;
 
 ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group, double eta,
-                                 bool invert_source) :
-    Pointers(lmp)
+                                 bool invert_source) : Pointers(lmp)
 {
   igroup = sensor_group;                // group of all atoms at which we calculate potential
   this->source_group = source_group;    // group of all atoms influencing potential

src/ELECTRODE/fix_electrode_conp.cpp

@@ -931,7 +931,8 @@ void FixElectrodeConp::update_charges()
       dot_old = dot_new;
     }
     recompute_potential(std::move(b), q_local);
-    if ((delta > cg_threshold) && (comm->me == 0)) error->warning(FLERR, "CG threshold not reached");
+    if ((delta > cg_threshold) && (comm->me == 0))
+      error->warning(FLERR, "CG threshold not reached");
   } else {
     error->all(FLERR, "This algorithm is not implemented, yet");
   }

src/H5MD/dump_h5md.cpp

@@ -47,7 +47,7 @@ static int element_args(int narg, char **arg, int *every)
   while (iarg<narg) {
     if (strcmp(arg[iarg], "every")==0) {
       if (narg<2) return -1;
-      *every = atoi(arg[iarg+1]);
+      *every = std::stoi(arg[iarg+1]);
       iarg+=2;
     } else {
       break;

src/INTEL/fix_intel.cpp

@@ -125,11 +125,11 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
       iarg += 2;
     } else if (strcmp(arg[iarg], "tpc") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
-      _offload_tpc = atoi(arg[iarg+1]);
+      _offload_tpc = std::stoi(arg[iarg+1]);
       iarg += 2;
     } else if (strcmp(arg[iarg],"tptask") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
-      _offload_threads = atoi(arg[iarg+1]);
+      _offload_threads = std::stoi(arg[iarg+1]);
       iarg += 2;
     } else if (strcmp(arg[iarg],"no_affinity") == 0) {
       no_affinity = 1;
@@ -150,7 +150,7 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
       iarg++;
     } else if (strcmp(arg[iarg],"buffers") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal package intel command");
-      _allow_separate_buffers = atoi(arg[iarg+1]);
+      _allow_separate_buffers = std::stoi(arg[iarg+1]);
       iarg += 2;
     } else error->all(FLERR,"Illegal package intel command");
   }
@@ -1198,7 +1198,7 @@ int FixIntel::set_host_affinity(const int nomp)
   if (p == nullptr) return -1;
   ncores = 0;
   while (fgets(readbuf, 512, p)) {
-    proc_list[ncores] = atoi(readbuf);
+    proc_list[ncores] = std::stoi(readbuf);
     ncores++;
   }
   pclose(p);
@@ -1218,7 +1218,7 @@ int FixIntel::set_host_affinity(const int nomp)
   if (nthreads == 0) {
     estring = getenv("OMP_NUM_THREADS");
     if (estring != nullptr) {
-      nthreads = atoi(estring);
+      nthreads = std::stoi(estring);
       if (nthreads < 2) nthreads = 1;
     } else
       nthreads = 1;
@@ -1251,7 +1251,7 @@ int FixIntel::set_host_affinity(const int nomp)
     if (p == nullptr) return -1;
 
     while (fgets(readbuf, 512, p)) {
-      lwp = atoi(readbuf);
+      lwp = std::stoi(readbuf);
       int first = coi_cores + node_rank * mpi_cores;
       CPU_ZERO(&cpuset);
       for (int i = first; i < first + mpi_cores; i++)
@@ -1287,7 +1287,7 @@ int FixIntel::set_host_affinity(const int nomp)
     if (p == nullptr) return -1;
 
     while (fgets(readbuf, 512, p)) {
-      lwp = atoi(readbuf);
+      lwp = std::stoi(readbuf);
       nlwp++;
       if (nlwp <= plwp) continue;
 

src/KIM/kim_param.cpp

@@ -204,14 +204,14 @@ void KimParam::command(int narg, char **arg)
           if (npos != std::string::npos) {
             argtostr[npos] = ' ';
             auto words = utils::split_words(argtostr);
-            nlbound = atoi(words[0].c_str());
-            nubound = atoi(words[1].c_str());
+            nlbound = std::stoi(words[0]);
+            nubound = std::stoi(words[1]);
 
             if ((nubound < 1) || (nubound > extent) || (nlbound < 1) || (nlbound > nubound))
               error->all(FLERR, "Illegal index_range '{}-{}' for '{}' parameter with the "
                          "extent of '{}'",nlbound, nubound, paramname, extent);
           } else {
-            nlbound = atoi(argtostr.c_str());
+            nlbound = std::stoi(argtostr);
 
             if (nlbound < 1 || nlbound > extent)
               error->all(FLERR, "Illegal index '{}' for '{}' parameter with the extent of '{}'",

src/KIM/pair_kim.cpp

@@ -491,14 +491,14 @@ void PairKIM::coeff(int narg, char **arg)
         if (npos != std::string::npos) {
           argtostr[npos] = ' ';
           auto words = utils::split_words(argtostr);
-          nlbound = atoi(words[0].c_str());
-          nubound = atoi(words[1].c_str());
+          nlbound = std::stoi(words[0]);
+          nubound = std::stoi(words[1]);
 
           if ((nubound < 1) || (nubound > extent) || (nlbound < 1) || (nlbound > nubound))
             error->all(FLERR,"Illegal index_range '{}-{}' for '{}' parameter with the extent "
                        "of '{}'", nlbound, nubound, paramname, extent);
         } else {
-          nlbound = atoi(argtostr.c_str());
+          nlbound = std::stoi(argtostr);
 
           if ((nlbound < 1) || (nlbound > extent))
             error->all(FLERR,"Illegal index '{}' for '{}' parameter with the extent of '{}'",