[pull] develop from lammps:develop

cmake/Modules/Testing.cmake

@@ -11,7 +11,11 @@ if(ENABLE_TESTING)
     file(READ ${SUPP} SUPPRESSIONS)
     file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
   endforeach()
-  set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
+  # blocks that are still reachable when the process exits are not leaks. reporting
+  # them buries the actual defects under thousands of one-time initializations in
+  # OpenSSL, libcurl, CPython, and GoogleTest, plus everything that is still in use
+  # when a command like "quit" or an error exit terminates the process on purpose.
+  set(VALGRIND_DEFAULT_OPTIONS "--leak-check=full --show-leak-kinds=definite,indirect,possible --track-origins=yes --suppressions=${CMAKE_BINARY_DIR}/lammps.supp")
 
   set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
   set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")

src/DIFFRACTION/compute_saed.cpp

@@ -55,7 +55,7 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) :
   nlocalgroup = 0;
   if (lmp->citeme) lmp->citeme->add(cite_compute_saed_c);
 
-  int ntypes = atom->ntypes;
+  ntypes = atom->ntypes;
   int natoms = group->count(igroup);
   int dimension = domain->dimension;
   int *periodicity = domain->periodicity;

src/DIFFRACTION/compute_xrd.cpp

@@ -56,7 +56,7 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
   nlocalgroup = 0;
   if (lmp->citeme) lmp->citeme->add(cite_compute_xrd_c);
 
-  int ntypes = atom->ntypes;
+  ntypes = atom->ntypes;
   int natoms = group->count(igroup);
   int dimension = domain->dimension;
   int *periodicity = domain->periodicity;

src/DPD-MESO/pair_edpd.cpp

@@ -283,6 +283,7 @@ void PairEDPD::settings(int narg, char **arg)
 
   delete random;
   random = new RanMars(lmp,(seed + comm->me) % 900000000);
+  delete randomT;
   randomT = new RanMars(lmp,(2*seed + comm->me) % 900000000);
 
   // reset cutoffs that have been explicitly set

src/DPD-SMOOTH/pair_sdpd_taitwater_isothermal.cpp

@@ -259,6 +259,7 @@ void PairSDPDTaitwaterIsothermal::settings (int narg, char **arg) {
 #ifdef USE_ZEST
   generator.seed (seed);
 #else
+  delete random;
   random = new RanMars (lmp, seed);
 #endif
 }

src/EFF/pair_eff_cut.h

@@ -49,9 +49,12 @@ class PairEffCut : public Pair {
   int ecp_found;
   double cut_global;
   double **cut;
-  int ecp_type[100];
-  double PAULI_CORE_A[100], PAULI_CORE_B[100], PAULI_CORE_C[100];
-  double PAULI_CORE_D[100], PAULI_CORE_E[100];
+  // only the entries of ECP types set with the "ecp" keyword are filled in,
+  // but write_restart_settings() stores the arrays as a whole, so they must
+  // not contain uninitialized data
+  int ecp_type[100] = {};
+  double PAULI_CORE_A[100] = {}, PAULI_CORE_B[100] = {}, PAULI_CORE_C[100] = {};
+  double PAULI_CORE_D[100] = {}, PAULI_CORE_E[100] = {};
   double hhmss2e, h2e;
 
   int nmax;

src/KSPACE/pppm.cpp

@@ -98,7 +98,7 @@ PPPM::PPPM(LAMMPS *lmp) : KSpace(lmp),
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);
 
-  nfft_both = 0;
+  ngrid = nfft_both = 0;
   nxhi_in = nxlo_in = nxhi_out = nxlo_out = 0;
   nyhi_in = nylo_in = nyhi_out = nylo_out = 0;
   nzhi_in = nzlo_in = nzhi_out = nzlo_out = 0;

src/KSPACE/pppm_dipole_spin.cpp

@@ -202,6 +202,19 @@ void PPPMDipoleSpin::init()
 
   double estimated_accuracy = final_accuracy_dipole();
 
+  // allocate K-space dependent memory
+  // don't invoke allocate peratom(), will be allocated when needed
+  // must happen before printing the stats below, since allocate()
+  // is what sets ngrid and nfft_both
+
+  allocate();
+
+  // pre-compute Green's function denominator expansion
+  // pre-compute 1d charge distribution coefficients
+
+  compute_gf_denom();
+  compute_rho_coeff();
+
   // print stats
 
   int ngrid_max,nfft_both_max;
@@ -221,17 +234,6 @@ void PPPMDipoleSpin::init()
                        ngrid_max,nfft_both_max);
     utils::logmesg(lmp,mesg);
   }
-
-  // allocate K-space dependent memory
-  // don't invoke allocate peratom(), will be allocated when needed
-
-  allocate();
-
-  // pre-compute Green's function denominator expansion
-  // pre-compute 1d charge distribution coefficients
-
-  compute_gf_denom();
-  compute_rho_coeff();
 }
 
 /* ----------------------------------------------------------------------

src/MANYBODY/pair_local_density.cpp

@@ -690,6 +690,22 @@ void PairLocalDensity::parse_file(char *filename) {
   double *ftmp; // tmp var to extract the complete 2D frho array from file
 
   // setting up all arrays to be read from files and broadcasted
+  // free any storage from a previous pair_coeff command first
+
+  memory->destroy(uppercut);
+  memory->destroy(lowercut);
+  memory->destroy(uppercutsq);
+  memory->destroy(lowercutsq);
+  memory->destroy(c0);
+  memory->destroy(c2);
+  memory->destroy(c4);
+  memory->destroy(c6);
+  memory->destroy(rho_min);
+  memory->destroy(rho_max);
+  memory->destroy(delta_rho);
+  memory->destroy(a);
+  memory->destroy(b);
+
   memory->create(uppercut, nLD, "pairLD:uppercut");
   memory->create(lowercut, nLD, "pairLD:lowercut");
   memory->create(uppercutsq, nLD, "pairLD:uppercutsq");
@@ -804,6 +820,8 @@ void PairLocalDensity::parse_file(char *filename) {
   MPI_Bcast(&ftmp[0], nLD*nrho, MPI_DOUBLE, 0, world);
 
   // set up rho and frho arrays
+  memory->destroy(rho);
+  memory->destroy(frho);
   memory->create(rho, nLD, nrho, "pairLD:rho");
   memory->create(frho, nLD, nrho, "pairLD:frho");
 

src/MC/pair_dsmc.cpp

@@ -293,6 +293,12 @@ void PairDSMC::init_style()
   total_ncells = ncellsx*ncellsy*ncellsz;
   vol = cellx*celly*cellz;
 
+  // free storage from a previous init_style() call
+
+  memory->destroy(particle_list);
+  memory->destroy(first);
+  memory->destroy(number);
+
   memory->create(particle_list,atom->ntypes+1,0,"pair:particle_list");
   memory->create(first,atom->ntypes+1,total_ncells,"pair:first");
   memory->create(number,atom->ntypes+1,total_ncells,"pair:number");

src/ML-QUIP/pair_quip.cpp

@@ -251,7 +251,9 @@ void PairQUIP::coeff(int narg, char **arg)
   }
 
   // use expanded file name, including LAMMPS_POTENTIALS search path
+  delete[] quip_file;
   quip_file = utils::strdup(utils::get_potential_file_path(arg[2]));
+  delete[] quip_string;
   quip_string = utils::strdup(arg[3]);
   n_quip_file = strlen(quip_file);
   n_quip_string = strlen(quip_string);
@@ -286,6 +288,7 @@ void PairQUIP::coeff(int narg, char **arg)
   // and returns the necessary size of quip_potential. This behavior
   // is invoked by setting n_potential_quip to 0.
   n_quip_potential = 0;
+  delete[] quip_potential;
   quip_potential = new int[1];
   quip_lammps_potential_initialise(quip_potential, &n_quip_potential, &cutoff, quip_file,
                                    &n_quip_file, quip_string, &n_quip_string);

src/OPENMP/pair_local_density_omp.cpp

@@ -73,6 +73,15 @@ void PairLocalDensityOMP::compute(int eflag, int vflag)
     for (int k = 0; k < nLD; k++)
       memset(&localrho[k][tid*nall], 0, nall * sizeof(double));
 
+    // zero fp. pass 2 assigns it only for those local densities that apply
+    // to the type of the central atom, while pass 3 reads all of them.
+    // fp is shared, so each thread only zeroes its own chunk of atoms.
+
+    int kfrom, kto;
+    loop_setup_thr(kfrom, kto, tid, nall, nthreads);
+    for (int k = 0; k < nLD; k++)
+      memset(&fp[k][kfrom], 0, (kto-kfrom) * sizeof(double));
+
     // -------------------------------------------------------------------
     // Pass 1: compute per-thread local densities
 

src/SPIN/fix_nve_spin.cpp

@@ -297,6 +297,7 @@ void FixNVESpin::init()
   // setting the sector variables/lists
 
   nsectors = 0;
+  memory->destroy(rsec);
   memory->create(rsec,3,"nve/spin:rsec");
 
   // perform the sectoring operation

src/atom_vec_ellipsoid.cpp

@@ -682,6 +682,10 @@ void AtomVecEllipsoid::data_atom_post(int ilocal)
 
   if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
 
+  // data_atom_bonus() overrides this for atoms listed in the Ellipsoids section
+
+  if (atom->superellipsoid_flag) radius[ilocal] = 0.0;
+
   angmom[ilocal][0] = 0.0;
   angmom[ilocal][1] = 0.0;
   angmom[ilocal][2] = 0.0;

src/delete_atoms.cpp

@@ -237,6 +237,13 @@ void DeleteAtoms::command(int narg, char **arg)
       // overwrite tags with condensed values
       for (int i = 0; i < nlocal; ++i) tag[i] = newtags[i];
 
+      // tagproc is only needed by the settags() callback above
+      // newtags points to mynewtags and thus must not be deleted
+
+      delete[] tagproc;
+      tagproc = nullptr;
+      newtags = nullptr;
+
       // update atom map since we changed the tags
       atom->map_tag_max = -1;
       atom->map_style_set();

tools/valgrind/README

@@ -5,7 +5,8 @@ and fixing real issues. When using CMake, these are automatically included
 when running "ctest -T memcheck". To manually add them to do a memory check
 on running LAMMPS, use a command line like following:
 
-valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes \
+valgrind --leak-check=full --track-origins=yes \
+   --show-leak-kinds=definite,indirect,possible \
    --suppressions=/path/to/lammps/tools/valgrind/FlexiBLAS.supp \
    --suppressions=/path/to/lammps/tools/valgrind/GTest.supp \
    --suppressions=/path/to/lammps/tools/valgrind/Kokkos.supp \
@@ -21,7 +22,7 @@ valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes \
 Or you can create a file $HOME/.valgrindrc with one option per line:
 
 --leak-check=full
---show-leak-kinds=all
+--show-leak-kinds=definite,indirect,possible
 --track-origins=yes
 --suppressions=/path/to/lammps/tools/valgrind/FlexiBLAS.supp
 --suppressions=/path/to/lammps/tools/valgrind/GTest.supp
@@ -37,4 +38,4 @@ Or you can create a file $HOME/.valgrindrc with one option per line:
 These options will be automatically added to the valgrind
 command line, so it becomes: valgrind lmp -in in.melt
 
-Last update: 2026-06-27
+Last update: 2026-07-26

unittest/cplusplus/test_advanced_utils.cpp

@@ -163,6 +163,9 @@ TEST_F(AdvancedUtils, expand_args)
     args[8]            = utils::strdup("c_gofr[*][*]");
 
     // disable use of input->command and input->arg which point to the last run command right now
+    // must be restored afterwards, or Input cannot free its argument list
+    char *saved_command = lmp->input->command;
+    char **saved_arg    = lmp->input->arg;
     lmp->input->command = nullptr;
     lmp->input->arg     = nullptr;
 
@@ -253,6 +256,9 @@ TEST_F(AdvancedUtils, expand_args)
     for (int i = 0; i < oarg; ++i)
         delete[] args[i];
     delete[] args;
+
+    lmp->input->command = saved_command;
+    lmp->input->arg     = saved_arg;
 }
 
 TEST_F(AdvancedUtils, check_packages_for_style)