Merge pull request #2395 from rbberger/collected-small-fixes

Fixes issues found via Static Code Analysis and from bug reports

.github/CODEOWNERS

@@ -114,6 +114,7 @@ src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
 src/utils.*               @akohlmey @rbberger
+src/math_eigen_impl.h     @jewettaij
 
 # tools
 tools/msi2lmp/*       @akohlmey
@@ -134,6 +135,9 @@ cmake/presets/*.cmake @junghans @rbberger @akohlmey
 # python
 python/*              @rbberger
 
+# fortran
+fortran/*             @akohlmey
+
 # docs
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger

cmake/presets/intel.cmake

@@ -1,7 +1,8 @@
-# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
 set(MPI_CXX "icpc" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
@@ -12,5 +13,6 @@ set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpc" CACHE STRING "" FORCE)
 set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

doc/src/Tools.rst

@@ -663,6 +663,7 @@ The singularity sub-directory contains container definitions files
 that can be used to build container images for building and testing
 LAMMPS on specific OS variants using the `Singularity <https://sylabs.io>`_
 container software. Contributions for additional variants are welcome.
+For more details please see the README.md file in that folder.
 
 ----------
 

src/ASPHERE/pair_line_lj.cpp

@@ -74,7 +74,6 @@ void PairLineLJ::compute(int eflag, int vflag)
   double xi[2],xj[2],fi[2],dxi,dxj,dyi,dyj;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
-  evdwl = 0.0;
   ev_init(eflag,vflag);
 
   double **x = atom->x;

src/ASPHERE/pair_tri_lj.cpp

@@ -74,7 +74,6 @@ void PairTriLJ::compute(int eflag, int vflag)
   double dc1[3],dc2[3],dc3[3];
   int *ilist,*jlist,*numneigh,**firstneigh;
 
-  evdwl = 0.0;
   ev_init(eflag,vflag);
 
   AtomVecTri::Bonus *bonus = avec->bonus;

src/BODY/compute_body_local.cpp

@@ -123,7 +123,7 @@ void ComputeBodyLocal::compute_local()
   int ncount = compute_body(0);
   if (ncount > nmax) reallocate(ncount);
   size_local_rows = ncount;
-  ncount = compute_body(1);
+  compute_body(1);
 }
 
 /* ----------------------------------------------------------------------

src/BODY/compute_temp_body.cpp

@@ -343,7 +343,6 @@ void ComputeTempBody::compute_vector()
 
         inertia = bonus[body[i]].inertia;
         quat = bonus[body[i]].quat;
-        massone = rmass[i];
 
         // wbody = angular velocity in body frame
 

src/CLASS2/angle_class2.cpp

@@ -447,10 +447,6 @@ double AngleClass2::single(int type, int i1, int i2, int i3)
   if (c > 1.0) c = 1.0;
   if (c < -1.0) c = -1.0;
 
-  double s = sqrt(1.0 - c*c);
-  if (s < SMALL) s = SMALL;
-  s = 1.0/s;
-
   double dtheta = acos(c) - theta0[type];
   double dtheta2 = dtheta*dtheta;
   double dtheta3 = dtheta2*dtheta;

src/SPIN/neb_spin.cpp

@@ -298,7 +298,7 @@ void NEBSpin::run()
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc EBF EBR RDT "
                 "RD1 PE1 RD2 PE2 ... RDN PEN "
-                "GradV0dottan DN0... GradVNdottan DNN\n");
+                "GradV0dottan DN0 ... GradVNdottan DNN\n");
       } else {
         fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
                 "GradV0 GradV1 GradVc "

src/SPIN/pair_spin_dipole_cut.cpp

@@ -379,7 +379,7 @@ void PairSpinDipoleCut::compute_dipolar(int /* i */, int /* j */, double eij[3],
 ------------------------------------------------------------------------- */
 
 void PairSpinDipoleCut::compute_dipolar_mech(int /* i */, int /* j */, double eij[3],
-    double fi[3], double spi[3], double spj[3], double r2inv)
+    double fi[3], double spi[4], double spj[4], double r2inv)
 {
   double sisj,sieij,sjeij;
   double gigjri4,bij,pre;

src/SPIN/pair_spin_dipole_long.cpp

@@ -453,7 +453,7 @@ void PairSpinDipoleLong::compute_long(int /* i */, int /* j */, double eij[3],
 ------------------------------------------------------------------------- */
 
 void PairSpinDipoleLong::compute_long_mech(int /* i */, int /* j */, double eij[3],
-    double bij[4], double fi[3], double spi[3], double spj[3])
+    double bij[4], double fi[3], double spi[4], double spj[4])
 {
   double sisj,sieij,sjeij,b2,b3;
   double g1,g2,g1b2_g2b3,gigj,pre;

src/USER-INTEL/fix_intel.cpp

@@ -160,9 +160,9 @@ FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) :  Fix(lmp, narg, arg)
 
   // if using LRT mode, create the integrate style
   if (_lrt) {
-    char *str;
-    str = (char *) "verlet/lrt/intel";
-    update->create_integrate(1,&str,0);
+    char *cmd[1];
+    cmd[0] = (char *) "verlet/lrt/intel";
+    update->create_integrate(1,cmd,0);
   }
 
   // error check

src/USER-MISC/bond_special.cpp

@@ -184,8 +184,8 @@ void BondSpecial::read_restart(FILE *fp)
   allocate();
 
   if (comm->me == 0) {
-    fread(&factor_lj[1],sizeof(double),atom->nbondtypes,fp);
-    fread(&factor_coul[1],sizeof(double),atom->nbondtypes,fp);
+    utils::sfread(FLERR,&factor_lj[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
+    utils::sfread(FLERR,&factor_coul[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
   }
   MPI_Bcast(&factor_lj[1],atom->nbondtypes,MPI_DOUBLE,0,world);
   MPI_Bcast(&factor_coul[1],atom->nbondtypes,MPI_DOUBLE,0,world);

src/USER-MISC/fix_propel_self.cpp

@@ -160,13 +160,13 @@ template <int filter_by_type>
 void FixPropelSelf::post_force_quaternion(int /* vflag */ )
 {
   double **f = atom->f;
-  AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->avec);
 
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
   int *type = atom->type;
   int* ellipsoid = atom->ellipsoid;
 
+  AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->style_match("ellipsoid"));
   AtomVecEllipsoid::Bonus *bonus = av->bonus;
 
   // Add the active force to the atom force:

src/USER-MISC/pair_coul_slater_cut.cpp

@@ -152,10 +152,10 @@ void PairCoulSlaterCut::write_restart_settings(FILE *fp)
 void PairCoulSlaterCut::read_restart_settings(FILE *fp)
 {
   if (comm->me == 0) {
-    fread(&cut_global,sizeof(double),1,fp);
-    fread(&lamda,sizeof(double),1,fp);
-    fread(&offset_flag,sizeof(int),1,fp);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&lamda,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
   }
   MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);

src/USER-OMP/fix_omp.cpp

@@ -78,10 +78,10 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg)
 #endif
   }
 
+#if defined(_OPENMP)
   if (nthreads < 1)
     error->all(FLERR,"Illegal number of OpenMP threads requested");
 
-#if defined(_OPENMP)
   int reset_thr = 0;
 #endif
   if (nthreads != comm->nthreads) {

src/USER-UEF/compute_pressure_uef.cpp

@@ -78,7 +78,7 @@ double ComputePressureUef::compute_scalar()
   addstep(update->ntimestep+1);
 
   int k =0;
-  scalar = 0;
+  scalar = 0.0;
   if (ext_flags[0]) {
     scalar += vector[0];
     k++;
@@ -92,7 +92,7 @@ double ComputePressureUef::compute_scalar()
     k++;
   }
 
-  scalar /= k;
+  if (k > 1) scalar /= k;
   return scalar;
 }
 

src/change_box.cpp

@@ -176,7 +176,7 @@ void ChangeBox::command(int narg, char **arg)
 
   int move_atoms = 0;
   for (int m = 0; m < nops; m++) {
-    if (ops[m].style != ORTHO || ops[m].style != TRICLINIC) move_atoms = 1;
+    if (ops[m].style != ORTHO && ops[m].style != TRICLINIC) move_atoms = 1;
   }
 
   // error if moving atoms and there is stored per-atom restart state

src/compute_pressure.cpp

@@ -36,7 +36,7 @@ using namespace LAMMPS_NS;
 
 ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  vptr(nullptr), id_temp(nullptr)
+  vptr(nullptr), id_temp(nullptr), pstyle(nullptr)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute pressure command");
   if (igroup) error->all(FLERR,"Compute pressure must use group all");
@@ -146,6 +146,7 @@ ComputePressure::~ComputePressure()
   delete [] id_temp;
   delete [] vector;
   delete [] vptr;
+  delete [] pstyle;
 }
 
 /* ---------------------------------------------------------------------- */

src/input.cpp

@@ -1234,12 +1234,11 @@ void Input::shell()
   } else if (strcmp(arg[0],"putenv") == 0) {
     if (narg < 2) error->all(FLERR,"Illegal shell putenv command");
     for (int i = 1; i < narg; i++) {
-      char *ptr = strdup(arg[i]);
       rv = 0;
 #ifdef _WIN32
-      if (ptr != nullptr) rv = _putenv(ptr);
+      if (arg[i]) rv = _putenv(arg[i]);
 #else
-      if (ptr != nullptr) rv = putenv(ptr);
+      if (arg[i]) rv = putenv(arg[i]);
 #endif
       rv = (rv < 0) ? errno : 0;
       MPI_Reduce(&rv,&err,1,MPI_INT,MPI_MAX,0,world);

src/math_eigen_impl.h

@@ -849,6 +849,8 @@ void Jacobi<Scalar, Vector, Matrix, ConstMatrix>::
 Dealloc() {
   //assert(! is_preallocated);
   Dealloc2D(&M);
+  delete[] max_idx_row;
+  max_idx_row = nullptr;
   Init();
 }
 

src/reset_atom_ids.cpp

@@ -368,9 +368,9 @@ void ResetIDs::sort()
   // bins are numbered from 0 to Nbins-1
 
   bigint nbins = (bigint) nbinx*nbiny*nbinz;
-  int nlo = nbins / nprocs;
-  int nhi = nlo + 1;
-  int nplo = nprocs - (nbins % nprocs);
+  bigint nlo = nbins / nprocs;
+  bigint nhi = nlo + 1;
+  bigint nplo = nprocs - (nbins % nprocs);
   bigint nbinlo = nplo*nlo;
 
   if (me < nplo) {

tools/singularity/README.md

@@ -5,12 +5,12 @@ for [Singularity](https://sylabs.io), suitable for compiling and testing
 LAMMPS on a variety of OS variants with support for most standard
 packages and - for some of them - also building/spellchecking the manual
 in all supported formats. This allows to test and debug LAMMPS code on
-different OS variants than what is locally installed on your development
+different OS variants without doing a full installation on your development
 workstation, e.g. when bugs are reported that can only be reproduced on
 a specific OS or with specific (mostly older) versions of tools,
 compilers, or libraries.
 
-Ready-to-use container images built from these definition files are
+Ready-to-use container images built from some these definition files are
 occasionally uploaded to the container library at sylabs.io. They
 can be found here: https://cloud.sylabs.io/library/lammps/default/lammps_development#
 and will be signed with a GPG key that has the fingerprint:
@@ -25,7 +25,7 @@ git clone --depth 500  git://github.com/lammps/lammps.git lammps
 mkdir build-centos7
 cd build-centos7
 sudo singularity build centos7.sif ../tools/singularity/centos7.def
-singularity shell centos7.sif
+singularity exec centos7.sif bash --login
 cmake -C ../cmake/presets/most.cmake ../cmake
 make
 ```
@@ -39,7 +39,7 @@ git clone --depth 500  git://github.com/lammps/lammps.git lammps
 mkdir build-ubuntu18
 cd build-ubuntu18
 singularity pull library://lammps/default/lammps_development:ubuntu18.04
-singularity shell lammps_development_ubuntu18.04.sif
+singularity exec lammps_development_ubuntu18.04.sif bash --login
 cmake -C ../cmake/presets/most.cmake ../cmake
 make
 ```

unittest/commands/test_simple_commands.cpp

@@ -312,6 +312,32 @@ TEST_F(SimpleCommandsTest, Units)
 
     TEST_FAILURE(".*ERROR: Illegal units command.*", lmp->input->one("units unknown"););
 }
+
+TEST_F(SimpleCommandsTest, Shell)
+{
+    if (!verbose) ::testing::internal::CaptureStdout();
+    lmp->input->one("shell putenv TEST_VARIABLE=simpletest");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    char * test_var = getenv("TEST_VARIABLE");
+    ASSERT_NE(test_var, nullptr);
+    ASSERT_THAT(test_var, StrEq("simpletest"));
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    lmp->input->one("shell putenv TEST_VARIABLE=simpletest");
+    lmp->input->one("shell putenv TEST_VARIABLE2=simpletest2 OTHER_VARIABLE=2");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    char * test_var2 = getenv("TEST_VARIABLE2");
+    char * other_var = getenv("OTHER_VARIABLE");
+
+    ASSERT_NE(test_var2, nullptr);
+    ASSERT_THAT(test_var2, StrEq("simpletest2"));
+
+    ASSERT_NE(other_var, nullptr);
+    ASSERT_THAT(other_var, StrEq("2"));
+}
+
 } // namespace LAMMPS_NS
 
 int main(int argc, char **argv)