Merge pull request #2761 from rbberger/collected-small-changes

Collected small changes and fixes for the next patch release

SECURITY.md

@@ -0,0 +1,35 @@
+# Security Policy
+
+LAMMPS is designed as a user-level application to conduct computer
+simulations for research using classical mechanics.  As such LAMMPS
+depends to some degrees on users providing correctly formatted input and
+LAMMPS needs to read and write files based on uncontrolled user input.
+As a parallel application for use in high-performance computing
+environments, performance critical steps are also done without checking
+data.
+
+LAMMPS also is interfaced to a number of external libraries, including
+libraries with experimental research software, that are not validated
+and tested by the LAMMPS developers, so it is easy to import bad
+behavior from calling functions in one of those libraries.
+
+Thus is is quite easy to crash LAMMPS through malicious input and do all
+kinds of filesystem manipulations.  And because of that LAMMPS should
+**NEVER** be compiled or **run** as superuser, either from a "root" or
+"administrator" account directly or indirectly via "sudo" or "su".
+
+Therefore what could be seen as a security vulnerability is usually
+either a user mistake or a bug in the code.  Bugs can be reported in
+the LAMMPS project
+[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
+
+
+# Version Updates
+
+LAMMPS follows continuous release development model.  We aim to keep all
+release versions (stable or patch) fully functional and employ a variety
+of automatic testing procedures to detect failures of existing
+functionality from adding new features before releases are made.  Thus
+bugfixes and updates are only integrated into the current development
+branch and thus the next (patch) release and users are recommended to
+update regularly.

doc/src/fix_grem.rst

@@ -92,6 +92,11 @@ The :doc:`thermo_modify <thermo_modify>` *press* option is supported
 by this fix to add the rescaled kinetic pressure as part of
 :doc:`thermodynamic output <thermo_style>`.
 
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the effective
+temperature :math:`T_{eff}`.  The scalar value calculated by this
+fix is "intensive".
+
 Restrictions
 """"""""""""
 

src/USER-BROWNIAN/fix_brownian_asphere.cpp

@@ -38,8 +38,8 @@ using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixBrownianAsphere::FixBrownianAsphere(LAMMPS *lmp, int narg, char **arg) :
-    FixBrownianBase(lmp, narg, arg)
+FixBrownianAsphere::FixBrownianAsphere(LAMMPS *lmp, int narg, char **arg)
+  : FixBrownianBase(lmp, narg, arg), avec(nullptr)
 {
   if (!gamma_t_eigen_flag || !gamma_r_eigen_flag) {
     error->all(FLERR, "Illegal fix brownian command.");

src/USER-BROWNIAN/fix_brownian_base.cpp

@@ -46,6 +46,7 @@ FixBrownianBase::FixBrownianBase(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, n
   gamma_t_flag = gamma_r_flag = 0;
   gamma_t_eigen_flag = gamma_r_eigen_flag = 0;
   dipole_flag = 0;
+  g2 = 0.0;
 
   if (narg < 5) error->all(FLERR, "Illegal fix brownian command.");
 
@@ -201,7 +202,7 @@ void FixBrownianBase::init()
 
   g1 = force->ftm2v;
   if (noise_flag == 0) {
-    g2 = 0;
+    g2 = 0.0;
   } else if (gaussian_noise_flag == 1) {
     g2 = sqrt(2 * force->boltz * temp / dt / force->mvv2e);
   } else {

src/USER-BROWNIAN/fix_propel_self.cpp

@@ -42,7 +42,8 @@ enum { DIPOLE, VELOCITY, QUAT };
 
 /* ---------------------------------------------------------------------- */
 
-FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg)
+  : Fix(lmp, narg, arg), avec(nullptr)
 {
 
   virial_global_flag = virial_peratom_flag = 1;

src/USER-REACTION/fix_bond_react.cpp

@@ -2212,6 +2212,7 @@ double FixBondReact::rxnfunction(std::string rxnfunc, std::string varid,
 
   if (rxnfunc == "rxnsum") return sumvvec;
   if (rxnfunc == "rxnave") return sumvvec/nsum;
+  return 0.0;
 }
 
 /* ----------------------------------------------------------------------

src/fix_temp_csvr.cpp

@@ -39,6 +39,7 @@ using namespace FixConst;
 enum{NOBIAS,BIAS};
 enum{CONSTANT,EQUAL};
 
+static constexpr int PRNGSIZE = 98+2+3;
 /* ---------------------------------------------------------------------- */
 
 FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
@@ -330,7 +331,6 @@ double FixTempCSVR::compute_scalar()
 
 void FixTempCSVR::write_restart(FILE *fp)
 {
-  const int PRNGSIZE = 98+2+3;
   int nsize = PRNGSIZE*comm->nprocs+2; // pRNG state per proc + nprocs + energy
   double *list = nullptr;
   if (comm->me == 0) {
@@ -363,7 +363,7 @@ void FixTempCSVR::restart(char *buf)
   if (nprocs != comm->nprocs) {
     if (comm->me == 0)
       error->warning(FLERR,"Different number of procs. Cannot restore RNG state.");
-  } else random->set_state(list+2+comm->me*103);
+  } else random->set_state(list+2+comm->me*PRNGSIZE);
 }
 
 /* ----------------------------------------------------------------------

src/utils.h

@@ -379,7 +379,6 @@ namespace LAMMPS_NS {
    :cpp:class:`Tokenizer`, :cpp:class:`ValueTokenizer`
 
 \endverbatim
-     *
      * \param text string that should be split
      * \return STL vector with the words */