Merge branch 'master' into snap-launch-bounds

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "24 December 2020" "2020-12-24"
+.TH LAMMPS "10 February 2021" "2021-02-10"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Intro_citing.rst

@@ -38,17 +38,18 @@ In addition there are DOIs for individual stable releases. Currently there are:
 Home page
 ^^^^^^^^^
 
-The LAMMPS website at `https://lammps.sandia.gov/ <https://lammps.sandia.gov>`_ is the canonical
-location for information about LAMMPS and more detailed lists of publications
-using LAMMPS and contributing features.
+The LAMMPS website at `https://lammps.sandia.gov/
+<https://lammps.sandia.gov>`_ is the canonical location for information
+about LAMMPS and its features.
 
 Citing contributions
 ^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS has many features and uses previously published methods and
-algorithms or novel features. It also includes potential parameter
-filed for specific models.  You can look up relevant publications either
-in the LAMMPS output to the screen, the ``log.cite`` file (which is
-populated with references to relevant papers through embedding them into
-the source code) and in the documentation of the :doc:`corresponding commands
+LAMMPS has many features and that use either previously published
+methods and algorithms or novel features.  It also includes potential
+parameter filed for specific models.  Where available, a reminder about
+references for optional features used in a specific run is printed to
+the screen and log file.  Style and output location can be selected with
+the :ref:`-cite command-line switch <cite>`.  Additional references are
+given in the documentation of the :doc:`corresponding commands
 <Commands_all>` or in the :doc:`Howto tutorials <Howto>`.

doc/src/Modify_contribute.rst

@@ -206,16 +206,22 @@ packages in the src directory for examples. If you are uncertain, please ask.
   algorithm/science behind the feature itself, or its initial usage, or
   its implementation in LAMMPS), you can add the citation to the \*.cpp
   source file.  See src/USER-EFF/atom_vec_electron.cpp for an example.
-  A LaTeX citation is stored in a variable at the top of the file and a
-  single line of code that references the variable is added to the
-  constructor of the class.  Whenever a user invokes your feature from
-  their input script, this will cause LAMMPS to output the citation to a
-  log.cite file and prompt the user to examine the file.  Note that you
-  should only use this for a paper you or your group authored.
-  E.g. adding a cite in the code for a paper by Nose and Hoover if you
-  write a fix that implements their integrator is not the intended
-  usage.  That kind of citation should just be in the doc page you
-  provide.
+  A LaTeX citation is stored in a variable at the top of the file and
+  a single line of code registering this variable is added to the
+  constructor of the class.  If there is additional functionality (which
+  may have been added later) described in a different publication,
+  additional citation descriptions may be added for as long as they
+  are only registered when the corresponding keyword activating this
+  functionality is used.  With these options it is possible to have
+  LAMMPS output a specific citation reminder whenever a user invokes
+  your feature from their input script.  Note that you should only use
+  this for the most relevant paper for a feature and a publication that
+  you or your group authored.  E.g. adding a citation in the code for
+  a paper by Nose and Hoover if you write a fix that implements their
+  integrator is not the intended usage.  That kind of citation should
+  just be included in the documentation page you provide describing
+  your contribution.  If you are not sure what the best option would
+  be, please contact the LAMMPS developers for advice.
 
 Finally, as a general rule-of-thumb, the more clear and
 self-explanatory you make your documentation and README files, and the

doc/src/Run_options.rst

@@ -11,6 +11,7 @@ letter abbreviation can be used:
 * :ref:`-k or -kokkos <run-kokkos>`
 * :ref:`-l or -log <log>`
 * :ref:`-m or -mpicolor <mpicolor>`
+* :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
 * :ref:`-pk or -package <package>`
 * :ref:`-p or -partition <partition>`
@@ -220,14 +221,31 @@ links with from the lib/message directory.  See the
 
 ----------
 
+.. _cite:
+
+**-cite style or file name**
+
+Select how and where to output a reminder about citing contributions
+to the LAMMPS code that were used during the run. Available styles are
+"both", "none", "screen", or "log".  Any flag will be considered a file
+name to write the detailed citation info to.  Default is the "log" style
+where there is a short summary in the screen output and detailed citations
+in BibTeX format in the logfile.  The option "both" selects the detailed
+output for both, "none", the short output for both, and "screen" will
+write the detailed info to the screen and the short version to the log
+file.  If a dedicated citation info file is requested, the screen and
+log file output will be in the short format (same as with "none").
+
+See the :doc:`citation page <Intro_citing>` for more details on
+how to correctly reference and cite LAMMPS.
+
+----------
+
 .. _nocite:
 
 **-nocite**
 
-Disable writing the log.cite file which is normally written to list
-references for specific cite-able features used during a LAMMPS run.
-See the `citation page <https://lammps.sandia.gov/cite.html>`_ for more
-details.
+Disable generating a citation reminder (see above) at all.
 
 ----------
 

doc/src/compute_pressure.rst

@@ -122,8 +122,11 @@ Output info
 This compute calculates a global scalar (the pressure) and a global
 vector of length 6 (pressure tensor), which can be accessed by indices
 1-6.  These values can be used by any command that uses global scalar
-or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
-options.
+or vector values from a compute as input.  See the :doc:`Howto output
+<Howto_output>` doc page for an overview of LAMMPS output options.
+
+The ordering of values in the symmetric pressure tensor is as follows:
+pxx, pyy, pzz, pxy, pxz, pyz.
 
 The scalar and vector values calculated by this compute are
 "intensive".  The scalar and vector values will be in pressure

doc/src/compute_stress_atom.rst

@@ -216,6 +216,11 @@ an identical manner to compute *stress/atom*.  See the :doc:`Howto
 output <Howto_output>` doc page for an overview of LAMMPS output
 options.
 
+The ordering of the 6 columns for *stress/atom* is as follows: xx, yy,
+zz, xy, xz, yz.  The ordering of the 9 columns for
+*centroid/stress/atom* is as follows: xx, yy, zz, xy, xz, yz, yx, zx,
+zy.
+
 The per-atom array values will be in pressure\*volume :doc:`units
 <units>` as discussed above.
 

doc/src/create_bonds.rst

@@ -125,6 +125,16 @@ cannot appear in the neighbor list, to avoid creation of duplicate
 bonds.  The neighbor list for all atom type pairs must also extend to
 a distance that encompasses the *rmax* for new bonds to create.
 
+.. note::
+
+   If you want to create bonds between pairs of 1-3 or 1-4 atoms in
+   the current bond topology, then you need to use :doc:`special_bonds
+   lj 0 1 1 <special_bonds>` to insure those pairs appear in the
+   neighbor list.  They will not appear with the default special_bonds
+   settings which are zero for 1-2, 1-3, and 1-4 atoms.  1-3 or 1-4
+   atoms are those which are 2 hops or 3 hops apart in the bond
+   topology.
+
 An additional requirement for this style is that your system must be
 ready to perform a simulation.  This means, for example, that all
 :doc:`pair_style <pair_style>` coefficients be set via the

doc/src/fix_bond_react.rst

@@ -650,8 +650,8 @@ reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
 
 .. _Gissinger:
 
-**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
+**(Gissinger2017)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
 
 .. _Gissinger2020:
 
-**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
+**(Gissinger2020)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).

doc/src/kim_commands.rst

@@ -1286,7 +1286,7 @@ to cite the OpenKIM project :ref:`(Tadmor) <kim-mainpaper>`, KIM API
 in addition to the relevant scientific references for the IM.
 The citation format for an IM is displayed on its page on
 `OpenKIM <https://openkim.org>`_ along with the corresponding BibTex file,
-and is automatically added to the LAMMPS *log.cite* file.
+and is automatically added to the LAMMPS citation reminder.
 
 Citing the IM software (KIM infrastructure and specific PM or SM codes)
 used in the simulation gives credit to the researchers who developed them

doc/utils/sphinx-config/false_positives.txt

@@ -2540,6 +2540,8 @@ Px
 pxx
 Pxx
 Pxy
+pxy
+pxz
 py
 Py
 pydir
@@ -2551,10 +2553,13 @@ pymol
 pypar
 pythonic
 pytorch
+pyy
 Pyy
+pyz
 pz
 Pz
 Pzz
+pzz
 qbmsst
 qcore
 qdist

src/USER-INTEL/npair_skip_intel.cpp

@@ -55,8 +55,8 @@ void NPairSkipIntel::copy_neighbor_info()
 {
   NPair::copy_neighbor_info();
   if (_full_props) delete []_full_props;
-  _full_props = new int[neighbor->nlist];
-  for (int i = 0; i < neighbor->nlist; i++)
+  _full_props = new int[neighbor->nrequest];
+  for (int i = 0; i < neighbor->nrequest; i++)
     _full_props[i] = neighbor->requests[i]->full;
 }
 

src/angle.h

@@ -26,7 +26,7 @@ class Angle : protected Pointers {
   int *setflag;
   int writedata;                  // 1 if writes coeffs to data file
   double energy;                  // accumulated energies
-  double virial[6];               // accumulated virial
+  double virial[6];               // accumulated virial: xx,yy,zz,xy,xz,yz
   double *eatom,**vatom;          // accumulated per-atom energy/virial
   double **cvatom;                // accumulated per-atom centroid virial
 

src/atom_vec_tri.cpp

@@ -539,7 +539,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
   double area = 0.5 * MathExtra::len3(norm);
   rmass[m] *= area;
 
-  // inertia = inertia tensor of triangle as 6-vector in Voigt notation
+  // inertia = inertia tensor of triangle as 6-vector in Voigt ordering
 
   double inertia[6];
   MathExtra::inertia_triangle(c1,c2,c3,rmass[m],inertia);

src/bond.h

@@ -26,7 +26,7 @@ class Bond : protected Pointers {
   int *setflag;
   int writedata;                  // 1 if writes coeffs to data file
   double energy;                  // accumulated energies
-  double virial[6];               // accumulated virial
+  double virial[6];               // accumulated virial: xx,yy,zz,xy,xz,yz
   double *eatom,**vatom;          // accumulated per-atom energy/virial
 
   int reinitflag;                // 1 if compatible with fix adapt and alike

src/citeme.cpp

@@ -12,64 +12,118 @@
 ------------------------------------------------------------------------- */
 
 #include "citeme.h"
+#include "comm.h"
 #include "universe.h"
 
 using namespace LAMMPS_NS;
 
-static const char cite_header[] =
-  "This LAMMPS simulation made specific use of work described in the\n"
-  "following references.  See https://lammps.sandia.gov/cite.html\n"
-  "for details.\n\n";
+static const char cite_separator[] =
+  "CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE\n\n";
 
-static const char cite_nagline[] = "\nPlease see the log.cite file "
-  "for references relevant to this simulation\n\n";
+static const char cite_nagline[] =
+  "Your simulation uses code contributions which should be cited:\n";
+
+static const char cite_file[] = "The {} {} lists these citations in "
+                                "BibTeX format.\n\n";
 
 /* ---------------------------------------------------------------------- */
 
-CiteMe::CiteMe(LAMMPS *lmp) : Pointers(lmp)
+CiteMe::CiteMe(LAMMPS *lmp, int _screen, int _logfile, const char *_file)
+  : Pointers(lmp)
 {
   fp = nullptr;
   cs = new citeset();
+
+  screen_flag = _screen;
+  scrbuffer.clear();
+  logfile_flag = _logfile;
+  logbuffer.clear();
+
+  if (_file && universe->me == 0) {
+    citefile = _file;
+    fp = fopen(_file,"w");
+    if (fp) {
+      fputs(cite_nagline,fp);
+      fflush(fp);
+    } else {
+      utils::logmesg(lmp, "Unable to open citation file '" + citefile
+                     + "': " + utils::getsyserror() + "\n");
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
-   write out nag-line at the end of the regular output and clean up
+   write out remaining citations at end of the regular output and clean up
 ------------------------------------------------------------------------- */
 
 CiteMe::~CiteMe()
 {
-  if (universe->me || cs->size() == 0) {
-    delete cs;
-    return;
-  }
-
+  flush();
   delete cs;
 
-  if (fp) {
-    if (screen) fprintf(screen,cite_nagline);
-    if (logfile) fprintf(logfile,cite_nagline);
-
-    fclose(fp);
-  }
+  if (fp) fclose(fp);
 }
 
 /* ----------------------------------------------------------------------
-   write out and register a citation so it will be written only once
+   process an added citation so it will be shown only once and as requested
 ------------------------------------------------------------------------- */
 
 void CiteMe::add(const char *ref)
 {
-  if (universe->me) return;
+  if (comm->me != 0) return;
   if (cs->find(ref) != cs->end()) return;
   cs->insert(ref);
 
-  if (!fp) {
-    fp = fopen("log.cite","w");
-    if (!fp) return;
-    fputs(cite_header,fp);
+  if (fp) {
+    fputs(ref,fp);
     fflush(fp);
   }
 
-  fputs(ref,fp);
-  fflush(fp);
+  if (scrbuffer.empty()) {
+    scrbuffer += "\n";
+    scrbuffer += cite_separator;
+    scrbuffer += cite_nagline;
+    if (screen_flag == VERBOSE) scrbuffer += "\n";
+  }
+
+  if (logbuffer.empty()) {
+    logbuffer += "\n";
+    logbuffer += cite_separator;
+    logbuffer += cite_nagline;
+    if (logfile_flag == VERBOSE) logbuffer += "\n";
+  }
+
+  std::string reference = ref;
+  std::size_t found = reference.find_first_of("\n");
+  std::string header = reference.substr(0,found+1);
+  if (screen_flag == VERBOSE) scrbuffer += "- " + reference;
+  if (screen_flag == TERSE) scrbuffer += "- " + header;
+  if (logfile_flag == VERBOSE) logbuffer += "- " + reference;
+  if (logfile_flag == TERSE) logbuffer += "- " + header;
 }
+
+void CiteMe::flush()
+{
+  if (comm->me == 0) {
+    if (!scrbuffer.empty()) {
+      if (!citefile.empty())
+        scrbuffer += fmt::format(cite_file,"file",citefile);
+      if (logfile_flag == VERBOSE)
+        scrbuffer += fmt::format(cite_file,"log","file");
+      scrbuffer += cite_separator;
+      if (screen) fputs(scrbuffer.c_str(),screen);
+      scrbuffer.clear();
+    }
+    if (!logbuffer.empty()) {
+      if (!citefile.empty())
+        logbuffer += fmt::format(cite_file,"file",citefile);
+      if (screen_flag == VERBOSE)
+        scrbuffer += fmt::format(cite_file,"screen","output");
+      logbuffer += cite_separator;
+      if (logfile) fputs(logbuffer.c_str(),logfile);
+      logbuffer.clear();
+    }
+  }
+  return;
+}
+

src/citeme.h

@@ -21,27 +21,33 @@ namespace LAMMPS_NS {
 
 class CiteMe : protected Pointers {
  public:
-  CiteMe(class LAMMPS *);
+  CiteMe(class LAMMPS *, int, int, const char *);
   virtual ~CiteMe();
-  void add(const char *);       // print out and register publication
+  void add(const char *);       // register publication for output
+  void flush();                 // flush buffers to screen and logfile
+  enum {VERBOSE, TERSE};
 
  private:
-  FILE *fp;                    // opaque pointer to log.cite file object
+  FILE *fp;                    // explicit citation file pointer or NULL
+  std::string citefile;        // name of the explicit citation file.
+  int screen_flag;             // determine whether verbose or terse output
+  int logfile_flag;            // determine whether verbose or terse output
+  std::string scrbuffer;       // output buffer for screen
+  std::string logbuffer;       // output buffer for logfile
   typedef std::set<const char *> citeset;
   citeset *cs;                 // registered set of publications
 };
-
 }
 
 #endif
 
 /* ERROR/WARNING messages:
 
-E: Cannot open log.cite file
+E: Cannot open citation file
 
 This file is created when you use some LAMMPS features, to indicate
 what paper you should cite on behalf of those who implemented
-the feature.  Check that you have write privileges into the directory
+the feature.  Check that you have write privileges in the directory
 you are running in.
 
 */

src/compute_pressure.h

@@ -40,7 +40,7 @@ class ComputePressure : public Compute {
   double *kspace_virial;
   Compute *temperature;
   char *id_temp;
-  double virial[6];
+  double virial[6];                // ordering: xx,yy,zz,xy,xz,yz
   int pairhybridflag;
   class Pair *pairhybrid;
   int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;

src/create_bonds.cpp

@@ -233,7 +233,7 @@ void CreateBonds::many()
   // build neighbor list this command needs based on earlier request
 
   NeighList *list = neighbor->lists[irequest];
-  neighbor->build_one(list);
+  neighbor->build_one(list,1);
 
   // loop over all neighs of each atom
   // compute distance between two atoms consistently on both procs

src/dihedral.h

@@ -26,7 +26,7 @@ class Dihedral : protected Pointers {
   int *setflag;
   int writedata;                     // 1 if writes coeffs to data file
   double energy;                     // accumulated energy
-  double virial[6];                  // accumulated virial
+  double virial[6];                  // accumulated virial: xx,yy,zz,xy,xz,yz
   double *eatom,**vatom;             // accumulated per-atom energy/virial
   double **cvatom;                   // accumulated per-atom centroid virial
 

src/domain.h

@@ -75,7 +75,8 @@ class Domain : protected Pointers {
 
                                          // triclinic box
   double xy,xz,yz;                       // 3 tilt factors
-  double h[6],h_inv[6];                  // shape matrix in Voigt notation
+  double h[6],h_inv[6];                  // shape matrix in Voigt ordering
+                                         // Voigt = xx,yy,zz,yz,xz,xy
   double h_rate[6],h_ratelo[3];          // rate of box size/shape change
 
   int box_change;                // 1 if any of next 3 flags are set, else 0

src/fix_box_relax.cpp

@@ -738,7 +738,7 @@ void FixBoxRelax::couple()
   if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2]))
     error->all(FLERR,"Non-numeric pressure - simulation unstable");
 
-  // switch order from xy-xz-yz to Voigt
+  // switch order from xy-xz-yz to Voigt ordering
 
   if (pstyle == TRICLINIC) {
     p_current[3] = tensor[5];

src/fix_nh.cpp

@@ -1063,7 +1063,7 @@ void FixNH::couple()
   if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2]))
     error->all(FLERR,"Non-numeric pressure - simulation unstable");
 
-  // switch order from xy-xz-yz to Voigt
+  // switch order from xy-xz-yz to Voigt ordering
 
   if (pstyle == TRICLINIC) {
     p_current[3] = tensor[5];
@@ -1118,7 +1118,7 @@ void FixNH::remap()
   // h_dot = omega_dot * h
   //
   // where h_dot, omega_dot and h are all upper-triangular
-  // 3x3 tensors. In Voigt notation, the elements of the
+  // 3x3 tensors. In Voigt ordering, the elements of the
   // RHS product tensor are:
   // h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
   //

src/improper.h

@@ -26,7 +26,7 @@ class Improper : protected Pointers {
   int *setflag;
   int writedata;                  // 1 if writes coeffs to data file
   double energy;                  // accumulated energies
-  double virial[6];               // accumulated virial
+  double virial[6];               // accumulated virial: xx,yy,zz,xy,xz,yz
   double *eatom,**vatom;          // accumulated per-atom energy/virial
   double **cvatom;                // accumulated per-atom centroid virial
 

src/integrate.cpp

@@ -12,12 +12,14 @@
 ------------------------------------------------------------------------- */
 
 #include "integrate.h"
-#include "update.h"
+
+#include "citeme.h"
+#include "compute.h"
 #include "force.h"
-#include "pair.h"
 #include "kspace.h"
 #include "modify.h"
-#include "compute.h"
+#include "pair.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -45,6 +47,7 @@ Integrate::~Integrate()
 
 void Integrate::init()
 {
+  if (lmp->citeme) lmp->citeme->flush();
   update->atimestep = update->ntimestep;
 
   // allow pair and Kspace compute() to be turned off via modify flags

src/kspace.h

@@ -32,7 +32,7 @@ class KSpace : protected Pointers {
  public:
   double energy;                 // accumulated energies
   double energy_1,energy_6;
-  double virial[6];              // accumulated virial
+  double virial[6];              // accumulated virial: xx,yy,zz,xy,xz,yz
   double *eatom,**vatom;         // accumulated per-atom energy/virial
   double e2group;                // accumulated group-group energy
   double f2group[3];             // accumulated group-group force

src/lammps.cpp

@@ -171,6 +171,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
   int restart2dump = 0;
   int restartremap = 0;
   int citeflag = 1;
+  int citescreen = CiteMe::TERSE;
+  int citelogfile = CiteMe::VERBOSE;
+  char *citefile = nullptr;
   int helpflag = 0;
 
   suffix = suffix2 = suffixp = nullptr;
@@ -190,7 +193,35 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
   iarg = 1;
   while (iarg < narg) {
 
-    if (strcmp(arg[iarg],"-echo") == 0 ||
+    if (strcmp(arg[iarg],"-cite") == 0 ||
+               strcmp(arg[iarg],"-c") == 0) {
+      if (iarg+2 > narg)
+        error->universe_all(FLERR,"Invalid command-line argument");
+
+      if (strcmp(arg[iarg+1],"both") == 0) {
+        citescreen = CiteMe::VERBOSE;
+        citelogfile = CiteMe::VERBOSE;
+        citefile = nullptr;
+      } else if (strcmp(arg[iarg+1],"none") == 0) {
+        citescreen = CiteMe::TERSE;
+        citelogfile = CiteMe::TERSE;
+        citefile = nullptr;
+      } else if (strcmp(arg[iarg+1],"screen") == 0) {
+        citescreen = CiteMe::VERBOSE;
+        citelogfile = CiteMe::TERSE;
+        citefile = nullptr;
+      } else if (strcmp(arg[iarg+1],"log") == 0) {
+        citescreen = CiteMe::TERSE;
+        citelogfile = CiteMe::VERBOSE;
+        citefile = nullptr;
+      } else {
+        citescreen = CiteMe::TERSE;
+        citelogfile = CiteMe::TERSE;
+        citefile = arg[iarg+1];
+      }
+      iarg += 2;
+
+    } else if (strcmp(arg[iarg],"-echo") == 0 ||
                strcmp(arg[iarg],"-e") == 0) {
       if (iarg+2 > narg)
         error->universe_all(FLERR,"Invalid command-line argument");
@@ -605,7 +636,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
 
   // allocate CiteMe class if enabled
 
-  if (citeflag) citeme = new CiteMe(this);
+  if (citeflag) citeme = new CiteMe(this,citescreen,citelogfile,citefile);
   else citeme = nullptr;
 
   // allocate input class now that MPI is fully setup
@@ -669,8 +700,8 @@ LAMMPS::~LAMMPS()
 {
   const int me = comm->me;
 
-  destroy();
   delete citeme;
+  destroy();
 
   if (num_package) {
     for (int i = 0; i < num_package; i++) {
@@ -1111,7 +1142,8 @@ void _noopt LAMMPS::help()
           "-kokkos on/off ...          : turn KOKKOS mode on or off (-k)\n"
           "-log none/filename          : where to send log output (-l)\n"
           "-mpicolor color             : which exe in a multi-exe mpirun cmd (-m)\n"
-          "-nocite                     : disable writing log.cite file (-nc)\n"
+          "-cite                       : select citation reminder style (-c)\n"
+          "-nocite                     : disable citation reminder (-nc)\n"
           "-package style ...          : invoke package command (-pk)\n"
           "-partition size1 size2 ...  : assign partition sizes (-p)\n"
           "-plog basename              : basename for partition logs (-pl)\n"

src/lammps.h

@@ -56,7 +56,6 @@ class LAMMPS {
   char *exename;                 // pointer to argv[0]
   char ***packargs;              // arguments for cmdline package commands
   int num_package;               // number of cmdline package commands
-  int cite_enable;               // 1 if generating log.cite, 0 if disabled
 
   int clientserver;              // 0 = neither, 1 = client, 2 = server
   void *cslib;                   // client/server messaging via CSlib
@@ -66,9 +65,9 @@ class LAMMPS {
   class AtomKokkos *atomKK;      // KOKKOS version of Atom class
   class MemoryKokkos *memoryKK;  // KOKKOS version of Memory class
 
-  class Python * python;         // Python interface
+  class Python *python;          // Python interface
 
-  class CiteMe *citeme;          // citation info
+  class CiteMe *citeme;          // handle citation info
 
   const char *match_style(const char *style, const char *name);
   static const char * installed_packages[];

src/math_extra.cpp

@@ -396,7 +396,7 @@ void quat_to_mat_trans(const double *quat, double mat[3][3])
    compute space-frame inertia tensor of an ellipsoid
    radii = 3 radii of ellipsoid
    quat = orientiation quaternion of ellipsoid
-   return symmetric inertia tensor as 6-vector in Voigt notation
+   return symmetric inertia tensor as 6-vector in Voigt ordering
 ------------------------------------------------------------------------- */
 
 void inertia_ellipsoid(double *radii, double *quat, double mass,
@@ -424,7 +424,7 @@ void inertia_ellipsoid(double *radii, double *quat, double mass,
    compute space-frame inertia tensor of a line segment in 2d
    length = length of line
    theta = orientiation of line
-   return symmetric inertia tensor as 6-vector in Voigt notation
+   return symmetric inertia tensor as 6-vector in Voigt ordering
 ------------------------------------------------------------------------- */
 
 void inertia_line(double length, double theta, double mass, double *inertia)
@@ -462,7 +462,7 @@ void inertia_line(double length, double theta, double mass, double *inertia)
    S = 1/24 [2 1 1]
             [1 2 1]
             [1 1 2]
-   return symmetric inertia tensor as 6-vector in Voigt notation
+   return symmetric inertia tensor as 6-vector in Voigt ordering
 ------------------------------------------------------------------------- */
 
 void inertia_triangle(double *v0, double *v1, double *v2,
@@ -503,7 +503,7 @@ void inertia_triangle(double *v0, double *v1, double *v2,
    compute space-frame inertia tensor of a triangle
    idiag = previously computed diagonal inertia tensor
    quat = orientiation quaternion of triangle
-   return symmetric inertia tensor as 6-vector in Voigt notation
+   return symmetric inertia tensor as 6-vector in Voigt ordering
 ------------------------------------------------------------------------- */
 
 void inertia_triangle(double *idiag, double *quat, double /*mass*/,

src/math_extra.h

@@ -95,7 +95,7 @@ namespace MathExtra {
                         double dt);
 
   // shape matrix operations
-  // upper-triangular 3x3 matrix stored in Voigt notation as 6-vector
+  // upper-triangular 3x3 matrix stored in Voigt ordering as 6-vector
 
   inline void multiply_shape_shape(const double *one, const double *two,
                                    double *ans);
@@ -593,7 +593,7 @@ inline void MathExtra::scalar_times3(const double f, double m[3][3])
 
 /* ----------------------------------------------------------------------
    multiply 2 shape matrices
-   upper-triangular 3x3, stored as 6-vector in Voigt notation
+   upper-triangular 3x3, stored as 6-vector in Voigt ordering
 ------------------------------------------------------------------------- */
 
 inline void MathExtra::multiply_shape_shape(const double *one,

src/minimize.cpp

@@ -13,6 +13,7 @@
 
 #include "minimize.h"
 
+#include "citeme.h"
 #include "domain.h"
 #include "error.h"
 #include "finish.h"
@@ -46,6 +47,7 @@ void Minimize::command(int narg, char **arg)
   if (update->etol < 0.0 || update->ftol < 0.0)
     error->all(FLERR,"Illegal minimize command");
 
+  if (lmp->citeme) lmp->citeme->flush();
   update->whichflag = 2;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + update->nsteps;

src/neigh_request.cpp

@@ -225,6 +225,8 @@ void NeighRequest::copy_request(NeighRequest *other, int skipflag)
   int i,j;
   int ntypes = atom->ntypes;
 
+  skip = other->skip;
+
   if (other->iskip) {
     iskip = new int[ntypes+1];
     for (i = 1; i <= ntypes; i++)

src/pair.h

@@ -35,7 +35,7 @@ class Pair : protected Pointers {
   static int instance_total;     // # of Pair classes ever instantiated
 
   double eng_vdwl,eng_coul;      // accumulated energies
-  double virial[6];              // accumulated virial
+  double virial[6];              // accumulated virial: xx,yy,zz,xy,xz,yz
   double *eatom,**vatom;         // accumulated per-atom energy/virial
   double **cvatom;               // accumulated per-atom centroid virial
 

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "24 Dec 2020"
+#define LAMMPS_VERSION "10 Feb 2021"