Merge branch 'collected-small-changes' into collected-post-stable-patches

doc/github-development-workflow.md

@@ -6,7 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
 is likely to change as our experiences and needs change and we try to
-adapt accordingly. Last change 2018-11-15.
+adapt accordingly. Last change 2018-12-19.
 
 ## Table of Contents
 
@@ -129,16 +129,17 @@ Here are some items to check:
     * stdlib.h -> cstdlib
     * string.h -> cstring
     * time.h -> ctime
-  Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
+    * Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
   * Code should follow the C++-98 standard. C++-11 is only accepted
   in individual special purpose packages
-  * indentation is two spaces per level
-  * there should be no tabs and no trailing whitespace
+  * indentation is 2 spaces per level
+  * there should be NO tabs and no trailing whitespace
   * header files, especially of new styles, should not include any
   other headers, except the header with the base class or cstdio.
   Forward declarations should be used instead when possible.
   * iostreams should be avoided. LAMMPS uses stdio from the C-library.
   * use of STL in headers and class definitions should be avoided.
+  * there MUST NOT be any "using namespace XXX;" statements in headers.
   * static class members should be avoided at all cost.
   * anything storing atom IDs should be using `tagint` and not `int`.
   This can be flagged by the compiler only for pointers and only when

doc/src/Intro_nonfeatures.txt

@@ -16,7 +16,7 @@ functionality for setting up simulations and analyzing their output.
 Specifically, LAMMPS was not conceived and designed for:
 
 being run thru a GUI
-build molecular systems, or building molecular topologies
+building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
 perform sophisticated analysis of your MD simulation
 visualize your MD simulation interactively
@@ -24,18 +24,18 @@ plot your output data :ul
 
 Although over the years these limitations have been somewhat
 reduced through features added to LAMMPS or external tools
-that either interface with LAMMPS or extend LAMMPS.
+that either closely interface with LAMMPS or extend LAMMPS.
 
 Here are suggestions on how to perform these tasks:
 
-GUI: LAMMPS can be built as a library and a Python wrapper that wraps
+[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
 the library interface is provided.  Thus, GUI interfaces can be
 written in Python (or C or C++ if desired) that run LAMMPS and
 visualize or plot its output.  Examples of this are provided in the
 python directory and described on the "Python"_Python_head.html doc
-page.  Also, there are several external wrappers or GUI front ends.:ulb,l
+page.  Also, there are several external wrappers or GUI front ends. :ulb,l
 
-Builder: Several pre-processing tools are packaged with LAMMPS.  Some
+[Builder:] Several pre-processing tools are packaged with LAMMPS.  Some
 of them convert input files in formats produced by other MD codes such
 as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of them
 are simple programs that will build simple molecular systems, such as
@@ -45,15 +45,20 @@ the "Tools"_Tools.html doc page for details on tools packaged with
 LAMMPS.  The "Pre/post processing
 page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
 describes a variety of 3rd party tools for this task.  Furthermore,
-some LAMMPS internal commands to reconstruct topology, as well as
-the option to insert molecule templates instead of atoms.:l
+some LAMMPS internal commands allow to reconstruct, or selectively add
+topology information, as well as provide the option to insert molecule
+templates instead of atoms for building bulk molecular systems. :l
 
-Force-field assignment: The conversion tools described in the previous
+[Force-field assignment:] The conversion tools described in the previous
 bullet for CHARMM, AMBER, and Insight will also assign force field
 coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
-or BIOVIA (formerly Accelrys) force field files. :l
+or BIOVIA (formerly Accelrys) force field files. The tools
+"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
+"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
+powerful and flexible in converting force field and topology data
+between various MD simulation programs.  :l
 
-Simulation analysis: If you want to perform analysis on-the-fly as
+[Simulation analysis:] If you want to perform analysis on-the-fly as
 your simulation runs, see the "compute"_compute.html and
 "fix"_fix.html doc pages, which list commands that can be used in a
 LAMMPS input script.  Also see the "Modify"_Modify.html doc page for
@@ -71,22 +76,22 @@ tools/python directory can extract and massage data in dump files to
 make it easier to import into other programs.  See the
 "Tools"_Tools.html doc page for details on these various options. :l
 
-Visualization: LAMMPS can produce JPG or PNG snapshot images
+[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
 on-the-fly via its "dump image"_dump_image.html command and pass
-them to an external program FFmpeg to generate movies from them.  For
-high-quality, interactive visualization there are many excellent and
-free tools available.  See the "Other Codes
+them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate
+movies from them.  For high-quality, interactive visualization there are
+many excellent and free tools available.  See the "Other Codes
 page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
 visualization packages that can use LAMMPS output data. :l
 
-Plotting: See the next bullet about Pizza.py as well as the
+[Plotting:] See the next bullet about Pizza.py as well as the
 "Python"_Python_head.html doc page for examples of plotting LAMMPS
 output.  Scripts provided with the {python} tool in the tools
 directory will extract and massage data in log and dump files to make
 it easier to analyze and plot.  See the "Tools"_Tools.html doc page
 for more discussion of the various tools. :l
 
-Pizza.py: Our group has also written a separate toolkit called
+[Pizza.py:] Our group has also written a separate toolkit called
 "Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
 setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
 simulations.  It thus provides some functionality for several of the

doc/src/Modify_contribute.txt

@@ -108,9 +108,13 @@ your contribution(s) to be added to main LAMMPS code or one of its
 standard packages, it needs to be written in a style compatible with
 other LAMMPS source files. This means: 2-character indentation per
 level, [no tabs], no lines over 80 characters. I/O is done via
-the C-style stdio library, class header files should not import any
-system headers outside <stdio.h>, STL containers should be avoided
-in headers, and forward declarations used where possible or needed.
+the C-style stdio library (mixing of stdio and iostreams is generally
+discouraged), class header files should not import any system headers
+outside of <cstdio>, STL containers should be avoided in headers,
+system header from the C library should use the C++-style names
+(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
+<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
+used where possible or needed to avoid including headers.
 All added code should be placed into the LAMMPS_NS namespace or a
 sub-namespace; global or static variables should be avoided, as they
 conflict with the modular nature of LAMMPS and the C++ class structure.

doc/utils/sphinx-config/false_positives.txt

@@ -435,6 +435,9 @@ CSiC
 csld
 cslib
 CSlib
+cstdio
+cstdlib
+cstring
 cstyle
 csvr
 Ctypes
@@ -1135,6 +1138,7 @@ inv
 invariants
 inversed
 ionocovalent
+iostreams
 iparam
 ipi
 ipp
@@ -2507,7 +2511,9 @@ Startstep
 statcoul
 statcoulombs
 statvolt
+stdlib
 stdin
+stdio
 steelblue
 Stegailov
 Steinbach

src/CLASS2/pair_lj_class2_coul_cut.cpp

@@ -217,7 +217,9 @@ void PairLJClass2CoulCut::settings(int narg, char **arg)
 
 void PairLJClass2CoulCut::coeff(int narg, char **arg)
 {
-  if (narg < 4 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
+  if (narg < 4 || narg > 6)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
   if (!allocated) allocate();
 
   int ilo,ihi,jlo,jhi;

src/CLASS2/pair_lj_class2_coul_long.cpp

@@ -252,8 +252,9 @@ void PairLJClass2CoulLong::settings(int narg, char **arg)
 
 void PairLJClass2CoulLong::coeff(int narg, char **arg)
 {
-  if (narg < 4 || narg > 6)
+  if (narg < 4 || narg > 5)
     error->all(FLERR,"Incorrect args for pair coefficients");
+
   if (!allocated) allocate();
 
   int ilo,ihi,jlo,jhi;

src/atom.cpp

@@ -1886,7 +1886,7 @@ void Atom::setup_sort_bins()
   // check if neighbor cutoff = 0.0
   // and in that case, disable sorting
 
-  double binsize;
+  double binsize = 0.0;
   if (userbinsize > 0.0) binsize = userbinsize;
   else if (neighbor->cutneighmax > 0.0) binsize = 0.5 * neighbor->cutneighmax;
 

src/variable.h

@@ -88,17 +88,15 @@ class Variable : protected Pointers {
     int nvector;           // length of array for vector-style variable
     int nstride;           // stride between atoms if array is a 2d array
     int selfalloc;         // 1 if array is allocated here, else 0
-    int ivalue1,ivalue2;   // extra values for needed for gmask,rmask,grmask
+    int ivalue1,ivalue2;   // extra values needed for gmask,rmask,grmask
     int nextra;            // # of additional args beyond first 2
     Tree *first,*second;   // ptrs further down tree for first 2 args
     Tree **extra;          // ptrs further down tree for nextra args
 
     Tree() :
       array(NULL), iarray(NULL), barray(NULL),
-      selfalloc(0), nextra(0),
-      first(NULL), second(NULL), extra(NULL)
-    {
-    }
+      selfalloc(0), ivalue1(0), ivalue2(0), nextra(0),
+      first(NULL), second(NULL), extra(NULL) {}
   };
 
   int compute_python(int);