Merge pull request #2260 from akohlmey/collected-small-changes

Collected small changes

.github/codecov.yml

@@ -0,0 +1,29 @@
+comment: false
+coverage:
+  notify:
+    slack:
+      default:
+        url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
+        threshold: 10%
+        only_pulls: false
+        branches:
+          - "master"
+        flags:
+          - "unit"
+        paths:
+          - "src"
+  status:
+    project:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true
+    patch:
+        default:
+            branches:
+              - "master"
+            paths:
+              - "src"
+            informational: true

cmake/Modules/Testing.cmake

@@ -23,14 +23,17 @@ if(ENABLE_TESTING)
         OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
-      check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER)
-      check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER)
-      check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER)
-      if(HAVE_LLD_LINKER)
+      check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
+      check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
+      check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
+      find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
+      find_program(HAVE_GOLD_LINKER_BIN ld.gold)
+      find_program(HAVE_BFD_LINKER_BIN ld.bfd)
+      if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
-      elseif(HAVE_GOLD_LINKER)
+      elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
-      elseif(HAVE_BFD_LINKER)
+      elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
       endif()
       set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)

doc/src/Errors_warnings.rst

@@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    incorrect periodic images of atoms in interaction lists.  To avoid, either use
    :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
 
+*Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
+
+   Since LAMMPS stores topology data with individual atoms, all atoms
+   comprising a bond, angle, dihedral or improper must be present on any
+   sub-domain that "owns" the atom with the information, either as a
+   local or a ghost atom. The communication cutoff is what determines up
+   to what distance from a sub-domain boundary ghost atoms are created.
+   The communication cutoff is by default the largest non-bonded cutoff
+   plus the neighbor skin distance, but for short or non-bonded cutoffs
+   and/or long bonds, this may not be sufficient. This warning indicates
+   that there is an increased risk of a simulation stopping unexpectedly
+   because of Bond/Angle/Dihedral/Improper atoms missing.  It can be
+   silenced by manually setting the communication cutoff via
+   :doc:`comm_modify cutoff <comm_modify>`.  However, since the
+   heuristic used to determine the estimate is not always accurate, it
+   is not changed automatically and the warning may be ignored depending
+   on the specific system being simulated.
+
 *Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
    Self-explanatory.
 

src/MC/fix_widom.h

@@ -32,7 +32,7 @@ class FixWidom : public Fix {
   int setmask();
   void init();
   void pre_exchange();
-  
+
   void attempt_atomic_insertion();
   void attempt_molecule_insertion();
 
@@ -207,7 +207,7 @@ is on.
 
 E: Cannot use fix Widom in a 2d simulation
 
-Fix Widom is set up to run in 3d only. No 2d simulations with fix Widom 
+Fix Widom is set up to run in 3d only. No 2d simulations with fix Widom
 are allowed.
 
 E: Could not find fix Widom exclusion group ID

src/USER-MISC/pair_lennard_mdf.cpp

@@ -32,11 +32,11 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairLJ_AB_MDF::PairLJ_AB_MDF(LAMMPS *lmp) : Pair(lmp) {}
+PairLennardMDF::PairLennardMDF(LAMMPS *lmp) : Pair(lmp) {}
 
 /* ---------------------------------------------------------------------- */
 
-PairLJ_AB_MDF::~PairLJ_AB_MDF()
+PairLennardMDF::~PairLennardMDF()
 {
   if (allocated) {
     memory->destroy(setflag);
@@ -56,7 +56,7 @@ PairLJ_AB_MDF::~PairLJ_AB_MDF()
 
 /* ---------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::compute(int eflag, int vflag)
+void PairLennardMDF::compute(int eflag, int vflag)
 {
   int i,j,ii,jj,inum,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@@ -153,7 +153,7 @@ void PairLJ_AB_MDF::compute(int eflag, int vflag)
    allocate all arrays
 ------------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::allocate()
+void PairLennardMDF::allocate()
 {
   allocated = 1;
   int n = atom->ntypes;
@@ -180,7 +180,7 @@ void PairLJ_AB_MDF::allocate()
    global settings
 ------------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::settings(int narg, char **arg)
+void PairLennardMDF::settings(int narg, char **arg)
 {
   if (narg != 2) error->all(FLERR,"Illegal pair_style command");
 
@@ -207,7 +207,7 @@ void PairLJ_AB_MDF::settings(int narg, char **arg)
    set coeffs for one or more type pairs
 ------------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::coeff(int narg, char **arg)
+void PairLennardMDF::coeff(int narg, char **arg)
 {
   if (narg != 4 && narg != 6)
     error->all(FLERR,"Incorrect args for pair coefficients");
@@ -248,7 +248,7 @@ void PairLJ_AB_MDF::coeff(int narg, char **arg)
    init for one type pair i,j and corresponding j,i
 ------------------------------------------------------------------------- */
 
-double PairLJ_AB_MDF::init_one(int i, int j)
+double PairLennardMDF::init_one(int i, int j)
 {
   if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
 
@@ -259,6 +259,7 @@ double PairLJ_AB_MDF::init_one(int i, int j)
   lj3[i][j] = aparm[i][j];
   lj4[i][j] = bparm[i][j];
 
+  cut[j][i] = cut[i][j];
   cut_inner[j][i] = cut_inner[i][j];
   cut_inner_sq[j][i] = cut_inner_sq[i][j];
   lj1[j][i] = lj1[i][j];
@@ -273,7 +274,7 @@ double PairLJ_AB_MDF::init_one(int i, int j)
   proc 0 writes to restart file
 ------------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::write_restart(FILE *fp)
+void PairLennardMDF::write_restart(FILE *fp)
 {
   write_restart_settings(fp);
 
@@ -294,7 +295,7 @@ void PairLJ_AB_MDF::write_restart(FILE *fp)
   proc 0 reads from restart file, bcasts
 ------------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::read_restart(FILE *fp)
+void PairLennardMDF::read_restart(FILE *fp)
 {
   read_restart_settings(fp);
   allocate();
@@ -324,7 +325,7 @@ void PairLJ_AB_MDF::read_restart(FILE *fp)
   proc 0 writes to restart file
 ------------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::write_restart_settings(FILE *fp)
+void PairLennardMDF::write_restart_settings(FILE *fp)
 {
   fwrite(&mix_flag,sizeof(int),1,fp);
 }
@@ -333,7 +334,7 @@ void PairLJ_AB_MDF::write_restart_settings(FILE *fp)
   proc 0 reads from restart file, bcasts
 ------------------------------------------------------------------------- */
 
-void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
+void PairLennardMDF::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
@@ -342,9 +343,32 @@ void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }
 
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairLennardMDF::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d %g %g\n",i,aparm[i][i],bparm[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLennardMDF::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g %g %g %g\n",
+              i,j,aparm[i][j],bparm[i][j],
+              cut_inner[i][j],cut[i][j]);
+}
+
 /* ---------------------------------------------------------------------- */
 
-double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype,
+double PairLennardMDF::single(int /*i*/, int /*j*/, int itype, int jtype,
                              double rsq,
                              double /*factor_coul*/, double factor_lj,
                              double &fforce)
@@ -368,7 +392,7 @@ double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype,
     dt = 30.* d*d * dd*dd * rr / dp;
 
     forcelj = forcelj*tt + philj*dt;
-    philj *= dt;
+    philj *= tt;
   }
 
   fforce = factor_lj*forcelj*r2inv;
@@ -378,7 +402,7 @@ double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype,
 
 /* ---------------------------------------------------------------------- */
 
-void *PairLJ_AB_MDF::extract(const char *str, int &dim)
+void *PairLennardMDF::extract(const char *str, int &dim)
 {
   dim = 2;
   if (strcmp(str,"a") == 0) return (void *) aparm;

src/USER-MISC/pair_lennard_mdf.h

@@ -13,21 +13,21 @@
 
 #ifdef PAIR_CLASS
 
-PairStyle(lennard/mdf,PairLJ_AB_MDF)
+PairStyle(lennard/mdf,PairLennardMDF)
 
 #else
 
-#ifndef LMP_PAIR_LJ_AB_MDF_H
-#define LMP_PAIR_LJ_AB_MDF_H
+#ifndef LMP_PAIR_LENNARD_MDF_H
+#define LMP_PAIR_LENNARD_MDF_H
 
 #include "pair.h"
 
 namespace LAMMPS_NS {
 
-class PairLJ_AB_MDF : public Pair {
+class PairLennardMDF : public Pair {
  public:
-  PairLJ_AB_MDF(class LAMMPS *);
-  virtual ~PairLJ_AB_MDF();
+  PairLennardMDF(class LAMMPS *);
+  virtual ~PairLennardMDF();
 
   virtual void compute(int, int);
   void settings(int, char **);
@@ -37,6 +37,8 @@ class PairLJ_AB_MDF : public Pair {
   void read_restart(FILE *);
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
   double single(int, int, int, int, double, double, double, double &);
   void *extract(const char *, int &);