Merge remote-tracking branch 'origin/master' into refactor-table-reading

lib/kokkos/Makefile.kokkos

@@ -4,7 +4,11 @@
 ifndef KOKKOS_PATH
   KOKKOS_PATH=../../lib/kokkos
 endif
+
 CXXFLAGS=$(CCFLAGS)
+ifeq ($(mode),shared)
+CXXFLAGS += $(SHFLAGS)
+endif
 
 KOKKOS_VERSION_MAJOR = 3
 KOKKOS_VERSION_MINOR = 1

src/KOKKOS/pair_kokkos.h

@@ -51,7 +51,8 @@ struct DoCoul<1> {
 
 //Specialisation for Neighborlist types Half, HalfThread, Full
 template <class PairStyle, int NEIGHFLAG, bool STACKPARAMS, class Specialisation = void>
-struct PairComputeFunctor  {
+class PairComputeFunctor  {
+ public:
   typedef typename PairStyle::device_type device_type ;
   typedef ArrayTypes<device_type> AT;
 

src/MANYBODY/pair_bop.cpp

@@ -5075,11 +5075,13 @@ void _noopt PairBOP::read_table(char *filename)
         if(rcut3[i]>rcutall)
           rcutall=rcut3[i];
         rcutsq[i]=rcut[i]*rcut[i];
-        rcutsq3[i]=rcut3[i]*rcut3[i];
         dr[i]=rcut[i]/((double)nr-1.0);
         rdr[i]=1.0/dr[i];
-        dr3[i]=rcut3[i]/((double)nr-1.0);
-        rdr3[i]=1.0/dr3[i];
+        if (format == 3) {
+          rcutsq3[i]=rcut3[i]*rcut3[i];
+          dr3[i]=rcut3[i]/((double)nr-1.0);
+          rdr3[i]=1.0/dr3[i];
+        }
       }
 
       rctroot=rcutall;
@@ -5170,9 +5172,11 @@ void _noopt PairBOP::read_table(char *filename)
           pRepul4[i][k]=pRepul1[i][k]/dr[i];
           pRepul5[i][k]=2.0*pRepul2[i][k]/dr[i];
           pRepul6[i][k]=3.0*pRepul3[i][k]/dr[i];
-          pLong4[i][k]=pLong1[i][k]/dr3[i];
-          pLong5[i][k]=2.0*pLong2[i][k]/dr3[i];
-          pLong6[i][k]=3.0*pLong3[i][k]/dr3[i];
+          if (format == 3) {
+            pLong4[i][k]=pLong1[i][k]/dr3[i];
+            pLong5[i][k]=2.0*pLong2[i][k]/dr3[i];
+            pLong6[i][k]=3.0*pLong3[i][k]/dr3[i];
+          }
         }
         for (int k=0; k < nBOt; k++) {
           FsigBO4[i][k]=FsigBO1[i][k]/dBO;

src/MANYBODY/pair_tersoff.cpp

@@ -524,10 +524,14 @@ void PairTersoff::setup_params()
     params[m].cut = params[m].bigr + params[m].bigd;
     params[m].cutsq = params[m].cut*params[m].cut;
 
-    params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
-    params[m].c2 = pow(2.0*params[m].powern*1.0e-8,-1.0/params[m].powern);
-    params[m].c3 = 1.0/params[m].c2;
-    params[m].c4 = 1.0/params[m].c1;
+    if (params[m].powern > 0.0) {
+      params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
+      params[m].c2 = pow(2.0*params[m].powern*1.0e-8,-1.0/params[m].powern);
+      params[m].c3 = 1.0/params[m].c2;
+      params[m].c4 = 1.0/params[m].c1;
+    } else {
+      params[m].c1 = params[m].c2 = params[m].c3 = params[m].c4 = 0.0;
+    }
   }
 
   // set cutmax to max of all params

src/MANYBODY/pair_tersoff_mod.cpp

@@ -178,8 +178,10 @@ void PairTersoffMOD::setup_params()
     params[m].cut = params[m].bigr + params[m].bigd;
     params[m].cutsq = params[m].cut*params[m].cut;
 
-    params[m].ca1 = pow(2.0*params[m].powern_del*1.0e-16,-1.0/params[m].powern);
-    params[m].ca4 = 1.0/params[m].ca1;
+    if (params[m].powern > 0.0) {
+      params[m].ca1 = pow(2.0*params[m].powern_del*1.0e-16,-1.0/params[m].powern);
+      params[m].ca4 = 1.0/params[m].ca1;
+    } else params[m].ca1 = params[m].ca4 = 0.0;
   }
 
   // set cutmax to max of all params

src/library.cpp

@@ -137,7 +137,7 @@ void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
     *ptr = (void *) lmp;
   }
   catch(LAMMPSException & e) {
-    fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
+    fmt::print(stderr, "LAMMPS Exception: {}", e.message);
     *ptr = (void *) NULL;
   }
 #else
@@ -172,7 +172,7 @@ void lammps_open_no_mpi(int argc, char **argv, void **ptr)
     *ptr = (void *) lmp;
   }
   catch(LAMMPSException & e) {
-    fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
+    fmt::print(stderr, "LAMMPS Exception: {}", e.message);
     *ptr = (void*) NULL;
   }
 #else

src/pair_coul_dsf.cpp

@@ -65,7 +65,7 @@ void PairCoulDSF::compute(int eflag, int vflag)
 {
   int i,j,ii,jj,inum,jnum;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
-  double r,rsq,r2inv,forcecoul,factor_coul;
+  double r,rsq,forcecoul,factor_coul;
   double prefactor,erfcc,erfcd,t;
   int *ilist,*jlist,*numneigh,**firstneigh;
 

src/write_data.cpp

@@ -123,7 +123,7 @@ void WriteData::command(int narg, char **arg)
     if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
   }
 
-  write(file.c_str());
+  write(file);
 }
 
 /* ----------------------------------------------------------------------
@@ -131,7 +131,7 @@ void WriteData::command(int narg, char **arg)
    might later let it be directly called within run/minimize loop
 ------------------------------------------------------------------------- */
 
-void WriteData::write(const char *file)
+void WriteData::write(const std::string &file)
 {
   // special case where reneighboring is not done in integrator
   //   on timestep data file is written (due to build_once being set)
@@ -187,7 +187,7 @@ void WriteData::write(const char *file)
   // open data file
 
   if (me == 0) {
-    fp = fopen(file,"w");
+    fp = fopen(file.c_str(),"w");
     if (fp == NULL)
       error->one(FLERR,fmt::format("Cannot open data file {}: {}",
                                    file, utils::getsyserror()));

src/write_data.h

@@ -21,6 +21,7 @@ CommandStyle(write_data,WriteData)
 #define LMP_WRITE_DATA_H
 
 #include "pointers.h"
+#include <string>
 
 namespace LAMMPS_NS {
 
@@ -28,7 +29,7 @@ class WriteData : protected Pointers {
  public:
   WriteData(class LAMMPS *);
   void command(int, char **);
-  void write(const char *);
+  void write(const std::string &);
 
  private:
   int me,nprocs;

src/write_restart.cpp

@@ -293,9 +293,6 @@ void WriteRestart::write(std::string file)
 
     std::string multiname = file;
     multiname.replace(multiname.find("%"),1,fmt::format("{}",icluster));
-    fp = fopen(multiname.c_str(),"wb");
-    if (fp == NULL)
-      error->one(FLERR,fmt::format("Cannot open restart file {}",multiname).c_str());
 
     if (filewriter) {
       fp = fopen(multiname.c_str(),"wb");