undo cosmetic differences between LAMMPS-ICMS and LAMMPS

src/MPIIO/restart_mpiio.cpp

@@ -16,7 +16,6 @@
 ------------------------------------------------------------------------- */
 
 #include "mpi.h"
-#include "mpiio.h"
 #include "restart_mpiio.h"
 #include "error.h"
 #include "limits.h"

src/REPLICA/verlet_split.cpp

@@ -194,7 +194,7 @@ VerletSplit::VerletSplit(LAMMPS *lmp, int narg, char **arg) :
   // f_kspace = Rspace copy of Kspace forces
   // allocate dummy version for Kspace partition
 
-  maxatom = -1;
+  maxatom = 0;
   f_kspace = NULL;
   if (!master) memory->create(f_kspace,1,1,"verlet/split:f_kspace");
 }

src/RIGID/fix_rigid_nh.h

@@ -72,7 +72,7 @@ class FixRigidNH : public FixRigid {
   int tcomputeflag,pcomputeflag;
 
   void couple();
-  virtual void remap();  
+  void remap();  
   void nhc_temp_integrate();
   void nhc_press_integrate();
 

src/USER-MISC/compute_basal_atom.cpp

@@ -204,10 +204,8 @@ void ComputeBasalAtom::compute_peratom()
       double bond_angle;
       double norm_j, norm_k;
       chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
-      double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,
+      double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,x3[n0],y3[n0],z3[n0],
         xmean5, ymean5, zmean5, xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
-      double *x3,*y3,*z3; 
-      x3 = new double[n0]; y3 = new double[n0]; z3 = new double[n0];
       for (j = 0; j < n0; j++) {
 	x_ij = x[i][0]-x[nearest_n0[j]][0];
 	y_ij = x[i][1]-x[nearest_n0[j]][1];
@@ -415,7 +413,6 @@ void ComputeBasalAtom::compute_peratom()
       //if there are less than two ~180 degree bond angles, the algorithm returns null
       else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
 
-      delete[] x3; delete[] y3; delete[] z3;
       //normalize BPV:
       double Mag = sqrt(BPV[i][0]*BPV[i][0] + 
                         BPV[i][1]*BPV[i][1] + BPV[i][2]*BPV[i][2]);

src/USER-MISC/fix_ipi.cpp

@@ -380,8 +380,7 @@ void FixIPI::final_integrate()
 
   int nat=bsize/3;
   double **f= atom->f;
-  double *lbuf;
-  lbuf = new double[bsize];
+  double lbuf[bsize];
 
   // reassembles the force vector from the local arrays
   int nlocal = atom->nlocal;
@@ -393,7 +392,6 @@ void FixIPI::final_integrate()
     lbuf[3*(atom->tag[i]-1)+2]=f[i][2]*forceconv;
   }
   MPI_Allreduce(lbuf,buffer,bsize,MPI_DOUBLE,MPI_SUM,world);
-  delete[] lbuf;
 
   for (int i = 0; i < 9; ++i) vir[i]=0.0;
 

src/USER-OMP/fix_rigid_omp.cpp

@@ -155,7 +155,7 @@ void FixRigidOMP::final_integrate()
 
   } else if (rstyle == GROUP) {
 
-     // we likely have only a rather number of groups so we loop
+     // we likely have only a rather number of groups so we loops
      // over bodies and thread over all atoms for each of them.
      
      for (int ib = 0; ib < nbody; ++ib) {

src/USER-OMP/thr_omp.cpp

@@ -22,7 +22,6 @@
 #include "force.h"
 #include "memory.h"
 #include "modify.h"
-#include "compute.h"
 #include "neighbor.h"
 #include "timer.h"
 

src/USER-PHONON/fix_phonon.cpp

@@ -666,10 +666,9 @@ void FixPhonon::postprocess( )
   }
 
   // to get Phi = KT.G^-1; normalization of FFTW data is done here
-  double boltz = force->boltz, *kbtsqrt, TempAve = 0.;
+  double boltz = force->boltz, kbtsqrt[sysdim], TempAve = 0.;
   double TempFac = inv_neval*inv_nTemp;
   double NormFac = TempFac*double(ntotal);
-  kbtsqrt = new double[sysdim];
 
   for (idim = 0; idim < sysdim; ++idim){
     kbtsqrt[idim] = sqrt(TempSum[idim]*NormFac);
@@ -683,7 +682,6 @@ void FixPhonon::postprocess( )
     for (idim = 0; idim < fft_dim; ++idim)
     for (jdim = 0; jdim < fft_dim; ++jdim) Phi_q[idq][ndim++] *= kbtsqrt[idim%sysdim]*kbtsqrt[jdim%sysdim];
   }
-  delete[] kbtsqrt;
 
   // to collect all local Phi_q to root
   displs[0]=0;
@@ -692,8 +690,7 @@ void FixPhonon::postprocess( )
   MPI_Gatherv(Phi_q[0],mynq*fft_dim2*2,MPI_DOUBLE,Phi_all[0],recvcnts,displs,MPI_DOUBLE,0,world);
   
   // to collect all basis info and averaged it on root
-  double *basis_root;
-  basis_root = new double[fft_dim];
+  double basis_root[fft_dim];
   if (fft_dim > sysdim) MPI_Reduce(&basis[1][0], &basis_root[sysdim], fft_dim-sysdim, MPI_DOUBLE, MPI_SUM, 0, world);
 
   if (me == 0){ // output dynamic matrix by root
@@ -733,7 +730,6 @@ void FixPhonon::postprocess( )
     fwrite(M_inv_sqrt,    sizeof(double),nucell, fp_bin);
 
     fclose(fp_bin);
-    delete[] basis_root;
 
     // write log file, here however, it is the dynamical matrix that is written
     for (int i = 0; i < 60; ++i) fprintf(flog,"#"); fprintf(flog,"\n");

src/atom_vec_body.cpp

@@ -65,8 +65,8 @@ AtomVecBody::~AtomVecBody()
 {
   int nall = nlocal_bonus + nghost_bonus;
   for (int i = 0; i < nall; i++) {
-    bptr->icp->put(bonus[i].iindex);
-    bptr->dcp->put(bonus[i].dindex);
+    icp->put(bonus[i].iindex);
+    dcp->put(bonus[i].dindex);
   }
   memory->sfree(bonus);
 
@@ -95,6 +95,8 @@ void AtomVecBody::process_args(int narg, char **arg)
   else error->all(FLERR,"Unknown body style");
 
   bptr->avec = this;
+  icp = bptr->icp;
+  dcp = bptr->dcp;
 
   // max size of forward/border comm
   // 7,16 are packed in pack_comm/pack_border
@@ -189,8 +191,8 @@ void AtomVecBody::copy(int i, int j, int delflag)
   // if deleting atom J via delflag and J has bonus data, then delete it
 
   if (delflag && body[j] >= 0) {
-    bptr->icp->put(bonus[body[j]].iindex);
-    bptr->dcp->put(bonus[body[j]].dindex);
+    icp->put(bonus[body[j]].iindex);
+    dcp->put(bonus[body[j]].dindex);
     copy_bonus(nlocal_bonus-1,body[j]);
     nlocal_bonus--;
   }
@@ -226,8 +228,8 @@ void AtomVecBody::clear_bonus()
 {
   int nall = nlocal_bonus + nghost_bonus;
   for (int i = nlocal_bonus; i < nall; i++) {
-    bptr->icp->put(bonus[i].iindex);
-    bptr->dcp->put(bonus[i].dindex);
+    icp->put(bonus[i].iindex);
+    dcp->put(bonus[i].dindex);
   }
   nghost_bonus = 0;
 }
@@ -828,8 +830,8 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
       inertia[2] = buf[m++];
       bonus[j].ninteger = (int) ubuf(buf[m++]).i;
       bonus[j].ndouble = (int) ubuf(buf[m++]).i;
-      bonus[j].ivalue = bptr->icp->get(bonus[j].ninteger,bonus[j].iindex);
-      bonus[j].dvalue = bptr->dcp->get(bonus[j].ndouble,bonus[j].dindex);
+      bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
+      bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
       m += bptr->unpack_border_body(&bonus[j],&buf[m]);
       bonus[j].ilocal = i;
       body[i] = j;
@@ -876,8 +878,8 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
       inertia[2] = buf[m++];
       bonus[j].ninteger = (int) ubuf(buf[m++]).i;
       bonus[j].ndouble = (int) ubuf(buf[m++]).i;
-      bonus[j].ivalue = bptr->icp->get(bonus[j].ninteger,bonus[j].iindex);
-      bonus[j].dvalue = bptr->dcp->get(bonus[j].ndouble,bonus[j].dindex);
+      bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
+      bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
       m += bptr->unpack_border_body(&bonus[j],&buf[m]);
       bonus[j].ilocal = i;
       body[i] = j;
@@ -923,8 +925,8 @@ int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
       inertia[2] = buf[m++];
       bonus[j].ninteger = (int) ubuf(buf[m++]).i;
       bonus[j].ndouble = (int) ubuf(buf[m++]).i;
-      bonus[j].ivalue = bptr->icp->get(bonus[j].ninteger,bonus[j].iindex);
-      bonus[j].dvalue = bptr->dcp->get(bonus[j].ndouble,bonus[j].dindex);
+      bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
+      bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
       m += bptr->unpack_border_body(&bonus[j],&buf[m]);
       bonus[j].ilocal = i;
       body[i] = j;
@@ -1027,9 +1029,9 @@ int AtomVecBody::unpack_exchange(double *buf)
     inertia[2] = buf[m++];
     bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
     bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
-    bonus[nlocal_bonus].ivalue = bptr->icp->get(bonus[nlocal_bonus].ninteger,
+    bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
 					  bonus[nlocal_bonus].iindex);
-    bonus[nlocal_bonus].dvalue = bptr->dcp->get(bonus[nlocal_bonus].ndouble,
+    bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
 					  bonus[nlocal_bonus].dindex);
     memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
            bonus[nlocal_bonus].ninteger*sizeof(int));
@@ -1179,9 +1181,9 @@ int AtomVecBody::unpack_restart(double *buf)
     inertia[2] = buf[m++];
     bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
     bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
-    bonus[nlocal_bonus].ivalue = bptr->icp->get(bonus[nlocal_bonus].ninteger,
+    bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
 					  bonus[nlocal_bonus].iindex);
-    bonus[nlocal_bonus].dvalue = bptr->dcp->get(bonus[nlocal_bonus].ndouble,
+    bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
 					  bonus[nlocal_bonus].dindex);
     memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
            bonus[nlocal_bonus].ninteger*sizeof(int));
@@ -1469,7 +1471,7 @@ bigint AtomVecBody::memory_usage()
   if (atom->memcheck("body")) bytes += memory->usage(body,nmax);
 
   bytes += nmax_bonus*sizeof(Bonus);
-  bytes += bptr->icp->size + bptr->dcp->size;
+  bytes += icp->size + dcp->size;
 
   int nall = nlocal_bonus + nghost_bonus;
   for (int i = 0; i < nall; i++) {

src/delete_bonds.cpp

@@ -25,8 +25,6 @@
 #include "special.h"
 #include "error.h"
 
-#include <stdlib.h>
-
 using namespace LAMMPS_NS;
 
 enum{MULTI,ATOM,BOND,ANGLE,DIHEDRAL,IMPROPER,STATS};

src/error.h

@@ -21,7 +21,6 @@ namespace LAMMPS_NS {
 class Error : protected Pointers {
  public:
   Error(class LAMMPS *);
-  virtual ~Error() {}
 
   void universe_all(const char *, int, const char *);
   void universe_one(const char *, int, const char *);

src/fix_ave_spatial.cpp

@@ -413,7 +413,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
   maxvar = 0;
   varatom = NULL;
 
-  maxatom = -1;
+  maxatom = 0;
   bin = NULL;
 
   nbins = maxbin = 0;

src/fix_heat.cpp

@@ -81,7 +81,7 @@ FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 
   scale = 1.0;
 
-  maxatom = -1;
+  maxatom = 0;
   vheat = NULL;
   vscale = NULL;
 }

src/fix_nh.h

@@ -120,11 +120,10 @@ class FixNH : public Fix {
   double fixedpoint[3];            // location of dilation fixed-point
 
   void couple();
+  void remap();
   void nhc_temp_integrate();
   void nhc_press_integrate();
 
-  virtual void remap();
-
   virtual void nve_x();            // may be overwritten by child classes
   virtual void nve_v();
   virtual void nh_v_press();

src/force.h

@@ -75,7 +75,7 @@ class Force : protected Pointers {
   int special_extra;         // extra space for added bonds
 
   Force(class LAMMPS *);
-  virtual ~Force();
+  ~Force();
   void init();
 
   void create_pair(const char *, int);

src/image.cpp

@@ -1065,8 +1065,7 @@ void Image::write_PNG(FILE *fp)
   png_set_text(png_ptr,info_ptr,text_ptr,1);
   png_write_info(png_ptr,info_ptr);
 
-  png_bytep *row_pointers;
-  row_pointers = new png_bytep[height];
+  png_bytep row_pointers[height];
   for (int i=0; i < height; ++i)
     row_pointers[i] = (png_bytep) &writeBuffer[(height-i-1)*3*width];
 
@@ -1074,7 +1073,6 @@ void Image::write_PNG(FILE *fp)
   png_write_end(png_ptr, info_ptr);
 
   png_destroy_write_struct(&png_ptr, &info_ptr);
-  delete[] row_pointers;
 #endif
 }
 

src/lattice.cpp

@@ -18,8 +18,8 @@
 #include "update.h"
 #include "domain.h"
 #include "comm.h"
-#include "memory.h"
 #include "force.h"
+#include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;

src/memory.h

@@ -25,7 +25,6 @@ namespace LAMMPS_NS {
 class Memory : protected Pointers {
  public:
   Memory(class LAMMPS *);
-  virtual ~Memory() {}
 
   void *smalloc(bigint n, const char *);
   void *srealloc(void *, bigint n, const char *);

src/pair.cpp

@@ -223,10 +223,10 @@ void Pair::init()
   // I,I coeffs must be set
   // init_one() will check if I,J is set explicitly or inferred by mixing
 
-  if (!allocated) error->all(FLERR,"Not all pair coeffs are set");
+  if (!allocated) error->all(FLERR,"All pair coeffs are not set");
 
   for (i = 1; i <= atom->ntypes; i++)
-    if (setflag[i][i] == 0) error->all(FLERR,"Not all pair coeffs are set");
+    if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");
 
   // style-specific initialization
 

src/pair.h

@@ -277,10 +277,10 @@ This is likely not what you want to do.  The exclusion settings will
 eliminate neighbors in the neighbor list, which the manybody potential
 needs to calculated its terms correctly.
 
-E: Not all pair coeffs are set
+E: All pair coeffs are not set
 
-Pair coefficients must be set for all pairs of atom types in either the
-data file or by the pair_coeff command before running a simulation.
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
 
 E: Fix adapt interface to this pair style not supported
 

src/random_mars.cpp

@@ -17,7 +17,6 @@
 #include "math.h"
 #include "random_mars.h"
 #include "error.h"
-#include "math_inline.h"
 
 using namespace LAMMPS_NS;
 
@@ -105,8 +104,7 @@ double RanMars::gaussian()
       rsq = v1*v1 + v2*v2;
       if (rsq < 1.0 && rsq != 0.0) again = 0;
     }
-    // fac = sqrt(-2.0*log(rsq)/rsq);
-    fac = MathInline::sqrtlgx2byx(rsq);
+    fac = sqrt(-2.0*log(rsq)/rsq);
     second = v1*fac;
     first = v2*fac;
     save = 1;

src/random_park.cpp

@@ -15,7 +15,6 @@
 
 #include "math.h"
 #include "random_park.h"
-#include "math_inline.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -65,8 +64,7 @@ double RanPark::gaussian()
       rsq = v1*v1 + v2*v2;
       if (rsq < 1.0 && rsq != 0.0) again = 0;
     }
-    // fac = sqrt(-2.0*log(rsq)/rsq);
-    fac = MathInline::sqrtlgx2byx(rsq);
+    fac = sqrt(-2.0*log(rsq)/rsq);
     second = v1*fac;
     first = v2*fac;
     save = 1;

src/universe.h

@@ -42,7 +42,7 @@ class Universe : protected Pointers {
                           // proc uni2orig[I] in original communicator
 
   Universe(class LAMMPS *, MPI_Comm);
-  virtual ~Universe();
+  ~Universe();
   void reorder(char *, char *);
   void add_world(char *);
   int consistent();

src/update.h

@@ -47,7 +47,7 @@ class Update : protected Pointers {
   char *minimize_style;
 
   Update(class LAMMPS *);
-  virtual ~Update();
+  ~Update();
   void init();
   void set_units(const char *);
   void create_integrate(int, char **, int);