Merge pull request #1831 from akohlmey/pair-bop-updates

Correct some issues with pair style bop and its potential files

potentials/AlCu.bop.table

@@ -1,4 +1,4 @@
-# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, J. Alloys Compd., 680, 752 (2016).
+# DATE: 2015-07-06 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, Don Ward, donward@sandia.gov, CITATION: Zhou, Ward, and Foster, Phys. Chem. Chem. Phys., under consideration
     2
    13  2.69800000e+01 Al
    29  6.35500000e+01 Cu
@@ -4835,7 +4835,7 @@
   0.00000000e+00
   0.00000000e+00
   0.00000000e+00
-  0.00000000e+00
+  4.90000000e+00
   0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00
   0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00  0.00000000e+00

src/.gitignore

@@ -27,8 +27,8 @@
 /*_ssa.h
 /*_ssa.cpp
 
-/kim_query.cpp
+/kim_*.cpp
-/kim_query.h
+/kim_*.h
 /pair_kim.cpp
 /pair_kim.h
 
@@ -116,6 +116,8 @@
 /compute_snad_atom.h
 /compute_snav_atom.cpp
 /compute_snav_atom.h
+/compute_snap.cpp
+/compute_snap.h
 /openmp_snap.h
 /pair_snap.cpp
 /pair_snap.h
@@ -318,8 +320,14 @@
 /compute_fep.h
 /compute_force_tally.cpp
 /compute_force_tally.h
+/compute_gyration_shape.cpp
+/compute_gyration_shape.h
+/compute_gyration_shape_chunk.cpp
+/compute_gyration_shape_chunk.h
 /compute_heat_flux_tally.cpp
 /compute_heat_flux_tally.h
+/compute_hma.cpp
+/compute_hma.h
 /compute_ke_atom_eff.cpp
 /compute_ke_atom_eff.h
 /compute_ke_eff.cpp
@@ -332,6 +340,8 @@
 /compute_meso_rho_atom.h
 /compute_meso_t_atom.cpp
 /compute_meso_t_atom.h
+/compute_momentum.cpp
+/compute_momentum.h
 /compute_msd_nongauss.cpp
 /compute_msd_nongauss.h
 /compute_pe_tally.cpp
@@ -422,6 +432,8 @@
 /dump_custom_mpiio.h
 /dump_h5md.cpp
 /dump_h5md.h
+/dump_local_gz.cpp
+/dump_local_gz.h
 /dump_netcdf.cpp
 /dump_netcdf.h
 /dump_netcdf_mpiio.cpp
@@ -564,6 +576,8 @@
 /fix_nph_asphere.h
 /fix_npt_asphere.cpp
 /fix_npt_asphere.h
+/fix_npt_cauchy.cpp
+/fix_npt_cauchy.h
 /fix_nve_asphere.cpp
 /fix_nve_asphere.h
 /fix_nve_asphere_noforce.cpp
@@ -673,6 +687,8 @@
 /fix_spring_pull.h
 /fix_srd.cpp
 /fix_srd.h
+/fix_store_kim.cpp
+/fix_store_kim.h
 /fix_temp_rescale_eff.cpp
 /fix_temp_rescale_eff.h
 /fix_thermal_conductivity.cpp
@@ -695,6 +711,8 @@
 /fix_wall_ees.h
 /fix_wall_region_ees.cpp
 /fix_wall_region_ees.h
+/fix_wall_reflect_stochastic.cpp
+/fix_wall_reflect_stochastic.h
 /fix_wall_gran.cpp
 /fix_wall_gran.h
 /fix_wall_gran_region.cpp
@@ -843,6 +861,8 @@
 /pair_lebedeva_z.h
 /pair_lj_expand_coul_long.cpp
 /pair_lj_expand_coul_long.h
+/pair_local_density.cpp
+/pair_local_density.h
 /pair_edip.cpp
 /pair_edip.h
 /pair_edip_multi.cpp
@@ -968,6 +988,8 @@
 /pair_meam_spline.h
 /pair_meam_sw_spline.cpp
 /pair_meam_sw_spline.h
+/pair_mesocnt.cpp
+/pair_mesocnt.h
 /pair_mm3_switch3_coulgauss_long.cpp
 /pair_mm3_switch3_coulgauss_long.h
 /pair_morse_soft.cpp
@@ -1128,6 +1150,7 @@
 /remap_wrap.h
 /restart_mpiio.cpp
 /restart_mpiio.h
+/rigid_const.h
 /scafacos.cpp
 /scafacos.h
 /server.cpp
@@ -1148,6 +1171,8 @@
 /temper_grem.h
 /temper_npt.cpp
 /temper_npt.h
+/third_order.cpp
+/third_order.h
 /thr_data.cpp
 /thr_data.h
 /verlet_split.cpp

src/MANYBODY/pair_bop.cpp

@@ -61,6 +61,7 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
   one_coeff = 1;
   manybody_flag = 1;
   ghostneigh = 1;
+  allocated = 0;
 
   BOP_index = NULL;
   BOP_index3 = NULL;
@@ -495,6 +496,53 @@ void PairBOP::allocate()
   allocated = 1;
   int n = atom->ntypes;
 
+  memory->destroy(rcut);
+  memory->destroy(rcut3);
+  memory->destroy(rcutsq);
+  memory->destroy(rcutsq3);
+  memory->destroy(dr);
+  memory->destroy(rdr);
+  memory->destroy(dr3);
+  memory->destroy(rdr3);
+  memory->destroy(setflag);
+  memory->destroy(cutsq);
+  memory->destroy(cutghost);
+  memory->destroy(pBetaS);
+  memory->destroy(pBetaS1);
+  memory->destroy(pBetaS2);
+  memory->destroy(pBetaS3);
+  memory->destroy(pBetaS4);
+  memory->destroy(pBetaS5);
+  memory->destroy(pBetaS6);
+  memory->destroy(pLong);
+  memory->destroy(pLong1);
+  memory->destroy(pLong2);
+  memory->destroy(pLong3);
+  memory->destroy(pLong4);
+  memory->destroy(pLong5);
+  memory->destroy(pLong6);
+  memory->destroy(pBetaP);
+  memory->destroy(pBetaP1);
+  memory->destroy(pBetaP2);
+  memory->destroy(pBetaP3);
+  memory->destroy(pBetaP4);
+  memory->destroy(pBetaP5);
+  memory->destroy(pBetaP6);
+  memory->destroy(pRepul);
+  memory->destroy(pRepul1);
+  memory->destroy(pRepul2);
+  memory->destroy(pRepul3);
+  memory->destroy(pRepul4);
+  memory->destroy(pRepul5);
+  memory->destroy(pRepul6);
+  memory->destroy(FsigBO);
+  memory->destroy(FsigBO1);
+  memory->destroy(FsigBO2);
+  memory->destroy(FsigBO3);
+  memory->destroy(FsigBO4);
+  memory->destroy(FsigBO5);
+  memory->destroy(FsigBO6);
+
   memory->create(rcut,npairs,"BOP:rcut");
   memory->create(rcut3,npairs,"BOP:rcut3");
   memory->create(rcutsq,npairs,"BOP:rcutsq");
@@ -569,6 +617,8 @@ void PairBOP::coeff(int narg, char **arg)
   int i,j;
   int n = atom->ntypes;
   MPI_Comm_rank(world,&me);
+
+  delete[] map;
   map = new int[n+1];
 
   if (narg != 3 + atom->ntypes)
@@ -5056,6 +5106,29 @@ void PairBOP::read_table(char *filename)
   MPI_Bcast(&bop_types,1,MPI_INT,0,world);
   MPI_Bcast(&npairs,1,MPI_INT,0,world);
   MPI_Bcast(&npower,1,MPI_INT,0,world);
+
+  memory->destroy(pi_a);
+  memory->destroy(pro_delta);
+  memory->destroy(pi_delta);
+  memory->destroy(pi_p);
+  memory->destroy(pi_c);
+  memory->destroy(r1);
+  memory->destroy(pro);
+  memory->destroy(sigma_delta);
+  memory->destroy(sigma_c);
+  memory->destroy(sigma_a);
+  memory->destroy(sigma_f);
+  memory->destroy(sigma_k);
+  memory->destroy(small3);
+  memory->destroy(gfunc);
+  memory->destroy(gfunc1);
+  memory->destroy(gfunc2);
+  memory->destroy(gfunc3);
+  memory->destroy(gfunc4);
+  memory->destroy(gfunc5);
+  memory->destroy(gfunc6);
+  memory->destroy(gpara);
+
   memory->create(pi_a,npairs,"BOP:pi_a");
   memory->create(pro_delta,bop_types,"BOP:pro_delta");
   memory->create(pi_delta,npairs,"BOP:pi_delta");
@@ -5225,22 +5298,23 @@ void PairBOP::read_table(char *filename)
     pass=0;
     i=0;
     if(nws==3) {
-      while(fgets(s,MAXLINE,fp)!=NULL&&i<npairs) {
+      for(i=0;i<npairs;i++) {
+        utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
         sscanf(s,"%lf",&rcut3[i]);
-        pass=1;
-        i++;
       }
-      if(pass==1) {
+      for(i=0;i<npairs;i++) {
-        for(i=0;i<npairs;i++) {
+        for(j=0;j<nr;j++) {
-          for(j=0;j<nr;j++) {
+          pass=0;
-            utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
+          while(fgets(s,MAXLINE,fp)!=NULL&&pass==0) {
             sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1]
-                ,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
+              ,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
             j+=4;
+            pass=1;
           }
         }
       }
     }
+
     rcutall=0.0;
     for(i=0;i<npairs;i++) {
       if(rcut[i]>rcutall)