forked from lijiext/lammps
Merge pull request #1831 from akohlmey/pair-bop-updates
Correct some issues with pair style bop and its potential files
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
77a28c404a
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@ -1,4 +1,4 @@
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# 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).
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# 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
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2
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13 2.69800000e+01 Al
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29 6.35500000e+01 Cu
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@ -4835,7 +4835,7 @@
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0.00000000e+00
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0.00000000e+00
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0.00000000e+00
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0.00000000e+00
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4.90000000e+00
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0.00000000e+00
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0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
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0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
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File diff suppressed because it is too large
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File diff suppressed because it is too large
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@ -27,8 +27,8 @@
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/*_ssa.h
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/*_ssa.cpp
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/kim_query.cpp
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/kim_query.h
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/kim_*.cpp
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/kim_*.h
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/pair_kim.cpp
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/pair_kim.h
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@ -116,6 +116,8 @@
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/compute_snad_atom.h
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/compute_snav_atom.cpp
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/compute_snav_atom.h
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/compute_snap.cpp
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/compute_snap.h
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/openmp_snap.h
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/pair_snap.cpp
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/pair_snap.h
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@ -318,8 +320,14 @@
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/compute_fep.h
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/compute_force_tally.cpp
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/compute_force_tally.h
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/compute_gyration_shape.cpp
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/compute_gyration_shape.h
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/compute_gyration_shape_chunk.cpp
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/compute_gyration_shape_chunk.h
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/compute_heat_flux_tally.cpp
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/compute_heat_flux_tally.h
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/compute_hma.cpp
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/compute_hma.h
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/compute_ke_atom_eff.cpp
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/compute_ke_atom_eff.h
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/compute_ke_eff.cpp
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@ -332,6 +340,8 @@
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/compute_meso_rho_atom.h
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/compute_meso_t_atom.cpp
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/compute_meso_t_atom.h
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/compute_momentum.cpp
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/compute_momentum.h
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/compute_msd_nongauss.cpp
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/compute_msd_nongauss.h
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/compute_pe_tally.cpp
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@ -422,6 +432,8 @@
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/dump_custom_mpiio.h
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/dump_h5md.cpp
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/dump_h5md.h
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/dump_local_gz.cpp
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/dump_local_gz.h
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/dump_netcdf.cpp
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/dump_netcdf.h
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/dump_netcdf_mpiio.cpp
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@ -564,6 +576,8 @@
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/fix_nph_asphere.h
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/fix_npt_asphere.cpp
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/fix_npt_asphere.h
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/fix_npt_cauchy.cpp
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/fix_npt_cauchy.h
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/fix_nve_asphere.cpp
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/fix_nve_asphere.h
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/fix_nve_asphere_noforce.cpp
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@ -673,6 +687,8 @@
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/fix_spring_pull.h
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/fix_srd.cpp
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/fix_srd.h
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/fix_store_kim.cpp
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/fix_store_kim.h
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/fix_temp_rescale_eff.cpp
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/fix_temp_rescale_eff.h
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/fix_thermal_conductivity.cpp
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@ -695,6 +711,8 @@
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/fix_wall_ees.h
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/fix_wall_region_ees.cpp
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/fix_wall_region_ees.h
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/fix_wall_reflect_stochastic.cpp
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/fix_wall_reflect_stochastic.h
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/fix_wall_gran.cpp
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/fix_wall_gran.h
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/fix_wall_gran_region.cpp
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@ -843,6 +861,8 @@
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/pair_lebedeva_z.h
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/pair_lj_expand_coul_long.cpp
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/pair_lj_expand_coul_long.h
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/pair_local_density.cpp
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/pair_local_density.h
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/pair_edip.cpp
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/pair_edip.h
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/pair_edip_multi.cpp
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@ -968,6 +988,8 @@
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/pair_meam_spline.h
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/pair_meam_sw_spline.cpp
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/pair_meam_sw_spline.h
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/pair_mesocnt.cpp
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/pair_mesocnt.h
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/pair_mm3_switch3_coulgauss_long.cpp
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/pair_mm3_switch3_coulgauss_long.h
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/pair_morse_soft.cpp
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@ -1128,6 +1150,7 @@
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/remap_wrap.h
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/restart_mpiio.cpp
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/restart_mpiio.h
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/rigid_const.h
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/scafacos.cpp
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/scafacos.h
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/server.cpp
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@ -1148,6 +1171,8 @@
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/temper_grem.h
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/temper_npt.cpp
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/temper_npt.h
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/third_order.cpp
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/third_order.h
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/thr_data.cpp
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/thr_data.h
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/verlet_split.cpp
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@ -61,6 +61,7 @@ PairBOP::PairBOP(LAMMPS *lmp) : Pair(lmp)
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one_coeff = 1;
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manybody_flag = 1;
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ghostneigh = 1;
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allocated = 0;
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BOP_index = NULL;
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BOP_index3 = NULL;
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@ -495,6 +496,53 @@ void PairBOP::allocate()
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allocated = 1;
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int n = atom->ntypes;
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memory->destroy(rcut);
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memory->destroy(rcut3);
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memory->destroy(rcutsq);
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memory->destroy(rcutsq3);
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memory->destroy(dr);
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memory->destroy(rdr);
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memory->destroy(dr3);
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memory->destroy(rdr3);
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(cutghost);
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memory->destroy(pBetaS);
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memory->destroy(pBetaS1);
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memory->destroy(pBetaS2);
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memory->destroy(pBetaS3);
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memory->destroy(pBetaS4);
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memory->destroy(pBetaS5);
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memory->destroy(pBetaS6);
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memory->destroy(pLong);
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memory->destroy(pLong1);
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memory->destroy(pLong2);
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memory->destroy(pLong3);
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memory->destroy(pLong4);
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memory->destroy(pLong5);
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memory->destroy(pLong6);
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memory->destroy(pBetaP);
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memory->destroy(pBetaP1);
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memory->destroy(pBetaP2);
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memory->destroy(pBetaP3);
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memory->destroy(pBetaP4);
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memory->destroy(pBetaP5);
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memory->destroy(pBetaP6);
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memory->destroy(pRepul);
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memory->destroy(pRepul1);
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memory->destroy(pRepul2);
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memory->destroy(pRepul3);
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memory->destroy(pRepul4);
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memory->destroy(pRepul5);
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memory->destroy(pRepul6);
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memory->destroy(FsigBO);
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memory->destroy(FsigBO1);
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memory->destroy(FsigBO2);
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memory->destroy(FsigBO3);
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memory->destroy(FsigBO4);
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memory->destroy(FsigBO5);
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memory->destroy(FsigBO6);
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memory->create(rcut,npairs,"BOP:rcut");
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memory->create(rcut3,npairs,"BOP:rcut3");
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memory->create(rcutsq,npairs,"BOP:rcutsq");
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@ -569,6 +617,8 @@ void PairBOP::coeff(int narg, char **arg)
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int i,j;
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int n = atom->ntypes;
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MPI_Comm_rank(world,&me);
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delete[] map;
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map = new int[n+1];
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if (narg != 3 + atom->ntypes)
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@ -5056,6 +5106,29 @@ void PairBOP::read_table(char *filename)
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MPI_Bcast(&bop_types,1,MPI_INT,0,world);
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MPI_Bcast(&npairs,1,MPI_INT,0,world);
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MPI_Bcast(&npower,1,MPI_INT,0,world);
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memory->destroy(pi_a);
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memory->destroy(pro_delta);
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memory->destroy(pi_delta);
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memory->destroy(pi_p);
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memory->destroy(pi_c);
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memory->destroy(r1);
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memory->destroy(pro);
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memory->destroy(sigma_delta);
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memory->destroy(sigma_c);
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memory->destroy(sigma_a);
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memory->destroy(sigma_f);
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memory->destroy(sigma_k);
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memory->destroy(small3);
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memory->destroy(gfunc);
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memory->destroy(gfunc1);
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memory->destroy(gfunc2);
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memory->destroy(gfunc3);
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memory->destroy(gfunc4);
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memory->destroy(gfunc5);
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memory->destroy(gfunc6);
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memory->destroy(gpara);
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memory->create(pi_a,npairs,"BOP:pi_a");
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memory->create(pro_delta,bop_types,"BOP:pro_delta");
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memory->create(pi_delta,npairs,"BOP:pi_delta");
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@ -5225,22 +5298,23 @@ void PairBOP::read_table(char *filename)
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pass=0;
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i=0;
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if(nws==3) {
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while(fgets(s,MAXLINE,fp)!=NULL&&i<npairs) {
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for(i=0;i<npairs;i++) {
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utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
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sscanf(s,"%lf",&rcut3[i]);
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pass=1;
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i++;
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}
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if(pass==1) {
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for(i=0;i<npairs;i++) {
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for(j=0;j<nr;j++) {
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utils::sfgets(FLERR,s,MAXLINE,fp,filename,error);
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for(i=0;i<npairs;i++) {
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for(j=0;j<nr;j++) {
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pass=0;
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while(fgets(s,MAXLINE,fp)!=NULL&&pass==0) {
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sscanf(s,"%lf%lf%lf%lf%lf",&pLong[i][j],&pLong[i][j+1]
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,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
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,&pLong[i][j+2],&pLong[i][j+3],&pLong[i][j+4]);
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j+=4;
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pass=1;
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}
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}
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}
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}
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rcutall=0.0;
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for(i=0;i<npairs;i++) {
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if(rcut[i]>rcutall)
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