diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 5fa03a098925430d50f5dd09bc59612398a9d759..b2b107284ec26109843db5092bf1dc9594acee8e 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -119,7 +119,7 @@ void VerletKokkos::setup(int flag) atomKK->modified(Host,ALL_MASK); - neighbor->build(); + neighbor->build(1); neighbor->ncalls = 0; // compute all forces @@ -222,7 +222,7 @@ void VerletKokkos::setup_minimal(int flag) atomKK->modified(Host,ALL_MASK); - neighbor->build(); + neighbor->build(1); neighbor->ncalls = 0; } @@ -378,7 +378,7 @@ void VerletKokkos::run(int n) modify->pre_neighbor(); timer->stamp(Timer::MODIFY); } - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); } diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 80bebefec027304bcf020a2cb5d989d523d7ba89..6500707bf3f1812ef3e84b0a46dd5d8c45e4a669 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -316,7 +316,7 @@ void FixAtomSwap::pre_exchange() comm->borders(); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (modify->n_pre_neighbor) modify->pre_neighbor(); - neighbor->build(); + neighbor->build(1); energy_stored = energy_full(); @@ -366,7 +366,7 @@ int FixAtomSwap::attempt_semi_grand() comm->borders(); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (modify->n_pre_neighbor) modify->pre_neighbor(); - neighbor->build(); + neighbor->build(1); } else { comm->forward_comm_fix(this); } @@ -408,7 +408,7 @@ int FixAtomSwap::attempt_semi_grand() comm->borders(); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (modify->n_pre_neighbor) modify->pre_neighbor(); - neighbor->build(); + neighbor->build(1); } else { comm->forward_comm_fix(this); } @@ -447,7 +447,7 @@ int FixAtomSwap::attempt_swap() comm->borders(); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (modify->n_pre_neighbor) modify->pre_neighbor(); - neighbor->build(); + neighbor->build(1); } else { comm->forward_comm_fix(this); } @@ -489,7 +489,7 @@ int FixAtomSwap::attempt_swap() comm->borders(); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (modify->n_pre_neighbor) modify->pre_neighbor(); - neighbor->build(); + neighbor->build(1); } else { comm->forward_comm_fix(this); } diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index f6843eb0a3a420a0d18f0e15fe1036990c565a50..02300844907b16767986019acc77af28f2edc1c3 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -2250,7 +2250,7 @@ double FixGCMC::energy_full() comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (modify->n_pre_neighbor) modify->pre_neighbor(); - neighbor->build(); + neighbor->build(1); int eflag = 1; int vflag = 0; diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index 4572170f34f6132fa4ca6ef1b081147142a8d011..4a30f8c00b672824a93f580a89f86b2cb58d75cd 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -344,7 +344,7 @@ void VerletSplit::run(int n) if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); timer->stamp(Timer::COMM); if (n_pre_neighbor) modify->pre_neighbor(); - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); } } diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index 9ff5f8517608fa74c7c9916824aa723247ef3fa6..1b9c305e9c69377906b0346de8b6803c37b307b9 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -142,7 +142,7 @@ void VerletLRTIntel::setup(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); neighbor->ncalls = 0; // compute all forces @@ -276,7 +276,7 @@ void VerletLRTIntel::run(int n) modify->pre_neighbor(); timer->stamp(Timer::MODIFY); } - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); } diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index e1e5f579b875c31f16c70c3f55ba3d44a3f14494..aeaf2f78ba8500660cf758261a4b6de92709f90d 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -304,7 +304,7 @@ void FixSRP::setup_pre_force(int zz) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); neighbor->ncalls = 0; // new atom counts diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index aa4aa65a4fcefec8bc143367d63347306c1c3bc6..e721842e4814b168512d1f793201bc74fbf7ce98 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -107,7 +107,7 @@ void RespaOMP::setup() domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; @@ -200,7 +200,7 @@ void RespaOMP::setup_minimal(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; } @@ -311,7 +311,7 @@ void RespaOMP::recurse(int ilevel) modify->pre_neighbor(); timer->stamp(Timer::MODIFY); } - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); if (modify->n_post_neighbor) { modify->post_neighbor(); diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index dd639c34dbc3e4442a16c60875d01587f085ff1d..36494b0d493809c4ae10e9314bc58765a19ee674 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -734,7 +734,7 @@ void FixNHUef::end_of_step() comm->borders(); domain->lamda2x(atom->nlocal+atom->nghost); timer->stamp(Timer::COMM); - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); } } @@ -754,7 +754,7 @@ void FixNHUef::post_run() comm->borders(); domain->lamda2x(atom->nlocal+atom->nghost); timer->stamp(Timer::COMM); - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); } diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 4752002ac9319d4096fbeb5f1a3f1c4ae5d6ef83..48f12406b6ea06cb4fda7a20ed90fd4b85ef8bf0 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -209,7 +209,7 @@ void CreateBonds::many() comm->exchange(); comm->borders(); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); - neighbor->build(); + neighbor->build(1); // build neighbor list this command needs based on earlier request diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 489c5bf5d5f4ce5837d42ee64d8fcd04be3103f3..a5b15f5f52a848894b35467639f772779c9d831e 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -311,7 +311,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg) comm->exchange(); comm->borders(); if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost); - neighbor->build(); + neighbor->build(1); // build neighbor list this command needs based on earlier request diff --git a/src/min.cpp b/src/min.cpp index 653cac71e6af5b3a52a00d808a47319242593def..0caa9a9acf0584eac39ad0a55c8ddf634f56906e 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -245,7 +245,7 @@ void Min::setup(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; @@ -345,7 +345,7 @@ void Min::setup_minimal(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; } @@ -508,7 +508,7 @@ double Min::energy_force(int resetflag) modify->min_pre_neighbor(); timer->stamp(Timer::MODIFY); } - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); if (modify->n_min_post_neighbor) { modify->min_post_neighbor(); diff --git a/src/neighbor.h b/src/neighbor.h index 9244bc575d9b355780996e98e6fb4b63f9aa0651..c054cddb2b59d04dbfd723d8c405e66ea8cf2ad5 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -111,7 +111,7 @@ class Neighbor : protected Pointers { int decide(); // decide whether to build or not virtual int check_distance(); // check max distance moved since last build void setup_bins(); // setup bins based on box and cutoff - virtual void build(int topoflag=1); // build all perpetual neighbor lists + virtual void build(int); // build all perpetual neighbor lists virtual void build_topology(); // pairwise topology neighbor lists void build_one(class NeighList *list, int preflag=0); // create a one-time pairwise neigh list diff --git a/src/respa.cpp b/src/respa.cpp index 23cd941834482d3f5047602c8fa98e426f901ba4..18630c06d6fe8c525716cebd9bf5d689406dfe86 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -441,7 +441,7 @@ void Respa::setup(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; @@ -517,7 +517,7 @@ void Respa::setup_minimal(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; } @@ -668,7 +668,7 @@ void Respa::recurse(int ilevel) modify->pre_neighbor(); timer->stamp(Timer::MODIFY); } - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); if (modify->n_post_neighbor) { modify->post_neighbor(); diff --git a/src/verlet.cpp b/src/verlet.cpp index d74906556b35c32bde5da26114a31cf7c9441b13..019f3f2f05b3f539cd9619b441dd77f290c804dd 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -120,7 +120,7 @@ void Verlet::setup(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; @@ -182,7 +182,7 @@ void Verlet::setup_minimal(int flag) domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); - neighbor->build(); + neighbor->build(1); modify->setup_post_neighbor(); neighbor->ncalls = 0; } @@ -284,7 +284,7 @@ void Verlet::run(int n) modify->pre_neighbor(); timer->stamp(Timer::MODIFY); } - neighbor->build(); + neighbor->build(1); timer->stamp(Timer::NEIGH); if (n_post_neighbor) { modify->post_neighbor();