Loading src/neighbor.cpp +26 −1 Original line number Diff line number Diff line Loading @@ -104,6 +104,11 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp) maxbin = 0; bins = NULL; // SSA AIR binning len_ssa_airnum = 0; ssa_airnum = NULL; // pair exclusion list info includegroup = 0; Loading Loading @@ -157,6 +162,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp) improperlist = NULL; copymode = 0; last_binning_timestep = -1; } /* ---------------------------------------------------------------------- */ Loading @@ -176,6 +182,8 @@ Neighbor::~Neighbor() memory->destroy(binhead); memory->destroy(bins); memory->destroy(ssa_airnum); memory->destroy(ex1_type); memory->destroy(ex2_type); memory->destroy(ex_type); Loading Loading @@ -1019,6 +1027,7 @@ int Neighbor::request(void *requestor, int instance) skip -> granular function if gran with granhistory, respa function if respaouter, skip_from function for everything else ssa -> special case for USER-DPD pair styles half_from_full, half, full, gran, respaouter -> choose by newton and rq->newton and tri settings style NSQ options = newton off, newton on Loading @@ -1042,6 +1051,10 @@ void Neighbor::choose_build(int index, NeighRequest *rq) else if (rq->respaouter) pb = &Neighbor::skip_from_respa; else pb = &Neighbor::skip_from; } else if (rq->ssa) { if (rq->half_from_full) pb = &Neighbor::half_from_full_newton_ssa; else pb = &Neighbor::half_bin_newton_ssa; } else if (rq->half_from_full) { if (rq->newton == 0) { if (newton_pair == 0) pb = &Neighbor::half_from_full_no_newton; Loading Loading @@ -1286,6 +1299,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq) determine which stencil_create function each neigh list needs based on settings of neigh request, only called if style != NSQ skip or copy or half_from_full -> no stencil ssa = special case for USER-DPD pair styles half, gran, respaouter, full -> choose by newton and tri and dimension if none of these, ptr = NULL since this list needs no stencils use "else if" b/c skip,copy can be set in addition to half,full,etc Loading @@ -1297,7 +1311,11 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq) if (rq->skip || rq->copy || rq->half_from_full) sc = NULL; else if (rq->half || rq->gran || rq->respaouter) { else if (rq->ssa) { if (dimension == 2) sc = &Neighbor::stencil_half_bin_2d_ssa; else if (dimension == 3) sc = &Neighbor::stencil_half_bin_3d_ssa; } else if (rq->half || rq->gran || rq->respaouter) { if (style == BIN) { if (rq->newton == 0) { if (newton_pair == 0) { Loading Loading @@ -1997,6 +2015,11 @@ void Neighbor::bin_atoms() { int i,ibin; // NOTE: added for USER-DPD, why do we need this? if (last_binning_timestep == update->ntimestep) return; last_binning_timestep = update->ntimestep; for (i = 0; i < mbins; i++) binhead[i] = -1; // bin in reverse order so linked list will be in forward order Loading Loading @@ -2152,6 +2175,8 @@ bigint Neighbor::memory_usage() bytes += memory->usage(binhead,maxhead); } bytes += memory->usage(ssa_airnum,len_ssa_airnum); for (int i = 0; i < nrequest; i++) if (lists[i]) bytes += lists[i]->memory_usage(); Loading src/neighbor.h +27 −3 Original line number Diff line number Diff line Loading @@ -69,6 +69,14 @@ class Neighbor : protected Pointers { int nimproperlist; // list of impropers to compute int **improperlist; int cluster_check; // 1 if check bond/angle/etc satisfies minimg // USER-DPD package - better to make this private? int *ssa_airnum; // AIR number of each atom for SSA in USER-DPD // methods Neighbor(class LAMMPS *); virtual ~Neighbor(); virtual void init(); Loading @@ -79,14 +87,13 @@ class Neighbor : protected Pointers { void setup_bins(); // setup bins based on box and cutoff virtual void build(int topoflag=1); // create all neighbor lists (pair,bond) virtual void build_topology(); // create all topology neighbor lists void build_one(class NeighList *list, int preflag=0); // create a single neighbor list void build_one(class NeighList *list, int preflag=0); // create a single one-time neigh list void set(int, char **); // set neighbor style and skin distance void modify_params(int, char**); // modify parameters that control builds bigint memory_usage(); int exclude_setting(); int cluster_check; // 1 if check bond/angle/etc satisfies minimg protected: int me,nprocs; Loading Loading @@ -114,6 +121,7 @@ class Neighbor : protected Pointers { int binatomflag; // bin atoms or not when build neigh list // turned off by build_one() bigint last_binning_timestep; // last step neighbor binning was done int nbinx,nbiny,nbinz; // # of global bins int *bins; // ptr to next atom in each bin Loading Loading @@ -170,6 +178,12 @@ class Neighbor : protected Pointers { int *glist; // lists to grow atom arrays every reneigh int *slist; // lists to grow stencil arrays every reneigh // USER-DPD package int len_ssa_airnum; // length of ssa_airnum array // methods void bin_atoms(); // bin all atoms double bin_distance(int, int, int); // distance between binx int coord2bin(double *); // mapping atom coord to a bin Loading Loading @@ -304,6 +318,16 @@ class Neighbor : protected Pointers { void improper_template(); // improper list with templated bonds void improper_partial(); // exclude certain impropers // SSA neighboring for USER-DPD //int coord2ssa_airnum(double *); // map atom coord to an AIR number //void assign_ssa_airnums(); // set ssa_airnum values void half_bin_newton_ssa(NeighList *) {} void half_from_full_newton_ssa(class NeighList *) {} void stencil_half_bin_2d_ssa(class NeighList *, int, int, int) {} void stencil_half_bin_3d_ssa(class NeighList *, int, int, int) {} // find_special: determine if atom j is in special list of atom i // if it is not, return 0 // if it is and special flag is 0 (both coeffs are 0.0), return -1 Loading Loading
src/neighbor.cpp +26 −1 Original line number Diff line number Diff line Loading @@ -104,6 +104,11 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp) maxbin = 0; bins = NULL; // SSA AIR binning len_ssa_airnum = 0; ssa_airnum = NULL; // pair exclusion list info includegroup = 0; Loading Loading @@ -157,6 +162,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp) improperlist = NULL; copymode = 0; last_binning_timestep = -1; } /* ---------------------------------------------------------------------- */ Loading @@ -176,6 +182,8 @@ Neighbor::~Neighbor() memory->destroy(binhead); memory->destroy(bins); memory->destroy(ssa_airnum); memory->destroy(ex1_type); memory->destroy(ex2_type); memory->destroy(ex_type); Loading Loading @@ -1019,6 +1027,7 @@ int Neighbor::request(void *requestor, int instance) skip -> granular function if gran with granhistory, respa function if respaouter, skip_from function for everything else ssa -> special case for USER-DPD pair styles half_from_full, half, full, gran, respaouter -> choose by newton and rq->newton and tri settings style NSQ options = newton off, newton on Loading @@ -1042,6 +1051,10 @@ void Neighbor::choose_build(int index, NeighRequest *rq) else if (rq->respaouter) pb = &Neighbor::skip_from_respa; else pb = &Neighbor::skip_from; } else if (rq->ssa) { if (rq->half_from_full) pb = &Neighbor::half_from_full_newton_ssa; else pb = &Neighbor::half_bin_newton_ssa; } else if (rq->half_from_full) { if (rq->newton == 0) { if (newton_pair == 0) pb = &Neighbor::half_from_full_no_newton; Loading Loading @@ -1286,6 +1299,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq) determine which stencil_create function each neigh list needs based on settings of neigh request, only called if style != NSQ skip or copy or half_from_full -> no stencil ssa = special case for USER-DPD pair styles half, gran, respaouter, full -> choose by newton and tri and dimension if none of these, ptr = NULL since this list needs no stencils use "else if" b/c skip,copy can be set in addition to half,full,etc Loading @@ -1297,7 +1311,11 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq) if (rq->skip || rq->copy || rq->half_from_full) sc = NULL; else if (rq->half || rq->gran || rq->respaouter) { else if (rq->ssa) { if (dimension == 2) sc = &Neighbor::stencil_half_bin_2d_ssa; else if (dimension == 3) sc = &Neighbor::stencil_half_bin_3d_ssa; } else if (rq->half || rq->gran || rq->respaouter) { if (style == BIN) { if (rq->newton == 0) { if (newton_pair == 0) { Loading Loading @@ -1997,6 +2015,11 @@ void Neighbor::bin_atoms() { int i,ibin; // NOTE: added for USER-DPD, why do we need this? if (last_binning_timestep == update->ntimestep) return; last_binning_timestep = update->ntimestep; for (i = 0; i < mbins; i++) binhead[i] = -1; // bin in reverse order so linked list will be in forward order Loading Loading @@ -2152,6 +2175,8 @@ bigint Neighbor::memory_usage() bytes += memory->usage(binhead,maxhead); } bytes += memory->usage(ssa_airnum,len_ssa_airnum); for (int i = 0; i < nrequest; i++) if (lists[i]) bytes += lists[i]->memory_usage(); Loading
src/neighbor.h +27 −3 Original line number Diff line number Diff line Loading @@ -69,6 +69,14 @@ class Neighbor : protected Pointers { int nimproperlist; // list of impropers to compute int **improperlist; int cluster_check; // 1 if check bond/angle/etc satisfies minimg // USER-DPD package - better to make this private? int *ssa_airnum; // AIR number of each atom for SSA in USER-DPD // methods Neighbor(class LAMMPS *); virtual ~Neighbor(); virtual void init(); Loading @@ -79,14 +87,13 @@ class Neighbor : protected Pointers { void setup_bins(); // setup bins based on box and cutoff virtual void build(int topoflag=1); // create all neighbor lists (pair,bond) virtual void build_topology(); // create all topology neighbor lists void build_one(class NeighList *list, int preflag=0); // create a single neighbor list void build_one(class NeighList *list, int preflag=0); // create a single one-time neigh list void set(int, char **); // set neighbor style and skin distance void modify_params(int, char**); // modify parameters that control builds bigint memory_usage(); int exclude_setting(); int cluster_check; // 1 if check bond/angle/etc satisfies minimg protected: int me,nprocs; Loading Loading @@ -114,6 +121,7 @@ class Neighbor : protected Pointers { int binatomflag; // bin atoms or not when build neigh list // turned off by build_one() bigint last_binning_timestep; // last step neighbor binning was done int nbinx,nbiny,nbinz; // # of global bins int *bins; // ptr to next atom in each bin Loading Loading @@ -170,6 +178,12 @@ class Neighbor : protected Pointers { int *glist; // lists to grow atom arrays every reneigh int *slist; // lists to grow stencil arrays every reneigh // USER-DPD package int len_ssa_airnum; // length of ssa_airnum array // methods void bin_atoms(); // bin all atoms double bin_distance(int, int, int); // distance between binx int coord2bin(double *); // mapping atom coord to a bin Loading Loading @@ -304,6 +318,16 @@ class Neighbor : protected Pointers { void improper_template(); // improper list with templated bonds void improper_partial(); // exclude certain impropers // SSA neighboring for USER-DPD //int coord2ssa_airnum(double *); // map atom coord to an AIR number //void assign_ssa_airnums(); // set ssa_airnum values void half_bin_newton_ssa(NeighList *) {} void half_from_full_newton_ssa(class NeighList *) {} void stencil_half_bin_2d_ssa(class NeighList *, int, int, int) {} void stencil_half_bin_3d_ssa(class NeighList *, int, int, int) {} // find_special: determine if atom j is in special list of atom i // if it is not, return 0 // if it is and special flag is 0 (both coeffs are 0.0), return -1 Loading
