diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index a9501dac9d..8b36019881 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -141,10 +141,10 @@ PairReaxC::~PairReaxC() if (control->tabulate ) Deallocate_Lookup_Tables( system); - if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS, world); - Delete_List( lists+BONDS, world ); - Delete_List( lists+THREE_BODIES, world ); - Delete_List( lists+FAR_NBRS, world ); + if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS ); + Delete_List( lists+BONDS ); + Delete_List( lists+THREE_BODIES ); + Delete_List( lists+FAR_NBRS ); DeAllocate_Workspace( control, workspace ); DeAllocate_System( system ); @@ -439,12 +439,12 @@ void PairReaxC::setup( ) // initialize my data structures - PreAllocate_Space( system, control, workspace, world ); + PreAllocate_Space( system, control, workspace ); write_reax_atoms(); int num_nbrs = estimate_reax_lists(); if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR, - lists+FAR_NBRS, world)) + lists+FAR_NBRS)) error->one(FLERR,"Pair reax/c problem in far neighbor list"); (lists+FAR_NBRS)->error_ptr=lmp->error; @@ -469,7 +469,7 @@ void PairReaxC::setup( ) // check if I need to shrink/extend my data-structs - ReAllocate( system, control, data, workspace, &lists, mpi_data ); + ReAllocate( system, control, data, workspace, &lists ); } bigint local_ngroup = list->inum; @@ -521,7 +521,7 @@ void PairReaxC::compute(int eflag, int vflag) setup(); - Reset( system, control, data, workspace, &lists, world ); + Reset( system, control, data, workspace, &lists ); workspace->realloc.num_far = write_reax_lists(); // timing for filling in the reax lists if (comm->me == 0) { diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index 8784c854b5..7649c110ef 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -44,7 +44,7 @@ using namespace LAMMPS_NS; process's box throughout the whole simulation. therefore we need to make upper bound estimates for various data structures */ int PreAllocate_Space( reax_system *system, control_params * /*control*/, - storage * workspace, MPI_Comm comm ) + storage * workspace ) { int mincap = system->mincap; double safezone = system->safezone; @@ -55,7 +55,7 @@ int PreAllocate_Space( reax_system *system, control_params * /*control*/, system->total_cap = MAX( (int)(system->N * safezone), mincap ); system->my_atoms = (reax_atom*) - scalloc(system->error_ptr, system->total_cap, sizeof(reax_atom), "my_atoms", comm ); + scalloc(system->error_ptr, system->total_cap, sizeof(reax_atom), "my_atoms"); // Nullify some arrays only used in omp styles // Should be safe to do here since called in pair->setup(); @@ -212,7 +212,7 @@ void DeAllocate_Workspace( control_params * control, storage *workspace ) int Allocate_Workspace( reax_system * /*system*/, control_params * control, storage *workspace, int local_cap, int total_cap, - MPI_Comm comm, char * /*msg*/ ) + char * /*msg*/ ) { int i, total_real, total_rvec, local_rvec; @@ -224,84 +224,84 @@ int Allocate_Workspace( reax_system * /*system*/, control_params * control, /* communication storage */ for( i = 0; i < MAX_NBRS; ++i ) { workspace->tmp_dbl[i] = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "tmp_dbl", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "tmp_dbl"); workspace->tmp_rvec[i] = (rvec*) - scalloc(control->error_ptr, total_cap, sizeof(rvec), "tmp_rvec", comm ); + scalloc(control->error_ptr, total_cap, sizeof(rvec), "tmp_rvec"); workspace->tmp_rvec2[i] = (rvec2*) - scalloc(control->error_ptr, total_cap, sizeof(rvec2), "tmp_rvec2", comm ); + scalloc(control->error_ptr, total_cap, sizeof(rvec2), "tmp_rvec2"); } /* bond order related storage */ workspace->within_bond_box = (int*) - scalloc(control->error_ptr, total_cap, sizeof(int), "skin", comm ); - workspace->total_bond_order = (double*) smalloc(control->error_ptr, total_real, "total_bo", comm ); - workspace->Deltap = (double*) smalloc(control->error_ptr, total_real, "Deltap", comm ); - workspace->Deltap_boc = (double*) smalloc(control->error_ptr, total_real, "Deltap_boc", comm ); - workspace->dDeltap_self = (rvec*) smalloc(control->error_ptr, total_rvec, "dDeltap_self", comm ); - workspace->Delta = (double*) smalloc(control->error_ptr, total_real, "Delta", comm ); - workspace->Delta_lp = (double*) smalloc(control->error_ptr, total_real, "Delta_lp", comm ); + scalloc(control->error_ptr, total_cap, sizeof(int), "skin"); + workspace->total_bond_order = (double*) smalloc(control->error_ptr, total_real, "total_bo"); + workspace->Deltap = (double*) smalloc(control->error_ptr, total_real, "Deltap"); + workspace->Deltap_boc = (double*) smalloc(control->error_ptr, total_real, "Deltap_boc"); + workspace->dDeltap_self = (rvec*) smalloc(control->error_ptr, total_rvec, "dDeltap_self"); + workspace->Delta = (double*) smalloc(control->error_ptr, total_real, "Delta"); + workspace->Delta_lp = (double*) smalloc(control->error_ptr, total_real, "Delta_lp"); workspace->Delta_lp_temp = (double*) - smalloc(control->error_ptr, total_real, "Delta_lp_temp", comm ); - workspace->dDelta_lp = (double*) smalloc(control->error_ptr, total_real, "dDelta_lp", comm ); + smalloc(control->error_ptr, total_real, "Delta_lp_temp"); + workspace->dDelta_lp = (double*) smalloc(control->error_ptr, total_real, "dDelta_lp"); workspace->dDelta_lp_temp = (double*) - smalloc(control->error_ptr, total_real, "dDelta_lp_temp", comm ); - workspace->Delta_e = (double*) smalloc(control->error_ptr, total_real, "Delta_e", comm ); - workspace->Delta_boc = (double*) smalloc(control->error_ptr, total_real, "Delta_boc", comm ); - workspace->Delta_val = (double*) smalloc(control->error_ptr, total_real, "Delta_val", comm ); - workspace->nlp = (double*) smalloc(control->error_ptr, total_real, "nlp", comm ); - workspace->nlp_temp = (double*) smalloc(control->error_ptr, total_real, "nlp_temp", comm ); - workspace->Clp = (double*) smalloc(control->error_ptr, total_real, "Clp", comm ); - workspace->vlpex = (double*) smalloc(control->error_ptr, total_real, "vlpex", comm ); + smalloc(control->error_ptr, total_real, "dDelta_lp_temp"); + workspace->Delta_e = (double*) smalloc(control->error_ptr, total_real, "Delta_e"); + workspace->Delta_boc = (double*) smalloc(control->error_ptr, total_real, "Delta_boc"); + workspace->Delta_val = (double*) smalloc(control->error_ptr, total_real, "Delta_val"); + workspace->nlp = (double*) smalloc(control->error_ptr, total_real, "nlp"); + workspace->nlp_temp = (double*) smalloc(control->error_ptr, total_real, "nlp_temp"); + workspace->Clp = (double*) smalloc(control->error_ptr, total_real, "Clp"); + workspace->vlpex = (double*) smalloc(control->error_ptr, total_real, "vlpex"); workspace->bond_mark = (int*) - scalloc(control->error_ptr, total_cap, sizeof(int), "bond_mark", comm ); + scalloc(control->error_ptr, total_cap, sizeof(int), "bond_mark"); workspace->done_after = (int*) - scalloc(control->error_ptr, total_cap, sizeof(int), "done_after", comm ); + scalloc(control->error_ptr, total_cap, sizeof(int), "done_after"); /* QEq storage */ workspace->Hdia_inv = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "Hdia_inv", comm ); - workspace->b_s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_s", comm ); - workspace->b_t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_t", comm ); - workspace->b_prc = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prc", comm ); - workspace->b_prm = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prm", comm ); - workspace->s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "s", comm ); - workspace->t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "t", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "Hdia_inv"); + workspace->b_s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_s"); + workspace->b_t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_t"); + workspace->b_prc = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prc"); + workspace->b_prm = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prm"); + workspace->s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "s"); + workspace->t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "t"); workspace->droptol = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "droptol", comm ); - workspace->b = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "b", comm ); - workspace->x = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "x", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "droptol"); + workspace->b = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "b"); + workspace->x = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "x"); /* GMRES storage */ - workspace->y = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "y", comm ); - workspace->z = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "z", comm ); - workspace->g = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "g", comm ); - workspace->h = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "h", comm ); - workspace->hs = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hs", comm ); - workspace->hc = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hc", comm ); - workspace->v = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "v", comm ); + workspace->y = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "y"); + workspace->z = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "z"); + workspace->g = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "g"); + workspace->h = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "h"); + workspace->hs = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hs"); + workspace->hc = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hc"); + workspace->v = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "v"); for( i = 0; i < RESTART+1; ++i ) { - workspace->h[i] = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "h[i]", comm ); - workspace->v[i] = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "v[i]", comm ); + workspace->h[i] = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "h[i]"); + workspace->v[i] = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "v[i]"); } /* CG storage */ - workspace->r = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "r", comm ); - workspace->d = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "d", comm ); - workspace->q = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "q", comm ); - workspace->p = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "p", comm ); - workspace->r2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "r2", comm ); - workspace->d2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "d2", comm ); - workspace->q2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "q2", comm ); - workspace->p2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "p2", comm ); + workspace->r = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "r"); + workspace->d = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "d"); + workspace->q = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "q"); + workspace->p = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "p"); + workspace->r2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "r2"); + workspace->d2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "d2"); + workspace->q2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "q2"); + workspace->p2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "p2"); /* integrator storage */ - workspace->v_const = (rvec*) smalloc(control->error_ptr, local_rvec, "v_const", comm ); + workspace->v_const = (rvec*) smalloc(control->error_ptr, local_rvec, "v_const"); /* force related storage */ - workspace->f = (rvec*) scalloc(control->error_ptr, total_cap, sizeof(rvec), "f", comm ); + workspace->f = (rvec*) scalloc(control->error_ptr, total_cap, sizeof(rvec), "f"); workspace->CdDelta = (double*) - scalloc(control->error_ptr, total_cap, sizeof(double), "CdDelta", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "CdDelta"); // storage for reductions with multiple threads #ifdef LMP_USER_OMP @@ -322,17 +322,16 @@ int Allocate_Workspace( reax_system * /*system*/, control_params * control, static void Reallocate_Neighbor_List( reax_list *far_nbrs, int n, - int num_intrs, MPI_Comm comm ) + int num_intrs ) { - Delete_List( far_nbrs, comm ); - if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs, comm )){ + Delete_List( far_nbrs); + if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs )){ far_nbrs->error_ptr->one(FLERR,"Problem in initializing far neighbors list"); } } -static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds, - MPI_Comm comm ) +static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds ) { int i, total_hbonds; @@ -346,8 +345,8 @@ static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds, } total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS )); - Delete_List( hbonds, comm ); - if (!Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds, comm )) { + Delete_List( hbonds); + if (!Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds )) { hbonds->error_ptr->one(FLERR, "Not enough space for hydrogen bonds list"); } @@ -356,8 +355,7 @@ static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds, static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, - int *total_bonds, int *est_3body, - MPI_Comm comm ) + int *total_bonds, int *est_3body ) { int i; @@ -378,8 +376,8 @@ static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, sfree(system->error_ptr, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); #endif - Delete_List( bonds, comm ); - if(!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds, comm)) { + Delete_List( bonds); + if(!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds)) { bonds->error_ptr->one(FLERR, "Not enough space for bonds list"); } @@ -401,14 +399,12 @@ static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, void ReAllocate( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, reax_list **lists, - mpi_datatypes *mpi_data ) + simulation_data *data, storage *workspace, reax_list **lists ) { int num_bonds, est_3body, Hflag, ret; int renbr, newsize; reallocate_data *realloc; reax_list *far_nbrs; - MPI_Comm comm; char msg[200]; int mincap = system->mincap; @@ -416,7 +412,6 @@ void ReAllocate( reax_system *system, control_params *control, double saferzone = system->saferzone; realloc = &(workspace->realloc); - comm = mpi_data->world; if( system->n >= DANGER_ZONE * system->local_cap || (0 && system->n <= LOOSE_ZONE * system->local_cap) ) { @@ -434,18 +429,18 @@ void ReAllocate( reax_system *system, control_params *control, /* system */ ret = Allocate_System( system, system->local_cap, system->total_cap, msg ); if (ret != SUCCESS) { - char errmsg[128]; - snprintf(errmsg, 128, "Not enough space for atom_list: total_cap=%d", system->total_cap); + char errmsg[256]; + snprintf(errmsg, 256, "Not enough space for atom_list: total_cap=%d", system->total_cap); system->error_ptr->one(FLERR, errmsg); } /* workspace */ DeAllocate_Workspace( control, workspace ); ret = Allocate_Workspace( system, control, workspace, system->local_cap, - system->total_cap, comm, msg ); + system->total_cap, msg ); if (ret != SUCCESS) { - char errmsg[128]; - snprintf(errmsg, 128, "Not enough space for workspace: local_cap=%d total_cap=%d", system->local_cap, system->total_cap); + char errmsg[256]; + snprintf(errmsg, 256, "Not enough space for workspace: local_cap=%d total_cap=%d", system->local_cap, system->total_cap); system->error_ptr->one(FLERR, errmsg); } } @@ -458,15 +453,15 @@ void ReAllocate( reax_system *system, control_params *control, if (Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE) { if (realloc->num_far > far_nbrs->num_intrs) { - char errmsg[128]; - snprintf(errmsg, 128, "step%d-ran out of space on far_nbrs: top=%d, max=%d", data->step, realloc->num_far, far_nbrs->num_intrs); + char errmsg[256]; + snprintf(errmsg, 256, "step%d-ran out of space on far_nbrs: top=%d, max=%d", data->step, realloc->num_far, far_nbrs->num_intrs); system->error_ptr->one(FLERR, errmsg); } newsize = static_cast (MAX( realloc->num_far*safezone, mincap*MIN_NBRS )); - Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize, comm ); + Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize); realloc->num_far = 0; } } @@ -481,7 +476,7 @@ void ReAllocate( reax_system *system, control_params *control, } if (Hflag || realloc->hbonds) { - ret = Reallocate_HBonds_List( system, (*lists)+HBONDS, comm ); + ret = Reallocate_HBonds_List( system, (*lists)+HBONDS); realloc->hbonds = 0; } } @@ -490,14 +485,14 @@ void ReAllocate( reax_system *system, control_params *control, num_bonds = est_3body = -1; if (Nflag || realloc->bonds) { Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds, - &est_3body, comm ); + &est_3body); realloc->bonds = 0; realloc->num_3body = MAX( realloc->num_3body, est_3body ) * 2; } /* 3-body list */ if (realloc->num_3body > 0) { - Delete_List( (*lists)+THREE_BODIES, comm ); + Delete_List( (*lists)+THREE_BODIES); if (num_bonds == -1) num_bonds = ((*lists)+BONDS)->num_intrs; @@ -505,7 +500,7 @@ void ReAllocate( reax_system *system, control_params *control, realloc->num_3body = (int)(MAX(realloc->num_3body*safezone, MIN_3BODIES)); if( !Make_List( num_bonds, realloc->num_3body, TYP_THREE_BODY, - (*lists)+THREE_BODIES, comm ) ) { + (*lists)+THREE_BODIES ) ) { system->error_ptr->one(FLERR, "Problem in initializing angles list"); } realloc->num_3body = -1; diff --git a/src/USER-REAXC/reaxc_allocate.h b/src/USER-REAXC/reaxc_allocate.h index f813204006..be203340f6 100644 --- a/src/USER-REAXC/reaxc_allocate.h +++ b/src/USER-REAXC/reaxc_allocate.h @@ -28,20 +28,15 @@ #define __ALLOCATE_H_ #include "reaxc_types.h" - -#include "lammps.h" -#include "error.h" -using namespace LAMMPS_NS; - -int PreAllocate_Space( reax_system*, control_params*, storage*, MPI_Comm ); +int PreAllocate_Space( reax_system*, control_params*, storage* ); int Allocate_System( reax_system*, int, int, char* ); void DeAllocate_System( reax_system* ); int Allocate_Workspace( reax_system*, control_params*, storage*, - int, int, MPI_Comm, char* ); + int, int, char* ); void DeAllocate_Workspace( control_params*, storage* ); void ReAllocate( reax_system*, control_params*, simulation_data*, storage*, - reax_list**, mpi_datatypes* ); + reax_list** ); #endif diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp index 14b28615fb..0caae40156 100644 --- a/src/USER-REAXC/reaxc_control.cpp +++ b/src/USER-REAXC/reaxc_control.cpp @@ -28,7 +28,6 @@ #include "reaxc_control.h" #include "reaxc_tool_box.h" - char Read_Control_File( char *control_file, control_params* control, output_controls *out_control ) { diff --git a/src/USER-REAXC/reaxc_control.h b/src/USER-REAXC/reaxc_control.h index 47627aed61..b2b455d6b8 100644 --- a/src/USER-REAXC/reaxc_control.h +++ b/src/USER-REAXC/reaxc_control.h @@ -29,9 +29,6 @@ #include "reaxc_types.h" -#include "lammps.h" -#include "error.h" - char Read_Control_File( char*, control_params*, output_controls* ); #endif diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index 987a11d252..28bc0429cc 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -44,7 +44,6 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, double val; MPI_Comm comm; int me; - comm = MPI_COMM_WORLD; MPI_Comm_rank(comm, &me); @@ -99,55 +98,45 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Allocating structures in reax_interaction */ reax->sbp = (single_body_parameters*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(single_body_parameters), "sbp", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(single_body_parameters), "sbp"); reax->tbp = (two_body_parameters**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters*), "tbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters*), "tbp"); reax->thbp= (three_body_header***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header**), "thbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header**), "thbp"); reax->hbp = (hbond_parameters***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters**), "hbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters**), "hbp"); reax->fbp = (four_body_header****) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header***), "fbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header***), "fbp"); tor_flag = (char****) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char***), "tor_flag", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char***), "tor_flag"); for( i = 0; i < reax->num_atom_types; i++ ) { reax->tbp[i] = (two_body_parameters*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]"); reax->thbp[i]= (three_body_header**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]"); reax->hbp[i] = (hbond_parameters**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]"); reax->fbp[i] = (four_body_header***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]"); tor_flag[i] = (char***) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char**), "tor_flag[i]", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char**), "tor_flag[i]"); for( j = 0; j < reax->num_atom_types; j++ ) { reax->thbp[i][j]= (three_body_header*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]"); reax->hbp[i][j] = (hbond_parameters*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]"); reax->fbp[i][j] = (four_body_header**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]"); tor_flag[i][j] = (char**) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char*), "tor_flag[i,j]", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char*), "tor_flag[i,j]"); for (k=0; k < reax->num_atom_types; k++) { reax->fbp[i][j][k] = (four_body_header*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]"); tor_flag[i][j][k] = (char*) - scalloc(control->error_ptr, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]"); } } } @@ -163,7 +152,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity checks */ if (c < 9) { - control->error_ptr->one(FLERR,"Inconsistent ffield file"); + control->error_ptr->all(FLERR,"Inconsistent ffield file"); } for( j = 0; j < (int)(strlen(tmp[0])); ++j ) @@ -185,7 +174,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c < 8) { - control->error_ptr->one(FLERR,"Inconsistent ffield file"); + control->error_ptr->all(FLERR,"Inconsistent ffield file"); } val = atof(tmp[0]); reax->sbp[i].alpha = val; @@ -203,7 +192,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c < 8) { - control->error_ptr->one(FLERR,"Inconsistent ffield file"); + control->error_ptr->all(FLERR,"Inconsistent ffield file"); } val = atof(tmp[0]); reax->sbp[i].r_pi_pi = val; @@ -221,7 +210,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c < 8) { - control->error_ptr->one(FLERR,"Inconsistent ffield file"); + control->error_ptr->all(FLERR,"Inconsistent ffield file"); } val = atof(tmp[0]); reax->sbp[i].p_ovun2 = val; @@ -240,7 +229,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c > 2) { - control->error_ptr->one(FLERR,"Force field file incompatible with 'lgvdw yes'"); + control->error_ptr->all(FLERR,"Force field file incompatible with 'lgvdw yes'"); } val = atof(tmp[0]); reax->sbp[i].lgcij = val; @@ -337,8 +326,6 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, fgets(s,MAX_LINE,fp); c=Tokenize(s,&tmp); - - j = atoi(tmp[0]) - 1; k = atoi(tmp[1]) - 1; diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index ff1dd839fb..afe9a059ed 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -116,7 +116,7 @@ void Compute_Total_Force( reax_system *system, control_params *control, } void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **lists, - int step, int /*n*/, int N, int numH, MPI_Comm comm ) + int step, int /*n*/, int N, int numH ) { int i, comp, Hindex; reax_list *bonds, *hbonds; @@ -176,8 +176,7 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l void Init_Forces_noQEq( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /*out_control*/, - MPI_Comm comm ) { + reax_list **lists, output_controls * /*out_control*/ ) { int i, j, pj; int start_i, end_i; int type_i, type_j; @@ -311,13 +310,13 @@ void Init_Forces_noQEq( reax_system *system, control_params *control, workspace->realloc.num_hbonds = num_hbonds; Validate_Lists( system, workspace, lists, data->step, - system->n, system->N, system->numH, comm ); + system->n, system->N, system->numH); } void Estimate_Storages( reax_system *system, control_params *control, reax_list **lists, int *Htop, int *hb_top, - int *bond_top, int *num_3body, MPI_Comm /*comm*/ ) + int *bond_top, int *num_3body ) { int i, j, pj; int start_i, end_i; @@ -439,10 +438,9 @@ void Compute_Forces( reax_system *system, control_params *control, reax_list **lists, output_controls *out_control, mpi_datatypes *mpi_data ) { - MPI_Comm comm = mpi_data->world; Init_Forces_noQEq( system, control, data, workspace, - lists, out_control, comm ); + lists, out_control); /********* bonded interactions ************/ Compute_Bonded_Forces( system, control, data, workspace, diff --git a/src/USER-REAXC/reaxc_forces.h b/src/USER-REAXC/reaxc_forces.h index 6c839a7023..bfad2e9b71 100644 --- a/src/USER-REAXC/reaxc_forces.h +++ b/src/USER-REAXC/reaxc_forces.h @@ -36,5 +36,5 @@ void Init_Force_Functions( control_params* ); void Compute_Forces( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes* ); void Estimate_Storages( reax_system*, control_params*, reax_list**, - int*, int*, int*, int*, MPI_Comm ); + int*, int*, int*, int* ); #endif diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index 27e60c580c..913bc241de 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -81,7 +81,7 @@ int Init_Simulation_Data( reax_system *system, control_params *control, return SUCCESS; } -void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm ) +void Init_Taper( control_params *control, storage *workspace ) { double d1, d7; double swa, swa2, swa3; @@ -122,12 +122,12 @@ void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm ) int Init_Workspace( reax_system *system, control_params *control, - storage *workspace, MPI_Comm comm, char *msg ) + storage *workspace, char *msg ) { int ret; ret = Allocate_Workspace( system, control, workspace, - system->local_cap, system->total_cap, comm, msg ); + system->local_cap, system->total_cap, msg ); if (ret != SUCCESS) return ret; @@ -135,7 +135,7 @@ int Init_Workspace( reax_system *system, control_params *control, Reset_Workspace( system, workspace ); /* Initialize the Taper function */ - Init_Taper( control, workspace, comm ); + Init_Taper( control, workspace); return SUCCESS; } @@ -159,17 +159,15 @@ int Init_Lists( reax_system *system, control_params *control, { int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; int *hb_top, *bond_top; - MPI_Comm comm; int mincap = system->mincap; double safezone = system->safezone; double saferzone = system->saferzone; - comm = mpi_data->world; bond_top = (int*) calloc( system->total_cap, sizeof(int) ); hb_top = (int*) calloc( system->local_cap, sizeof(int) ); Estimate_Storages( system, control, lists, - &Htop, hb_top, bond_top, &num_3body, comm ); + &Htop, hb_top, bond_top, &num_3body); if (control->hbond_cut > 0) { /* init H indexes */ @@ -181,7 +179,7 @@ int Init_Lists( reax_system *system, control_params *control, total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS )); if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND, - *lists+HBONDS, comm ) ) { + *lists+HBONDS ) ) { control->error_ptr->one(FLERR, "Not enough space for hbonds list."); } (*lists+HBONDS)->error_ptr = system->error_ptr; @@ -195,7 +193,7 @@ int Init_Lists( reax_system *system, control_params *control, bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS )); if( !Make_List( system->total_cap, bond_cap, TYP_BOND, - *lists+BONDS, comm ) ) { + *lists+BONDS ) ) { control->error_ptr->one(FLERR, "Not enough space for bonds list."); } (*lists+BONDS)->error_ptr = system->error_ptr; @@ -203,7 +201,7 @@ int Init_Lists( reax_system *system, control_params *control, /* 3bodies list */ cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES )); if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY, - *lists+THREE_BODIES, comm ) ){ + *lists+THREE_BODIES ) ){ control->error_ptr->one(FLERR,"Problem in initializing angles list."); } (*lists+THREE_BODIES)->error_ptr = system->error_ptr; @@ -242,7 +240,7 @@ void Initialize( reax_system *system, control_params *control, control->error_ptr->one(FLERR,errmsg); } - if (Init_Workspace( system, control, workspace, mpi_data->world, msg ) == + if (Init_Workspace( system, control, workspace, msg ) == FAILURE) { snprintf(errmsg, 128, "Workspace could not be initialized on thread %d", system->my_rank); diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h index 546a9e33c9..ab519a4c72 100644 --- a/src/USER-REAXC/reaxc_init_md.h +++ b/src/USER-REAXC/reaxc_init_md.h @@ -29,8 +29,6 @@ #include "reaxc_types.h" -#include "lammps.h" -#include "error.h" void Initialize( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp index f103e520e8..d0143ec9ae 100644 --- a/src/USER-REAXC/reaxc_list.cpp +++ b/src/USER-REAXC/reaxc_list.cpp @@ -29,7 +29,7 @@ #include "reaxc_tool_box.h" /************* allocate list space ******************/ -int Make_List( int n, int num_intrs, int type, reax_list *l, MPI_Comm comm) +int Make_List(int n, int num_intrs, int type, reax_list *l ) { l->allocated = 1; @@ -38,52 +38,52 @@ int Make_List( int n, int num_intrs, int type, reax_list *l, MPI_Comm comm) if (l->index) sfree(l->error_ptr, l->index, "list:index"); if (l->end_index) sfree(l->error_ptr, l->end_index, "list:end_index"); - l->index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:index", comm ); - l->end_index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:end_index", comm ); + l->index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:index"); + l->end_index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:end_index"); l->type = type; switch(l->type) { case TYP_VOID: if (l->select.v) sfree(l->error_ptr, l->select.v, "list:v"); - l->select.v = (void*) smalloc(l->error_ptr, l->num_intrs * sizeof(void*), "list:v", comm); + l->select.v = (void*) smalloc(l->error_ptr, l->num_intrs * sizeof(void*), "list:v"); break; case TYP_THREE_BODY: if (l->select.three_body_list) sfree(l->error_ptr, l->select.three_body_list,"list:three_bodies"); l->select.three_body_list = (three_body_interaction_data*) smalloc(l->error_ptr, l->num_intrs * sizeof(three_body_interaction_data), - "list:three_bodies", comm ); + "list:three_bodies"); break; case TYP_BOND: if (l->select.bond_list) sfree(l->error_ptr, l->select.bond_list,"list:bonds"); l->select.bond_list = (bond_data*) - smalloc(l->error_ptr, l->num_intrs * sizeof(bond_data), "list:bonds", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(bond_data), "list:bonds"); break; case TYP_DBO: if (l->select.dbo_list) sfree(l->error_ptr, l->select.dbo_list,"list:dbonds"); l->select.dbo_list = (dbond_data*) - smalloc(l->error_ptr, l->num_intrs * sizeof(dbond_data), "list:dbonds", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(dbond_data), "list:dbonds"); break; case TYP_DDELTA: if (l->select.dDelta_list) sfree(l->error_ptr, l->select.dDelta_list,"list:dDeltas"); l->select.dDelta_list = (dDelta_data*) - smalloc(l->error_ptr, l->num_intrs * sizeof(dDelta_data), "list:dDeltas", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(dDelta_data), "list:dDeltas"); break; case TYP_FAR_NEIGHBOR: if (l->select.far_nbr_list) sfree(l->error_ptr, l->select.far_nbr_list,"list:far_nbrs"); l->select.far_nbr_list = (far_neighbor_data*) - smalloc(l->error_ptr, l->num_intrs * sizeof(far_neighbor_data), "list:far_nbrs", comm); + smalloc(l->error_ptr, l->num_intrs * sizeof(far_neighbor_data), "list:far_nbrs"); break; case TYP_HBOND: if (l->select.hbond_list) sfree(l->error_ptr, l->select.hbond_list,"list:hbonds"); l->select.hbond_list = (hbond_data*) - smalloc(l->error_ptr, l->num_intrs * sizeof(hbond_data), "list:hbonds", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(hbond_data), "list:hbonds"); break; default: @@ -96,7 +96,7 @@ int Make_List( int n, int num_intrs, int type, reax_list *l, MPI_Comm comm) } -void Delete_List( reax_list *l, MPI_Comm comm ) +void Delete_List( reax_list *l ) { if (l->allocated == 0) return; diff --git a/src/USER-REAXC/reaxc_list.h b/src/USER-REAXC/reaxc_list.h index ab7fbce19c..28567252da 100644 --- a/src/USER-REAXC/reaxc_list.h +++ b/src/USER-REAXC/reaxc_list.h @@ -29,8 +29,8 @@ #include "reaxc_types.h" -int Make_List( int, int, int, reax_list*, MPI_Comm ); -void Delete_List( reax_list*, MPI_Comm ); +int Make_List( int, int, int, reax_list* ); +void Delete_List( reax_list* ); inline int Num_Entries(int,reax_list*); inline int Start_Index( int, reax_list* ); diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index b140b0cadf..74d8176522 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -51,18 +51,17 @@ void Tridiagonal_Solve( const double *a, const double *b, void Natural_Cubic_Spline( LAMMPS_NS::Error* error_ptr, const double *h, const double *f, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ) + cubic_spline_coef *coef, unsigned int n ) { int i; double *a, *b, *c, *d, *v; /* allocate space for the linear system */ - a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); + a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); /* build the linear system */ a[0] = a[1] = a[n-1] = 0; @@ -102,18 +101,17 @@ void Natural_Cubic_Spline( LAMMPS_NS::Error* error_ptr, const double *h, const d void Complete_Cubic_Spline( LAMMPS_NS::Error* error_ptr, const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ) + cubic_spline_coef *coef, unsigned int n ) { int i; double *a, *b, *c, *d, *v; /* allocate space for the linear system */ - a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); - v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a", comm ); + a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); /* build the linear system */ a[0] = 0; @@ -159,35 +157,33 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, double dr; double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb; double v0_vdw, v0_ele, vlast_vdw, vlast_ele; - MPI_Comm comm; /* initializations */ v0_vdw = 0; v0_ele = 0; vlast_vdw = 0; vlast_ele = 0; - comm = mpi_data->world; num_atom_types = system->reax_param.num_atom_types; dr = control->nonb_cut / control->tabulate; h = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h"); fh = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh"); fvdw = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw"); fCEvd = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd"); fele = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele"); fCEclmb = (double*) - smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb"); LR = (LR_lookup_table**) - scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table*), "lookup:LR", comm ); + scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table*), "lookup:LR"); for( i = 0; i < num_atom_types; ++i ) LR[i] = (LR_lookup_table*) - scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]", comm ); + scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]"); for( i = 0; i < MAX_ATOM_TYPES; ++i ) existing_types[i] = 0; @@ -207,22 +203,18 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, LR[i][j].dx = dr; LR[i][j].inv_dx = control->tabulate / control->nonb_cut; LR[i][j].y = (LR_data*) - smalloc(system->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y", comm ); + smalloc(system->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y"); LR[i][j].H = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H" , - comm ); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H"); LR[i][j].vdW = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW", - comm); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW"); LR[i][j].CEvd = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd", - comm); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd"); LR[i][j].ele = (cubic_spline_coef*) - smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele", - comm ); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele"); LR[i][j].CEclmb = (cubic_spline_coef*) smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef), - "lookup:LR[i,j].CEclmb", comm ); + "lookup:LR[i,j].CEclmb"); for( r = 1; r <= control->tabulate; ++r ) { LR_vdW_Coulomb( system, workspace, control, i, j, r * dr, &(LR[i][j].y[r]) ); @@ -247,23 +239,19 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, vlast_ele = fele[r-1]; Natural_Cubic_Spline( control->error_ptr, &h[1], &fh[1], - &(LR[i][j].H[1]), control->tabulate+1, comm ); + &(LR[i][j].H[1]), control->tabulate+1); Complete_Cubic_Spline( control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw, - &(LR[i][j].vdW[1]), control->tabulate+1, - comm ); + &(LR[i][j].vdW[1]), control->tabulate+1); Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEvd[1], - &(LR[i][j].CEvd[1]), control->tabulate+1, - comm ); + &(LR[i][j].CEvd[1]), control->tabulate+1); Complete_Cubic_Spline( control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele, - &(LR[i][j].ele[1]), control->tabulate+1, - comm ); + &(LR[i][j].ele[1]), control->tabulate+1); Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEclmb[1], - &(LR[i][j].CEclmb[1]), control->tabulate+1, - comm ); + &(LR[i][j].CEclmb[1]), control->tabulate+1); } else { LR[i][j].n = 0; } diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h index 9b1b14a34d..6d6aae2f8e 100644 --- a/src/USER-REAXC/reaxc_lookup.h +++ b/src/USER-REAXC/reaxc_lookup.h @@ -33,12 +33,10 @@ void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n); void Natural_Cubic_Spline( LAMMPS_NS::LAMMPS*, const double *h, const double *f, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ); + cubic_spline_coef *coef, unsigned int n ); void Complete_Cubic_Spline( LAMMPS_NS::LAMMPS*, const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ); + cubic_spline_coef *coef, unsigned int n ); int Init_Lookup_Tables( reax_system*, control_params*, storage*, mpi_datatypes*, char* ); diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index d273a417f8..8954e344df 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -121,8 +121,7 @@ void Reset_Workspace( reax_system *system, storage *workspace ) void Reset_Neighbor_Lists( reax_system *system, control_params *control, - storage *workspace, reax_list **lists, - MPI_Comm comm ) + storage *workspace, reax_list **lists ) { int i, total_bonds, Hindex, total_hbonds; reax_list *bonds, *hbonds; @@ -144,8 +143,8 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, workspace->realloc.bonds = 1; if (total_bonds >= bonds->num_intrs) { char errmsg[256]; - snprintf(errmsg, 256, "p%d: not enough space for bonds! total=%d allocated=%d\n", - system->my_rank, total_bonds, bonds->num_intrs); + snprintf(errmsg, 256, "Not enough space for bonds! total=%d allocated=%d\n", + total_bonds, bonds->num_intrs); control->error_ptr->one(FLERR, errmsg); } } @@ -170,8 +169,8 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, workspace->realloc.hbonds = 1; if (total_hbonds >= hbonds->num_intrs) { char errmsg[256]; - snprintf(errmsg, 256, "p%d: not enough space for hbonds! total=%d allocated=%d\n", - system->my_rank, total_hbonds, hbonds->num_intrs); + snprintf(errmsg, 256, "Not enough space for hbonds! total=%d allocated=%d\n", + total_hbonds, hbonds->num_intrs); control->error_ptr->one(FLERR, errmsg); } } @@ -180,7 +179,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, void Reset( reax_system *system, control_params *control, simulation_data *data, - storage *workspace, reax_list **lists, MPI_Comm comm ) + storage *workspace, reax_list **lists ) { Reset_Atoms( system, control ); @@ -188,6 +187,6 @@ void Reset( reax_system *system, control_params *control, simulation_data *data, Reset_Workspace( system, workspace ); - Reset_Neighbor_Lists( system, control, workspace, lists, comm ); + Reset_Neighbor_Lists( system, control, workspace, lists ); } diff --git a/src/USER-REAXC/reaxc_reset_tools.h b/src/USER-REAXC/reaxc_reset_tools.h index c2a90072d5..20d1ab6964 100644 --- a/src/USER-REAXC/reaxc_reset_tools.h +++ b/src/USER-REAXC/reaxc_reset_tools.h @@ -34,7 +34,7 @@ void Reset_Simulation_Data( simulation_data*, int ); void Reset_Timing( reax_timing* ); void Reset_Workspace( reax_system*, storage* ); void Reset_Neighbor_Lists( reax_system*, control_params*, storage*, - reax_list**, MPI_Comm ); + reax_list** ); void Reset( reax_system*, control_params*, simulation_data*, storage*, - reax_list**, MPI_Comm ); + reax_list** ); #endif diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index cd339af556..05ebc34c1b 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -56,7 +56,7 @@ int Tokenize( char* s, char*** tok ) /* safe malloc */ -void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name, MPI_Comm comm ) +void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name ) { void *ptr; char errmsg[256]; @@ -79,7 +79,7 @@ void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name, MPI_C /* safe calloc */ -void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name, MPI_Comm comm ) +void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name ) { void *ptr; char errmsg[256]; diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h index 257ff1813f..0465376dba 100644 --- a/src/USER-REAXC/reaxc_tool_box.h +++ b/src/USER-REAXC/reaxc_tool_box.h @@ -37,7 +37,7 @@ double Get_Time( ); int Tokenize( char*, char*** ); /* from lammps */ -void *smalloc( LAMMPS_NS::Error*, rc_bigint, const char*, MPI_Comm ); -void *scalloc( LAMMPS_NS::Error*, rc_bigint, rc_bigint, const char*, MPI_Comm ); +void *smalloc( LAMMPS_NS::Error*, rc_bigint, const char* ); +void *scalloc( LAMMPS_NS::Error*, rc_bigint, rc_bigint, const char* ); void sfree( LAMMPS_NS::Error*, void*, const char* ); #endif diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index 90f3d1e668..27bebb6327 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -29,8 +29,7 @@ #include "reaxc_list.h" #include "reaxc_tool_box.h" -int Reallocate_Output_Buffer( LAMMPS_NS::Error *error_ptr, output_controls *out_control, int req_space, - MPI_Comm comm ) +int Reallocate_Output_Buffer( LAMMPS_NS::Error *error_ptr, output_controls *out_control, int req_space ) { if (out_control->buffer_len > 0) free( out_control->buffer ); @@ -82,7 +81,7 @@ int Write_Header( reax_system *system, control_params *control, my_hdr_lines = num_hdr_lines * ( system->my_rank == MASTER_NODE ); buffer_req = my_hdr_lines * HEADER_LINE_LEN; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req ); /* only the master node writes into trajectory header */ if (system->my_rank == MASTER_NODE) { @@ -277,7 +276,7 @@ int Write_Init_Desc( reax_system *system, control_params * /*control*/, else buffer_req = system->n * INIT_DESC_LEN + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); out_control->line[0] = 0; out_control->buffer[0] = 0; @@ -366,7 +365,7 @@ int Write_Frame_Header( reax_system *system, control_params *control, my_frm_hdr_lines = num_frm_hdr_lines * ( me == MASTER_NODE ); buffer_req = my_frm_hdr_lines * HEADER_LINE_LEN; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req ); /* only the master node writes into trajectory header */ if (me == MASTER_NODE) { @@ -499,7 +498,7 @@ int Write_Atoms( reax_system *system, control_params * /*control*/, else buffer_req = system->n * line_len + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); /* fill in buffer */ out_control->line[0] = 0; @@ -589,7 +588,7 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds, else buffer_req = my_bonds * line_len + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); /* fill in the buffer */ out_control->line[0] = 0; @@ -689,7 +688,7 @@ int Write_Angles( reax_system *system, control_params *control, else buffer_req = my_angles * line_len + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); /* fill in the buffer */ my_angles = 0; diff --git a/src/USER-REAXC/reaxc_valence_angles.h b/src/USER-REAXC/reaxc_valence_angles.h index 51eac5a95e..31936ba190 100644 --- a/src/USER-REAXC/reaxc_valence_angles.h +++ b/src/USER-REAXC/reaxc_valence_angles.h @@ -30,7 +30,7 @@ #include "reaxc_types.h" void Valence_Angles( reax_system*, control_params*, simulation_data*, - storage*, reax_list**, output_controls*); + storage*, reax_list**, output_controls* ); void Calculate_Theta( rvec, double, rvec, double, double*, double* );