lammps-sys 0.6.0

/*----------------------------------------------------------------------
  PuReMD - Purdue ReaxFF Molecular Dynamics Program

  Copyright (2010) Purdue University
  Hasan Metin Aktulga, hmaktulga@lbl.gov
  Joseph Fogarty, jcfogart@mail.usf.edu
  Sagar Pandit, pandit@usf.edu
  Ananth Y Grama, ayg@cs.purdue.edu

  Please cite the related publication:
  H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
  "Parallel Reactive Molecular Dynamics: Numerical Methods and
  Algorithmic Techniques", Parallel Computing, in press.

  This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 2 of
  the License, or (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  See the GNU General Public License for more details:
  <http://www.gnu.org/licenses/>.
  ----------------------------------------------------------------------*/

#include "reaxc_reset_tools.h"
#include <cstring>
#include "reaxc_defs.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"

#include "error.h"


void Reset_Atoms( reax_system* system, control_params *control )
{
  int i;
  reax_atom *atom;

  system->numH = 0;
  if (control->hbond_cut > 0)
    for( i = 0; i < system->n; ++i ) {
      atom = &(system->my_atoms[i]);
      if (atom->type < 0) continue;
      if (system->reax_param.sbp[ atom->type ].p_hbond == 1)
        atom->Hindex = system->numH++;
      else atom->Hindex = -1;
    }
}


void Reset_Energies( energy_data *en )
{
  en->e_bond = 0;
  en->e_ov = 0;
  en->e_un = 0;
  en->e_lp = 0;
  en->e_ang = 0;
  en->e_pen = 0;
  en->e_coa = 0;
  en->e_hb = 0;
  en->e_tor = 0;
  en->e_con = 0;
  en->e_vdW = 0;
  en->e_ele = 0;
  en->e_pol = 0;

  en->e_pot = 0;
  en->e_kin = 0;
  en->e_tot = 0;
}


void Reset_Temperatures( simulation_data *data )
{
  data->therm.T = 0;
}


void Reset_Pressures( simulation_data *data )
{
  data->flex_bar.P_scalar = 0;
  rtensor_MakeZero( data->flex_bar.P );

  data->iso_bar.P = 0;
  rvec_MakeZero( data->int_press );
  rvec_MakeZero( data->my_ext_press );
  rvec_MakeZero( data->ext_press );
}


void Reset_Simulation_Data( simulation_data* data, int /*virial*/ )
{
  Reset_Energies( &data->my_en );
  Reset_Energies( &data->sys_en );
  Reset_Temperatures( data );
  Reset_Pressures( data );
}


void Reset_Timing( reax_timing *rt )
{
  rt->total = Get_Time();
  rt->comm = 0;
  rt->nbrs = 0;
  rt->init_forces = 0;
  rt->bonded = 0;
  rt->nonb = 0;
  rt->qEq = 0;
  rt->s_matvecs = 0;
  rt->t_matvecs = 0;
}

void Reset_Workspace( reax_system *system, storage *workspace )
{
  memset( workspace->total_bond_order, 0, system->total_cap * sizeof( double ) );
  memset( workspace->dDeltap_self, 0, system->total_cap * sizeof( rvec ) );
  memset( workspace->CdDelta, 0, system->total_cap * sizeof( double ) );
  memset( workspace->f, 0, system->total_cap * sizeof( rvec ) );

}


void Reset_Neighbor_Lists( reax_system *system, control_params *control,
                           storage *workspace, reax_list **lists )
{
  int i, total_bonds, Hindex, total_hbonds;
  reax_list *bonds, *hbonds;

  /* bonds list */
  if (system->N > 0) {
    bonds = (*lists) + BONDS;
    total_bonds = 0;

    /* reset start-end indexes */
    for( i = 0; i < system->N; ++i ) {
      Set_Start_Index( i, total_bonds, bonds );
      Set_End_Index( i, total_bonds, bonds );
      total_bonds += system->my_atoms[i].num_bonds;
    }

    /* is reallocation needed? */
    if (total_bonds >= bonds->num_intrs * DANGER_ZONE) {
      workspace->realloc.bonds = 1;
      if (total_bonds >= bonds->num_intrs) {
        char errmsg[256];
        snprintf(errmsg, 256, "Not enough space for bonds! total=%d allocated=%d\n",
                total_bonds, bonds->num_intrs);
        control->error_ptr->one(FLERR, errmsg);
      }
    }
  }

  if (control->hbond_cut > 0 && system->numH > 0) {
    hbonds = (*lists) + HBONDS;
    total_hbonds = 0;

    /* reset start-end indexes */
    for( i = 0; i < system->n; ++i ) {
      Hindex = system->my_atoms[i].Hindex;
      if (Hindex > -1) {
        Set_Start_Index( Hindex, total_hbonds, hbonds );
        Set_End_Index( Hindex, total_hbonds, hbonds );
        total_hbonds += system->my_atoms[i].num_hbonds;
      }
    }

    /* is reallocation needed? */
    if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) {
      workspace->realloc.hbonds = 1;
      if (total_hbonds >= hbonds->num_intrs) {
        char errmsg[256];
        snprintf(errmsg, 256, "Not enough space for hbonds! total=%d allocated=%d\n",
                total_hbonds, hbonds->num_intrs);
        control->error_ptr->one(FLERR, errmsg);
      }
    }
  }
}


void Reset( reax_system *system, control_params *control, simulation_data *data,
            storage *workspace, reax_list **lists )
{
  Reset_Atoms( system, control );

  Reset_Simulation_Data( data, control->virial );

  Reset_Workspace( system, workspace );

  Reset_Neighbor_Lists( system, control, workspace, lists );

}