lammps-sys 0.6.0

Generates bindings to LAMMPS' C interface (with optional builds from source)
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244

/*----------------------------------------------------------------------
  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_multi_body.h"
#include <cmath>
#include <cstring>
#include "pair.h"
#include "reaxc_defs.h"
#include "reaxc_list.h"

void Atom_Energy( reax_system *system, control_params *control,
                  simulation_data *data, storage *workspace, reax_list **lists,
                  output_controls * /*out_control*/ )
{
  int i, j, pj, type_i, type_j;
  double Delta_lpcorr, dfvl;
  double e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi;
  double e_lph, Di, vov3, deahu2dbo, deahu2dsbo;
  double e_ov, CEover1, CEover2, CEover3, CEover4;
  double exp_ovun1, exp_ovun2, sum_ovun1, sum_ovun2;
  double exp_ovun2n, exp_ovun6, exp_ovun8;
  double inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
  double e_un, CEunder1, CEunder2, CEunder3, CEunder4;
  double p_lp2, p_lp3;
  double p_ovun2, p_ovun3, p_ovun4, p_ovun5, p_ovun6, p_ovun7, p_ovun8;
  double eng_tmp;
  int numbonds;

  single_body_parameters *sbp_i;
  two_body_parameters *twbp;
  bond_data *pbond;
  bond_order_data *bo_ij;
  reax_list *bonds = (*lists) + BONDS;

  /* Initialize parameters */
  p_lp3 = system->reax_param.gp.l[5];
  p_ovun3 = system->reax_param.gp.l[32];
  p_ovun4 = system->reax_param.gp.l[31];
  p_ovun6 = system->reax_param.gp.l[6];
  p_ovun7 = system->reax_param.gp.l[8];
  p_ovun8 = system->reax_param.gp.l[9];

  for( i = 0; i < system->n; ++i ) {
    /* set the parameter pointer */
    type_i = system->my_atoms[i].type;
    if (type_i < 0) continue;
    sbp_i = &(system->reax_param.sbp[ type_i ]);

    /* lone-pair Energy */
    p_lp2 = sbp_i->p_lp2;
    expvd2 = exp( -75 * workspace->Delta_lp[i] );
    inv_expvd2 = 1. / (1. + expvd2 );

    numbonds = 0;
    e_lp = 0.0;
    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
      numbonds ++;

    /* calculate the energy */
    if (numbonds > 0 || control->enobondsflag)
      data->my_en.e_lp += e_lp =
        p_lp2 * workspace->Delta_lp[i] * inv_expvd2;

    dElp = p_lp2 * inv_expvd2 +
      75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
    CElp = dElp * workspace->dDelta_lp[i];

    if (numbonds > 0 || control->enobondsflag)
      workspace->CdDelta[i] += CElp;  // lp - 1st term

    /* tally into per-atom energy */
    if (system->pair_ptr->evflag)
      system->pair_ptr->ev_tally(i,i,system->n,1,e_lp,0.0,0.0,0.0,0.0,0.0);

    /* correction for C2 */
    if (p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C"))
      for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
        j = bonds->select.bond_list[pj].nbr;
        type_j = system->my_atoms[j].type;
        if (type_j < 0) continue;

        if (!strcmp( system->reax_param.sbp[type_j].name, "C" )) {
          twbp = &( system->reax_param.tbp[type_i][type_j]);
          bo_ij = &( bonds->select.bond_list[pj].bo_data );
          Di = workspace->Delta[i];
          vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.);

          if (vov3 > 3.) {
            data->my_en.e_lp += e_lph = p_lp3 * SQR(vov3-3.0);

            deahu2dbo = 2.*p_lp3*(vov3 - 3.);
            deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.));

            bo_ij->Cdbo += deahu2dbo;
            workspace->CdDelta[i] += deahu2dsbo;

            /* tally into per-atom energy */
            if (system->pair_ptr->evflag)
              system->pair_ptr->ev_tally(i,j,system->n,1,e_lph,0.0,0.0,0.0,0.0,0.0);

          }
        }
      }
  }


  for( i = 0; i < system->n; ++i ) {
    type_i = system->my_atoms[i].type;
    if (type_i < 0) continue;
    sbp_i = &(system->reax_param.sbp[ type_i ]);

    /* over-coordination energy */
    if (sbp_i->mass > 21.0)
      dfvl = 0.0;
    else dfvl = 1.0; // only for 1st-row elements

    p_ovun2 = sbp_i->p_ovun2;
    sum_ovun1 = sum_ovun2 = 0;
    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
        j = bonds->select.bond_list[pj].nbr;
        type_j = system->my_atoms[j].type;
        if (type_j < 0) continue;
        bo_ij = &(bonds->select.bond_list[pj].bo_data);
        twbp = &(system->reax_param.tbp[ type_i ][ type_j ]);

        sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
        sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])*
          ( bo_ij->BO_pi + bo_ij->BO_pi2 );

      }

    exp_ovun1 = p_ovun3 * exp( p_ovun4 * sum_ovun2 );
    inv_exp_ovun1 = 1.0 / (1 + exp_ovun1);
    Delta_lpcorr  = workspace->Delta[i] -
      (dfvl * workspace->Delta_lp_temp[i]) * inv_exp_ovun1;

    exp_ovun2 = exp( p_ovun2 * Delta_lpcorr );
    inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2);

    DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8);
    CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2;

    data->my_en.e_ov += e_ov = sum_ovun1 * CEover1;

    CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 *
      (1.0 - Delta_lpcorr * ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ));

    CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1 );

    CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) *
      p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1);


    /* under-coordination potential */
    p_ovun2 = sbp_i->p_ovun2;
    p_ovun5 = sbp_i->p_ovun5;

    exp_ovun2n = 1.0 / exp_ovun2;
    exp_ovun6 = exp( p_ovun6 * Delta_lpcorr );
    exp_ovun8 = p_ovun7 * exp(p_ovun8 * sum_ovun2);
    inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n);
    inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);

    numbonds = 0;
    e_un = 0.0;
    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
      numbonds ++;

    if (numbonds > 0 || control->enobondsflag)
      data->my_en.e_un += e_un =
        -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;

    CEunder1 = inv_exp_ovun2n *
      ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 +
        p_ovun2 * e_un * exp_ovun2n );
    CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8;
    CEunder3 = CEunder1 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1);
    CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) *
      p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2;

    /* tally into per-atom energy */
    if (system->pair_ptr->evflag) {
      eng_tmp = e_ov;
      if (numbonds > 0 || control->enobondsflag)
        eng_tmp += e_un;
      system->pair_ptr->ev_tally(i,i,system->n,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
    }

    /* forces */
    workspace->CdDelta[i] += CEover3;   // OvCoor - 2nd term
    if (numbonds > 0 || control->enobondsflag)
      workspace->CdDelta[i] += CEunder3;  // UnCoor - 1st term

    for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
      pbond = &(bonds->select.bond_list[pj]);
      j = pbond->nbr;
      bo_ij = &(pbond->bo_data);
      twbp  = &(system->reax_param.tbp[ system->my_atoms[i].type ]
                [system->my_atoms[pbond->nbr].type]);


      bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s;// OvCoor-1st
      workspace->CdDelta[j] += CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
        (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a
      bo_ij->Cdbopi += CEover4 *
        (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
      bo_ij->Cdbopi2 += CEover4 *
        (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);  // OvCoor-3b


      workspace->CdDelta[j] += CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
        (bo_ij->BO_pi + bo_ij->BO_pi2);   // UnCoor - 2a
      bo_ij->Cdbopi += CEunder4 *
        (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);  // UnCoor-2b
      bo_ij->Cdbopi2 += CEunder4 *
        (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);  // UnCoor-2b

    }

  }
}