1 // clang-format off
2 /* ----------------------------------------------------------------------
3 LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
4 https://www.lammps.org/, Sandia National Laboratories
5 Steve Plimpton, sjplimp@sandia.gov
6
7 Copyright (2003) Sandia Corporation. Under the terms of Contract
8 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
9 certain rights in this software. This software is distributed under
10 the GNU General Public License.
11
12 See the README file in the top-level LAMMPS directory.
13 ------------------------------------------------------------------------- */
14
15 /* ----------------------------------------------------------------------
16 Contributing author: Steven Vandenbrande
17 ------------------------------------------------------------------------- */
18
19 #include "angle_cross.h"
20
21 #include <cmath>
22 #include "atom.h"
23 #include "neighbor.h"
24 #include "domain.h"
25 #include "comm.h"
26 #include "force.h"
27 #include "math_const.h"
28 #include "memory.h"
29 #include "error.h"
30
31
32 using namespace LAMMPS_NS;
33 using namespace MathConst;
34
35 #define SMALL 0.001
36
37 /* ---------------------------------------------------------------------- */
38
AngleCross(LAMMPS * lmp)39 AngleCross::AngleCross(LAMMPS *lmp) : Angle(lmp) {}
40
41 /* ---------------------------------------------------------------------- */
42
~AngleCross()43 AngleCross::~AngleCross()
44 {
45 if (copymode) return;
46
47 if (allocated) {
48 memory->destroy(setflag);
49 memory->destroy(kss);
50 memory->destroy(kbs0);
51 memory->destroy(kbs1);
52 memory->destroy(r00);
53 memory->destroy(r01);
54 memory->destroy(theta0);
55 }
56 }
57
58 /* ---------------------------------------------------------------------- */
59
compute(int eflag,int vflag)60 void AngleCross::compute(int eflag, int vflag)
61 {
62 int i1,i2,i3,n,type;
63 double delx1,dely1,delz1,delx2,dely2,delz2;
64 double eangle,f1[3],f3[3];
65 double dtheta;
66 double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22;
67 double rsq1,rsq2,r1,r2,c,s,b1,b2;
68 double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
69
70 eangle = 0.0;
71 ev_init(eflag,vflag);
72
73 double **x = atom->x;
74 double **f = atom->f;
75 int **anglelist = neighbor->anglelist;
76 int nanglelist = neighbor->nanglelist;
77 int nlocal = atom->nlocal;
78 int newton_bond = force->newton_bond;
79
80 for (n = 0; n < nanglelist; n++) {
81 i1 = anglelist[n][0];
82 i2 = anglelist[n][1];
83 i3 = anglelist[n][2];
84 type = anglelist[n][3];
85
86 // 1st bond
87
88 delx1 = x[i1][0] - x[i2][0];
89 dely1 = x[i1][1] - x[i2][1];
90 delz1 = x[i1][2] - x[i2][2];
91
92 rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
93 r1 = sqrt(rsq1);
94
95 // 2nd bond
96
97 delx2 = x[i3][0] - x[i2][0];
98 dely2 = x[i3][1] - x[i2][1];
99 delz2 = x[i3][2] - x[i2][2];
100
101 rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
102 r2 = sqrt(rsq2);
103
104 // angle (cos and sin)
105
106 c = delx1*delx2 + dely1*dely2 + delz1*delz2;
107 c /= r1*r2;
108
109 if (c > 1.0) c = 1.0;
110 if (c < -1.0) c = -1.0;
111
112 s = sqrt(1.0 - c*c);
113 if (s < SMALL) s = SMALL;
114 s = 1.0/s;
115
116 // force & energy for bond-bond term
117 dr1 = r1 - r00[type];
118 dr2 = r2 - r01[type];
119 tk1 = kss[type] * dr1;
120 tk2 = kss[type] * dr2;
121
122 f1[0] = -delx1*tk2/r1;
123 f1[1] = -dely1*tk2/r1;
124 f1[2] = -delz1*tk2/r1;
125
126 f3[0] = -delx2*tk1/r2;
127 f3[1] = -dely2*tk1/r2;
128 f3[2] = -delz2*tk1/r2;
129
130 if (eflag) eangle = kss[type]*dr1*dr2;
131
132 // force & energy for bond-angle term
133 dtheta = acos(c) - theta0[type];
134
135 aa1 = s * dr1 * kbs0[type];
136 aa2 = s * dr2 * kbs1[type];
137
138 aa11 = aa1 * c / rsq1;
139 aa12 = -aa1 / (r1 * r2);
140 aa21 = aa2 * c / rsq1;
141 aa22 = -aa2 / (r1 * r2);
142
143 vx11 = (aa11 * delx1) + (aa12 * delx2);
144 vx12 = (aa21 * delx1) + (aa22 * delx2);
145 vy11 = (aa11 * dely1) + (aa12 * dely2);
146 vy12 = (aa21 * dely1) + (aa22 * dely2);
147 vz11 = (aa11 * delz1) + (aa12 * delz2);
148 vz12 = (aa21 * delz1) + (aa22 * delz2);
149
150 aa11 = aa1 * c / rsq2;
151 aa21 = aa2 * c / rsq2;
152
153 vx21 = (aa11 * delx2) + (aa12 * delx1);
154 vx22 = (aa21 * delx2) + (aa22 * delx1);
155 vy21 = (aa11 * dely2) + (aa12 * dely1);
156 vy22 = (aa21 * dely2) + (aa22 * dely1);
157 vz21 = (aa11 * delz2) + (aa12 * delz1);
158 vz22 = (aa21 * delz2) + (aa22 * delz1);
159
160 b1 = kbs0[type] * dtheta / r1;
161 b2 = kbs1[type] * dtheta / r2;
162
163 f1[0] -= vx11 + b1*delx1 + vx12;
164 f1[1] -= vy11 + b1*dely1 + vy12;
165 f1[2] -= vz11 + b1*delz1 + vz12;
166
167 f3[0] -= vx21 + b2*delx2 + vx22;
168 f3[1] -= vy21 + b2*dely2 + vy22;
169 f3[2] -= vz21 + b2*delz2 + vz22;
170
171 if (eflag) eangle += kbs0[type]*dr1*dtheta + kbs1[type]*dr2*dtheta;
172
173 // apply force to each of 3 atoms
174
175 if (newton_bond || i1 < nlocal) {
176 f[i1][0] += f1[0];
177 f[i1][1] += f1[1];
178 f[i1][2] += f1[2];
179 }
180
181 if (newton_bond || i2 < nlocal) {
182 f[i2][0] -= f1[0] + f3[0];
183 f[i2][1] -= f1[1] + f3[1];
184 f[i2][2] -= f1[2] + f3[2];
185 }
186
187 if (newton_bond || i3 < nlocal) {
188 f[i3][0] += f3[0];
189 f[i3][1] += f3[1];
190 f[i3][2] += f3[2];
191 }
192
193 if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
194 delx1,dely1,delz1,delx2,dely2,delz2);
195 }
196 }
197
198 /* ---------------------------------------------------------------------- */
199
allocate()200 void AngleCross::allocate()
201 {
202 allocated = 1;
203 int n = atom->nangletypes;
204
205 memory->create(kss,n+1,"angle:kss");
206 memory->create(kbs0,n+1,"angle:kbs0");
207 memory->create(kbs1,n+1,"angle:kbs1");
208 memory->create(r00,n+1,"angle:r00");
209 memory->create(r01,n+1,"angle:r01");
210 memory->create(theta0,n+1,"angle:theta0");
211 memory->create(setflag,n+1,"angle:setflag");
212
213 for (int i = 1; i <= n; i++)
214 setflag[i] = 0;
215 }
216
217 /* ----------------------------------------------------------------------
218 set coeffs
219 ------------------------------------------------------------------------- */
220
coeff(int narg,char ** arg)221 void AngleCross::coeff(int narg, char **arg)
222 {
223 if (narg != 7) error->all(FLERR,"Incorrect args for angle coefficients");
224 if (!allocated) allocate();
225
226 int ilo,ihi;
227 utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
228
229 int count = 0;
230
231 double kss_one = utils::numeric(FLERR,arg[1],false,lmp);
232 double kbs0_one = utils::numeric(FLERR,arg[2],false,lmp);
233 double kbs1_one = utils::numeric(FLERR,arg[3],false,lmp);
234 double r0_one = utils::numeric(FLERR,arg[4],false,lmp);
235 double r1_one = utils::numeric(FLERR,arg[5],false,lmp);
236 double theta0_one = utils::numeric(FLERR,arg[6],false,lmp);
237
238 for (int i = ilo; i <= ihi; i++) {
239 kss[i] = kss_one;
240 kbs0[i] = kbs0_one;
241 kbs1[i] = kbs1_one;
242 r00[i] = r0_one;
243 r01[i] = r1_one;
244 // Convert theta0 from degrees to radians
245 theta0[i] = theta0_one*MY_PI/180.0;
246 setflag[i] = 1;
247 count++;
248 }
249
250 if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
251 }
252
253 /* ---------------------------------------------------------------------- */
254
equilibrium_angle(int i)255 double AngleCross::equilibrium_angle(int i)
256 {
257 return theta0[i];
258 }
259
260 /* ----------------------------------------------------------------------
261 proc 0 writes out coeffs to restart file
262 ------------------------------------------------------------------------- */
263
write_restart(FILE * fp)264 void AngleCross::write_restart(FILE *fp)
265 {
266 fwrite(&kss[1],sizeof(double),atom->nangletypes,fp);
267 fwrite(&kbs0[1],sizeof(double),atom->nangletypes,fp);
268 fwrite(&kbs1[1],sizeof(double),atom->nangletypes,fp);
269 fwrite(&r00[1],sizeof(double),atom->nangletypes,fp);
270 fwrite(&r01[1],sizeof(double),atom->nangletypes,fp);
271 fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
272 }
273
274 /* ----------------------------------------------------------------------
275 proc 0 reads coeffs from restart file, bcasts them
276 ------------------------------------------------------------------------- */
277
read_restart(FILE * fp)278 void AngleCross::read_restart(FILE *fp)
279 {
280 allocate();
281
282 if (comm->me == 0) {
283 utils::sfread(FLERR,&kss[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
284 utils::sfread(FLERR,&kbs0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
285 utils::sfread(FLERR,&kbs1[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
286 utils::sfread(FLERR,&r00[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
287 utils::sfread(FLERR,&r01[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
288 utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
289 }
290
291 MPI_Bcast(&kss[1],atom->nangletypes,MPI_DOUBLE,0,world);
292 MPI_Bcast(&kbs0[1],atom->nangletypes,MPI_DOUBLE,0,world);
293 MPI_Bcast(&kbs1[1],atom->nangletypes,MPI_DOUBLE,0,world);
294 MPI_Bcast(&r00[1],atom->nangletypes,MPI_DOUBLE,0,world);
295 MPI_Bcast(&r01[1],atom->nangletypes,MPI_DOUBLE,0,world);
296 MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
297
298 for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
299 }
300
301 /* ----------------------------------------------------------------------
302 proc 0 writes to data file
303 ------------------------------------------------------------------------- */
304
write_data(FILE * fp)305 void AngleCross::write_data(FILE *fp)
306 {
307 for (int i = 1; i <= atom->nangletypes; i++)
308 fprintf(fp,"%d %g %g %g %g %g %g\n",
309 i,kss[i],kbs0[i],kbs1[i],r00[i],r01[i],theta0[i]/MY_PI*180.0);
310 }
311
312 /* ---------------------------------------------------------------------- */
313
single(int type,int i1,int i2,int i3)314 double AngleCross::single(int type, int i1, int i2, int i3)
315 {
316 double **x = atom->x;
317
318 double delx1 = x[i1][0] - x[i2][0];
319 double dely1 = x[i1][1] - x[i2][1];
320 double delz1 = x[i1][2] - x[i2][2];
321 domain->minimum_image(delx1,dely1,delz1);
322 double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
323
324 double delx2 = x[i3][0] - x[i2][0];
325 double dely2 = x[i3][1] - x[i2][1];
326 double delz2 = x[i3][2] - x[i2][2];
327 domain->minimum_image(delx2,dely2,delz2);
328 double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
329
330 double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
331 c /= r1*r2;
332 if (c > 1.0) c = 1.0;
333 if (c < -1.0) c = -1.0;
334
335 double s = sqrt(1.0 - c*c);
336 if (s < SMALL) s = SMALL;
337 s = 1.0/s;
338
339 double dtheta = acos(c) - theta0[type];
340 double dr1 = r1 - r00[type];
341 double dr2 = r2 - r01[type];
342 double energy = kss[type]*dr1*dr2+kbs0[type]*dr1*dtheta + kbs1[type]*dr2*dtheta;
343 return energy;
344 }
345