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 #include "angle_cosine.h"
16
17 #include <cmath>
18 #include "atom.h"
19 #include "neighbor.h"
20 #include "domain.h"
21 #include "comm.h"
22 #include "force.h"
23 #include "math_const.h"
24 #include "memory.h"
25 #include "error.h"
26
27
28 using namespace LAMMPS_NS;
29 using namespace MathConst;
30
31 #define SMALL 0.001
32
33 /* ---------------------------------------------------------------------- */
34
AngleCosine(LAMMPS * lmp)35 AngleCosine::AngleCosine(LAMMPS *lmp) : Angle(lmp) {}
36
37 /* ---------------------------------------------------------------------- */
38
~AngleCosine()39 AngleCosine::~AngleCosine()
40 {
41 if (allocated && !copymode) {
42 memory->destroy(setflag);
43 memory->destroy(k);
44 }
45 }
46
47 /* ---------------------------------------------------------------------- */
48
compute(int eflag,int vflag)49 void AngleCosine::compute(int eflag, int vflag)
50 {
51 int i1,i2,i3,n,type;
52 double delx1,dely1,delz1,delx2,dely2,delz2;
53 double eangle,f1[3],f3[3];
54 double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
55
56 eangle = 0.0;
57 ev_init(eflag,vflag);
58
59 double **x = atom->x;
60 double **f = atom->f;
61 int **anglelist = neighbor->anglelist;
62 int nanglelist = neighbor->nanglelist;
63 int nlocal = atom->nlocal;
64 int newton_bond = force->newton_bond;
65
66 for (n = 0; n < nanglelist; n++) {
67 i1 = anglelist[n][0];
68 i2 = anglelist[n][1];
69 i3 = anglelist[n][2];
70 type = anglelist[n][3];
71
72 // 1st bond
73
74 delx1 = x[i1][0] - x[i2][0];
75 dely1 = x[i1][1] - x[i2][1];
76 delz1 = x[i1][2] - x[i2][2];
77
78 rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
79 r1 = sqrt(rsq1);
80
81 // 2nd bond
82
83 delx2 = x[i3][0] - x[i2][0];
84 dely2 = x[i3][1] - x[i2][1];
85 delz2 = x[i3][2] - x[i2][2];
86
87 rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
88 r2 = sqrt(rsq2);
89
90 // c = cosine of angle
91
92 c = delx1*delx2 + dely1*dely2 + delz1*delz2;
93 c /= r1*r2;
94 if (c > 1.0) c = 1.0;
95 if (c < -1.0) c = -1.0;
96
97 // force & energy
98
99 if (eflag) eangle = k[type]*(1.0+c);
100
101 a = k[type];
102 a11 = a*c / rsq1;
103 a12 = -a / (r1*r2);
104 a22 = a*c / rsq2;
105
106 f1[0] = a11*delx1 + a12*delx2;
107 f1[1] = a11*dely1 + a12*dely2;
108 f1[2] = a11*delz1 + a12*delz2;
109 f3[0] = a22*delx2 + a12*delx1;
110 f3[1] = a22*dely2 + a12*dely1;
111 f3[2] = a22*delz2 + a12*delz1;
112
113 // apply force to each of 3 atoms
114
115 if (newton_bond || i1 < nlocal) {
116 f[i1][0] += f1[0];
117 f[i1][1] += f1[1];
118 f[i1][2] += f1[2];
119 }
120
121 if (newton_bond || i2 < nlocal) {
122 f[i2][0] -= f1[0] + f3[0];
123 f[i2][1] -= f1[1] + f3[1];
124 f[i2][2] -= f1[2] + f3[2];
125 }
126
127 if (newton_bond || i3 < nlocal) {
128 f[i3][0] += f3[0];
129 f[i3][1] += f3[1];
130 f[i3][2] += f3[2];
131 }
132
133 if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
134 delx1,dely1,delz1,delx2,dely2,delz2);
135 }
136 }
137
138 /* ---------------------------------------------------------------------- */
139
allocate()140 void AngleCosine::allocate()
141 {
142 allocated = 1;
143 int n = atom->nangletypes;
144
145 memory->create(k,n+1,"angle:k");
146 memory->create(setflag,n+1,"angle:setflag");
147 for (int i = 1; i <= n; i++) setflag[i] = 0;
148 }
149
150 /* ----------------------------------------------------------------------
151 set coeffs for one type
152 ------------------------------------------------------------------------- */
153
coeff(int narg,char ** arg)154 void AngleCosine::coeff(int narg, char **arg)
155 {
156 if (narg != 2) error->all(FLERR,"Incorrect args for angle coefficients");
157 if (!allocated) allocate();
158
159 int ilo,ihi;
160 utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
161
162 double k_one = utils::numeric(FLERR,arg[1],false,lmp);
163
164 int count = 0;
165 for (int i = ilo; i <= ihi; i++) {
166 k[i] = k_one;
167 setflag[i] = 1;
168 count++;
169 }
170
171 if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
172 }
173
174 /* ---------------------------------------------------------------------- */
175
equilibrium_angle(int)176 double AngleCosine::equilibrium_angle(int /*i*/)
177 {
178 return MY_PI;
179 }
180
181 /* ----------------------------------------------------------------------
182 proc 0 writes out coeffs to restart file
183 ------------------------------------------------------------------------- */
184
write_restart(FILE * fp)185 void AngleCosine::write_restart(FILE *fp)
186 {
187 fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
188 }
189
190 /* ----------------------------------------------------------------------
191 proc 0 reads coeffs from restart file, bcasts them
192 ------------------------------------------------------------------------- */
193
read_restart(FILE * fp)194 void AngleCosine::read_restart(FILE *fp)
195 {
196 allocate();
197
198 if (comm->me == 0) utils::sfread(FLERR,&k[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
199 MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
200
201 for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
202 }
203
204 /* ----------------------------------------------------------------------
205 proc 0 writes to data file
206 ------------------------------------------------------------------------- */
207
write_data(FILE * fp)208 void AngleCosine::write_data(FILE *fp)
209 {
210 for (int i = 1; i <= atom->nangletypes; i++)
211 fprintf(fp,"%d %g\n",i,k[i]);
212 }
213
214 /* ---------------------------------------------------------------------- */
215
single(int type,int i1,int i2,int i3)216 double AngleCosine::single(int type, int i1, int i2, int i3)
217 {
218 double **x = atom->x;
219
220 double delx1 = x[i1][0] - x[i2][0];
221 double dely1 = x[i1][1] - x[i2][1];
222 double delz1 = x[i1][2] - x[i2][2];
223 domain->minimum_image(delx1,dely1,delz1);
224 double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
225
226 double delx2 = x[i3][0] - x[i2][0];
227 double dely2 = x[i3][1] - x[i2][1];
228 double delz2 = x[i3][2] - x[i2][2];
229 domain->minimum_image(delx2,dely2,delz2);
230 double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
231
232 double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
233 c /= r1*r2;
234 if (c > 1.0) c = 1.0;
235 if (c < -1.0) c = -1.0;
236
237 return k[type]*(1.0+c);
238 }
239