1 /* ----------------------------------------------------------------------
2    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
3    https://www.lammps.org/, Sandia National Laboratories
4    Steve Plimpton, sjplimp@sandia.gov
5 
6    Copyright (2003) Sandia Corporation.  Under the terms of Contract
7    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
8    certain rights in this software.  This software is distributed under
9    the GNU General Public License.
10 
11    See the README file in the top-level LAMMPS directory.
12 ------------------------------------------------------------------------- */
13 
14 #include "angle_hybrid.h"
15 
16 #include "atom.h"
17 #include "comm.h"
18 #include "error.h"
19 #include "force.h"
20 #include "memory.h"
21 #include "neighbor.h"
22 
23 #include <cctype>
24 #include <cstring>
25 
26 using namespace LAMMPS_NS;
27 
28 #define EXTRA 1000
29 
30 /* ---------------------------------------------------------------------- */
31 
AngleHybrid(LAMMPS * lmp)32 AngleHybrid::AngleHybrid(LAMMPS *lmp) : Angle(lmp)
33 {
34   writedata = 0;
35   nstyles = 0;
36   nanglelist = nullptr;
37   maxangle = nullptr;
38   anglelist = nullptr;
39 }
40 
41 /* ---------------------------------------------------------------------- */
42 
~AngleHybrid()43 AngleHybrid::~AngleHybrid()
44 {
45   if (nstyles) {
46     for (int i = 0; i < nstyles; i++) delete styles[i];
47     delete[] styles;
48     for (int i = 0; i < nstyles; i++) delete[] keywords[i];
49     delete[] keywords;
50   }
51 
52   if (allocated) {
53     memory->destroy(setflag);
54     memory->destroy(map);
55     delete[] nanglelist;
56     delete[] maxangle;
57     for (int i = 0; i < nstyles; i++) memory->destroy(anglelist[i]);
58     delete[] anglelist;
59   }
60 }
61 
62 /* ---------------------------------------------------------------------- */
63 
compute(int eflag,int vflag)64 void AngleHybrid::compute(int eflag, int vflag)
65 {
66   int i, j, m, n;
67 
68   // save ptrs to original anglelist
69 
70   int nanglelist_orig = neighbor->nanglelist;
71   int **anglelist_orig = neighbor->anglelist;
72 
73   // if this is re-neighbor step, create sub-style anglelists
74   // nanglelist[] = length of each sub-style list
75   // realloc sub-style anglelist if necessary
76   // load sub-style anglelist with 4 values from original anglelist
77 
78   if (neighbor->ago == 0) {
79     for (m = 0; m < nstyles; m++) nanglelist[m] = 0;
80     for (i = 0; i < nanglelist_orig; i++) {
81       m = map[anglelist_orig[i][3]];
82       if (m >= 0) nanglelist[m]++;
83     }
84     for (m = 0; m < nstyles; m++) {
85       if (nanglelist[m] > maxangle[m]) {
86         memory->destroy(anglelist[m]);
87         maxangle[m] = nanglelist[m] + EXTRA;
88         memory->create(anglelist[m], maxangle[m], 4, "angle_hybrid:anglelist");
89       }
90       nanglelist[m] = 0;
91     }
92     for (i = 0; i < nanglelist_orig; i++) {
93       m = map[anglelist_orig[i][3]];
94       if (m < 0) continue;
95       n = nanglelist[m];
96       anglelist[m][n][0] = anglelist_orig[i][0];
97       anglelist[m][n][1] = anglelist_orig[i][1];
98       anglelist[m][n][2] = anglelist_orig[i][2];
99       anglelist[m][n][3] = anglelist_orig[i][3];
100       nanglelist[m]++;
101     }
102   }
103 
104   // call each sub-style's compute function
105   // set neighbor->anglelist to sub-style anglelist before call
106   // accumulate sub-style global/peratom energy/virial in hybrid
107 
108   ev_init(eflag, vflag);
109 
110   // need to clear per-thread storage here, when using multiple threads
111   // with thread-enabled substyles to avoid uninitlialized data access.
112 
113   const int nthreads = comm->nthreads;
114   if (comm->nthreads > 1) {
115     const bigint nall = atom->nlocal + atom->nghost;
116     if (eflag_atom) memset(&eatom[0], 0, nall * nthreads * sizeof(double));
117     if (vflag_atom) memset(&vatom[0][0], 0, 6 * nall * nthreads * sizeof(double));
118   }
119 
120   for (m = 0; m < nstyles; m++) {
121     neighbor->nanglelist = nanglelist[m];
122     neighbor->anglelist = anglelist[m];
123 
124     styles[m]->compute(eflag, vflag);
125 
126     if (eflag_global) energy += styles[m]->energy;
127     if (vflag_global)
128       for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
129     if (eflag_atom) {
130       n = atom->nlocal;
131       if (force->newton_bond) n += atom->nghost;
132       double *eatom_substyle = styles[m]->eatom;
133       for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
134     }
135     if (vflag_atom) {
136       n = atom->nlocal;
137       if (force->newton_bond) n += atom->nghost;
138       double **vatom_substyle = styles[m]->vatom;
139       for (i = 0; i < n; i++)
140         for (j = 0; j < 6; j++) vatom[i][j] += vatom_substyle[i][j];
141     }
142     if (cvflag_atom) {
143       n = atom->nlocal;
144       if (force->newton_bond) n += atom->nghost;
145       double **cvatom_substyle = styles[m]->cvatom;
146       for (i = 0; i < n; i++)
147         for (j = 0; j < 9; j++) cvatom[i][j] += cvatom_substyle[i][j];
148     }
149   }
150 
151   // restore ptrs to original anglelist
152 
153   neighbor->nanglelist = nanglelist_orig;
154   neighbor->anglelist = anglelist_orig;
155 }
156 
157 /* ---------------------------------------------------------------------- */
158 
allocate()159 void AngleHybrid::allocate()
160 {
161   allocated = 1;
162   int n = atom->nangletypes;
163 
164   memory->create(map, n + 1, "angle:map");
165   memory->create(setflag, n + 1, "angle:setflag");
166   for (int i = 1; i <= n; i++) setflag[i] = 0;
167 
168   nanglelist = new int[nstyles];
169   maxangle = new int[nstyles];
170   anglelist = new int **[nstyles];
171   for (int m = 0; m < nstyles; m++) maxangle[m] = 0;
172   for (int m = 0; m < nstyles; m++) anglelist[m] = nullptr;
173 }
174 
175 /* ----------------------------------------------------------------------
176    create one angle style for each arg in list
177 ------------------------------------------------------------------------- */
178 
settings(int narg,char ** arg)179 void AngleHybrid::settings(int narg, char **arg)
180 {
181   int i, m, istyle;
182 
183   if (narg < 1) error->all(FLERR, "Illegal angle_style command");
184 
185   // delete old lists, since cannot just change settings
186 
187   if (nstyles) {
188     for (i = 0; i < nstyles; i++) delete styles[i];
189     delete[] styles;
190     for (i = 0; i < nstyles; i++) delete[] keywords[i];
191     delete[] keywords;
192   }
193 
194   if (allocated) {
195     memory->destroy(setflag);
196     memory->destroy(map);
197     delete[] nanglelist;
198     delete[] maxangle;
199     for (i = 0; i < nstyles; i++) memory->destroy(anglelist[i]);
200     delete[] anglelist;
201   }
202   allocated = 0;
203 
204   // count sub-styles by skipping numeric args
205   // one exception is 1st arg of style "table", which is non-numeric word
206   // need a better way to skip these exceptions
207 
208   nstyles = 0;
209   i = 0;
210   while (i < narg) {
211     if (strcmp(arg[i], "table") == 0) i++;
212     i++;
213     while (i < narg && !isalpha(arg[i][0])) i++;
214     nstyles++;
215   }
216 
217   // allocate list of sub-styles
218 
219   styles = new Angle *[nstyles];
220   keywords = new char *[nstyles];
221 
222   // allocate each sub-style and call its settings() with subset of args
223   // allocate uses suffix, but don't store suffix version in keywords,
224   //   else syntax in coeff() will not match
225   // define subset of args for a sub-style by skipping numeric args
226   // one exception is 1st arg of style "table", which is non-numeric
227   // need a better way to skip these exceptions
228 
229   int dummy;
230   nstyles = 0;
231   i = 0;
232 
233   while (i < narg) {
234     for (m = 0; m < nstyles; m++)
235       if (strcmp(arg[i], keywords[m]) == 0)
236         error->all(FLERR, "Angle style hybrid cannot use same angle style twice");
237     if (strcmp(arg[i], "hybrid") == 0)
238       error->all(FLERR, "Angle style hybrid cannot have hybrid as an argument");
239     if (strcmp(arg[i], "none") == 0)
240       error->all(FLERR, "Angle style hybrid cannot have none as an argument");
241 
242     styles[nstyles] = force->new_angle(arg[i], 1, dummy);
243     force->store_style(keywords[nstyles], arg[i], 0);
244 
245     istyle = i;
246     if (strcmp(arg[i], "table") == 0) i++;
247     i++;
248     while (i < narg && !isalpha(arg[i][0])) i++;
249     styles[nstyles]->settings(i - istyle - 1, &arg[istyle + 1]);
250     nstyles++;
251   }
252 }
253 
254 /* ----------------------------------------------------------------------
255    set coeffs for one type
256 ---------------------------------------------------------------------- */
257 
coeff(int narg,char ** arg)258 void AngleHybrid::coeff(int narg, char **arg)
259 {
260   if (!allocated) allocate();
261 
262   int ilo, ihi;
263   utils::bounds(FLERR, arg[0], 1, atom->nangletypes, ilo, ihi, error);
264 
265   // 2nd arg = angle sub-style name
266   // allow for "none" or "skip" as valid sub-style name
267 
268   int m;
269   for (m = 0; m < nstyles; m++)
270     if (strcmp(arg[1], keywords[m]) == 0) break;
271 
272   int none = 0;
273   int skip = 0;
274   if (m == nstyles) {
275     if (strcmp(arg[1], "none") == 0)
276       none = 1;
277     else if (strcmp(arg[1], "skip") == 0)
278       none = skip = 1;
279     else if (strcmp(arg[1], "ba") == 0)
280       error->all(FLERR, "BondAngle coeff for hybrid angle has invalid format");
281     else if (strcmp(arg[1], "bb") == 0)
282       error->all(FLERR, "BondBond coeff for hybrid angle has invalid format");
283     else
284       error->all(FLERR, "Angle coeff for hybrid has invalid style");
285   }
286 
287   // move 1st arg to 2nd arg
288   // just copy ptrs, since arg[] points into original input line
289 
290   arg[1] = arg[0];
291 
292   // invoke sub-style coeff() starting with 1st arg
293 
294   if (!none) styles[m]->coeff(narg - 1, &arg[1]);
295 
296   // set setflag and which type maps to which sub-style
297   // if sub-style is skip: auxiliary class2 setting in data file so ignore
298   // if sub-style is none: set hybrid setflag, wipe out map
299 
300   for (int i = ilo; i <= ihi; i++) {
301     if (skip)
302       continue;
303     else if (none) {
304       setflag[i] = 1;
305       map[i] = -1;
306     } else {
307       setflag[i] = styles[m]->setflag[i];
308       map[i] = m;
309     }
310   }
311 }
312 
313 /* ----------------------------------------------------------------------
314    run angle style specific initialization
315 ------------------------------------------------------------------------- */
316 
init_style()317 void AngleHybrid::init_style()
318 {
319   for (int m = 0; m < nstyles; m++)
320     if (styles[m]) styles[m]->init_style();
321 }
322 
323 /* ----------------------------------------------------------------------
324    return an equilbrium angle length
325 ------------------------------------------------------------------------- */
326 
equilibrium_angle(int i)327 double AngleHybrid::equilibrium_angle(int i)
328 {
329   if (map[i] < 0) error->one(FLERR, "Invoked angle equil angle on angle style none");
330   return styles[map[i]]->equilibrium_angle(i);
331 }
332 
333 /* ----------------------------------------------------------------------
334    proc 0 writes to restart file
335 ------------------------------------------------------------------------- */
336 
write_restart(FILE * fp)337 void AngleHybrid::write_restart(FILE *fp)
338 {
339   fwrite(&nstyles, sizeof(int), 1, fp);
340 
341   int n;
342   for (int m = 0; m < nstyles; m++) {
343     n = strlen(keywords[m]) + 1;
344     fwrite(&n, sizeof(int), 1, fp);
345     fwrite(keywords[m], sizeof(char), n, fp);
346     styles[m]->write_restart_settings(fp);
347   }
348 }
349 
350 /* ----------------------------------------------------------------------
351    proc 0 reads from restart file, bcasts
352 ------------------------------------------------------------------------- */
353 
read_restart(FILE * fp)354 void AngleHybrid::read_restart(FILE *fp)
355 {
356   int me = comm->me;
357   if (me == 0) utils::sfread(FLERR, &nstyles, sizeof(int), 1, fp, nullptr, error);
358   MPI_Bcast(&nstyles, 1, MPI_INT, 0, world);
359   styles = new Angle *[nstyles];
360   keywords = new char *[nstyles];
361 
362   allocate();
363 
364   int n, dummy;
365   for (int m = 0; m < nstyles; m++) {
366     if (me == 0) utils::sfread(FLERR, &n, sizeof(int), 1, fp, nullptr, error);
367     MPI_Bcast(&n, 1, MPI_INT, 0, world);
368     keywords[m] = new char[n];
369     if (me == 0) utils::sfread(FLERR, keywords[m], sizeof(char), n, fp, nullptr, error);
370     MPI_Bcast(keywords[m], n, MPI_CHAR, 0, world);
371     styles[m] = force->new_angle(keywords[m], 0, dummy);
372     styles[m]->read_restart_settings(fp);
373   }
374 }
375 
376 /* ---------------------------------------------------------------------- */
377 
single(int type,int i1,int i2,int i3)378 double AngleHybrid::single(int type, int i1, int i2, int i3)
379 {
380   if (map[type] < 0) error->one(FLERR, "Invoked angle single on angle style none");
381   return styles[map[type]]->single(type, i1, i2, i3);
382 }
383 
384 /* ----------------------------------------------------------------------
385    memory usage
386 ------------------------------------------------------------------------- */
387 
memory_usage()388 double AngleHybrid::memory_usage()
389 {
390   double bytes = (double) maxeatom * sizeof(double);
391   bytes += (double) maxvatom * 6 * sizeof(double);
392   bytes += (double) maxcvatom * 9 * sizeof(double);
393   for (int m = 0; m < nstyles; m++) bytes += (double) maxangle[m] * 4 * sizeof(int);
394   for (int m = 0; m < nstyles; m++)
395     if (styles[m]) bytes += styles[m]->memory_usage();
396   return bytes;
397 }
398