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 "dihedral_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
DihedralHybrid(LAMMPS * lmp)32 DihedralHybrid::DihedralHybrid(LAMMPS *lmp) : Dihedral(lmp)
33 {
34 writedata = 0;
35 nstyles = 0;
36 ndihedrallist = nullptr;
37 dihedrallist = nullptr;
38 maxdihedral = nullptr;
39 }
40
41 /* ---------------------------------------------------------------------- */
42
~DihedralHybrid()43 DihedralHybrid::~DihedralHybrid()
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[] ndihedrallist;
56 delete[] maxdihedral;
57 for (int i = 0; i < nstyles; i++) memory->destroy(dihedrallist[i]);
58 delete[] dihedrallist;
59 }
60 }
61
62 /* ---------------------------------------------------------------------- */
63
compute(int eflag,int vflag)64 void DihedralHybrid::compute(int eflag, int vflag)
65 {
66 int i, j, m, n;
67
68 // save ptrs to original dihedrallist
69
70 int ndihedrallist_orig = neighbor->ndihedrallist;
71 int **dihedrallist_orig = neighbor->dihedrallist;
72
73 // if this is re-neighbor step, create sub-style dihedrallists
74 // ndihedrallist[] = length of each sub-style list
75 // realloc sub-style dihedrallist if necessary
76 // load sub-style dihedrallist with 5 values from original dihedrallist
77
78 if (neighbor->ago == 0) {
79 for (m = 0; m < nstyles; m++) ndihedrallist[m] = 0;
80 for (i = 0; i < ndihedrallist_orig; i++) {
81 m = map[dihedrallist_orig[i][4]];
82 if (m >= 0) ndihedrallist[m]++;
83 }
84 for (m = 0; m < nstyles; m++) {
85 if (ndihedrallist[m] > maxdihedral[m]) {
86 memory->destroy(dihedrallist[m]);
87 maxdihedral[m] = ndihedrallist[m] + EXTRA;
88 memory->create(dihedrallist[m], maxdihedral[m], 5, "dihedral_hybrid:dihedrallist");
89 }
90 ndihedrallist[m] = 0;
91 }
92 for (i = 0; i < ndihedrallist_orig; i++) {
93 m = map[dihedrallist_orig[i][4]];
94 if (m < 0) continue;
95 n = ndihedrallist[m];
96 dihedrallist[m][n][0] = dihedrallist_orig[i][0];
97 dihedrallist[m][n][1] = dihedrallist_orig[i][1];
98 dihedrallist[m][n][2] = dihedrallist_orig[i][2];
99 dihedrallist[m][n][3] = dihedrallist_orig[i][3];
100 dihedrallist[m][n][4] = dihedrallist_orig[i][4];
101 ndihedrallist[m]++;
102 }
103 }
104
105 // call each sub-style's compute function
106 // set neighbor->dihedrallist to sub-style dihedrallist before call
107 // accumulate sub-style global/peratom energy/virial in hybrid
108
109 ev_init(eflag, vflag);
110
111 // need to clear per-thread storage here, when using multiple threads
112 // with thread-enabled substyles to avoid uninitlialized data access.
113
114 const int nthreads = comm->nthreads;
115 if (comm->nthreads > 1) {
116 const bigint nall = atom->nlocal + atom->nghost;
117 if (eflag_atom) memset(&eatom[0], 0, nall * nthreads * sizeof(double));
118 if (vflag_atom) memset(&vatom[0][0], 0, 6 * nall * nthreads * sizeof(double));
119 }
120
121 for (m = 0; m < nstyles; m++) {
122 neighbor->ndihedrallist = ndihedrallist[m];
123 neighbor->dihedrallist = dihedrallist[m];
124
125 styles[m]->compute(eflag, vflag);
126
127 if (eflag_global) energy += styles[m]->energy;
128 if (vflag_global)
129 for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
130 if (eflag_atom) {
131 n = atom->nlocal;
132 if (force->newton_bond) n += atom->nghost;
133 double *eatom_substyle = styles[m]->eatom;
134 for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
135 }
136 if (vflag_atom) {
137 n = atom->nlocal;
138 if (force->newton_bond) n += atom->nghost;
139 double **vatom_substyle = styles[m]->vatom;
140 for (i = 0; i < n; i++)
141 for (j = 0; j < 6; j++) vatom[i][j] += vatom_substyle[i][j];
142 }
143 if (cvflag_atom) {
144 n = atom->nlocal;
145 if (force->newton_bond) n += atom->nghost;
146 double **cvatom_substyle = styles[m]->cvatom;
147 for (i = 0; i < n; i++)
148 for (j = 0; j < 9; j++) cvatom[i][j] += cvatom_substyle[i][j];
149 }
150 }
151
152 // restore ptrs to original dihedrallist
153
154 neighbor->ndihedrallist = ndihedrallist_orig;
155 neighbor->dihedrallist = dihedrallist_orig;
156 }
157
158 /* ---------------------------------------------------------------------- */
159
allocate()160 void DihedralHybrid::allocate()
161 {
162 allocated = 1;
163 int n = atom->ndihedraltypes;
164
165 memory->create(map, n + 1, "dihedral:map");
166 memory->create(setflag, n + 1, "dihedral:setflag");
167 for (int i = 1; i <= n; i++) setflag[i] = 0;
168
169 ndihedrallist = new int[nstyles];
170 maxdihedral = new int[nstyles];
171 dihedrallist = new int **[nstyles];
172 for (int m = 0; m < nstyles; m++) maxdihedral[m] = 0;
173 for (int m = 0; m < nstyles; m++) dihedrallist[m] = nullptr;
174 }
175
176 /* ----------------------------------------------------------------------
177 create one dihedral style for each arg in list
178 ------------------------------------------------------------------------- */
179
settings(int narg,char ** arg)180 void DihedralHybrid::settings(int narg, char **arg)
181 {
182 int i, m, istyle;
183
184 if (narg < 1) error->all(FLERR, "Illegal dihedral_style command");
185
186 // delete old lists, since cannot just change settings
187
188 if (nstyles) {
189 for (i = 0; i < nstyles; i++) delete styles[i];
190 delete[] styles;
191 for (i = 0; i < nstyles; i++) delete[] keywords[i];
192 delete[] keywords;
193 }
194
195 if (allocated) {
196 memory->destroy(setflag);
197 memory->destroy(map);
198 delete[] ndihedrallist;
199 delete[] maxdihedral;
200 for (i = 0; i < nstyles; i++) memory->destroy(dihedrallist[i]);
201 delete[] dihedrallist;
202 }
203 allocated = 0;
204
205 // count sub-styles by skipping numeric args
206 // one exception is 1st arg of style "table", which is non-numeric word
207 // need a better way to skip these exceptions
208
209 nstyles = 0;
210 i = 0;
211 while (i < narg) {
212 if (strcmp(arg[i], "table") == 0) i++;
213 i++;
214 while (i < narg && !isalpha(arg[i][0])) i++;
215 nstyles++;
216 }
217
218 // allocate list of sub-styles
219
220 styles = new Dihedral *[nstyles];
221 keywords = new char *[nstyles];
222
223 // allocate each sub-style and call its settings() with subset of args
224 // allocate uses suffix, but don't store suffix version in keywords,
225 // else syntax in coeff() will not match
226 // define subset of args for a sub-style by skipping numeric args
227 // one exception is 1st arg of style "table", which is non-numeric
228 // need a better way to skip these exceptions
229
230 int dummy;
231 nstyles = 0;
232 i = 0;
233
234 while (i < narg) {
235 for (m = 0; m < nstyles; m++)
236 if (strcmp(arg[i], keywords[m]) == 0)
237 error->all(FLERR, "Dihedral style hybrid cannot use same dihedral style twice");
238 if (strcmp(arg[i], "hybrid") == 0)
239 error->all(FLERR, "Dihedral style hybrid cannot have hybrid as an argument");
240 if (strcmp(arg[i], "none") == 0)
241 error->all(FLERR, "Dihedral style hybrid cannot have none as an argument");
242
243 styles[nstyles] = force->new_dihedral(arg[i], 1, dummy);
244 force->store_style(keywords[nstyles], arg[i], 0);
245
246 istyle = i;
247 if (strcmp(arg[i], "table") == 0) i++;
248 i++;
249 while (i < narg && !isalpha(arg[i][0])) i++;
250 styles[nstyles]->settings(i - istyle - 1, &arg[istyle + 1]);
251 nstyles++;
252 }
253 }
254
255 /* ----------------------------------------------------------------------
256 set coeffs for one type
257 ---------------------------------------------------------------------- */
258
coeff(int narg,char ** arg)259 void DihedralHybrid::coeff(int narg, char **arg)
260 {
261 if (!allocated) allocate();
262
263 int ilo, ihi;
264 utils::bounds(FLERR, arg[0], 1, atom->ndihedraltypes, ilo, ihi, error);
265
266 // 2nd arg = dihedral sub-style name
267 // allow for "none" or "skip" as valid sub-style name
268
269 int m;
270 for (m = 0; m < nstyles; m++)
271 if (strcmp(arg[1], keywords[m]) == 0) break;
272
273 int none = 0;
274 int skip = 0;
275 if (m == nstyles) {
276 if (strcmp(arg[1], "none") == 0)
277 none = 1;
278 else if (strcmp(arg[1], "skip") == 0)
279 none = skip = 1;
280 else if (strcmp(arg[1], "mbt") == 0)
281 error->all(FLERR, "MiddleBondTorsion coeff for hybrid dihedral has invalid format");
282 else if (strcmp(arg[1], "ebt") == 0)
283 error->all(FLERR, "EndBondTorsion coeff for hybrid dihedral has invalid format");
284 else if (strcmp(arg[1], "at") == 0)
285 error->all(FLERR, "AngleTorsion coeff for hybrid dihedral has invalid format");
286 else if (strcmp(arg[1], "aat") == 0)
287 error->all(FLERR, "AngleAngleTorsion coeff for hybrid dihedral has invalid format");
288 else if (strcmp(arg[1], "bb13") == 0)
289 error->all(FLERR, "BondBond13 coeff for hybrid dihedral has invalid format");
290 else
291 error->all(FLERR, "Dihedral coeff for hybrid has invalid style");
292 }
293
294 // move 1st arg to 2nd arg
295 // just copy ptrs, since arg[] points into original input line
296
297 arg[1] = arg[0];
298
299 // invoke sub-style coeff() starting with 1st arg
300
301 if (!none) styles[m]->coeff(narg - 1, &arg[1]);
302
303 // set setflag and which type maps to which sub-style
304 // if sub-style is skip: auxiliary class2 setting in data file so ignore
305 // if sub-style is none and not skip: set hybrid setflag, wipe out map
306
307 for (int i = ilo; i <= ihi; i++) {
308 if (skip)
309 continue;
310 else if (none) {
311 setflag[i] = 1;
312 map[i] = -1;
313 } else {
314 setflag[i] = styles[m]->setflag[i];
315 map[i] = m;
316 }
317 }
318 }
319
320 /* ----------------------------------------------------------------------
321 run dihedral style specific initialization
322 ------------------------------------------------------------------------- */
323
init_style()324 void DihedralHybrid::init_style()
325 {
326 for (int m = 0; m < nstyles; m++)
327 if (styles[m]) styles[m]->init_style();
328 }
329
330 /* ----------------------------------------------------------------------
331 proc 0 writes to restart file
332 ------------------------------------------------------------------------- */
333
write_restart(FILE * fp)334 void DihedralHybrid::write_restart(FILE *fp)
335 {
336 fwrite(&nstyles, sizeof(int), 1, fp);
337
338 int n;
339 for (int m = 0; m < nstyles; m++) {
340 n = strlen(keywords[m]) + 1;
341 fwrite(&n, sizeof(int), 1, fp);
342 fwrite(keywords[m], sizeof(char), n, fp);
343 styles[m]->write_restart_settings(fp);
344 }
345 }
346
347 /* ----------------------------------------------------------------------
348 proc 0 reads from restart file, bcasts
349 ------------------------------------------------------------------------- */
350
read_restart(FILE * fp)351 void DihedralHybrid::read_restart(FILE *fp)
352 {
353 int me = comm->me;
354 if (me == 0) utils::sfread(FLERR, &nstyles, sizeof(int), 1, fp, nullptr, error);
355 MPI_Bcast(&nstyles, 1, MPI_INT, 0, world);
356 styles = new Dihedral *[nstyles];
357 keywords = new char *[nstyles];
358
359 allocate();
360
361 int n, dummy;
362 for (int m = 0; m < nstyles; m++) {
363 if (me == 0) utils::sfread(FLERR, &n, sizeof(int), 1, fp, nullptr, error);
364 MPI_Bcast(&n, 1, MPI_INT, 0, world);
365 keywords[m] = new char[n];
366 if (me == 0) utils::sfread(FLERR, keywords[m], sizeof(char), n, fp, nullptr, error);
367 MPI_Bcast(keywords[m], n, MPI_CHAR, 0, world);
368 styles[m] = force->new_dihedral(keywords[m], 0, dummy);
369 styles[m]->read_restart_settings(fp);
370 }
371 }
372
373 /* ----------------------------------------------------------------------
374 memory usage
375 ------------------------------------------------------------------------- */
376
memory_usage()377 double DihedralHybrid::memory_usage()
378 {
379 double bytes = (double) maxeatom * sizeof(double);
380 bytes += (double) maxvatom * 6 * sizeof(double);
381 bytes += (double) maxcvatom * 9 * sizeof(double);
382 for (int m = 0; m < nstyles; m++) bytes += (double) maxdihedral[m] * 5 * sizeof(int);
383 for (int m = 0; m < nstyles; m++)
384 if (styles[m]) bytes += styles[m]->memory_usage();
385 return bytes;
386 }
387