1 /* ----------------------------------------------------------------------
2 This is the
3
4 ██╗ ██╗ ██████╗ ██████╗ ██████╗ ██╗ ██╗████████╗███████╗
5 ██║ ██║██╔════╝ ██╔════╝ ██╔════╝ ██║ ██║╚══██╔══╝██╔════╝
6 ██║ ██║██║ ███╗██║ ███╗██║ ███╗███████║ ██║ ███████╗
7 ██║ ██║██║ ██║██║ ██║██║ ██║██╔══██║ ██║ ╚════██║
8 ███████╗██║╚██████╔╝╚██████╔╝╚██████╔╝██║ ██║ ██║ ███████║
9 ╚══════╝╚═╝ ╚═════╝ ╚═════╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝ ╚══════╝®
10
11 DEM simulation engine, released by
12 DCS Computing Gmbh, Linz, Austria
13 http://www.dcs-computing.com, office@dcs-computing.com
14
15 LIGGGHTS® is part of CFDEM®project:
16 http://www.liggghts.com | http://www.cfdem.com
17
18 Core developer and main author:
19 Christoph Kloss, christoph.kloss@dcs-computing.com
20
21 LIGGGHTS® is open-source, distributed under the terms of the GNU Public
22 License, version 2 or later. It is distributed in the hope that it will
23 be useful, but WITHOUT ANY WARRANTY; without even the implied warranty
24 of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. You should have
25 received a copy of the GNU General Public License along with LIGGGHTS®.
26 If not, see http://www.gnu.org/licenses . See also top-level README
27 and LICENSE files.
28
29 LIGGGHTS® and CFDEM® are registered trade marks of DCS Computing GmbH,
30 the producer of the LIGGGHTS® software and the CFDEM®coupling software
31 See http://www.cfdem.com/terms-trademark-policy for details.
32
33 -------------------------------------------------------------------------
34 Contributing author and copyright for this file:
35 This file is from LAMMPS
36 LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
37 http://lammps.sandia.gov, Sandia National Laboratories
38 Steve Plimpton, sjplimp@sandia.gov
39
40 Copyright (2003) Sandia Corporation. Under the terms of Contract
41 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
42 certain rights in this software. This software is distributed under
43 the GNU General Public License.
44 ------------------------------------------------------------------------- */
45
46 #include <cmath>
47 #include <string.h>
48 #include "ctype.h"
49 #include "angle_hybrid.h"
50 #include "atom.h"
51 #include "neighbor.h"
52 #include "domain.h"
53 #include "comm.h"
54 #include "force.h"
55 #include "memory.h"
56 #include "error.h"
57
58 using namespace LAMMPS_NS;
59
60 #define EXTRA 1000
61
62 /* ---------------------------------------------------------------------- */
63
AngleHybrid(LAMMPS * lmp)64 AngleHybrid::AngleHybrid(LAMMPS *lmp) : Angle(lmp)
65 {
66 writedata = 0;
67 nstyles = 0;
68 }
69
70 /* ---------------------------------------------------------------------- */
71
~AngleHybrid()72 AngleHybrid::~AngleHybrid()
73 {
74 if (nstyles) {
75 for (int i = 0; i < nstyles; i++) delete styles[i];
76 delete [] styles;
77 for (int i = 0; i < nstyles; i++) delete [] keywords[i];
78 delete [] keywords;
79 }
80
81 if (allocated) {
82 memory->destroy(setflag);
83 memory->destroy(map);
84 delete [] nanglelist;
85 delete [] maxangle;
86 for (int i = 0; i < nstyles; i++)
87 memory->destroy(anglelist[i]);
88 delete [] anglelist;
89 }
90 }
91
92 /* ---------------------------------------------------------------------- */
93
compute(int eflag,int vflag)94 void AngleHybrid::compute(int eflag, int vflag)
95 {
96 int i,j,m,n;
97
98 // save ptrs to original anglelist
99
100 int nanglelist_orig = neighbor->nanglelist;
101 int **anglelist_orig = neighbor->anglelist;
102
103 // if this is re-neighbor step, create sub-style anglelists
104 // nanglelist[] = length of each sub-style list
105 // realloc sub-style anglelist if necessary
106 // load sub-style anglelist with 4 values from original anglelist
107
108 if (neighbor->ago == 0) {
109 for (m = 0; m < nstyles; m++) nanglelist[m] = 0;
110 for (i = 0; i < nanglelist_orig; i++) {
111 m = map[anglelist_orig[i][3]];
112 if (m >= 0) nanglelist[m]++;
113 }
114 for (m = 0; m < nstyles; m++) {
115 if (nanglelist[m] > maxangle[m]) {
116 memory->destroy(anglelist[m]);
117 maxangle[m] = nanglelist[m] + EXTRA;
118 memory->create(anglelist[m],maxangle[m],4,"angle_hybrid:anglelist");
119 }
120 nanglelist[m] = 0;
121 }
122 for (i = 0; i < nanglelist_orig; i++) {
123 m = map[anglelist_orig[i][3]];
124 if (m < 0) continue;
125 n = nanglelist[m];
126 anglelist[m][n][0] = anglelist_orig[i][0];
127 anglelist[m][n][1] = anglelist_orig[i][1];
128 anglelist[m][n][2] = anglelist_orig[i][2];
129 anglelist[m][n][3] = anglelist_orig[i][3];
130 nanglelist[m]++;
131 }
132 }
133
134 // call each sub-style's compute function
135 // set neighbor->anglelist to sub-style anglelist before call
136 // accumulate sub-style global/peratom energy/virial in hybrid
137
138 if (eflag || vflag) ev_setup(eflag,vflag);
139 else evflag = 0;
140
141 for (m = 0; m < nstyles; m++) {
142 neighbor->nanglelist = nanglelist[m];
143 neighbor->anglelist = anglelist[m];
144
145 styles[m]->compute(eflag,vflag);
146
147 if (eflag_global) energy += styles[m]->energy;
148 if (vflag_global)
149 for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
150 if (eflag_atom) {
151 n = atom->nlocal;
152 if (force->newton_bond) n += atom->nghost;
153 double *eatom_substyle = styles[m]->eatom;
154 for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
155 }
156 if (vflag_atom) {
157 n = atom->nlocal;
158 if (force->newton_bond) n += atom->nghost;
159 double **vatom_substyle = styles[m]->vatom;
160 for (i = 0; i < n; i++)
161 for (j = 0; j < 6; j++)
162 vatom[i][j] += vatom_substyle[i][j];
163 }
164 }
165
166 // restore ptrs to original anglelist
167
168 neighbor->nanglelist = nanglelist_orig;
169 neighbor->anglelist = anglelist_orig;
170 }
171
172 /* ---------------------------------------------------------------------- */
173
allocate()174 void AngleHybrid::allocate()
175 {
176 allocated = 1;
177 int n = atom->nangletypes;
178
179 memory->create(map,n+1,"angle:map");
180 memory->create(setflag,n+1,"angle:setflag");
181 for (int i = 1; i <= n; i++) setflag[i] = 0;
182
183 nanglelist = new int[nstyles];
184 maxangle = new int[nstyles];
185 anglelist = new int**[nstyles];
186 for (int m = 0; m < nstyles; m++) maxangle[m] = 0;
187 for (int m = 0; m < nstyles; m++) anglelist[m] = NULL;
188 }
189
190 /* ----------------------------------------------------------------------
191 create one angle style for each arg in list
192 ------------------------------------------------------------------------- */
193
settings(int narg,char ** arg)194 void AngleHybrid::settings(int narg, char **arg)
195 {
196 int i,m,istyle;
197
198 if (narg < 1) error->all(FLERR,"Illegal angle_style command");
199
200 // delete old lists, since cannot just change settings
201
202 if (nstyles) {
203 for (int i = 0; i < nstyles; i++) delete styles[i];
204 delete [] styles;
205 for (int i = 0; i < nstyles; i++) delete [] keywords[i];
206 delete [] keywords;
207 }
208
209 if (allocated) {
210 memory->destroy(setflag);
211 memory->destroy(map);
212 delete [] nanglelist;
213 delete [] maxangle;
214 for (int i = 0; i < nstyles; i++)
215 memory->destroy(anglelist[i]);
216 delete [] anglelist;
217 }
218 allocated = 0;
219
220 // count sub-styles by skipping numeric args
221 // one exception is 1st arg of style "table", which is non-numeric word
222 // need a better way to skip these exceptions
223
224 nstyles = 0;
225 i = 0;
226 while (i < narg) {
227 if (strcmp(arg[i],"table") == 0) i++;
228 i++;
229 while (i < narg && !isalpha(arg[i][0])) i++;
230 nstyles++;
231 }
232
233 // allocate list of sub-styles
234
235 styles = new Angle*[nstyles];
236 keywords = new char*[nstyles];
237
238 // allocate each sub-style and call its settings() with subset of args
239 // define subset of args for a sub-style by skipping numeric args
240 // one exception is 1st arg of style "table", which is non-numeric
241 // need a better way to skip these exceptions
242
243 int dummy;
244 nstyles = 0;
245 i = 0;
246
247 while (i < narg) {
248 for (m = 0; m < nstyles; m++)
249 if (strcmp(arg[i],keywords[m]) == 0)
250 error->all(FLERR,"Angle style hybrid cannot use "
251 "same angle style twice");
252 if (strcmp(arg[i],"hybrid") == 0)
253 error->all(FLERR,"Angle style hybrid cannot have hybrid as an argument");
254 if (strcmp(arg[i],"none") == 0)
255 error->all(FLERR,"Angle style hybrid cannot have none as an argument");
256 styles[nstyles] = force->new_angle(arg[i],lmp->suffix,dummy);
257 keywords[nstyles] = new char[strlen(arg[i])+1];
258 strcpy(keywords[nstyles],arg[i]);
259 istyle = i;
260 if (strcmp(arg[i],"table") == 0) i++;
261 i++;
262 while (i < narg && !isalpha(arg[i][0])) i++;
263 styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
264 nstyles++;
265 }
266 }
267
268 /* ----------------------------------------------------------------------
269 set coeffs for one type
270 ---------------------------------------------------------------------- */
271
coeff(int narg,char ** arg)272 void AngleHybrid::coeff(int narg, char **arg)
273 {
274 if (!allocated) allocate();
275
276 int ilo,ihi;
277 force->bounds(arg[0],atom->nangletypes,ilo,ihi);
278
279 // 2nd arg = angle sub-style name
280 // allow for "none" or "skip" as valid sub-style name
281
282 int m;
283 for (m = 0; m < nstyles; m++)
284 if (strcmp(arg[1],keywords[m]) == 0) break;
285
286 int none = 0;
287 int skip = 0;
288 if (m == nstyles) {
289 if (strcmp(arg[1],"none") == 0) none = 1;
290 else if (strcmp(arg[1],"skip") == 0) none = skip = 1;
291 else error->all(FLERR,"Angle 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: set hybrid setflag, wipe out map
306
307 for (int i = ilo; i <= ihi; i++) {
308 if (skip) continue;
309 else if (none) {
310 setflag[i] = 1;
311 map[i] = -1;
312 } else {
313 setflag[i] = styles[m]->setflag[i];
314 map[i] = m;
315 }
316 }
317 }
318
319 /* ----------------------------------------------------------------------
320 run angle style specific initialization
321 ------------------------------------------------------------------------- */
322
init_style()323 void AngleHybrid::init_style()
324 {
325 for (int m = 0; m < nstyles; m++)
326 if (styles[m]) styles[m]->init_style();
327 }
328
329 /* ----------------------------------------------------------------------
330 return an equilbrium angle length
331 ------------------------------------------------------------------------- */
332
equilibrium_angle(int i)333 double AngleHybrid::equilibrium_angle(int i)
334 {
335 if (map[i] < 0)
336 error->one(FLERR,"Invoked angle equil angle on angle style none");
337 return styles[map[i]]->equilibrium_angle(i);
338 }
339
340 /* ----------------------------------------------------------------------
341 proc 0 writes to restart file
342 ------------------------------------------------------------------------- */
343
write_restart(FILE * fp)344 void AngleHybrid::write_restart(FILE *fp)
345 {
346 fwrite(&nstyles,sizeof(int),1,fp);
347
348 int n;
349 for (int m = 0; m < nstyles; m++) {
350 n = strlen(keywords[m]) + 1;
351 fwrite(&n,sizeof(int),1,fp);
352 fwrite(keywords[m],sizeof(char),n,fp);
353 }
354 }
355
356 /* ----------------------------------------------------------------------
357 proc 0 reads from restart file, bcasts
358 ------------------------------------------------------------------------- */
359
read_restart(FILE * fp)360 void AngleHybrid::read_restart(FILE *fp)
361 {
362 int me = comm->me;
363 if (me == 0) fread(&nstyles,sizeof(int),1,fp);
364 MPI_Bcast(&nstyles,1,MPI_INT,0,world);
365 styles = new Angle*[nstyles];
366 keywords = new char*[nstyles];
367
368 allocate();
369
370 int n,dummy;
371 for (int m = 0; m < nstyles; m++) {
372 if (me == 0) fread(&n,sizeof(int),1,fp);
373 MPI_Bcast(&n,1,MPI_INT,0,world);
374 keywords[m] = new char[n];
375 if (me == 0) fread(keywords[m],sizeof(char),n,fp);
376 MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
377 styles[m] = force->new_angle(keywords[m],lmp->suffix,dummy);
378 }
379 }
380
381 /* ---------------------------------------------------------------------- */
382
single(int type,int i1,int i2,int i3)383 double AngleHybrid::single(int type, int i1, int i2, int i3)
384 {
385 if (map[type] < 0) error->one(FLERR,"Invoked angle single on angle style none");
386 return styles[map[type]]->single(type,i1,i2,i3);
387 }
388
389 /* ----------------------------------------------------------------------
390 memory usage
391 ------------------------------------------------------------------------- */
392
memory_usage()393 double AngleHybrid::memory_usage()
394 {
395 double bytes = maxeatom * sizeof(double);
396 bytes += maxvatom*6 * sizeof(double);
397 for (int m = 0; m < nstyles; m++) bytes += maxangle[m]*4 * sizeof(int);
398 for (int m = 0; m < nstyles; m++)
399 if (styles[m]) bytes += styles[m]->memory_usage();
400 return bytes;
401 }
402