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 "compute_gyration_chunk.h"
16
17 #include <cmath>
18 #include <cstring>
19 #include "atom.h"
20 #include "update.h"
21 #include "modify.h"
22 #include "compute_chunk_atom.h"
23 #include "domain.h"
24 #include "memory.h"
25 #include "error.h"
26
27 using namespace LAMMPS_NS;
28
29 /* ---------------------------------------------------------------------- */
30
ComputeGyrationChunk(LAMMPS * lmp,int narg,char ** arg)31 ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) :
32 Compute(lmp, narg, arg),
33 idchunk(nullptr), massproc(nullptr), masstotal(nullptr), com(nullptr), comall(nullptr),
34 rg(nullptr), rgall(nullptr), rgt(nullptr), rgtall(nullptr)
35 {
36 if (narg < 4) error->all(FLERR,"Illegal compute gyration/chunk command");
37
38 // ID of compute chunk/atom
39
40 idchunk = utils::strdup(arg[3]);
41
42 ComputeGyrationChunk::init();
43
44 // optional args
45
46 tensor = 0;
47 int iarg = 4;
48 while (iarg < narg) {
49 if (strcmp(arg[iarg],"tensor") == 0) {
50 tensor = 1;
51 iarg++;
52 } else error->all(FLERR,"Illegal compute gyration/chunk command");
53 }
54
55 if (tensor) {
56 array_flag = 1;
57 size_array_cols = 6;
58 size_array_rows = 0;
59 size_array_rows_variable = 1;
60 extarray = 0;
61 } else {
62 vector_flag = 1;
63 size_vector = 0;
64 size_vector_variable = 1;
65 extvector = 0;
66 }
67
68 // chunk-based data
69
70 nchunk = 1;
71 maxchunk = 0;
72 allocate();
73 }
74
75 /* ---------------------------------------------------------------------- */
76
~ComputeGyrationChunk()77 ComputeGyrationChunk::~ComputeGyrationChunk()
78 {
79 delete [] idchunk;
80 memory->destroy(massproc);
81 memory->destroy(masstotal);
82 memory->destroy(com);
83 memory->destroy(comall);
84 memory->destroy(rg);
85 memory->destroy(rgall);
86 memory->destroy(rgt);
87 memory->destroy(rgtall);
88 }
89
90 /* ---------------------------------------------------------------------- */
91
init()92 void ComputeGyrationChunk::init()
93 {
94 int icompute = modify->find_compute(idchunk);
95 if (icompute < 0)
96 error->all(FLERR,"Chunk/atom compute does not exist for "
97 "compute gyration/chunk");
98 cchunk = (ComputeChunkAtom *) modify->compute[icompute];
99 if (strcmp(cchunk->style,"chunk/atom") != 0)
100 error->all(FLERR,"Compute gyration/chunk does not use chunk/atom compute");
101 }
102
103 /* ---------------------------------------------------------------------- */
104
compute_vector()105 void ComputeGyrationChunk::compute_vector()
106 {
107 int i,index;
108 double dx,dy,dz,massone;
109 double unwrap[3];
110
111 invoked_array = update->ntimestep;
112
113 com_chunk();
114 int *ichunk = cchunk->ichunk;
115
116 for (i = 0; i < nchunk; i++) rg[i] = 0.0;
117
118 // compute Rg for each chunk
119
120 double **x = atom->x;
121 int *mask = atom->mask;
122 int *type = atom->type;
123 imageint *image = atom->image;
124 double *mass = atom->mass;
125 double *rmass = atom->rmass;
126 int nlocal = atom->nlocal;
127
128 for (i = 0; i < nlocal; i++)
129 if (mask[i] & groupbit) {
130 index = ichunk[i]-1;
131 if (index < 0) continue;
132 domain->unmap(x[i],image[i],unwrap);
133 dx = unwrap[0] - comall[index][0];
134 dy = unwrap[1] - comall[index][1];
135 dz = unwrap[2] - comall[index][2];
136 if (rmass) massone = rmass[i];
137 else massone = mass[type[i]];
138 rg[index] += (dx*dx + dy*dy + dz*dz) * massone;
139 }
140
141 MPI_Allreduce(rg,rgall,nchunk,MPI_DOUBLE,MPI_SUM,world);
142
143 for (i = 0; i < nchunk; i++)
144 if (masstotal[i] > 0.0)
145 rgall[i] = sqrt(rgall[i]/masstotal[i]);
146 }
147
148 /* ---------------------------------------------------------------------- */
149
compute_array()150 void ComputeGyrationChunk::compute_array()
151 {
152 int i,j,index;
153 double dx,dy,dz,massone;
154 double unwrap[3];
155
156 invoked_array = update->ntimestep;
157
158 com_chunk();
159 int *ichunk = cchunk->ichunk;
160
161 for (i = 0; i < nchunk; i++)
162 for (j = 0; j < 6; j++) rgt[i][j] = 0.0;
163
164 double **x = atom->x;
165 int *mask = atom->mask;
166 int *type = atom->type;
167 imageint *image = atom->image;
168 double *mass = atom->mass;
169 double *rmass = atom->rmass;
170 int nlocal = atom->nlocal;
171
172 for (i = 0; i < nlocal; i++)
173 if (mask[i] & groupbit) {
174 index = ichunk[i]-1;
175 if (index < 0) continue;
176 domain->unmap(x[i],image[i],unwrap);
177 dx = unwrap[0] - comall[index][0];
178 dy = unwrap[1] - comall[index][1];
179 dz = unwrap[2] - comall[index][2];
180 if (rmass) massone = rmass[i];
181 else massone = mass[type[i]];
182 rgt[index][0] += dx*dx * massone;
183 rgt[index][1] += dy*dy * massone;
184 rgt[index][2] += dz*dz * massone;
185 rgt[index][3] += dx*dy * massone;
186 rgt[index][4] += dx*dz * massone;
187 rgt[index][5] += dy*dz * massone;
188 }
189
190 if (nchunk)
191 MPI_Allreduce(&rgt[0][0],&rgtall[0][0],nchunk*6,MPI_DOUBLE,MPI_SUM,world);
192
193 for (i = 0; i < nchunk; i++) {
194 if (masstotal[i] > 0.0) {
195 for (j = 0; j < 6; j++)
196 rgtall[i][j] = rgtall[i][j]/masstotal[i];
197 }
198 }
199 }
200
201
202 /* ----------------------------------------------------------------------
203 calculate per-chunk COM, used by both scalar and tensor
204 ------------------------------------------------------------------------- */
205
com_chunk()206 void ComputeGyrationChunk::com_chunk()
207 {
208 int index;
209 double massone;
210 double unwrap[3];
211
212 // compute chunk/atom assigns atoms to chunk IDs
213 // extract ichunk index vector from compute
214 // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms
215
216 nchunk = cchunk->setup_chunks();
217 cchunk->compute_ichunk();
218 int *ichunk = cchunk->ichunk;
219
220 if (nchunk > maxchunk) allocate();
221 if (tensor) size_array_rows = nchunk;
222 else size_vector = nchunk;
223
224 // zero local per-chunk values
225
226 for (int i = 0; i < nchunk; i++) {
227 massproc[i] = 0.0;
228 com[i][0] = com[i][1] = com[i][2] = 0.0;
229 }
230
231 // compute COM for each chunk
232
233 double **x = atom->x;
234 int *mask = atom->mask;
235 int *type = atom->type;
236 imageint *image = atom->image;
237 double *mass = atom->mass;
238 double *rmass = atom->rmass;
239 int nlocal = atom->nlocal;
240
241 for (int i = 0; i < nlocal; i++)
242 if (mask[i] & groupbit) {
243 index = ichunk[i]-1;
244 if (index < 0) continue;
245 if (rmass) massone = rmass[i];
246 else massone = mass[type[i]];
247 domain->unmap(x[i],image[i],unwrap);
248 massproc[index] += massone;
249 com[index][0] += unwrap[0] * massone;
250 com[index][1] += unwrap[1] * massone;
251 com[index][2] += unwrap[2] * massone;
252 }
253
254 MPI_Allreduce(massproc,masstotal,nchunk,MPI_DOUBLE,MPI_SUM,world);
255 MPI_Allreduce(&com[0][0],&comall[0][0],3*nchunk,MPI_DOUBLE,MPI_SUM,world);
256
257 for (int i = 0; i < nchunk; i++) {
258 if (masstotal[i] > 0.0) {
259 comall[i][0] /= masstotal[i];
260 comall[i][1] /= masstotal[i];
261 comall[i][2] /= masstotal[i];
262 }
263 }
264 }
265
266 /* ----------------------------------------------------------------------
267 lock methods: called by fix ave/time
268 these methods insure vector/array size is locked for Nfreq epoch
269 by passing lock info along to compute chunk/atom
270 ------------------------------------------------------------------------- */
271
272 /* ----------------------------------------------------------------------
273 increment lock counter
274 ------------------------------------------------------------------------- */
275
lock_enable()276 void ComputeGyrationChunk::lock_enable()
277 {
278 cchunk->lockcount++;
279 }
280
281 /* ----------------------------------------------------------------------
282 decrement lock counter in compute chunk/atom, it if still exists
283 ------------------------------------------------------------------------- */
284
lock_disable()285 void ComputeGyrationChunk::lock_disable()
286 {
287 int icompute = modify->find_compute(idchunk);
288 if (icompute >= 0) {
289 cchunk = (ComputeChunkAtom *) modify->compute[icompute];
290 cchunk->lockcount--;
291 }
292 }
293
294 /* ----------------------------------------------------------------------
295 calculate and return # of chunks = length of vector/array
296 ------------------------------------------------------------------------- */
297
lock_length()298 int ComputeGyrationChunk::lock_length()
299 {
300 nchunk = cchunk->setup_chunks();
301 return nchunk;
302 }
303
304 /* ----------------------------------------------------------------------
305 set the lock from startstep to stopstep
306 ------------------------------------------------------------------------- */
307
lock(Fix * fixptr,bigint startstep,bigint stopstep)308 void ComputeGyrationChunk::lock(Fix *fixptr, bigint startstep, bigint stopstep)
309 {
310 cchunk->lock(fixptr,startstep,stopstep);
311 }
312
313 /* ----------------------------------------------------------------------
314 unset the lock
315 ------------------------------------------------------------------------- */
316
unlock(Fix * fixptr)317 void ComputeGyrationChunk::unlock(Fix *fixptr)
318 {
319 cchunk->unlock(fixptr);
320 }
321
322 /* ----------------------------------------------------------------------
323 free and reallocate per-chunk arrays
324 ------------------------------------------------------------------------- */
325
allocate()326 void ComputeGyrationChunk::allocate()
327 {
328 memory->destroy(massproc);
329 memory->destroy(masstotal);
330 memory->destroy(com);
331 memory->destroy(comall);
332 memory->destroy(rg);
333 memory->destroy(rgall);
334 memory->destroy(rgt);
335 memory->destroy(rgtall);
336 maxchunk = nchunk;
337 memory->create(massproc,maxchunk,"gyration/chunk:massproc");
338 memory->create(masstotal,maxchunk,"gyration/chunk:masstotal");
339 memory->create(com,maxchunk,3,"gyration/chunk:com");
340 memory->create(comall,maxchunk,3,"gyration/chunk:comall");
341 if (tensor) {
342 memory->create(rgt,maxchunk,6,"gyration/chunk:rgt");
343 memory->create(rgtall,maxchunk,6,"gyration/chunk:rgtall");
344 array = rgtall;
345 } else {
346 memory->create(rg,maxchunk,"gyration/chunk:rg");
347 memory->create(rgall,maxchunk,"gyration/chunk:rgall");
348 vector = rgall;
349 }
350 }
351
352 /* ----------------------------------------------------------------------
353 memory usage of local data
354 ------------------------------------------------------------------------- */
355
memory_usage()356 double ComputeGyrationChunk::memory_usage()
357 {
358 double bytes = (bigint) maxchunk * 2 * sizeof(double);
359 bytes += (double) maxchunk * 2*3 * sizeof(double);
360 if (tensor) bytes += (double) maxchunk * 2*6 * sizeof(double);
361 else bytes += (double) maxchunk * 2 * sizeof(double);
362 return bytes;
363 }
364