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 /* ----------------------------------------------------------------------
16 Contributing author: Stan Moore (SNL)
17 ------------------------------------------------------------------------- */
18
19 #include "angle_harmonic_kokkos.h"
20
21 #include "atom_kokkos.h"
22 #include "atom_masks.h"
23 #include "comm.h"
24 #include "force.h"
25 #include "math_const.h"
26 #include "memory_kokkos.h"
27 #include "neighbor_kokkos.h"
28
29 #include <cmath>
30
31 using namespace LAMMPS_NS;
32 using namespace MathConst;
33
34 #define SMALL 0.001
35
36 /* ---------------------------------------------------------------------- */
37
38 template<class DeviceType>
AngleHarmonicKokkos(LAMMPS * lmp)39 AngleHarmonicKokkos<DeviceType>::AngleHarmonicKokkos(LAMMPS *lmp) : AngleHarmonic(lmp)
40 {
41 atomKK = (AtomKokkos *) atom;
42 neighborKK = (NeighborKokkos *) neighbor;
43 execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
44 datamask_read = X_MASK | F_MASK | ENERGY_MASK | VIRIAL_MASK;
45 datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
46
47 centroidstressflag = CENTROID_NOTAVAIL;
48 }
49
50 /* ---------------------------------------------------------------------- */
51
52 template<class DeviceType>
~AngleHarmonicKokkos()53 AngleHarmonicKokkos<DeviceType>::~AngleHarmonicKokkos()
54 {
55 if (!copymode) {
56 memoryKK->destroy_kokkos(k_eatom,eatom);
57 memoryKK->destroy_kokkos(k_vatom,vatom);
58 }
59 }
60
61 /* ---------------------------------------------------------------------- */
62
63 template<class DeviceType>
compute(int eflag_in,int vflag_in)64 void AngleHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
65 {
66 eflag = eflag_in;
67 vflag = vflag_in;
68
69 ev_init(eflag,vflag,0);
70
71 // reallocate per-atom arrays if necessary
72
73 if (eflag_atom) {
74 memoryKK->destroy_kokkos(k_eatom,eatom);
75 memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");
76 d_eatom = k_eatom.template view<DeviceType>();
77 }
78 if (vflag_atom) {
79 memoryKK->destroy_kokkos(k_vatom,vatom);
80 memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"angle:vatom");
81 d_vatom = k_vatom.template view<DeviceType>();
82 }
83
84 //atomKK->sync(execution_space,datamask_read);
85 k_k.template sync<DeviceType>();
86 k_theta0.template sync<DeviceType>();
87 // if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
88 // else atomKK->modified(execution_space,F_MASK);
89
90 x = atomKK->k_x.template view<DeviceType>();
91 f = atomKK->k_f.template view<DeviceType>();
92 neighborKK->k_anglelist.template sync<DeviceType>();
93 anglelist = neighborKK->k_anglelist.template view<DeviceType>();
94 int nanglelist = neighborKK->nanglelist;
95 nlocal = atom->nlocal;
96 newton_bond = force->newton_bond;
97
98 copymode = 1;
99
100 // loop over neighbors of my atoms
101
102 EV_FLOAT ev;
103
104 if (evflag) {
105 if (newton_bond) {
106 Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<1,1> >(0,nanglelist),*this,ev);
107 } else {
108 Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<0,1> >(0,nanglelist),*this,ev);
109 }
110 } else {
111 if (newton_bond) {
112 Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<1,0> >(0,nanglelist),*this);
113 } else {
114 Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleHarmonicCompute<0,0> >(0,nanglelist),*this);
115 }
116 }
117
118 if (eflag_global) energy += ev.evdwl;
119 if (vflag_global) {
120 virial[0] += ev.v[0];
121 virial[1] += ev.v[1];
122 virial[2] += ev.v[2];
123 virial[3] += ev.v[3];
124 virial[4] += ev.v[4];
125 virial[5] += ev.v[5];
126 }
127
128 if (eflag_atom) {
129 k_eatom.template modify<DeviceType>();
130 k_eatom.template sync<LMPHostType>();
131 }
132
133 if (vflag_atom) {
134 k_vatom.template modify<DeviceType>();
135 k_vatom.template sync<LMPHostType>();
136 }
137
138 copymode = 0;
139 }
140
141 template<class DeviceType>
142 template<int NEWTON_BOND, int EVFLAG>
143 KOKKOS_INLINE_FUNCTION
operator ()(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>,const int & n,EV_FLOAT & ev) const144 void AngleHarmonicKokkos<DeviceType>::operator()(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {
145
146 // The f array is atomic
147 Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > a_f = f;
148
149 const int i1 = anglelist(n,0);
150 const int i2 = anglelist(n,1);
151 const int i3 = anglelist(n,2);
152 const int type = anglelist(n,3);
153
154 // 1st bond
155
156 const F_FLOAT delx1 = x(i1,0) - x(i2,0);
157 const F_FLOAT dely1 = x(i1,1) - x(i2,1);
158 const F_FLOAT delz1 = x(i1,2) - x(i2,2);
159
160 const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
161 const F_FLOAT r1 = sqrt(rsq1);
162
163 // 2nd bond
164
165 const F_FLOAT delx2 = x(i3,0) - x(i2,0);
166 const F_FLOAT dely2 = x(i3,1) - x(i2,1);
167 const F_FLOAT delz2 = x(i3,2) - x(i2,2);
168
169 const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
170 const F_FLOAT r2 = sqrt(rsq2);
171
172 // angle (cos and sin)
173
174 F_FLOAT c = delx1*delx2 + dely1*dely2 + delz1*delz2;
175 c /= r1*r2;
176
177 if (c > 1.0) c = 1.0;
178 if (c < -1.0) c = -1.0;
179
180 F_FLOAT s = sqrt(1.0 - c*c);
181 if (s < SMALL) s = SMALL;
182 s = 1.0/s;
183
184 // force & energy
185
186 const F_FLOAT dtheta = acos(c) - d_theta0[type];
187 const F_FLOAT tk = d_k[type] * dtheta;
188
189 F_FLOAT eangle = 0.0;
190 if (eflag) eangle = tk*dtheta;
191
192 const F_FLOAT a = -2.0 * tk * s;
193 const F_FLOAT a11 = a*c / rsq1;
194 const F_FLOAT a12 = -a / (r1*r2);
195 const F_FLOAT a22 = a*c / rsq2;
196
197 F_FLOAT f1[3],f3[3];
198 f1[0] = a11*delx1 + a12*delx2;
199 f1[1] = a11*dely1 + a12*dely2;
200 f1[2] = a11*delz1 + a12*delz2;
201 f3[0] = a22*delx2 + a12*delx1;
202 f3[1] = a22*dely2 + a12*dely1;
203 f3[2] = a22*delz2 + a12*delz1;
204
205 // apply force to each of 3 atoms
206
207 if (NEWTON_BOND || i1 < nlocal) {
208 a_f(i1,0) += f1[0];
209 a_f(i1,1) += f1[1];
210 a_f(i1,2) += f1[2];
211 }
212
213 if (NEWTON_BOND || i2 < nlocal) {
214 a_f(i2,0) -= f1[0] + f3[0];
215 a_f(i2,1) -= f1[1] + f3[1];
216 a_f(i2,2) -= f1[2] + f3[2];
217 }
218
219 if (NEWTON_BOND || i3 < nlocal) {
220 a_f(i3,0) += f3[0];
221 a_f(i3,1) += f3[1];
222 a_f(i3,2) += f3[2];
223 }
224
225 if (EVFLAG) ev_tally(ev,i1,i2,i3,eangle,f1,f3,
226 delx1,dely1,delz1,delx2,dely2,delz2);
227 }
228
229 template<class DeviceType>
230 template<int NEWTON_BOND, int EVFLAG>
231 KOKKOS_INLINE_FUNCTION
operator ()(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>,const int & n) const232 void AngleHarmonicKokkos<DeviceType>::operator()(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>, const int &n) const {
233 EV_FLOAT ev;
234 this->template operator()<NEWTON_BOND,EVFLAG>(TagAngleHarmonicCompute<NEWTON_BOND,EVFLAG>(), n, ev);
235 }
236
237 /* ---------------------------------------------------------------------- */
238
239 template<class DeviceType>
allocate()240 void AngleHarmonicKokkos<DeviceType>::allocate()
241 {
242 AngleHarmonic::allocate();
243
244 int n = atom->nangletypes;
245 k_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleHarmonic::k",n+1);
246 k_theta0 = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleHarmonic::theta0",n+1);
247
248 d_k = k_k.template view<DeviceType>();
249 d_theta0 = k_theta0.template view<DeviceType>();
250 }
251
252 /* ----------------------------------------------------------------------
253 set coeffs for one or more types
254 ------------------------------------------------------------------------- */
255
256 template<class DeviceType>
coeff(int narg,char ** arg)257 void AngleHarmonicKokkos<DeviceType>::coeff(int narg, char **arg)
258 {
259 AngleHarmonic::coeff(narg, arg);
260
261 int n = atom->nangletypes;
262 for (int i = 1; i <= n; i++) {
263 k_k.h_view[i] = k[i];
264 k_theta0.h_view[i] = theta0[i];
265 }
266
267 k_k.template modify<LMPHostType>();
268 k_theta0.template modify<LMPHostType>();
269 }
270
271 /* ----------------------------------------------------------------------
272 proc 0 reads coeffs from restart file, bcasts them
273 ------------------------------------------------------------------------- */
274
275 template<class DeviceType>
read_restart(FILE * fp)276 void AngleHarmonicKokkos<DeviceType>::read_restart(FILE *fp)
277 {
278 AngleHarmonic::read_restart(fp);
279
280 int n = atom->nangletypes;
281 for (int i = 1; i <= n; i++) {
282 k_k.h_view[i] = k[i];
283 k_theta0.h_view[i] = theta0[i];
284 }
285
286 k_k.template modify<LMPHostType>();
287 k_theta0.template modify<LMPHostType>();
288 }
289
290 /* ----------------------------------------------------------------------
291 tally energy and virial into global and per-atom accumulators
292 virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3
293 ------------------------------------------------------------------------- */
294
295 template<class DeviceType>
296 //template<int NEWTON_BOND>
297 KOKKOS_INLINE_FUNCTION
ev_tally(EV_FLOAT & ev,const int i,const int j,const int k,F_FLOAT & eangle,F_FLOAT * f1,F_FLOAT * f3,const F_FLOAT & delx1,const F_FLOAT & dely1,const F_FLOAT & delz1,const F_FLOAT & delx2,const F_FLOAT & dely2,const F_FLOAT & delz2) const298 void AngleHarmonicKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const int j, const int k,
299 F_FLOAT &eangle, F_FLOAT *f1, F_FLOAT *f3,
300 const F_FLOAT &delx1, const F_FLOAT &dely1, const F_FLOAT &delz1,
301 const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const
302 {
303 E_FLOAT eanglethird;
304 F_FLOAT v[6];
305
306 // The eatom and vatom arrays are atomic
307 Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_eatom = k_eatom.template view<DeviceType>();
308 Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_vatom = k_vatom.template view<DeviceType>();
309
310 if (eflag_either) {
311 if (eflag_global) {
312 if (newton_bond) ev.evdwl += eangle;
313 else {
314 eanglethird = THIRD*eangle;
315
316 if (i < nlocal) ev.evdwl += eanglethird;
317 if (j < nlocal) ev.evdwl += eanglethird;
318 if (k < nlocal) ev.evdwl += eanglethird;
319 }
320 }
321 if (eflag_atom) {
322 eanglethird = THIRD*eangle;
323
324 if (newton_bond || i < nlocal) v_eatom[i] += eanglethird;
325 if (newton_bond || j < nlocal) v_eatom[j] += eanglethird;
326 if (newton_bond || k < nlocal) v_eatom[k] += eanglethird;
327 }
328 }
329
330 if (vflag_either) {
331 v[0] = delx1*f1[0] + delx2*f3[0];
332 v[1] = dely1*f1[1] + dely2*f3[1];
333 v[2] = delz1*f1[2] + delz2*f3[2];
334 v[3] = delx1*f1[1] + delx2*f3[1];
335 v[4] = delx1*f1[2] + delx2*f3[2];
336 v[5] = dely1*f1[2] + dely2*f3[2];
337
338 if (vflag_global) {
339 if (newton_bond) {
340 ev.v[0] += v[0];
341 ev.v[1] += v[1];
342 ev.v[2] += v[2];
343 ev.v[3] += v[3];
344 ev.v[4] += v[4];
345 ev.v[5] += v[5];
346 } else {
347 if (i < nlocal) {
348 ev.v[0] += THIRD*v[0];
349 ev.v[1] += THIRD*v[1];
350 ev.v[2] += THIRD*v[2];
351 ev.v[3] += THIRD*v[3];
352 ev.v[4] += THIRD*v[4];
353 ev.v[5] += THIRD*v[5];
354 }
355 if (j < nlocal) {
356 ev.v[0] += THIRD*v[0];
357 ev.v[1] += THIRD*v[1];
358 ev.v[2] += THIRD*v[2];
359 ev.v[3] += THIRD*v[3];
360 ev.v[4] += THIRD*v[4];
361 ev.v[5] += THIRD*v[5];
362 }
363 if (k < nlocal) {
364 ev.v[0] += THIRD*v[0];
365
366 ev.v[1] += THIRD*v[1];
367 ev.v[2] += THIRD*v[2];
368 ev.v[3] += THIRD*v[3];
369 ev.v[4] += THIRD*v[4];
370 ev.v[5] += THIRD*v[5];
371 }
372 }
373 }
374
375 if (vflag_atom) {
376 if (newton_bond || i < nlocal) {
377 v_vatom(i,0) += THIRD*v[0];
378 v_vatom(i,1) += THIRD*v[1];
379 v_vatom(i,2) += THIRD*v[2];
380 v_vatom(i,3) += THIRD*v[3];
381 v_vatom(i,4) += THIRD*v[4];
382 v_vatom(i,5) += THIRD*v[5];
383 }
384 if (newton_bond || j < nlocal) {
385 v_vatom(j,0) += THIRD*v[0];
386 v_vatom(j,1) += THIRD*v[1];
387 v_vatom(j,2) += THIRD*v[2];
388 v_vatom(j,3) += THIRD*v[3];
389 v_vatom(j,4) += THIRD*v[4];
390 v_vatom(j,5) += THIRD*v[5];
391 }
392 if (newton_bond || k < nlocal) {
393 v_vatom(k,0) += THIRD*v[0];
394 v_vatom(k,1) += THIRD*v[1];
395 v_vatom(k,2) += THIRD*v[2];
396 v_vatom(k,3) += THIRD*v[3];
397 v_vatom(k,4) += THIRD*v[4];
398 v_vatom(k,5) += THIRD*v[5];
399
400 }
401 }
402 }
403 }
404
405 /* ---------------------------------------------------------------------- */
406
407 namespace LAMMPS_NS {
408 template class AngleHarmonicKokkos<LMPDeviceType>;
409 #ifdef LMP_KOKKOS_GPU
410 template class AngleHarmonicKokkos<LMPHostType>;
411 #endif
412 }
413
414