Bug Summary

File:gromacs/gmxlib/bondfree.c
Location:line 2007, column 5
Description:Value stored to 'msf_l' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
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18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
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24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 *
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
33 *
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <math.h>
42#include <assert.h>
43#include "physics.h"
44#include "gromacs/math/vec.h"
45#include "gromacs/math/utilities.h"
46#include "txtdump.h"
47#include "bondf.h"
48#include "gromacs/utility/smalloc.h"
49#include "pbc.h"
50#include "ns.h"
51#include "macros.h"
52#include "names.h"
53#include "gromacs/utility/fatalerror.h"
54#include "mshift.h"
55#include "disre.h"
56#include "orires.h"
57#include "force.h"
58#include "nonbonded.h"
59#include "restcbt.h"
60
61#include "gromacs/simd/simd.h"
62#include "gromacs/simd/simd_math.h"
63#include "gromacs/simd/vector_operations.h"
64
65/* Find a better place for this? */
66const int cmap_coeff_matrix[] = {
67 1, 0, -3, 2, 0, 0, 0, 0, -3, 0, 9, -6, 2, 0, -6, 4,
68 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, -9, 6, -2, 0, 6, -4,
69 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, -6, 0, 0, -6, 4,
70 0, 0, 3, -2, 0, 0, 0, 0, 0, 0, -9, 6, 0, 0, 6, -4,
71 0, 0, 0, 0, 1, 0, -3, 2, -2, 0, 6, -4, 1, 0, -3, 2,
72 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 3, -2, 1, 0, -3, 2,
73 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 2, 0, 0, 3, -2,
74 0, 0, 0, 0, 0, 0, 3, -2, 0, 0, -6, 4, 0, 0, 3, -2,
75 0, 1, -2, 1, 0, 0, 0, 0, 0, -3, 6, -3, 0, 2, -4, 2,
76 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, -6, 3, 0, -2, 4, -2,
77 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 3, 0, 0, 2, -2,
78 0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 3, -3, 0, 0, -2, 2,
79 0, 0, 0, 0, 0, 1, -2, 1, 0, -2, 4, -2, 0, 1, -2, 1,
80 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 2, -1, 0, 1, -2, 1,
81 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, -1, 1,
82 0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 2, -2, 0, 0, -1, 1
83};
84
85
86
87int glatnr(int *global_atom_index, int i)
88{
89 int atnr;
90
91 if (global_atom_index == NULL((void*)0))
92 {
93 atnr = i + 1;
94 }
95 else
96 {
97 atnr = global_atom_index[i] + 1;
98 }
99
100 return atnr;
101}
102
103static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
104{
105 if (pbc)
106 {
107 return pbc_dx_aiuc(pbc, xi, xj, dx);
108 }
109 else
110 {
111 rvec_sub(xi, xj, dx);
112 return CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2);
113 }
114}
115
116#ifdef GMX_SIMD_HAVE_REAL
117
118/* SIMD PBC data structure, containing 1/boxdiag and the box vectors */
119typedef struct {
120 gmx_simd_real_t__m128 inv_bzz;
121 gmx_simd_real_t__m128 inv_byy;
122 gmx_simd_real_t__m128 inv_bxx;
123 gmx_simd_real_t__m128 bzx;
124 gmx_simd_real_t__m128 bzy;
125 gmx_simd_real_t__m128 bzz;
126 gmx_simd_real_t__m128 byx;
127 gmx_simd_real_t__m128 byy;
128 gmx_simd_real_t__m128 bxx;
129} pbc_simd_t;
130
131/* Set the SIMD pbc data from a normal t_pbc struct */
132static void set_pbc_simd(const t_pbc *pbc, pbc_simd_t *pbc_simd)
133{
134 rvec inv_bdiag;
135 int d;
136
137 /* Setting inv_bdiag to 0 effectively turns off PBC */
138 clear_rvec(inv_bdiag);
139 if (pbc != NULL((void*)0))
140 {
141 for (d = 0; d < pbc->ndim_ePBC; d++)
142 {
143 inv_bdiag[d] = 1.0/pbc->box[d][d];
144 }
145 }
146
147 pbc_simd->inv_bzz = gmx_simd_set1_r_mm_set1_ps(inv_bdiag[ZZ2]);
148 pbc_simd->inv_byy = gmx_simd_set1_r_mm_set1_ps(inv_bdiag[YY1]);
149 pbc_simd->inv_bxx = gmx_simd_set1_r_mm_set1_ps(inv_bdiag[XX0]);
150
151 if (pbc != NULL((void*)0))
152 {
153 pbc_simd->bzx = gmx_simd_set1_r_mm_set1_ps(pbc->box[ZZ2][XX0]);
154 pbc_simd->bzy = gmx_simd_set1_r_mm_set1_ps(pbc->box[ZZ2][YY1]);
155 pbc_simd->bzz = gmx_simd_set1_r_mm_set1_ps(pbc->box[ZZ2][ZZ2]);
156 pbc_simd->byx = gmx_simd_set1_r_mm_set1_ps(pbc->box[YY1][XX0]);
157 pbc_simd->byy = gmx_simd_set1_r_mm_set1_ps(pbc->box[YY1][YY1]);
158 pbc_simd->bxx = gmx_simd_set1_r_mm_set1_ps(pbc->box[XX0][XX0]);
159 }
160 else
161 {
162 pbc_simd->bzx = gmx_simd_setzero_r_mm_setzero_ps();
163 pbc_simd->bzy = gmx_simd_setzero_r_mm_setzero_ps();
164 pbc_simd->bzz = gmx_simd_setzero_r_mm_setzero_ps();
165 pbc_simd->byx = gmx_simd_setzero_r_mm_setzero_ps();
166 pbc_simd->byy = gmx_simd_setzero_r_mm_setzero_ps();
167 pbc_simd->bxx = gmx_simd_setzero_r_mm_setzero_ps();
168 }
169}
170
171/* Correct distance vector *dx,*dy,*dz for PBC using SIMD */
172static gmx_inlineinline void
173pbc_dx_simd(gmx_simd_real_t__m128 *dx, gmx_simd_real_t__m128 *dy, gmx_simd_real_t__m128 *dz,
174 const pbc_simd_t *pbc)
175{
176 gmx_simd_real_t__m128 sh;
177
178 sh = gmx_simd_round_r(gmx_simd_mul_r(*dz, pbc->inv_bzz))__extension__ ({ __m128 __X = (_mm_mul_ps(*dz, pbc->inv_bzz
)); (__m128) __builtin_ia32_roundps((__v4sf)__X, ((0x00 | 0x00
))); });
179 *dx = gmx_simd_fnmadd_r(sh, pbc->bzx, *dx)_mm_sub_ps(*dx, _mm_mul_ps(sh, pbc->bzx));
180 *dy = gmx_simd_fnmadd_r(sh, pbc->bzy, *dy)_mm_sub_ps(*dy, _mm_mul_ps(sh, pbc->bzy));
181 *dz = gmx_simd_fnmadd_r(sh, pbc->bzz, *dz)_mm_sub_ps(*dz, _mm_mul_ps(sh, pbc->bzz));
182
183 sh = gmx_simd_round_r(gmx_simd_mul_r(*dy, pbc->inv_byy))__extension__ ({ __m128 __X = (_mm_mul_ps(*dy, pbc->inv_byy
)); (__m128) __builtin_ia32_roundps((__v4sf)__X, ((0x00 | 0x00
))); });
184 *dx = gmx_simd_fnmadd_r(sh, pbc->byx, *dx)_mm_sub_ps(*dx, _mm_mul_ps(sh, pbc->byx));
185 *dy = gmx_simd_fnmadd_r(sh, pbc->byy, *dy)_mm_sub_ps(*dy, _mm_mul_ps(sh, pbc->byy));
186
187 sh = gmx_simd_round_r(gmx_simd_mul_r(*dx, pbc->inv_bxx))__extension__ ({ __m128 __X = (_mm_mul_ps(*dx, pbc->inv_bxx
)); (__m128) __builtin_ia32_roundps((__v4sf)__X, ((0x00 | 0x00
))); });
188 *dx = gmx_simd_fnmadd_r(sh, pbc->bxx, *dx)_mm_sub_ps(*dx, _mm_mul_ps(sh, pbc->bxx));
189}
190
191#endif /* GMX_SIMD_HAVE_REAL */
192
193/*
194 * Morse potential bond by Frank Everdij
195 *
196 * Three parameters needed:
197 *
198 * b0 = equilibrium distance in nm
199 * be = beta in nm^-1 (actually, it's nu_e*Sqrt(2*pi*pi*mu/D_e))
200 * cb = well depth in kJ/mol
201 *
202 * Note: the potential is referenced to be +cb at infinite separation
203 * and zero at the equilibrium distance!
204 */
205
206real morse_bonds(int nbonds,
207 const t_iatom forceatoms[], const t_iparams forceparams[],
208 const rvec x[], rvec f[], rvec fshift[],
209 const t_pbc *pbc, const t_graph *g,
210 real lambda, real *dvdlambda,
211 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
212 int gmx_unused__attribute__ ((unused)) *global_atom_index)
213{
214 const real one = 1.0;
215 const real two = 2.0;
216 real dr, dr2, temp, omtemp, cbomtemp, fbond, vbond, fij, vtot;
217 real b0, be, cb, b0A, beA, cbA, b0B, beB, cbB, L1;
218 rvec dx;
219 int i, m, ki, type, ai, aj;
220 ivec dt;
221
222 vtot = 0.0;
223 for (i = 0; (i < nbonds); )
224 {
225 type = forceatoms[i++];
226 ai = forceatoms[i++];
227 aj = forceatoms[i++];
228
229 b0A = forceparams[type].morse.b0A;
230 beA = forceparams[type].morse.betaA;
231 cbA = forceparams[type].morse.cbA;
232
233 b0B = forceparams[type].morse.b0B;
234 beB = forceparams[type].morse.betaB;
235 cbB = forceparams[type].morse.cbB;
236
237 L1 = one-lambda; /* 1 */
238 b0 = L1*b0A + lambda*b0B; /* 3 */
239 be = L1*beA + lambda*beB; /* 3 */
240 cb = L1*cbA + lambda*cbB; /* 3 */
241
242 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
243 dr2 = iprod(dx, dx); /* 5 */
244 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
245 temp = exp(-be*(dr-b0)); /* 12 */
246
247 if (temp == one)
248 {
249 /* bonds are constrainted. This may _not_ include bond constraints if they are lambda dependent */
250 *dvdlambda += cbB-cbA;
251 continue;
252 }
253
254 omtemp = one-temp; /* 1 */
255 cbomtemp = cb*omtemp; /* 1 */
256 vbond = cbomtemp*omtemp; /* 1 */
257 fbond = -two*be*temp*cbomtemp*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 9 */
258 vtot += vbond; /* 1 */
259
260 *dvdlambda += (cbB - cbA) * omtemp * omtemp - (2-2*omtemp)*omtemp * cb * ((b0B-b0A)*be - (beB-beA)*(dr-b0)); /* 15 */
261
262 if (g)
263 {
264 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
265 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
266 }
267
268 for (m = 0; (m < DIM3); m++) /* 15 */
269 {
270 fij = fbond*dx[m];
271 f[ai][m] += fij;
272 f[aj][m] -= fij;
273 fshift[ki][m] += fij;
274 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
275 }
276 } /* 83 TOTAL */
277 return vtot;
278}
279
280real cubic_bonds(int nbonds,
281 const t_iatom forceatoms[], const t_iparams forceparams[],
282 const rvec x[], rvec f[], rvec fshift[],
283 const t_pbc *pbc, const t_graph *g,
284 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
285 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
286 int gmx_unused__attribute__ ((unused)) *global_atom_index)
287{
288 const real three = 3.0;
289 const real two = 2.0;
290 real kb, b0, kcub;
291 real dr, dr2, dist, kdist, kdist2, fbond, vbond, fij, vtot;
292 rvec dx;
293 int i, m, ki, type, ai, aj;
294 ivec dt;
295
296 vtot = 0.0;
297 for (i = 0; (i < nbonds); )
298 {
299 type = forceatoms[i++];
300 ai = forceatoms[i++];
301 aj = forceatoms[i++];
302
303 b0 = forceparams[type].cubic.b0;
304 kb = forceparams[type].cubic.kb;
305 kcub = forceparams[type].cubic.kcub;
306
307 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
308 dr2 = iprod(dx, dx); /* 5 */
309
310 if (dr2 == 0.0)
311 {
312 continue;
313 }
314
315 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
316 dist = dr-b0;
317 kdist = kb*dist;
318 kdist2 = kdist*dist;
319
320 vbond = kdist2 + kcub*kdist2*dist;
321 fbond = -(two*kdist + three*kdist2*kcub)/dr;
322
323 vtot += vbond; /* 21 */
324
325 if (g)
326 {
327 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
328 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
329 }
330 for (m = 0; (m < DIM3); m++) /* 15 */
331 {
332 fij = fbond*dx[m];
333 f[ai][m] += fij;
334 f[aj][m] -= fij;
335 fshift[ki][m] += fij;
336 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
337 }
338 } /* 54 TOTAL */
339 return vtot;
340}
341
342real FENE_bonds(int nbonds,
343 const t_iatom forceatoms[], const t_iparams forceparams[],
344 const rvec x[], rvec f[], rvec fshift[],
345 const t_pbc *pbc, const t_graph *g,
346 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
347 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
348 int *global_atom_index)
349{
350 const real half = 0.5;
351 const real one = 1.0;
352 real bm, kb;
353 real dr, dr2, bm2, omdr2obm2, fbond, vbond, fij, vtot;
354 rvec dx;
355 int i, m, ki, type, ai, aj;
356 ivec dt;
357
358 vtot = 0.0;
359 for (i = 0; (i < nbonds); )
360 {
361 type = forceatoms[i++];
362 ai = forceatoms[i++];
363 aj = forceatoms[i++];
364
365 bm = forceparams[type].fene.bm;
366 kb = forceparams[type].fene.kb;
367
368 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
369 dr2 = iprod(dx, dx); /* 5 */
370
371 if (dr2 == 0.0)
372 {
373 continue;
374 }
375
376 bm2 = bm*bm;
377
378 if (dr2 >= bm2)
379 {
380 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 380,
381 "r^2 (%f) >= bm^2 (%f) in FENE bond between atoms %d and %d",
382 dr2, bm2,
383 glatnr(global_atom_index, ai),
384 glatnr(global_atom_index, aj));
385 }
386
387 omdr2obm2 = one - dr2/bm2;
388
389 vbond = -half*kb*bm2*log(omdr2obm2);
390 fbond = -kb/omdr2obm2;
391
392 vtot += vbond; /* 35 */
393
394 if (g)
395 {
396 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
397 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
398 }
399 for (m = 0; (m < DIM3); m++) /* 15 */
400 {
401 fij = fbond*dx[m];
402 f[ai][m] += fij;
403 f[aj][m] -= fij;
404 fshift[ki][m] += fij;
405 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
406 }
407 } /* 58 TOTAL */
408 return vtot;
409}
410
411real harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
412 real *V, real *F)
413{
414 const real half = 0.5;
415 real L1, kk, x0, dx, dx2;
416 real v, f, dvdlambda;
417
418 L1 = 1.0-lambda;
419 kk = L1*kA+lambda*kB;
420 x0 = L1*xA+lambda*xB;
421
422 dx = x-x0;
423 dx2 = dx*dx;
424
425 f = -kk*dx;
426 v = half*kk*dx2;
427 dvdlambda = half*(kB-kA)*dx2 + (xA-xB)*kk*dx;
428
429 *F = f;
430 *V = v;
431
432 return dvdlambda;
433
434 /* That was 19 flops */
435}
436
437
438real bonds(int nbonds,
439 const t_iatom forceatoms[], const t_iparams forceparams[],
440 const rvec x[], rvec f[], rvec fshift[],
441 const t_pbc *pbc, const t_graph *g,
442 real lambda, real *dvdlambda,
443 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
444 int gmx_unused__attribute__ ((unused)) *global_atom_index)
445{
446 int i, m, ki, ai, aj, type;
447 real dr, dr2, fbond, vbond, fij, vtot;
448 rvec dx;
449 ivec dt;
450
451 vtot = 0.0;
452 for (i = 0; (i < nbonds); )
453 {
454 type = forceatoms[i++];
455 ai = forceatoms[i++];
456 aj = forceatoms[i++];
457
458 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
459 dr2 = iprod(dx, dx); /* 5 */
460 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
461
462 *dvdlambda += harmonic(forceparams[type].harmonic.krA,
463 forceparams[type].harmonic.krB,
464 forceparams[type].harmonic.rA,
465 forceparams[type].harmonic.rB,
466 dr, lambda, &vbond, &fbond); /* 19 */
467
468 if (dr2 == 0.0)
469 {
470 continue;
471 }
472
473
474 vtot += vbond; /* 1*/
475 fbond *= gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 6 */
476#ifdef DEBUG
477 if (debug)
478 {
479 fprintf(debug, "BONDS: dr = %10g vbond = %10g fbond = %10g\n",
480 dr, vbond, fbond);
481 }
482#endif
483 if (g)
484 {
485 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
486 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
487 }
488 for (m = 0; (m < DIM3); m++) /* 15 */
489 {
490 fij = fbond*dx[m];
491 f[ai][m] += fij;
492 f[aj][m] -= fij;
493 fshift[ki][m] += fij;
494 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
495 }
496 } /* 59 TOTAL */
497 return vtot;
498}
499
500real restraint_bonds(int nbonds,
501 const t_iatom forceatoms[], const t_iparams forceparams[],
502 const rvec x[], rvec f[], rvec fshift[],
503 const t_pbc *pbc, const t_graph *g,
504 real lambda, real *dvdlambda,
505 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
506 int gmx_unused__attribute__ ((unused)) *global_atom_index)
507{
508 int i, m, ki, ai, aj, type;
509 real dr, dr2, fbond, vbond, fij, vtot;
510 real L1;
511 real low, dlow, up1, dup1, up2, dup2, k, dk;
512 real drh, drh2;
513 rvec dx;
514 ivec dt;
515
516 L1 = 1.0 - lambda;
517
518 vtot = 0.0;
519 for (i = 0; (i < nbonds); )
520 {
521 type = forceatoms[i++];
522 ai = forceatoms[i++];
523 aj = forceatoms[i++];
524
525 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
526 dr2 = iprod(dx, dx); /* 5 */
527 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
528
529 low = L1*forceparams[type].restraint.lowA + lambda*forceparams[type].restraint.lowB;
530 dlow = -forceparams[type].restraint.lowA + forceparams[type].restraint.lowB;
531 up1 = L1*forceparams[type].restraint.up1A + lambda*forceparams[type].restraint.up1B;
532 dup1 = -forceparams[type].restraint.up1A + forceparams[type].restraint.up1B;
533 up2 = L1*forceparams[type].restraint.up2A + lambda*forceparams[type].restraint.up2B;
534 dup2 = -forceparams[type].restraint.up2A + forceparams[type].restraint.up2B;
535 k = L1*forceparams[type].restraint.kA + lambda*forceparams[type].restraint.kB;
536 dk = -forceparams[type].restraint.kA + forceparams[type].restraint.kB;
537 /* 24 */
538
539 if (dr < low)
540 {
541 drh = dr - low;
542 drh2 = drh*drh;
543 vbond = 0.5*k*drh2;
544 fbond = -k*drh;
545 *dvdlambda += 0.5*dk*drh2 - k*dlow*drh;
546 } /* 11 */
547 else if (dr <= up1)
548 {
549 vbond = 0;
550 fbond = 0;
551 }
552 else if (dr <= up2)
553 {
554 drh = dr - up1;
555 drh2 = drh*drh;
556 vbond = 0.5*k*drh2;
557 fbond = -k*drh;
558 *dvdlambda += 0.5*dk*drh2 - k*dup1*drh;
559 } /* 11 */
560 else
561 {
562 drh = dr - up2;
563 vbond = k*(up2 - up1)*(0.5*(up2 - up1) + drh);
564 fbond = -k*(up2 - up1);
565 *dvdlambda += dk*(up2 - up1)*(0.5*(up2 - up1) + drh)
566 + k*(dup2 - dup1)*(up2 - up1 + drh)
567 - k*(up2 - up1)*dup2;
568 }
569
570 if (dr2 == 0.0)
571 {
572 continue;
573 }
574
575 vtot += vbond; /* 1*/
576 fbond *= gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 6 */
577#ifdef DEBUG
578 if (debug)
579 {
580 fprintf(debug, "BONDS: dr = %10g vbond = %10g fbond = %10g\n",
581 dr, vbond, fbond);
582 }
583#endif
584 if (g)
585 {
586 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
587 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
588 }
589 for (m = 0; (m < DIM3); m++) /* 15 */
590 {
591 fij = fbond*dx[m];
592 f[ai][m] += fij;
593 f[aj][m] -= fij;
594 fshift[ki][m] += fij;
595 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
596 }
597 } /* 59 TOTAL */
598
599 return vtot;
600}
601
602real polarize(int nbonds,
603 const t_iatom forceatoms[], const t_iparams forceparams[],
604 const rvec x[], rvec f[], rvec fshift[],
605 const t_pbc *pbc, const t_graph *g,
606 real lambda, real *dvdlambda,
607 const t_mdatoms *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
608 int gmx_unused__attribute__ ((unused)) *global_atom_index)
609{
610 int i, m, ki, ai, aj, type;
611 real dr, dr2, fbond, vbond, fij, vtot, ksh;
612 rvec dx;
613 ivec dt;
614
615 vtot = 0.0;
616 for (i = 0; (i < nbonds); )
617 {
618 type = forceatoms[i++];
619 ai = forceatoms[i++];
620 aj = forceatoms[i++];
621 ksh = sqr(md->chargeA[aj])*ONE_4PI_EPS0((332.0636930*(4.184))*0.1)/forceparams[type].polarize.alpha;
622 if (debug)
623 {
624 fprintf(debug, "POL: local ai = %d aj = %d ksh = %.3f\n", ai, aj, ksh);
625 }
626
627 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
628 dr2 = iprod(dx, dx); /* 5 */
629 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
630
631 *dvdlambda += harmonic(ksh, ksh, 0, 0, dr, lambda, &vbond, &fbond); /* 19 */
632
633 if (dr2 == 0.0)
634 {
635 continue;
636 }
637
638 vtot += vbond; /* 1*/
639 fbond *= gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 6 */
640
641 if (g)
642 {
643 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
644 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
645 }
646 for (m = 0; (m < DIM3); m++) /* 15 */
647 {
648 fij = fbond*dx[m];
649 f[ai][m] += fij;
650 f[aj][m] -= fij;
651 fshift[ki][m] += fij;
652 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
653 }
654 } /* 59 TOTAL */
655 return vtot;
656}
657
658real anharm_polarize(int nbonds,
659 const t_iatom forceatoms[], const t_iparams forceparams[],
660 const rvec x[], rvec f[], rvec fshift[],
661 const t_pbc *pbc, const t_graph *g,
662 real lambda, real *dvdlambda,
663 const t_mdatoms *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
664 int gmx_unused__attribute__ ((unused)) *global_atom_index)
665{
666 int i, m, ki, ai, aj, type;
667 real dr, dr2, fbond, vbond, fij, vtot, ksh, khyp, drcut, ddr, ddr3;
668 rvec dx;
669 ivec dt;
670
671 vtot = 0.0;
672 for (i = 0; (i < nbonds); )
673 {
674 type = forceatoms[i++];
675 ai = forceatoms[i++];
676 aj = forceatoms[i++];
677 ksh = sqr(md->chargeA[aj])*ONE_4PI_EPS0((332.0636930*(4.184))*0.1)/forceparams[type].anharm_polarize.alpha; /* 7*/
678 khyp = forceparams[type].anharm_polarize.khyp;
679 drcut = forceparams[type].anharm_polarize.drcut;
680 if (debug)
681 {
682 fprintf(debug, "POL: local ai = %d aj = %d ksh = %.3f\n", ai, aj, ksh);
683 }
684
685 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
686 dr2 = iprod(dx, dx); /* 5 */
687 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
688
689 *dvdlambda += harmonic(ksh, ksh, 0, 0, dr, lambda, &vbond, &fbond); /* 19 */
690
691 if (dr2 == 0.0)
692 {
693 continue;
694 }
695
696 if (dr > drcut)
697 {
698 ddr = dr-drcut;
699 ddr3 = ddr*ddr*ddr;
700 vbond += khyp*ddr*ddr3;
701 fbond -= 4*khyp*ddr3;
702 }
703 fbond *= gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 6 */
704 vtot += vbond; /* 1*/
705
706 if (g)
707 {
708 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
709 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
710 }
711 for (m = 0; (m < DIM3); m++) /* 15 */
712 {
713 fij = fbond*dx[m];
714 f[ai][m] += fij;
715 f[aj][m] -= fij;
716 fshift[ki][m] += fij;
717 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
718 }
719 } /* 72 TOTAL */
720 return vtot;
721}
722
723real water_pol(int nbonds,
724 const t_iatom forceatoms[], const t_iparams forceparams[],
725 const rvec x[], rvec f[], rvec gmx_unused__attribute__ ((unused)) fshift[],
726 const t_pbc gmx_unused__attribute__ ((unused)) *pbc, const t_graph gmx_unused__attribute__ ((unused)) *g,
727 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
728 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
729 int gmx_unused__attribute__ ((unused)) *global_atom_index)
730{
731 /* This routine implements anisotropic polarizibility for water, through
732 * a shell connected to a dummy with spring constant that differ in the
733 * three spatial dimensions in the molecular frame.
734 */
735 int i, m, aO, aH1, aH2, aD, aS, type, type0;
736 rvec dOH1, dOH2, dHH, dOD, dDS, nW, kk, dx, kdx, proj;
737#ifdef DEBUG
738 rvec df;
739#endif
740 real vtot, fij, r_HH, r_OD, r_nW, tx, ty, tz, qS;
741
742 vtot = 0.0;
743 if (nbonds > 0)
744 {
745 type0 = forceatoms[0];
746 aS = forceatoms[5];
747 qS = md->chargeA[aS];
748 kk[XX0] = sqr(qS)*ONE_4PI_EPS0((332.0636930*(4.184))*0.1)/forceparams[type0].wpol.al_x;
749 kk[YY1] = sqr(qS)*ONE_4PI_EPS0((332.0636930*(4.184))*0.1)/forceparams[type0].wpol.al_y;
750 kk[ZZ2] = sqr(qS)*ONE_4PI_EPS0((332.0636930*(4.184))*0.1)/forceparams[type0].wpol.al_z;
751 r_HH = 1.0/forceparams[type0].wpol.rHH;
752 r_OD = 1.0/forceparams[type0].wpol.rOD;
753 if (debug)
754 {
755 fprintf(debug, "WPOL: qS = %10.5f aS = %5d\n", qS, aS);
756 fprintf(debug, "WPOL: kk = %10.3f %10.3f %10.3f\n",
757 kk[XX0], kk[YY1], kk[ZZ2]);
758 fprintf(debug, "WPOL: rOH = %10.3f rHH = %10.3f rOD = %10.3f\n",
759 forceparams[type0].wpol.rOH,
760 forceparams[type0].wpol.rHH,
761 forceparams[type0].wpol.rOD);
762 }
763 for (i = 0; (i < nbonds); i += 6)
764 {
765 type = forceatoms[i];
766 if (type != type0)
767 {
768 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 768, "Sorry, type = %d, type0 = %d, file = %s, line = %d",
769 type, type0, __FILE__"/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c", __LINE__769);
770 }
771 aO = forceatoms[i+1];
772 aH1 = forceatoms[i+2];
773 aH2 = forceatoms[i+3];
774 aD = forceatoms[i+4];
775 aS = forceatoms[i+5];
776
777 /* Compute vectors describing the water frame */
778 rvec_sub(x[aH1], x[aO], dOH1);
779 rvec_sub(x[aH2], x[aO], dOH2);
780 rvec_sub(x[aH2], x[aH1], dHH);
781 rvec_sub(x[aD], x[aO], dOD);
782 rvec_sub(x[aS], x[aD], dDS);
783 cprod(dOH1, dOH2, nW);
784
785 /* Compute inverse length of normal vector
786 * (this one could be precomputed, but I'm too lazy now)
787 */
788 r_nW = gmx_invsqrt(iprod(nW, nW))gmx_software_invsqrt(iprod(nW, nW));
789 /* This is for precision, but does not make a big difference,
790 * it can go later.
791 */
792 r_OD = gmx_invsqrt(iprod(dOD, dOD))gmx_software_invsqrt(iprod(dOD, dOD));
793
794 /* Normalize the vectors in the water frame */
795 svmul(r_nW, nW, nW);
796 svmul(r_HH, dHH, dHH);
797 svmul(r_OD, dOD, dOD);
798
799 /* Compute displacement of shell along components of the vector */
800 dx[ZZ2] = iprod(dDS, dOD);
801 /* Compute projection on the XY plane: dDS - dx[ZZ]*dOD */
802 for (m = 0; (m < DIM3); m++)
803 {
804 proj[m] = dDS[m]-dx[ZZ2]*dOD[m];
805 }
806
807 /*dx[XX] = iprod(dDS,nW);
808 dx[YY] = iprod(dDS,dHH);*/
809 dx[XX0] = iprod(proj, nW);
810 for (m = 0; (m < DIM3); m++)
811 {
812 proj[m] -= dx[XX0]*nW[m];
813 }
814 dx[YY1] = iprod(proj, dHH);
815 /*#define DEBUG*/
816#ifdef DEBUG
817 if (debug)
818 {
819 fprintf(debug, "WPOL: dx2=%10g dy2=%10g dz2=%10g sum=%10g dDS^2=%10g\n",
820 sqr(dx[XX0]), sqr(dx[YY1]), sqr(dx[ZZ2]), iprod(dx, dx), iprod(dDS, dDS));
821 fprintf(debug, "WPOL: dHH=(%10g,%10g,%10g)\n", dHH[XX0], dHH[YY1], dHH[ZZ2]);
822 fprintf(debug, "WPOL: dOD=(%10g,%10g,%10g), 1/r_OD = %10g\n",
823 dOD[XX0], dOD[YY1], dOD[ZZ2], 1/r_OD);
824 fprintf(debug, "WPOL: nW =(%10g,%10g,%10g), 1/r_nW = %10g\n",
825 nW[XX0], nW[YY1], nW[ZZ2], 1/r_nW);
826 fprintf(debug, "WPOL: dx =%10g, dy =%10g, dz =%10g\n",
827 dx[XX0], dx[YY1], dx[ZZ2]);
828 fprintf(debug, "WPOL: dDSx=%10g, dDSy=%10g, dDSz=%10g\n",
829 dDS[XX0], dDS[YY1], dDS[ZZ2]);
830 }
831#endif
832 /* Now compute the forces and energy */
833 kdx[XX0] = kk[XX0]*dx[XX0];
834 kdx[YY1] = kk[YY1]*dx[YY1];
835 kdx[ZZ2] = kk[ZZ2]*dx[ZZ2];
836 vtot += iprod(dx, kdx);
837 for (m = 0; (m < DIM3); m++)
838 {
839 /* This is a tensor operation but written out for speed */
840 tx = nW[m]*kdx[XX0];
841 ty = dHH[m]*kdx[YY1];
842 tz = dOD[m]*kdx[ZZ2];
843 fij = -tx-ty-tz;
844#ifdef DEBUG
845 df[m] = fij;
846#endif
847 f[aS][m] += fij;
848 f[aD][m] -= fij;
849 }
850#ifdef DEBUG
851 if (debug)
852 {
853 fprintf(debug, "WPOL: vwpol=%g\n", 0.5*iprod(dx, kdx));
854 fprintf(debug, "WPOL: df = (%10g, %10g, %10g)\n", df[XX0], df[YY1], df[ZZ2]);
855 }
856#endif
857 }
858 }
859 return 0.5*vtot;
860}
861
862static real do_1_thole(const rvec xi, const rvec xj, rvec fi, rvec fj,
863 const t_pbc *pbc, real qq,
864 rvec fshift[], real afac)
865{
866 rvec r12;
867 real r12sq, r12_1, r12n, r12bar, v0, v1, fscal, ebar, fff;
868 int m, t;
869
870 t = pbc_rvec_sub(pbc, xi, xj, r12); /* 3 */
871
872 r12sq = iprod(r12, r12); /* 5 */
873 r12_1 = gmx_invsqrt(r12sq)gmx_software_invsqrt(r12sq); /* 5 */
874 r12bar = afac/r12_1; /* 5 */
875 v0 = qq*ONE_4PI_EPS0((332.0636930*(4.184))*0.1)*r12_1; /* 2 */
876 ebar = exp(-r12bar); /* 5 */
877 v1 = (1-(1+0.5*r12bar)*ebar); /* 4 */
878 fscal = ((v0*r12_1)*v1 - v0*0.5*afac*ebar*(r12bar+1))*r12_1; /* 9 */
879 if (debug)
880 {
881 fprintf(debug, "THOLE: v0 = %.3f v1 = %.3f r12= % .3f r12bar = %.3f fscal = %.3f ebar = %.3f\n", v0, v1, 1/r12_1, r12bar, fscal, ebar);
882 }
883
884 for (m = 0; (m < DIM3); m++)
885 {
886 fff = fscal*r12[m];
887 fi[m] += fff;
888 fj[m] -= fff;
889 fshift[t][m] += fff;
890 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fff;
891 } /* 15 */
892
893 return v0*v1; /* 1 */
894 /* 54 */
895}
896
897real thole_pol(int nbonds,
898 const t_iatom forceatoms[], const t_iparams forceparams[],
899 const rvec x[], rvec f[], rvec fshift[],
900 const t_pbc *pbc, const t_graph gmx_unused__attribute__ ((unused)) *g,
901 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
902 const t_mdatoms *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
903 int gmx_unused__attribute__ ((unused)) *global_atom_index)
904{
905 /* Interaction between two pairs of particles with opposite charge */
906 int i, type, a1, da1, a2, da2;
907 real q1, q2, qq, a, al1, al2, afac;
908 real V = 0;
909
910 for (i = 0; (i < nbonds); )
911 {
912 type = forceatoms[i++];
913 a1 = forceatoms[i++];
914 da1 = forceatoms[i++];
915 a2 = forceatoms[i++];
916 da2 = forceatoms[i++];
917 q1 = md->chargeA[da1];
918 q2 = md->chargeA[da2];
919 a = forceparams[type].thole.a;
920 al1 = forceparams[type].thole.alpha1;
921 al2 = forceparams[type].thole.alpha2;
922 qq = q1*q2;
923 afac = a*pow(al1*al2, -1.0/6.0);
924 V += do_1_thole(x[a1], x[a2], f[a1], f[a2], pbc, qq, fshift, afac);
925 V += do_1_thole(x[da1], x[a2], f[da1], f[a2], pbc, -qq, fshift, afac);
926 V += do_1_thole(x[a1], x[da2], f[a1], f[da2], pbc, -qq, fshift, afac);
927 V += do_1_thole(x[da1], x[da2], f[da1], f[da2], pbc, qq, fshift, afac);
928 }
929 /* 290 flops */
930 return V;
931}
932
933real bond_angle(const rvec xi, const rvec xj, const rvec xk, const t_pbc *pbc,
934 rvec r_ij, rvec r_kj, real *costh,
935 int *t1, int *t2)
936/* Return value is the angle between the bonds i-j and j-k */
937{
938 /* 41 FLOPS */
939 real th;
940
941 *t1 = pbc_rvec_sub(pbc, xi, xj, r_ij); /* 3 */
942 *t2 = pbc_rvec_sub(pbc, xk, xj, r_kj); /* 3 */
943
944 *costh = cos_angle(r_ij, r_kj); /* 25 */
945 th = acos(*costh); /* 10 */
946 /* 41 TOTAL */
947 return th;
948}
949
950real angles(int nbonds,
951 const t_iatom forceatoms[], const t_iparams forceparams[],
952 const rvec x[], rvec f[], rvec fshift[],
953 const t_pbc *pbc, const t_graph *g,
954 real lambda, real *dvdlambda,
955 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
956 int gmx_unused__attribute__ ((unused)) *global_atom_index)
957{
958 int i, ai, aj, ak, t1, t2, type;
959 rvec r_ij, r_kj;
960 real cos_theta, cos_theta2, theta, dVdt, va, vtot;
961 ivec jt, dt_ij, dt_kj;
962
963 vtot = 0.0;
964 for (i = 0; i < nbonds; )
965 {
966 type = forceatoms[i++];
967 ai = forceatoms[i++];
968 aj = forceatoms[i++];
969 ak = forceatoms[i++];
970
971 theta = bond_angle(x[ai], x[aj], x[ak], pbc,
972 r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
973
974 *dvdlambda += harmonic(forceparams[type].harmonic.krA,
975 forceparams[type].harmonic.krB,
976 forceparams[type].harmonic.rA*DEG2RAD(3.14159265358979323846/180.0),
977 forceparams[type].harmonic.rB*DEG2RAD(3.14159265358979323846/180.0),
978 theta, lambda, &va, &dVdt); /* 21 */
979 vtot += va;
980
981 cos_theta2 = sqr(cos_theta);
982 if (cos_theta2 < 1)
983 {
984 int m;
985 real st, sth;
986 real cik, cii, ckk;
987 real nrkj2, nrij2;
988 real nrkj_1, nrij_1;
989 rvec f_i, f_j, f_k;
990
991 st = dVdt*gmx_invsqrt(1 - cos_theta2)gmx_software_invsqrt(1 - cos_theta2); /* 12 */
992 sth = st*cos_theta; /* 1 */
993#ifdef DEBUG
994 if (debug)
995 {
996 fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
997 theta*RAD2DEG(180.0/3.14159265358979323846), va, dVdt);
998 }
999#endif
1000 nrij2 = iprod(r_ij, r_ij); /* 5 */
1001 nrkj2 = iprod(r_kj, r_kj); /* 5 */
1002
1003 nrij_1 = gmx_invsqrt(nrij2)gmx_software_invsqrt(nrij2); /* 10 */
1004 nrkj_1 = gmx_invsqrt(nrkj2)gmx_software_invsqrt(nrkj2); /* 10 */
1005
1006 cik = st*nrij_1*nrkj_1; /* 2 */
1007 cii = sth*nrij_1*nrij_1; /* 2 */
1008 ckk = sth*nrkj_1*nrkj_1; /* 2 */
1009
1010 for (m = 0; m < DIM3; m++)
1011 { /* 39 */
1012 f_i[m] = -(cik*r_kj[m] - cii*r_ij[m]);
1013 f_k[m] = -(cik*r_ij[m] - ckk*r_kj[m]);
1014 f_j[m] = -f_i[m] - f_k[m];
1015 f[ai][m] += f_i[m];
1016 f[aj][m] += f_j[m];
1017 f[ak][m] += f_k[m];
1018 }
1019 if (g != NULL((void*)0))
1020 {
1021 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
1022
1023 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
1024 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
1025 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
1026 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
1027 }
1028 rvec_inc(fshift[t1], f_i);
1029 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
1030 rvec_inc(fshift[t2], f_k);
1031 } /* 161 TOTAL */
1032 }
1033
1034 return vtot;
1035}
1036
1037#ifdef GMX_SIMD_HAVE_REAL
1038
1039/* As angles, but using SIMD to calculate many dihedrals at once.
1040 * This routines does not calculate energies and shift forces.
1041 */
1042static gmx_inlineinline void
1043angles_noener_simd(int nbonds,
1044 const t_iatom forceatoms[], const t_iparams forceparams[],
1045 const rvec x[], rvec f[],
1046 const t_pbc *pbc, const t_graph gmx_unused__attribute__ ((unused)) *g,
1047 real gmx_unused__attribute__ ((unused)) lambda,
1048 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
1049 int gmx_unused__attribute__ ((unused)) *global_atom_index)
1050{
1051 const int nfa1 = 4;
1052 int i, iu, s, m;
1053 int type, ai[GMX_SIMD_REAL_WIDTH4], aj[GMX_SIMD_REAL_WIDTH4];
1054 int ak[GMX_SIMD_REAL_WIDTH4];
1055 real coeff_array[2*GMX_SIMD_REAL_WIDTH4+GMX_SIMD_REAL_WIDTH4], *coeff;
1056 real dr_array[2*DIM3*GMX_SIMD_REAL_WIDTH4+GMX_SIMD_REAL_WIDTH4], *dr;
1057 real f_buf_array[6*GMX_SIMD_REAL_WIDTH4+GMX_SIMD_REAL_WIDTH4], *f_buf;
1058 gmx_simd_real_t__m128 k_S, theta0_S;
1059 gmx_simd_real_t__m128 rijx_S, rijy_S, rijz_S;
1060 gmx_simd_real_t__m128 rkjx_S, rkjy_S, rkjz_S;
1061 gmx_simd_real_t__m128 one_S;
1062 gmx_simd_real_t__m128 min_one_plus_eps_S;
1063 gmx_simd_real_t__m128 rij_rkj_S;
1064 gmx_simd_real_t__m128 nrij2_S, nrij_1_S;
1065 gmx_simd_real_t__m128 nrkj2_S, nrkj_1_S;
1066 gmx_simd_real_t__m128 cos_S, invsin_S;
1067 gmx_simd_real_t__m128 theta_S;
1068 gmx_simd_real_t__m128 st_S, sth_S;
1069 gmx_simd_real_t__m128 cik_S, cii_S, ckk_S;
1070 gmx_simd_real_t__m128 f_ix_S, f_iy_S, f_iz_S;
1071 gmx_simd_real_t__m128 f_kx_S, f_ky_S, f_kz_S;
1072 pbc_simd_t pbc_simd;
1073
1074 /* Ensure register memory alignment */
1075 coeff = gmx_simd_align_rgmx_simd_align_f(coeff_array);
1076 dr = gmx_simd_align_rgmx_simd_align_f(dr_array);
1077 f_buf = gmx_simd_align_rgmx_simd_align_f(f_buf_array);
1078
1079 set_pbc_simd(pbc, &pbc_simd);
1080
1081 one_S = gmx_simd_set1_r_mm_set1_ps(1.0);
1082
1083 /* The smallest number > -1 */
1084 min_one_plus_eps_S = gmx_simd_set1_r_mm_set1_ps(-1.0 + 2*GMX_REAL_EPS5.96046448E-08);
1085
1086 /* nbonds is the number of angles times nfa1, here we step GMX_SIMD_REAL_WIDTH angles */
1087 for (i = 0; (i < nbonds); i += GMX_SIMD_REAL_WIDTH4*nfa1)
1088 {
1089 /* Collect atoms for GMX_SIMD_REAL_WIDTH angles.
1090 * iu indexes into forceatoms, we should not let iu go beyond nbonds.
1091 */
1092 iu = i;
1093 for (s = 0; s < GMX_SIMD_REAL_WIDTH4; s++)
1094 {
1095 type = forceatoms[iu];
1096 ai[s] = forceatoms[iu+1];
1097 aj[s] = forceatoms[iu+2];
1098 ak[s] = forceatoms[iu+3];
1099
1100 coeff[s] = forceparams[type].harmonic.krA;
1101 coeff[GMX_SIMD_REAL_WIDTH4+s] = forceparams[type].harmonic.rA*DEG2RAD(3.14159265358979323846/180.0);
1102
1103 /* If you can't use pbc_dx_simd below for PBC, e.g. because
1104 * you can't round in SIMD, use pbc_rvec_sub here.
1105 */
1106 /* Store the non PBC corrected distances packed and aligned */
1107 for (m = 0; m < DIM3; m++)
1108 {
1109 dr[s + m *GMX_SIMD_REAL_WIDTH4] = x[ai[s]][m] - x[aj[s]][m];
1110 dr[s + (DIM3+m)*GMX_SIMD_REAL_WIDTH4] = x[ak[s]][m] - x[aj[s]][m];
1111 }
1112
1113 /* At the end fill the arrays with identical entries */
1114 if (iu + nfa1 < nbonds)
1115 {
1116 iu += nfa1;
1117 }
1118 }
1119
1120 k_S = gmx_simd_load_r_mm_load_ps(coeff);
1121 theta0_S = gmx_simd_load_r_mm_load_ps(coeff+GMX_SIMD_REAL_WIDTH4);
1122
1123 rijx_S = gmx_simd_load_r_mm_load_ps(dr + 0*GMX_SIMD_REAL_WIDTH4);
1124 rijy_S = gmx_simd_load_r_mm_load_ps(dr + 1*GMX_SIMD_REAL_WIDTH4);
1125 rijz_S = gmx_simd_load_r_mm_load_ps(dr + 2*GMX_SIMD_REAL_WIDTH4);
1126 rkjx_S = gmx_simd_load_r_mm_load_ps(dr + 3*GMX_SIMD_REAL_WIDTH4);
1127 rkjy_S = gmx_simd_load_r_mm_load_ps(dr + 4*GMX_SIMD_REAL_WIDTH4);
1128 rkjz_S = gmx_simd_load_r_mm_load_ps(dr + 5*GMX_SIMD_REAL_WIDTH4);
1129
1130 pbc_dx_simd(&rijx_S, &rijy_S, &rijz_S, &pbc_simd);
1131 pbc_dx_simd(&rkjx_S, &rkjy_S, &rkjz_S, &pbc_simd);
1132
1133 rij_rkj_S = gmx_simd_iprod_rgmx_simd_iprod_f(rijx_S, rijy_S, rijz_S,
1134 rkjx_S, rkjy_S, rkjz_S);
1135
1136 nrij2_S = gmx_simd_norm2_rgmx_simd_norm2_f(rijx_S, rijy_S, rijz_S);
1137 nrkj2_S = gmx_simd_norm2_rgmx_simd_norm2_f(rkjx_S, rkjy_S, rkjz_S);
1138
1139 nrij_1_S = gmx_simd_invsqrt_rgmx_simd_invsqrt_f(nrij2_S);
1140 nrkj_1_S = gmx_simd_invsqrt_rgmx_simd_invsqrt_f(nrkj2_S);
1141
1142 cos_S = gmx_simd_mul_r_mm_mul_ps(rij_rkj_S, gmx_simd_mul_r_mm_mul_ps(nrij_1_S, nrkj_1_S));
1143
1144 /* To allow for 180 degrees, we take the max of cos and -1 + 1bit,
1145 * so we can safely get the 1/sin from 1/sqrt(1 - cos^2).
1146 * This also ensures that rounding errors would cause the argument
1147 * of gmx_simd_acos_r to be < -1.
1148 * Note that we do not take precautions for cos(0)=1, so the outer
1149 * atoms in an angle should not be on top of each other.
1150 */
1151 cos_S = gmx_simd_max_r_mm_max_ps(cos_S, min_one_plus_eps_S);
1152
1153 theta_S = gmx_simd_acos_rgmx_simd_acos_f(cos_S);
1154
1155 invsin_S = gmx_simd_invsqrt_rgmx_simd_invsqrt_f(gmx_simd_sub_r_mm_sub_ps(one_S, gmx_simd_mul_r_mm_mul_ps(cos_S, cos_S)));
1156
1157 st_S = gmx_simd_mul_r_mm_mul_ps(gmx_simd_mul_r_mm_mul_ps(k_S, gmx_simd_sub_r_mm_sub_ps(theta0_S, theta_S)),
1158 invsin_S);
1159 sth_S = gmx_simd_mul_r_mm_mul_ps(st_S, cos_S);
1160
1161 cik_S = gmx_simd_mul_r_mm_mul_ps(st_S, gmx_simd_mul_r_mm_mul_ps(nrij_1_S, nrkj_1_S));
1162 cii_S = gmx_simd_mul_r_mm_mul_ps(sth_S, gmx_simd_mul_r_mm_mul_ps(nrij_1_S, nrij_1_S));
1163 ckk_S = gmx_simd_mul_r_mm_mul_ps(sth_S, gmx_simd_mul_r_mm_mul_ps(nrkj_1_S, nrkj_1_S));
1164
1165 f_ix_S = gmx_simd_mul_r_mm_mul_ps(cii_S, rijx_S);
1166 f_ix_S = gmx_simd_fnmadd_r(cik_S, rkjx_S, f_ix_S)_mm_sub_ps(f_ix_S, _mm_mul_ps(cik_S, rkjx_S));
1167 f_iy_S = gmx_simd_mul_r_mm_mul_ps(cii_S, rijy_S);
1168 f_iy_S = gmx_simd_fnmadd_r(cik_S, rkjy_S, f_iy_S)_mm_sub_ps(f_iy_S, _mm_mul_ps(cik_S, rkjy_S));
1169 f_iz_S = gmx_simd_mul_r_mm_mul_ps(cii_S, rijz_S);
1170 f_iz_S = gmx_simd_fnmadd_r(cik_S, rkjz_S, f_iz_S)_mm_sub_ps(f_iz_S, _mm_mul_ps(cik_S, rkjz_S));
1171 f_kx_S = gmx_simd_mul_r_mm_mul_ps(ckk_S, rkjx_S);
1172 f_kx_S = gmx_simd_fnmadd_r(cik_S, rijx_S, f_kx_S)_mm_sub_ps(f_kx_S, _mm_mul_ps(cik_S, rijx_S));
1173 f_ky_S = gmx_simd_mul_r_mm_mul_ps(ckk_S, rkjy_S);
1174 f_ky_S = gmx_simd_fnmadd_r(cik_S, rijy_S, f_ky_S)_mm_sub_ps(f_ky_S, _mm_mul_ps(cik_S, rijy_S));
1175 f_kz_S = gmx_simd_mul_r_mm_mul_ps(ckk_S, rkjz_S);
1176 f_kz_S = gmx_simd_fnmadd_r(cik_S, rijz_S, f_kz_S)_mm_sub_ps(f_kz_S, _mm_mul_ps(cik_S, rijz_S));
1177
1178 gmx_simd_store_r_mm_store_ps(f_buf + 0*GMX_SIMD_REAL_WIDTH4, f_ix_S);
1179 gmx_simd_store_r_mm_store_ps(f_buf + 1*GMX_SIMD_REAL_WIDTH4, f_iy_S);
1180 gmx_simd_store_r_mm_store_ps(f_buf + 2*GMX_SIMD_REAL_WIDTH4, f_iz_S);
1181 gmx_simd_store_r_mm_store_ps(f_buf + 3*GMX_SIMD_REAL_WIDTH4, f_kx_S);
1182 gmx_simd_store_r_mm_store_ps(f_buf + 4*GMX_SIMD_REAL_WIDTH4, f_ky_S);
1183 gmx_simd_store_r_mm_store_ps(f_buf + 5*GMX_SIMD_REAL_WIDTH4, f_kz_S);
1184
1185 iu = i;
1186 s = 0;
1187 do
1188 {
1189 for (m = 0; m < DIM3; m++)
1190 {
1191 f[ai[s]][m] += f_buf[s + m*GMX_SIMD_REAL_WIDTH4];
1192 f[aj[s]][m] -= f_buf[s + m*GMX_SIMD_REAL_WIDTH4] + f_buf[s + (DIM3+m)*GMX_SIMD_REAL_WIDTH4];
1193 f[ak[s]][m] += f_buf[s + (DIM3+m)*GMX_SIMD_REAL_WIDTH4];
1194 }
1195 s++;
1196 iu += nfa1;
1197 }
1198 while (s < GMX_SIMD_REAL_WIDTH4 && iu < nbonds);
1199 }
1200}
1201
1202#endif /* GMX_SIMD_HAVE_REAL */
1203
1204real linear_angles(int nbonds,
1205 const t_iatom forceatoms[], const t_iparams forceparams[],
1206 const rvec x[], rvec f[], rvec fshift[],
1207 const t_pbc *pbc, const t_graph *g,
1208 real lambda, real *dvdlambda,
1209 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
1210 int gmx_unused__attribute__ ((unused)) *global_atom_index)
1211{
1212 int i, m, ai, aj, ak, t1, t2, type;
1213 rvec f_i, f_j, f_k;
1214 real L1, kA, kB, aA, aB, dr, dr2, va, vtot, a, b, klin;
1215 ivec jt, dt_ij, dt_kj;
1216 rvec r_ij, r_kj, r_ik, dx;
1217
1218 L1 = 1-lambda;
1219 vtot = 0.0;
1220 for (i = 0; (i < nbonds); )
1221 {
1222 type = forceatoms[i++];
1223 ai = forceatoms[i++];
1224 aj = forceatoms[i++];
1225 ak = forceatoms[i++];
1226
1227 kA = forceparams[type].linangle.klinA;
1228 kB = forceparams[type].linangle.klinB;
1229 klin = L1*kA + lambda*kB;
1230
1231 aA = forceparams[type].linangle.aA;
1232 aB = forceparams[type].linangle.aB;
1233 a = L1*aA+lambda*aB;
1234 b = 1-a;
1235
1236 t1 = pbc_rvec_sub(pbc, x[ai], x[aj], r_ij);
1237 t2 = pbc_rvec_sub(pbc, x[ak], x[aj], r_kj);
1238 rvec_sub(r_ij, r_kj, r_ik);
1239
1240 dr2 = 0;
1241 for (m = 0; (m < DIM3); m++)
1242 {
1243 dr = -a * r_ij[m] - b * r_kj[m];
1244 dr2 += dr*dr;
1245 dx[m] = dr;
1246 f_i[m] = a*klin*dr;
1247 f_k[m] = b*klin*dr;
1248 f_j[m] = -(f_i[m]+f_k[m]);
1249 f[ai][m] += f_i[m];
1250 f[aj][m] += f_j[m];
1251 f[ak][m] += f_k[m];
1252 }
1253 va = 0.5*klin*dr2;
1254 *dvdlambda += 0.5*(kB-kA)*dr2 + klin*(aB-aA)*iprod(dx, r_ik);
1255
1256 vtot += va;
1257
1258 if (g)
1259 {
1260 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
1261
1262 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
1263 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
1264 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
1265 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
1266 }
1267 rvec_inc(fshift[t1], f_i);
1268 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
1269 rvec_inc(fshift[t2], f_k);
1270 } /* 57 TOTAL */
1271 return vtot;
1272}
1273
1274real urey_bradley(int nbonds,
1275 const t_iatom forceatoms[], const t_iparams forceparams[],
1276 const rvec x[], rvec f[], rvec fshift[],
1277 const t_pbc *pbc, const t_graph *g,
1278 real lambda, real *dvdlambda,
1279 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
1280 int gmx_unused__attribute__ ((unused)) *global_atom_index)
1281{
1282 int i, m, ai, aj, ak, t1, t2, type, ki;
1283 rvec r_ij, r_kj, r_ik;
1284 real cos_theta, cos_theta2, theta;
1285 real dVdt, va, vtot, dr, dr2, vbond, fbond, fik;
1286 real kthA, th0A, kUBA, r13A, kthB, th0B, kUBB, r13B;
1287 ivec jt, dt_ij, dt_kj, dt_ik;
1288
1289 vtot = 0.0;
1290 for (i = 0; (i < nbonds); )
1291 {
1292 type = forceatoms[i++];
1293 ai = forceatoms[i++];
1294 aj = forceatoms[i++];
1295 ak = forceatoms[i++];
1296 th0A = forceparams[type].u_b.thetaA*DEG2RAD(3.14159265358979323846/180.0);
1297 kthA = forceparams[type].u_b.kthetaA;
1298 r13A = forceparams[type].u_b.r13A;
1299 kUBA = forceparams[type].u_b.kUBA;
1300 th0B = forceparams[type].u_b.thetaB*DEG2RAD(3.14159265358979323846/180.0);
1301 kthB = forceparams[type].u_b.kthetaB;
1302 r13B = forceparams[type].u_b.r13B;
1303 kUBB = forceparams[type].u_b.kUBB;
1304
1305 theta = bond_angle(x[ai], x[aj], x[ak], pbc,
1306 r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
1307
1308 *dvdlambda += harmonic(kthA, kthB, th0A, th0B, theta, lambda, &va, &dVdt); /* 21 */
1309 vtot += va;
1310
1311 ki = pbc_rvec_sub(pbc, x[ai], x[ak], r_ik); /* 3 */
1312 dr2 = iprod(r_ik, r_ik); /* 5 */
1313 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
1314
1315 *dvdlambda += harmonic(kUBA, kUBB, r13A, r13B, dr, lambda, &vbond, &fbond); /* 19 */
1316
1317 cos_theta2 = sqr(cos_theta); /* 1 */
1318 if (cos_theta2 < 1)
1319 {
1320 real st, sth;
1321 real cik, cii, ckk;
1322 real nrkj2, nrij2;
1323 rvec f_i, f_j, f_k;
1324
1325 st = dVdt*gmx_invsqrt(1 - cos_theta2)gmx_software_invsqrt(1 - cos_theta2); /* 12 */
1326 sth = st*cos_theta; /* 1 */
1327#ifdef DEBUG
1328 if (debug)
1329 {
1330 fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
1331 theta*RAD2DEG(180.0/3.14159265358979323846), va, dVdt);
1332 }
1333#endif
1334 nrkj2 = iprod(r_kj, r_kj); /* 5 */
1335 nrij2 = iprod(r_ij, r_ij);
1336
1337 cik = st*gmx_invsqrt(nrkj2*nrij2)gmx_software_invsqrt(nrkj2*nrij2); /* 12 */
1338 cii = sth/nrij2; /* 10 */
1339 ckk = sth/nrkj2; /* 10 */
1340
1341 for (m = 0; (m < DIM3); m++) /* 39 */
1342 {
1343 f_i[m] = -(cik*r_kj[m]-cii*r_ij[m]);
1344 f_k[m] = -(cik*r_ij[m]-ckk*r_kj[m]);
1345 f_j[m] = -f_i[m]-f_k[m];
1346 f[ai][m] += f_i[m];
1347 f[aj][m] += f_j[m];
1348 f[ak][m] += f_k[m];
1349 }
1350 if (g)
1351 {
1352 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
1353
1354 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
1355 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
1356 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
1357 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
1358 }
1359 rvec_inc(fshift[t1], f_i);
1360 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
1361 rvec_inc(fshift[t2], f_k);
1362 } /* 161 TOTAL */
1363 /* Time for the bond calculations */
1364 if (dr2 == 0.0)
1365 {
1366 continue;
1367 }
1368
1369 vtot += vbond; /* 1*/
1370 fbond *= gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 6 */
1371
1372 if (g)
1373 {
1374 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, ak)((g)->ishift[ak]), dt_ik);
1375 ki = IVEC2IS(dt_ik)(((2*2 +1)*((2*1 +1)*(((dt_ik)[2])+1)+((dt_ik)[1])+1)+((dt_ik
)[0])+2));
1376 }
1377 for (m = 0; (m < DIM3); m++) /* 15 */
1378 {
1379 fik = fbond*r_ik[m];
1380 f[ai][m] += fik;
1381 f[ak][m] -= fik;
1382 fshift[ki][m] += fik;
1383 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fik;
1384 }
1385 }
1386 return vtot;
1387}
1388
1389real quartic_angles(int nbonds,
1390 const t_iatom forceatoms[], const t_iparams forceparams[],
1391 const rvec x[], rvec f[], rvec fshift[],
1392 const t_pbc *pbc, const t_graph *g,
1393 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
1394 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
1395 int gmx_unused__attribute__ ((unused)) *global_atom_index)
1396{
1397 int i, j, ai, aj, ak, t1, t2, type;
1398 rvec r_ij, r_kj;
1399 real cos_theta, cos_theta2, theta, dt, dVdt, va, dtp, c, vtot;
1400 ivec jt, dt_ij, dt_kj;
1401
1402 vtot = 0.0;
1403 for (i = 0; (i < nbonds); )
1404 {
1405 type = forceatoms[i++];
1406 ai = forceatoms[i++];
1407 aj = forceatoms[i++];
1408 ak = forceatoms[i++];
1409
1410 theta = bond_angle(x[ai], x[aj], x[ak], pbc,
1411 r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
1412
1413 dt = theta - forceparams[type].qangle.theta*DEG2RAD(3.14159265358979323846/180.0); /* 2 */
1414
1415 dVdt = 0;
1416 va = forceparams[type].qangle.c[0];
1417 dtp = 1.0;
1418 for (j = 1; j <= 4; j++)
1419 {
1420 c = forceparams[type].qangle.c[j];
1421 dVdt -= j*c*dtp;
1422 dtp *= dt;
1423 va += c*dtp;
1424 }
1425 /* 20 */
1426
1427 vtot += va;
1428
1429 cos_theta2 = sqr(cos_theta); /* 1 */
1430 if (cos_theta2 < 1)
1431 {
1432 int m;
1433 real st, sth;
1434 real cik, cii, ckk;
1435 real nrkj2, nrij2;
1436 rvec f_i, f_j, f_k;
1437
1438 st = dVdt*gmx_invsqrt(1 - cos_theta2)gmx_software_invsqrt(1 - cos_theta2); /* 12 */
1439 sth = st*cos_theta; /* 1 */
1440#ifdef DEBUG
1441 if (debug)
1442 {
1443 fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
1444 theta*RAD2DEG(180.0/3.14159265358979323846), va, dVdt);
1445 }
1446#endif
1447 nrkj2 = iprod(r_kj, r_kj); /* 5 */
1448 nrij2 = iprod(r_ij, r_ij);
1449
1450 cik = st*gmx_invsqrt(nrkj2*nrij2)gmx_software_invsqrt(nrkj2*nrij2); /* 12 */
1451 cii = sth/nrij2; /* 10 */
1452 ckk = sth/nrkj2; /* 10 */
1453
1454 for (m = 0; (m < DIM3); m++) /* 39 */
1455 {
1456 f_i[m] = -(cik*r_kj[m]-cii*r_ij[m]);
1457 f_k[m] = -(cik*r_ij[m]-ckk*r_kj[m]);
1458 f_j[m] = -f_i[m]-f_k[m];
1459 f[ai][m] += f_i[m];
1460 f[aj][m] += f_j[m];
1461 f[ak][m] += f_k[m];
1462 }
1463 if (g)
1464 {
1465 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
1466
1467 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
1468 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
1469 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
1470 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
1471 }
1472 rvec_inc(fshift[t1], f_i);
1473 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
1474 rvec_inc(fshift[t2], f_k);
1475 } /* 153 TOTAL */
1476 }
1477 return vtot;
1478}
1479
1480real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
1481 const t_pbc *pbc,
1482 rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n,
1483 real *sign, int *t1, int *t2, int *t3)
1484{
1485 real ipr, phi;
1486
1487 *t1 = pbc_rvec_sub(pbc, xi, xj, r_ij); /* 3 */
1488 *t2 = pbc_rvec_sub(pbc, xk, xj, r_kj); /* 3 */
1489 *t3 = pbc_rvec_sub(pbc, xk, xl, r_kl); /* 3 */
1490
1491 cprod(r_ij, r_kj, m); /* 9 */
1492 cprod(r_kj, r_kl, n); /* 9 */
1493 phi = gmx_angle(m, n); /* 49 (assuming 25 for atan2) */
1494 ipr = iprod(r_ij, n); /* 5 */
1495 (*sign) = (ipr < 0.0) ? -1.0 : 1.0;
1496 phi = (*sign)*phi; /* 1 */
1497 /* 82 TOTAL */
1498 return phi;
1499}
1500
1501
1502#ifdef GMX_SIMD_HAVE_REAL
1503
1504/* As dih_angle above, but calculates 4 dihedral angles at once using SIMD,
1505 * also calculates the pre-factor required for the dihedral force update.
1506 * Note that bv and buf should be register aligned.
1507 */
1508static gmx_inlineinline void
1509dih_angle_simd(const rvec *x,
1510 const int *ai, const int *aj, const int *ak, const int *al,
1511 const pbc_simd_t *pbc,
1512 real *dr,
1513 gmx_simd_real_t__m128 *phi_S,
1514 gmx_simd_real_t__m128 *mx_S, gmx_simd_real_t__m128 *my_S, gmx_simd_real_t__m128 *mz_S,
1515 gmx_simd_real_t__m128 *nx_S, gmx_simd_real_t__m128 *ny_S, gmx_simd_real_t__m128 *nz_S,
1516 gmx_simd_real_t__m128 *nrkj_m2_S,
1517 gmx_simd_real_t__m128 *nrkj_n2_S,
1518 real *p,
1519 real *q)
1520{
1521 int s, m;
1522 gmx_simd_real_t__m128 rijx_S, rijy_S, rijz_S;
1523 gmx_simd_real_t__m128 rkjx_S, rkjy_S, rkjz_S;
1524 gmx_simd_real_t__m128 rklx_S, rkly_S, rklz_S;
1525 gmx_simd_real_t__m128 cx_S, cy_S, cz_S;
1526 gmx_simd_real_t__m128 cn_S;
1527 gmx_simd_real_t__m128 s_S;
1528 gmx_simd_real_t__m128 ipr_S;
1529 gmx_simd_real_t__m128 iprm_S, iprn_S;
1530 gmx_simd_real_t__m128 nrkj2_S, nrkj_1_S, nrkj_2_S, nrkj_S;
1531 gmx_simd_real_t__m128 toler_S;
1532 gmx_simd_real_t__m128 p_S, q_S;
1533 gmx_simd_real_t__m128 nrkj2_min_S;
1534 gmx_simd_real_t__m128 real_eps_S;
1535
1536 /* Used to avoid division by zero.
1537 * We take into acount that we multiply the result by real_eps_S.
1538 */
1539 nrkj2_min_S = gmx_simd_set1_r_mm_set1_ps(GMX_REAL_MIN1.17549435E-38/(2*GMX_REAL_EPS5.96046448E-08));
1540
1541 /* The value of the last significant bit (GMX_REAL_EPS is half of that) */
1542 real_eps_S = gmx_simd_set1_r_mm_set1_ps(2*GMX_REAL_EPS5.96046448E-08);
1543
1544 for (s = 0; s < GMX_SIMD_REAL_WIDTH4; s++)
1545 {
1546 /* If you can't use pbc_dx_simd below for PBC, e.g. because
1547 * you can't round in SIMD, use pbc_rvec_sub here.
1548 */
1549 for (m = 0; m < DIM3; m++)
1550 {
1551 dr[s + (0*DIM3 + m)*GMX_SIMD_REAL_WIDTH4] = x[ai[s]][m] - x[aj[s]][m];
1552 dr[s + (1*DIM3 + m)*GMX_SIMD_REAL_WIDTH4] = x[ak[s]][m] - x[aj[s]][m];
1553 dr[s + (2*DIM3 + m)*GMX_SIMD_REAL_WIDTH4] = x[ak[s]][m] - x[al[s]][m];
1554 }
1555 }
1556
1557 rijx_S = gmx_simd_load_r_mm_load_ps(dr + 0*GMX_SIMD_REAL_WIDTH4);
1558 rijy_S = gmx_simd_load_r_mm_load_ps(dr + 1*GMX_SIMD_REAL_WIDTH4);
1559 rijz_S = gmx_simd_load_r_mm_load_ps(dr + 2*GMX_SIMD_REAL_WIDTH4);
1560 rkjx_S = gmx_simd_load_r_mm_load_ps(dr + 3*GMX_SIMD_REAL_WIDTH4);
1561 rkjy_S = gmx_simd_load_r_mm_load_ps(dr + 4*GMX_SIMD_REAL_WIDTH4);
1562 rkjz_S = gmx_simd_load_r_mm_load_ps(dr + 5*GMX_SIMD_REAL_WIDTH4);
1563 rklx_S = gmx_simd_load_r_mm_load_ps(dr + 6*GMX_SIMD_REAL_WIDTH4);
1564 rkly_S = gmx_simd_load_r_mm_load_ps(dr + 7*GMX_SIMD_REAL_WIDTH4);
1565 rklz_S = gmx_simd_load_r_mm_load_ps(dr + 8*GMX_SIMD_REAL_WIDTH4);
1566
1567 pbc_dx_simd(&rijx_S, &rijy_S, &rijz_S, pbc);
1568 pbc_dx_simd(&rkjx_S, &rkjy_S, &rkjz_S, pbc);
1569 pbc_dx_simd(&rklx_S, &rkly_S, &rklz_S, pbc);
1570
1571 gmx_simd_cprod_rgmx_simd_cprod_f(rijx_S, rijy_S, rijz_S,
1572 rkjx_S, rkjy_S, rkjz_S,
1573 mx_S, my_S, mz_S);
1574
1575 gmx_simd_cprod_rgmx_simd_cprod_f(rkjx_S, rkjy_S, rkjz_S,
1576 rklx_S, rkly_S, rklz_S,
1577 nx_S, ny_S, nz_S);
1578
1579 gmx_simd_cprod_rgmx_simd_cprod_f(*mx_S, *my_S, *mz_S,
1580 *nx_S, *ny_S, *nz_S,
1581 &cx_S, &cy_S, &cz_S);
1582
1583 cn_S = gmx_simd_sqrt_rgmx_simd_sqrt_f(gmx_simd_norm2_rgmx_simd_norm2_f(cx_S, cy_S, cz_S));
1584
1585 s_S = gmx_simd_iprod_rgmx_simd_iprod_f(*mx_S, *my_S, *mz_S, *nx_S, *ny_S, *nz_S);
1586
1587 /* Determine the dihedral angle, the sign might need correction */
1588 *phi_S = gmx_simd_atan2_rgmx_simd_atan2_f(cn_S, s_S);
1589
1590 ipr_S = gmx_simd_iprod_rgmx_simd_iprod_f(rijx_S, rijy_S, rijz_S,
1591 *nx_S, *ny_S, *nz_S);
1592
1593 iprm_S = gmx_simd_norm2_rgmx_simd_norm2_f(*mx_S, *my_S, *mz_S);
1594 iprn_S = gmx_simd_norm2_rgmx_simd_norm2_f(*nx_S, *ny_S, *nz_S);
1595
1596 nrkj2_S = gmx_simd_norm2_rgmx_simd_norm2_f(rkjx_S, rkjy_S, rkjz_S);
1597
1598 /* Avoid division by zero. When zero, the result is multiplied by 0
1599 * anyhow, so the 3 max below do not affect the final result.
1600 */
1601 nrkj2_S = gmx_simd_max_r_mm_max_ps(nrkj2_S, nrkj2_min_S);
1602 nrkj_1_S = gmx_simd_invsqrt_rgmx_simd_invsqrt_f(nrkj2_S);
1603 nrkj_2_S = gmx_simd_mul_r_mm_mul_ps(nrkj_1_S, nrkj_1_S);
1604 nrkj_S = gmx_simd_mul_r_mm_mul_ps(nrkj2_S, nrkj_1_S);
1605
1606 toler_S = gmx_simd_mul_r_mm_mul_ps(nrkj2_S, real_eps_S);
1607
1608 /* Here the plain-C code uses a conditional, but we can't do that in SIMD.
1609 * So we take a max with the tolerance instead. Since we multiply with
1610 * m or n later, the max does not affect the results.
1611 */
1612 iprm_S = gmx_simd_max_r_mm_max_ps(iprm_S, toler_S);
1613 iprn_S = gmx_simd_max_r_mm_max_ps(iprn_S, toler_S);
1614 *nrkj_m2_S = gmx_simd_mul_r_mm_mul_ps(nrkj_S, gmx_simd_inv_rgmx_simd_inv_f(iprm_S));
1615 *nrkj_n2_S = gmx_simd_mul_r_mm_mul_ps(nrkj_S, gmx_simd_inv_rgmx_simd_inv_f(iprn_S));
1616
1617 /* Set sign of phi_S with the sign of ipr_S; phi_S is currently positive */
1618 *phi_S = gmx_simd_xor_sign_rgmx_simd_xor_sign_f(*phi_S, ipr_S);
1619 p_S = gmx_simd_iprod_rgmx_simd_iprod_f(rijx_S, rijy_S, rijz_S,
1620 rkjx_S, rkjy_S, rkjz_S);
1621 p_S = gmx_simd_mul_r_mm_mul_ps(p_S, nrkj_2_S);
1622
1623 q_S = gmx_simd_iprod_rgmx_simd_iprod_f(rklx_S, rkly_S, rklz_S,
1624 rkjx_S, rkjy_S, rkjz_S);
1625 q_S = gmx_simd_mul_r_mm_mul_ps(q_S, nrkj_2_S);
1626
1627 gmx_simd_store_r_mm_store_ps(p, p_S);
1628 gmx_simd_store_r_mm_store_ps(q, q_S);
1629}
1630
1631#endif /* GMX_SIMD_HAVE_REAL */
1632
1633
1634void do_dih_fup(int i, int j, int k, int l, real ddphi,
1635 rvec r_ij, rvec r_kj, rvec r_kl,
1636 rvec m, rvec n, rvec f[], rvec fshift[],
1637 const t_pbc *pbc, const t_graph *g,
1638 const rvec x[], int t1, int t2, int t3)
1639{
1640 /* 143 FLOPS */
1641 rvec f_i, f_j, f_k, f_l;
1642 rvec uvec, vvec, svec, dx_jl;
1643 real iprm, iprn, nrkj, nrkj2, nrkj_1, nrkj_2;
1644 real a, b, p, q, toler;
1645 ivec jt, dt_ij, dt_kj, dt_lj;
1646
1647 iprm = iprod(m, m); /* 5 */
1648 iprn = iprod(n, n); /* 5 */
1649 nrkj2 = iprod(r_kj, r_kj); /* 5 */
1650 toler = nrkj2*GMX_REAL_EPS5.96046448E-08;
1651 if ((iprm > toler) && (iprn > toler))
1652 {
1653 nrkj_1 = gmx_invsqrt(nrkj2)gmx_software_invsqrt(nrkj2); /* 10 */
1654 nrkj_2 = nrkj_1*nrkj_1; /* 1 */
1655 nrkj = nrkj2*nrkj_1; /* 1 */
1656 a = -ddphi*nrkj/iprm; /* 11 */
1657 svmul(a, m, f_i); /* 3 */
1658 b = ddphi*nrkj/iprn; /* 11 */
1659 svmul(b, n, f_l); /* 3 */
1660 p = iprod(r_ij, r_kj); /* 5 */
1661 p *= nrkj_2; /* 1 */
1662 q = iprod(r_kl, r_kj); /* 5 */
1663 q *= nrkj_2; /* 1 */
1664 svmul(p, f_i, uvec); /* 3 */
1665 svmul(q, f_l, vvec); /* 3 */
1666 rvec_sub(uvec, vvec, svec); /* 3 */
1667 rvec_sub(f_i, svec, f_j); /* 3 */
1668 rvec_add(f_l, svec, f_k); /* 3 */
1669 rvec_inc(f[i], f_i); /* 3 */
1670 rvec_dec(f[j], f_j); /* 3 */
1671 rvec_dec(f[k], f_k); /* 3 */
1672 rvec_inc(f[l], f_l); /* 3 */
1673
1674 if (g)
1675 {
1676 copy_ivec(SHIFT_IVEC(g, j)((g)->ishift[j]), jt);
1677 ivec_sub(SHIFT_IVEC(g, i)((g)->ishift[i]), jt, dt_ij);
1678 ivec_sub(SHIFT_IVEC(g, k)((g)->ishift[k]), jt, dt_kj);
1679 ivec_sub(SHIFT_IVEC(g, l)((g)->ishift[l]), jt, dt_lj);
1680 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
1681 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
1682 t3 = IVEC2IS(dt_lj)(((2*2 +1)*((2*1 +1)*(((dt_lj)[2])+1)+((dt_lj)[1])+1)+((dt_lj
)[0])+2));
1683 }
1684 else if (pbc)
1685 {
1686 t3 = pbc_rvec_sub(pbc, x[l], x[j], dx_jl);
1687 }
1688 else
1689 {
1690 t3 = CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2);
1691 }
1692
1693 rvec_inc(fshift[t1], f_i);
1694 rvec_dec(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
1695 rvec_dec(fshift[t2], f_k);
1696 rvec_inc(fshift[t3], f_l);
1697 }
1698 /* 112 TOTAL */
1699}
1700
1701/* As do_dih_fup above, but without shift forces */
1702static void
1703do_dih_fup_noshiftf(int i, int j, int k, int l, real ddphi,
1704 rvec r_ij, rvec r_kj, rvec r_kl,
1705 rvec m, rvec n, rvec f[])
1706{
1707 rvec f_i, f_j, f_k, f_l;
1708 rvec uvec, vvec, svec, dx_jl;
1709 real iprm, iprn, nrkj, nrkj2, nrkj_1, nrkj_2;
1710 real a, b, p, q, toler;
1711 ivec jt, dt_ij, dt_kj, dt_lj;
1712
1713 iprm = iprod(m, m); /* 5 */
1714 iprn = iprod(n, n); /* 5 */
1715 nrkj2 = iprod(r_kj, r_kj); /* 5 */
1716 toler = nrkj2*GMX_REAL_EPS5.96046448E-08;
1717 if ((iprm > toler) && (iprn > toler))
1718 {
1719 nrkj_1 = gmx_invsqrt(nrkj2)gmx_software_invsqrt(nrkj2); /* 10 */
1720 nrkj_2 = nrkj_1*nrkj_1; /* 1 */
1721 nrkj = nrkj2*nrkj_1; /* 1 */
1722 a = -ddphi*nrkj/iprm; /* 11 */
1723 svmul(a, m, f_i); /* 3 */
1724 b = ddphi*nrkj/iprn; /* 11 */
1725 svmul(b, n, f_l); /* 3 */
1726 p = iprod(r_ij, r_kj); /* 5 */
1727 p *= nrkj_2; /* 1 */
1728 q = iprod(r_kl, r_kj); /* 5 */
1729 q *= nrkj_2; /* 1 */
1730 svmul(p, f_i, uvec); /* 3 */
1731 svmul(q, f_l, vvec); /* 3 */
1732 rvec_sub(uvec, vvec, svec); /* 3 */
1733 rvec_sub(f_i, svec, f_j); /* 3 */
1734 rvec_add(f_l, svec, f_k); /* 3 */
1735 rvec_inc(f[i], f_i); /* 3 */
1736 rvec_dec(f[j], f_j); /* 3 */
1737 rvec_dec(f[k], f_k); /* 3 */
1738 rvec_inc(f[l], f_l); /* 3 */
1739 }
1740}
1741
1742/* As do_dih_fup_noshiftf above, but with pre-calculated pre-factors */
1743static gmx_inlineinline void
1744do_dih_fup_noshiftf_precalc(int i, int j, int k, int l,
1745 real p, real q,
1746 real f_i_x, real f_i_y, real f_i_z,
1747 real mf_l_x, real mf_l_y, real mf_l_z,
1748 rvec f[])
1749{
1750 rvec f_i, f_j, f_k, f_l;
1751 rvec uvec, vvec, svec;
1752
1753 f_i[XX0] = f_i_x;
1754 f_i[YY1] = f_i_y;
1755 f_i[ZZ2] = f_i_z;
1756 f_l[XX0] = -mf_l_x;
1757 f_l[YY1] = -mf_l_y;
1758 f_l[ZZ2] = -mf_l_z;
1759 svmul(p, f_i, uvec);
1760 svmul(q, f_l, vvec);
1761 rvec_sub(uvec, vvec, svec);
1762 rvec_sub(f_i, svec, f_j);
1763 rvec_add(f_l, svec, f_k);
1764 rvec_inc(f[i], f_i);
1765 rvec_dec(f[j], f_j);
1766 rvec_dec(f[k], f_k);
1767 rvec_inc(f[l], f_l);
1768}
1769
1770
1771real dopdihs(real cpA, real cpB, real phiA, real phiB, int mult,
1772 real phi, real lambda, real *V, real *F)
1773{
1774 real v, dvdlambda, mdphi, v1, sdphi, ddphi;
1775 real L1 = 1.0 - lambda;
1776 real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD(3.14159265358979323846/180.0);
1777 real dph0 = (phiB - phiA)*DEG2RAD(3.14159265358979323846/180.0);
1778 real cp = L1*cpA + lambda*cpB;
1779
1780 mdphi = mult*phi - ph0;
1781 sdphi = sin(mdphi);
1782 ddphi = -cp*mult*sdphi;
1783 v1 = 1.0 + cos(mdphi);
1784 v = cp*v1;
1785
1786 dvdlambda = (cpB - cpA)*v1 + cp*dph0*sdphi;
1787
1788 *V = v;
1789 *F = ddphi;
1790
1791 return dvdlambda;
1792
1793 /* That was 40 flops */
1794}
1795
1796static void
1797dopdihs_noener(real cpA, real cpB, real phiA, real phiB, int mult,
1798 real phi, real lambda, real *F)
1799{
1800 real mdphi, sdphi, ddphi;
1801 real L1 = 1.0 - lambda;
1802 real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD(3.14159265358979323846/180.0);
1803 real cp = L1*cpA + lambda*cpB;
1804
1805 mdphi = mult*phi - ph0;
1806 sdphi = sin(mdphi);
1807 ddphi = -cp*mult*sdphi;
1808
1809 *F = ddphi;
1810
1811 /* That was 20 flops */
1812}
1813
1814static void
1815dopdihs_mdphi(real cpA, real cpB, real phiA, real phiB, int mult,
1816 real phi, real lambda, real *cp, real *mdphi)
1817{
1818 real L1 = 1.0 - lambda;
1819 real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD(3.14159265358979323846/180.0);
1820
1821 *cp = L1*cpA + lambda*cpB;
1822
1823 *mdphi = mult*phi - ph0;
1824}
1825
1826static real dopdihs_min(real cpA, real cpB, real phiA, real phiB, int mult,
1827 real phi, real lambda, real *V, real *F)
1828/* similar to dopdihs, except for a minus sign *
1829 * and a different treatment of mult/phi0 */
1830{
1831 real v, dvdlambda, mdphi, v1, sdphi, ddphi;
1832 real L1 = 1.0 - lambda;
1833 real ph0 = (L1*phiA + lambda*phiB)*DEG2RAD(3.14159265358979323846/180.0);
1834 real dph0 = (phiB - phiA)*DEG2RAD(3.14159265358979323846/180.0);
1835 real cp = L1*cpA + lambda*cpB;
1836
1837 mdphi = mult*(phi-ph0);
1838 sdphi = sin(mdphi);
1839 ddphi = cp*mult*sdphi;
1840 v1 = 1.0-cos(mdphi);
1841 v = cp*v1;
1842
1843 dvdlambda = (cpB-cpA)*v1 + cp*dph0*sdphi;
1844
1845 *V = v;
1846 *F = ddphi;
1847
1848 return dvdlambda;
1849
1850 /* That was 40 flops */
1851}
1852
1853real pdihs(int nbonds,
1854 const t_iatom forceatoms[], const t_iparams forceparams[],
1855 const rvec x[], rvec f[], rvec fshift[],
1856 const t_pbc *pbc, const t_graph *g,
1857 real lambda, real *dvdlambda,
1858 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
1859 int gmx_unused__attribute__ ((unused)) *global_atom_index)
1860{
1861 int i, type, ai, aj, ak, al;
1862 int t1, t2, t3;
1863 rvec r_ij, r_kj, r_kl, m, n;
1864 real phi, sign, ddphi, vpd, vtot;
1865
1866 vtot = 0.0;
1867
1868 for (i = 0; (i < nbonds); )
1869 {
1870 type = forceatoms[i++];
1871 ai = forceatoms[i++];
1872 aj = forceatoms[i++];
1873 ak = forceatoms[i++];
1874 al = forceatoms[i++];
1875
1876 phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
1877 &sign, &t1, &t2, &t3); /* 84 */
1878 *dvdlambda += dopdihs(forceparams[type].pdihs.cpA,
1879 forceparams[type].pdihs.cpB,
1880 forceparams[type].pdihs.phiA,
1881 forceparams[type].pdihs.phiB,
1882 forceparams[type].pdihs.mult,
1883 phi, lambda, &vpd, &ddphi);
1884
1885 vtot += vpd;
1886 do_dih_fup(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n,
1887 f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
1888
1889#ifdef DEBUG
1890 fprintf(debug, "pdih: (%d,%d,%d,%d) phi=%g\n",
1891 ai, aj, ak, al, phi);
1892#endif
1893 } /* 223 TOTAL */
1894
1895 return vtot;
1896}
1897
1898void make_dp_periodic(real *dp) /* 1 flop? */
1899{
1900 /* dp cannot be outside (-pi,pi) */
1901 if (*dp >= M_PI3.14159265358979323846)
1902 {
1903 *dp -= 2*M_PI3.14159265358979323846;
1904 }
1905 else if (*dp < -M_PI3.14159265358979323846)
1906 {
1907 *dp += 2*M_PI3.14159265358979323846;
1908 }
1909 return;
1910}
1911
1912/* As pdihs above, but without calculating energies and shift forces */
1913static void
1914pdihs_noener(int nbonds,
1915 const t_iatom forceatoms[], const t_iparams forceparams[],
1916 const rvec x[], rvec f[],
1917 const t_pbc gmx_unused__attribute__ ((unused)) *pbc, const t_graph gmx_unused__attribute__ ((unused)) *g,
1918 real lambda,
1919 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
1920 int gmx_unused__attribute__ ((unused)) *global_atom_index)
1921{
1922 int i, type, ai, aj, ak, al;
1923 int t1, t2, t3;
1924 rvec r_ij, r_kj, r_kl, m, n;
1925 real phi, sign, ddphi_tot, ddphi;
1926
1927 for (i = 0; (i < nbonds); )
1928 {
1929 ai = forceatoms[i+1];
1930 aj = forceatoms[i+2];
1931 ak = forceatoms[i+3];
1932 al = forceatoms[i+4];
1933
1934 phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
1935 &sign, &t1, &t2, &t3);
1936
1937 ddphi_tot = 0;
1938
1939 /* Loop over dihedrals working on the same atoms,
1940 * so we avoid recalculating angles and force distributions.
1941 */
1942 do
1943 {
1944 type = forceatoms[i];
1945 dopdihs_noener(forceparams[type].pdihs.cpA,
1946 forceparams[type].pdihs.cpB,
1947 forceparams[type].pdihs.phiA,
1948 forceparams[type].pdihs.phiB,
1949 forceparams[type].pdihs.mult,
1950 phi, lambda, &ddphi);
1951 ddphi_tot += ddphi;
1952
1953 i += 5;
1954 }
1955 while (i < nbonds &&
1956 forceatoms[i+1] == ai &&
1957 forceatoms[i+2] == aj &&
1958 forceatoms[i+3] == ak &&
1959 forceatoms[i+4] == al);
1960
1961 do_dih_fup_noshiftf(ai, aj, ak, al, ddphi_tot, r_ij, r_kj, r_kl, m, n, f);
1962 }
1963}
1964
1965
1966#ifdef GMX_SIMD_HAVE_REAL
1967
1968/* As pdihs_noner above, but using SIMD to calculate many dihedrals at once */
1969static void
1970pdihs_noener_simd(int nbonds,
1971 const t_iatom forceatoms[], const t_iparams forceparams[],
1972 const rvec x[], rvec f[],
1973 const t_pbc *pbc, const t_graph gmx_unused__attribute__ ((unused)) *g,
1974 real gmx_unused__attribute__ ((unused)) lambda,
1975 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
1976 int gmx_unused__attribute__ ((unused)) *global_atom_index)
1977{
1978 const int nfa1 = 5;
1979 int i, iu, s;
1980 int type, ai[GMX_SIMD_REAL_WIDTH4], aj[GMX_SIMD_REAL_WIDTH4], ak[GMX_SIMD_REAL_WIDTH4], al[GMX_SIMD_REAL_WIDTH4];
1981 int t1[GMX_SIMD_REAL_WIDTH4], t2[GMX_SIMD_REAL_WIDTH4], t3[GMX_SIMD_REAL_WIDTH4];
1982 real ddphi;
1983 real dr_array[3*DIM3*GMX_SIMD_REAL_WIDTH4+GMX_SIMD_REAL_WIDTH4], *dr;
1984 real buf_array[7*GMX_SIMD_REAL_WIDTH4+GMX_SIMD_REAL_WIDTH4], *buf;
1985 real *cp, *phi0, *mult, *phi, *p, *q, *sf_i, *msf_l;
1986 gmx_simd_real_t__m128 phi0_S, phi_S;
1987 gmx_simd_real_t__m128 mx_S, my_S, mz_S;
1988 gmx_simd_real_t__m128 nx_S, ny_S, nz_S;
1989 gmx_simd_real_t__m128 nrkj_m2_S, nrkj_n2_S;
1990 gmx_simd_real_t__m128 cp_S, mdphi_S, mult_S;
1991 gmx_simd_real_t__m128 sin_S, cos_S;
1992 gmx_simd_real_t__m128 mddphi_S;
1993 gmx_simd_real_t__m128 sf_i_S, msf_l_S;
1994 pbc_simd_t pbc_simd;
1995
1996 /* Ensure SIMD register alignment */
1997 dr = gmx_simd_align_rgmx_simd_align_f(dr_array);
1998 buf = gmx_simd_align_rgmx_simd_align_f(buf_array);
1999
2000 /* Extract aligned pointer for parameters and variables */
2001 cp = buf + 0*GMX_SIMD_REAL_WIDTH4;
2002 phi0 = buf + 1*GMX_SIMD_REAL_WIDTH4;
2003 mult = buf + 2*GMX_SIMD_REAL_WIDTH4;
2004 p = buf + 3*GMX_SIMD_REAL_WIDTH4;
2005 q = buf + 4*GMX_SIMD_REAL_WIDTH4;
2006 sf_i = buf + 5*GMX_SIMD_REAL_WIDTH4;
2007 msf_l = buf + 6*GMX_SIMD_REAL_WIDTH4;
Value stored to 'msf_l' is never read
2008
2009 set_pbc_simd(pbc, &pbc_simd);
2010
2011 /* nbonds is the number of dihedrals times nfa1, here we step GMX_SIMD_REAL_WIDTH dihs */
2012 for (i = 0; (i < nbonds); i += GMX_SIMD_REAL_WIDTH4*nfa1)
2013 {
2014 /* Collect atoms quadruplets for GMX_SIMD_REAL_WIDTH dihedrals.
2015 * iu indexes into forceatoms, we should not let iu go beyond nbonds.
2016 */
2017 iu = i;
2018 for (s = 0; s < GMX_SIMD_REAL_WIDTH4; s++)
2019 {
2020 type = forceatoms[iu];
2021 ai[s] = forceatoms[iu+1];
2022 aj[s] = forceatoms[iu+2];
2023 ak[s] = forceatoms[iu+3];
2024 al[s] = forceatoms[iu+4];
2025
2026 cp[s] = forceparams[type].pdihs.cpA;
2027 phi0[s] = forceparams[type].pdihs.phiA*DEG2RAD(3.14159265358979323846/180.0);
2028 mult[s] = forceparams[type].pdihs.mult;
2029
2030 /* At the end fill the arrays with identical entries */
2031 if (iu + nfa1 < nbonds)
2032 {
2033 iu += nfa1;
2034 }
2035 }
2036
2037 /* Caclulate GMX_SIMD_REAL_WIDTH dihedral angles at once */
2038 dih_angle_simd(x, ai, aj, ak, al, &pbc_simd,
2039 dr,
2040 &phi_S,
2041 &mx_S, &my_S, &mz_S,
2042 &nx_S, &ny_S, &nz_S,
2043 &nrkj_m2_S,
2044 &nrkj_n2_S,
2045 p, q);
2046
2047 cp_S = gmx_simd_load_r_mm_load_ps(cp);
2048 phi0_S = gmx_simd_load_r_mm_load_ps(phi0);
2049 mult_S = gmx_simd_load_r_mm_load_ps(mult);
2050
2051 mdphi_S = gmx_simd_sub_r_mm_sub_ps(gmx_simd_mul_r_mm_mul_ps(mult_S, phi_S), phi0_S);
2052
2053 /* Calculate GMX_SIMD_REAL_WIDTH sines at once */
2054 gmx_simd_sincos_rgmx_simd_sincos_f(mdphi_S, &sin_S, &cos_S);
2055 mddphi_S = gmx_simd_mul_r_mm_mul_ps(gmx_simd_mul_r_mm_mul_ps(cp_S, mult_S), sin_S);
2056 sf_i_S = gmx_simd_mul_r_mm_mul_ps(mddphi_S, nrkj_m2_S);
2057 msf_l_S = gmx_simd_mul_r_mm_mul_ps(mddphi_S, nrkj_n2_S);
2058
2059 /* After this m?_S will contain f[i] */
2060 mx_S = gmx_simd_mul_r_mm_mul_ps(sf_i_S, mx_S);
2061 my_S = gmx_simd_mul_r_mm_mul_ps(sf_i_S, my_S);
2062 mz_S = gmx_simd_mul_r_mm_mul_ps(sf_i_S, mz_S);
2063
2064 /* After this m?_S will contain -f[l] */
2065 nx_S = gmx_simd_mul_r_mm_mul_ps(msf_l_S, nx_S);
2066 ny_S = gmx_simd_mul_r_mm_mul_ps(msf_l_S, ny_S);
2067 nz_S = gmx_simd_mul_r_mm_mul_ps(msf_l_S, nz_S);
2068
2069 gmx_simd_store_r_mm_store_ps(dr + 0*GMX_SIMD_REAL_WIDTH4, mx_S);
2070 gmx_simd_store_r_mm_store_ps(dr + 1*GMX_SIMD_REAL_WIDTH4, my_S);
2071 gmx_simd_store_r_mm_store_ps(dr + 2*GMX_SIMD_REAL_WIDTH4, mz_S);
2072 gmx_simd_store_r_mm_store_ps(dr + 3*GMX_SIMD_REAL_WIDTH4, nx_S);
2073 gmx_simd_store_r_mm_store_ps(dr + 4*GMX_SIMD_REAL_WIDTH4, ny_S);
2074 gmx_simd_store_r_mm_store_ps(dr + 5*GMX_SIMD_REAL_WIDTH4, nz_S);
2075
2076 iu = i;
2077 s = 0;
2078 do
2079 {
2080 do_dih_fup_noshiftf_precalc(ai[s], aj[s], ak[s], al[s],
2081 p[s], q[s],
2082 dr[ XX0 *GMX_SIMD_REAL_WIDTH4+s],
2083 dr[ YY1 *GMX_SIMD_REAL_WIDTH4+s],
2084 dr[ ZZ2 *GMX_SIMD_REAL_WIDTH4+s],
2085 dr[(DIM3+XX0)*GMX_SIMD_REAL_WIDTH4+s],
2086 dr[(DIM3+YY1)*GMX_SIMD_REAL_WIDTH4+s],
2087 dr[(DIM3+ZZ2)*GMX_SIMD_REAL_WIDTH4+s],
2088 f);
2089 s++;
2090 iu += nfa1;
2091 }
2092 while (s < GMX_SIMD_REAL_WIDTH4 && iu < nbonds);
2093 }
2094}
2095
2096#endif /* GMX_SIMD_HAVE_REAL */
2097
2098
2099real idihs(int nbonds,
2100 const t_iatom forceatoms[], const t_iparams forceparams[],
2101 const rvec x[], rvec f[], rvec fshift[],
2102 const t_pbc *pbc, const t_graph *g,
2103 real lambda, real *dvdlambda,
2104 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2105 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2106{
2107 int i, type, ai, aj, ak, al;
2108 int t1, t2, t3;
2109 real phi, phi0, dphi0, ddphi, sign, vtot;
2110 rvec r_ij, r_kj, r_kl, m, n;
2111 real L1, kk, dp, dp2, kA, kB, pA, pB, dvdl_term;
2112
2113 L1 = 1.0-lambda;
2114 dvdl_term = 0;
2115 vtot = 0.0;
2116 for (i = 0; (i < nbonds); )
2117 {
2118 type = forceatoms[i++];
2119 ai = forceatoms[i++];
2120 aj = forceatoms[i++];
2121 ak = forceatoms[i++];
2122 al = forceatoms[i++];
2123
2124 phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
2125 &sign, &t1, &t2, &t3); /* 84 */
2126
2127 /* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
2128 * force changes if we just apply a normal harmonic.
2129 * Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
2130 * This means we will never have the periodicity problem, unless
2131 * the dihedral is Pi away from phiO, which is very unlikely due to
2132 * the potential.
2133 */
2134 kA = forceparams[type].harmonic.krA;
2135 kB = forceparams[type].harmonic.krB;
2136 pA = forceparams[type].harmonic.rA;
2137 pB = forceparams[type].harmonic.rB;
2138
2139 kk = L1*kA + lambda*kB;
2140 phi0 = (L1*pA + lambda*pB)*DEG2RAD(3.14159265358979323846/180.0);
2141 dphi0 = (pB - pA)*DEG2RAD(3.14159265358979323846/180.0);
2142
2143 dp = phi-phi0;
2144
2145 make_dp_periodic(&dp);
2146
2147 dp2 = dp*dp;
2148
2149 vtot += 0.5*kk*dp2;
2150 ddphi = -kk*dp;
2151
2152 dvdl_term += 0.5*(kB - kA)*dp2 - kk*dphi0*dp;
2153
2154 do_dih_fup(ai, aj, ak, al, (real)(-ddphi), r_ij, r_kj, r_kl, m, n,
2155 f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
2156 /* 218 TOTAL */
2157#ifdef DEBUG
2158 if (debug)
2159 {
2160 fprintf(debug, "idih: (%d,%d,%d,%d) phi=%g\n",
2161 ai, aj, ak, al, phi);
2162 }
2163#endif
2164 }
2165
2166 *dvdlambda += dvdl_term;
2167 return vtot;
2168}
2169
2170
2171/*! \brief returns dx, rdist, and dpdl for functions posres() and fbposres()
2172 */
2173static void posres_dx(const rvec x, const rvec pos0A, const rvec pos0B,
2174 const rvec comA_sc, const rvec comB_sc,
2175 real lambda,
2176 t_pbc *pbc, int refcoord_scaling, int npbcdim,
2177 rvec dx, rvec rdist, rvec dpdl)
2178{
2179 int m, d;
2180 real posA, posB, L1, ref = 0.;
2181 rvec pos;
2182
2183 L1 = 1.0-lambda;
2184
2185 for (m = 0; m < DIM3; m++)
2186 {
2187 posA = pos0A[m];
2188 posB = pos0B[m];
2189 if (m < npbcdim)
2190 {
2191 switch (refcoord_scaling)
2192 {
2193 case erscNO:
2194 ref = 0;
2195 rdist[m] = L1*posA + lambda*posB;
2196 dpdl[m] = posB - posA;
2197 break;
2198 case erscALL:
2199 /* Box relative coordinates are stored for dimensions with pbc */
2200 posA *= pbc->box[m][m];
2201 posB *= pbc->box[m][m];
2202 assert(npbcdim <= DIM)((void) (0));
2203 for (d = m+1; d < npbcdim; d++)
2204 {
2205 posA += pos0A[d]*pbc->box[d][m];
2206 posB += pos0B[d]*pbc->box[d][m];
2207 }
2208 ref = L1*posA + lambda*posB;
2209 rdist[m] = 0;
2210 dpdl[m] = posB - posA;
2211 break;
2212 case erscCOM:
2213 ref = L1*comA_sc[m] + lambda*comB_sc[m];
2214 rdist[m] = L1*posA + lambda*posB;
2215 dpdl[m] = comB_sc[m] - comA_sc[m] + posB - posA;
2216 break;
2217 default:
2218 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 2218, "No such scaling method implemented");
2219 }
2220 }
2221 else
2222 {
2223 ref = L1*posA + lambda*posB;
2224 rdist[m] = 0;
2225 dpdl[m] = posB - posA;
2226 }
2227
2228 /* We do pbc_dx with ref+rdist,
2229 * since with only ref we can be up to half a box vector wrong.
2230 */
2231 pos[m] = ref + rdist[m];
2232 }
2233
2234 if (pbc)
2235 {
2236 pbc_dx(pbc, x, pos, dx);
2237 }
2238 else
2239 {
2240 rvec_sub(x, pos, dx);
2241 }
2242}
2243
2244/*! \brief Adds forces of flat-bottomed positions restraints to f[]
2245 * and fixes vir_diag. Returns the flat-bottomed potential. */
2246real fbposres(int nbonds,
2247 const t_iatom forceatoms[], const t_iparams forceparams[],
2248 const rvec x[], rvec f[], rvec vir_diag,
2249 t_pbc *pbc,
2250 int refcoord_scaling, int ePBC, rvec com)
2251/* compute flat-bottomed positions restraints */
2252{
2253 int i, ai, m, d, type, npbcdim = 0, fbdim;
2254 const t_iparams *pr;
2255 real vtot, kk, v;
2256 real ref = 0, dr, dr2, rpot, rfb, rfb2, fact, invdr;
2257 rvec com_sc, rdist, pos, dx, dpdl, fm;
2258 gmx_bool bInvert;
2259
2260 npbcdim = ePBC2npbcdim(ePBC);
2261
2262 if (refcoord_scaling == erscCOM)
2263 {
2264 clear_rvec(com_sc);
2265 for (m = 0; m < npbcdim; m++)
2266 {
2267 assert(npbcdim <= DIM)((void) (0));
2268 for (d = m; d < npbcdim; d++)
2269 {
2270 com_sc[m] += com[d]*pbc->box[d][m];
2271 }
2272 }
2273 }
2274
2275 vtot = 0.0;
2276 for (i = 0; (i < nbonds); )
2277 {
2278 type = forceatoms[i++];
2279 ai = forceatoms[i++];
2280 pr = &forceparams[type];
2281
2282 /* same calculation as for normal posres, but with identical A and B states, and lambda==0 */
2283 posres_dx(x[ai], forceparams[type].fbposres.pos0, forceparams[type].fbposres.pos0,
2284 com_sc, com_sc, 0.0,
2285 pbc, refcoord_scaling, npbcdim,
2286 dx, rdist, dpdl);
2287
2288 clear_rvec(fm);
2289 v = 0.0;
2290
2291 kk = pr->fbposres.k;
2292 rfb = pr->fbposres.r;
2293 rfb2 = sqr(rfb);
2294
2295 /* with rfb<0, push particle out of the sphere/cylinder/layer */
2296 bInvert = FALSE0;
2297 if (rfb < 0.)
2298 {
2299 bInvert = TRUE1;
2300 rfb = -rfb;
2301 }
2302
2303 switch (pr->fbposres.geom)
2304 {
2305 case efbposresSPHERE:
2306 /* spherical flat-bottom posres */
2307 dr2 = norm2(dx);
2308 if (dr2 > 0.0 &&
2309 ( (dr2 > rfb2 && bInvert == FALSE0 ) || (dr2 < rfb2 && bInvert == TRUE1 ) )
2310 )
2311 {
2312 dr = sqrt(dr2);
2313 v = 0.5*kk*sqr(dr - rfb);
2314 fact = -kk*(dr-rfb)/dr; /* Force pointing to the center pos0 */
2315 svmul(fact, dx, fm);
2316 }
2317 break;
2318 case efbposresCYLINDER:
2319 /* cylidrical flat-bottom posres in x-y plane. fm[ZZ] = 0. */
2320 dr2 = sqr(dx[XX0])+sqr(dx[YY1]);
2321 if (dr2 > 0.0 &&
2322 ( (dr2 > rfb2 && bInvert == FALSE0 ) || (dr2 < rfb2 && bInvert == TRUE1 ) )
2323 )
2324 {
2325 dr = sqrt(dr2);
2326 invdr = 1./dr;
2327 v = 0.5*kk*sqr(dr - rfb);
2328 fm[XX0] = -kk*(dr-rfb)*dx[XX0]*invdr; /* Force pointing to the center */
2329 fm[YY1] = -kk*(dr-rfb)*dx[YY1]*invdr;
2330 }
2331 break;
2332 case efbposresX: /* fbdim=XX */
2333 case efbposresY: /* fbdim=YY */
2334 case efbposresZ: /* fbdim=ZZ */
2335 /* 1D flat-bottom potential */
2336 fbdim = pr->fbposres.geom - efbposresX;
2337 dr = dx[fbdim];
2338 if ( ( dr > rfb && bInvert == FALSE0 ) || ( 0 < dr && dr < rfb && bInvert == TRUE1 ) )
2339 {
2340 v = 0.5*kk*sqr(dr - rfb);
2341 fm[fbdim] = -kk*(dr - rfb);
2342 }
2343 else if ( (dr < (-rfb) && bInvert == FALSE0 ) || ( (-rfb) < dr && dr < 0 && bInvert == TRUE1 ))
2344 {
2345 v = 0.5*kk*sqr(dr + rfb);
2346 fm[fbdim] = -kk*(dr + rfb);
2347 }
2348 break;
2349 }
2350
2351 vtot += v;
2352
2353 for (m = 0; (m < DIM3); m++)
2354 {
2355 f[ai][m] += fm[m];
2356 /* Here we correct for the pbc_dx which included rdist */
2357 vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
2358 }
2359 }
2360
2361 return vtot;
2362}
2363
2364
2365real posres(int nbonds,
2366 const t_iatom forceatoms[], const t_iparams forceparams[],
2367 const rvec x[], rvec f[], rvec vir_diag,
2368 t_pbc *pbc,
2369 real lambda, real *dvdlambda,
2370 int refcoord_scaling, int ePBC, rvec comA, rvec comB)
2371{
2372 int i, ai, m, d, type, ki, npbcdim = 0;
2373 const t_iparams *pr;
2374 real L1;
2375 real vtot, kk, fm;
2376 real posA, posB, ref = 0;
2377 rvec comA_sc, comB_sc, rdist, dpdl, pos, dx;
2378 gmx_bool bForceValid = TRUE1;
2379
2380 if ((f == NULL((void*)0)) || (vir_diag == NULL((void*)0))) /* should both be null together! */
2381 {
2382 bForceValid = FALSE0;
2383 }
2384
2385 npbcdim = ePBC2npbcdim(ePBC);
2386
2387 if (refcoord_scaling == erscCOM)
2388 {
2389 clear_rvec(comA_sc);
2390 clear_rvec(comB_sc);
2391 for (m = 0; m < npbcdim; m++)
2392 {
2393 assert(npbcdim <= DIM)((void) (0));
2394 for (d = m; d < npbcdim; d++)
2395 {
2396 comA_sc[m] += comA[d]*pbc->box[d][m];
2397 comB_sc[m] += comB[d]*pbc->box[d][m];
2398 }
2399 }
2400 }
2401
2402 L1 = 1.0 - lambda;
2403
2404 vtot = 0.0;
2405 for (i = 0; (i < nbonds); )
2406 {
2407 type = forceatoms[i++];
2408 ai = forceatoms[i++];
2409 pr = &forceparams[type];
2410
2411 /* return dx, rdist, and dpdl */
2412 posres_dx(x[ai], forceparams[type].posres.pos0A, forceparams[type].posres.pos0B,
2413 comA_sc, comB_sc, lambda,
2414 pbc, refcoord_scaling, npbcdim,
2415 dx, rdist, dpdl);
2416
2417 for (m = 0; (m < DIM3); m++)
2418 {
2419 kk = L1*pr->posres.fcA[m] + lambda*pr->posres.fcB[m];
2420 fm = -kk*dx[m];
2421 vtot += 0.5*kk*dx[m]*dx[m];
2422 *dvdlambda +=
2423 0.5*(pr->posres.fcB[m] - pr->posres.fcA[m])*dx[m]*dx[m]
2424 -fm*dpdl[m];
2425
2426 /* Here we correct for the pbc_dx which included rdist */
2427 if (bForceValid)
2428 {
2429 f[ai][m] += fm;
2430 vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm;
2431 }
2432 }
2433 }
2434
2435 return vtot;
2436}
2437
2438static real low_angres(int nbonds,
2439 const t_iatom forceatoms[], const t_iparams forceparams[],
2440 const rvec x[], rvec f[], rvec fshift[],
2441 const t_pbc *pbc, const t_graph *g,
2442 real lambda, real *dvdlambda,
2443 gmx_bool bZAxis)
2444{
2445 int i, m, type, ai, aj, ak, al;
2446 int t1, t2;
2447 real phi, cos_phi, cos_phi2, vid, vtot, dVdphi;
2448 rvec r_ij, r_kl, f_i, f_k = {0, 0, 0};
2449 real st, sth, nrij2, nrkl2, c, cij, ckl;
2450
2451 ivec dt;
2452 t2 = 0; /* avoid warning with gcc-3.3. It is never used uninitialized */
2453
2454 vtot = 0.0;
2455 ak = al = 0; /* to avoid warnings */
2456 for (i = 0; i < nbonds; )
2457 {
2458 type = forceatoms[i++];
2459 ai = forceatoms[i++];
2460 aj = forceatoms[i++];
2461 t1 = pbc_rvec_sub(pbc, x[aj], x[ai], r_ij); /* 3 */
2462 if (!bZAxis)
2463 {
2464 ak = forceatoms[i++];
2465 al = forceatoms[i++];
2466 t2 = pbc_rvec_sub(pbc, x[al], x[ak], r_kl); /* 3 */
2467 }
2468 else
2469 {
2470 r_kl[XX0] = 0;
2471 r_kl[YY1] = 0;
2472 r_kl[ZZ2] = 1;
2473 }
2474
2475 cos_phi = cos_angle(r_ij, r_kl); /* 25 */
2476 phi = acos(cos_phi); /* 10 */
2477
2478 *dvdlambda += dopdihs_min(forceparams[type].pdihs.cpA,
2479 forceparams[type].pdihs.cpB,
2480 forceparams[type].pdihs.phiA,
2481 forceparams[type].pdihs.phiB,
2482 forceparams[type].pdihs.mult,
2483 phi, lambda, &vid, &dVdphi); /* 40 */
2484
2485 vtot += vid;
2486
2487 cos_phi2 = sqr(cos_phi); /* 1 */
2488 if (cos_phi2 < 1)
2489 {
2490 st = -dVdphi*gmx_invsqrt(1 - cos_phi2)gmx_software_invsqrt(1 - cos_phi2); /* 12 */
2491 sth = st*cos_phi; /* 1 */
2492 nrij2 = iprod(r_ij, r_ij); /* 5 */
2493 nrkl2 = iprod(r_kl, r_kl); /* 5 */
2494
2495 c = st*gmx_invsqrt(nrij2*nrkl2)gmx_software_invsqrt(nrij2*nrkl2); /* 11 */
2496 cij = sth/nrij2; /* 10 */
2497 ckl = sth/nrkl2; /* 10 */
2498
2499 for (m = 0; m < DIM3; m++) /* 18+18 */
2500 {
2501 f_i[m] = (c*r_kl[m]-cij*r_ij[m]);
2502 f[ai][m] += f_i[m];
2503 f[aj][m] -= f_i[m];
2504 if (!bZAxis)
2505 {
2506 f_k[m] = (c*r_ij[m]-ckl*r_kl[m]);
2507 f[ak][m] += f_k[m];
2508 f[al][m] -= f_k[m];
2509 }
2510 }
2511
2512 if (g)
2513 {
2514 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
2515 t1 = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
2516 }
2517 rvec_inc(fshift[t1], f_i);
2518 rvec_dec(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_i);
2519 if (!bZAxis)
2520 {
2521 if (g)
2522 {
2523 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), SHIFT_IVEC(g, al)((g)->ishift[al]), dt);
2524 t2 = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
2525 }
2526 rvec_inc(fshift[t2], f_k);
2527 rvec_dec(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_k);
2528 }
2529 }
2530 }
2531
2532 return vtot; /* 184 / 157 (bZAxis) total */
2533}
2534
2535real angres(int nbonds,
2536 const t_iatom forceatoms[], const t_iparams forceparams[],
2537 const rvec x[], rvec f[], rvec fshift[],
2538 const t_pbc *pbc, const t_graph *g,
2539 real lambda, real *dvdlambda,
2540 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2541 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2542{
2543 return low_angres(nbonds, forceatoms, forceparams, x, f, fshift, pbc, g,
2544 lambda, dvdlambda, FALSE0);
2545}
2546
2547real angresz(int nbonds,
2548 const t_iatom forceatoms[], const t_iparams forceparams[],
2549 const rvec x[], rvec f[], rvec fshift[],
2550 const t_pbc *pbc, const t_graph *g,
2551 real lambda, real *dvdlambda,
2552 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2553 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2554{
2555 return low_angres(nbonds, forceatoms, forceparams, x, f, fshift, pbc, g,
2556 lambda, dvdlambda, TRUE1);
2557}
2558
2559real dihres(int nbonds,
2560 const t_iatom forceatoms[], const t_iparams forceparams[],
2561 const rvec x[], rvec f[], rvec fshift[],
2562 const t_pbc *pbc, const t_graph *g,
2563 real lambda, real *dvdlambda,
2564 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2565 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2566{
2567 real vtot = 0;
2568 int ai, aj, ak, al, i, k, type, t1, t2, t3;
2569 real phi0A, phi0B, dphiA, dphiB, kfacA, kfacB, phi0, dphi, kfac;
2570 real phi, ddphi, ddp, ddp2, dp, sign, d2r, fc, L1;
2571 rvec r_ij, r_kj, r_kl, m, n;
2572
2573 L1 = 1.0-lambda;
2574
2575 d2r = DEG2RAD(3.14159265358979323846/180.0);
2576 k = 0;
2577
2578 for (i = 0; (i < nbonds); )
2579 {
2580 type = forceatoms[i++];
2581 ai = forceatoms[i++];
2582 aj = forceatoms[i++];
2583 ak = forceatoms[i++];
2584 al = forceatoms[i++];
2585
2586 phi0A = forceparams[type].dihres.phiA*d2r;
2587 dphiA = forceparams[type].dihres.dphiA*d2r;
2588 kfacA = forceparams[type].dihres.kfacA;
2589
2590 phi0B = forceparams[type].dihres.phiB*d2r;
2591 dphiB = forceparams[type].dihres.dphiB*d2r;
2592 kfacB = forceparams[type].dihres.kfacB;
2593
2594 phi0 = L1*phi0A + lambda*phi0B;
2595 dphi = L1*dphiA + lambda*dphiB;
2596 kfac = L1*kfacA + lambda*kfacB;
2597
2598 phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
2599 &sign, &t1, &t2, &t3);
2600 /* 84 flops */
2601
2602 if (debug)
2603 {
2604 fprintf(debug, "dihres[%d]: %d %d %d %d : phi=%f, dphi=%f, kfac=%f\n",
2605 k++, ai, aj, ak, al, phi0, dphi, kfac);
2606 }
2607 /* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
2608 * force changes if we just apply a normal harmonic.
2609 * Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
2610 * This means we will never have the periodicity problem, unless
2611 * the dihedral is Pi away from phiO, which is very unlikely due to
2612 * the potential.
2613 */
2614 dp = phi-phi0;
2615 make_dp_periodic(&dp);
2616
2617 if (dp > dphi)
2618 {
2619 ddp = dp-dphi;
2620 }
2621 else if (dp < -dphi)
2622 {
2623 ddp = dp+dphi;
2624 }
2625 else
2626 {
2627 ddp = 0;
2628 }
2629
2630 if (ddp != 0.0)
2631 {
2632 ddp2 = ddp*ddp;
2633 vtot += 0.5*kfac*ddp2;
2634 ddphi = kfac*ddp;
2635
2636 *dvdlambda += 0.5*(kfacB - kfacA)*ddp2;
2637 /* lambda dependence from changing restraint distances */
2638 if (ddp > 0)
2639 {
2640 *dvdlambda -= kfac*ddp*((dphiB - dphiA)+(phi0B - phi0A));
2641 }
2642 else if (ddp < 0)
2643 {
2644 *dvdlambda += kfac*ddp*((dphiB - dphiA)-(phi0B - phi0A));
2645 }
2646 do_dih_fup(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n,
2647 f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
2648 }
2649 }
2650 return vtot;
2651}
2652
2653
2654real unimplemented(int gmx_unused__attribute__ ((unused)) nbonds,
2655 const t_iatom gmx_unused__attribute__ ((unused)) forceatoms[], const t_iparams gmx_unused__attribute__ ((unused)) forceparams[],
2656 const rvec gmx_unused__attribute__ ((unused)) x[], rvec gmx_unused__attribute__ ((unused)) f[], rvec gmx_unused__attribute__ ((unused)) fshift[],
2657 const t_pbc gmx_unused__attribute__ ((unused)) *pbc, const t_graph gmx_unused__attribute__ ((unused)) *g,
2658 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
2659 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2660 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2661{
2662 gmx_impl("*** you are using a not implemented function")_gmx_error("impl", "*** you are using a not implemented function"
, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 2662);
2663
2664 return 0.0; /* To make the compiler happy */
2665}
2666
2667real restrangles(int nbonds,
2668 const t_iatom forceatoms[], const t_iparams forceparams[],
2669 const rvec x[], rvec f[], rvec fshift[],
2670 const t_pbc *pbc, const t_graph *g,
2671 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
2672 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2673 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2674{
2675 int i, d, ai, aj, ak, type, m;
2676 int t1, t2;
2677 rvec r_ij, r_kj;
2678 real v, vtot;
2679 ivec jt, dt_ij, dt_kj;
2680 rvec f_i, f_j, f_k;
2681 real prefactor, ratio_ante, ratio_post;
2682 rvec delta_ante, delta_post, vec_temp;
2683
2684 vtot = 0.0;
2685 for (i = 0; (i < nbonds); )
2686 {
2687 type = forceatoms[i++];
2688 ai = forceatoms[i++];
2689 aj = forceatoms[i++];
2690 ak = forceatoms[i++];
2691
2692 t1 = pbc_rvec_sub(pbc, x[ai], x[aj], vec_temp);
2693 pbc_rvec_sub(pbc, x[aj], x[ai], delta_ante);
2694 t2 = pbc_rvec_sub(pbc, x[ak], x[aj], delta_post);
2695
2696
2697 /* This function computes factors needed for restricted angle potential.
2698 * The restricted angle potential is used in coarse-grained simulations to avoid singularities
2699 * when three particles align and the dihedral angle and dihedral potential
2700 * cannot be calculated. This potential is calculated using the formula:
2701 real restrangles(int nbonds,
2702 const t_iatom forceatoms[],const t_iparams forceparams[],
2703 const rvec x[],rvec f[],rvec fshift[],
2704 const t_pbc *pbc,const t_graph *g,
2705 real gmx_unused lambda,real gmx_unused *dvdlambda,
2706 const t_mdatoms gmx_unused *md,t_fcdata gmx_unused *fcd,
2707 int gmx_unused *global_atom_index)
2708 {
2709 int i, d, ai, aj, ak, type, m;
2710 int t1, t2;
2711 rvec r_ij,r_kj;
2712 real v, vtot;
2713 ivec jt,dt_ij,dt_kj;
2714 rvec f_i, f_j, f_k;
2715 real prefactor, ratio_ante, ratio_post;
2716 rvec delta_ante, delta_post, vec_temp;
2717
2718 vtot = 0.0;
2719 for(i=0; (i<nbonds); )
2720 {
2721 type = forceatoms[i++];
2722 ai = forceatoms[i++];
2723 aj = forceatoms[i++];
2724 ak = forceatoms[i++];
2725
2726 * \f[V_{\rm ReB}(\theta_i) = \frac{1}{2} k_{\theta} \frac{(\cos\theta_i - \cos\theta_0)^2}
2727 * {\sin^2\theta_i}\f] ({eq:ReB} and ref \cite{MonicaGoga2013} from the manual).
2728 * For more explanations see comments file "restcbt.h". */
2729
2730 compute_factors_restangles(type, forceparams, delta_ante, delta_post,
2731 &prefactor, &ratio_ante, &ratio_post, &v);
2732
2733 /* Forces are computed per component */
2734 for (d = 0; d < DIM3; d++)
2735 {
2736 f_i[d] = prefactor * (ratio_ante * delta_ante[d] - delta_post[d]);
2737 f_j[d] = prefactor * ((ratio_post + 1.0) * delta_post[d] - (ratio_ante + 1.0) * delta_ante[d]);
2738 f_k[d] = prefactor * (delta_ante[d] - ratio_post * delta_post[d]);
2739 }
2740
2741 /* Computation of potential energy */
2742
2743 vtot += v;
2744
2745 /* Update forces */
2746
2747 for (m = 0; (m < DIM3); m++)
2748 {
2749 f[ai][m] += f_i[m];
2750 f[aj][m] += f_j[m];
2751 f[ak][m] += f_k[m];
2752 }
2753
2754 if (g)
2755 {
2756 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
2757 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
2758 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
2759 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
2760 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
2761 }
2762
2763 rvec_inc(fshift[t1], f_i);
2764 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
2765 rvec_inc(fshift[t2], f_k);
2766 }
2767 return vtot;
2768}
2769
2770
2771real restrdihs(int nbonds,
2772 const t_iatom forceatoms[], const t_iparams forceparams[],
2773 const rvec x[], rvec f[], rvec fshift[],
2774 const t_pbc *pbc, const t_graph *g,
2775 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvlambda,
2776 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2777 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2778{
2779 int i, d, type, ai, aj, ak, al;
2780 rvec f_i, f_j, f_k, f_l;
2781 rvec dx_jl;
2782 ivec jt, dt_ij, dt_kj, dt_lj;
2783 int t1, t2, t3;
2784 real v, vtot;
2785 rvec delta_ante, delta_crnt, delta_post, vec_temp;
2786 real factor_phi_ai_ante, factor_phi_ai_crnt, factor_phi_ai_post;
2787 real factor_phi_aj_ante, factor_phi_aj_crnt, factor_phi_aj_post;
2788 real factor_phi_ak_ante, factor_phi_ak_crnt, factor_phi_ak_post;
2789 real factor_phi_al_ante, factor_phi_al_crnt, factor_phi_al_post;
2790 real prefactor_phi;
2791
2792
2793 vtot = 0.0;
2794 for (i = 0; (i < nbonds); )
2795 {
2796 type = forceatoms[i++];
2797 ai = forceatoms[i++];
2798 aj = forceatoms[i++];
2799 ak = forceatoms[i++];
2800 al = forceatoms[i++];
2801
2802 t1 = pbc_rvec_sub(pbc, x[ai], x[aj], vec_temp);
2803 pbc_rvec_sub(pbc, x[aj], x[ai], delta_ante);
2804 t2 = pbc_rvec_sub(pbc, x[ak], x[aj], delta_crnt);
2805 t3 = pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
2806 pbc_rvec_sub(pbc, x[al], x[ak], delta_post);
2807
2808 /* This function computes factors needed for restricted angle potential.
2809 * The restricted angle potential is used in coarse-grained simulations to avoid singularities
2810 * when three particles align and the dihedral angle and dihedral potential cannot be calculated.
2811 * This potential is calculated using the formula:
2812 * \f[V_{\rm ReB}(\theta_i) = \frac{1}{2} k_{\theta}
2813 * \frac{(\cos\theta_i - \cos\theta_0)^2}{\sin^2\theta_i}\f]
2814 * ({eq:ReB} and ref \cite{MonicaGoga2013} from the manual).
2815 * For more explanations see comments file "restcbt.h" */
2816
2817 compute_factors_restrdihs(type, forceparams,
2818 delta_ante, delta_crnt, delta_post,
2819 &factor_phi_ai_ante, &factor_phi_ai_crnt, &factor_phi_ai_post,
2820 &factor_phi_aj_ante, &factor_phi_aj_crnt, &factor_phi_aj_post,
2821 &factor_phi_ak_ante, &factor_phi_ak_crnt, &factor_phi_ak_post,
2822 &factor_phi_al_ante, &factor_phi_al_crnt, &factor_phi_al_post,
2823 &prefactor_phi, &v);
2824
2825
2826 /* Computation of forces per component */
2827 for (d = 0; d < DIM3; d++)
2828 {
2829 f_i[d] = prefactor_phi * (factor_phi_ai_ante * delta_ante[d] + factor_phi_ai_crnt * delta_crnt[d] + factor_phi_ai_post * delta_post[d]);
2830 f_j[d] = prefactor_phi * (factor_phi_aj_ante * delta_ante[d] + factor_phi_aj_crnt * delta_crnt[d] + factor_phi_aj_post * delta_post[d]);
2831 f_k[d] = prefactor_phi * (factor_phi_ak_ante * delta_ante[d] + factor_phi_ak_crnt * delta_crnt[d] + factor_phi_ak_post * delta_post[d]);
2832 f_l[d] = prefactor_phi * (factor_phi_al_ante * delta_ante[d] + factor_phi_al_crnt * delta_crnt[d] + factor_phi_al_post * delta_post[d]);
2833 }
2834 /* Computation of the energy */
2835
2836 vtot += v;
2837
2838
2839
2840 /* Updating the forces */
2841
2842 rvec_inc(f[ai], f_i);
2843 rvec_inc(f[aj], f_j);
2844 rvec_inc(f[ak], f_k);
2845 rvec_inc(f[al], f_l);
2846
2847
2848 /* Updating the fshift forces for the pressure coupling */
2849 if (g)
2850 {
2851 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
2852 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
2853 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
2854 ivec_sub(SHIFT_IVEC(g, al)((g)->ishift[al]), jt, dt_lj);
2855 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
2856 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
2857 t3 = IVEC2IS(dt_lj)(((2*2 +1)*((2*1 +1)*(((dt_lj)[2])+1)+((dt_lj)[1])+1)+((dt_lj
)[0])+2));
2858 }
2859 else if (pbc)
2860 {
2861 t3 = pbc_rvec_sub(pbc, x[al], x[aj], dx_jl);
2862 }
2863 else
2864 {
2865 t3 = CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2);
2866 }
2867
2868 rvec_inc(fshift[t1], f_i);
2869 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
2870 rvec_inc(fshift[t2], f_k);
2871 rvec_inc(fshift[t3], f_l);
2872
2873 }
2874
2875 return vtot;
2876}
2877
2878
2879real cbtdihs(int nbonds,
2880 const t_iatom forceatoms[], const t_iparams forceparams[],
2881 const rvec x[], rvec f[], rvec fshift[],
2882 const t_pbc *pbc, const t_graph *g,
2883 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
2884 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2885 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2886{
2887 int type, ai, aj, ak, al, i, d;
2888 int t1, t2, t3;
2889 real v, vtot;
2890 rvec vec_temp;
2891 rvec f_i, f_j, f_k, f_l;
2892 ivec jt, dt_ij, dt_kj, dt_lj;
2893 rvec dx_jl;
2894 rvec delta_ante, delta_crnt, delta_post;
2895 rvec f_phi_ai, f_phi_aj, f_phi_ak, f_phi_al;
2896 rvec f_theta_ante_ai, f_theta_ante_aj, f_theta_ante_ak;
2897 rvec f_theta_post_aj, f_theta_post_ak, f_theta_post_al;
2898
2899
2900
2901
2902 vtot = 0.0;
2903 for (i = 0; (i < nbonds); )
2904 {
2905 type = forceatoms[i++];
2906 ai = forceatoms[i++];
2907 aj = forceatoms[i++];
2908 ak = forceatoms[i++];
2909 al = forceatoms[i++];
2910
2911
2912 t1 = pbc_rvec_sub(pbc, x[ai], x[aj], vec_temp);
2913 pbc_rvec_sub(pbc, x[aj], x[ai], delta_ante);
2914 t2 = pbc_rvec_sub(pbc, x[ak], x[aj], vec_temp);
2915 pbc_rvec_sub(pbc, x[ak], x[aj], delta_crnt);
2916 t3 = pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
2917 pbc_rvec_sub(pbc, x[al], x[ak], delta_post);
2918
2919 /* \brief Compute factors for CBT potential
2920 * The combined bending-torsion potential goes to zero in a very smooth manner, eliminating the numerical
2921 * instabilities, when three coarse-grained particles align and the dihedral angle and standard
2922 * dihedral potentials cannot be calculated. The CBT potential is calculated using the formula:
2923 * \f[V_{\rm CBT}(\theta_{i-1}, \theta_i, \phi_i) = k_{\phi} \sin^3\theta_{i-1} \sin^3\theta_{i}
2924 * \sum_{n=0}^4 { a_n \cos^n\phi_i}\f] ({eq:CBT} and ref \cite{MonicaGoga2013} from the manual).
2925 * It contains in its expression not only the dihedral angle \f$\phi\f$
2926 * but also \f[\theta_{i-1}\f] (theta_ante bellow) and \f[\theta_{i}\f] (theta_post bellow)
2927 * --- the adjacent bending angles.
2928 * For more explanations see comments file "restcbt.h". */
2929
2930 compute_factors_cbtdihs(type, forceparams, delta_ante, delta_crnt, delta_post,
2931 f_phi_ai, f_phi_aj, f_phi_ak, f_phi_al,
2932 f_theta_ante_ai, f_theta_ante_aj, f_theta_ante_ak,
2933 f_theta_post_aj, f_theta_post_ak, f_theta_post_al,
2934 &v);
2935
2936
2937 /* Acumulate the resuts per beads */
2938 for (d = 0; d < DIM3; d++)
2939 {
2940 f_i[d] = f_phi_ai[d] + f_theta_ante_ai[d];
2941 f_j[d] = f_phi_aj[d] + f_theta_ante_aj[d] + f_theta_post_aj[d];
2942 f_k[d] = f_phi_ak[d] + f_theta_ante_ak[d] + f_theta_post_ak[d];
2943 f_l[d] = f_phi_al[d] + f_theta_post_al[d];
2944 }
2945
2946 /* Compute the potential energy */
2947
2948 vtot += v;
2949
2950
2951 /* Updating the forces */
2952 rvec_inc(f[ai], f_i);
2953 rvec_inc(f[aj], f_j);
2954 rvec_inc(f[ak], f_k);
2955 rvec_inc(f[al], f_l);
2956
2957
2958 /* Updating the fshift forces for the pressure coupling */
2959 if (g)
2960 {
2961 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
2962 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
2963 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
2964 ivec_sub(SHIFT_IVEC(g, al)((g)->ishift[al]), jt, dt_lj);
2965 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
2966 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
2967 t3 = IVEC2IS(dt_lj)(((2*2 +1)*((2*1 +1)*(((dt_lj)[2])+1)+((dt_lj)[1])+1)+((dt_lj
)[0])+2));
2968 }
2969 else if (pbc)
2970 {
2971 t3 = pbc_rvec_sub(pbc, x[al], x[aj], dx_jl);
2972 }
2973 else
2974 {
2975 t3 = CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2);
2976 }
2977
2978 rvec_inc(fshift[t1], f_i);
2979 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
2980 rvec_inc(fshift[t2], f_k);
2981 rvec_inc(fshift[t3], f_l);
2982 }
2983
2984 return vtot;
2985}
2986
2987real rbdihs(int nbonds,
2988 const t_iatom forceatoms[], const t_iparams forceparams[],
2989 const rvec x[], rvec f[], rvec fshift[],
2990 const t_pbc *pbc, const t_graph *g,
2991 real lambda, real *dvdlambda,
2992 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
2993 int gmx_unused__attribute__ ((unused)) *global_atom_index)
2994{
2995 const real c0 = 0.0, c1 = 1.0, c2 = 2.0, c3 = 3.0, c4 = 4.0, c5 = 5.0;
2996 int type, ai, aj, ak, al, i, j;
2997 int t1, t2, t3;
2998 rvec r_ij, r_kj, r_kl, m, n;
2999 real parmA[NR_RBDIHS6];
3000 real parmB[NR_RBDIHS6];
3001 real parm[NR_RBDIHS6];
3002 real cos_phi, phi, rbp, rbpBA;
3003 real v, sign, ddphi, sin_phi;
3004 real cosfac, vtot;
3005 real L1 = 1.0-lambda;
3006 real dvdl_term = 0;
3007
3008 vtot = 0.0;
3009 for (i = 0; (i < nbonds); )
3010 {
3011 type = forceatoms[i++];
3012 ai = forceatoms[i++];
3013 aj = forceatoms[i++];
3014 ak = forceatoms[i++];
3015 al = forceatoms[i++];
3016
3017 phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
3018 &sign, &t1, &t2, &t3); /* 84 */
3019
3020 /* Change to polymer convention */
3021 if (phi < c0)
3022 {
3023 phi += M_PI3.14159265358979323846;
3024 }
3025 else
3026 {
3027 phi -= M_PI3.14159265358979323846; /* 1 */
3028
3029 }
3030 cos_phi = cos(phi);
3031 /* Beware of accuracy loss, cannot use 1-sqrt(cos^2) ! */
3032 sin_phi = sin(phi);
3033
3034 for (j = 0; (j < NR_RBDIHS6); j++)
3035 {
3036 parmA[j] = forceparams[type].rbdihs.rbcA[j];
3037 parmB[j] = forceparams[type].rbdihs.rbcB[j];
3038 parm[j] = L1*parmA[j]+lambda*parmB[j];
3039 }
3040 /* Calculate cosine powers */
3041 /* Calculate the energy */
3042 /* Calculate the derivative */
3043
3044 v = parm[0];
3045 dvdl_term += (parmB[0]-parmA[0]);
3046 ddphi = c0;
3047 cosfac = c1;
3048
3049 rbp = parm[1];
3050 rbpBA = parmB[1]-parmA[1];
3051 ddphi += rbp*cosfac;
3052 cosfac *= cos_phi;
3053 v += cosfac*rbp;
3054 dvdl_term += cosfac*rbpBA;
3055 rbp = parm[2];
3056 rbpBA = parmB[2]-parmA[2];
3057 ddphi += c2*rbp*cosfac;
3058 cosfac *= cos_phi;
3059 v += cosfac*rbp;
3060 dvdl_term += cosfac*rbpBA;
3061 rbp = parm[3];
3062 rbpBA = parmB[3]-parmA[3];
3063 ddphi += c3*rbp*cosfac;
3064 cosfac *= cos_phi;
3065 v += cosfac*rbp;
3066 dvdl_term += cosfac*rbpBA;
3067 rbp = parm[4];
3068 rbpBA = parmB[4]-parmA[4];
3069 ddphi += c4*rbp*cosfac;
3070 cosfac *= cos_phi;
3071 v += cosfac*rbp;
3072 dvdl_term += cosfac*rbpBA;
3073 rbp = parm[5];
3074 rbpBA = parmB[5]-parmA[5];
3075 ddphi += c5*rbp*cosfac;
3076 cosfac *= cos_phi;
3077 v += cosfac*rbp;
3078 dvdl_term += cosfac*rbpBA;
3079
3080 ddphi = -ddphi*sin_phi; /* 11 */
3081
3082 do_dih_fup(ai, aj, ak, al, ddphi, r_ij, r_kj, r_kl, m, n,
3083 f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
3084 vtot += v;
3085 }
3086 *dvdlambda += dvdl_term;
3087
3088 return vtot;
3089}
3090
3091int cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
3092{
3093 int im1, ip1, ip2;
3094
3095 if (ip < 0)
3096 {
3097 ip = ip + grid_spacing - 1;
3098 }
3099 else if (ip > grid_spacing)
3100 {
3101 ip = ip - grid_spacing - 1;
3102 }
3103
3104 im1 = ip - 1;
3105 ip1 = ip + 1;
3106 ip2 = ip + 2;
3107
3108 if (ip == 0)
3109 {
3110 im1 = grid_spacing - 1;
3111 }
3112 else if (ip == grid_spacing-2)
3113 {
3114 ip2 = 0;
3115 }
3116 else if (ip == grid_spacing-1)
3117 {
3118 ip1 = 0;
3119 ip2 = 1;
3120 }
3121
3122 *ipm1 = im1;
3123 *ipp1 = ip1;
3124 *ipp2 = ip2;
3125
3126 return ip;
3127
3128}
3129
3130real cmap_dihs(int nbonds,
3131 const t_iatom forceatoms[], const t_iparams forceparams[],
3132 const gmx_cmap_t *cmap_grid,
3133 const rvec x[], rvec f[], rvec fshift[],
3134 const t_pbc *pbc, const t_graph *g,
3135 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
3136 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
3137 int gmx_unused__attribute__ ((unused)) *global_atom_index)
3138{
3139 int i, j, k, n, idx;
3140 int ai, aj, ak, al, am;
3141 int a1i, a1j, a1k, a1l, a2i, a2j, a2k, a2l;
3142 int type, cmapA;
3143 int t11, t21, t31, t12, t22, t32;
3144 int iphi1, ip1m1, ip1p1, ip1p2;
3145 int iphi2, ip2m1, ip2p1, ip2p2;
3146 int l1, l2, l3, l4;
3147 int pos1, pos2, pos3, pos4, tmp;
3148
3149 real ty[4], ty1[4], ty2[4], ty12[4], tc[16], tx[16];
3150 real phi1, psi1, cos_phi1, sin_phi1, sign1, xphi1;
3151 real phi2, psi2, cos_phi2, sin_phi2, sign2, xphi2;
3152 real dx, xx, tt, tu, e, df1, df2, ddf1, ddf2, ddf12, vtot;
3153 real ra21, rb21, rg21, rg1, rgr1, ra2r1, rb2r1, rabr1;
3154 real ra22, rb22, rg22, rg2, rgr2, ra2r2, rb2r2, rabr2;
3155 real fg1, hg1, fga1, hgb1, gaa1, gbb1;
3156 real fg2, hg2, fga2, hgb2, gaa2, gbb2;
3157 real fac;
3158
3159 rvec r1_ij, r1_kj, r1_kl, m1, n1;
3160 rvec r2_ij, r2_kj, r2_kl, m2, n2;
3161 rvec f1_i, f1_j, f1_k, f1_l;
3162 rvec f2_i, f2_j, f2_k, f2_l;
3163 rvec a1, b1, a2, b2;
3164 rvec f1, g1, h1, f2, g2, h2;
3165 rvec dtf1, dtg1, dth1, dtf2, dtg2, dth2;
3166 ivec jt1, dt1_ij, dt1_kj, dt1_lj;
3167 ivec jt2, dt2_ij, dt2_kj, dt2_lj;
3168
3169 const real *cmapd;
3170
3171 int loop_index[4][4] = {
3172 {0, 4, 8, 12},
3173 {1, 5, 9, 13},
3174 {2, 6, 10, 14},
3175 {3, 7, 11, 15}
3176 };
3177
3178 /* Total CMAP energy */
3179 vtot = 0;
3180
3181 for (n = 0; n < nbonds; )
3182 {
3183 /* Five atoms are involved in the two torsions */
3184 type = forceatoms[n++];
3185 ai = forceatoms[n++];
3186 aj = forceatoms[n++];
3187 ak = forceatoms[n++];
3188 al = forceatoms[n++];
3189 am = forceatoms[n++];
3190
3191 /* Which CMAP type is this */
3192 cmapA = forceparams[type].cmap.cmapA;
3193 cmapd = cmap_grid->cmapdata[cmapA].cmap;
3194
3195 /* First torsion */
3196 a1i = ai;
3197 a1j = aj;
3198 a1k = ak;
3199 a1l = al;
3200
3201 phi1 = dih_angle(x[a1i], x[a1j], x[a1k], x[a1l], pbc, r1_ij, r1_kj, r1_kl, m1, n1,
3202 &sign1, &t11, &t21, &t31); /* 84 */
3203
3204 cos_phi1 = cos(phi1);
3205
3206 a1[0] = r1_ij[1]*r1_kj[2]-r1_ij[2]*r1_kj[1];
3207 a1[1] = r1_ij[2]*r1_kj[0]-r1_ij[0]*r1_kj[2];
3208 a1[2] = r1_ij[0]*r1_kj[1]-r1_ij[1]*r1_kj[0]; /* 9 */
3209
3210 b1[0] = r1_kl[1]*r1_kj[2]-r1_kl[2]*r1_kj[1];
3211 b1[1] = r1_kl[2]*r1_kj[0]-r1_kl[0]*r1_kj[2];
3212 b1[2] = r1_kl[0]*r1_kj[1]-r1_kl[1]*r1_kj[0]; /* 9 */
3213
3214 tmp = pbc_rvec_sub(pbc, x[a1l], x[a1k], h1);
3215
3216 ra21 = iprod(a1, a1); /* 5 */
3217 rb21 = iprod(b1, b1); /* 5 */
3218 rg21 = iprod(r1_kj, r1_kj); /* 5 */
3219 rg1 = sqrt(rg21);
3220
3221 rgr1 = 1.0/rg1;
3222 ra2r1 = 1.0/ra21;
3223 rb2r1 = 1.0/rb21;
3224 rabr1 = sqrt(ra2r1*rb2r1);
3225
3226 sin_phi1 = rg1 * rabr1 * iprod(a1, h1) * (-1);
3227
3228 if (cos_phi1 < -0.5 || cos_phi1 > 0.5)
3229 {
3230 phi1 = asin(sin_phi1);
3231
3232 if (cos_phi1 < 0)
3233 {
3234 if (phi1 > 0)
3235 {
3236 phi1 = M_PI3.14159265358979323846 - phi1;
3237 }
3238 else
3239 {
3240 phi1 = -M_PI3.14159265358979323846 - phi1;
3241 }
3242 }
3243 }
3244 else
3245 {
3246 phi1 = acos(cos_phi1);
3247
3248 if (sin_phi1 < 0)
3249 {
3250 phi1 = -phi1;
3251 }
3252 }
3253
3254 xphi1 = phi1 + M_PI3.14159265358979323846; /* 1 */
3255
3256 /* Second torsion */
3257 a2i = aj;
3258 a2j = ak;
3259 a2k = al;
3260 a2l = am;
3261
3262 phi2 = dih_angle(x[a2i], x[a2j], x[a2k], x[a2l], pbc, r2_ij, r2_kj, r2_kl, m2, n2,
3263 &sign2, &t12, &t22, &t32); /* 84 */
3264
3265 cos_phi2 = cos(phi2);
3266
3267 a2[0] = r2_ij[1]*r2_kj[2]-r2_ij[2]*r2_kj[1];
3268 a2[1] = r2_ij[2]*r2_kj[0]-r2_ij[0]*r2_kj[2];
3269 a2[2] = r2_ij[0]*r2_kj[1]-r2_ij[1]*r2_kj[0]; /* 9 */
3270
3271 b2[0] = r2_kl[1]*r2_kj[2]-r2_kl[2]*r2_kj[1];
3272 b2[1] = r2_kl[2]*r2_kj[0]-r2_kl[0]*r2_kj[2];
3273 b2[2] = r2_kl[0]*r2_kj[1]-r2_kl[1]*r2_kj[0]; /* 9 */
3274
3275 tmp = pbc_rvec_sub(pbc, x[a2l], x[a2k], h2);
3276
3277 ra22 = iprod(a2, a2); /* 5 */
3278 rb22 = iprod(b2, b2); /* 5 */
3279 rg22 = iprod(r2_kj, r2_kj); /* 5 */
3280 rg2 = sqrt(rg22);
3281
3282 rgr2 = 1.0/rg2;
3283 ra2r2 = 1.0/ra22;
3284 rb2r2 = 1.0/rb22;
3285 rabr2 = sqrt(ra2r2*rb2r2);
3286
3287 sin_phi2 = rg2 * rabr2 * iprod(a2, h2) * (-1);
3288
3289 if (cos_phi2 < -0.5 || cos_phi2 > 0.5)
3290 {
3291 phi2 = asin(sin_phi2);
3292
3293 if (cos_phi2 < 0)
3294 {
3295 if (phi2 > 0)
3296 {
3297 phi2 = M_PI3.14159265358979323846 - phi2;
3298 }
3299 else
3300 {
3301 phi2 = -M_PI3.14159265358979323846 - phi2;
3302 }
3303 }
3304 }
3305 else
3306 {
3307 phi2 = acos(cos_phi2);
3308
3309 if (sin_phi2 < 0)
3310 {
3311 phi2 = -phi2;
3312 }
3313 }
3314
3315 xphi2 = phi2 + M_PI3.14159265358979323846; /* 1 */
3316
3317 /* Range mangling */
3318 if (xphi1 < 0)
3319 {
3320 xphi1 = xphi1 + 2*M_PI3.14159265358979323846;
3321 }
3322 else if (xphi1 >= 2*M_PI3.14159265358979323846)
3323 {
3324 xphi1 = xphi1 - 2*M_PI3.14159265358979323846;
3325 }
3326
3327 if (xphi2 < 0)
3328 {
3329 xphi2 = xphi2 + 2*M_PI3.14159265358979323846;
3330 }
3331 else if (xphi2 >= 2*M_PI3.14159265358979323846)
3332 {
3333 xphi2 = xphi2 - 2*M_PI3.14159265358979323846;
3334 }
3335
3336 /* Number of grid points */
3337 dx = 2*M_PI3.14159265358979323846 / cmap_grid->grid_spacing;
3338
3339 /* Where on the grid are we */
3340 iphi1 = (int)(xphi1/dx);
3341 iphi2 = (int)(xphi2/dx);
3342
3343 iphi1 = cmap_setup_grid_index(iphi1, cmap_grid->grid_spacing, &ip1m1, &ip1p1, &ip1p2);
3344 iphi2 = cmap_setup_grid_index(iphi2, cmap_grid->grid_spacing, &ip2m1, &ip2p1, &ip2p2);
3345
3346 pos1 = iphi1*cmap_grid->grid_spacing+iphi2;
3347 pos2 = ip1p1*cmap_grid->grid_spacing+iphi2;
3348 pos3 = ip1p1*cmap_grid->grid_spacing+ip2p1;
3349 pos4 = iphi1*cmap_grid->grid_spacing+ip2p1;
3350
3351 ty[0] = cmapd[pos1*4];
3352 ty[1] = cmapd[pos2*4];
3353 ty[2] = cmapd[pos3*4];
3354 ty[3] = cmapd[pos4*4];
3355
3356 ty1[0] = cmapd[pos1*4+1];
3357 ty1[1] = cmapd[pos2*4+1];
3358 ty1[2] = cmapd[pos3*4+1];
3359 ty1[3] = cmapd[pos4*4+1];
3360
3361 ty2[0] = cmapd[pos1*4+2];
3362 ty2[1] = cmapd[pos2*4+2];
3363 ty2[2] = cmapd[pos3*4+2];
3364 ty2[3] = cmapd[pos4*4+2];
3365
3366 ty12[0] = cmapd[pos1*4+3];
3367 ty12[1] = cmapd[pos2*4+3];
3368 ty12[2] = cmapd[pos3*4+3];
3369 ty12[3] = cmapd[pos4*4+3];
3370
3371 /* Switch to degrees */
3372 dx = 360.0 / cmap_grid->grid_spacing;
3373 xphi1 = xphi1 * RAD2DEG(180.0/3.14159265358979323846);
3374 xphi2 = xphi2 * RAD2DEG(180.0/3.14159265358979323846);
3375
3376 for (i = 0; i < 4; i++) /* 16 */
3377 {
3378 tx[i] = ty[i];
3379 tx[i+4] = ty1[i]*dx;
3380 tx[i+8] = ty2[i]*dx;
3381 tx[i+12] = ty12[i]*dx*dx;
3382 }
3383
3384 idx = 0;
3385 for (i = 0; i < 4; i++) /* 1056 */
3386 {
3387 for (j = 0; j < 4; j++)
3388 {
3389 xx = 0;
3390 for (k = 0; k < 16; k++)
3391 {
3392 xx = xx + cmap_coeff_matrix[k*16+idx]*tx[k];
3393 }
3394
3395 idx++;
3396 tc[i*4+j] = xx;
3397 }
3398 }
3399
3400 tt = (xphi1-iphi1*dx)/dx;
3401 tu = (xphi2-iphi2*dx)/dx;
3402
3403 e = 0;
3404 df1 = 0;
3405 df2 = 0;
3406 ddf1 = 0;
3407 ddf2 = 0;
3408 ddf12 = 0;
3409
3410 for (i = 3; i >= 0; i--)
3411 {
3412 l1 = loop_index[i][3];
3413 l2 = loop_index[i][2];
3414 l3 = loop_index[i][1];
3415
3416 e = tt * e + ((tc[i*4+3]*tu+tc[i*4+2])*tu + tc[i*4+1])*tu+tc[i*4];
3417 df1 = tu * df1 + (3.0*tc[l1]*tt+2.0*tc[l2])*tt+tc[l3];
3418 df2 = tt * df2 + (3.0*tc[i*4+3]*tu+2.0*tc[i*4+2])*tu+tc[i*4+1];
3419 ddf1 = tu * ddf1 + 2.0*3.0*tc[l1]*tt+2.0*tc[l2];
3420 ddf2 = tt * ddf2 + 2.0*3.0*tc[4*i+3]*tu+2.0*tc[4*i+2];
3421 }
3422
3423 ddf12 = tc[5] + 2.0*tc[9]*tt + 3.0*tc[13]*tt*tt + 2.0*tu*(tc[6]+2.0*tc[10]*tt+3.0*tc[14]*tt*tt) +
3424 3.0*tu*tu*(tc[7]+2.0*tc[11]*tt+3.0*tc[15]*tt*tt);
3425
3426 fac = RAD2DEG(180.0/3.14159265358979323846)/dx;
3427 df1 = df1 * fac;
3428 df2 = df2 * fac;
3429 ddf1 = ddf1 * fac * fac;
3430 ddf2 = ddf2 * fac * fac;
3431 ddf12 = ddf12 * fac * fac;
3432
3433 /* CMAP energy */
3434 vtot += e;
3435
3436 /* Do forces - first torsion */
3437 fg1 = iprod(r1_ij, r1_kj);
3438 hg1 = iprod(r1_kl, r1_kj);
3439 fga1 = fg1*ra2r1*rgr1;
3440 hgb1 = hg1*rb2r1*rgr1;
3441 gaa1 = -ra2r1*rg1;
3442 gbb1 = rb2r1*rg1;
3443
3444 for (i = 0; i < DIM3; i++)
3445 {
3446 dtf1[i] = gaa1 * a1[i];
3447 dtg1[i] = fga1 * a1[i] - hgb1 * b1[i];
3448 dth1[i] = gbb1 * b1[i];
3449
3450 f1[i] = df1 * dtf1[i];
3451 g1[i] = df1 * dtg1[i];
3452 h1[i] = df1 * dth1[i];
3453
3454 f1_i[i] = f1[i];
3455 f1_j[i] = -f1[i] - g1[i];
3456 f1_k[i] = h1[i] + g1[i];
3457 f1_l[i] = -h1[i];
3458
3459 f[a1i][i] = f[a1i][i] + f1_i[i];
3460 f[a1j][i] = f[a1j][i] + f1_j[i]; /* - f1[i] - g1[i] */
3461 f[a1k][i] = f[a1k][i] + f1_k[i]; /* h1[i] + g1[i] */
3462 f[a1l][i] = f[a1l][i] + f1_l[i]; /* h1[i] */
3463 }
3464
3465 /* Do forces - second torsion */
3466 fg2 = iprod(r2_ij, r2_kj);
3467 hg2 = iprod(r2_kl, r2_kj);
3468 fga2 = fg2*ra2r2*rgr2;
3469 hgb2 = hg2*rb2r2*rgr2;
3470 gaa2 = -ra2r2*rg2;
3471 gbb2 = rb2r2*rg2;
3472
3473 for (i = 0; i < DIM3; i++)
3474 {
3475 dtf2[i] = gaa2 * a2[i];
3476 dtg2[i] = fga2 * a2[i] - hgb2 * b2[i];
3477 dth2[i] = gbb2 * b2[i];
3478
3479 f2[i] = df2 * dtf2[i];
3480 g2[i] = df2 * dtg2[i];
3481 h2[i] = df2 * dth2[i];
3482
3483 f2_i[i] = f2[i];
3484 f2_j[i] = -f2[i] - g2[i];
3485 f2_k[i] = h2[i] + g2[i];
3486 f2_l[i] = -h2[i];
3487
3488 f[a2i][i] = f[a2i][i] + f2_i[i]; /* f2[i] */
3489 f[a2j][i] = f[a2j][i] + f2_j[i]; /* - f2[i] - g2[i] */
3490 f[a2k][i] = f[a2k][i] + f2_k[i]; /* h2[i] + g2[i] */
3491 f[a2l][i] = f[a2l][i] + f2_l[i]; /* - h2[i] */
3492 }
3493
3494 /* Shift forces */
3495 if (g)
3496 {
3497 copy_ivec(SHIFT_IVEC(g, a1j)((g)->ishift[a1j]), jt1);
3498 ivec_sub(SHIFT_IVEC(g, a1i)((g)->ishift[a1i]), jt1, dt1_ij);
3499 ivec_sub(SHIFT_IVEC(g, a1k)((g)->ishift[a1k]), jt1, dt1_kj);
3500 ivec_sub(SHIFT_IVEC(g, a1l)((g)->ishift[a1l]), jt1, dt1_lj);
3501 t11 = IVEC2IS(dt1_ij)(((2*2 +1)*((2*1 +1)*(((dt1_ij)[2])+1)+((dt1_ij)[1])+1)+((dt1_ij
)[0])+2));
3502 t21 = IVEC2IS(dt1_kj)(((2*2 +1)*((2*1 +1)*(((dt1_kj)[2])+1)+((dt1_kj)[1])+1)+((dt1_kj
)[0])+2));
3503 t31 = IVEC2IS(dt1_lj)(((2*2 +1)*((2*1 +1)*(((dt1_lj)[2])+1)+((dt1_lj)[1])+1)+((dt1_lj
)[0])+2));
3504
3505 copy_ivec(SHIFT_IVEC(g, a2j)((g)->ishift[a2j]), jt2);
3506 ivec_sub(SHIFT_IVEC(g, a2i)((g)->ishift[a2i]), jt2, dt2_ij);
3507 ivec_sub(SHIFT_IVEC(g, a2k)((g)->ishift[a2k]), jt2, dt2_kj);
3508 ivec_sub(SHIFT_IVEC(g, a2l)((g)->ishift[a2l]), jt2, dt2_lj);
3509 t12 = IVEC2IS(dt2_ij)(((2*2 +1)*((2*1 +1)*(((dt2_ij)[2])+1)+((dt2_ij)[1])+1)+((dt2_ij
)[0])+2));
3510 t22 = IVEC2IS(dt2_kj)(((2*2 +1)*((2*1 +1)*(((dt2_kj)[2])+1)+((dt2_kj)[1])+1)+((dt2_kj
)[0])+2));
3511 t32 = IVEC2IS(dt2_lj)(((2*2 +1)*((2*1 +1)*(((dt2_lj)[2])+1)+((dt2_lj)[1])+1)+((dt2_lj
)[0])+2));
3512 }
3513 else if (pbc)
3514 {
3515 t31 = pbc_rvec_sub(pbc, x[a1l], x[a1j], h1);
3516 t32 = pbc_rvec_sub(pbc, x[a2l], x[a2j], h2);
3517 }
3518 else
3519 {
3520 t31 = CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2);
3521 t32 = CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2);
3522 }
3523
3524 rvec_inc(fshift[t11], f1_i);
3525 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f1_j);
3526 rvec_inc(fshift[t21], f1_k);
3527 rvec_inc(fshift[t31], f1_l);
3528
3529 rvec_inc(fshift[t21], f2_i);
3530 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f2_j);
3531 rvec_inc(fshift[t22], f2_k);
3532 rvec_inc(fshift[t32], f2_l);
3533 }
3534 return vtot;
3535}
3536
3537
3538
3539/***********************************************************
3540 *
3541 * G R O M O S 9 6 F U N C T I O N S
3542 *
3543 ***********************************************************/
3544real g96harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
3545 real *V, real *F)
3546{
3547 const real half = 0.5;
3548 real L1, kk, x0, dx, dx2;
3549 real v, f, dvdlambda;
3550
3551 L1 = 1.0-lambda;
3552 kk = L1*kA+lambda*kB;
3553 x0 = L1*xA+lambda*xB;
3554
3555 dx = x-x0;
3556 dx2 = dx*dx;
3557
3558 f = -kk*dx;
3559 v = half*kk*dx2;
3560 dvdlambda = half*(kB-kA)*dx2 + (xA-xB)*kk*dx;
3561
3562 *F = f;
3563 *V = v;
3564
3565 return dvdlambda;
3566
3567 /* That was 21 flops */
3568}
3569
3570real g96bonds(int nbonds,
3571 const t_iatom forceatoms[], const t_iparams forceparams[],
3572 const rvec x[], rvec f[], rvec fshift[],
3573 const t_pbc *pbc, const t_graph *g,
3574 real lambda, real *dvdlambda,
3575 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
3576 int gmx_unused__attribute__ ((unused)) *global_atom_index)
3577{
3578 int i, m, ki, ai, aj, type;
3579 real dr2, fbond, vbond, fij, vtot;
3580 rvec dx;
3581 ivec dt;
3582
3583 vtot = 0.0;
3584 for (i = 0; (i < nbonds); )
3585 {
3586 type = forceatoms[i++];
3587 ai = forceatoms[i++];
3588 aj = forceatoms[i++];
3589
3590 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
3591 dr2 = iprod(dx, dx); /* 5 */
3592
3593 *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
3594 forceparams[type].harmonic.krB,
3595 forceparams[type].harmonic.rA,
3596 forceparams[type].harmonic.rB,
3597 dr2, lambda, &vbond, &fbond);
3598
3599 vtot += 0.5*vbond; /* 1*/
3600#ifdef DEBUG
3601 if (debug)
3602 {
3603 fprintf(debug, "G96-BONDS: dr = %10g vbond = %10g fbond = %10g\n",
3604 sqrt(dr2), vbond, fbond);
3605 }
3606#endif
3607
3608 if (g)
3609 {
3610 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
3611 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
3612 }
3613 for (m = 0; (m < DIM3); m++) /* 15 */
3614 {
3615 fij = fbond*dx[m];
3616 f[ai][m] += fij;
3617 f[aj][m] -= fij;
3618 fshift[ki][m] += fij;
3619 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
3620 }
3621 } /* 44 TOTAL */
3622 return vtot;
3623}
3624
3625real g96bond_angle(const rvec xi, const rvec xj, const rvec xk, const t_pbc *pbc,
3626 rvec r_ij, rvec r_kj,
3627 int *t1, int *t2)
3628/* Return value is the angle between the bonds i-j and j-k */
3629{
3630 real costh;
3631
3632 *t1 = pbc_rvec_sub(pbc, xi, xj, r_ij); /* 3 */
3633 *t2 = pbc_rvec_sub(pbc, xk, xj, r_kj); /* 3 */
3634
3635 costh = cos_angle(r_ij, r_kj); /* 25 */
3636 /* 41 TOTAL */
3637 return costh;
3638}
3639
3640real g96angles(int nbonds,
3641 const t_iatom forceatoms[], const t_iparams forceparams[],
3642 const rvec x[], rvec f[], rvec fshift[],
3643 const t_pbc *pbc, const t_graph *g,
3644 real lambda, real *dvdlambda,
3645 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
3646 int gmx_unused__attribute__ ((unused)) *global_atom_index)
3647{
3648 int i, ai, aj, ak, type, m, t1, t2;
3649 rvec r_ij, r_kj;
3650 real cos_theta, dVdt, va, vtot;
3651 real rij_1, rij_2, rkj_1, rkj_2, rijrkj_1;
3652 rvec f_i, f_j, f_k;
3653 ivec jt, dt_ij, dt_kj;
3654
3655 vtot = 0.0;
3656 for (i = 0; (i < nbonds); )
3657 {
3658 type = forceatoms[i++];
3659 ai = forceatoms[i++];
3660 aj = forceatoms[i++];
3661 ak = forceatoms[i++];
3662
3663 cos_theta = g96bond_angle(x[ai], x[aj], x[ak], pbc, r_ij, r_kj, &t1, &t2);
3664
3665 *dvdlambda += g96harmonic(forceparams[type].harmonic.krA,
3666 forceparams[type].harmonic.krB,
3667 forceparams[type].harmonic.rA,
3668 forceparams[type].harmonic.rB,
3669 cos_theta, lambda, &va, &dVdt);
3670 vtot += va;
3671
3672 rij_1 = gmx_invsqrt(iprod(r_ij, r_ij))gmx_software_invsqrt(iprod(r_ij, r_ij));
3673 rkj_1 = gmx_invsqrt(iprod(r_kj, r_kj))gmx_software_invsqrt(iprod(r_kj, r_kj));
3674 rij_2 = rij_1*rij_1;
3675 rkj_2 = rkj_1*rkj_1;
3676 rijrkj_1 = rij_1*rkj_1; /* 23 */
3677
3678#ifdef DEBUG
3679 if (debug)
3680 {
3681 fprintf(debug, "G96ANGLES: costheta = %10g vth = %10g dV/dct = %10g\n",
3682 cos_theta, va, dVdt);
3683 }
3684#endif
3685 for (m = 0; (m < DIM3); m++) /* 42 */
3686 {
3687 f_i[m] = dVdt*(r_kj[m]*rijrkj_1 - r_ij[m]*rij_2*cos_theta);
3688 f_k[m] = dVdt*(r_ij[m]*rijrkj_1 - r_kj[m]*rkj_2*cos_theta);
3689 f_j[m] = -f_i[m]-f_k[m];
3690 f[ai][m] += f_i[m];
3691 f[aj][m] += f_j[m];
3692 f[ak][m] += f_k[m];
3693 }
3694
3695 if (g)
3696 {
3697 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
3698
3699 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
3700 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
3701 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
3702 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
3703 }
3704 rvec_inc(fshift[t1], f_i);
3705 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
3706 rvec_inc(fshift[t2], f_k); /* 9 */
3707 /* 163 TOTAL */
3708 }
3709 return vtot;
3710}
3711
3712real cross_bond_bond(int nbonds,
3713 const t_iatom forceatoms[], const t_iparams forceparams[],
3714 const rvec x[], rvec f[], rvec fshift[],
3715 const t_pbc *pbc, const t_graph *g,
3716 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
3717 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
3718 int gmx_unused__attribute__ ((unused)) *global_atom_index)
3719{
3720 /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
3721 * pp. 842-847
3722 */
3723 int i, ai, aj, ak, type, m, t1, t2;
3724 rvec r_ij, r_kj;
3725 real vtot, vrr, s1, s2, r1, r2, r1e, r2e, krr;
3726 rvec f_i, f_j, f_k;
3727 ivec jt, dt_ij, dt_kj;
3728
3729 vtot = 0.0;
3730 for (i = 0; (i < nbonds); )
3731 {
3732 type = forceatoms[i++];
3733 ai = forceatoms[i++];
3734 aj = forceatoms[i++];
3735 ak = forceatoms[i++];
3736 r1e = forceparams[type].cross_bb.r1e;
3737 r2e = forceparams[type].cross_bb.r2e;
3738 krr = forceparams[type].cross_bb.krr;
3739
3740 /* Compute distance vectors ... */
3741 t1 = pbc_rvec_sub(pbc, x[ai], x[aj], r_ij);
3742 t2 = pbc_rvec_sub(pbc, x[ak], x[aj], r_kj);
3743
3744 /* ... and their lengths */
3745 r1 = norm(r_ij);
3746 r2 = norm(r_kj);
3747
3748 /* Deviations from ideality */
3749 s1 = r1-r1e;
3750 s2 = r2-r2e;
3751
3752 /* Energy (can be negative!) */
3753 vrr = krr*s1*s2;
3754 vtot += vrr;
3755
3756 /* Forces */
3757 svmul(-krr*s2/r1, r_ij, f_i);
3758 svmul(-krr*s1/r2, r_kj, f_k);
3759
3760 for (m = 0; (m < DIM3); m++) /* 12 */
3761 {
3762 f_j[m] = -f_i[m] - f_k[m];
3763 f[ai][m] += f_i[m];
3764 f[aj][m] += f_j[m];
3765 f[ak][m] += f_k[m];
3766 }
3767
3768 /* Virial stuff */
3769 if (g)
3770 {
3771 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
3772
3773 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
3774 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
3775 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
3776 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
3777 }
3778 rvec_inc(fshift[t1], f_i);
3779 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
3780 rvec_inc(fshift[t2], f_k); /* 9 */
3781 /* 163 TOTAL */
3782 }
3783 return vtot;
3784}
3785
3786real cross_bond_angle(int nbonds,
3787 const t_iatom forceatoms[], const t_iparams forceparams[],
3788 const rvec x[], rvec f[], rvec fshift[],
3789 const t_pbc *pbc, const t_graph *g,
3790 real gmx_unused__attribute__ ((unused)) lambda, real gmx_unused__attribute__ ((unused)) *dvdlambda,
3791 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata gmx_unused__attribute__ ((unused)) *fcd,
3792 int gmx_unused__attribute__ ((unused)) *global_atom_index)
3793{
3794 /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
3795 * pp. 842-847
3796 */
3797 int i, ai, aj, ak, type, m, t1, t2, t3;
3798 rvec r_ij, r_kj, r_ik;
3799 real vtot, vrt, s1, s2, s3, r1, r2, r3, r1e, r2e, r3e, krt, k1, k2, k3;
3800 rvec f_i, f_j, f_k;
3801 ivec jt, dt_ij, dt_kj;
3802
3803 vtot = 0.0;
3804 for (i = 0; (i < nbonds); )
3805 {
3806 type = forceatoms[i++];
3807 ai = forceatoms[i++];
3808 aj = forceatoms[i++];
3809 ak = forceatoms[i++];
3810 r1e = forceparams[type].cross_ba.r1e;
3811 r2e = forceparams[type].cross_ba.r2e;
3812 r3e = forceparams[type].cross_ba.r3e;
3813 krt = forceparams[type].cross_ba.krt;
3814
3815 /* Compute distance vectors ... */
3816 t1 = pbc_rvec_sub(pbc, x[ai], x[aj], r_ij);
3817 t2 = pbc_rvec_sub(pbc, x[ak], x[aj], r_kj);
3818 t3 = pbc_rvec_sub(pbc, x[ai], x[ak], r_ik);
3819
3820 /* ... and their lengths */
3821 r1 = norm(r_ij);
3822 r2 = norm(r_kj);
3823 r3 = norm(r_ik);
3824
3825 /* Deviations from ideality */
3826 s1 = r1-r1e;
3827 s2 = r2-r2e;
3828 s3 = r3-r3e;
3829
3830 /* Energy (can be negative!) */
3831 vrt = krt*s3*(s1+s2);
3832 vtot += vrt;
3833
3834 /* Forces */
3835 k1 = -krt*(s3/r1);
3836 k2 = -krt*(s3/r2);
3837 k3 = -krt*(s1+s2)/r3;
3838 for (m = 0; (m < DIM3); m++)
3839 {
3840 f_i[m] = k1*r_ij[m] + k3*r_ik[m];
3841 f_k[m] = k2*r_kj[m] - k3*r_ik[m];
3842 f_j[m] = -f_i[m] - f_k[m];
3843 }
3844
3845 for (m = 0; (m < DIM3); m++) /* 12 */
3846 {
3847 f[ai][m] += f_i[m];
3848 f[aj][m] += f_j[m];
3849 f[ak][m] += f_k[m];
3850 }
3851
3852 /* Virial stuff */
3853 if (g)
3854 {
3855 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
3856
3857 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
3858 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
3859 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
3860 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
3861 }
3862 rvec_inc(fshift[t1], f_i);
3863 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
3864 rvec_inc(fshift[t2], f_k); /* 9 */
3865 /* 163 TOTAL */
3866 }
3867 return vtot;
3868}
3869
3870static real bonded_tab(const char *type, int table_nr,
3871 const bondedtable_t *table, real kA, real kB, real r,
3872 real lambda, real *V, real *F)
3873{
3874 real k, tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps2, Fp, VV, FF;
3875 int n0, nnn;
3876 real v, f, dvdlambda;
3877
3878 k = (1.0 - lambda)*kA + lambda*kB;
3879
3880 tabscale = table->scale;
3881 VFtab = table->data;
3882
3883 rt = r*tabscale;
3884 n0 = rt;
3885 if (n0 >= table->n)
3886 {
3887 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 3887, "A tabulated %s interaction table number %d is out of the table range: r %f, between table indices %d and %d, table length %d",
3888 type, table_nr, r, n0, n0+1, table->n);
3889 }
3890 eps = rt - n0;
3891 eps2 = eps*eps;
3892 nnn = 4*n0;
3893 Yt = VFtab[nnn];
3894 Ft = VFtab[nnn+1];
3895 Geps = VFtab[nnn+2]*eps;
3896 Heps2 = VFtab[nnn+3]*eps2;
3897 Fp = Ft + Geps + Heps2;
3898 VV = Yt + Fp*eps;
3899 FF = Fp + Geps + 2.0*Heps2;
3900
3901 *F = -k*FF*tabscale;
3902 *V = k*VV;
3903 dvdlambda = (kB - kA)*VV;
3904
3905 return dvdlambda;
3906
3907 /* That was 22 flops */
3908}
3909
3910real tab_bonds(int nbonds,
3911 const t_iatom forceatoms[], const t_iparams forceparams[],
3912 const rvec x[], rvec f[], rvec fshift[],
3913 const t_pbc *pbc, const t_graph *g,
3914 real lambda, real *dvdlambda,
3915 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata *fcd,
3916 int gmx_unused__attribute__ ((unused)) *global_atom_index)
3917{
3918 int i, m, ki, ai, aj, type, table;
3919 real dr, dr2, fbond, vbond, fij, vtot;
3920 rvec dx;
3921 ivec dt;
3922
3923 vtot = 0.0;
3924 for (i = 0; (i < nbonds); )
3925 {
3926 type = forceatoms[i++];
3927 ai = forceatoms[i++];
3928 aj = forceatoms[i++];
3929
3930 ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx); /* 3 */
3931 dr2 = iprod(dx, dx); /* 5 */
3932 dr = dr2*gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 10 */
3933
3934 table = forceparams[type].tab.table;
3935
3936 *dvdlambda += bonded_tab("bond", table,
3937 &fcd->bondtab[table],
3938 forceparams[type].tab.kA,
3939 forceparams[type].tab.kB,
3940 dr, lambda, &vbond, &fbond); /* 22 */
3941
3942 if (dr2 == 0.0)
3943 {
3944 continue;
3945 }
3946
3947
3948 vtot += vbond; /* 1*/
3949 fbond *= gmx_invsqrt(dr2)gmx_software_invsqrt(dr2); /* 6 */
3950#ifdef DEBUG
3951 if (debug)
3952 {
3953 fprintf(debug, "TABBONDS: dr = %10g vbond = %10g fbond = %10g\n",
3954 dr, vbond, fbond);
3955 }
3956#endif
3957 if (g)
3958 {
3959 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), SHIFT_IVEC(g, aj)((g)->ishift[aj]), dt);
3960 ki = IVEC2IS(dt)(((2*2 +1)*((2*1 +1)*(((dt)[2])+1)+((dt)[1])+1)+((dt)[0])+2));
3961 }
3962 for (m = 0; (m < DIM3); m++) /* 15 */
3963 {
3964 fij = fbond*dx[m];
3965 f[ai][m] += fij;
3966 f[aj][m] -= fij;
3967 fshift[ki][m] += fij;
3968 fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)][m] -= fij;
3969 }
3970 } /* 62 TOTAL */
3971 return vtot;
3972}
3973
3974real tab_angles(int nbonds,
3975 const t_iatom forceatoms[], const t_iparams forceparams[],
3976 const rvec x[], rvec f[], rvec fshift[],
3977 const t_pbc *pbc, const t_graph *g,
3978 real lambda, real *dvdlambda,
3979 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata *fcd,
3980 int gmx_unused__attribute__ ((unused)) *global_atom_index)
3981{
3982 int i, ai, aj, ak, t1, t2, type, table;
3983 rvec r_ij, r_kj;
3984 real cos_theta, cos_theta2, theta, dVdt, va, vtot;
3985 ivec jt, dt_ij, dt_kj;
3986
3987 vtot = 0.0;
3988 for (i = 0; (i < nbonds); )
3989 {
3990 type = forceatoms[i++];
3991 ai = forceatoms[i++];
3992 aj = forceatoms[i++];
3993 ak = forceatoms[i++];
3994
3995 theta = bond_angle(x[ai], x[aj], x[ak], pbc,
3996 r_ij, r_kj, &cos_theta, &t1, &t2); /* 41 */
3997
3998 table = forceparams[type].tab.table;
3999
4000 *dvdlambda += bonded_tab("angle", table,
4001 &fcd->angletab[table],
4002 forceparams[type].tab.kA,
4003 forceparams[type].tab.kB,
4004 theta, lambda, &va, &dVdt); /* 22 */
4005 vtot += va;
4006
4007 cos_theta2 = sqr(cos_theta); /* 1 */
4008 if (cos_theta2 < 1)
4009 {
4010 int m;
4011 real snt, st, sth;
4012 real cik, cii, ckk;
4013 real nrkj2, nrij2;
4014 rvec f_i, f_j, f_k;
4015
4016 st = dVdt*gmx_invsqrt(1 - cos_theta2)gmx_software_invsqrt(1 - cos_theta2); /* 12 */
4017 sth = st*cos_theta; /* 1 */
4018#ifdef DEBUG
4019 if (debug)
4020 {
4021 fprintf(debug, "ANGLES: theta = %10g vth = %10g dV/dtheta = %10g\n",
4022 theta*RAD2DEG(180.0/3.14159265358979323846), va, dVdt);
4023 }
4024#endif
4025 nrkj2 = iprod(r_kj, r_kj); /* 5 */
4026 nrij2 = iprod(r_ij, r_ij);
4027
4028 cik = st*gmx_invsqrt(nrkj2*nrij2)gmx_software_invsqrt(nrkj2*nrij2); /* 12 */
4029 cii = sth/nrij2; /* 10 */
4030 ckk = sth/nrkj2; /* 10 */
4031
4032 for (m = 0; (m < DIM3); m++) /* 39 */
4033 {
4034 f_i[m] = -(cik*r_kj[m]-cii*r_ij[m]);
4035 f_k[m] = -(cik*r_ij[m]-ckk*r_kj[m]);
4036 f_j[m] = -f_i[m]-f_k[m];
4037 f[ai][m] += f_i[m];
4038 f[aj][m] += f_j[m];
4039 f[ak][m] += f_k[m];
4040 }
4041 if (g)
4042 {
4043 copy_ivec(SHIFT_IVEC(g, aj)((g)->ishift[aj]), jt);
4044
4045 ivec_sub(SHIFT_IVEC(g, ai)((g)->ishift[ai]), jt, dt_ij);
4046 ivec_sub(SHIFT_IVEC(g, ak)((g)->ishift[ak]), jt, dt_kj);
4047 t1 = IVEC2IS(dt_ij)(((2*2 +1)*((2*1 +1)*(((dt_ij)[2])+1)+((dt_ij)[1])+1)+((dt_ij
)[0])+2));
4048 t2 = IVEC2IS(dt_kj)(((2*2 +1)*((2*1 +1)*(((dt_kj)[2])+1)+((dt_kj)[1])+1)+((dt_kj
)[0])+2));
4049 }
4050 rvec_inc(fshift[t1], f_i);
4051 rvec_inc(fshift[CENTRAL(((2*1 +1)*(2*1 +1)*(2*2 +1))/2)], f_j);
4052 rvec_inc(fshift[t2], f_k);
4053 } /* 169 TOTAL */
4054 }
4055 return vtot;
4056}
4057
4058real tab_dihs(int nbonds,
4059 const t_iatom forceatoms[], const t_iparams forceparams[],
4060 const rvec x[], rvec f[], rvec fshift[],
4061 const t_pbc *pbc, const t_graph *g,
4062 real lambda, real *dvdlambda,
4063 const t_mdatoms gmx_unused__attribute__ ((unused)) *md, t_fcdata *fcd,
4064 int gmx_unused__attribute__ ((unused)) *global_atom_index)
4065{
4066 int i, type, ai, aj, ak, al, table;
4067 int t1, t2, t3;
4068 rvec r_ij, r_kj, r_kl, m, n;
4069 real phi, sign, ddphi, vpd, vtot;
4070
4071 vtot = 0.0;
4072 for (i = 0; (i < nbonds); )
4073 {
4074 type = forceatoms[i++];
4075 ai = forceatoms[i++];
4076 aj = forceatoms[i++];
4077 ak = forceatoms[i++];
4078 al = forceatoms[i++];
4079
4080 phi = dih_angle(x[ai], x[aj], x[ak], x[al], pbc, r_ij, r_kj, r_kl, m, n,
4081 &sign, &t1, &t2, &t3); /* 84 */
4082
4083 table = forceparams[type].tab.table;
4084
4085 /* Hopefully phi+M_PI never results in values < 0 */
4086 *dvdlambda += bonded_tab("dihedral", table,
4087 &fcd->dihtab[table],
4088 forceparams[type].tab.kA,
4089 forceparams[type].tab.kB,
4090 phi+M_PI3.14159265358979323846, lambda, &vpd, &ddphi);
4091
4092 vtot += vpd;
4093 do_dih_fup(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n,
4094 f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
4095
4096#ifdef DEBUG
4097 fprintf(debug, "pdih: (%d,%d,%d,%d) phi=%g\n",
4098 ai, aj, ak, al, phi);
4099#endif
4100 } /* 227 TOTAL */
4101
4102 return vtot;
4103}
4104
4105/* Return if this is a potential calculated in bondfree.c,
4106 * i.e. an interaction that actually calculates a potential and
4107 * works on multiple atoms (not e.g. a connection or a position restraint).
4108 */
4109static gmx_inlineinline gmx_bool ftype_is_bonded_potential(int ftype)
4110{
4111 return
4112 (interaction_function[ftype].flags & IF_BOND1) &&
4113 !(ftype == F_CONNBONDS || ftype == F_POSRES || ftype == F_FBPOSRES) &&
4114 (ftype < F_GB12 || ftype > F_GB14);
4115}
4116
4117static void divide_bondeds_over_threads(t_idef *idef, int nthreads)
4118{
4119 int ftype;
4120 int nat1;
4121 int t;
4122 int il_nr_thread;
4123
4124 idef->nthreads = nthreads;
4125
4126 if (F_NRE*(nthreads+1) > idef->il_thread_division_nalloc)
4127 {
4128 idef->il_thread_division_nalloc = F_NRE*(nthreads+1);
4129 snew(idef->il_thread_division, idef->il_thread_division_nalloc)(idef->il_thread_division) = save_calloc("idef->il_thread_division"
, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4129, (idef->il_thread_division_nalloc), sizeof(*(idef->
il_thread_division)));
4130 }
4131
4132 for (ftype = 0; ftype < F_NRE; ftype++)
4133 {
4134 if (ftype_is_bonded_potential(ftype))
4135 {
4136 nat1 = interaction_function[ftype].nratoms + 1;
4137
4138 for (t = 0; t <= nthreads; t++)
4139 {
4140 /* Divide the interactions equally over the threads.
4141 * When the different types of bonded interactions
4142 * are distributed roughly equally over the threads,
4143 * this should lead to well localized output into
4144 * the force buffer on each thread.
4145 * If this is not the case, a more advanced scheme
4146 * (not implemented yet) will do better.
4147 */
4148 il_nr_thread = (((idef->il[ftype].nr/nat1)*t)/nthreads)*nat1;
4149
4150 /* Ensure that distance restraint pairs with the same label
4151 * end up on the same thread.
4152 * This is slighlty tricky code, since the next for iteration
4153 * may have an initial il_nr_thread lower than the final value
4154 * in the previous iteration, but this will anyhow be increased
4155 * to the approriate value again by this while loop.
4156 */
4157 while (ftype == F_DISRES &&
4158 il_nr_thread > 0 &&
4159 il_nr_thread < idef->il[ftype].nr &&
4160 idef->iparams[idef->il[ftype].iatoms[il_nr_thread]].disres.label ==
4161 idef->iparams[idef->il[ftype].iatoms[il_nr_thread-nat1]].disres.label)
4162 {
4163 il_nr_thread += nat1;
4164 }
4165
4166 idef->il_thread_division[ftype*(nthreads+1)+t] = il_nr_thread;
4167 }
4168 }
4169 }
4170}
4171
4172static unsigned
4173calc_bonded_reduction_mask(const t_idef *idef,
4174 int shift,
4175 int t, int nt)
4176{
4177 unsigned mask;
4178 int ftype, nb, nat1, nb0, nb1, i, a;
4179
4180 mask = 0;
4181
4182 for (ftype = 0; ftype < F_NRE; ftype++)
4183 {
4184 if (ftype_is_bonded_potential(ftype))
4185 {
4186 nb = idef->il[ftype].nr;
4187 if (nb > 0)
4188 {
4189 nat1 = interaction_function[ftype].nratoms + 1;
4190
4191 /* Divide this interaction equally over the threads.
4192 * This is not stored: should match division in calc_bonds.
4193 */
4194 nb0 = idef->il_thread_division[ftype*(nt+1)+t];
4195 nb1 = idef->il_thread_division[ftype*(nt+1)+t+1];
4196
4197 for (i = nb0; i < nb1; i += nat1)
4198 {
4199 for (a = 1; a < nat1; a++)
4200 {
4201 mask |= (1U << (idef->il[ftype].iatoms[i+a]>>shift));
4202 }
4203 }
4204 }
4205 }
4206 }
4207
4208 return mask;
4209}
4210
4211void setup_bonded_threading(t_forcerec *fr, t_idef *idef)
4212{
4213#define MAX_BLOCK_BITS32 32
4214 int t;
4215 int ctot, c, b;
4216
4217 assert(fr->nthreads >= 1)((void) (0));
4218
4219 /* Divide the bonded interaction over the threads */
4220 divide_bondeds_over_threads(idef, fr->nthreads);
4221
4222 if (fr->nthreads == 1)
4223 {
4224 fr->red_nblock = 0;
4225
4226 return;
4227 }
4228
4229 /* We divide the force array in a maximum of 32 blocks.
4230 * Minimum force block reduction size is 2^6=64.
4231 */
4232 fr->red_ashift = 6;
4233 while (fr->natoms_force > (int)(MAX_BLOCK_BITS32*(1U<<fr->red_ashift)))
4234 {
4235 fr->red_ashift++;
4236 }
4237 if (debug)
4238 {
4239 fprintf(debug, "bonded force buffer block atom shift %d bits\n",
4240 fr->red_ashift);
4241 }
4242
4243 /* Determine to which blocks each thread's bonded force calculation
4244 * contributes. Store this is a mask for each thread.
4245 */
4246#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
4247 for (t = 1; t < fr->nthreads; t++)
4248 {
4249 fr->f_t[t].red_mask =
4250 calc_bonded_reduction_mask(idef, fr->red_ashift, t, fr->nthreads);
4251 }
4252
4253 /* Determine the maximum number of blocks we need to reduce over */
4254 fr->red_nblock = 0;
4255 ctot = 0;
4256 for (t = 0; t < fr->nthreads; t++)
4257 {
4258 c = 0;
4259 for (b = 0; b < MAX_BLOCK_BITS32; b++)
4260 {
4261 if (fr->f_t[t].red_mask & (1U<<b))
4262 {
4263 fr->red_nblock = max(fr->red_nblock, b+1)(((fr->red_nblock) > (b+1)) ? (fr->red_nblock) : (b+
1) );
4264 c++;
4265 }
4266 }
4267 if (debug)
4268 {
4269 fprintf(debug, "thread %d flags %x count %d\n",
4270 t, fr->f_t[t].red_mask, c);
4271 }
4272 ctot += c;
4273 }
4274 if (debug)
4275 {
4276 fprintf(debug, "Number of blocks to reduce: %d of size %d\n",
4277 fr->red_nblock, 1<<fr->red_ashift);
4278 fprintf(debug, "Reduction density %.2f density/#thread %.2f\n",
4279 ctot*(1<<fr->red_ashift)/(double)fr->natoms_force,
4280 ctot*(1<<fr->red_ashift)/(double)(fr->natoms_force*fr->nthreads));
4281 }
4282}
4283
4284static void zero_thread_forces(f_thread_t *f_t, int n,
4285 int nblock, int blocksize)
4286{
4287 int b, a0, a1, a, i, j;
4288
4289 if (n > f_t->f_nalloc)
4290 {
4291 f_t->f_nalloc = over_alloc_large(n)(int)(1.19*(n) + 1000);
4292 srenew(f_t->f, f_t->f_nalloc)(f_t->f) = save_realloc("f_t->f", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4292, (f_t->f), (f_t->f_nalloc), sizeof(*(f_t->f))
);
4293 }
4294
4295 if (f_t->red_mask != 0)
4296 {
4297 for (b = 0; b < nblock; b++)
4298 {
4299 if (f_t->red_mask && (1U<<b))
4300 {
4301 a0 = b*blocksize;
4302 a1 = min((b+1)*blocksize, n)((((b+1)*blocksize) < (n)) ? ((b+1)*blocksize) : (n) );
4303 for (a = a0; a < a1; a++)
4304 {
4305 clear_rvec(f_t->f[a]);
4306 }
4307 }
4308 }
4309 }
4310 for (i = 0; i < SHIFTS((2*1 +1)*(2*1 +1)*(2*2 +1)); i++)
4311 {
4312 clear_rvec(f_t->fshift[i]);
4313 }
4314 for (i = 0; i < F_NRE; i++)
4315 {
4316 f_t->ener[i] = 0;
4317 }
4318 for (i = 0; i < egNR; i++)
4319 {
4320 for (j = 0; j < f_t->grpp.nener; j++)
4321 {
4322 f_t->grpp.ener[i][j] = 0;
4323 }
4324 }
4325 for (i = 0; i < efptNR; i++)
4326 {
4327 f_t->dvdl[i] = 0;
4328 }
4329}
4330
4331static void reduce_thread_force_buffer(int n, rvec *f,
4332 int nthreads, f_thread_t *f_t,
4333 int nblock, int block_size)
4334{
4335 /* The max thread number is arbitrary,
4336 * we used a fixed number to avoid memory management.
4337 * Using more than 16 threads is probably never useful performance wise.
4338 */
4339#define MAX_BONDED_THREADS256 256
4340 int b;
4341
4342 if (nthreads > MAX_BONDED_THREADS256)
4343 {
4344 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4344, "Can not reduce bonded forces on more than %d threads",
4345 MAX_BONDED_THREADS256);
4346 }
4347
4348 /* This reduction can run on any number of threads,
4349 * independently of nthreads.
4350 */
4351#pragma omp parallel for num_threads(nthreads) schedule(static)
4352 for (b = 0; b < nblock; b++)
4353 {
4354 rvec *fp[MAX_BONDED_THREADS256];
4355 int nfb, ft, fb;
4356 int a0, a1, a;
4357
4358 /* Determine which threads contribute to this block */
4359 nfb = 0;
4360 for (ft = 1; ft < nthreads; ft++)
4361 {
4362 if (f_t[ft].red_mask & (1U<<b))
4363 {
4364 fp[nfb++] = f_t[ft].f;
4365 }
4366 }
4367 if (nfb > 0)
4368 {
4369 /* Reduce force buffers for threads that contribute */
4370 a0 = b *block_size;
4371 a1 = (b+1)*block_size;
4372 a1 = min(a1, n)(((a1) < (n)) ? (a1) : (n) );
4373 for (a = a0; a < a1; a++)
4374 {
4375 for (fb = 0; fb < nfb; fb++)
4376 {
4377 rvec_inc(f[a], fp[fb][a]);
4378 }
4379 }
4380 }
4381 }
4382}
4383
4384static void reduce_thread_forces(int n, rvec *f, rvec *fshift,
4385 real *ener, gmx_grppairener_t *grpp, real *dvdl,
4386 int nthreads, f_thread_t *f_t,
4387 int nblock, int block_size,
4388 gmx_bool bCalcEnerVir,
4389 gmx_bool bDHDL)
4390{
4391 if (nblock > 0)
4392 {
4393 /* Reduce the bonded force buffer */
4394 reduce_thread_force_buffer(n, f, nthreads, f_t, nblock, block_size);
4395 }
4396
4397 /* When necessary, reduce energy and virial using one thread only */
4398 if (bCalcEnerVir)
4399 {
4400 int t, i, j;
4401
4402 for (i = 0; i < SHIFTS((2*1 +1)*(2*1 +1)*(2*2 +1)); i++)
4403 {
4404 for (t = 1; t < nthreads; t++)
4405 {
4406 rvec_inc(fshift[i], f_t[t].fshift[i]);
4407 }
4408 }
4409 for (i = 0; i < F_NRE; i++)
4410 {
4411 for (t = 1; t < nthreads; t++)
4412 {
4413 ener[i] += f_t[t].ener[i];
4414 }
4415 }
4416 for (i = 0; i < egNR; i++)
4417 {
4418 for (j = 0; j < f_t[1].grpp.nener; j++)
4419 {
4420 for (t = 1; t < nthreads; t++)
4421 {
4422
4423 grpp->ener[i][j] += f_t[t].grpp.ener[i][j];
4424 }
4425 }
4426 }
4427 if (bDHDL)
4428 {
4429 for (i = 0; i < efptNR; i++)
4430 {
4431
4432 for (t = 1; t < nthreads; t++)
4433 {
4434 dvdl[i] += f_t[t].dvdl[i];
4435 }
4436 }
4437 }
4438 }
4439}
4440
4441static real calc_one_bond(FILE *fplog, int thread,
4442 int ftype, const t_idef *idef,
4443 rvec x[], rvec f[], rvec fshift[],
4444 t_forcerec *fr,
4445 const t_pbc *pbc, const t_graph *g,
4446 gmx_grppairener_t *grpp,
4447 t_nrnb *nrnb,
4448 real *lambda, real *dvdl,
4449 const t_mdatoms *md, t_fcdata *fcd,
4450 gmx_bool bCalcEnerVir,
4451 int *global_atom_index, gmx_bool bPrintSepPot)
4452{
4453 int nat1, nbonds, efptFTYPE;
4454 real v = 0;
4455 t_iatom *iatoms;
4456 int nb0, nbn;
4457
4458 if (IS_RESTRAINT_TYPE(ftype)(((ftype == F_POSRES) || (ftype == F_FBPOSRES) || (ftype == F_DISRES
) || (ftype == F_RESTRBONDS) || (ftype == F_DISRESVIOL) || (ftype
== F_ORIRES) || (ftype == F_ORIRESDEV) || (ftype == F_ANGRES
) || (ftype == F_ANGRESZ) || (ftype == F_DIHRES))))
4459 {
4460 efptFTYPE = efptRESTRAINT;
4461 }
4462 else
4463 {
4464 efptFTYPE = efptBONDED;
4465 }
4466
4467 nat1 = interaction_function[ftype].nratoms + 1;
4468 nbonds = idef->il[ftype].nr/nat1;
4469 iatoms = idef->il[ftype].iatoms;
4470
4471 nb0 = idef->il_thread_division[ftype*(idef->nthreads+1)+thread];
4472 nbn = idef->il_thread_division[ftype*(idef->nthreads+1)+thread+1] - nb0;
4473
4474 if (!IS_LISTED_LJ_C(ftype)((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB
))
4475 {
4476 if (ftype == F_CMAP)
4477 {
4478 v = cmap_dihs(nbn, iatoms+nb0,
4479 idef->iparams, &idef->cmap_grid,
4480 (const rvec*)x, f, fshift,
4481 pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
4482 md, fcd, global_atom_index);
4483 }
4484#ifdef GMX_SIMD_HAVE_REAL
4485 else if (ftype == F_ANGLES &&
4486 !bCalcEnerVir && fr->efep == efepNO)
4487 {
4488 /* No energies, shift forces, dvdl */
4489 angles_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
4490 idef->iparams,
4491 (const rvec*)x, f,
4492 pbc, g, lambda[efptFTYPE], md, fcd,
4493 global_atom_index);
4494 v = 0;
4495 }
4496#endif
4497 else if (ftype == F_PDIHS &&
4498 !bCalcEnerVir && fr->efep == efepNO)
4499 {
4500 /* No energies, shift forces, dvdl */
4501#ifdef GMX_SIMD_HAVE_REAL
4502 pdihs_noener_simd
4503#else
4504 pdihs_noener
4505#endif
4506 (nbn, idef->il[ftype].iatoms+nb0,
4507 idef->iparams,
4508 (const rvec*)x, f,
4509 pbc, g, lambda[efptFTYPE], md, fcd,
4510 global_atom_index);
4511 v = 0;
4512 }
4513 else
4514 {
4515 v = interaction_function[ftype].ifunc(nbn, iatoms+nb0,
4516 idef->iparams,
4517 (const rvec*)x, f, fshift,
4518 pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
4519 md, fcd, global_atom_index);
4520 }
4521 if (bPrintSepPot)
4522 {
4523 fprintf(fplog, " %-23s #%4d V %12.5e dVdl %12.5e\n",
4524 interaction_function[ftype].longname,
4525 nbonds, v, lambda[efptFTYPE]);
4526 }
4527 }
4528 else
4529 {
4530 v = do_nonbonded_listed(ftype, nbn, iatoms+nb0, idef->iparams, (const rvec*)x, f, fshift,
4531 pbc, g, lambda, dvdl, md, fr, grpp, global_atom_index);
4532
4533 if (bPrintSepPot)
4534 {
4535 fprintf(fplog, " %-5s + %-15s #%4d dVdl %12.5e\n",
4536 interaction_function[ftype].longname,
4537 interaction_function[F_LJ14].longname, nbonds, dvdl[efptVDW]);
4538 fprintf(fplog, " %-5s + %-15s #%4d dVdl %12.5e\n",
4539 interaction_function[ftype].longname,
4540 interaction_function[F_COUL14].longname, nbonds, dvdl[efptCOUL]);
4541 }
4542 }
4543
4544 if (thread == 0)
4545 {
4546 inc_nrnb(nrnb, interaction_function[ftype].nrnb_ind, nbonds)(nrnb)->n[interaction_function[ftype].nrnb_ind] += nbonds;
4547 }
4548
4549 return v;
4550}
4551
4552void calc_bonds(FILE *fplog, const gmx_multisim_t *ms,
4553 const t_idef *idef,
4554 rvec x[], history_t *hist,
4555 rvec f[], t_forcerec *fr,
4556 const t_pbc *pbc, const t_graph *g,
4557 gmx_enerdata_t *enerd, t_nrnb *nrnb,
4558 real *lambda,
4559 const t_mdatoms *md,
4560 t_fcdata *fcd, int *global_atom_index,
4561 t_atomtypes gmx_unused__attribute__ ((unused)) *atype, gmx_genborn_t gmx_unused__attribute__ ((unused)) *born,
4562 int force_flags,
4563 gmx_bool bPrintSepPot, gmx_int64_t step)
4564{
4565 gmx_bool bCalcEnerVir;
4566 int i;
4567 real v, dvdl[efptNR], dvdl_dum[efptNR]; /* The dummy array is to have a place to store the dhdl at other values
4568 of lambda, which will be thrown away in the end*/
4569 const t_pbc *pbc_null;
4570 char buf[22];
4571 int thread;
4572
4573 assert(fr->nthreads == idef->nthreads)((void) (0));
4574
4575 bCalcEnerVir = (force_flags & (GMX_FORCE_VIRIAL(1<<8) | GMX_FORCE_ENERGY(1<<9)));
4576
4577 for (i = 0; i < efptNR; i++)
4578 {
4579 dvdl[i] = 0.0;
4580 }
4581 if (fr->bMolPBC)
4582 {
4583 pbc_null = pbc;
4584 }
4585 else
4586 {
4587 pbc_null = NULL((void*)0);
4588 }
4589 if (bPrintSepPot)
4590 {
4591 fprintf(fplog, "Step %s: bonded V and dVdl for this node\n",
4592 gmx_step_str(step, buf));
4593 }
4594
4595#ifdef DEBUG
4596 if (g && debug)
4597 {
4598 p_graph(debug, "Bondage is fun", g);
4599 }
4600#endif
4601
4602 /* Do pre force calculation stuff which might require communication */
4603 if (idef->il[F_ORIRES].nr)
4604 {
4605 enerd->term[F_ORIRESDEV] =
4606 calc_orires_dev(ms, idef->il[F_ORIRES].nr,
4607 idef->il[F_ORIRES].iatoms,
4608 idef->iparams, md, (const rvec*)x,
4609 pbc_null, fcd, hist);
4610 }
4611 if (idef->il[F_DISRES].nr)
4612 {
4613 calc_disres_R_6(idef->il[F_DISRES].nr,
4614 idef->il[F_DISRES].iatoms,
4615 idef->iparams, (const rvec*)x, pbc_null,
4616 fcd, hist);
4617#ifdef GMX_MPI
4618 if (fcd->disres.nsystems > 1)
4619 {
4620 gmx_sum_simgmx_sumf_sim(2*fcd->disres.nres, fcd->disres.Rt_6, ms);
4621 }
4622#endif
4623 }
4624
4625#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
4626 for (thread = 0; thread < fr->nthreads; thread++)
4627 {
4628 int ftype;
4629 real *epot, v;
4630 /* thread stuff */
4631 rvec *ft, *fshift;
4632 real *dvdlt;
4633 gmx_grppairener_t *grpp;
4634
4635 if (thread == 0)
4636 {
4637 ft = f;
4638 fshift = fr->fshift;
4639 epot = enerd->term;
4640 grpp = &enerd->grpp;
4641 dvdlt = dvdl;
4642 }
4643 else
4644 {
4645 zero_thread_forces(&fr->f_t[thread], fr->natoms_force,
4646 fr->red_nblock, 1<<fr->red_ashift);
4647
4648 ft = fr->f_t[thread].f;
4649 fshift = fr->f_t[thread].fshift;
4650 epot = fr->f_t[thread].ener;
4651 grpp = &fr->f_t[thread].grpp;
4652 dvdlt = fr->f_t[thread].dvdl;
4653 }
4654 /* Loop over all bonded force types to calculate the bonded forces */
4655 for (ftype = 0; (ftype < F_NRE); ftype++)
4656 {
4657 if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype))
4658 {
4659 v = calc_one_bond(fplog, thread, ftype, idef, x,
4660 ft, fshift, fr, pbc_null, g, grpp,
4661 nrnb, lambda, dvdlt,
4662 md, fcd, bCalcEnerVir,
4663 global_atom_index, bPrintSepPot);
4664 epot[ftype] += v;
4665 }
4666 }
4667 }
4668 if (fr->nthreads > 1)
4669 {
4670 reduce_thread_forces(fr->natoms_force, f, fr->fshift,
4671 enerd->term, &enerd->grpp, dvdl,
4672 fr->nthreads, fr->f_t,
4673 fr->red_nblock, 1<<fr->red_ashift,
4674 bCalcEnerVir,
4675 force_flags & GMX_FORCE_DHDL(1<<10));
4676 }
4677 if (force_flags & GMX_FORCE_DHDL(1<<10))
4678 {
4679 for (i = 0; i < efptNR; i++)
4680 {
4681 enerd->dvdl_nonlin[i] += dvdl[i];
4682 }
4683 }
4684
4685 /* Copy the sum of violations for the distance restraints from fcd */
4686 if (fcd)
4687 {
4688 enerd->term[F_DISRESVIOL] = fcd->disres.sumviol;
4689
4690 }
4691}
4692
4693void calc_bonds_lambda(FILE *fplog,
4694 const t_idef *idef,
4695 rvec x[],
4696 t_forcerec *fr,
4697 const t_pbc *pbc, const t_graph *g,
4698 gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
4699 real *lambda,
4700 const t_mdatoms *md,
4701 t_fcdata *fcd,
4702 int *global_atom_index)
4703{
4704 int i, ftype, nr_nonperturbed, nr;
4705 real v;
4706 real dvdl_dum[efptNR];
4707 rvec *f, *fshift;
4708 const t_pbc *pbc_null;
4709 t_idef idef_fe;
4710
4711 if (fr->bMolPBC)
4712 {
4713 pbc_null = pbc;
4714 }
4715 else
4716 {
4717 pbc_null = NULL((void*)0);
4718 }
4719
4720 /* Copy the whole idef, so we can modify the contents locally */
4721 idef_fe = *idef;
4722 idef_fe.nthreads = 1;
4723 snew(idef_fe.il_thread_division, F_NRE*(idef_fe.nthreads+1))(idef_fe.il_thread_division) = save_calloc("idef_fe.il_thread_division"
, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4723, (F_NRE*(idef_fe.nthreads+1)), sizeof(*(idef_fe.il_thread_division
)));
4724
4725 /* We already have the forces, so we use temp buffers here */
4726 snew(f, fr->natoms_force)(f) = save_calloc("f", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4726, (fr->natoms_force), sizeof(*(f)));
4727 snew(fshift, SHIFTS)(fshift) = save_calloc("fshift", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4727, (((2*1 +1)*(2*1 +1)*(2*2 +1))), sizeof(*(fshift)));
4728
4729 /* Loop over all bonded force types to calculate the bonded energies */
4730 for (ftype = 0; (ftype < F_NRE); ftype++)
4731 {
4732 if (ftype_is_bonded_potential(ftype))
4733 {
4734 /* Set the work range of thread 0 to the perturbed bondeds only */
4735 nr_nonperturbed = idef->il[ftype].nr_nonperturbed;
4736 nr = idef->il[ftype].nr;
4737 idef_fe.il_thread_division[ftype*2+0] = nr_nonperturbed;
4738 idef_fe.il_thread_division[ftype*2+1] = nr;
4739
4740 /* This is only to get the flop count correct */
4741 idef_fe.il[ftype].nr = nr - nr_nonperturbed;
4742
4743 if (nr - nr_nonperturbed > 0)
4744 {
4745 v = calc_one_bond(fplog, 0, ftype, &idef_fe,
4746 x, f, fshift, fr, pbc_null, g,
4747 grpp, nrnb, lambda, dvdl_dum,
4748 md, fcd, TRUE1,
4749 global_atom_index, FALSE0);
4750 epot[ftype] += v;
4751 }
4752 }
4753 }
4754
4755 sfree(fshift)save_free("fshift", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4755, (fshift));
4756 sfree(f)save_free("f", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4756, (f));
4757
4758 sfree(idef_fe.il_thread_division)save_free("idef_fe.il_thread_division", "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/bondfree.c"
, 4758, (idef_fe.il_thread_division));
4759}