Prepared t_mdatoms for using vector
[gromacs.git] / src / gromacs / mdlib / tgroup.cpp
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37 /* This file is completely threadsafe - keep it that way! */
38 #include "gmxpre.h"
40 #include "tgroup.h"
42 #include <cmath>
44 #include "gromacs/gmxlib/network.h"
45 #include "gromacs/math/vec.h"
46 #include "gromacs/mdlib/gmx_omp_nthreads.h"
47 #include "gromacs/mdlib/rbin.h"
48 #include "gromacs/mdlib/update.h"
49 #include "gromacs/mdtypes/group.h"
50 #include "gromacs/mdtypes/inputrec.h"
51 #include "gromacs/mdtypes/mdatom.h"
52 #include "gromacs/topology/mtop_util.h"
53 #include "gromacs/topology/topology.h"
54 #include "gromacs/utility/exceptions.h"
55 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/futil.h"
57 #include "gromacs/utility/smalloc.h"
59 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
61 int i;
63 for (i = 0; (i < ngtc); i++)
65 tcstat[i].T = 0;
66 clear_mat(tcstat[i].ekinh);
67 clear_mat(tcstat[i].ekinh_old);
68 clear_mat(tcstat[i].ekinf);
72 static void init_grpstat(gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
74 gmx_groups_t *groups;
75 gmx_mtop_atomloop_all_t aloop;
76 int i, grp;
77 const t_atom *atom;
79 if (ngacc > 0)
81 groups = &mtop->groups;
82 aloop = gmx_mtop_atomloop_all_init(mtop);
83 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
85 grp = ggrpnr(groups, egcACC, i);
86 if ((grp < 0) && (grp >= ngacc))
88 gmx_incons("Input for acceleration groups wrong");
90 gstat[grp].nat++;
91 /* This will not work for integrator BD */
92 gstat[grp].mA += atom->m;
93 gstat[grp].mB += atom->mB;
98 void init_ekindata(FILE gmx_unused *log, gmx_mtop_t *mtop, t_grpopts *opts,
99 gmx_ekindata_t *ekind)
101 int i;
102 int nthread, thread;
103 #ifdef DEBUG
104 fprintf(log, "ngtc: %d, ngacc: %d, ngener: %d\n", opts->ngtc, opts->ngacc,
105 opts->ngener);
106 #endif
108 /* bNEMD tells if we should remove remove the COM velocity
109 * from the velocities during velocity scaling in T-coupling.
110 * Turn this on when we have multiple acceleration groups
111 * or one accelerated group.
113 ekind->bNEMD = (opts->ngacc > 1 || norm2(opts->acc[0]) > 0);
115 ekind->ngtc = opts->ngtc;
116 snew(ekind->tcstat, opts->ngtc);
117 init_grptcstat(opts->ngtc, ekind->tcstat);
118 /* Set Berendsen tcoupl lambda's to 1,
119 * so runs without Berendsen coupling are not affected.
121 for (i = 0; i < opts->ngtc; i++)
123 ekind->tcstat[i].lambda = 1.0;
124 ekind->tcstat[i].vscale_nhc = 1.0;
125 ekind->tcstat[i].ekinscaleh_nhc = 1.0;
126 ekind->tcstat[i].ekinscalef_nhc = 1.0;
129 nthread = gmx_omp_nthreads_get(emntUpdate);
131 snew(ekind->ekin_work_alloc, nthread);
132 snew(ekind->ekin_work, nthread);
133 snew(ekind->dekindl_work, nthread);
134 #pragma omp parallel for num_threads(nthread) schedule(static)
135 for (thread = 0; thread < nthread; thread++)
139 #define EKIN_WORK_BUFFER_SIZE 2
140 /* Allocate 2 extra elements on both sides, so in single
141 * precision we have
142 * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
143 * buffer on both sides to avoid cache pollution.
145 snew(ekind->ekin_work_alloc[thread], ekind->ngtc+2*EKIN_WORK_BUFFER_SIZE);
146 ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
147 /* Nasty hack so we can have the per-thread accumulation
148 * variable for dekindl in the same thread-local cache lines
149 * as the per-thread accumulation tensors for ekin[fh],
150 * because they are accumulated in the same loop. */
151 ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
152 #undef EKIN_WORK_BUFFER_SIZE
154 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
157 ekind->ngacc = opts->ngacc;
158 snew(ekind->grpstat, opts->ngacc);
159 init_grpstat(mtop, opts->ngacc, ekind->grpstat);
162 void accumulate_u(t_commrec *cr, t_grpopts *opts, gmx_ekindata_t *ekind)
164 /* This routine will only be called when it's necessary */
165 t_bin *rb;
166 int g;
168 rb = mk_bin();
170 for (g = 0; (g < opts->ngacc); g++)
172 add_binr(rb, DIM, ekind->grpstat[g].u);
174 sum_bin(rb, cr);
176 for (g = 0; (g < opts->ngacc); g++)
178 extract_binr(rb, DIM*g, DIM, ekind->grpstat[g].u);
180 destroy_bin(rb);
183 /* I don't think accumulate_ekin is used anymore? */
185 #if 0
186 static void accumulate_ekin(t_commrec *cr, t_grpopts *opts,
187 gmx_ekindata_t *ekind)
189 int g;
191 if (PAR(cr))
193 for (g = 0; (g < opts->ngtc); g++)
195 gmx_sum(DIM*DIM, ekind->tcstat[g].ekinf[0], cr);
199 #endif
201 void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
202 t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda)
204 int d, g, n;
205 real mv;
207 /* calculate mean velocities at whole timestep */
208 for (g = 0; (g < opts->ngtc); g++)
210 ekind->tcstat[g].T = 0;
213 if (ekind->bNEMD)
215 for (g = 0; (g < opts->ngacc); g++)
217 clear_rvec(ekind->grpstat[g].u);
220 g = 0;
221 for (n = start; (n < start+homenr); n++)
223 if (md->cACC)
225 g = md->cACC[n];
227 for (d = 0; (d < DIM); d++)
229 mv = md->massT[n]*v[n][d];
230 ekind->grpstat[g].u[d] += mv;
234 for (g = 0; (g < opts->ngacc); g++)
236 for (d = 0; (d < DIM); d++)
238 ekind->grpstat[g].u[d] /=
239 (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
245 real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
246 gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
248 int i, j, m, ngtc;
249 real T;
250 t_grp_tcstat *tcstat;
251 real nrdf, nd, *ndf;
253 ngtc = opts->ngtc;
254 ndf = opts->nrdf;
256 T = 0;
257 nrdf = 0;
259 clear_mat(ekind->ekin);
261 for (i = 0; (i < ngtc); i++)
264 nd = ndf[i];
265 tcstat = &ekind->tcstat[i];
266 /* Sometimes a group does not have degrees of freedom, e.g.
267 * when it consists of shells and virtual sites, then we just
268 * set the temperatue to 0 and also neglect the kinetic
269 * energy, which should be zero anyway.
272 if (nd > 0)
274 if (bEkinAveVel)
276 if (!bScaleEkin)
278 /* in this case, kinetic energy is from the current velocities already */
279 msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
282 else
284 /* Calculate the full step Ekin as the average of the half steps */
285 for (j = 0; (j < DIM); j++)
287 for (m = 0; (m < DIM); m++)
289 tcstat->ekinf[j][m] =
290 0.5*(tcstat->ekinh[j][m]*tcstat->ekinscaleh_nhc + tcstat->ekinh_old[j][m]);
294 m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
296 tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
297 tcstat->T = calc_temp(trace(tcstat->ekinf), nd);
299 /* after the scaling factors have been multiplied in, we can remove them */
300 if (bEkinAveVel)
302 tcstat->ekinscalef_nhc = 1.0;
304 else
306 tcstat->ekinscaleh_nhc = 1.0;
309 else
311 tcstat->T = 0;
312 tcstat->Th = 0;
314 T += nd*tcstat->T;
315 nrdf += nd;
317 if (nrdf > 0)
319 T /= nrdf;
321 if (dekindlambda)
323 if (bEkinAveVel)
325 *dekindlambda = ekind->dekindl;
327 else
329 *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);
332 return T;