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Remove the rest of the device coordinates management from PME
[gromacs.git] / src / gromacs / mdlib / energyoutput.cpp
blob01ef7b2cc9860e27ea03a6fae670a8d4eeae7274
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) 2013,2014,2015,2016,2017 by the GROMACS development team.
7 * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
9 * and including many others, as listed in the AUTHORS file in the
10 * top-level source directory and at http://www.gromacs.org.
11 *
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
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23 * License along with GROMACS; if not, see
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37 */
38 /*! \internal \file
39 * \brief Defines code that writes energy-like quantities.
40 *
41 * \author Mark Abraham <mark.j.abraham@gmail.com>
42 * \author Paul Bauer <paul.bauer.q@gmail.com>
43 * \author Artem Zhmurov <zhmurov@gmail.com>
44 *
45 * \ingroup module_mdlib
46 */
47 #include "gmxpre.h"
48
49 #include "energyoutput.h"
50
51 #include <cfloat>
52 #include <cstdlib>
53 #include <cstring>
54
55 #include <array>
56 #include <string>
57
58 #include "gromacs/awh/awh.h"
59 #include "gromacs/fileio/enxio.h"
60 #include "gromacs/fileio/gmxfio.h"
61 #include "gromacs/fileio/xvgr.h"
62 #include "gromacs/gmxlib/network.h"
63 #include "gromacs/listed_forces/disre.h"
64 #include "gromacs/listed_forces/orires.h"
65 #include "gromacs/math/functions.h"
66 #include "gromacs/math/units.h"
67 #include "gromacs/math/vec.h"
68 #include "gromacs/mdlib/constr.h"
69 #include "gromacs/mdlib/ebin.h"
70 #include "gromacs/mdlib/mdebin_bar.h"
71 #include "gromacs/mdrunutility/handlerestart.h"
72 #include "gromacs/mdtypes/energyhistory.h"
73 #include "gromacs/mdtypes/fcdata.h"
74 #include "gromacs/mdtypes/group.h"
75 #include "gromacs/mdtypes/inputrec.h"
76 #include "gromacs/mdtypes/md_enums.h"
77 #include "gromacs/mdtypes/state.h"
78 #include "gromacs/pbcutil/pbc.h"
79 #include "gromacs/pulling/pull.h"
80 #include "gromacs/topology/mtop_util.h"
81 #include "gromacs/trajectory/energyframe.h"
82 #include "gromacs/utility/arraysize.h"
83 #include "gromacs/utility/fatalerror.h"
84 #include "gromacs/utility/mdmodulenotification.h"
85 #include "gromacs/utility/smalloc.h"
86 #include "gromacs/utility/stringutil.h"
87
88 //! Labels for energy file quantities
89 //! \{
90 static const char* conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
91
92 static std::array<const char*, 3> boxs_nm = { "Box-X", "Box-Y", "Box-Z" };
93
94 static std::array<const char*, 6> tricl_boxs_nm = { "Box-XX", "Box-YY", "Box-ZZ",
95 "Box-YX", "Box-ZX", "Box-ZY" };
96
97 static const char* vol_nm[] = { "Volume" };
98
99 static const char* dens_nm[] = { "Density" };
100
101 static const char* pv_nm[] = { "pV" };
102
103 static const char* enthalpy_nm[] = { "Enthalpy" };
104
105 static std::array<const char*, 6> boxvel_nm = { "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
106 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY" };
107
108 const char* egrp_nm[egNR + 1] = { "Coul-SR", "LJ-SR", "Buck-SR", "Coul-14", "LJ-14", nullptr };
109 //! \}
110
111 namespace gmx
112 {
113
114 /*! \brief Energy output class
115 *
116 * This is the collection of energy averages collected during mdrun, and to
117 * be written out to the .edr file.
118 *
119 * \todo Use more std containers.
120 * \todo Remove GMX_CONSTRAINTVIR
121 * \todo Write free-energy output also to energy file (after adding more tests)
122 */
123 EnergyOutput::EnergyOutput(ener_file* fp_ene,
124 const gmx_mtop_t* mtop,
125 const t_inputrec* ir,
126 const pull_t* pull_work,
127 FILE* fp_dhdl,
128 bool isRerun,
129 const StartingBehavior startingBehavior,
130 const MdModulesNotifier& mdModulesNotifier)
131 {
132 const char* ener_nm[F_NRE];
133 static const char* vir_nm[] = { "Vir-XX", "Vir-XY", "Vir-XZ", "Vir-YX", "Vir-YY",
134 "Vir-YZ", "Vir-ZX", "Vir-ZY", "Vir-ZZ" };
135 static const char* sv_nm[] = { "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
136 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
137 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ" };
138 static const char* fv_nm[] = { "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
139 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
140 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ" };
141 static const char* pres_nm[] = { "Pres-XX", "Pres-XY", "Pres-XZ", "Pres-YX", "Pres-YY",
142 "Pres-YZ", "Pres-ZX", "Pres-ZY", "Pres-ZZ" };
143 static const char* surft_nm[] = { "#Surf*SurfTen" };
144 static const char* mu_nm[] = { "Mu-X", "Mu-Y", "Mu-Z" };
145 static const char* vcos_nm[] = { "2CosZ*Vel-X" };
146 static const char* visc_nm[] = { "1/Viscosity" };
147 static const char* baro_nm[] = { "Barostat" };
148
149 const SimulationGroups* groups;
150 char** gnm;
151 char buf[256];
152 const char* bufi;
153 int i, j, ni, nj, n, k, kk, ncon, nset;
154 bool bBHAM, b14;
155
156 if (EI_DYNAMICS(ir->eI))
157 {
158 delta_t_ = ir->delta_t;
159 }
160 else
161 {
162 delta_t_ = 0;
163 }
164
165 groups = &mtop->groups;
166
167 bBHAM = (mtop->ffparams.numTypes() > 0) && (mtop->ffparams.functype[0] == F_BHAM);
168 b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 || gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
169
170 ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
171 nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
172 bool bConstr = (ncon > 0 || nset > 0) && !isRerun;
173 bConstrVir_ = false;
174 nCrmsd_ = 0;
175 if (bConstr)
176 {
177 if (ncon > 0 && ir->eConstrAlg == econtLINCS)
178 {
179 nCrmsd_ = 1;
180 }
181 bConstrVir_ = (getenv("GMX_CONSTRAINTVIR") != nullptr);
182 }
183 else
184 {
185 nCrmsd_ = 0;
186 }
187
188 /* Energy monitoring */
189 for (i = 0; i < egNR; i++)
190 {
191 bEInd_[i] = false;
192 }
193
194 // Setting true only to those energy terms, that have active interactions and
195 // are not vsite terms (not VSITE2, VSITE3, VSITE3FD, VSITE3FAD, VSITE3OUT, VSITE4FD, VSITE4FDN, or VSITEN)
196 for (i = 0; i < F_NRE; i++)
197 {
198 bEner_[i] = (gmx_mtop_ftype_count(mtop, i) > 0)
199 && ((interaction_function[i].flags & IF_VSITE) == 0);
200 }
201
202 if (!isRerun)
203 {
204 bEner_[F_EKIN] = EI_DYNAMICS(ir->eI);
205 bEner_[F_ETOT] = EI_DYNAMICS(ir->eI);
206 bEner_[F_TEMP] = EI_DYNAMICS(ir->eI);
207
208 bEner_[F_ECONSERVED] = integratorHasConservedEnergyQuantity(ir);
209 bEner_[F_PDISPCORR] = (ir->eDispCorr != edispcNO);
210 bEner_[F_PRES] = true;
211 }
212
213 bEner_[F_LJ] = !bBHAM;
214 bEner_[F_BHAM] = bBHAM;
215 bEner_[F_EQM] = ir->bQMMM;
216 bEner_[F_RF_EXCL] = (EEL_RF(ir->coulombtype) && ir->cutoff_scheme == ecutsGROUP);
217 bEner_[F_COUL_RECIP] = EEL_FULL(ir->coulombtype);
218 bEner_[F_LJ_RECIP] = EVDW_PME(ir->vdwtype);
219 bEner_[F_LJ14] = b14;
220 bEner_[F_COUL14] = b14;
221 bEner_[F_LJC14_Q] = false;
222 bEner_[F_LJC_PAIRS_NB] = false;
223
224
225 bEner_[F_DVDL_COUL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptCOUL];
226 bEner_[F_DVDL_VDW] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptVDW];
227 bEner_[F_DVDL_BONDED] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptBONDED];
228 bEner_[F_DVDL_RESTRAINT] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptRESTRAINT];
229 bEner_[F_DKDL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptMASS];
230 bEner_[F_DVDL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptFEP];
231
232 bEner_[F_CONSTR] = false;
233 bEner_[F_CONSTRNC] = false;
234 bEner_[F_SETTLE] = false;
235
236 bEner_[F_COUL_SR] = true;
237 bEner_[F_EPOT] = true;
238
239 bEner_[F_DISPCORR] = (ir->eDispCorr != edispcNO);
240 bEner_[F_DISRESVIOL] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
241 bEner_[F_ORIRESDEV] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
242 bEner_[F_COM_PULL] = ((ir->bPull && pull_have_potential(pull_work)) || ir->bRot);
243
244 MdModulesEnergyOutputToDensityFittingRequestChecker mdModulesAddOutputToDensityFittingFieldRequest;
245 mdModulesNotifier.notifier_.notify(&mdModulesAddOutputToDensityFittingFieldRequest);
246
247 bEner_[F_DENSITYFITTING] = mdModulesAddOutputToDensityFittingFieldRequest.energyOutputToDensityFitting_;
248
249
250 // Counting the energy terms that will be printed and saving their names
251 f_nre_ = 0;
252 for (i = 0; i < F_NRE; i++)
253 {
254 if (bEner_[i])
255 {
256 ener_nm[f_nre_] = interaction_function[i].longname;
257 f_nre_++;
258 }
259 }
260
261 epc_ = isRerun ? epcNO : ir->epc;
262 bDiagPres_ = !TRICLINIC(ir->ref_p) && !isRerun;
263 ref_p_ = (ir->ref_p[XX][XX] + ir->ref_p[YY][YY] + ir->ref_p[ZZ][ZZ]) / DIM;
264 bTricl_ = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
265 bDynBox_ = inputrecDynamicBox(ir);
266 etc_ = isRerun ? etcNO : ir->etc;
267 bNHC_trotter_ = inputrecNvtTrotter(ir) && !isRerun;
268 bPrintNHChains_ = ir->bPrintNHChains && !isRerun;
269 bMTTK_ = (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)) && !isRerun;
270 bMu_ = inputrecNeedMutot(ir);
271 bPres_ = !isRerun;
272
273 ebin_ = mk_ebin();
274 /* Pass NULL for unit to let get_ebin_space determine the units
275 * for interaction_function[i].longname
276 */
277 ie_ = get_ebin_space(ebin_, f_nre_, ener_nm, nullptr);
278 if (nCrmsd_)
279 {
280 /* This should be called directly after the call for ie_,
281 * such that iconrmsd_ follows directly in the list.
282 */
283 iconrmsd_ = get_ebin_space(ebin_, nCrmsd_, conrmsd_nm, "");
284 }
285 if (bDynBox_)
286 {
287 ib_ = get_ebin_space(ebin_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(),
288 bTricl_ ? tricl_boxs_nm.data() : boxs_nm.data(), unit_length);
289 ivol_ = get_ebin_space(ebin_, 1, vol_nm, unit_volume);
290 idens_ = get_ebin_space(ebin_, 1, dens_nm, unit_density_SI);
291 if (bDiagPres_)
292 {
293 ipv_ = get_ebin_space(ebin_, 1, pv_nm, unit_energy);
294 ienthalpy_ = get_ebin_space(ebin_, 1, enthalpy_nm, unit_energy);
295 }
296 }
297 if (bConstrVir_)
298 {
299 isvir_ = get_ebin_space(ebin_, asize(sv_nm), sv_nm, unit_energy);
300 ifvir_ = get_ebin_space(ebin_, asize(fv_nm), fv_nm, unit_energy);
301 }
302 if (bPres_)
303 {
304 ivir_ = get_ebin_space(ebin_, asize(vir_nm), vir_nm, unit_energy);
305 ipres_ = get_ebin_space(ebin_, asize(pres_nm), pres_nm, unit_pres_bar);
306 isurft_ = get_ebin_space(ebin_, asize(surft_nm), surft_nm, unit_surft_bar);
307 }
308 if (epc_ == epcPARRINELLORAHMAN || epc_ == epcMTTK)
309 {
310 ipc_ = get_ebin_space(ebin_, bTricl_ ? boxvel_nm.size() : DIM, boxvel_nm.data(), unit_vel);
311 }
312 if (bMu_)
313 {
314 imu_ = get_ebin_space(ebin_, asize(mu_nm), mu_nm, unit_dipole_D);
315 }
316 if (ir->cos_accel != 0)
317 {
318 ivcos_ = get_ebin_space(ebin_, asize(vcos_nm), vcos_nm, unit_vel);
319 ivisc_ = get_ebin_space(ebin_, asize(visc_nm), visc_nm, unit_invvisc_SI);
320 }
321
322 /* Energy monitoring */
323 for (i = 0; i < egNR; i++)
324 {
325 bEInd_[i] = false;
326 }
327 bEInd_[egCOULSR] = true;
328 bEInd_[egLJSR] = true;
329
330 if (bBHAM)
331 {
332 bEInd_[egLJSR] = false;
333 bEInd_[egBHAMSR] = true;
334 }
335 if (b14)
336 {
337 bEInd_[egLJ14] = true;
338 bEInd_[egCOUL14] = true;
339 }
340 nEc_ = 0;
341 for (i = 0; (i < egNR); i++)
342 {
343 if (bEInd_[i])
344 {
345 nEc_++;
346 }
347 }
348 n = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
349 nEg_ = n;
350 nE_ = (n * (n + 1)) / 2;
351
352 snew(igrp_, nE_);
353 if (nE_ > 1)
354 {
355 n = 0;
356 snew(gnm, nEc_);
357 for (k = 0; (k < nEc_); k++)
358 {
359 snew(gnm[k], STRLEN);
360 }
361 for (i = 0; (i < gmx::ssize(groups->groups[SimulationAtomGroupType::EnergyOutput])); i++)
362 {
363 ni = groups->groups[SimulationAtomGroupType::EnergyOutput][i];
364 for (j = i; (j < gmx::ssize(groups->groups[SimulationAtomGroupType::EnergyOutput])); j++)
365 {
366 nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
367 for (k = kk = 0; (k < egNR); k++)
368 {
369 if (bEInd_[k])
370 {
371 sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k], *(groups->groupNames[ni]),
372 *(groups->groupNames[nj]));
373 kk++;
374 }
375 }
376 igrp_[n] = get_ebin_space(ebin_, nEc_, gnm, unit_energy);
377 n++;
378 }
379 }
380 for (k = 0; (k < nEc_); k++)
381 {
382 sfree(gnm[k]);
383 }
384 sfree(gnm);
385
386 if (n != nE_)
387 {
388 gmx_incons("Number of energy terms wrong");
389 }
390 }
391
392 nTC_ = isRerun ? 0 : groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
393 nNHC_ = ir->opts.nhchainlength; /* shorthand for number of NH chains */
394 if (bMTTK_)
395 {
396 nTCP_ = 1; /* assume only one possible coupling system for barostat
397 for now */
398 }
399 else
400 {
401 nTCP_ = 0;
402 }
403 if (etc_ == etcNOSEHOOVER)
404 {
405 if (bNHC_trotter_)
406 {
407 mde_n_ = 2 * nNHC_ * nTC_;
408 }
409 else
410 {
411 mde_n_ = 2 * nTC_;
412 }
413 if (epc_ == epcMTTK)
414 {
415 mdeb_n_ = 2 * nNHC_ * nTCP_;
416 }
417 }
418 else
419 {
420 mde_n_ = nTC_;
421 mdeb_n_ = 0;
422 }
423
424 snew(tmp_r_, mde_n_);
425 // TODO redo the group name memory management to make it more clear
426 char** grpnms;
427 snew(grpnms, std::max(mde_n_, mdeb_n_)); // Just in case mdeb_n_ > mde_n_
428
429 for (i = 0; (i < nTC_); i++)
430 {
431 ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
432 sprintf(buf, "T-%s", *(groups->groupNames[ni]));
433 grpnms[i] = gmx_strdup(buf);
434 }
435 itemp_ = get_ebin_space(ebin_, nTC_, grpnms, unit_temp_K);
436 for (i = 0; i < nTC_; i++)
437 {
438 sfree(grpnms[i]);
439 }
440
441 int allocated = 0;
442 if (etc_ == etcNOSEHOOVER)
443 {
444 if (bPrintNHChains_)
445 {
446 if (bNHC_trotter_)
447 {
448 for (i = 0; (i < nTC_); i++)
449 {
450 ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
451 bufi = *(groups->groupNames[ni]);
452 for (j = 0; (j < nNHC_); j++)
453 {
454 sprintf(buf, "Xi-%d-%s", j, bufi);
455 grpnms[2 * (i * nNHC_ + j)] = gmx_strdup(buf);
456 sprintf(buf, "vXi-%d-%s", j, bufi);
457 grpnms[2 * (i * nNHC_ + j) + 1] = gmx_strdup(buf);
458 }
459 }
460 itc_ = get_ebin_space(ebin_, mde_n_, grpnms, unit_invtime);
461 allocated = mde_n_;
462 if (bMTTK_)
463 {
464 for (i = 0; (i < nTCP_); i++)
465 {
466 bufi = baro_nm[0]; /* All barostat DOF's together for now. */
467 for (j = 0; (j < nNHC_); j++)
468 {
469 sprintf(buf, "Xi-%d-%s", j, bufi);
470 grpnms[2 * (i * nNHC_ + j)] = gmx_strdup(buf);
471 sprintf(buf, "vXi-%d-%s", j, bufi);
472 grpnms[2 * (i * nNHC_ + j) + 1] = gmx_strdup(buf);
473 }
474 }
475 itcb_ = get_ebin_space(ebin_, mdeb_n_, grpnms, unit_invtime);
476 allocated = mdeb_n_;
477 }
478 }
479 else
480 {
481 for (i = 0; (i < nTC_); i++)
482 {
483 ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
484 bufi = *(groups->groupNames[ni]);
485 sprintf(buf, "Xi-%s", bufi);
486 grpnms[2 * i] = gmx_strdup(buf);
487 sprintf(buf, "vXi-%s", bufi);
488 grpnms[2 * i + 1] = gmx_strdup(buf);
489 }
490 itc_ = get_ebin_space(ebin_, mde_n_, grpnms, unit_invtime);
491 allocated = mde_n_;
492 }
493 }
494 }
495 else if (etc_ == etcBERENDSEN || etc_ == etcYES || etc_ == etcVRESCALE)
496 {
497 for (i = 0; (i < nTC_); i++)
498 {
499 ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
500 sprintf(buf, "Lamb-%s", *(groups->groupNames[ni]));
501 grpnms[i] = gmx_strdup(buf);
502 }
503 itc_ = get_ebin_space(ebin_, mde_n_, grpnms, "");
504 allocated = mde_n_;
505 }
506
507 for (i = 0; i < allocated; i++)
508 {
509 sfree(grpnms[i]);
510 }
511 sfree(grpnms);
512
513 nU_ = groups->groups[SimulationAtomGroupType::Acceleration].size();
514 snew(tmp_v_, nU_);
515 if (nU_ > 1)
516 {
517 snew(grpnms, 3 * nU_);
518 for (i = 0; (i < nU_); i++)
519 {
520 ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
521 sprintf(buf, "Ux-%s", *(groups->groupNames[ni]));
522 grpnms[3 * i + XX] = gmx_strdup(buf);
523 sprintf(buf, "Uy-%s", *(groups->groupNames[ni]));
524 grpnms[3 * i + YY] = gmx_strdup(buf);
525 sprintf(buf, "Uz-%s", *(groups->groupNames[ni]));
526 grpnms[3 * i + ZZ] = gmx_strdup(buf);
527 }
528 iu_ = get_ebin_space(ebin_, 3 * nU_, grpnms, unit_vel);
529 for (i = 0; i < 3 * nU_; i++)
530 {
531 sfree(grpnms[i]);
532 }
533 sfree(grpnms);
534 }
535
536 /* Note that fp_ene should be valid on the master rank and null otherwise */
537 if (fp_ene != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
538 {
539 do_enxnms(fp_ene, &ebin_->nener, &ebin_->enm);
540 }
541
542 /* check whether we're going to write dh histograms */
543 dhc_ = nullptr;
544 if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
545 {
546 /* Currently dh histograms are only written with dynamics */
547 if (EI_DYNAMICS(ir->eI))
548 {
549 snew(dhc_, 1);
550
551 mde_delta_h_coll_init(dhc_, ir);
552 }
553 fp_dhdl_ = nullptr;
554 snew(dE_, ir->fepvals->n_lambda);
555 }
556 else
557 {
558 fp_dhdl_ = fp_dhdl;
559 snew(dE_, ir->fepvals->n_lambda);
560 }
561 if (ir->bSimTemp)
562 {
563 int i;
564 snew(temperatures_, ir->fepvals->n_lambda);
565 numTemperatures_ = ir->fepvals->n_lambda;
566 for (i = 0; i < ir->fepvals->n_lambda; i++)
567 {
568 temperatures_[i] = ir->simtempvals->temperatures[i];
569 }
570 }
571 else
572 {
573 numTemperatures_ = 0;
574 }
575 }
576
577 EnergyOutput::~EnergyOutput()
578 {
579 sfree(igrp_);
580 sfree(tmp_r_);
581 sfree(tmp_v_);
582 done_ebin(ebin_);
583 done_mde_delta_h_coll(dhc_);
584 sfree(dE_);
585 if (numTemperatures_ > 0)
586 {
587 sfree(temperatures_);
588 }
589 }
590
591 } // namespace gmx
592
593 /*! \brief Print a lambda vector to a string
594 *
595 * \param[in] fep The inputrec's FEP input data
596 * \param[in] i The index of the lambda vector
597 * \param[in] get_native_lambda Whether to print the native lambda
598 * \param[in] get_names Whether to print the names rather than the values
599 * \param[in,out] str The pre-allocated string buffer to print to.
600 */
601 static void print_lambda_vector(t_lambda* fep, int i, bool get_native_lambda, bool get_names, char* str)
602 {
603 int j, k = 0;
604 int Nsep = 0;
605
606 for (j = 0; j < efptNR; j++)
607 {
608 if (fep->separate_dvdl[j])
609 {
610 Nsep++;
611 }
612 }
613 str[0] = 0; /* reset the string */
614 if (Nsep > 1)
615 {
616 str += sprintf(str, "("); /* set the opening parenthesis*/
617 }
618 for (j = 0; j < efptNR; j++)
619 {
620 if (fep->separate_dvdl[j])
621 {
622 if (!get_names)
623 {
624 if (get_native_lambda && fep->init_lambda >= 0)
625 {
626 str += sprintf(str, "%.4f", fep->init_lambda);
627 }
628 else
629 {
630 str += sprintf(str, "%.4f", fep->all_lambda[j][i]);
631 }
632 }
633 else
634 {
635 str += sprintf(str, "%s", efpt_singular_names[j]);
636 }
637 /* print comma for the next item */
638 if (k < Nsep - 1)
639 {
640 str += sprintf(str, ", ");
641 }
642 k++;
643 }
644 }
645 if (Nsep > 1)
646 {
647 /* and add the closing parenthesis */
648 sprintf(str, ")");
649 }
650 }
651
652 FILE* open_dhdl(const char* filename, const t_inputrec* ir, const gmx_output_env_t* oenv)
653 {
654 FILE* fp;
655 const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
656 *lambdastate = "\\lambda state";
657 int i, nsets, nsets_de, nsetsbegin;
658 int n_lambda_terms = 0;
659 t_lambda* fep = ir->fepvals; /* for simplicity */
660 t_expanded* expand = ir->expandedvals;
661 char lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
662
663 int nsets_dhdl = 0;
664 int s = 0;
665 int nsetsextend;
666 bool write_pV = false;
667
668 /* count the number of different lambda terms */
669 for (i = 0; i < efptNR; i++)
670 {
671 if (fep->separate_dvdl[i])
672 {
673 n_lambda_terms++;
674 }
675 }
676
677 std::string title, label_x, label_y;
678 if (fep->n_lambda == 0)
679 {
680 title = gmx::formatString("%s", dhdl);
681 label_x = gmx::formatString("Time (ps)");
682 label_y = gmx::formatString("%s (%s %s)", dhdl, unit_energy, "[\\lambda]\\S-1\\N");
683 }
684 else
685 {
686 title = gmx::formatString("%s and %s", dhdl, deltag);
687 label_x = gmx::formatString("Time (ps)");
688 label_y = gmx::formatString("%s and %s (%s %s)", dhdl, deltag, unit_energy,
689 "[\\8l\\4]\\S-1\\N");
690 }
691 fp = gmx_fio_fopen(filename, "w+");
692 xvgr_header(fp, title.c_str(), label_x, label_y, exvggtXNY, oenv);
693
694 std::string buf;
695 if (!(ir->bSimTemp))
696 {
697 buf = gmx::formatString("T = %g (K) ", ir->opts.ref_t[0]);
698 }
699 if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
700 {
701 if ((fep->init_lambda >= 0) && (n_lambda_terms == 1))
702 {
703 /* compatibility output */
704 buf += gmx::formatString("%s = %.4f", lambda, fep->init_lambda);
705 }
706 else
707 {
708 print_lambda_vector(fep, fep->init_fep_state, true, false, lambda_vec_str);
709 print_lambda_vector(fep, fep->init_fep_state, true, true, lambda_name_str);
710 buf += gmx::formatString("%s %d: %s = %s", lambdastate, fep->init_fep_state,
711 lambda_name_str, lambda_vec_str);
712 }
713 }
714 xvgr_subtitle(fp, buf.c_str(), oenv);
715
716
717 nsets_dhdl = 0;
718 if (fep->dhdl_derivatives == edhdlderivativesYES)
719 {
720 nsets_dhdl = n_lambda_terms;
721 }
722 /* count the number of delta_g states */
723 nsets_de = fep->lambda_stop_n - fep->lambda_start_n;
724
725 nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
726
727 if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
728 {
729 nsets += 1; /*add fep state for expanded ensemble */
730 }
731
732 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
733 {
734 nsets += 1; /* add energy to the dhdl as well */
735 }
736
737 nsetsextend = nsets;
738 if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
739 {
740 nsetsextend += 1; /* for PV term, other terms possible if required for
741 the reduced potential (only needed with foreign
742 lambda, and only output when init_lambda is not
743 set in order to maintain compatibility of the
744 dhdl.xvg file) */
745 write_pV = true;
746 }
747 std::vector<std::string> setname(nsetsextend);
748
749 if (expand->elmcmove > elmcmoveNO)
750 {
751 /* state for the fep_vals, if we have alchemical sampling */
752 setname[s++] = "Thermodynamic state";
753 }
754
755 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
756 {
757 std::string energy;
758 switch (fep->edHdLPrintEnergy)
759 {
760 case edHdLPrintEnergyPOTENTIAL:
761 energy = gmx::formatString("%s (%s)", "Potential Energy", unit_energy);
762 break;
763 case edHdLPrintEnergyTOTAL:
764 case edHdLPrintEnergyYES:
765 default: energy = gmx::formatString("%s (%s)", "Total Energy", unit_energy);
766 }
767 setname[s++] = energy;
768 }
769
770 if (fep->dhdl_derivatives == edhdlderivativesYES)
771 {
772 for (i = 0; i < efptNR; i++)
773 {
774 if (fep->separate_dvdl[i])
775 {
776 std::string derivative;
777 if ((fep->init_lambda >= 0) && (n_lambda_terms == 1))
778 {
779 /* compatibility output */
780 derivative = gmx::formatString("%s %s %.4f", dhdl, lambda, fep->init_lambda);
781 }
782 else
783 {
784 double lam = fep->init_lambda;
785 if (fep->init_lambda < 0)
786 {
787 lam = fep->all_lambda[i][fep->init_fep_state];
788 }
789 derivative = gmx::formatString("%s %s = %.4f", dhdl, efpt_singular_names[i], lam);
790 }
791 setname[s++] = derivative;
792 }
793 }
794 }
795
796 if (fep->n_lambda > 0)
797 {
798 /* g_bar has to determine the lambda values used in this simulation
799 * from this xvg legend.
800 */
801
802 if (expand->elmcmove > elmcmoveNO)
803 {
804 nsetsbegin = 1; /* for including the expanded ensemble */
805 }
806 else
807 {
808 nsetsbegin = 0;
809 }
810
811 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
812 {
813 nsetsbegin += 1;
814 }
815 nsetsbegin += nsets_dhdl;
816
817 for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
818 {
819 print_lambda_vector(fep, i, false, false, lambda_vec_str);
820 std::string buf;
821 if ((fep->init_lambda >= 0) && (n_lambda_terms == 1))
822 {
823 /* for compatible dhdl.xvg files */
824 buf = gmx::formatString("%s %s %s", deltag, lambda, lambda_vec_str);
825 }
826 else
827 {
828 buf = gmx::formatString("%s %s to %s", deltag, lambda, lambda_vec_str);
829 }
830
831 if (ir->bSimTemp)
832 {
833 /* print the temperature for this state if doing simulated annealing */
834 buf += gmx::formatString(
835 "T = %g (%s)", ir->simtempvals->temperatures[s - (nsetsbegin)], unit_temp_K);
836 }
837 setname[s++] = buf;
838 }
839 if (write_pV)
840 {
841 setname[s++] = gmx::formatString("pV (%s)", unit_energy);
842 }
843
844 xvgrLegend(fp, setname, oenv);
845 }
846
847 return fp;
848 }
849
850 namespace gmx
851 {
852
853 void EnergyOutput::addDataAtEnergyStep(bool bDoDHDL,
854 bool bSum,
855 double time,
856 real tmass,
857 const gmx_enerdata_t* enerd,
858 const t_state* state,
859 const t_lambda* fep,
860 const t_expanded* expand,
861 const matrix box,
862 const tensor svir,
863 const tensor fvir,
864 const tensor vir,
865 const tensor pres,
866 const gmx_ekindata_t* ekind,
867 const rvec mu_tot,
868 const gmx::Constraints* constr)
869 {
870 int j, k, kk, n, gid;
871 real crmsd[2], tmp6[6];
872 real bs[tricl_boxs_nm.size()], vol, dens, pv, enthalpy;
873 real eee[egNR];
874 double store_dhdl[efptNR];
875 real store_energy = 0;
876 real tmp;
877
878 /* Do NOT use the box in the state variable, but the separate box provided
879 * as an argument. This is because we sometimes need to write the box from
880 * the last timestep to match the trajectory frames.
881 */
882 add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
883 if (nCrmsd_)
884 {
885 crmsd[0] = constr->rmsd();
886 add_ebin(ebin_, iconrmsd_, nCrmsd_, crmsd, false);
887 }
888 if (bDynBox_)
889 {
890 int nboxs;
891 if (bTricl_)
892 {
893 bs[0] = box[XX][XX];
894 bs[1] = box[YY][YY];
895 bs[2] = box[ZZ][ZZ];
896 bs[3] = box[YY][XX];
897 bs[4] = box[ZZ][XX];
898 bs[5] = box[ZZ][YY];
899 nboxs = tricl_boxs_nm.size();
900 }
901 else
902 {
903 bs[0] = box[XX][XX];
904 bs[1] = box[YY][YY];
905 bs[2] = box[ZZ][ZZ];
906 nboxs = boxs_nm.size();
907 }
908 vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
909 dens = (tmass * AMU) / (vol * NANO * NANO * NANO);
910 add_ebin(ebin_, ib_, nboxs, bs, bSum);
911 add_ebin(ebin_, ivol_, 1, &vol, bSum);
912 add_ebin(ebin_, idens_, 1, &dens, bSum);
913
914 if (bDiagPres_)
915 {
916 /* This is pV (in kJ/mol). The pressure is the reference pressure,
917 not the instantaneous pressure */
918 pv = vol * ref_p_ / PRESFAC;
919
920 add_ebin(ebin_, ipv_, 1, &pv, bSum);
921 enthalpy = pv + enerd->term[F_ETOT];
922 add_ebin(ebin_, ienthalpy_, 1, &enthalpy, bSum);
923 }
924 }
925 if (bConstrVir_)
926 {
927 add_ebin(ebin_, isvir_, 9, svir[0], bSum);
928 add_ebin(ebin_, ifvir_, 9, fvir[0], bSum);
929 }
930 if (bPres_)
931 {
932 add_ebin(ebin_, ivir_, 9, vir[0], bSum);
933 add_ebin(ebin_, ipres_, 9, pres[0], bSum);
934 tmp = (pres[ZZ][ZZ] - (pres[XX][XX] + pres[YY][YY]) * 0.5) * box[ZZ][ZZ];
935 add_ebin(ebin_, isurft_, 1, &tmp, bSum);
936 }
937 if (epc_ == epcPARRINELLORAHMAN || epc_ == epcMTTK)
938 {
939 tmp6[0] = state->boxv[XX][XX];
940 tmp6[1] = state->boxv[YY][YY];
941 tmp6[2] = state->boxv[ZZ][ZZ];
942 tmp6[3] = state->boxv[YY][XX];
943 tmp6[4] = state->boxv[ZZ][XX];
944 tmp6[5] = state->boxv[ZZ][YY];
945 add_ebin(ebin_, ipc_, bTricl_ ? 6 : 3, tmp6, bSum);
946 }
947 if (bMu_)
948 {
949 add_ebin(ebin_, imu_, 3, mu_tot, bSum);
950 }
951 if (ekind && ekind->cosacc.cos_accel != 0)
952 {
953 vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
954 dens = (tmass * AMU) / (vol * NANO * NANO * NANO);
955 add_ebin(ebin_, ivcos_, 1, &(ekind->cosacc.vcos), bSum);
956 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
957 tmp = 1
958 / (ekind->cosacc.cos_accel / (ekind->cosacc.vcos * PICO) * dens
959 * gmx::square(box[ZZ][ZZ] * NANO / (2 * M_PI)));
960 add_ebin(ebin_, ivisc_, 1, &tmp, bSum);
961 }
962 if (nE_ > 1)
963 {
964 n = 0;
965 for (int i = 0; (i < nEg_); i++)
966 {
967 for (j = i; (j < nEg_); j++)
968 {
969 gid = GID(i, j, nEg_);
970 for (k = kk = 0; (k < egNR); k++)
971 {
972 if (bEInd_[k])
973 {
974 eee[kk++] = enerd->grpp.ener[k][gid];
975 }
976 }
977 add_ebin(ebin_, igrp_[n], nEc_, eee, bSum);
978 n++;
979 }
980 }
981 }
982
983 if (ekind)
984 {
985 for (int i = 0; (i < nTC_); i++)
986 {
987 tmp_r_[i] = ekind->tcstat[i].T;
988 }
989 add_ebin(ebin_, itemp_, nTC_, tmp_r_, bSum);
990
991 if (etc_ == etcNOSEHOOVER)
992 {
993 /* whether to print Nose-Hoover chains: */
994 if (bPrintNHChains_)
995 {
996 if (bNHC_trotter_)
997 {
998 for (int i = 0; (i < nTC_); i++)
999 {
1000 for (j = 0; j < nNHC_; j++)
1001 {
1002 k = i * nNHC_ + j;
1003 tmp_r_[2 * k] = state->nosehoover_xi[k];
1004 tmp_r_[2 * k + 1] = state->nosehoover_vxi[k];
1005 }
1006 }
1007 add_ebin(ebin_, itc_, mde_n_, tmp_r_, bSum);
1008
1009 if (bMTTK_)
1010 {
1011 for (int i = 0; (i < nTCP_); i++)
1012 {
1013 for (j = 0; j < nNHC_; j++)
1014 {
1015 k = i * nNHC_ + j;
1016 tmp_r_[2 * k] = state->nhpres_xi[k];
1017 tmp_r_[2 * k + 1] = state->nhpres_vxi[k];
1018 }
1019 }
1020 add_ebin(ebin_, itcb_, mdeb_n_, tmp_r_, bSum);
1021 }
1022 }
1023 else
1024 {
1025 for (int i = 0; (i < nTC_); i++)
1026 {
1027 tmp_r_[2 * i] = state->nosehoover_xi[i];
1028 tmp_r_[2 * i + 1] = state->nosehoover_vxi[i];
1029 }
1030 add_ebin(ebin_, itc_, mde_n_, tmp_r_, bSum);
1031 }
1032 }
1033 }
1034 else if (etc_ == etcBERENDSEN || etc_ == etcYES || etc_ == etcVRESCALE)
1035 {
1036 for (int i = 0; (i < nTC_); i++)
1037 {
1038 tmp_r_[i] = ekind->tcstat[i].lambda;
1039 }
1040 add_ebin(ebin_, itc_, nTC_, tmp_r_, bSum);
1041 }
1042 }
1043
1044 if (ekind && nU_ > 1)
1045 {
1046 for (int i = 0; (i < nU_); i++)
1047 {
1048 copy_rvec(ekind->grpstat[i].u, tmp_v_[i]);
1049 }
1050 add_ebin(ebin_, iu_, 3 * nU_, tmp_v_[0], bSum);
1051 }
1052
1053 ebin_increase_count(1, ebin_, bSum);
1054
1055 // BAR + thermodynamic integration values
1056 if ((fp_dhdl_ || dhc_) && bDoDHDL)
1057 {
1058 for (gmx::index i = 0; i < static_cast<gmx::index>(enerd->enerpart_lambda.size()) - 1; i++)
1059 {
1060 /* zero for simulated tempering */
1061 dE_[i] = enerd->enerpart_lambda[i + 1] - enerd->enerpart_lambda[0];
1062 if (numTemperatures_ > 0)
1063 {
1064 GMX_RELEASE_ASSERT(numTemperatures_ > state->fep_state,
1065 "Number of lambdas in state is bigger then in input record");
1066 GMX_RELEASE_ASSERT(
1067 numTemperatures_ >= static_cast<gmx::index>(enerd->enerpart_lambda.size()) - 1,
1068 "Number of lambdas in energy data is bigger then in input record");
1069 /* MRS: is this right, given the way we have defined the exchange probabilities? */
1070 /* is this even useful to have at all? */
1071 dE_[i] += (temperatures_[i] / temperatures_[state->fep_state] - 1.0) * enerd->term[F_EKIN];
1072 }
1073 }
1074
1075 if (fp_dhdl_)
1076 {
1077 fprintf(fp_dhdl_, "%.4f", time);
1078 /* the current free energy state */
1079
1080 /* print the current state if we are doing expanded ensemble */
1081 if (expand->elmcmove > elmcmoveNO)
1082 {
1083 fprintf(fp_dhdl_, " %4d", state->fep_state);
1084 }
1085 /* total energy (for if the temperature changes */
1086
1087 if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
1088 {
1089 switch (fep->edHdLPrintEnergy)
1090 {
1091 case edHdLPrintEnergyPOTENTIAL: store_energy = enerd->term[F_EPOT]; break;
1092 case edHdLPrintEnergyTOTAL:
1093 case edHdLPrintEnergyYES:
1094 default: store_energy = enerd->term[F_ETOT];
1095 }
1096 fprintf(fp_dhdl_, " %#.8g", store_energy);
1097 }
1098
1099 if (fep->dhdl_derivatives == edhdlderivativesYES)
1100 {
1101 for (int i = 0; i < efptNR; i++)
1102 {
1103 if (fep->separate_dvdl[i])
1104 {
1105 /* assumes F_DVDL is first */
1106 fprintf(fp_dhdl_, " %#.8g", enerd->term[F_DVDL + i]);
1107 }
1108 }
1109 }
1110 for (int i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
1111 {
1112 fprintf(fp_dhdl_, " %#.8g", dE_[i]);
1113 }
1114 if (bDynBox_ && bDiagPres_ && (epc_ != epcNO) && !enerd->enerpart_lambda.empty()
1115 && (fep->init_lambda < 0))
1116 {
1117 fprintf(fp_dhdl_, " %#.8g", pv); /* PV term only needed when
1118 there are alternate state
1119 lambda and we're not in
1120 compatibility mode */
1121 }
1122 fprintf(fp_dhdl_, "\n");
1123 /* and the binary free energy output */
1124 }
1125 if (dhc_ && bDoDHDL)
1126 {
1127 int idhdl = 0;
1128 for (int i = 0; i < efptNR; i++)
1129 {
1130 if (fep->separate_dvdl[i])
1131 {
1132 /* assumes F_DVDL is first */
1133 store_dhdl[idhdl] = enerd->term[F_DVDL + i];
1134 idhdl += 1;
1135 }
1136 }
1137 store_energy = enerd->term[F_ETOT];
1138 /* store_dh is dE */
1139 mde_delta_h_coll_add_dh(dhc_, static_cast<double>(state->fep_state), store_energy, pv,
1140 store_dhdl, dE_ + fep->lambda_start_n, time);
1141 }
1142 }
1143 }
1144
1145 void EnergyOutput::recordNonEnergyStep()
1146 {
1147 ebin_increase_count(1, ebin_, false);
1148 }
1149
1150 void EnergyOutput::printHeader(FILE* log, int64_t steps, double time)
1151 {
1152 char buf[22];
1153
1154 fprintf(log,
1155 " %12s %12s\n"
1156 " %12s %12.5f\n\n",
1157 "Step", "Time", gmx_step_str(steps, buf), time);
1158 }
1159
1160 void EnergyOutput::printStepToEnergyFile(ener_file* fp_ene,
1161 bool bEne,
1162 bool bDR,
1163 bool bOR,
1164 FILE* log,
1165 int64_t step,
1166 double time,
1167 t_fcdata* fcd,
1168 gmx::Awh* awh)
1169 {
1170 t_enxframe fr;
1171 init_enxframe(&fr);
1172 fr.t = time;
1173 fr.step = step;
1174 fr.nsteps = ebin_->nsteps;
1175 fr.dt = delta_t_;
1176 fr.nsum = ebin_->nsum;
1177 fr.nre = (bEne) ? ebin_->nener : 0;
1178 fr.ener = ebin_->e;
1179 int ndisre = bDR ? fcd->disres.npair : 0;
1180 /* these are for the old-style blocks (1 subblock, only reals), because
1181 there can be only one per ID for these */
1182 int nr[enxNR];
1183 int id[enxNR];
1184 real* block[enxNR];
1185 /* Optional additional old-style (real-only) blocks. */
1186 for (int i = 0; i < enxNR; i++)
1187 {
1188 nr[i] = 0;
1189 }
1190
1191 if (bOR && fcd->orires.nr > 0)
1192 {
1193 diagonalize_orires_tensors(&(fcd->orires));
1194 nr[enxOR] = fcd->orires.nr;
1195 block[enxOR] = fcd->orires.otav;
1196 id[enxOR] = enxOR;
1197 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ? fcd->orires.nr : 0;
1198 block[enxORI] = fcd->orires.oinsl;
1199 id[enxORI] = enxORI;
1200 nr[enxORT] = fcd->orires.nex * 12;
1201 block[enxORT] = fcd->orires.eig;
1202 id[enxORT] = enxORT;
1203 }
1204
1205 /* whether we are going to write anything out: */
1206 if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
1207 {
1208 /* the old-style blocks go first */
1209 fr.nblock = 0;
1210 for (int i = 0; i < enxNR; i++)
1211 {
1212 if (nr[i] > 0)
1213 {
1214 fr.nblock = i + 1;
1215 }
1216 }
1217 add_blocks_enxframe(&fr, fr.nblock);
1218 for (int b = 0; b < fr.nblock; b++)
1219 {
1220 add_subblocks_enxblock(&(fr.block[b]), 1);
1221 fr.block[b].id = id[b];
1222 fr.block[b].sub[0].nr = nr[b];
1223 #if !GMX_DOUBLE
1224 fr.block[b].sub[0].type = xdr_datatype_float;
1225 fr.block[b].sub[0].fval = block[b];
1226 #else
1227 fr.block[b].sub[0].type = xdr_datatype_double;
1228 fr.block[b].sub[0].dval = block[b];
1229 #endif
1230 }
1231
1232 /* check for disre block & fill it. */
1233 if (ndisre > 0)
1234 {
1235 int db = fr.nblock;
1236 fr.nblock += 1;
1237 add_blocks_enxframe(&fr, fr.nblock);
1238
1239 add_subblocks_enxblock(&(fr.block[db]), 2);
1240 fr.block[db].id = enxDISRE;
1241 fr.block[db].sub[0].nr = ndisre;
1242 fr.block[db].sub[1].nr = ndisre;
1243 #if !GMX_DOUBLE
1244 fr.block[db].sub[0].type = xdr_datatype_float;
1245 fr.block[db].sub[1].type = xdr_datatype_float;
1246 fr.block[db].sub[0].fval = fcd->disres.rt;
1247 fr.block[db].sub[1].fval = fcd->disres.rm3tav;
1248 #else
1249 fr.block[db].sub[0].type = xdr_datatype_double;
1250 fr.block[db].sub[1].type = xdr_datatype_double;
1251 fr.block[db].sub[0].dval = fcd->disres.rt;
1252 fr.block[db].sub[1].dval = fcd->disres.rm3tav;
1253 #endif
1254 }
1255 /* here we can put new-style blocks */
1256
1257 /* Free energy perturbation blocks */
1258 if (dhc_)
1259 {
1260 mde_delta_h_coll_handle_block(dhc_, &fr, fr.nblock);
1261 }
1262
1263 /* we can now free & reset the data in the blocks */
1264 if (dhc_)
1265 {
1266 mde_delta_h_coll_reset(dhc_);
1267 }
1268
1269 /* AWH bias blocks. */
1270 if (awh != nullptr) // TODO: add boolean flag.
1271 {
1272 awh->writeToEnergyFrame(step, &fr);
1273 }
1274
1275 /* do the actual I/O */
1276 do_enx(fp_ene, &fr);
1277 if (fr.nre)
1278 {
1279 /* We have stored the sums, so reset the sum history */
1280 reset_ebin_sums(ebin_);
1281 }
1282 }
1283 free_enxframe(&fr);
1284 if (log)
1285 {
1286 if (bOR && fcd->orires.nr > 0)
1287 {
1288 print_orires_log(log, &(fcd->orires));
1289 }
1290
1291 fprintf(log, " Energies (%s)\n", unit_energy);
1292 pr_ebin(log, ebin_, ie_, f_nre_ + nCrmsd_, 5, eprNORMAL, true);
1293 fprintf(log, "\n");
1294 }
1295 }
1296
1297 void EnergyOutput::printAnnealingTemperatures(FILE* log, SimulationGroups* groups, t_grpopts* opts)
1298 {
1299 if (log)
1300 {
1301 if (opts)
1302 {
1303 for (int i = 0; i < opts->ngtc; i++)
1304 {
1305 if (opts->annealing[i] != eannNO)
1306 {
1307 fprintf(log, "Current ref_t for group %s: %8.1f\n",
1308 *(groups->groupNames[groups->groups[SimulationAtomGroupType::TemperatureCoupling][i]]),
1309 opts->ref_t[i]);
1310 }
1311 }
1312 fprintf(log, "\n");
1313 }
1314 }
1315 }
1316
1317 void EnergyOutput::printAverages(FILE* log, const SimulationGroups* groups)
1318 {
1319 if (ebin_->nsum_sim <= 0)
1320 {
1321 if (log)
1322 {
1323 fprintf(log, "Not enough data recorded to report energy averages\n");
1324 }
1325 return;
1326 }
1327 if (log)
1328 {
1329
1330 char buf1[22], buf2[22];
1331
1332 fprintf(log, "\t<====== ############### ==>\n");
1333 fprintf(log, "\t<==== A V E R A G E S ====>\n");
1334 fprintf(log, "\t<== ############### ======>\n\n");
1335
1336 fprintf(log, "\tStatistics over %s steps using %s frames\n",
1337 gmx_step_str(ebin_->nsteps_sim, buf1), gmx_step_str(ebin_->nsum_sim, buf2));
1338 fprintf(log, "\n");
1339
1340 fprintf(log, " Energies (%s)\n", unit_energy);
1341 pr_ebin(log, ebin_, ie_, f_nre_ + nCrmsd_, 5, eprAVER, true);
1342 fprintf(log, "\n");
1343
1344 if (bDynBox_)
1345 {
1346 pr_ebin(log, ebin_, ib_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(), 5, eprAVER, true);
1347 fprintf(log, "\n");
1348 }
1349 if (bConstrVir_)
1350 {
1351 fprintf(log, " Constraint Virial (%s)\n", unit_energy);
1352 pr_ebin(log, ebin_, isvir_, 9, 3, eprAVER, false);
1353 fprintf(log, "\n");
1354 fprintf(log, " Force Virial (%s)\n", unit_energy);
1355 pr_ebin(log, ebin_, ifvir_, 9, 3, eprAVER, false);
1356 fprintf(log, "\n");
1357 }
1358 if (bPres_)
1359 {
1360 fprintf(log, " Total Virial (%s)\n", unit_energy);
1361 pr_ebin(log, ebin_, ivir_, 9, 3, eprAVER, false);
1362 fprintf(log, "\n");
1363 fprintf(log, " Pressure (%s)\n", unit_pres_bar);
1364 pr_ebin(log, ebin_, ipres_, 9, 3, eprAVER, false);
1365 fprintf(log, "\n");
1366 }
1367 if (bMu_)
1368 {
1369 fprintf(log, " Total Dipole (%s)\n", unit_dipole_D);
1370 pr_ebin(log, ebin_, imu_, 3, 3, eprAVER, false);
1371 fprintf(log, "\n");
1372 }
1373
1374 if (nE_ > 1)
1375 {
1376 int padding = 8 - strlen(unit_energy);
1377 fprintf(log, "%*sEpot (%s) ", padding, "", unit_energy);
1378 for (int i = 0; (i < egNR); i++)
1379 {
1380 if (bEInd_[i])
1381 {
1382 fprintf(log, "%12s ", egrp_nm[i]);
1383 }
1384 }
1385 fprintf(log, "\n");
1386
1387 int n = 0;
1388 for (int i = 0; (i < nEg_); i++)
1389 {
1390 int ni = groups->groups[SimulationAtomGroupType::EnergyOutput][i];
1391 for (int j = i; (j < nEg_); j++)
1392 {
1393 int nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
1394 int padding =
1395 14 - (strlen(*(groups->groupNames[ni])) + strlen(*(groups->groupNames[nj])));
1396 fprintf(log, "%*s%s-%s", padding, "", *(groups->groupNames[ni]),
1397 *(groups->groupNames[nj]));
1398 pr_ebin(log, ebin_, igrp_[n], nEc_, nEc_, eprAVER, false);
1399 n++;
1400 }
1401 }
1402 fprintf(log, "\n");
1403 }
1404 if (nTC_ > 1)
1405 {
1406 pr_ebin(log, ebin_, itemp_, nTC_, 4, eprAVER, true);
1407 fprintf(log, "\n");
1408 }
1409 if (nU_ > 1)
1410 {
1411 fprintf(log, "%15s %12s %12s %12s\n", "Group", "Ux", "Uy", "Uz");
1412 for (int i = 0; (i < nU_); i++)
1413 {
1414 int ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
1415 fprintf(log, "%15s", *groups->groupNames[ni]);
1416 pr_ebin(log, ebin_, iu_ + 3 * i, 3, 3, eprAVER, false);
1417 }
1418 fprintf(log, "\n");
1419 }
1420 }
1421 }
1422
1423 void EnergyOutput::fillEnergyHistory(energyhistory_t* enerhist) const
1424 {
1425 const t_ebin* const ebin = ebin_;
1426
1427 enerhist->nsteps = ebin->nsteps;
1428 enerhist->nsum = ebin->nsum;
1429 enerhist->nsteps_sim = ebin->nsteps_sim;
1430 enerhist->nsum_sim = ebin->nsum_sim;
1431
1432 if (ebin->nsum > 0)
1433 {
1434 /* This will only actually resize the first time */
1435 enerhist->ener_ave.resize(ebin->nener);
1436 enerhist->ener_sum.resize(ebin->nener);
1437
1438 for (int i = 0; i < ebin->nener; i++)
1439 {
1440 enerhist->ener_ave[i] = ebin->e[i].eav;
1441 enerhist->ener_sum[i] = ebin->e[i].esum;
1442 }
1443 }
1444
1445 if (ebin->nsum_sim > 0)
1446 {
1447 /* This will only actually resize the first time */
1448 enerhist->ener_sum_sim.resize(ebin->nener);
1449
1450 for (int i = 0; i < ebin->nener; i++)
1451 {
1452 enerhist->ener_sum_sim[i] = ebin->e_sim[i].esum;
1453 }
1454 }
1455 if (dhc_)
1456 {
1457 mde_delta_h_coll_update_energyhistory(dhc_, enerhist);
1458 }
1459 }
1460
1461 void EnergyOutput::restoreFromEnergyHistory(const energyhistory_t& enerhist)
1462 {
1463 unsigned int nener = static_cast<unsigned int>(ebin_->nener);
1464
1465 if ((enerhist.nsum > 0 && nener != enerhist.ener_sum.size())
1466 || (enerhist.nsum_sim > 0 && nener != enerhist.ener_sum_sim.size()))
1467 {
1468 gmx_fatal(FARGS,
1469 "Mismatch between number of energies in run input (%u) and checkpoint file (%zu "
1470 "or %zu).",
1471 nener, enerhist.ener_sum.size(), enerhist.ener_sum_sim.size());
1472 }
1473
1474 ebin_->nsteps = enerhist.nsteps;
1475 ebin_->nsum = enerhist.nsum;
1476 ebin_->nsteps_sim = enerhist.nsteps_sim;
1477 ebin_->nsum_sim = enerhist.nsum_sim;
1478
1479 for (int i = 0; i < ebin_->nener; i++)
1480 {
1481 ebin_->e[i].eav = (enerhist.nsum > 0 ? enerhist.ener_ave[i] : 0);
1482 ebin_->e[i].esum = (enerhist.nsum > 0 ? enerhist.ener_sum[i] : 0);
1483 ebin_->e_sim[i].esum = (enerhist.nsum_sim > 0 ? enerhist.ener_sum_sim[i] : 0);
1484 }
1485 if (dhc_)
1486 {
1487 mde_delta_h_coll_restore_energyhistory(dhc_, enerhist.deltaHForeignLambdas.get());
1488 }
1489 }
1490
1491 int EnergyOutput::numEnergyTerms() const
1492 {
1493 return ebin_->nener;
1494 }
1495
1496 } // namespace gmx
The ultimate molecular dynamics simulation package