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37 * Implements functions in swapcoords.h.
39 * \author Carsten Kutzner <ckutzne@gwdg.de>
40 * \ingroup module_swap
49 #include "gromacs/legacyheaders/typedefs.h"
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/mdlib/groupcoord.h"
53 #include "gromacs/topology/mtop_util.h"
54 #include "gromacs/legacyheaders/macros.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/legacyheaders/names.h"
57 #include "gromacs/legacyheaders/network.h"
58 #include "gromacs/legacyheaders/mdrun.h"
59 #include "gromacs/fileio/xvgr.h"
60 #include "gromacs/legacyheaders/copyrite.h"
61 #include "gromacs/fileio/confio.h"
62 #include "gromacs/timing/wallcycle.h"
63 #include "swapcoords.h"
65 #include "gromacs/pbcutil/pbc.h"
67 static char *SwS = {"SWAP:"}; /**< For output that comes from the swap module */
68 static char *SwSEmpty = {" "}; /**< Placeholder for multi-line output */
69 static char* IonString[eIonNR] = {"anion", "cation" }; /**< Type of ion, used for verbose output */
70 static char* IonStr[eIonNR] = {"-", "+" }; /**< Type of ion, used for short output */
71 static char* CompStr[eCompNR] = {"A", "B" }; /**< Compartment name */
72 static char *SwapStr[eSwapTypesNR+1] = { "", "X-", "Y-", "Z-", NULL}; /**< Name for the swap types. */
73 static char *DimStr[DIM+1] = { "X", "Y", "Z", NULL}; /**< Name for the swap dimension. */
75 /* eGrpSplit0 and eGrpSplit1 _must_ be neighbors in this list because
76 * we sometimes loop from eGrpSplit0 to eGrpSplit1 */
78 eGrpIons, eGrpSplit0, eGrpSplit1, eGrpSolvent, eGrpNr
79 }; /**< Group identifier */
80 static char* GrpString[eGrpNr] = { "ion", "split0", "split1", "solvent" }; /**< Group name */
82 /** Keep track of through which channel the ions have passed */
83 enum eChannelHistory {
84 eChHistPassedNone, eChHistPassedCh0, eChHistPassedCh1, eChHistNr
86 static char* ChannelString[eChHistNr] = { "none", "channel0", "channel1" }; /**< Name for the channels */
88 /*! \brief Domain identifier.
90 * Keeps track of from which compartment the ions came before passing the
94 eDomainNotset, eDomainA, eDomainB, eDomainNr
96 static char* DomainString[eDomainNr] = { "not_assigned", "Domain_A", "Domain_B" }; /**< Name for the domains */
101 * Structure containing compartment-specific data.
103 typedef struct swap_compartment
105 int nat; /**< Number of atoms matching the
106 compartment conditions. */
107 int nat_old; /**< Number of atoms before swapping. */
108 int nat_req; /**< Requested number of atoms. */
109 real nat_av; /**< Time-averaged number of atoms matching
110 the compartment conditions. */
111 int *nat_past; /**< Past ion counts for time-averaging. */
112 int *ind; /**< Indices to coll array of atoms. */
113 real *dist; /**< Distance of atom to compartment center. */
114 int nalloc; /**< Allocation size for ind array. */
115 int inflow_netto; /**< Net inflow of ions into this compartment. */
120 * This structure contains data needed for each of the groups involved in swapping: ions, water,
123 typedef struct swap_group
125 int nat; /**< Number of atoms in the group */
126 int apm; /**< Number of atoms in each molecule */
127 atom_id *ind; /**< Global atom indices of the group */
128 atom_id *ind_loc; /**< Local atom indices of the group */
129 int nat_loc; /**< Number of local group atoms */
130 int nalloc_loc; /**< Allocation size for ind_loc */
131 rvec *xc; /**< Collective array of group atom positions */
132 ivec *xc_shifts; /**< Current (collective) shifts */
133 ivec *xc_eshifts; /**< Extra shifts since last DD step */
134 rvec *xc_old; /**< Old (collective) positions */
135 real *qc; /**< Collective array of charges */
136 int *c_ind_loc; /**< Position of local atoms in the
137 collective array, [0..nat_loc] */
138 real *m; /**< Masses (can be omitted) */
139 unsigned char *comp_from; /**< (Collective) Stores from which compartment this
140 atom has come. This way we keep track of through
141 which channel an ion permeates (only used for
143 unsigned char *comp_now; /**< In which compartment this ion is now */
144 unsigned char *channel_label; /**< Which channel was passed at last by this ion? */
145 rvec center; /**< Center of the group; COM if masses are used */
150 * Main (private) data structure for the position swapping protocol.
154 int swapdim; /**< One of XX, YY, ZZ */
155 t_pbc *pbc; /**< Needed to make molecules whole. */
156 FILE *fpout; /**< Output file. */
157 t_group group[eGrpNr]; /**< Ions, solvent or channels? */
158 t_compartment comp[eCompNR][eIonNR]; /**< Data for a specific compartment and ion type. */
159 t_compartment compsol[eCompNR]; /**< Solvent compartments. */
160 int fluxfromAtoB[eChanNR][eIonNR]; /**< Net flux per channels and ion type. */
161 int ncyl0ions; /**< Number of ions residing in channel 0. */
162 int ncyl1ions; /**< Same for channel 1. */
163 int cyl0and1; /**< Ions assigned to cyl0 and cyl1. Not good. */
164 int *fluxleak; /**< Pointer to a single int value holding the
165 flux not going through any of the channels. */
166 real deltaQ; /**< The charge imbalance between the compartments. */
171 /*! \brief Check whether point is in channel.
173 * A channel is a cylinder defined by a disc
174 * with radius r around its center c. The thickness of the cylinder is
181 * <---------c--------->
187 static gmx_bool is_in_channel(
188 rvec point, /* Point under consideration */
189 rvec center, /* 'Center' of cylinder */
190 real d_up, /* Upper extension */
191 real d_down, /* Lower extensions */
192 real r_cyl2, /* Cylinder radius squared */
194 int normal) /* The membrane normal direction is typically 3, i.e. ZZ, but can be X or Y also */
197 int plane1, plane2; /* Directions tangential to membrane */
200 plane1 = (normal + 1) % 3; /* typically 0, i.e. XX */
201 plane2 = (normal + 2) % 3; /* typically 1, i.e. YY */
203 /* Get the distance vector dr between the point and the center of the cylinder */
204 pbc_dx(pbc, point, center, dr); /* This puts center in the origin */
206 /* Check vertical direction */
207 if ( (dr[normal] > d_up) || (dr[normal] < -d_down) )
212 /* Check radial direction */
213 if ( (dr[plane1]*dr[plane1] + dr[plane2]*dr[plane2]) > r_cyl2)
218 /* All check passed, this point is in the cylinder */
223 /*! \brief Prints to swap output file which ions are in which compartment. */
224 static void print_ionlist(
229 int itype, icomp, i, j;
233 fprintf(s->fpout, "%12.5e", time);
234 for (icomp = 0; icomp < eCompNR; icomp++)
236 for (itype = 0; itype < eIonNR; itype++)
238 comp = &(s->comp[icomp][itype]);
239 fprintf(s->fpout, "%7d%7.1f%7d", comp->nat, comp->nat_av-comp->nat_req, comp->inflow_netto);
242 fprintf(s->fpout, "%12.3e%12.3e",
243 s->group[eGrpSplit0].center[s->swapdim],
244 s->group[eGrpSplit1].center[s->swapdim]);
246 for (i = 0; i < eChanNR; i++)
248 for (j = 0; j < eIonNR; j++)
250 fprintf(s->fpout, "%12d", s->fluxfromAtoB[i][j]);
254 /* Also print the number of ions that leaked from A to B: */
255 fprintf(s->fpout, "%12d", *s->fluxleak);
257 fprintf(s->fpout, "%s\n", comment);
261 /*! \brief Get the center of a group of nat atoms.
263 * Since with PBC an atom group might not be whole, use the first atom as the
264 * reference atom and determine the center with respect to this reference.
266 static void get_molecule_center(
274 rvec weightedPBCimage;
276 rvec reference, correctPBCimage, dx;
279 /* Use the first atom as the reference and put other atoms near that one */
280 /* This does not work for large molecules that span > half of the box! */
281 copy_rvec(x[0], reference);
283 /* Calculate either the weighted center or simply the center of geometry */
286 for (i = 0; i < nat; i++)
288 /* PBC distance between position and reference */
289 pbc_dx(pbc, x[i], reference, dx);
291 /* Add PBC distance to reference */
292 rvec_add(reference, dx, correctPBCimage);
294 /* Take weight into account */
304 svmul(wi, correctPBCimage, weightedPBCimage);
307 rvec_inc(center, weightedPBCimage);
311 svmul(1.0/wsum, center, center);
316 /*! \brief Return TRUE if ion is found in the compartment.
318 * Returns TRUE if x is between (w1+gap) and (w2-gap)
322 * ||-----------|--+--|----------o----------|--+--|---------------------||
323 * w1 ????????????????????? w2
327 static gmx_bool compartment_contains_atom(
328 real w1, /* position of wall atom 1 */
329 real w2, /* position of wall atom 2 */
332 real l, /* length of the box, from || to || in the sketch */
333 real *distance_from_center)
338 /* First set the origin in the middle of w1 and w2 */
344 /* Now choose the PBC image of x that is closest to the origin: */
355 *distance_from_center = (real)fabs(x);
357 /* Return TRUE if we now are in area "????" */
358 if ( (x >= (w1+gap)) && (x < (w2-gap)) )
369 /*! \brief Updates the time-averaged number of ions in a compartment. */
370 static void update_time_window(t_compartment *comp, int values, int replace)
376 /* Put in the new value */
379 comp->nat_past[replace] = comp->nat;
382 /* Compute the new time-average */
384 for (i = 0; i < values; i++)
386 average += comp->nat_past[i];
389 comp->nat_av = average;
393 /*! \brief Add atom with collective index ci to the list 'comp'. */
394 static void add_to_list(
395 int ci, /* index of this ion in the collective array xc, qc */
396 t_compartment *comp, /* Compartment to add this atom to */
397 real distance) /* Shortest distance of this atom to the compartment center */
404 if (nr >= comp->nalloc)
406 comp->nalloc = over_alloc_dd(nr+1);
407 srenew(comp->ind, comp->nalloc);
408 srenew(comp->dist, comp->nalloc);
411 comp->dist[nr] = distance;
416 /*! \brief Determine the compartment boundaries from the channel centers. */
417 static void get_compartment_boundaries(
421 real *left, real *right)
424 real leftpos, rightpos, leftpos_orig;
429 gmx_fatal(FARGS, "No compartment %d.", c);
432 pos0 = s->group[eGrpSplit0].center[s->swapdim];
433 pos1 = s->group[eGrpSplit1].center[s->swapdim];
446 /* This gets us the other compartment: */
449 leftpos_orig = leftpos;
451 rightpos = leftpos_orig + box[s->swapdim][s->swapdim];
459 /*! \brief Determine the per-channel ion flux.
461 * To determine the flux through the individual channels, we
462 * remember the compartment and channel history of each ion. An ion can be
463 * either in channel0 or channel1, or in the remaining volume of compartment
467 * +-----------------+
470 * ||||||||||0|||||||| bilayer with channel 0
475 * |||||1||||||||||||| bilayer with channel 1
478 * +-----------------+
482 static void detect_flux_per_channel(
487 unsigned char *comp_now,
488 unsigned char *comp_from,
489 unsigned char *channel_label,
499 gmx_bool in_cyl0, in_cyl1;
506 /* Check whether ion is inside any of the channels */
507 in_cyl0 = is_in_channel(ion_pos, s->group[eGrpSplit0].center, sc->cyl0u, sc->cyl0l, cyl0_r2, s->pbc, sd);
508 in_cyl1 = is_in_channel(ion_pos, s->group[eGrpSplit1].center, sc->cyl1u, sc->cyl1l, cyl1_r2, s->pbc, sd);
510 if (in_cyl0 && in_cyl1)
512 /* Ion appears to be in both channels. Something is severely wrong! */
514 *comp_now = eDomainNotset;
515 *comp_from = eDomainNotset;
516 *channel_label = eChHistPassedNone;
520 /* Ion is in channel 0 now */
521 *channel_label = eChHistPassedCh0;
522 *comp_now = eDomainNotset;
527 /* Ion is in channel 1 now */
528 *channel_label = eChHistPassedCh1;
529 *comp_now = eDomainNotset;
534 /* Ion is not in any of the channels, so it must be in domain A or B */
537 *comp_now = eDomainA;
541 *comp_now = eDomainB;
545 /* Only take action, if ion is now in domain A or B, and was before
546 * in the other domain!
548 if (eDomainNotset == *comp_from)
550 /* Maybe we can set the domain now */
551 *comp_from = *comp_now; /* Could still be eDomainNotset, though */
553 else if ( (*comp_now != eDomainNotset ) /* if in channel */
554 && (*comp_from != *comp_now) )
556 /* Obviously the ion changed its domain.
557 * Count this for the channel through which it has passed. */
558 switch (*channel_label)
560 case eChHistPassedNone:
561 *s->fluxleak = *s->fluxleak + 1;
563 fprintf(stderr, " %s Warning! Step %s, ion %d (%s) moved from %s to %s\n",
564 SwS, gmx_step_str(step, buf), iion, IonStr[iontype], DomainString[*comp_from], DomainString[*comp_now]);
567 fprintf(stderr, ", possibly due to a swap in the original simulation.\n");
571 fprintf(stderr, "but did not pass cyl0 or cyl1 as defined in the .mdp file.\n"
572 "Do you have an ion somewhere within the membrane?\n");
573 /* Write this info to the CompEL output file: */
574 fprintf(s->fpout, " # Warning: step %s, ion %d (%s) moved from %s to %s (probably through the membrane)\n",
575 gmx_step_str(step, buf), iion, IonStr[iontype],
576 DomainString[*comp_from], DomainString[*comp_now]);
580 case eChHistPassedCh0:
581 case eChHistPassedCh1:
582 if (*channel_label == eChHistPassedCh0)
591 if (eDomainA == *comp_from)
593 s->fluxfromAtoB[chan_nr][iontype]++;
597 s->fluxfromAtoB[chan_nr][iontype]--;
599 fprintf(fpout, "# Atom nr. %d finished passing %s.\n", iion, ChannelString[*channel_label]);
602 gmx_fatal(FARGS, "%s Unknown channel history entry!\n", SwS);
606 /* This ion has moved to the _other_ compartment ... */
607 *comp_from = *comp_now;
608 /* ... and it did not pass any channel yet */
609 *channel_label = eChHistPassedNone;
614 /*! \brief Get the lists of ions for the two compartments */
615 static void compartmentalize_ions(
628 real cyl0_r2, cyl1_r2;
630 int sum, not_in_comp[eCompNR]; /* consistency check */
635 iong = &s->group[eGrpIons];
638 cyl0_r2 = sc->cyl0r * sc->cyl0r;
639 cyl1_r2 = sc->cyl1r * sc->cyl1r;
642 /* Get us a counter that cycles in the range of [0 ... sc->nAverage[ */
643 replace = (step/sc->nstswap) % sc->nAverage;
645 for (comp = eCompA; comp <= eCompB; comp++)
647 /* Get lists of atoms that match criteria for this compartment */
648 get_compartment_boundaries(comp, sc->si_priv, box, &left, &right);
650 /* First clear the ion lists */
651 s->comp[comp][eIonNEG].nat = 0;
652 s->comp[comp][eIonPOS].nat = 0;
653 not_in_comp[comp] = 0; /* consistency check */
655 /* Loop over the IONS */
656 for (i = 0; i < iong->nat; i++)
658 /* Anion or cation? */
659 type = iong->qc[i] < 0 ? eIonNEG : eIonPOS;
661 /* Is this ion in the compartment that we look at? */
662 if (compartment_contains_atom(left, right, 0, iong->xc[i][sd], box[sd][sd], &dist) )
664 /* Now put it into the list containing only ions of its type */
665 add_to_list(i, &s->comp[comp][type], dist);
667 /* Master also checks through which channel each ion has passed */
668 if (MASTER(cr) && (iong->comp_now != NULL))
670 ion_nr_global = iong->ind[i] + 1; /* PDB index starts at 1 ... */
671 detect_flux_per_channel(ion_nr_global, comp, type, iong->xc[i],
672 &iong->comp_now[i], &iong->comp_from[i], &iong->channel_label[i],
673 sc, cyl0_r2, cyl1_r2, step, bRerun, fpout);
678 not_in_comp[comp] += 1;
681 /* Correct the time-averaged number of ions in both compartments */
682 update_time_window(&s->comp[comp][eIonNEG], sc->nAverage, replace);
683 update_time_window(&s->comp[comp][eIonPOS], sc->nAverage, replace);
686 /* Flux detection warnings */
692 "%s Warning: %d atoms were detected as being in both channels! Probably your split\n"
693 "%s cylinder is way too large, or one compartment has collapsed (step %"GMX_PRId64 ")\n",
694 SwS, s->cyl0and1, SwS, step);
696 fprintf(s->fpout, "Warning: %d atoms were assigned to both channels!\n", s->cyl0and1);
703 /* Consistency checks */
704 if (not_in_comp[eCompA] + not_in_comp[eCompB] != iong->nat)
708 fprintf(fpout, "# Warning: Inconsistency during ion compartmentalization. !inA: %d, !inB: %d, total ions %d\n",
709 not_in_comp[eCompA], not_in_comp[eCompB], iong->nat);
714 fprintf(stderr, "%s rank %d: Inconsistency during ion compartmentalization. !inA: %d, !inB: %d, total ions %d\n",
715 SwS, cr->nodeid, not_in_comp[eCompA], not_in_comp[eCompB], iong->nat);
719 sum = s->comp[eCompA][eIonNEG].nat + s->comp[eCompA][eIonPOS].nat
720 + s->comp[eCompB][eIonNEG].nat + s->comp[eCompB][eIonPOS].nat;
721 if (sum != iong->nat)
725 fprintf(fpout, "# Warning: %d atoms are in the ion group, but altogether %d have been assigned to the compartments.\n",
731 fprintf(stderr, "%s rank %d: %d atoms are in the ion group, but altogether %d have been assigned to the compartments.\n",
732 SwS, cr->nodeid, iong->nat, sum);
740 /*! \brief Set up the compartments and get lists of solvent atoms in each compartment */
741 static void compartmentalize_solvent(
753 int sum, not_in_comp[eCompNR]; /* consistency check */
757 solg = &s->group[eGrpSolvent];
761 for (comp = eCompA; comp <= eCompB; comp++)
763 /* Get lists of atoms that match criteria for this compartment */
764 get_compartment_boundaries(comp, sc->si_priv, box, &left, &right);
766 /* First clear the solvent molecule lists */
767 s->compsol[comp].nat = 0;
768 not_in_comp[comp] = 0; /* consistency check */
770 /* Loop over the solvent MOLECULES */
771 for (i = 0; i < sc->nat_sol; i += apm)
773 if (compartment_contains_atom(left, right, 0, solg->xc[i][sd], box[sd][sd], &dist))
775 /* Add the whole molecule to the list */
776 for (j = 0; j < apm; j++)
778 add_to_list(i+j, &s->compsol[comp], dist);
783 not_in_comp[comp] += apm;
790 fprintf(fpout, "# Solv. molecules in comp.%s: %d comp.%s: %d\n",
791 CompStr[eCompA], s->compsol[eCompA].nat/apm,
792 CompStr[eCompB], s->compsol[eCompB].nat/apm);
795 /* Consistency checks */
796 if (not_in_comp[eCompA] + not_in_comp[eCompB] != solg->nat)
800 fprintf(fpout, "# Warning: Inconsistency during solvent compartmentalization. !inA: %d, !inB: %d, solvent atoms %d\n",
801 not_in_comp[eCompA], not_in_comp[eCompB], solg->nat);
806 fprintf(stderr, "%s rank %d: Inconsistency during solvent compartmentalization. !inA: %d, !inB: %d, solvent atoms %d\n",
807 SwS, cr->nodeid, not_in_comp[eCompA], not_in_comp[eCompB], solg->nat);
810 sum = s->compsol[eCompA].nat + s->compsol[eCompB].nat;
811 if (sum != solg->nat)
815 fprintf(fpout, "# Warning: %d atoms in solvent group, but %d have been assigned to the compartments.\n",
821 fprintf(stderr, "%s rank %d: %d atoms in solvent group, but %d have been assigned to the compartments.\n",
822 SwS, cr->nodeid, solg->nat, sum);
828 /*! \brief Find out how many group atoms are in the compartments initially */
829 static void get_initial_ioncounts(
831 rvec x[], /* the initial positions */
845 /* Copy the initial swap group positions to the collective array so
846 * that we can compartmentalize */
847 for (i = 0; i < sc->nat; i++)
850 copy_rvec(x[ind], s->group[eGrpIons].xc[i]);
853 /* Set up the compartments and get lists of atoms in each compartment */
854 compartmentalize_ions(cr, sc, box, 0, s->fpout, bRerun);
856 /* Set initial concentrations if requested */
857 for (ic = 0; ic < eCompNR; ic++)
859 s->comp[ic][eIonPOS].nat_req = sc->ncations[ic];
860 s->comp[ic][eIonNEG].nat_req = sc->nanions[ic];
862 for (ic = 0; ic < eCompNR; ic++)
864 for (ii = 0; ii < eIonNR; ii++)
866 if (s->comp[ic][ii].nat_req < 0)
868 s->comp[ic][ii].nat_req = s->comp[ic][ii].nat;
873 /* Check whether the number of requested ions adds up to the total number of ions */
874 for (ii = 0; ii < eIonNR; ii++)
876 req[ii] = s->comp[eCompA][ii].nat_req + s->comp[eCompB][ii].nat_req;
877 tot[ii] = s->comp[eCompA][ii].nat + s->comp[eCompB][ii].nat;
879 if ( (req[eCompA] != tot[eCompA]) || (req[eCompB] != tot[eCompB ]) )
881 gmx_fatal(FARGS, "Mismatch of the number of ions summed over both compartments.\n"
882 "You requested a total of %d anions and %d cations,\n"
883 "but there are a total of %d anions and %d cations in the system.\n",
884 req[eIonNEG], req[eIonPOS],
885 tot[eIonNEG], tot[eIonPOS]);
888 /* Initialize time-averaging:
889 * Write initial concentrations to all time bins to start with */
890 for (ic = 0; ic < eCompNR; ic++)
892 for (ii = 0; ii < eIonNR; ii++)
894 s->comp[ic][ii].nat_av = s->comp[ic][ii].nat;
895 for (i = 0; i < sc->nAverage; i++)
897 s->comp[ic][ii].nat_past[i] = s->comp[ic][ii].nat;
904 /*! \brief Copy history of ion counts from checkpoint file.
906 * When called, the checkpoint file has already been read in. Here we copy
907 * over the values from .cpt file to the swap data structure.
909 static void get_initial_ioncounts_from_cpt(
910 t_inputrec *ir, swapstate_t *swapstate,
911 t_commrec *cr, gmx_bool bVerbose)
922 /* Copy the past values from the checkpoint values that have been read in already */
925 fprintf(stderr, "%s Copying values from checkpoint\n", SwS);
928 for (ic = 0; ic < eCompNR; ic++)
930 for (ii = 0; ii < eIonNR; ii++)
932 s->comp[ic][ii].nat_req = swapstate->nat_req[ic][ii];
933 s->comp[ic][ii].inflow_netto = swapstate->inflow_netto[ic][ii];
937 fprintf(stderr, "%s ... Influx netto: %d Requested: %d Past values: ", SwS,
938 s->comp[ic][ii].inflow_netto, s->comp[ic][ii].nat_req);
941 for (j = 0; j < sc->nAverage; j++)
943 s->comp[ic][ii].nat_past[j] = swapstate->nat_past[ic][ii][j];
946 fprintf(stderr, "%d ", s->comp[ic][ii].nat_past[j]);
951 fprintf(stderr, "\n");
959 /*! \brief The master lets all others know about the initial ion counts. */
960 static void bc_initial_concentrations(
969 for (ic = 0; ic < eCompNR; ic++)
971 for (ii = 0; ii < eIonNR; ii++)
973 gmx_bcast(sizeof(s->comp[ic][ii].nat_req), &(s->comp[ic][ii].nat_req), cr);
974 gmx_bcast(sizeof(s->comp[ic][ii].nat ), &(s->comp[ic][ii].nat ), cr);
975 gmx_bcast( swap->nAverage * sizeof(s->comp[ic][ii].nat_past[0]), s->comp[ic][ii].nat_past, cr);
981 /*! \brief Ensure that each atom belongs to at most one of the swap groups. */
982 static void check_swap_groups(t_swap *s, int nat, gmx_bool bVerbose)
986 atom_id *nGroup = NULL; /* This array counts for each atom in the MD system to
987 how many swap groups it belongs (should be 0 or 1!) */
989 int nMultiple = 0; /* Number of atoms belonging to multiple groups */
994 fprintf(stderr, "%s Making sure each atom belongs to at most one of the swap groups.\n", SwS);
997 /* Add one to the group count of atoms belonging to a swap group: */
999 for (i = 0; i < eGrpNr; i++)
1002 for (j = 0; j < g->nat; j++)
1004 /* Get the global index of this atom of this group: */
1009 /* Make sure each atom belongs to at most one swap group: */
1010 for (j = 0; j < g->nat; j++)
1021 gmx_fatal(FARGS, "%s Cannot perform swapping since %d atom%s allocated to more than one swap index group.\n"
1022 "%s Each atom must be allocated to at most one of the split groups, the swap group, or the solvent.\n"
1023 "%s Check the .mdp file settings regarding the swap index groups or the index groups themselves.\n",
1024 SwS, nMultiple, (1 == nMultiple) ? " is" : "s are", SwSEmpty, SwSEmpty);
1029 /*! \brief Get the number of atoms per molecule for this group.
1031 * Also ensure that all the molecules in this group have this number of atoms.
1033 static int get_group_apm_check(
1037 const gmx_mtop_atomlookup_t alook,
1042 int molb, molnr, atnr_mol;
1045 ind = s->group[group].ind;
1046 nat = s->group[group].nat;
1048 /* Determine the number of solvent atoms per solvent molecule from the
1049 * first solvent atom: */
1051 gmx_mtop_atomnr_to_molblock_ind(alook, ind[i], &molb, &molnr, &atnr_mol);
1052 apm = mtop->molblock[molb].natoms_mol;
1056 fprintf(stderr, "%s Checking whether all %s molecules consist of %d atom%s\n",
1057 SwS, GrpString[group], apm, apm > 1 ? "s" : "");
1060 /* Check whether this is also true for all other solvent atoms */
1061 for (i = 1; i < nat; i++)
1063 gmx_mtop_atomnr_to_molblock_ind(alook, ind[i], &molb, &molnr, &atnr_mol);
1064 if (apm != mtop->molblock[molb].natoms_mol)
1066 gmx_fatal(FARGS, "Not all %s group molecules consist of %d atoms.",
1067 GrpString[group], apm);
1075 /*! \brief Print the legend to the swap output file.
1077 * Also print the initial ion counts
1079 static void print_ionlist_legend(t_inputrec *ir, const output_env_t oenv)
1081 const char **legend;
1087 s = ir->swap->si_priv;
1089 snew(legend, eCompNR*eIonNR*3 + 2 + eChanNR*eIonNR + 1);
1090 for (ic = count = 0; ic < eCompNR; ic++)
1092 for (ii = 0; ii < eIonNR; ii++)
1094 sprintf(buf, "%s %ss", CompStr[ic], IonString[ii]);
1095 legend[count++] = gmx_strdup(buf);
1096 sprintf(buf, "%s av. mismatch to %d%s",
1097 CompStr[ic], s->comp[ic][ii].nat_req, IonStr[ii]);
1098 legend[count++] = gmx_strdup(buf);
1099 sprintf(buf, "%s netto %s influx", CompStr[ic], IonString[ii]);
1100 legend[count++] = gmx_strdup(buf);
1103 sprintf(buf, "%scenter of %s of split group 0", SwapStr[ir->eSwapCoords], (NULL != s->group[eGrpSplit0].m) ? "mass" : "geometry");
1104 legend[count++] = gmx_strdup(buf);
1105 sprintf(buf, "%scenter of %s of split group 1", SwapStr[ir->eSwapCoords], (NULL != s->group[eGrpSplit1].m) ? "mass" : "geometry");
1106 legend[count++] = gmx_strdup(buf);
1108 for (ic = 0; ic < eChanNR; ic++)
1110 for (ii = 0; ii < eIonNR; ii++)
1112 sprintf(buf, "A->ch%d->B %s permeations", ic, IonString[ii]);
1113 legend[count++] = gmx_strdup(buf);
1117 sprintf(buf, "leakage");
1118 legend[count++] = gmx_strdup(buf);
1120 xvgr_legend(s->fpout, count, legend, oenv);
1122 fprintf(s->fpout, "# Instantaneous ion counts and time-averaged differences to requested numbers\n");
1123 fprintf(s->fpout, "# time[ps] A_an diff t_in A_cat diff t_in B_an diff t_in B_cat diff t_in ");
1124 fprintf(s->fpout, " %s-Split0 %s-Split1", DimStr[s->swapdim], DimStr[s->swapdim]);
1125 fprintf(s->fpout, " A-ch0-B_an A-ch0-B_cat A-ch1-B_an A-ch1-B_cat ion_leakage\n");
1130 /*! \brief Initialize channel ion flux detection routine.
1132 * Initialize arrays that keep track of where the ions come from and where
1135 static void detect_flux_per_channel_init(
1138 swapstate_t *swapstate,
1139 gmx_bool bStartFromCpt)
1145 g = &(s->group[eGrpIons]);
1147 /* All these flux detection routines run on the master only */
1151 g->comp_from = NULL;
1152 g->channel_label = NULL;
1157 /******************************************************/
1158 /* Channel and domain history for the individual ions */
1159 /******************************************************/
1160 if (bStartFromCpt) /* set the pointers right */
1162 g->comp_from = swapstate->comp_from;
1163 g->channel_label = swapstate->channel_label;
1165 else /* allocate memory */
1167 snew(g->comp_from, g->nat);
1168 swapstate->comp_from = g->comp_from;
1169 snew(g->channel_label, g->nat);
1170 swapstate->channel_label = g->channel_label;
1172 snew(g->comp_now, g->nat);
1174 /* Initialize the channel and domain history counters */
1175 for (i = 0; i < g->nat; i++)
1177 g->comp_now[i] = eDomainNotset;
1180 g->comp_from[i] = eDomainNotset;
1181 g->channel_label[i] = eChHistPassedNone;
1185 /************************************/
1186 /* Channel fluxes for both channels */
1187 /************************************/
1194 fprintf(stderr, "%s Copying channel fluxes from checkpoint file data\n", SwS);
1197 for (ic = 0; ic < eChanNR; ic++)
1199 fprintf(stderr, "%s Channel %d flux history: ", SwS, ic);
1200 for (ii = 0; ii < eIonNR; ii++)
1204 s->fluxfromAtoB[ic][ii] = swapstate->fluxfromAtoB[ic][ii];
1208 s->fluxfromAtoB[ic][ii] = 0;
1211 fprintf(stderr, "%d %s%s ", s->fluxfromAtoB[ic][ii], IonString[ii], s->fluxfromAtoB[ic][ii] == 1 ? "" : "s");
1213 fprintf(stderr, "\n");
1217 s->fluxleak = swapstate->fluxleak;
1221 snew(s->fluxleak, 1);
1223 /* Set pointer for checkpoint writing */
1224 swapstate->fluxleak = s->fluxleak;
1227 /* Set pointers for checkpoint writing */
1228 for (ic = 0; ic < eChanNR; ic++)
1230 for (ii = 0; ii < eIonNR; ii++)
1232 swapstate->fluxfromAtoB_p[ic][ii] = &(s->fluxfromAtoB[ic][ii]);
1238 /*! \brief Outputs the initial structure to PDB file for debugging reasons.
1240 * Output the starting structure so that in case of multimeric channels
1241 * the user can check whether we have the correct PBC image for all atoms.
1242 * If this is not correct, the ion counts per channel will be very likely
1245 static void outputStartStructureIfWanted(gmx_mtop_t *mtop, rvec *x, int ePBC, matrix box)
1247 char *env = getenv("GMX_COMPELDUMP");
1251 fprintf(stderr, "\n%s Found env.var. GMX_COMPELDUMP, will output CompEL starting structure made whole.\n"
1252 "%s In case of multimeric channels, please check whether they have the correct PBC representation.\n",
1255 write_sto_conf_mtop("CompELAssumedWholeConfiguration.pdb", *mtop->name, mtop, x, NULL, ePBC, box);
1260 /*! \brief Initialize the swapstate structure, used for checkpoint writing.
1262 * The swapstate struct stores the information we need to make the channels
1263 * whole again after restarts from a checkpoint file. Here we do the following:\n
1264 * a) If we did not start from .cpt, we prepare the struct for proper .cpt writing,\n
1265 * b) if we did start from .cpt, we copy over the last whole structures from .cpt,\n
1266 * c) in any case, for subsequent checkpoint writing, we set the pointers in\n
1267 * swapstate to the x_old arrays, which contain the correct PBC representation of
1268 * multimeric channels at the last time step.
1270 static void init_swapstate(
1271 swapstate_t *swapstate,
1274 rvec x[], /* the initial positions */
1279 rvec *x_pbc = NULL; /* positions of the whole MD system with molecules made whole */
1286 /* We always need the last whole positions such that
1287 * in the next time step we can make the channels whole again in PBC */
1288 if (swapstate->bFromCpt)
1290 /* Copy the last whole positions of each channel from .cpt */
1291 g = &(s->group[eGrpSplit0]);
1292 for (i = 0; i < g->nat; i++)
1294 copy_rvec(swapstate->xc_old_whole[eChan0][i], g->xc_old[i]);
1296 g = &(s->group[eGrpSplit1]);
1297 for (i = 0; i < g->nat; i++)
1299 copy_rvec(swapstate->xc_old_whole[eChan1][i], g->xc_old[i]);
1304 /* Extract the initial split group positions. */
1306 /* Remove pbc, make molecule whole. */
1307 snew(x_pbc, mtop->natoms);
1308 m_rveccopy(mtop->natoms, x, x_pbc);
1310 /* This can only make individual molecules whole, not multimers */
1311 do_pbc_mtop(NULL, ePBC, box, mtop, x_pbc);
1313 /* Output the starting structure? */
1314 outputStartStructureIfWanted(mtop, x_pbc, ePBC, box);
1316 /* If this is the first run (i.e. no checkpoint present) we assume
1317 * that the starting positions give us the correct PBC representation */
1318 for (ig = eGrpSplit0; ig <= eGrpSplit1; ig++)
1320 g = &(s->group[ig]);
1321 for (i = 0; i < g->nat; i++)
1323 copy_rvec(x_pbc[g->ind[i]], g->xc_old[i]);
1328 /* Prepare swapstate arrays for later checkpoint writing */
1329 swapstate->nat[eChan0] = s->group[eGrpSplit0].nat;
1330 swapstate->nat[eChan1] = s->group[eGrpSplit1].nat;
1333 /* For subsequent checkpoint writing, set the swapstate pointers to the xc_old
1334 * arrays that get updated at every swapping step */
1335 swapstate->xc_old_whole_p[eChan0] = &s->group[eGrpSplit0].xc_old;
1336 swapstate->xc_old_whole_p[eChan1] = &s->group[eGrpSplit1].xc_old;
1340 extern void init_swapcoords(
1348 swapstate_t *swapstate,
1350 const output_env_t oenv,
1351 unsigned long Flags)
1353 int i, ic, ig, ii, j;
1358 gmx_bool bAppend, bStartFromCpt, bRerun;
1359 gmx_mtop_atomlookup_t alook = NULL;
1362 alook = gmx_mtop_atomlookup_init(mtop);
1364 if ( (PAR(cr)) && !DOMAINDECOMP(cr) )
1366 gmx_fatal(FARGS, "Position swapping is only implemented for domain decomposition!");
1369 bAppend = Flags & MD_APPENDFILES;
1370 bStartFromCpt = Flags & MD_STARTFROMCPT;
1371 bRerun = Flags & MD_RERUN;
1374 snew(sc->si_priv, 1);
1381 gmx_fatal(FARGS, "%s This module does not support reruns in parallel\nPlease request a serial run with -nt 1 / -np 1\n", SwS);
1384 fprintf(stderr, "%s Rerun - using every available frame\n", SwS);
1386 sc->nAverage = 1; /* averaging makes no sense for reruns */
1389 if (MASTER(cr) && !bAppend)
1391 fprintf(fplog, "\nInitializing ion/water position exchanges\n");
1392 please_cite(fplog, "Kutzner2011b");
1395 switch (ir->eSwapCoords)
1411 /* Copy some data to the group structures for convenience */
1412 /* Number of atoms in the group */
1413 s->group[eGrpIons ].nat = sc->nat;
1414 s->group[eGrpSplit0 ].nat = sc->nat_split[0];
1415 s->group[eGrpSplit1 ].nat = sc->nat_split[1];
1416 s->group[eGrpSolvent].nat = sc->nat_sol;
1417 /* Pointer to the indices */
1418 s->group[eGrpIons ].ind = sc->ind;
1419 s->group[eGrpSplit0 ].ind = sc->ind_split[0];
1420 s->group[eGrpSplit1 ].ind = sc->ind_split[1];
1421 s->group[eGrpSolvent].ind = sc->ind_sol;
1423 check_swap_groups(s, mtop->natoms, bVerbose && MASTER(cr));
1425 /* Allocate space for the collective arrays for all groups */
1426 for (ig = 0; ig < eGrpNr; ig++)
1428 g = &(s->group[ig]);
1429 snew(g->xc, g->nat);
1430 snew(g->c_ind_loc, g->nat);
1431 /* For the split groups (the channels) we need some extra memory to
1432 * be able to make the molecules whole even if they span more than
1433 * half of the box size. */
1434 if (eGrpSplit0 == ig || eGrpSplit1 == ig)
1436 snew(g->xc_shifts, g->nat);
1437 snew(g->xc_eshifts, g->nat);
1438 snew(g->xc_old, g->nat);
1444 init_swapstate(swapstate, sc, mtop, x, box, ir->ePBC);
1447 /* After init_swapstate we have a set of (old) whole positions for our
1448 * channels. Now transfer that to all nodes */
1451 for (ig = eGrpSplit0; ig <= eGrpSplit1; ig++)
1453 g = &(s->group[ig]);
1454 gmx_bcast((g->nat)*sizeof((g->xc_old)[0]), g->xc_old, (cr));
1458 /* Make sure that all molecules in the ion and solvent groups contain the
1459 * same number of atoms each */
1460 s->group[eGrpIons ].apm = get_group_apm_check(eGrpIons, s, MASTER(cr) && bVerbose, alook, mtop);
1461 s->group[eGrpSolvent].apm = get_group_apm_check(eGrpSolvent, s, MASTER(cr) && bVerbose, alook, mtop);
1463 /* Save masses where needed */
1464 s->group[eGrpIons ].m = NULL;
1465 /* We only need enough space to determine a single solvent molecule's
1466 * center at at time */
1467 g = &(s->group[eGrpSolvent]);
1470 /* Need mass-weighted center of split group? */
1471 for (j = 0, ig = eGrpSplit0; j < eChanNR; ig++, j++)
1473 g = &(s->group[ig]);
1474 if (TRUE == sc->massw_split[j])
1476 /* Save the split group charges if mass-weighting is requested */
1478 for (i = 0; i < g->nat; i++)
1480 gmx_mtop_atomnr_to_atom(alook, g->ind[i], &atom);
1490 /* Save the ionic charges */
1491 g = &(s->group[eGrpIons]);
1492 snew(g->qc, g->nat);
1493 for (i = 0; i < g->nat; i++)
1495 gmx_mtop_atomnr_to_atom(alook, g->ind[i], &atom);
1500 set_pbc(s->pbc, -1, box);
1507 fprintf(stderr, "%s Opening output file %s%s\n", SwS, fn, bAppend ? " for appending" : "");
1510 s->fpout = gmx_fio_fopen(fn, bAppend ? "a" : "w" );
1514 xvgr_header(s->fpout, "Ion counts", "Time (ps)", "counts", exvggtXNY, oenv);
1516 for (ig = 0; ig < eGrpNr; ig++)
1518 g = &(s->group[ig]);
1519 fprintf(s->fpout, "# %s group contains %d atom%s", GrpString[ig], g->nat, (g->nat > 1) ? "s" : "");
1520 if (eGrpSolvent == ig || eGrpIons == ig)
1522 fprintf(s->fpout, " with %d atom%s in each molecule", g->apm, (g->apm > 1) ? "s" : "");
1524 fprintf(s->fpout, ".\n");
1527 fprintf(s->fpout, "#\n# Initial positions of split groups:\n");
1530 for (j = 0, ig = eGrpSplit0; j < eChanNR; j++, ig++)
1532 g = &(s->group[ig]);
1533 for (i = 0; i < g->nat; i++)
1535 copy_rvec(x[sc->ind_split[j][i]], g->xc[i]);
1537 if (eGrpSplit0 == ig || eGrpSplit1 == ig)
1539 /* xc has the correct PBC representation for the two channels, so we do
1540 * not need to correct for that */
1541 get_center(g->xc, g->m, g->nat, g->center);
1545 /* For the water molecules, we need to make the molecules whole */
1546 get_molecule_center(g->xc, g->nat, g->m, g->center, s->pbc);
1550 fprintf(s->fpout, "# %s group %s-center %5f nm\n", GrpString[ig],
1551 DimStr[s->swapdim], g->center[s->swapdim]);
1557 fprintf(s->fpout, "#\n");
1558 fprintf(s->fpout, "# split0 cylinder radius %f nm, up %f nm, down %f nm\n",
1559 sc->cyl0r, sc->cyl0u, sc->cyl0l);
1560 fprintf(s->fpout, "# split1 cylinder radius %f nm, up %f nm, down %f nm\n",
1561 sc->cyl1r, sc->cyl1u, sc->cyl1l);
1566 fprintf(s->fpout, "#\n");
1569 fprintf(s->fpout, "# Coupling constant (number of swap attempt steps to average over): %d (translates to %f ps).\n",
1570 sc->nAverage, sc->nAverage*sc->nstswap*ir->delta_t);
1571 fprintf(s->fpout, "# Threshold is %f\n", sc->threshold);
1572 fprintf(s->fpout, "#\n");
1573 fprintf(s->fpout, "# Remarks about which atoms passed which channel use global atoms numbers starting at one.\n");
1582 /* Prepare for parallel or serial run */
1585 for (ig = 0; ig < eGrpNr; ig++)
1587 g = &(s->group[ig]);
1595 for (ig = 0; ig < eGrpNr; ig++)
1597 g = &(s->group[ig]);
1598 g->nat_loc = g->nat;
1599 g->ind_loc = g->ind;
1600 /* c_ind_loc needs to be set to identity in the serial case */
1601 for (i = 0; i < g->nat; i++)
1603 g->c_ind_loc[i] = i;
1608 /* Allocate memory for the ion counts time window */
1609 for (ic = 0; ic < eCompNR; ic++)
1611 for (ii = 0; ii < eIonNR; ii++)
1613 snew(s->comp[ic][ii].nat_past, sc->nAverage);
1617 /* Get the initial ion concentrations and let the other nodes know */
1620 swapstate->nions = s->group[eGrpIons].nat;
1624 get_initial_ioncounts_from_cpt(ir, swapstate, cr, bVerbose);
1628 fprintf(stderr, "%s Determining initial ion counts.\n", SwS);
1629 get_initial_ioncounts(ir, x, box, cr, bRerun);
1632 /* Prepare (further) checkpoint writes ... */
1635 /* Consistency check */
1636 if (swapstate->nAverage != sc->nAverage)
1638 gmx_fatal(FARGS, "%s Ion count averaging steps mismatch! checkpoint: %d, tpr: %d",
1639 SwS, swapstate->nAverage, sc->nAverage);
1644 swapstate->nAverage = sc->nAverage;
1646 fprintf(stderr, "%s Setting pointers for checkpoint writing\n", SwS);
1647 for (ic = 0; ic < eCompNR; ic++)
1649 for (ii = 0; ii < eIonNR; ii++)
1651 swapstate->nat_req_p[ic][ii] = &(s->comp[ic][ii].nat_req);
1652 swapstate->nat_past_p[ic][ii] = &(s->comp[ic][ii].nat_past[0]);
1653 swapstate->inflow_netto_p[ic][ii] = &(s->comp[ic][ii].inflow_netto);
1657 /* Determine the total charge imbalance */
1658 s->deltaQ = ( (-1) * s->comp[eCompA][eIonNEG].nat_req + s->comp[eCompA][eIonPOS].nat_req )
1659 - ( (-1) * s->comp[eCompB][eIonNEG].nat_req + s->comp[eCompB][eIonPOS].nat_req );
1663 fprintf(stderr, "%s Requested charge imbalance is Q(A) - Q(B) = %gz.\n", SwS, s->deltaQ);
1667 fprintf(s->fpout, "# Requested charge imbalance is Q(A)-Q(B) = %gz.\n", s->deltaQ);
1673 bc_initial_concentrations(cr, ir->swap);
1676 /* Put the time-averaged number of ions for all compartments */
1677 for (ic = 0; ic < eCompNR; ic++)
1679 for (ii = 0; ii < eIonNR; ii++)
1681 update_time_window(&(s->comp[ic][ii]), sc->nAverage, -1);
1685 /* Initialize arrays that keep track of through which channel the ions go */
1686 detect_flux_per_channel_init(cr, s, swapstate, bStartFromCpt);
1688 /* We need to print the legend if we open this file for the first time. */
1689 if (MASTER(cr) && !bAppend)
1691 print_ionlist_legend(ir, oenv);
1696 extern void dd_make_local_swap_groups(gmx_domdec_t *dd, t_swapcoords *sc)
1702 /* Make ion group, split groups and solvent group */
1703 for (ig = 0; ig < eGrpNr; ig++)
1705 g = &(sc->si_priv->group[ig]);
1706 dd_make_local_group_indices(dd->ga2la, g->nat, g->ind,
1707 &(g->nat_loc), &(g->ind_loc), &(g->nalloc_loc), g->c_ind_loc);
1712 /*! \brief Do we need to swap ions with water molecules at this step?
1714 * From the requested and average ion counts we determine whether a swap is needed
1715 * at this time step.
1717 static gmx_bool need_swap(t_swapcoords *sc)
1724 for (ic = 0; ic < eCompNR; ic++)
1726 for (ii = 0; ii < eIonNR; ii++)
1728 if (s->comp[ic][ii].nat_req - s->comp[ic][ii].nat_av >= sc->threshold)
1738 /*! \brief Return index of atom that we can use for swapping.
1740 * Returns the index of an atom that is far off the compartment boundaries.
1741 * Other atoms of the molecule (if any) will directly follow the returned index
1743 static int get_index_of_distant_atom(
1744 t_compartment *comp,
1745 int apm) /* Atoms per molecule - just return the first atom index of a molecule */
1748 real d = GMX_REAL_MAX;
1751 /* comp->nat contains the original number of atoms in this compartment
1752 * prior to doing any swaps. Some of these atoms may already have been
1753 * swapped out, but then they are marked with a distance of GMX_REAL_MAX
1755 for (i = 0; i < comp->nat_old; i += apm)
1757 if (comp->dist[i] < d)
1760 d = comp->dist[ibest];
1766 gmx_fatal(FARGS, "Could not get index of swap atom. Compartment atoms %d before swaps, atoms per molecule %d.",
1767 comp->nat_old, apm);
1770 /* Set the distance of this index to infinity such that it won't get selected again in
1773 comp->dist[ibest] = GMX_REAL_MAX;
1775 return comp->ind[ibest];
1779 /*! \brief Swaps centers of mass and makes molecule whole if broken */
1780 static void translate_positions(
1788 rvec reference, dx, correctPBCimage;
1791 /* Use the first atom as the reference for PBC */
1792 copy_rvec(x[0], reference);
1794 for (i = 0; i < apm; i++)
1796 /* PBC distance between position and reference */
1797 pbc_dx(pbc, x[i], reference, dx);
1799 /* Add PBC distance to reference */
1800 rvec_add(reference, dx, correctPBCimage);
1802 /* Subtract old_com from correct image and add new_com */
1803 rvec_dec(correctPBCimage, old_com);
1804 rvec_inc(correctPBCimage, new_com);
1806 copy_rvec(correctPBCimage, x[i]);
1811 /*! \brief Write back the the modified local positions from the collective array to the official positions. */
1812 static void apply_modified_positions(
1819 for (l = 0; l < g->nat_loc; l++)
1821 /* Get the right local index to write to */
1823 /* Where is the local atom in the collective array? */
1824 cind = g->c_ind_loc[l];
1826 /* Copy the possibly modified position */
1827 copy_rvec(g->xc[cind], x[ii]);
1832 extern gmx_bool do_swapcoords(
1837 gmx_wallcycle_t wcycle,
1846 int j, ii, ic, ig, im, gmax, nswaps;
1847 gmx_bool bSwap = FALSE;
1849 real vacancy[eCompNR][eIonNR];
1851 rvec solvent_center, ion_center;
1853 gmx_mtop_atomlookup_t alook = NULL;
1856 wallcycle_start(wcycle, ewcSWAP);
1861 /* Assemble all the positions of the swap group (ig = 0), the split groups
1862 * (ig = 1,2), and possibly the solvent group (ig = 3) */
1865 for (ig = 0; ig < gmax; ig++)
1867 g = &(s->group[ig]);
1868 if (eGrpSplit0 == ig || eGrpSplit1 == ig)
1870 /* The split groups, i.e. the channels. Here we need the full
1871 * communicate_group_positions(), so that we can make the molecules
1872 * whole even in cases where they span more than half of the box in
1874 communicate_group_positions(cr, g->xc, g->xc_shifts, g->xc_eshifts, TRUE,
1875 x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, g->xc_old, box);
1877 get_center(g->xc, g->m, g->nat, g->center); /* center of split groups == channels */
1881 /* Swap group (ions), and solvent group. These molecules are small
1882 * and we can always make them whole with a simple distance check.
1883 * Therefore we pass NULL as third argument. */
1884 communicate_group_positions(cr, g->xc, NULL, NULL, FALSE,
1885 x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, NULL, NULL);
1889 /* Set up the compartments and get lists of atoms in each compartment,
1890 * determine how many ions each compartment contains */
1891 compartmentalize_ions(cr, sc, box, step, s->fpout, bRerun);
1893 /* Output how many ions are in the compartments */
1896 print_ionlist(s, t, "");
1899 /* If we are doing a rerun, we are finished here, since we cannot perform
1906 /* Do we have to perform a swap? */
1907 bSwap = need_swap(sc);
1910 g = &(s->group[eGrpSolvent]);
1911 communicate_group_positions(cr, g->xc, NULL, NULL, FALSE,
1912 x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, NULL, NULL);
1914 compartmentalize_solvent(cr, sc, box, s->fpout);
1916 /* Determine where ions are missing and where ions are too many */
1917 for (ic = 0; ic < eCompNR; ic++)
1919 for (ii = 0; ii < eIonNR; ii++)
1921 vacancy[ic][ii] = s->comp[ic][ii].nat_req - s->comp[ic][ii].nat_av;
1925 /* Remember the original number of ions per compartment */
1926 for (ic = 0; ic < eCompNR; ic++)
1928 s->compsol[ic].nat_old = s->compsol[ic].nat;
1929 for (ii = 0; ii < eIonNR; ii++)
1931 s->comp[ic][ii].nat_old = s->comp[ic][ii].nat;
1935 /* Now actually correct the number of ions */
1936 g = &(s->group[eGrpSolvent]);
1938 alook = gmx_mtop_atomlookup_init(mtop);
1939 for (ic = 0; ic < eCompNR; ic++)
1941 for (ii = 0; ii < eIonNR; ii++)
1943 while (vacancy[ic][ii] >= sc->threshold)
1945 /* Swap in an ion */
1947 /* Get the xc-index of the first atom of a solvent molecule of this compartment */
1948 isol = get_index_of_distant_atom(&(s->compsol[ic]), s->group[eGrpSolvent].apm );
1950 /* Get the xc-index of an ion from the other compartment */
1951 iion = get_index_of_distant_atom(&(s->comp[(ic+1)%eCompNR][ii]), s->group[eGrpIons].apm );
1953 /* Get the solvent molecule's center of mass */
1954 for (im = 0; im < s->group[eGrpSolvent].apm; im++)
1956 gmx_mtop_atomnr_to_atom(alook, s->group[eGrpSolvent].ind[isol+im], &atom);
1957 s->group[eGrpSolvent].m[im] = atom->m;
1959 get_molecule_center(&(s->group[eGrpSolvent].xc[isol]), s->group[eGrpSolvent].apm, s->group[eGrpSolvent].m, solvent_center, s->pbc);
1960 get_molecule_center(&(s->group[eGrpIons ].xc[iion]), s->group[eGrpIons ].apm, NULL, ion_center, s->pbc);
1962 /* subtract com_solvent and add com_ion */
1963 translate_positions(&(s->group[eGrpSolvent].xc[isol]), s->group[eGrpSolvent].apm, solvent_center, ion_center, s->pbc);
1964 /* For the ion, subtract com_ion and add com_solvent */
1965 translate_positions(&(s->group[eGrpIons ].xc[iion]), s->group[eGrpIons ].apm, ion_center, solvent_center, s->pbc);
1968 vacancy[(ic+1) % eCompNR][ii]++;
1970 /* Keep track of the changes */
1971 s->comp[ic ][ii].nat++;
1972 s->comp[(ic+1) % eCompNR][ii].nat--;
1973 s->comp[ic ][ii].inflow_netto++;
1974 s->comp[(ic+1) % eCompNR][ii].inflow_netto--;
1975 /* Correct the past time window to still get the right averages from now on */
1976 s->comp[ic ][ii].nat_av++;
1977 s->comp[(ic+1) % eCompNR][ii].nat_av--;
1978 for (j = 0; j < sc->nAverage; j++)
1980 s->comp[ic ][ii].nat_past[j]++;
1981 s->comp[(ic+1) % eCompNR][ii].nat_past[j]--;
1983 /* Clear ion history */
1986 s->group[eGrpIons].channel_label[iion] = eChHistPassedNone;
1987 s->group[eGrpIons].comp_from[iion] = eDomainNotset;
1989 /* That was the swap */
1994 gmx_mtop_atomlookup_destroy(alook);
1998 fprintf(stderr, "%s Performed %d swap%s in step %"GMX_PRId64 ".\n", SwS, nswaps, nswaps > 1 ? "s" : "", step);
2000 if (s->fpout != NULL)
2002 print_ionlist(s, t, " # after swap");
2005 /* Write back the the modified local positions from the collective array to the official coordinates */
2006 apply_modified_positions(&(s->group[eGrpIons ]), x);
2007 apply_modified_positions(&(s->group[eGrpSolvent]), x);
2008 } /* end of if(bSwap) */
2010 wallcycle_stop(wcycle, ewcSWAP);