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37 * Implements functions in swapcoords.h.
39 * \author Carsten Kutzner <ckutzne@gwdg.de>
40 * \ingroup module_swap
53 #include "gromacs/mdlib/groupcoord.h"
54 #include "mtop_util.h"
62 #include "gromacs/fileio/confio.h"
63 #include "gromacs/timing/wallcycle.h"
64 #include "swapcoords.h"
66 static char *SwS = {"SWAP:"}; /**< For output that comes from the swap module */
67 static char *SwSEmpty = {" "}; /**< Placeholder for multi-line output */
68 static char* IonString[eIonNR] = {"anion", "cation" }; /**< Type of ion, used for verbose output */
69 static char* IonStr[eIonNR] = {"-", "+" }; /**< Type of ion, used for short output */
70 static char* CompStr[eCompNR] = {"A", "B" }; /**< Compartment name */
71 static char *SwapStr[eSwapTypesNR+1] = { "", "X-", "Y-", "Z-", NULL}; /**< Name for the swap types. */
72 static char *DimStr[DIM+1] = { "X", "Y", "Z", NULL}; /**< Name for the swap dimension. */
74 /* eGrpSplit0 and eGrpSplit1 _must_ be neighbors in this list because
75 * we sometimes loop from eGrpSplit0 to eGrpSplit1 */
77 eGrpIons, eGrpSplit0, eGrpSplit1, eGrpSolvent, eGrpNr
78 }; /**< Group identifier */
79 static char* GrpString[eGrpNr] = { "ion", "split0", "split1", "solvent" }; /**< Group name */
81 /** Keep track of through which channel the ions have passed */
82 enum eChannelHistory {
83 eChHistPassedNone, eChHistPassedCh0, eChHistPassedCh1, eChHistNr
85 static char* ChannelString[eChHistNr] = { "none", "channel0", "channel1" }; /**< Name for the channels */
87 /*! \brief Domain identifier.
89 * Keeps track of from which compartment the ions came before passing the
93 eDomainNotset, eDomainA, eDomainB, eDomainNr
95 static char* DomainString[eDomainNr] = { "not_assigned", "Domain_A", "Domain_B" }; /**< Name for the domains */
100 * Structure containing compartment-specific data
102 typedef struct swap_compartment
104 int nat; /**< Number of atoms matching the
105 compartment conditions. */
106 int nat_old; /**< Number of atoms before swapping. */
107 int nat_req; /**< Requested number of atoms. */
108 real nat_av; /**< Time-averaged number of atoms matching
109 the compartment conditions. */
110 int *nat_past; /**< Past ion counts for time-averaging. */
111 int *ind; /**< Indices to coll array of atoms. */
112 real *dist; /**< Distance of atom to compartment center. */
113 int nalloc; /**< Allocation size for ind array. */
114 int inflow_netto; /**< Net inflow of ions into this compartment. */
119 * This structure contains data needed for each of the groups involved in swapping: ions, water,
122 typedef struct swap_group
124 int nat; /**< Number of atoms in the group */
125 int apm; /**< Number of atoms in each molecule */
126 atom_id *ind; /**< Global atom indices of the group */
127 atom_id *ind_loc; /**< Local atom indices of the group */
128 int nat_loc; /**< Number of local group atoms */
129 int nalloc_loc; /**< Allocation size for ind_loc */
130 rvec *xc; /**< Collective array of group atom positions */
131 ivec *xc_shifts; /**< Current (collective) shifts */
132 ivec *xc_eshifts; /**< Extra shifts since last DD step */
133 rvec *xc_old; /**< Old (collective) positions */
134 real *qc; /**< Collective array of charges */
135 int *c_ind_loc; /**< Position of local atoms in the
136 collective array, [0..nat_loc] */
137 real *m; /**< Masses (can be omitted) */
138 unsigned char *comp_from; /**< (Collective) Stores from which compartment this
139 atom has come. This way we keep track of through
140 which channel an ion permeates (only used for
142 unsigned char *comp_now; /**< In which compartment this ion is now */
143 unsigned char *channel_label; /**< Which channel was passed at last by this ion? */
144 rvec center; /**< Center of the group; COM if masses are used */
149 * Main (private) data structure for the position swapping protocol.
153 int swapdim; /**< One of XX, YY, ZZ */
154 t_pbc *pbc; /**< Needed to make molecules whole. */
155 FILE *fpout; /**< Output file. */
156 t_group group[eGrpNr]; /**< Ions, solvent or channels? */
157 t_compartment comp[eCompNR][eIonNR]; /**< Data for a specific compartment and ion type. */
158 t_compartment compsol[eCompNR]; /**< Solvent compartments. */
159 int fluxfromAtoB[eChanNR][eIonNR]; /**< Net flux per channels and ion type. */
160 int ncyl0ions; /**< Number of ions residing in channel 0. */
161 int ncyl1ions; /**< Same for channel 1. */
162 int cyl0and1; /**< Ions assigned to cyl0 and cyl1. Not good. */
163 int *fluxleak; /**< Pointer to a single int value holding the
164 flux not going through any of the channels. */
165 real deltaQ; /**< The charge imbalance between the compartments. */
170 /*! Check whether point is in channel. Channel is a cylinder defined by a disc
171 * with radius r around its center c. The thickness of the cylinder is
178 * <---------c--------->
184 static gmx_bool is_in_channel(
185 rvec point, /* Point under consideration */
186 rvec center, /* 'Center' of cylinder */
187 real d_up, /* Upper extension */
188 real d_down, /* Lower extensions */
189 real r_cyl2, /* Cylinder radius squared */
191 int normal) /* The membrane normal direction is typically 3, i.e. ZZ, but can be X or Y also */
194 int plane1, plane2; /* Directions tangential to membrane */
197 plane1 = (normal + 1) % 3; /* typically 0, i.e. XX */
198 plane2 = (normal + 2) % 3; /* typically 1, i.e. YY */
200 /* Get the distance vector dr between the point and the center of the cylinder */
201 pbc_dx(pbc, point, center, dr); /* This puts center in the origin */
203 /* Check vertical direction */
204 if ( (dr[normal] > d_up) || (dr[normal] < -d_down) )
209 /* Check radial direction */
210 if ( (dr[plane1]*dr[plane1] + dr[plane2]*dr[plane2]) > r_cyl2)
215 /* All check passed, this point is in the cylinder */
220 /*! Prints to swap output file which ions are in which compartments. */
221 static void print_ionlist(
226 int itype, icomp, i, j;
230 fprintf(s->fpout, "%12.5e", time);
231 for (icomp = 0; icomp < eCompNR; icomp++)
233 for (itype = 0; itype < eIonNR; itype++)
235 comp = &(s->comp[icomp][itype]);
236 fprintf(s->fpout, "%7d%7.1f%7d", comp->nat, comp->nat_av-comp->nat_req, comp->inflow_netto);
239 fprintf(s->fpout, "%12.3e%12.3e",
240 s->group[eGrpSplit0].center[s->swapdim],
241 s->group[eGrpSplit1].center[s->swapdim]);
243 for (i = 0; i < eChanNR; i++)
245 for (j = 0; j < eIonNR; j++)
247 fprintf(s->fpout, "%12d", s->fluxfromAtoB[i][j]);
251 /* Also print the number of ions that leaked from A to B: */
252 fprintf(s->fpout, "%12d", *s->fluxleak);
254 fprintf(s->fpout, "%s\n", comment);
258 /*! Get the center of a group of nat atoms. Since with PBC an atom group might
259 * not be whole, Use the first atom as the reference atom and determine the
260 * center with respect to this reference. */
261 static void get_molecule_center(
269 rvec weightedPBCimage;
271 rvec reference, correctPBCimage, dx;
274 /* Use the first atom as the reference and put other atoms near that one */
275 /* This does not work for large molecules that span > half of the box! */
276 copy_rvec(x[0], reference);
278 /* Calculate either the weighted center or simply the center of geometry */
281 for (i = 0; i < nat; i++)
283 /* PBC distance between position and reference */
284 pbc_dx(pbc, x[i], reference, dx);
286 /* Add PBC distance to reference */
287 rvec_add(reference, dx, correctPBCimage);
289 /* Take weight into account */
299 svmul(wi, correctPBCimage, weightedPBCimage);
302 rvec_inc(center, weightedPBCimage);
306 svmul(1.0/wsum, center, center);
311 /*! Returns TRUE if x is between (w1+gap) and (w2-gap)
315 * ||-----------|--+--|----------o----------|--+--|---------------------||
316 * w1 ????????????????????? w2
320 static gmx_bool compartment_contains_atom(
321 real w1, /* position of wall atom 1 */
322 real w2, /* position of wall atom 2 */
325 real l, /* length of the box, from || to || in the sketch */
326 real *distance_from_center)
331 /* First set the origin in the middle of w1 and w2 */
337 /* Now choose the PBC image of x that is closest to the origin: */
348 *distance_from_center = (real)fabs(x);
350 /* Return TRUE if we now are in area "????" */
351 if ( (x >= (w1+gap)) && (x < (w2-gap)) )
362 /*! Updates the time-averaged number of ions in a compartment. */
363 static void update_time_window(t_compartment *comp, int values, int replace)
369 /* Put in the new value */
372 comp->nat_past[replace] = comp->nat;
375 /* Compute the new time-average */
377 for (i = 0; i < values; i++)
379 average += comp->nat_past[i];
382 comp->nat_av = average;
386 /*! Add atom with collective index ci to the list 'comp' */
387 static void add_to_list(
388 int ci, /* index of this ion in the collective array xc, qc */
389 t_compartment *comp, /* Compartment to add this atom to */
390 real distance) /* Shortest distance of this atom to the compartment center */
397 if (nr >= comp->nalloc)
399 comp->nalloc = over_alloc_dd(nr+1);
400 srenew(comp->ind, comp->nalloc);
401 srenew(comp->dist, comp->nalloc);
404 comp->dist[nr] = distance;
409 /*! Determine the compartment boundaries from the channel centers. */
410 static void get_compartment_boundaries(
414 real *left, real *right)
417 real leftpos, rightpos, leftpos_orig;
422 gmx_fatal(FARGS, "No compartment %d.", c);
425 pos0 = s->group[eGrpSplit0].center[s->swapdim];
426 pos1 = s->group[eGrpSplit1].center[s->swapdim];
439 /* This gets us the other compartment: */
442 leftpos_orig = leftpos;
444 rightpos = leftpos_orig + box[s->swapdim][s->swapdim];
452 /*! To determine the flux through the individual channels, we
453 * remember the compartment and channel history of each ion. An ion can be
454 * either in channel0 or channel1, or in the remaining volume of compartment
458 * +-----------------+
461 * ||||||||||0|||||||| bilayer with channel 0
466 * |||||1||||||||||||| bilayer with channel 1
469 * +-----------------+
473 static void detect_flux_per_channel(
478 unsigned char *comp_now,
479 unsigned char *comp_from,
480 unsigned char *channel_label,
490 gmx_bool in_cyl0, in_cyl1;
497 /* Check whether ion is inside any of the channels */
498 in_cyl0 = is_in_channel(ion_pos, s->group[eGrpSplit0].center, sc->cyl0u, sc->cyl0l, cyl0_r2, s->pbc, sd);
499 in_cyl1 = is_in_channel(ion_pos, s->group[eGrpSplit1].center, sc->cyl1u, sc->cyl1l, cyl1_r2, s->pbc, sd);
501 if (in_cyl0 && in_cyl1)
503 /* Ion appears to be in both channels. Something is severely wrong! */
505 *comp_now = eDomainNotset;
506 *comp_from = eDomainNotset;
507 *channel_label = eChHistPassedNone;
511 /* Ion is in channel 0 now */
512 *channel_label = eChHistPassedCh0;
513 *comp_now = eDomainNotset;
518 /* Ion is in channel 1 now */
519 *channel_label = eChHistPassedCh1;
520 *comp_now = eDomainNotset;
525 /* Ion is not in any of the channels, so it must be in domain A or B */
528 *comp_now = eDomainA;
532 *comp_now = eDomainB;
536 /* Only take action, if ion is now in domain A or B, and was before
537 * in the other domain!
539 if (eDomainNotset == *comp_from)
541 /* Maybe we can set the domain now */
542 *comp_from = *comp_now; /* Could still be eDomainNotset, though */
544 else if ( (*comp_now != eDomainNotset ) /* if in channel */
545 && (*comp_from != *comp_now) )
547 /* Obviously the ion changed its domain.
548 * Count this for the channel through which it has passed. */
549 switch (*channel_label)
551 case eChHistPassedNone:
552 *s->fluxleak = *s->fluxleak + 1;
554 fprintf(stderr, " %s Warning! Step %s, ion %d (%s) moved from %s to %s\n",
555 SwS, gmx_step_str(step, buf), iion, IonStr[iontype], DomainString[*comp_from], DomainString[*comp_now]);
558 fprintf(stderr, ", possibly due to a swap in the original simulation.\n");
562 fprintf(stderr, "but did not pass cyl0 or cyl1 as defined in the .mdp file.\n"
563 "Do you have an ion somewhere within the membrane?\n");
564 /* Write this info to the CompEL output file: */
565 fprintf(s->fpout, " # Warning: step %s, ion %d (%s) moved from %s to %s (probably through the membrane)\n",
566 gmx_step_str(step, buf), iion, IonStr[iontype],
567 DomainString[*comp_from], DomainString[*comp_now]);
571 case eChHistPassedCh0:
572 case eChHistPassedCh1:
573 if (*channel_label == eChHistPassedCh0)
582 if (eDomainA == *comp_from)
584 s->fluxfromAtoB[chan_nr][iontype]++;
588 s->fluxfromAtoB[chan_nr][iontype]--;
590 fprintf(fpout, "# Atom nr. %d finished passing %s.\n", iion, ChannelString[*channel_label]);
593 gmx_fatal(FARGS, "%s Unknown channel history entry!\n", SwS);
597 /* This ion has moved to the _other_ compartment ... */
598 *comp_from = *comp_now;
599 /* ... and it did not pass any channel yet */
600 *channel_label = eChHistPassedNone;
605 /*! Get the lists of ions for the two compartments */
606 static void compartmentalize_ions(
619 real cyl0_r2, cyl1_r2;
621 int sum, not_in_comp[eCompNR]; /* consistency check */
626 iong = &s->group[eGrpIons];
629 cyl0_r2 = sc->cyl0r * sc->cyl0r;
630 cyl1_r2 = sc->cyl1r * sc->cyl1r;
633 /* Get us a counter that cycles in the range of [0 ... sc->nAverage[ */
634 replace = (step/sc->nstswap) % sc->nAverage;
636 for (comp = eCompA; comp <= eCompB; comp++)
638 /* Get lists of atoms that match criteria for this compartment */
639 get_compartment_boundaries(comp, sc->si_priv, box, &left, &right);
641 /* First clear the ion lists */
642 s->comp[comp][eIonNEG].nat = 0;
643 s->comp[comp][eIonPOS].nat = 0;
644 not_in_comp[comp] = 0; /* consistency check */
646 /* Loop over the IONS */
647 for (i = 0; i < iong->nat; i++)
649 /* Anion or cation? */
650 type = iong->qc[i] < 0 ? eIonNEG : eIonPOS;
652 /* Is this ion in the compartment that we look at? */
653 if (compartment_contains_atom(left, right, 0, iong->xc[i][sd], box[sd][sd], &dist) )
655 /* Now put it into the list containing only ions of its type */
656 add_to_list(i, &s->comp[comp][type], dist);
658 /* Master also checks through which channel each ion has passed */
659 if (MASTER(cr) && (iong->comp_now != NULL))
661 ion_nr_global = iong->ind[i] + 1; /* PDB index starts at 1 ... */
662 detect_flux_per_channel(ion_nr_global, comp, type, iong->xc[i],
663 &iong->comp_now[i], &iong->comp_from[i], &iong->channel_label[i],
664 sc, cyl0_r2, cyl1_r2, step, bRerun, fpout);
669 not_in_comp[comp] += 1;
672 /* Correct the time-averaged number of ions in both compartments */
673 update_time_window(&s->comp[comp][eIonNEG], sc->nAverage, replace);
674 update_time_window(&s->comp[comp][eIonPOS], sc->nAverage, replace);
677 /* Flux detection warnings */
683 "%s Warning: %d atoms were detected as being in both channels! Probably your split\n"
684 "%s cylinder is way too large, or one compartment has collapsed (step %"GMX_PRId64 ")\n",
685 SwS, s->cyl0and1, SwS, step);
687 fprintf(s->fpout, "Warning: %d atoms were assigned to both channels!\n", s->cyl0and1);
694 /* Consistency checks */
695 if (not_in_comp[eCompA] + not_in_comp[eCompB] != iong->nat)
699 fprintf(fpout, "# Warning: Inconsistency during ion compartmentalization. !inA: %d, !inB: %d, total ions %d\n",
700 not_in_comp[eCompA], not_in_comp[eCompB], iong->nat);
705 fprintf(stderr, "%s node %d: Inconsistency during ion compartmentalization. !inA: %d, !inB: %d, total ions %d\n",
706 SwS, cr->nodeid, not_in_comp[eCompA], not_in_comp[eCompB], iong->nat);
710 sum = s->comp[eCompA][eIonNEG].nat + s->comp[eCompA][eIonPOS].nat
711 + s->comp[eCompB][eIonNEG].nat + s->comp[eCompB][eIonPOS].nat;
712 if (sum != iong->nat)
716 fprintf(fpout, "# Warning: %d atoms are in the ion group, but altogether %d have been assigned to the compartments.\n",
722 fprintf(stderr, "%s node %d: %d atoms are in the ion group, but altogether %d have been assigned to the compartments.\n",
723 SwS, cr->nodeid, iong->nat, sum);
731 /*! Set up the compartments and get lists of solvent atoms in each compartment */
732 static void compartmentalize_solvent(
744 int sum, not_in_comp[eCompNR]; /* consistency check */
748 solg = &s->group[eGrpSolvent];
752 for (comp = eCompA; comp <= eCompB; comp++)
754 /* Get lists of atoms that match criteria for this compartment */
755 get_compartment_boundaries(comp, sc->si_priv, box, &left, &right);
757 /* First clear the solvent molecule lists */
758 s->compsol[comp].nat = 0;
759 not_in_comp[comp] = 0; /* consistency check */
761 /* Loop over the solvent MOLECULES */
762 for (i = 0; i < sc->nat_sol; i += apm)
764 if (compartment_contains_atom(left, right, 0, solg->xc[i][sd], box[sd][sd], &dist))
766 /* Add the whole molecule to the list */
767 for (j = 0; j < apm; j++)
769 add_to_list(i+j, &s->compsol[comp], dist);
774 not_in_comp[comp] += apm;
781 fprintf(fpout, "# Solv. molecules in comp.%s: %d comp.%s: %d\n",
782 CompStr[eCompA], s->compsol[eCompA].nat/apm,
783 CompStr[eCompB], s->compsol[eCompB].nat/apm);
786 /* Consistency checks */
787 if (not_in_comp[eCompA] + not_in_comp[eCompB] != solg->nat)
791 fprintf(fpout, "# Warning: Inconsistency during solvent compartmentalization. !inA: %d, !inB: %d, solvent atoms %d\n",
792 not_in_comp[eCompA], not_in_comp[eCompB], solg->nat);
797 fprintf(stderr, "%s node %d: Inconsistency during solvent compartmentalization. !inA: %d, !inB: %d, solvent atoms %d\n",
798 SwS, cr->nodeid, not_in_comp[eCompA], not_in_comp[eCompB], solg->nat);
801 sum = s->compsol[eCompA].nat + s->compsol[eCompB].nat;
802 if (sum != solg->nat)
806 fprintf(fpout, "# Warning: %d atoms in solvent group, but %d have been assigned to the compartments.\n",
812 fprintf(stderr, "%s node %d: %d atoms in solvent group, but %d have been assigned to the compartments.\n",
813 SwS, cr->nodeid, solg->nat, sum);
819 /*! Find out how many group atoms are in the compartments initially */
820 static void get_initial_ioncounts(
822 rvec x[], /* the initial positions */
836 /* Copy the initial swap group positions to the collective array so
837 * that we can compartmentalize */
838 for (i = 0; i < sc->nat; i++)
841 copy_rvec(x[ind], s->group[eGrpIons].xc[i]);
844 /* Set up the compartments and get lists of atoms in each compartment */
845 compartmentalize_ions(cr, sc, box, 0, s->fpout, bRerun);
847 /* Set initial concentrations if requested */
848 for (ic = 0; ic < eCompNR; ic++)
850 s->comp[ic][eIonPOS].nat_req = sc->ncations[ic];
851 s->comp[ic][eIonNEG].nat_req = sc->nanions[ic];
853 for (ic = 0; ic < eCompNR; ic++)
855 for (ii = 0; ii < eIonNR; ii++)
857 if (s->comp[ic][ii].nat_req < 0)
859 s->comp[ic][ii].nat_req = s->comp[ic][ii].nat;
864 /* Check whether the number of requested ions adds up to the total number of ions */
865 for (ii = 0; ii < eIonNR; ii++)
867 req[ii] = s->comp[eCompA][ii].nat_req + s->comp[eCompB][ii].nat_req;
868 tot[ii] = s->comp[eCompA][ii].nat + s->comp[eCompB][ii].nat;
870 if ( (req[eCompA] != tot[eCompA]) || (req[eCompB] != tot[eCompB ]) )
872 gmx_fatal(FARGS, "Mismatch of the number of ions summed over both compartments.\n"
873 "You requested a total of %d anions and %d cations,\n"
874 "but there are a total of %d anions and %d cations in the system.\n",
875 req[eIonNEG], req[eIonPOS],
876 tot[eIonNEG], tot[eIonPOS]);
879 /* Initialize time-averaging:
880 * Write initial concentrations to all time bins to start with */
881 for (ic = 0; ic < eCompNR; ic++)
883 for (ii = 0; ii < eIonNR; ii++)
885 s->comp[ic][ii].nat_av = s->comp[ic][ii].nat;
886 for (i = 0; i < sc->nAverage; i++)
888 s->comp[ic][ii].nat_past[i] = s->comp[ic][ii].nat;
895 /*! When called, the checkpoint file has already been read in. Here we copy
896 * over the values from .cpt file to the swap data structure.
898 static void get_initial_ioncounts_from_cpt(
899 t_inputrec *ir, swapstate_t *swapstate,
900 t_commrec *cr, gmx_bool bVerbose)
911 /* Copy the past values from the checkpoint values that have been read in already */
914 fprintf(stderr, "%s Copying values from checkpoint\n", SwS);
917 for (ic = 0; ic < eCompNR; ic++)
919 for (ii = 0; ii < eIonNR; ii++)
921 s->comp[ic][ii].nat_req = swapstate->nat_req[ic][ii];
922 s->comp[ic][ii].inflow_netto = swapstate->inflow_netto[ic][ii];
926 fprintf(stderr, "%s ... Influx netto: %d Requested: %d Past values: ", SwS,
927 s->comp[ic][ii].inflow_netto, s->comp[ic][ii].nat_req);
930 for (j = 0; j < sc->nAverage; j++)
932 s->comp[ic][ii].nat_past[j] = swapstate->nat_past[ic][ii][j];
935 fprintf(stderr, "%d ", s->comp[ic][ii].nat_past[j]);
940 fprintf(stderr, "\n");
948 /*! Master node lets all other nodes know about the initial ion counts. */
949 static void bc_initial_concentrations(
958 for (ic = 0; ic < eCompNR; ic++)
960 for (ii = 0; ii < eIonNR; ii++)
962 gmx_bcast(sizeof(s->comp[ic][ii].nat_req), &(s->comp[ic][ii].nat_req), cr);
963 gmx_bcast(sizeof(s->comp[ic][ii].nat ), &(s->comp[ic][ii].nat ), cr);
964 gmx_bcast( swap->nAverage * sizeof(s->comp[ic][ii].nat_past[0]), s->comp[ic][ii].nat_past, cr);
970 /*! Ensure that each atom belongs to at most one of the swap groups. */
971 static void check_swap_groups(t_swap *s, int nat, gmx_bool bVerbose)
975 atom_id *nGroup = NULL; /* This array counts for each atom in the MD system to
976 how many swap groups it belongs (should be 0 or 1!) */
978 int nMultiple = 0; /* Number of atoms belonging to multiple groups */
983 fprintf(stderr, "%s Making sure each atom belongs to at most one of the swap groups.\n", SwS);
986 /* Add one to the group count of atoms belonging to a swap group: */
988 for (i = 0; i < eGrpNr; i++)
991 for (j = 0; j < g->nat; j++)
993 /* Get the global index of this atom of this group: */
998 /* Make sure each atom belongs to at most one swap group: */
999 for (j = 0; j < g->nat; j++)
1010 gmx_fatal(FARGS, "%s Cannot perform swapping since %d atom%s allocated to more than one swap index group.\n"
1011 "%s Each atom must be allocated to at most one of the split groups, the swap group, or the solvent.\n"
1012 "%s Check the .mdp file settings regarding the swap index groups or the index groups themselves.\n",
1013 SwS, nMultiple, (1 == nMultiple) ? " is" : "s are", SwSEmpty, SwSEmpty);
1018 /*! Get the number of atoms per molecule for this group.
1019 * Also ensure that all the molecules in this group have this number of atoms. */
1020 static int get_group_apm_check(
1024 const gmx_mtop_atomlookup_t alook,
1029 int molb, molnr, atnr_mol;
1032 ind = s->group[group].ind;
1033 nat = s->group[group].nat;
1035 /* Determine the number of solvent atoms per solvent molecule from the
1036 * first solvent atom: */
1038 gmx_mtop_atomnr_to_molblock_ind(alook, ind[i], &molb, &molnr, &atnr_mol);
1039 apm = mtop->molblock[molb].natoms_mol;
1043 fprintf(stderr, "%s Checking whether all %s molecules consist of %d atom%s\n",
1044 SwS, GrpString[group], apm, apm > 1 ? "s" : "");
1047 /* Check whether this is also true for all other solvent atoms */
1048 for (i = 1; i < nat; i++)
1050 gmx_mtop_atomnr_to_molblock_ind(alook, ind[i], &molb, &molnr, &atnr_mol);
1051 if (apm != mtop->molblock[molb].natoms_mol)
1053 gmx_fatal(FARGS, "Not all %s group molecules consist of %d atoms.",
1054 GrpString[group], apm);
1062 /*! Print the legend to the swapcoords output file as well as the
1063 * initial ion counts */
1064 static void print_ionlist_legend(t_inputrec *ir, const output_env_t oenv)
1066 const char **legend;
1072 s = ir->swap->si_priv;
1074 snew(legend, eCompNR*eIonNR*3 + 2 + eChanNR*eIonNR + 1);
1075 for (ic = count = 0; ic < eCompNR; ic++)
1077 for (ii = 0; ii < eIonNR; ii++)
1079 sprintf(buf, "%s %ss", CompStr[ic], IonString[ii]);
1080 legend[count++] = gmx_strdup(buf);
1081 sprintf(buf, "%s av. mismatch to %d%s",
1082 CompStr[ic], s->comp[ic][ii].nat_req, IonStr[ii]);
1083 legend[count++] = gmx_strdup(buf);
1084 sprintf(buf, "%s netto %s influx", CompStr[ic], IonString[ii]);
1085 legend[count++] = gmx_strdup(buf);
1088 sprintf(buf, "%scenter of %s of split group 0", SwapStr[ir->eSwapCoords], (NULL != s->group[eGrpSplit0].m) ? "mass" : "geometry");
1089 legend[count++] = gmx_strdup(buf);
1090 sprintf(buf, "%scenter of %s of split group 1", SwapStr[ir->eSwapCoords], (NULL != s->group[eGrpSplit1].m) ? "mass" : "geometry");
1091 legend[count++] = gmx_strdup(buf);
1093 for (ic = 0; ic < eChanNR; ic++)
1095 for (ii = 0; ii < eIonNR; ii++)
1097 sprintf(buf, "A->ch%d->B %s permeations", ic, IonString[ii]);
1098 legend[count++] = gmx_strdup(buf);
1102 sprintf(buf, "leakage");
1103 legend[count++] = gmx_strdup(buf);
1105 xvgr_legend(s->fpout, count, legend, oenv);
1107 fprintf(s->fpout, "# Instantaneous ion counts and time-averaged differences to requested numbers\n");
1108 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 ");
1109 fprintf(s->fpout, " %s-Split0 %s-Split1", DimStr[s->swapdim], DimStr[s->swapdim]);
1110 fprintf(s->fpout, " A-ch0-B_an A-ch0-B_cat A-ch1-B_an A-ch1-B_cat ion_leakage\n");
1115 /*! Initialize arrays that keep track of where the ions come from and where
1117 static void detect_flux_per_channel_init(
1120 swapstate_t *swapstate,
1121 gmx_bool bStartFromCpt)
1127 g = &(s->group[eGrpIons]);
1129 /* All these flux detection routines run on the master only */
1133 g->comp_from = NULL;
1134 g->channel_label = NULL;
1139 /******************************************************/
1140 /* Channel and domain history for the individual ions */
1141 /******************************************************/
1142 if (bStartFromCpt) /* set the pointers right */
1144 g->comp_from = swapstate->comp_from;
1145 g->channel_label = swapstate->channel_label;
1147 else /* allocate memory */
1149 snew(g->comp_from, g->nat);
1150 swapstate->comp_from = g->comp_from;
1151 snew(g->channel_label, g->nat);
1152 swapstate->channel_label = g->channel_label;
1154 snew(g->comp_now, g->nat);
1156 /* Initialize the channel and domain history counters */
1157 for (i = 0; i < g->nat; i++)
1159 g->comp_now[i] = eDomainNotset;
1162 g->comp_from[i] = eDomainNotset;
1163 g->channel_label[i] = eChHistPassedNone;
1167 /************************************/
1168 /* Channel fluxes for both channels */
1169 /************************************/
1176 fprintf(stderr, "%s Copying channel fluxes from checkpoint file data\n", SwS);
1179 for (ic = 0; ic < eChanNR; ic++)
1181 fprintf(stderr, "%s Channel %d flux history: ", SwS, ic);
1182 for (ii = 0; ii < eIonNR; ii++)
1186 s->fluxfromAtoB[ic][ii] = swapstate->fluxfromAtoB[ic][ii];
1190 s->fluxfromAtoB[ic][ii] = 0;
1193 fprintf(stderr, "%d %s%s ", s->fluxfromAtoB[ic][ii], IonString[ii], s->fluxfromAtoB[ic][ii] == 1 ? "" : "s");
1195 fprintf(stderr, "\n");
1199 s->fluxleak = swapstate->fluxleak;
1203 snew(s->fluxleak, 1);
1205 /* Set pointer for checkpoint writing */
1206 swapstate->fluxleak = s->fluxleak;
1209 /* Set pointers for checkpoint writing */
1210 for (ic = 0; ic < eChanNR; ic++)
1212 for (ii = 0; ii < eIonNR; ii++)
1214 swapstate->fluxfromAtoB_p[ic][ii] = &(s->fluxfromAtoB[ic][ii]);
1220 /*! Output the starting structure so that in case of multimeric channels
1221 * the user can check whether we have the correct PBC image for all atoms.
1222 * If this is not correct, the ion counts per channel will be very likely
1224 static void outputStartStructureIfWanted(gmx_mtop_t *mtop, rvec *x, int ePBC, matrix box)
1226 char *env = getenv("GMX_COMPELDUMP");
1230 fprintf(stderr, "\n%s Found env.var. GMX_COMPELDUMP, will output CompEL starting structure made whole.\n"
1231 "%s In case of multimeric channels, please check whether they have the correct PBC representation.\n",
1234 write_sto_conf_mtop("CompELAssumedWholeConfiguration.pdb", *mtop->name, mtop, x, NULL, ePBC, box);
1239 /*! The swapstate struct stores the information we need to make the channels
1240 * whole again after restarts from a checkpoint file. Here we do the following:
1241 * a) If we did not start from .cpt, we prepare the struct for proper .cpt writing,\n
1242 * b) if we did start from .cpt, we copy over the last whole structures from .cpt,\n
1243 * c) in any case, for subsequent checkpoint writing, we set the pointers in\n
1244 * swapstate to the x_old arrays, which contain the correct PBC representation of
1245 * multimeric channels at the last time step. */
1246 static void init_swapstate(
1247 swapstate_t *swapstate,
1250 rvec x[], /* the initial positions */
1255 rvec *x_pbc = NULL; /* positions of the whole MD system with molecules made whole */
1262 /* We always need the last whole positions such that
1263 * in the next time step we can make the channels whole again in PBC */
1264 if (swapstate->bFromCpt)
1266 /* Copy the last whole positions of each channel from .cpt */
1267 g = &(s->group[eGrpSplit0]);
1268 for (i = 0; i < g->nat; i++)
1270 copy_rvec(swapstate->xc_old_whole[eChan0][i], g->xc_old[i]);
1272 g = &(s->group[eGrpSplit1]);
1273 for (i = 0; i < g->nat; i++)
1275 copy_rvec(swapstate->xc_old_whole[eChan1][i], g->xc_old[i]);
1280 /* Extract the initial split group positions. */
1282 /* Remove pbc, make molecule whole. */
1283 snew(x_pbc, mtop->natoms);
1284 m_rveccopy(mtop->natoms, x, x_pbc);
1286 /* This can only make individual molecules whole, not multimers */
1287 do_pbc_mtop(NULL, ePBC, box, mtop, x_pbc);
1289 /* Output the starting structure? */
1290 outputStartStructureIfWanted(mtop, x_pbc, ePBC, box);
1292 /* If this is the first run (i.e. no checkpoint present) we assume
1293 * that the starting positions give us the correct PBC representation */
1294 for (ig = eGrpSplit0; ig <= eGrpSplit1; ig++)
1296 g = &(s->group[ig]);
1297 for (i = 0; i < g->nat; i++)
1299 copy_rvec(x_pbc[g->ind[i]], g->xc_old[i]);
1304 /* Prepare swapstate arrays for later checkpoint writing */
1305 swapstate->nat[eChan0] = s->group[eGrpSplit0].nat;
1306 swapstate->nat[eChan1] = s->group[eGrpSplit1].nat;
1309 /* For subsequent checkpoint writing, set the swapstate pointers to the xc_old
1310 * arrays that get updated at every swapping step */
1311 swapstate->xc_old_whole_p[eChan0] = &s->group[eGrpSplit0].xc_old;
1312 swapstate->xc_old_whole_p[eChan1] = &s->group[eGrpSplit1].xc_old;
1316 extern void init_swapcoords(
1324 swapstate_t *swapstate,
1326 const output_env_t oenv,
1327 unsigned long Flags)
1329 int i, ic, ig, ii, j;
1334 gmx_bool bAppend, bStartFromCpt, bRerun;
1335 gmx_mtop_atomlookup_t alook = NULL;
1338 alook = gmx_mtop_atomlookup_init(mtop);
1340 if ( (PAR(cr)) && !DOMAINDECOMP(cr) )
1342 gmx_fatal(FARGS, "Position swapping is only implemented for domain decomposition!");
1345 bAppend = Flags & MD_APPENDFILES;
1346 bStartFromCpt = Flags & MD_STARTFROMCPT;
1347 bRerun = Flags & MD_RERUN;
1350 snew(sc->si_priv, 1);
1357 gmx_fatal(FARGS, "%s This module does not support reruns in parallel\nPlease request a serial run with -nt 1 / -np 1\n", SwS);
1360 fprintf(stderr, "%s Rerun - using every available frame\n", SwS);
1362 sc->nAverage = 1; /* averaging makes no sense for reruns */
1365 if (MASTER(cr) && !bAppend)
1367 fprintf(fplog, "\nInitializing ion/water position exchanges\n");
1368 please_cite(fplog, "Kutzner2011b");
1371 switch (ir->eSwapCoords)
1387 /* Copy some data to the group structures for convenience */
1388 /* Number of atoms in the group */
1389 s->group[eGrpIons ].nat = sc->nat;
1390 s->group[eGrpSplit0 ].nat = sc->nat_split[0];
1391 s->group[eGrpSplit1 ].nat = sc->nat_split[1];
1392 s->group[eGrpSolvent].nat = sc->nat_sol;
1393 /* Pointer to the indices */
1394 s->group[eGrpIons ].ind = sc->ind;
1395 s->group[eGrpSplit0 ].ind = sc->ind_split[0];
1396 s->group[eGrpSplit1 ].ind = sc->ind_split[1];
1397 s->group[eGrpSolvent].ind = sc->ind_sol;
1399 check_swap_groups(s, mtop->natoms, bVerbose && MASTER(cr));
1401 /* Allocate space for the collective arrays for all groups */
1402 for (ig = 0; ig < eGrpNr; ig++)
1404 g = &(s->group[ig]);
1405 snew(g->xc, g->nat);
1406 snew(g->c_ind_loc, g->nat);
1407 /* For the split groups (the channels) we need some extra memory to
1408 * be able to make the molecules whole even if they span more than
1409 * half of the box size. */
1410 if (eGrpSplit0 == ig || eGrpSplit1 == ig)
1412 snew(g->xc_shifts, g->nat);
1413 snew(g->xc_eshifts, g->nat);
1414 snew(g->xc_old, g->nat);
1420 init_swapstate(swapstate, sc, mtop, x, box, ir->ePBC);
1423 /* After init_swapstate we have a set of (old) whole positions for our
1424 * channels. Now transfer that to all nodes */
1427 for (ig = eGrpSplit0; ig <= eGrpSplit1; ig++)
1429 g = &(s->group[ig]);
1430 gmx_bcast((g->nat)*sizeof((g->xc_old)[0]), g->xc_old, (cr));
1434 /* Make sure that all molecules in the ion and solvent groups contain the
1435 * same number of atoms each */
1436 s->group[eGrpIons ].apm = get_group_apm_check(eGrpIons, s, MASTER(cr) && bVerbose, alook, mtop);
1437 s->group[eGrpSolvent].apm = get_group_apm_check(eGrpSolvent, s, MASTER(cr) && bVerbose, alook, mtop);
1439 /* Save masses where needed */
1440 s->group[eGrpIons ].m = NULL;
1441 /* We only need enough space to determine a single solvent molecule's
1442 * center at at time */
1443 g = &(s->group[eGrpSolvent]);
1446 /* Need mass-weighted center of split group? */
1447 for (j = 0, ig = eGrpSplit0; j < eChanNR; ig++, j++)
1449 g = &(s->group[ig]);
1450 if (TRUE == sc->massw_split[j])
1452 /* Save the split group charges if mass-weighting is requested */
1454 for (i = 0; i < g->nat; i++)
1456 gmx_mtop_atomnr_to_atom(alook, g->ind[i], &atom);
1466 /* Save the ionic charges */
1467 g = &(s->group[eGrpIons]);
1468 snew(g->qc, g->nat);
1469 for (i = 0; i < g->nat; i++)
1471 gmx_mtop_atomnr_to_atom(alook, g->ind[i], &atom);
1476 set_pbc(s->pbc, -1, box);
1483 fprintf(stderr, "%s Opening output file %s%s\n", SwS, fn, bAppend ? " for appending" : "");
1486 s->fpout = gmx_fio_fopen(fn, bAppend ? "a" : "w" );
1490 xvgr_header(s->fpout, "Ion counts", "Time (ps)", "counts", exvggtXNY, oenv);
1492 for (ig = 0; ig < eGrpNr; ig++)
1494 g = &(s->group[ig]);
1495 fprintf(s->fpout, "# %s group contains %d atom%s", GrpString[ig], g->nat, (g->nat > 1) ? "s" : "");
1496 if (eGrpSolvent == ig || eGrpIons == ig)
1498 fprintf(s->fpout, " with %d atom%s in each molecule", g->apm, (g->apm > 1) ? "s" : "");
1500 fprintf(s->fpout, ".\n");
1503 fprintf(s->fpout, "#\n# Initial positions of split groups:\n");
1506 for (j = 0, ig = eGrpSplit0; j < eChanNR; j++, ig++)
1508 g = &(s->group[ig]);
1509 for (i = 0; i < g->nat; i++)
1511 copy_rvec(x[sc->ind_split[j][i]], g->xc[i]);
1513 if (eGrpSplit0 == ig || eGrpSplit1 == ig)
1515 /* xc has the correct PBC representation for the two channels, so we do
1516 * not need to correct for that */
1517 get_center(g->xc, g->m, g->nat, g->center);
1521 /* For the water molecules, we need to make the molecules whole */
1522 get_molecule_center(g->xc, g->nat, g->m, g->center, s->pbc);
1526 fprintf(s->fpout, "# %s group %s-center %5f nm\n", GrpString[ig],
1527 DimStr[s->swapdim], g->center[s->swapdim]);
1533 fprintf(s->fpout, "#\n");
1534 fprintf(s->fpout, "# split0 cylinder radius %f nm, up %f nm, down %f nm\n",
1535 sc->cyl0r, sc->cyl0u, sc->cyl0l);
1536 fprintf(s->fpout, "# split1 cylinder radius %f nm, up %f nm, down %f nm\n",
1537 sc->cyl1r, sc->cyl1u, sc->cyl1l);
1542 fprintf(s->fpout, "#\n");
1545 fprintf(s->fpout, "# Coupling constant (number of swap attempt steps to average over): %d (translates to %f ps).\n",
1546 sc->nAverage, sc->nAverage*sc->nstswap*ir->delta_t);
1547 fprintf(s->fpout, "# Threshold is %f\n", sc->threshold);
1548 fprintf(s->fpout, "#\n");
1549 fprintf(s->fpout, "# Remarks about which atoms passed which channel use global atoms numbers starting at one.\n");
1558 /* Prepare for parallel or serial run */
1561 for (ig = 0; ig < eGrpNr; ig++)
1563 g = &(s->group[ig]);
1571 for (ig = 0; ig < eGrpNr; ig++)
1573 g = &(s->group[ig]);
1574 g->nat_loc = g->nat;
1575 g->ind_loc = g->ind;
1576 /* c_ind_loc needs to be set to identity in the serial case */
1577 for (i = 0; i < g->nat; i++)
1579 g->c_ind_loc[i] = i;
1584 /* Allocate memory for the ion counts time window */
1585 for (ic = 0; ic < eCompNR; ic++)
1587 for (ii = 0; ii < eIonNR; ii++)
1589 snew(s->comp[ic][ii].nat_past, sc->nAverage);
1593 /* Get the initial ion concentrations and let the other nodes know */
1596 swapstate->nions = s->group[eGrpIons].nat;
1600 get_initial_ioncounts_from_cpt(ir, swapstate, cr, bVerbose);
1604 fprintf(stderr, "%s Determining initial ion counts.\n", SwS);
1605 get_initial_ioncounts(ir, x, box, cr, bRerun);
1608 /* Prepare (further) checkpoint writes ... */
1611 /* Consistency check */
1612 if (swapstate->nAverage != sc->nAverage)
1614 gmx_fatal(FARGS, "%s Ion count averaging steps mismatch! checkpoint: %d, tpr: %d",
1615 SwS, swapstate->nAverage, sc->nAverage);
1620 swapstate->nAverage = sc->nAverage;
1622 fprintf(stderr, "%s Setting pointers for checkpoint writing\n", SwS);
1623 for (ic = 0; ic < eCompNR; ic++)
1625 for (ii = 0; ii < eIonNR; ii++)
1627 swapstate->nat_req_p[ic][ii] = &(s->comp[ic][ii].nat_req);
1628 swapstate->nat_past_p[ic][ii] = &(s->comp[ic][ii].nat_past[0]);
1629 swapstate->inflow_netto_p[ic][ii] = &(s->comp[ic][ii].inflow_netto);
1633 /* Determine the total charge imbalance */
1634 s->deltaQ = ( (-1) * s->comp[eCompA][eIonNEG].nat_req + s->comp[eCompA][eIonPOS].nat_req )
1635 - ( (-1) * s->comp[eCompB][eIonNEG].nat_req + s->comp[eCompB][eIonPOS].nat_req );
1639 fprintf(stderr, "%s Requested charge imbalance is Q(A) - Q(B) = %gz.\n", SwS, s->deltaQ);
1643 fprintf(s->fpout, "# Requested charge imbalance is Q(A)-Q(B) = %gz.\n", s->deltaQ);
1649 bc_initial_concentrations(cr, ir->swap);
1652 /* Put the time-averaged number of ions for all compartments */
1653 for (ic = 0; ic < eCompNR; ic++)
1655 for (ii = 0; ii < eIonNR; ii++)
1657 update_time_window(&(s->comp[ic][ii]), sc->nAverage, -1);
1661 /* Initialize arrays that keep track of through which channel the ions go */
1662 detect_flux_per_channel_init(cr, s, swapstate, bStartFromCpt);
1664 /* We need to print the legend if we open this file for the first time. */
1665 if (MASTER(cr) && !bAppend)
1667 print_ionlist_legend(ir, oenv);
1672 extern void dd_make_local_swap_groups(gmx_domdec_t *dd, t_swapcoords *sc)
1678 /* Make ion group, split groups and solvent group */
1679 for (ig = 0; ig < eGrpNr; ig++)
1681 g = &(sc->si_priv->group[ig]);
1682 dd_make_local_group_indices(dd->ga2la, g->nat, g->ind,
1683 &(g->nat_loc), &(g->ind_loc), &(g->nalloc_loc), g->c_ind_loc);
1688 /*! From the requested and average ion counts we determine whether a swap is needed
1689 * at this time step. */
1690 static gmx_bool need_swap(t_swapcoords *sc)
1697 for (ic = 0; ic < eCompNR; ic++)
1699 for (ii = 0; ii < eIonNR; ii++)
1701 if (s->comp[ic][ii].nat_req - s->comp[ic][ii].nat_av >= sc->threshold)
1711 /*! Returns the index of an atom that is far off the compartment boundaries.
1712 * Other atoms of the molecule (if any) will directly follow the returned index
1714 static int get_index_of_distant_atom(
1715 t_compartment *comp,
1716 int apm) /* Atoms per molecule - just return the first atom index of a molecule */
1719 real d = GMX_REAL_MAX;
1722 /* comp->nat contains the original number of atoms in this compartment
1723 * prior to doing any swaps. Some of these atoms may already have been
1724 * swapped out, but then they are marked with a distance of GMX_REAL_MAX
1726 for (i = 0; i < comp->nat_old; i += apm)
1728 if (comp->dist[i] < d)
1731 d = comp->dist[ibest];
1737 gmx_fatal(FARGS, "Could not get index of swap atom. Compartment atoms %d before swaps, atoms per molecule %d.",
1738 comp->nat_old, apm);
1741 /* Set the distance of this index to infinity such that it won't get selected again in
1744 comp->dist[ibest] = GMX_REAL_MAX;
1746 return comp->ind[ibest];
1750 /*! Swaps centers of mass and makes molecule whole if broken */
1751 static void translate_positions(
1759 rvec reference, dx, correctPBCimage;
1762 /* Use the first atom as the reference for PBC */
1763 copy_rvec(x[0], reference);
1765 for (i = 0; i < apm; i++)
1767 /* PBC distance between position and reference */
1768 pbc_dx(pbc, x[i], reference, dx);
1770 /* Add PBC distance to reference */
1771 rvec_add(reference, dx, correctPBCimage);
1773 /* Subtract old_com from correct image and add new_com */
1774 rvec_dec(correctPBCimage, old_com);
1775 rvec_inc(correctPBCimage, new_com);
1777 copy_rvec(correctPBCimage, x[i]);
1782 /*! Write back the the modified local positions from the collective array to the official coordinates */
1783 static void apply_modified_positions(
1790 for (l = 0; l < g->nat_loc; l++)
1792 /* Get the right local index to write to */
1794 /* Where is the local atom in the collective array? */
1795 cind = g->c_ind_loc[l];
1797 /* Copy the possibly modified position */
1798 copy_rvec(g->xc[cind], x[ii]);
1803 extern gmx_bool do_swapcoords(
1808 gmx_wallcycle_t wcycle,
1817 int j, ii, ic, ig, im, gmax, nswaps;
1818 gmx_bool bSwap = FALSE;
1820 real vacancy[eCompNR][eIonNR];
1822 rvec solvent_center, ion_center;
1824 gmx_mtop_atomlookup_t alook = NULL;
1827 wallcycle_start(wcycle, ewcSWAP);
1832 /* Assemble all the positions of the swap group (ig = 0), the split groups
1833 * (ig = 1,2), and possibly the solvent group (ig = 3) */
1836 for (ig = 0; ig < gmax; ig++)
1838 g = &(s->group[ig]);
1839 if (eGrpSplit0 == ig || eGrpSplit1 == ig)
1841 /* The split groups, i.e. the channels. Here we need the full
1842 * communicate_group_positions(), so that we can make the molecules
1843 * whole even in cases where they span more than half of the box in
1845 communicate_group_positions(cr, g->xc, g->xc_shifts, g->xc_eshifts, TRUE,
1846 x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, g->xc_old, box);
1848 get_center(g->xc, g->m, g->nat, g->center); /* center of split groups == channels */
1852 /* Swap group (ions), and solvent group. These molecules are small
1853 * and we can always make them whole with a simple distance check.
1854 * Therefore we pass NULL as third argument. */
1855 communicate_group_positions(cr, g->xc, NULL, NULL, FALSE,
1856 x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, NULL, NULL);
1860 /* Set up the compartments and get lists of atoms in each compartment,
1861 * determine how many ions each compartment contains */
1862 compartmentalize_ions(cr, sc, box, step, s->fpout, bRerun);
1864 /* Output how many ions are in the compartments */
1867 print_ionlist(s, t, "");
1870 /* If we are doing a rerun, we are finished here, since we cannot perform
1877 /* Do we have to perform a swap? */
1878 bSwap = need_swap(sc);
1881 g = &(s->group[eGrpSolvent]);
1882 communicate_group_positions(cr, g->xc, NULL, NULL, FALSE,
1883 x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, NULL, NULL);
1885 compartmentalize_solvent(cr, sc, box, s->fpout);
1887 /* Determine where ions are missing and where ions are too many */
1888 for (ic = 0; ic < eCompNR; ic++)
1890 for (ii = 0; ii < eIonNR; ii++)
1892 vacancy[ic][ii] = s->comp[ic][ii].nat_req - s->comp[ic][ii].nat_av;
1896 /* Remember the original number of ions per compartment */
1897 for (ic = 0; ic < eCompNR; ic++)
1899 s->compsol[ic].nat_old = s->compsol[ic].nat;
1900 for (ii = 0; ii < eIonNR; ii++)
1902 s->comp[ic][ii].nat_old = s->comp[ic][ii].nat;
1906 /* Now actually correct the number of ions */
1907 g = &(s->group[eGrpSolvent]);
1909 alook = gmx_mtop_atomlookup_init(mtop);
1910 for (ic = 0; ic < eCompNR; ic++)
1912 for (ii = 0; ii < eIonNR; ii++)
1914 while (vacancy[ic][ii] >= sc->threshold)
1916 /* Swap in an ion */
1918 /* Get the xc-index of the first atom of a solvent molecule of this compartment */
1919 isol = get_index_of_distant_atom(&(s->compsol[ic]), s->group[eGrpSolvent].apm );
1921 /* Get the xc-index of an ion from the other compartment */
1922 iion = get_index_of_distant_atom(&(s->comp[(ic+1)%eCompNR][ii]), s->group[eGrpIons].apm );
1924 /* Get the solvent molecule's center of mass */
1925 for (im = 0; im < s->group[eGrpSolvent].apm; im++)
1927 gmx_mtop_atomnr_to_atom(alook, s->group[eGrpSolvent].ind[isol+im], &atom);
1928 s->group[eGrpSolvent].m[im] = atom->m;
1930 get_molecule_center(&(s->group[eGrpSolvent].xc[isol]), s->group[eGrpSolvent].apm, s->group[eGrpSolvent].m, solvent_center, s->pbc);
1931 get_molecule_center(&(s->group[eGrpIons ].xc[iion]), s->group[eGrpIons ].apm, NULL, ion_center, s->pbc);
1933 /* subtract com_solvent and add com_ion */
1934 translate_positions(&(s->group[eGrpSolvent].xc[isol]), s->group[eGrpSolvent].apm, solvent_center, ion_center, s->pbc);
1935 /* For the ion, subtract com_ion and add com_solvent */
1936 translate_positions(&(s->group[eGrpIons ].xc[iion]), s->group[eGrpIons ].apm, ion_center, solvent_center, s->pbc);
1939 vacancy[(ic+1) % eCompNR][ii]++;
1941 /* Keep track of the changes */
1942 s->comp[ic ][ii].nat++;
1943 s->comp[(ic+1) % eCompNR][ii].nat--;
1944 s->comp[ic ][ii].inflow_netto++;
1945 s->comp[(ic+1) % eCompNR][ii].inflow_netto--;
1946 /* Correct the past time window to still get the right averages from now on */
1947 s->comp[ic ][ii].nat_av++;
1948 s->comp[(ic+1) % eCompNR][ii].nat_av--;
1949 for (j = 0; j < sc->nAverage; j++)
1951 s->comp[ic ][ii].nat_past[j]++;
1952 s->comp[(ic+1) % eCompNR][ii].nat_past[j]--;
1954 /* Clear ion history */
1957 s->group[eGrpIons].channel_label[iion] = eChHistPassedNone;
1958 s->group[eGrpIons].comp_from[iion] = eDomainNotset;
1960 /* That was the swap */
1965 gmx_mtop_atomlookup_destroy(alook);
1969 fprintf(stderr, "%s Performed %d swap%s in step %"GMX_PRId64 ".\n", SwS, nswaps, nswaps > 1 ? "s" : "", step);
1971 if (s->fpout != NULL)
1973 print_ionlist(s, t, " # after swap");
1976 /* Write back the the modified local positions from the collective array to the official coordinates */
1977 apply_modified_positions(&(s->group[eGrpIons ]), x);
1978 apply_modified_positions(&(s->group[eGrpSolvent]), x);
1979 } /* end of if(bSwap) */
1981 wallcycle_stop(wcycle, ewcSWAP);