2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
37 * Implements functions in swapcoords.h.
39 * \author Carsten Kutzner <ckutzne@gwdg.de>
40 * \ingroup module_swap
44 #include "swapcoords.h"
54 #include "gromacs/domdec/domdec_struct.h"
55 #include "gromacs/domdec/localatomset.h"
56 #include "gromacs/domdec/localatomsetmanager.h"
57 #include "gromacs/fileio/confio.h"
58 #include "gromacs/fileio/gmxfio.h"
59 #include "gromacs/fileio/xvgr.h"
60 #include "gromacs/gmxlib/network.h"
61 #include "gromacs/math/vec.h"
62 #include "gromacs/mdlib/groupcoord.h"
63 #include "gromacs/mdtypes/commrec.h"
64 #include "gromacs/mdtypes/imdmodule.h"
65 #include "gromacs/mdtypes/inputrec.h"
66 #include "gromacs/mdtypes/md_enums.h"
67 #include "gromacs/mdtypes/mdrunoptions.h"
68 #include "gromacs/mdtypes/observableshistory.h"
69 #include "gromacs/mdtypes/state.h"
70 #include "gromacs/mdtypes/swaphistory.h"
71 #include "gromacs/pbcutil/pbc.h"
72 #include "gromacs/timing/wallcycle.h"
73 #include "gromacs/topology/mtop_lookup.h"
74 #include "gromacs/topology/topology.h"
75 #include "gromacs/utility/cstringutil.h"
76 #include "gromacs/utility/fatalerror.h"
77 #include "gromacs/utility/pleasecite.h"
78 #include "gromacs/utility/smalloc.h"
79 #include "gromacs/utility/snprintf.h"
81 static const char *SwS
= {"SWAP:"}; /**< For output that comes from the swap module */
82 static const char *SwSEmpty
= {" "}; /**< Placeholder for multi-line output */
83 static const char* CompStr
[eCompNR
] = {"A", "B" }; /**< Compartment name */
84 static const char *SwapStr
[eSwapTypesNR
+1] = { "", "X-", "Y-", "Z-", nullptr}; /**< Name for the swap types. */
85 static const char *DimStr
[DIM
+1] = { "X", "Y", "Z", nullptr}; /**< Name for the swap dimension. */
87 /** Keep track of through which channel the ions have passed */
88 enum eChannelHistory
{
89 eChHistPassedNone
, eChHistPassedCh0
, eChHistPassedCh1
, eChHistNr
91 static const char* ChannelString
[eChHistNr
] = { "none", "channel0", "channel1" }; /**< Name for the channels */
93 /*! \brief Domain identifier.
95 * Keeps track of from which compartment the ions came before passing the
99 eDomainNotset
, eDomainA
, eDomainB
, eDomainNr
101 static const char* DomainString
[eDomainNr
] = { "not_assigned", "Domain_A", "Domain_B" }; /**< Name for the domains */
107 * \brief Implement Computational Electrophysiology swapping.
109 class SwapCoordinates final
: public IMDModule
112 IMdpOptionProvider
*mdpOptionProvider() override
{ return nullptr; }
113 IMDOutputProvider
*outputProvider() override
{ return nullptr; }
114 void initForceProviders(ForceProviders
* /* forceProviders */) override
{}
117 std::unique_ptr
<IMDModule
> createSwapCoordinatesModule()
119 return std::make_unique
<SwapCoordinates
>();
126 * Structure containing compartment-specific data.
128 typedef struct swap_compartment
130 int nMol
; /**< Number of ion or water molecules detected
131 in this compartment. */
132 int nMolBefore
; /**< Number of molecules before swapping. */
133 int nMolReq
; /**< Requested number of molecules in compartment. */
134 real nMolAv
; /**< Time-averaged number of molecules matching
135 the compartment conditions. */
136 int *nMolPast
; /**< Past molecule counts for time-averaging. */
137 int *ind
; /**< Indices to collective array of atoms. */
138 real
*dist
; /**< Distance of atom to bulk layer, which is
139 normally the center layer of the compartment */
140 int nalloc
; /**< Allocation size for ind array. */
141 int inflow_net
; /**< Net inflow of ions into this compartment. */
146 * This structure contains data needed for the groups involved in swapping:
147 * split group 0, split group 1, solvent group, ion groups.
149 typedef struct swap_group
151 /*!\brief Construct a swap group given the managed swap atoms.
153 * \param[in] atomset Managed indices of atoms that are part of the swap group.
155 swap_group(const gmx::LocalAtomSet
&atomset
);
156 char *molname
= nullptr; /**< Name of the group or ion type */
157 int apm
= 0; /**< Number of atoms in each molecule */
158 gmx::LocalAtomSet atomset
; /**< The atom indices in the swap group */
159 rvec
*xc
= nullptr; /**< Collective array of group atom positions (size nat) */
160 ivec
*xc_shifts
= nullptr; /**< Current (collective) shifts (size nat) */
161 ivec
*xc_eshifts
= nullptr; /**< Extra shifts since last DD step (size nat) */
162 rvec
*xc_old
= nullptr; /**< Old (collective) positions (size nat) */
163 real q
= 0.; /**< Total charge of one molecule of this group */
164 real
*m
= nullptr; /**< Masses (can be omitted, size apm) */
165 unsigned char *comp_from
= nullptr; /**< (Collective) Stores from which compartment this
166 molecule has come. This way we keep track of
167 through which channel an ion permeates
168 (size nMol = nat/apm) */
169 unsigned char *comp_now
= nullptr; /**< In which compartment this ion is now (size nMol) */
170 unsigned char *channel_label
= nullptr; /**< Which channel was passed at last by this ion?
172 rvec center
; /**< Center of the group; COM if masses are used */
173 t_compartment comp
[eCompNR
]; /**< Distribution of particles of this group across
174 the two compartments */
175 real vacancy
[eCompNR
]; /**< How many molecules need to be swapped in? */
176 int fluxfromAtoB
[eChanNR
]; /**< Net flux of ions per channel */
177 int nCyl
[eChanNR
]; /**< Number of ions residing in a channel */
178 int nCylBoth
= 0; /**< Ions assigned to cyl0 and cyl1. Not good. */
181 t_swapgrp::swap_group(const gmx::LocalAtomSet
& atomset
) : atomset
{
187 for (int compartment
= eCompA
; compartment
< eCompNR
; ++compartment
)
189 comp
[compartment
] = {};
190 vacancy
[compartment
] = 0;
192 for (int channel
= eChan0
; channel
< eChanNR
; ++channel
)
194 fluxfromAtoB
[channel
] = 0;
200 * Main (private) data structure for the position swapping protocol.
202 typedef struct t_swap
204 int swapdim
; /**< One of XX, YY, ZZ */
205 t_pbc
*pbc
; /**< Needed to make molecules whole. */
206 FILE *fpout
; /**< Output file. */
207 int ngrp
; /**< Number of t_swapgrp groups */
208 std::vector
<t_swapgrp
> group
; /**< Separate groups for channels, solvent, ions */
209 int fluxleak
; /**< Flux not going through any of the channels. */
210 real deltaQ
; /**< The charge imbalance between the compartments. */
215 /*! \brief Check whether point is in channel.
217 * A channel is a cylinder defined by a disc
218 * with radius r around its center c. The thickness of the cylinder is
225 * <---------c--------->
231 * \param[in] point The position (xyz) under consideration.
232 * \param[in] center The center of the cylinder.
233 * \param[in] d_up The upper extension of the cylinder.
234 * \param[in] d_down The lower extension.
235 * \param[in] r_cyl2 Cylinder radius squared.
236 * \param[in] pbc Structure with info about periodic boundary conditions.
237 * \param[in] normal The membrane normal direction is typically 3, i.e. z, but can be x or y also.
239 * \returns Whether the point is inside the defined cylindric channel.
241 static gmx_bool
is_in_channel(
251 int plane1
, plane2
; /* Directions tangential to membrane */
254 plane1
= (normal
+ 1) % 3; /* typically 0, i.e. XX */
255 plane2
= (normal
+ 2) % 3; /* typically 1, i.e. YY */
257 /* Get the distance vector dr between the point and the center of the cylinder */
258 pbc_dx(pbc
, point
, center
, dr
); /* This puts center in the origin */
260 /* Check vertical direction */
261 if ( (dr
[normal
] > d_up
) || (dr
[normal
] < -d_down
) )
266 /* Check radial direction */
267 if ( (dr
[plane1
]*dr
[plane1
] + dr
[plane2
]*dr
[plane2
]) > r_cyl2
)
272 /* All check passed, this point is in the cylinder */
277 /*! \brief Prints output to CompEL output file.
279 * Prints to swap output file how many ions are in each compartment,
280 * where the centers of the split groups are, and how many ions of each type
281 * passed the channels.
283 static void print_ionlist(
286 const char comment
[])
289 fprintf(s
->fpout
, "%12.5e", time
);
291 // Output number of molecules and difference to reference counts for each
292 // compartment and ion type
293 for (int iComp
= 0; iComp
< eCompNR
; iComp
++)
295 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
297 t_compartment
*comp
= &s
->group
[ig
].comp
[iComp
];
299 fprintf(s
->fpout
, "%10d%10.1f%10d", comp
->nMol
, comp
->nMolAv
- comp
->nMolReq
, comp
->inflow_net
);
303 // Output center of split groups
304 fprintf(s
->fpout
, "%10g%10g",
305 s
->group
[eGrpSplit0
].center
[s
->swapdim
],
306 s
->group
[eGrpSplit1
].center
[s
->swapdim
]);
308 // Output ion flux for each channel and ion type
309 for (int iChan
= 0; iChan
< eChanNR
; iChan
++)
311 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
313 t_swapgrp
*g
= &s
->group
[ig
];
314 fprintf(s
->fpout
, "%10d", g
->fluxfromAtoB
[iChan
]);
318 /* Output the number of molecules that leaked from A to B */
319 fprintf(s
->fpout
, "%10d", s
->fluxleak
);
321 fprintf(s
->fpout
, "%s\n", comment
);
325 /*! \brief Get the center of a group of nat atoms.
327 * Since with PBC an atom group might not be whole, use the first atom as the
328 * reference atom and determine the center with respect to this reference.
330 static void get_molecule_center(
338 rvec weightedPBCimage
;
340 rvec reference
, correctPBCimage
, dx
;
343 /* Use the first atom as the reference and put other atoms near that one */
344 /* This does not work for large molecules that span > half of the box! */
345 copy_rvec(x
[0], reference
);
347 /* Calculate either the weighted center or simply the center of geometry */
350 for (i
= 0; i
< nat
; i
++)
352 /* PBC distance between position and reference */
353 pbc_dx(pbc
, x
[i
], reference
, dx
);
355 /* Add PBC distance to reference */
356 rvec_add(reference
, dx
, correctPBCimage
);
358 /* Take weight into account */
359 if (nullptr == weights
)
368 svmul(wi
, correctPBCimage
, weightedPBCimage
);
371 rvec_inc(center
, weightedPBCimage
);
375 svmul(1.0/wsum
, center
, center
);
380 /*! \brief Return TRUE if position x of ion (or water) is found in the compartment,
381 * i.e. between w1 and w2.
383 * One can define and additional offset "b" if one wants to exchange ions/water
384 * to or from a plane not directly in the middle of w1 and w2. The offset can be
385 * in ]-1.0, ..., +1.0 [.
386 * A bulkOffset of 0.0 means 'no offset', so the swap-layer is directly in the
387 * middle between w1 and w2. Offsets -1.0 < b < 0.0 will yield swaps nearer to w1,
388 * whereas offsets 0.0 < 0 < +1.0 will yield swaps nearer to w2.
392 * ||--------------+-------------|-------------+------------------------||
393 * w1 ? ? ? ? ? ? ? ? ? ? ? w2
394 * ||--------------+-------------|----b--------+------------------------||
399 * \param[in] w1 Position of 'wall' atom 1.
400 * \param[in] w2 Position of 'wall' atom 2.
401 * \param[in] x Position of the ion or the water molecule under consideration.
402 * \param[in] l Length of the box, from || to || in the sketch.
403 * \param[in] bulkOffset Where is the bulk layer "b" to be found between w1 and w2?
404 * \param[out] distance_from_b Distance of x to the bulk layer "b".
406 * \returns TRUE if x is between w1 and w2.
408 * Also computes the distance of x to the compartment center (the layer that is
409 * normally situated in the middle of w1 and w2 that would be considered as having
410 * the bulk concentration of ions).
412 static gmx_bool
compartment_contains_atom(
418 real
*distance_from_b
)
424 /* First set the origin in the middle of w1 and w2 */
431 /* Now choose the PBC image of x that is closest to the origin: */
442 *distance_from_b
= static_cast<real
>(fabs(x
- bulkOffset
*0.5*width
));
444 /* Return TRUE if we now are in area "????" */
445 return (x
>= w1
) && (x
< w2
);
449 /*! \brief Updates the time-averaged number of ions in a compartment. */
450 static void update_time_window(t_compartment
*comp
, int values
, int replace
)
456 /* Put in the new value */
459 comp
->nMolPast
[replace
] = comp
->nMol
;
462 /* Compute the new time-average */
464 for (i
= 0; i
< values
; i
++)
466 average
+= comp
->nMolPast
[i
];
469 comp
->nMolAv
= average
;
473 /*! \brief Add the atom with collective index ci to the atom list in compartment 'comp'.
475 * \param[in] ci Index of this ion in the collective xc array.
476 * \param[inout] comp Compartment to add this atom to.
477 * \param[in] distance Shortest distance of this atom to the bulk layer,
478 * from which ion/water pairs are selected for swapping.
480 static void add_to_list(
487 if (nr
>= comp
->nalloc
)
489 comp
->nalloc
= over_alloc_dd(nr
+1);
490 srenew(comp
->ind
, comp
->nalloc
);
491 srenew(comp
->dist
, comp
->nalloc
);
494 comp
->dist
[nr
] = distance
;
499 /*! \brief Determine the compartment boundaries from the channel centers. */
500 static void get_compartment_boundaries(
504 real
*left
, real
*right
)
507 real leftpos
, rightpos
, leftpos_orig
;
512 gmx_fatal(FARGS
, "No compartment %c.", c
+'A');
515 pos0
= s
->group
[eGrpSplit0
].center
[s
->swapdim
];
516 pos1
= s
->group
[eGrpSplit1
].center
[s
->swapdim
];
529 /* This gets us the other compartment: */
532 leftpos_orig
= leftpos
;
534 rightpos
= leftpos_orig
+ box
[s
->swapdim
][s
->swapdim
];
542 /*! \brief Determine the per-channel ion flux.
544 * To determine the flux through the individual channels, we
545 * remember the compartment and channel history of each ion. An ion can be
546 * either in channel0 or channel1, or in the remaining volume of compartment
550 * +-----------------+
553 * ||||||||||0|||||||| bilayer with channel 0
558 * |||||1||||||||||||| bilayer with channel 1
561 * +-----------------+
565 static void detect_flux_per_channel(
570 unsigned char *comp_now
,
571 unsigned char *comp_from
,
572 unsigned char *channel_label
,
582 gmx_bool in_cyl0
, in_cyl1
;
589 /* Check whether ion is inside any of the channels */
590 in_cyl0
= is_in_channel(atomPosition
, s
->group
[eGrpSplit0
].center
, sc
->cyl0u
, sc
->cyl0l
, cyl0_r2
, s
->pbc
, sd
);
591 in_cyl1
= is_in_channel(atomPosition
, s
->group
[eGrpSplit1
].center
, sc
->cyl1u
, sc
->cyl1l
, cyl1_r2
, s
->pbc
, sd
);
593 if (in_cyl0
&& in_cyl1
)
595 /* Ion appears to be in both channels. Something is severely wrong! */
597 *comp_now
= eDomainNotset
;
598 *comp_from
= eDomainNotset
;
599 *channel_label
= eChHistPassedNone
;
603 /* Ion is in channel 0 now */
604 *channel_label
= eChHistPassedCh0
;
605 *comp_now
= eDomainNotset
;
610 /* Ion is in channel 1 now */
611 *channel_label
= eChHistPassedCh1
;
612 *comp_now
= eDomainNotset
;
617 /* Ion is not in any of the channels, so it must be in domain A or B */
620 *comp_now
= eDomainA
;
624 *comp_now
= eDomainB
;
628 /* Only take action, if ion is now in domain A or B, and was before
629 * in the other domain!
631 if (eDomainNotset
== *comp_from
)
633 /* Maybe we can set the domain now */
634 *comp_from
= *comp_now
; /* Could still be eDomainNotset, though */
636 else if ( (*comp_now
!= eDomainNotset
) /* if in channel */
637 && (*comp_from
!= *comp_now
) )
639 /* Obviously the ion changed its domain.
640 * Count this for the channel through which it has passed. */
641 switch (*channel_label
)
643 case eChHistPassedNone
:
646 fprintf(stderr
, " %s Warning! Step %s, ion %d moved from %s to %s\n",
647 SwS
, gmx_step_str(step
, buf
), iAtom
, DomainString
[*comp_from
], DomainString
[*comp_now
]);
650 fprintf(stderr
, ", possibly due to a swap in the original simulation.\n");
654 fprintf(stderr
, "but did not pass cyl0 or cyl1 as defined in the .mdp file.\n"
655 "Do you have an ion somewhere within the membrane?\n");
656 /* Write this info to the CompEL output file: */
657 fprintf(s
->fpout
, " # Warning: step %s, ion %d moved from %s to %s (probably through the membrane)\n",
658 gmx_step_str(step
, buf
), iAtom
,
659 DomainString
[*comp_from
], DomainString
[*comp_now
]);
663 case eChHistPassedCh0
:
664 case eChHistPassedCh1
:
665 if (*channel_label
== eChHistPassedCh0
)
674 if (eDomainA
== *comp_from
)
676 g
->fluxfromAtoB
[chan_nr
]++;
680 g
->fluxfromAtoB
[chan_nr
]--;
682 fprintf(fpout
, "# Atom nr. %d finished passing %s.\n", iAtom
, ChannelString
[*channel_label
]);
685 gmx_fatal(FARGS
, "%s Unknown channel history entry for ion type '%s'\n",
689 /* This ion has moved to the _other_ compartment ... */
690 *comp_from
= *comp_now
;
691 /* ... and it did not pass any channel yet */
692 *channel_label
= eChHistPassedNone
;
697 /*! \brief Determines which ions or solvent molecules are in compartment A and B */
698 static void sortMoleculesIntoCompartments(
708 gmx_swapcoords_t s
= sc
->si_priv
;
709 int nMolNotInComp
[eCompNR
]; /* consistency check */
710 real cyl0_r2
= sc
->cyl0r
* sc
->cyl0r
;
711 real cyl1_r2
= sc
->cyl1r
* sc
->cyl1r
;
713 /* Get us a counter that cycles in the range of [0 ... sc->nAverage[ */
714 int replace
= (step
/sc
->nstswap
) % sc
->nAverage
;
716 for (int comp
= eCompA
; comp
<= eCompB
; comp
++)
720 /* Get lists of atoms that match criteria for this compartment */
721 get_compartment_boundaries(comp
, sc
->si_priv
, box
, &left
, &right
);
723 /* First clear the ion molecule lists */
724 g
->comp
[comp
].nMol
= 0;
725 nMolNotInComp
[comp
] = 0; /* consistency check */
727 /* Loop over the molecules and atoms of this group */
728 for (int iMol
= 0, iAtom
= 0; iAtom
< static_cast<int>(g
->atomset
.numAtomsGlobal()); iAtom
+= g
->apm
, iMol
++)
733 /* Is this first atom of the molecule in the compartment that we look at? */
734 if (compartment_contains_atom(left
, right
, g
->xc
[iAtom
][sd
], box
[sd
][sd
], sc
->bulkOffset
[comp
], &dist
) )
736 /* Add the first atom of this molecule to the list of molecules in this compartment */
737 add_to_list(iAtom
, &g
->comp
[comp
], dist
);
739 /* Master also checks for ion groups through which channel each ion has passed */
740 if (MASTER(cr
) && (g
->comp_now
!= nullptr) && !bIsSolvent
)
742 int globalAtomNr
= g
->atomset
.globalIndex()[iAtom
] + 1; /* PDB index starts at 1 ... */
743 detect_flux_per_channel(g
, globalAtomNr
, comp
, g
->xc
[iAtom
],
744 &g
->comp_now
[iMol
], &g
->comp_from
[iMol
], &g
->channel_label
[iMol
],
745 sc
, cyl0_r2
, cyl1_r2
, step
, bRerun
, fpout
);
750 nMolNotInComp
[comp
]++;
753 /* Correct the time-averaged number of ions in the compartment */
756 update_time_window(&g
->comp
[comp
], sc
->nAverage
, replace
);
760 /* Flux detection warnings */
761 if (MASTER(cr
) && !bIsSolvent
)
766 "%s Warning: %d atoms were detected as being in both channels! Probably your split\n"
767 "%s cylinder is way too large, or one compartment has collapsed (step %" PRId64
")\n",
768 SwS
, g
->nCylBoth
, SwS
, step
);
770 fprintf(s
->fpout
, "Warning: %d atoms were assigned to both channels!\n", g
->nCylBoth
);
776 if (bIsSolvent
&& nullptr != fpout
)
778 fprintf(fpout
, "# Solv. molecules in comp.%s: %d comp.%s: %d\n",
779 CompStr
[eCompA
], g
->comp
[eCompA
].nMol
,
780 CompStr
[eCompB
], g
->comp
[eCompB
].nMol
);
783 /* Consistency checks */
784 const auto numMolecules
= static_cast<int>(g
->atomset
.numAtomsGlobal() / g
->apm
);
785 if (nMolNotInComp
[eCompA
] + nMolNotInComp
[eCompB
] != numMolecules
)
787 fprintf(stderr
, "%s Warning: Inconsistency while assigning '%s' molecules to compartments. !inA: %d, !inB: %d, total molecules %d\n",
788 SwS
, g
->molname
, nMolNotInComp
[eCompA
], nMolNotInComp
[eCompB
], numMolecules
);
791 int sum
= g
->comp
[eCompA
].nMol
+ g
->comp
[eCompB
].nMol
;
792 if (sum
!= numMolecules
)
794 fprintf(stderr
, "%s Warning: %d molecules are in group '%s', but altogether %d have been assigned to the compartments.\n",
795 SwS
, numMolecules
, g
->molname
, sum
);
800 /*! \brief Find out how many group atoms are in the compartments initially */
801 static void get_initial_ioncounts(
803 const rvec x
[], /* the initial positions */
815 /* Loop over the user-defined (ion) groups */
816 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
820 /* Copy the initial positions of the atoms in the group
821 * to the collective array so that we can compartmentalize */
822 for (size_t i
= 0; i
< g
->atomset
.numAtomsGlobal(); i
++)
824 int ind
= g
->atomset
.globalIndex()[i
];
825 copy_rvec(x
[ind
], g
->xc
[i
]);
828 /* Set up the compartments and get lists of atoms in each compartment */
829 sortMoleculesIntoCompartments(g
, cr
, sc
, box
, 0, s
->fpout
, bRerun
, FALSE
);
831 /* Set initial molecule counts if requested (as signaled by "-1" value) */
832 for (int ic
= 0; ic
< eCompNR
; ic
++)
834 int requested
= sc
->grp
[ig
].nmolReq
[ic
];
837 g
->comp
[ic
].nMolReq
= g
->comp
[ic
].nMol
;
841 g
->comp
[ic
].nMolReq
= requested
;
845 /* Check whether the number of requested molecules adds up to the total number */
846 int req
= g
->comp
[eCompA
].nMolReq
+ g
->comp
[eCompB
].nMolReq
;
847 int tot
= g
->comp
[eCompA
].nMol
+ g
->comp
[eCompB
].nMol
;
851 gmx_fatal(FARGS
, "Mismatch of the number of %s ions summed over both compartments.\n"
852 "You requested a total of %d ions (%d in A and %d in B),\n"
853 "but there are a total of %d ions of this type in the system.\n",
854 g
->molname
, req
, g
->comp
[eCompA
].nMolReq
,
855 g
->comp
[eCompB
].nMolReq
, tot
);
858 /* Initialize time-averaging:
859 * Write initial concentrations to all time bins to start with */
860 for (int ic
= 0; ic
< eCompNR
; ic
++)
862 g
->comp
[ic
].nMolAv
= g
->comp
[ic
].nMol
;
863 for (int i
= 0; i
< sc
->nAverage
; i
++)
865 g
->comp
[ic
].nMolPast
[i
] = g
->comp
[ic
].nMol
;
872 /*! \brief Copy history of ion counts from checkpoint file.
874 * When called, the checkpoint file has already been read in. Here we copy
875 * over the values from .cpt file to the swap data structure.
877 static void get_initial_ioncounts_from_cpt(
878 t_inputrec
*ir
, swaphistory_t
*swapstate
,
879 t_commrec
*cr
, gmx_bool bVerbose
)
891 /* Copy the past values from the checkpoint values that have been read in already */
894 fprintf(stderr
, "%s Copying values from checkpoint\n", SwS
);
897 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
900 gs
= &swapstate
->ionType
[ig
- eSwapFixedGrpNR
];
902 for (int ic
= 0; ic
< eCompNR
; ic
++)
904 g
->comp
[ic
].nMolReq
= gs
->nMolReq
[ic
];
905 g
->comp
[ic
].inflow_net
= gs
->inflow_net
[ic
];
909 fprintf(stderr
, "%s ... Influx netto: %d Requested: %d Past values: ", SwS
,
910 g
->comp
[ic
].inflow_net
, g
->comp
[ic
].nMolReq
);
913 for (int j
= 0; j
< sc
->nAverage
; j
++)
915 g
->comp
[ic
].nMolPast
[j
] = gs
->nMolPast
[ic
][j
];
918 fprintf(stderr
, "%d ", g
->comp
[ic
].nMolPast
[j
]);
923 fprintf(stderr
, "\n");
931 /*! \brief The master lets all others know about the initial ion counts. */
932 static void bc_initial_concentrations(
943 for (ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
947 for (ic
= 0; ic
< eCompNR
; ic
++)
949 gmx_bcast(sizeof(g
->comp
[ic
].nMolReq
), &(g
->comp
[ic
].nMolReq
), cr
);
950 gmx_bcast(sizeof(g
->comp
[ic
].nMol
), &(g
->comp
[ic
].nMol
), cr
);
951 gmx_bcast( swap
->nAverage
* sizeof(g
->comp
[ic
].nMolPast
[0]), g
->comp
[ic
].nMolPast
, cr
);
957 /*! \brief Ensure that each atom belongs to at most one of the swap groups. */
958 static void check_swap_groups(t_swap
*s
, int nat
, gmx_bool bVerbose
)
960 int *nGroup
= nullptr; /* This array counts for each atom in the MD system to
961 how many swap groups it belongs (should be 0 or 1!) */
963 int nMultiple
= 0; /* Number of atoms belonging to multiple groups */
968 fprintf(stderr
, "%s Making sure each atom belongs to at most one of the swap groups.\n", SwS
);
971 /* Add one to the group count of atoms belonging to a swap group: */
973 for (int i
= 0; i
< s
->ngrp
; i
++)
975 t_swapgrp
*g
= &s
->group
[i
];
976 for (size_t j
= 0; j
< g
->atomset
.numAtomsGlobal(); j
++)
978 /* Get the global index of this atom of this group: */
979 ind
= g
->atomset
.globalIndex()[j
];
983 /* Make sure each atom belongs to at most one of the groups: */
984 for (int i
= 0; i
< nat
; i
++)
995 gmx_fatal(FARGS
, "%s Cannot perform swapping since %d atom%s allocated to more than one swap index group.\n"
996 "%s Each atom must be allocated to at most one of the split groups, the swap groups, or the solvent.\n"
997 "%s Check the .mdp file settings regarding the swap index groups or the index groups themselves.\n",
998 SwS
, nMultiple
, (1 == nMultiple
) ? " is" : "s are", SwSEmpty
, SwSEmpty
);
1003 /*! \brief Get the number of atoms per molecule for this group.
1005 * Also ensure that all the molecules in this group have this number of atoms.
1007 static int get_group_apm_check(
1013 t_swapgrp
*g
= &s
->group
[igroup
];
1014 const int *ind
= s
->group
[igroup
].atomset
.globalIndex().data();
1015 int nat
= s
->group
[igroup
].atomset
.numAtomsGlobal();
1017 /* Determine the number of solvent atoms per solvent molecule from the
1018 * first solvent atom: */
1020 mtopGetMolblockIndex(mtop
, ind
[0], &molb
, nullptr, nullptr);
1021 int apm
= mtop
->moleculeBlockIndices
[molb
].numAtomsPerMolecule
;
1025 fprintf(stderr
, "%s Checking whether all %s molecules consist of %d atom%s\n", SwS
,
1026 g
->molname
, apm
, apm
> 1 ? "s" : "");
1029 /* Check whether this is also true for all other solvent atoms */
1030 for (int i
= 1; i
< nat
; i
++)
1032 mtopGetMolblockIndex(mtop
, ind
[i
], &molb
, nullptr, nullptr);
1033 if (apm
!= mtop
->moleculeBlockIndices
[molb
].numAtomsPerMolecule
)
1035 gmx_fatal(FARGS
, "Not all molecules of swap group %d consist of %d atoms.",
1040 //TODO: check whether charges and masses of each molecule are identical!
1045 /*! \brief Print the legend to the swap output file.
1047 * Also print the initial values of ion counts and position of split groups.
1049 static void print_ionlist_legend(t_inputrec
*ir
,
1050 const gmx_output_env_t
*oenv
)
1052 const char **legend
;
1056 t_swap
*s
= ir
->swap
->si_priv
;
1057 int nIonTypes
= ir
->swap
->ngrp
- eSwapFixedGrpNR
;
1058 snew(legend
, eCompNR
*nIonTypes
*3 + 2 + eChanNR
*nIonTypes
+ 1);
1060 // Number of molecules and difference to reference counts for each
1061 // compartment and ion type
1062 for (int ic
= count
= 0; ic
< eCompNR
; ic
++)
1064 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1066 t_swapGroup
*g
= &ir
->swap
->grp
[ig
];
1067 real q
= s
->group
[ig
].q
;
1069 snprintf(buf
, STRLEN
, "%s %s ions (charge %s%g)", CompStr
[ic
], g
->molname
, q
> 0 ? "+" : "", q
);
1070 legend
[count
++] = gmx_strdup(buf
);
1072 snprintf(buf
, STRLEN
, "%s av. mismatch to %d %s ions",
1073 CompStr
[ic
], s
->group
[ig
].comp
[ic
].nMolReq
, g
->molname
);
1074 legend
[count
++] = gmx_strdup(buf
);
1076 snprintf(buf
, STRLEN
, "%s net %s ion influx", CompStr
[ic
], g
->molname
);
1077 legend
[count
++] = gmx_strdup(buf
);
1081 // Center of split groups
1082 snprintf(buf
, STRLEN
, "%scenter of %s of split group 0", SwapStr
[ir
->eSwapCoords
], (nullptr != s
->group
[eGrpSplit0
].m
) ? "mass" : "geometry");
1083 legend
[count
++] = gmx_strdup(buf
);
1084 snprintf(buf
, STRLEN
, "%scenter of %s of split group 1", SwapStr
[ir
->eSwapCoords
], (nullptr != s
->group
[eGrpSplit1
].m
) ? "mass" : "geometry");
1085 legend
[count
++] = gmx_strdup(buf
);
1087 // Ion flux for each channel and ion type
1088 for (int ic
= 0; ic
< eChanNR
; ic
++)
1090 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1092 t_swapGroup
*g
= &ir
->swap
->grp
[ig
];
1093 snprintf(buf
, STRLEN
, "A->ch%d->B %s permeations", ic
, g
->molname
);
1094 legend
[count
++] = gmx_strdup(buf
);
1098 // Number of molecules that leaked from A to B
1099 snprintf(buf
, STRLEN
, "leakage");
1100 legend
[count
++] = gmx_strdup(buf
);
1102 xvgr_legend(s
->fpout
, count
, legend
, oenv
);
1104 fprintf(s
->fpout
, "# Instantaneous ion counts and time-averaged differences to requested numbers\n");
1106 // We add a simple text legend helping to identify the columns with xvgr legend strings
1107 fprintf(s
->fpout
, "# time (ps)");
1108 for (int i
= 0; i
< count
; i
++)
1110 snprintf(buf
, STRLEN
, "s%d", i
);
1111 fprintf(s
->fpout
, "%10s", buf
);
1113 fprintf(s
->fpout
, "\n");
1118 /*! \brief Initialize channel ion flux detection routine.
1120 * Initialize arrays that keep track of where the ions come from and where
1123 static void detect_flux_per_channel_init(
1125 swaphistory_t
*swapstate
,
1126 gmx_bool bStartFromCpt
)
1129 swapstateIons_t
*gs
;
1131 /* All these flux detection routines run on the master only */
1132 if (swapstate
== nullptr)
1137 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1140 gs
= &swapstate
->ionType
[ig
- eSwapFixedGrpNR
];
1142 /******************************************************/
1143 /* Channel and domain history for the individual ions */
1144 /******************************************************/
1145 if (bStartFromCpt
) /* set the pointers right */
1147 g
->comp_from
= gs
->comp_from
;
1148 g
->channel_label
= gs
->channel_label
;
1150 else /* allocate memory for molecule counts */
1152 snew(g
->comp_from
, g
->atomset
.numAtomsGlobal()/g
->apm
);
1153 gs
->comp_from
= g
->comp_from
;
1154 snew(g
->channel_label
, g
->atomset
.numAtomsGlobal()/g
->apm
);
1155 gs
->channel_label
= g
->channel_label
;
1157 snew(g
->comp_now
, g
->atomset
.numAtomsGlobal()/g
->apm
);
1159 /* Initialize the channel and domain history counters */
1160 for (size_t i
= 0; i
< g
->atomset
.numAtomsGlobal()/g
->apm
; i
++)
1162 g
->comp_now
[i
] = eDomainNotset
;
1165 g
->comp_from
[i
] = eDomainNotset
;
1166 g
->channel_label
[i
] = eChHistPassedNone
;
1170 /************************************/
1171 /* Channel fluxes for both channels */
1172 /************************************/
1173 g
->nCyl
[eChan0
] = 0;
1174 g
->nCyl
[eChan1
] = 0;
1180 fprintf(stderr
, "%s Copying channel fluxes from checkpoint file data\n", SwS
);
1184 // Loop over ion types (and both channels)
1185 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1188 gs
= &swapstate
->ionType
[ig
- eSwapFixedGrpNR
];
1190 for (int ic
= 0; ic
< eChanNR
; ic
++)
1192 fprintf(stderr
, "%s Channel %d flux history for ion type %s (charge %g): ", SwS
, ic
, g
->molname
, g
->q
);
1195 g
->fluxfromAtoB
[ic
] = gs
->fluxfromAtoB
[ic
];
1199 g
->fluxfromAtoB
[ic
] = 0;
1202 fprintf(stderr
, "%d molecule%s",
1203 g
->fluxfromAtoB
[ic
], g
->fluxfromAtoB
[ic
] == 1 ? "" : "s");
1204 fprintf(stderr
, "\n");
1208 /* Set pointers for checkpoint writing */
1209 swapstate
->fluxleak_p
= &s
->fluxleak
;
1210 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1213 gs
= &swapstate
->ionType
[ig
- eSwapFixedGrpNR
];
1215 for (int ic
= 0; ic
< eChanNR
; ic
++)
1217 gs
->fluxfromAtoB_p
[ic
] = &g
->fluxfromAtoB
[ic
];
1223 /*! \brief Outputs the initial structure to PDB file for debugging reasons.
1225 * Output the starting structure so that in case of multimeric channels
1226 * the user can check whether we have the correct PBC image for all atoms.
1227 * If this is not correct, the ion counts per channel will be very likely
1230 static void outputStartStructureIfWanted(gmx_mtop_t
*mtop
, rvec
*x
, int ePBC
, const matrix box
)
1232 char *env
= getenv("GMX_COMPELDUMP");
1236 fprintf(stderr
, "\n%s Found env.var. GMX_COMPELDUMP, will output CompEL starting structure made whole.\n"
1237 "%s In case of multimeric channels, please check whether they have the correct PBC representation.\n",
1240 write_sto_conf_mtop("CompELAssumedWholeConfiguration.pdb", *mtop
->name
, mtop
, x
, nullptr, ePBC
, box
);
1245 /*! \brief Initialize the swapstate structure, used for checkpoint writing.
1247 * The swapstate struct stores the information we need to make the channels
1248 * whole again after restarts from a checkpoint file. Here we do the following:
1249 * a) If we did not start from .cpt, we prepare the struct for proper .cpt writing,
1250 * b) if we did start from .cpt, we copy over the last whole structures from .cpt,
1251 * c) in any case, for subsequent checkpoint writing, we set the pointers in
1252 * swapstate to the x_old arrays, which contain the correct PBC representation of
1253 * multimeric channels at the last time step.
1255 static void init_swapstate(
1256 swaphistory_t
*swapstate
,
1259 const rvec
*x
, /* the initial positions */
1263 rvec
*x_pbc
= nullptr; /* positions of the whole MD system with molecules made whole */
1270 /* We always need the last whole positions such that
1271 * in the next time step we can make the channels whole again in PBC */
1272 if (swapstate
->bFromCpt
)
1274 /* Copy the last whole positions of each channel from .cpt */
1275 g
= &(s
->group
[eGrpSplit0
]);
1276 for (size_t i
= 0; i
< g
->atomset
.numAtomsGlobal(); i
++)
1278 copy_rvec(swapstate
->xc_old_whole
[eChan0
][i
], g
->xc_old
[i
]);
1280 g
= &(s
->group
[eGrpSplit1
]);
1281 for (size_t i
= 0; i
< g
->atomset
.numAtomsGlobal(); i
++)
1283 copy_rvec(swapstate
->xc_old_whole
[eChan1
][i
], g
->xc_old
[i
]);
1288 swapstate
->eSwapCoords
= ir
->eSwapCoords
;
1290 /* Set the number of ion types and allocate memory for checkpointing */
1291 swapstate
->nIonTypes
= s
->ngrp
- eSwapFixedGrpNR
;
1292 snew(swapstate
->ionType
, swapstate
->nIonTypes
);
1294 /* Store the total number of ions of each type in the swapstateIons
1295 * structure that is accessible during checkpoint writing */
1296 for (int ii
= 0; ii
< swapstate
->nIonTypes
; ii
++)
1298 swapstateIons_t
*gs
= &swapstate
->ionType
[ii
];
1299 gs
->nMol
= sc
->grp
[ii
+ eSwapFixedGrpNR
].nat
;
1302 /* Extract the initial split group positions. */
1304 /* Remove pbc, make molecule whole. */
1305 snew(x_pbc
, mtop
->natoms
);
1306 copy_rvecn(x
, x_pbc
, 0, mtop
->natoms
);
1308 /* This can only make individual molecules whole, not multimers */
1309 do_pbc_mtop(ir
->ePBC
, box
, mtop
, x_pbc
);
1311 /* Output the starting structure? */
1312 outputStartStructureIfWanted(mtop
, x_pbc
, ir
->ePBC
, box
);
1314 /* If this is the first run (i.e. no checkpoint present) we assume
1315 * that the starting positions give us the correct PBC representation */
1316 for (int ig
= eGrpSplit0
; ig
<= eGrpSplit1
; ig
++)
1318 g
= &(s
->group
[ig
]);
1319 for (size_t i
= 0; i
< g
->atomset
.numAtomsGlobal(); i
++)
1321 copy_rvec(x_pbc
[g
->atomset
.globalIndex()[i
]], g
->xc_old
[i
]);
1326 /* Prepare swapstate arrays for later checkpoint writing */
1327 swapstate
->nat
[eChan0
] = s
->group
[eGrpSplit0
].atomset
.numAtomsGlobal();
1328 swapstate
->nat
[eChan1
] = s
->group
[eGrpSplit1
].atomset
.numAtomsGlobal();
1331 /* For subsequent checkpoint writing, set the swapstate pointers to the xc_old
1332 * arrays that get updated at every swapping step */
1333 swapstate
->xc_old_whole_p
[eChan0
] = &s
->group
[eGrpSplit0
].xc_old
;
1334 swapstate
->xc_old_whole_p
[eChan1
] = &s
->group
[eGrpSplit1
].xc_old
;
1337 /*! \brief Determine the total charge imbalance resulting from the swap groups */
1338 static real
getRequestedChargeImbalance(t_swap
*s
)
1343 real particle_charge
;
1344 real particle_number
[eCompNR
];
1346 // s->deltaQ = ( (-1) * s->comp[eCompA][eIonNEG].nat_req + s->comp[eCompA][eIonPOS].nat_req )
1347 // - ( (-1) * s->comp[eCompB][eIonNEG].nat_req + s->comp[eCompB][eIonPOS].nat_req );
1349 for (ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1353 particle_charge
= g
->q
;
1354 particle_number
[eCompA
] = g
->comp
[eCompA
].nMolReq
;
1355 particle_number
[eCompB
] = g
->comp
[eCompB
].nMolReq
;
1357 DeltaQ
+= particle_charge
* (particle_number
[eCompA
] - particle_number
[eCompB
]);
1364 /*! \brief Sorts anions and cations into two separate groups
1366 * This routine should be called for the 'anions' and 'cations' group,
1367 * of which the indices were lumped together in the older version of the code.
1369 static void copyIndicesToGroup(
1377 /* If explicit ion counts were requested in the .mdp file
1378 * (by setting positive values for the number of ions),
1379 * we can make an additional consistency check here */
1380 if ( (g
->nmolReq
[eCompA
] < 0) && (g
->nmolReq
[eCompB
] < 0) )
1382 if (g
->nat
!= (g
->nmolReq
[eCompA
] + g
->nmolReq
[eCompB
]) )
1384 gmx_fatal_collective(FARGS
, cr
->mpi_comm_mysim
, MASTER(cr
),
1385 "%s Inconsistency while importing swap-related data from an old input file version.\n"
1386 "%s The requested ion counts in compartments A (%d) and B (%d)\n"
1387 "%s do not add up to the number of ions (%d) of this type for the group '%s'.\n",
1388 SwS
, SwSEmpty
, g
->nmolReq
[eCompA
], g
->nmolReq
[eCompB
], SwSEmpty
, g
->nat
, g
->molname
);
1392 srenew(g
->ind
, g
->nat
);
1393 for (int i
= 0; i
< g
->nat
; i
++)
1395 g
->ind
[i
] = indIons
[i
];
1400 /*! \brief Converts old .tpr file CompEL contents to new data layout.
1402 * If we have read an old .tpr file (tpxv <= tpxv_CompElPolyatomicIonsAndMultipleIonTypes),
1403 * anions and cations are stored together in group #3. In the new
1404 * format we store each ion type in a separate group.
1405 * The 'classic' groups are:
1406 * #0 split group 0 - OK
1407 * #1 split group 1 - OK
1409 * #3 anions - contains also cations, needs to be converted
1410 * #4 cations - empty before conversion
1413 static void convertOldToNewGroupFormat(
1419 t_swapGroup
*g
= &sc
->grp
[3];
1421 /* Loop through the atom indices of group #3 (anions) and put all indices
1422 * that belong to cations into the cation group.
1426 int *indAnions
= nullptr;
1427 int *indCations
= nullptr;
1428 snew(indAnions
, g
->nat
);
1429 snew(indCations
, g
->nat
);
1432 for (int i
= 0; i
< g
->nat
; i
++)
1434 const t_atom
&atom
= mtopGetAtomParameters(mtop
, g
->ind
[i
], &molb
);
1437 // This is an anion, add it to the list of anions
1438 indAnions
[nAnions
++] = g
->ind
[i
];
1442 // This is a cation, add it to the list of cations
1443 indCations
[nCations
++] = g
->ind
[i
];
1449 fprintf(stdout
, "%s Sorted %d ions into separate groups of %d anions and %d cations.\n",
1450 SwS
, g
->nat
, nAnions
, nCations
);
1454 /* Now we have the correct lists of anions and cations.
1455 * Copy it to the right groups.
1457 copyIndicesToGroup(indAnions
, nAnions
, g
, cr
);
1459 copyIndicesToGroup(indCations
, nCations
, g
, cr
);
1465 /*! \brief Returns TRUE if we started from an old .tpr
1467 * Then we need to re-sort anions and cations into separate groups */
1468 static gmx_bool
bConvertFromOldTpr(t_swapcoords
*sc
)
1470 // If the last group has no atoms it means we need to convert!
1471 return (sc
->ngrp
>= 5) && (0 == sc
->grp
[4].nat
);
1475 void init_swapcoords(
1480 const t_state
*globalState
,
1481 ObservablesHistory
*oh
,
1483 gmx::LocalAtomSetManager
*atomSets
,
1484 const gmx_output_env_t
*oenv
,
1485 const gmx::MdrunOptions
&mdrunOptions
)
1490 swapstateIons_t
*gs
;
1491 gmx_bool bAppend
, bStartFromCpt
;
1492 swaphistory_t
*swapstate
= nullptr;
1494 if ( (PAR(cr
)) && !DOMAINDECOMP(cr
) )
1496 gmx_fatal(FARGS
, "Position swapping is only implemented for domain decomposition!");
1499 bAppend
= mdrunOptions
.continuationOptions
.appendFiles
;
1500 bStartFromCpt
= mdrunOptions
.continuationOptions
.startedFromCheckpoint
;
1503 sc
->si_priv
= new t_swap();
1506 if (mdrunOptions
.rerun
)
1510 gmx_fatal(FARGS
, "%s This module does not support reruns in parallel\nPlease request a serial run with -nt 1 / -np 1\n", SwS
);
1513 fprintf(stderr
, "%s Rerun - using every available frame\n", SwS
);
1515 sc
->nAverage
= 1; /* averaging makes no sense for reruns */
1518 if (MASTER(cr
) && !bAppend
)
1520 fprintf(fplog
, "\nInitializing ion/water position exchanges\n");
1521 please_cite(fplog
, "Kutzner2011b");
1524 switch (ir
->eSwapCoords
)
1540 const gmx_bool bVerbose
= mdrunOptions
.verbose
;
1542 // For compatibility with old .tpr files
1543 if (bConvertFromOldTpr(sc
) )
1545 convertOldToNewGroupFormat(sc
, mtop
, bVerbose
&& MASTER(cr
), cr
);
1548 /* Copy some data and pointers to the group structures for convenience */
1549 /* Number of atoms in the group */
1551 for (int i
= 0; i
< s
->ngrp
; i
++)
1553 s
->group
.emplace_back(atomSets
->add(gmx::ArrayRef
<const int>( sc
->grp
[i
].ind
, sc
->grp
[i
].ind
+sc
->grp
[i
].nat
)));
1554 s
->group
[i
].molname
= sc
->grp
[i
].molname
;
1557 /* Check for overlapping atoms */
1558 check_swap_groups(s
, mtop
->natoms
, bVerbose
&& MASTER(cr
));
1560 /* Allocate space for the collective arrays for all groups */
1561 /* For the collective position array */
1562 for (int i
= 0; i
< s
->ngrp
; i
++)
1565 snew(g
->xc
, g
->atomset
.numAtomsGlobal());
1567 /* For the split groups (the channels) we need some extra memory to
1568 * be able to make the molecules whole even if they span more than
1569 * half of the box size. */
1570 if ( (i
== eGrpSplit0
) || (i
== eGrpSplit1
) )
1572 snew(g
->xc_shifts
, g
->atomset
.numAtomsGlobal());
1573 snew(g
->xc_eshifts
, g
->atomset
.numAtomsGlobal());
1574 snew(g
->xc_old
, g
->atomset
.numAtomsGlobal());
1580 if (oh
->swapHistory
== nullptr)
1582 oh
->swapHistory
= std::make_unique
<swaphistory_t
>(swaphistory_t
{});
1584 swapstate
= oh
->swapHistory
.get();
1586 init_swapstate(swapstate
, sc
, mtop
, globalState
->x
.rvec_array(), globalState
->box
, ir
);
1589 /* After init_swapstate we have a set of (old) whole positions for our
1590 * channels. Now transfer that to all nodes */
1593 for (int ig
= eGrpSplit0
; ig
<= eGrpSplit1
; ig
++)
1595 g
= &(s
->group
[ig
]);
1596 gmx_bcast((g
->atomset
.numAtomsGlobal())*sizeof((g
->xc_old
)[0]), g
->xc_old
, (cr
));
1600 /* Make sure that all molecules in the solvent and ion groups contain the
1601 * same number of atoms each */
1602 for (int ig
= eGrpSolvent
; ig
< s
->ngrp
; ig
++)
1606 g
= &(s
->group
[ig
]);
1607 g
->apm
= get_group_apm_check(ig
, s
, MASTER(cr
) && bVerbose
, mtop
);
1609 /* Since all molecules of a group are equal, we only need enough space
1610 * to determine properties of a single molecule at at time */
1611 snew(g
->m
, g
->apm
); /* For the center of mass */
1612 charge
= 0; /* To determine the charge imbalance */
1614 for (int j
= 0; j
< g
->apm
; j
++)
1616 const t_atom
&atom
= mtopGetAtomParameters(mtop
, g
->atomset
.globalIndex()[j
], &molb
);
1620 /* Total charge of one molecule of this group: */
1625 /* Need mass-weighted center of split group? */
1626 for (int j
= eGrpSplit0
; j
<= eGrpSplit1
; j
++)
1629 if (sc
->massw_split
[j
])
1631 /* Save the split group masses if mass-weighting is requested */
1632 snew(g
->m
, g
->atomset
.numAtomsGlobal());
1634 for (size_t i
= 0; i
< g
->atomset
.numAtomsGlobal(); i
++)
1636 g
->m
[i
] = mtopGetAtomMass(mtop
, g
->atomset
.globalIndex()[i
], &molb
);
1641 /* Make a t_pbc struct on all nodes so that the molecules
1642 * chosen for an exchange can be made whole. */
1649 fprintf(stderr
, "%s Opening output file %s%s\n", SwS
, fn
, bAppend
? " for appending" : "");
1652 s
->fpout
= gmx_fio_fopen(fn
, bAppend
? "a" : "w" );
1656 xvgr_header(s
->fpout
, "Molecule counts", "Time (ps)", "counts", exvggtXNY
, oenv
);
1658 for (int ig
= 0; ig
< s
->ngrp
; ig
++)
1660 g
= &(s
->group
[ig
]);
1661 fprintf(s
->fpout
, "# %s group '%s' contains %d atom%s",
1662 ig
< eSwapFixedGrpNR
? eSwapFixedGrp_names
[ig
] : "Ion",
1663 g
->molname
, static_cast<int>(g
->atomset
.numAtomsGlobal()), (g
->atomset
.numAtomsGlobal() > 1) ? "s" : "");
1664 if (!(eGrpSplit0
== ig
|| eGrpSplit1
== ig
) )
1666 fprintf(s
->fpout
, " with %d atom%s in each molecule of charge %g",
1667 g
->apm
, (g
->apm
> 1) ? "s" : "", g
->q
);
1669 fprintf(s
->fpout
, ".\n");
1672 fprintf(s
->fpout
, "#\n# Initial positions of split groups:\n");
1675 for (int j
= eGrpSplit0
; j
<= eGrpSplit1
; j
++)
1678 for (size_t i
= 0; i
< g
->atomset
.numAtomsGlobal(); i
++)
1680 copy_rvec(globalState
->x
[sc
->grp
[j
].ind
[i
]], g
->xc
[i
]);
1682 /* xc has the correct PBC representation for the two channels, so we do
1683 * not need to correct for that */
1684 get_center(g
->xc
, g
->m
, g
->atomset
.numAtomsGlobal(), g
->center
);
1687 fprintf(s
->fpout
, "# %s group %s-center %5f nm\n", eSwapFixedGrp_names
[j
],
1688 DimStr
[s
->swapdim
], g
->center
[s
->swapdim
]);
1694 if ( (0 != sc
->bulkOffset
[eCompA
]) || (0 != sc
->bulkOffset
[eCompB
]) )
1696 fprintf(s
->fpout
, "#\n");
1697 fprintf(s
->fpout
, "# You provided an offset for the position of the bulk layer(s).\n");
1698 fprintf(s
->fpout
, "# That means the layers to/from which ions and water molecules are swapped\n");
1699 fprintf(s
->fpout
, "# are not midway (= at 0.0) between the compartment-defining layers (at +/- 1.0).\n");
1700 fprintf(s
->fpout
, "# bulk-offsetA = %g\n", sc
->bulkOffset
[eCompA
]);
1701 fprintf(s
->fpout
, "# bulk-offsetB = %g\n", sc
->bulkOffset
[eCompB
]);
1704 fprintf(s
->fpout
, "#\n");
1705 fprintf(s
->fpout
, "# Split0 cylinder radius %f nm, up %f nm, down %f nm\n",
1706 sc
->cyl0r
, sc
->cyl0u
, sc
->cyl0l
);
1707 fprintf(s
->fpout
, "# Split1 cylinder radius %f nm, up %f nm, down %f nm\n",
1708 sc
->cyl1r
, sc
->cyl1u
, sc
->cyl1l
);
1710 fprintf(s
->fpout
, "#\n");
1711 if (!mdrunOptions
.rerun
)
1713 fprintf(s
->fpout
, "# Coupling constant (number of swap attempt steps to average over): %d (translates to %f ps).\n",
1714 sc
->nAverage
, sc
->nAverage
*sc
->nstswap
*ir
->delta_t
);
1715 fprintf(s
->fpout
, "# Threshold is %f\n", sc
->threshold
);
1716 fprintf(s
->fpout
, "#\n");
1717 fprintf(s
->fpout
, "# Remarks about which atoms passed which channel use global atoms numbers starting at one.\n");
1726 /* Allocate memory to remember the past particle counts for time averaging */
1727 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1729 g
= &(s
->group
[ig
]);
1730 for (int ic
= 0; ic
< eCompNR
; ic
++)
1732 snew(g
->comp
[ic
].nMolPast
, sc
->nAverage
);
1736 /* Get the initial particle concentrations and let the other nodes know */
1741 get_initial_ioncounts_from_cpt(ir
, swapstate
, cr
, bVerbose
);
1745 fprintf(stderr
, "%s Determining initial numbers of ions per compartment.\n", SwS
);
1746 get_initial_ioncounts(ir
, globalState
->x
.rvec_array(), globalState
->box
, cr
, mdrunOptions
.rerun
);
1749 /* Prepare (further) checkpoint writes ... */
1752 /* Consistency check */
1753 if (swapstate
->nAverage
!= sc
->nAverage
)
1755 gmx_fatal(FARGS
, "%s Ion count averaging steps mismatch! checkpoint: %d, tpr: %d",
1756 SwS
, swapstate
->nAverage
, sc
->nAverage
);
1761 swapstate
->nAverage
= sc
->nAverage
;
1763 fprintf(stderr
, "%s Setting pointers for checkpoint writing\n", SwS
);
1764 for (int ic
= 0; ic
< eCompNR
; ic
++)
1766 for (int ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1769 gs
= &swapstate
->ionType
[ig
- eSwapFixedGrpNR
];
1771 gs
->nMolReq_p
[ic
] = &(g
->comp
[ic
].nMolReq
);
1772 gs
->nMolPast_p
[ic
] = &(g
->comp
[ic
].nMolPast
[0]);
1773 gs
->inflow_net_p
[ic
] = &(g
->comp
[ic
].inflow_net
);
1777 /* Determine the total charge imbalance */
1778 s
->deltaQ
= getRequestedChargeImbalance(s
);
1782 fprintf(stderr
, "%s Requested charge imbalance is Q(A) - Q(B) = %g e.\n", SwS
, s
->deltaQ
);
1786 fprintf(s
->fpout
, "# Requested charge imbalance is Q(A)-Q(B) = %g e.\n", s
->deltaQ
);
1792 bc_initial_concentrations(cr
, ir
->swap
);
1795 /* Update the time-averaged number of molecules for all groups and compartments */
1796 for (int ig
= eSwapFixedGrpNR
; ig
< sc
->ngrp
; ig
++)
1799 for (int ic
= 0; ic
< eCompNR
; ic
++)
1801 update_time_window(&g
->comp
[ic
], sc
->nAverage
, -1);
1805 /* Initialize arrays that keep track of through which channel the ions go */
1806 detect_flux_per_channel_init(s
, swapstate
, bStartFromCpt
);
1808 /* We need to print the legend if we open this file for the first time. */
1809 if (MASTER(cr
) && !bAppend
)
1811 print_ionlist_legend(ir
, oenv
);
1816 void finish_swapcoords(t_swapcoords
*sc
)
1818 if (sc
->si_priv
->fpout
)
1820 // Close the swap output file
1821 gmx_fio_fclose(sc
->si_priv
->fpout
);
1825 /*! \brief Do we need to swap a molecule in any of the ion groups with a water molecule at this step?
1827 * From the requested and average molecule counts we determine whether a swap is needed
1828 * at this time step.
1830 static gmx_bool
need_swap(t_swapcoords
*sc
)
1838 for (ig
= eSwapFixedGrpNR
; ig
< sc
->ngrp
; ig
++)
1842 for (ic
= 0; ic
< eCompNR
; ic
++)
1844 if (g
->comp
[ic
].nMolReq
- g
->comp
[ic
].nMolAv
>= sc
->threshold
)
1854 /*! \brief Return the index of an atom or molecule suitable for swapping.
1856 * Returns the index of an atom that is far off the compartment boundaries,
1857 * that is near to the bulk layer to/from which the swaps take place.
1858 * Other atoms of the molecule (if any) will directly follow the returned index.
1860 * \param[in] comp Structure containing compartment-specific data.
1861 * \param[in] molname Name of the molecule.
1863 * \returns Index of the first atom of the molecule chosen for a position exchange.
1865 static int get_index_of_distant_atom(
1866 t_compartment
*comp
,
1867 const char molname
[])
1870 real d
= GMX_REAL_MAX
;
1873 /* comp->nat contains the original number of atoms in this compartment
1874 * prior to doing any swaps. Some of these atoms may already have been
1875 * swapped out, but then they are marked with a distance of GMX_REAL_MAX
1877 for (int iMol
= 0; iMol
< comp
->nMolBefore
; iMol
++)
1879 if (comp
->dist
[iMol
] < d
)
1882 d
= comp
->dist
[ibest
];
1888 gmx_fatal(FARGS
, "Could not get index of %s atom. Compartment contains %d %s molecules before swaps.",
1889 molname
, comp
->nMolBefore
, molname
);
1892 /* Set the distance of this index to infinity such that it won't get selected again in
1895 comp
->dist
[ibest
] = GMX_REAL_MAX
;
1897 return comp
->ind
[ibest
];
1901 /*! \brief Swaps centers of mass and makes molecule whole if broken */
1902 static void translate_positions(
1910 rvec reference
, dx
, correctPBCimage
;
1913 /* Use the first atom as the reference for PBC */
1914 copy_rvec(x
[0], reference
);
1916 for (i
= 0; i
< apm
; i
++)
1918 /* PBC distance between position and reference */
1919 pbc_dx(pbc
, x
[i
], reference
, dx
);
1921 /* Add PBC distance to reference */
1922 rvec_add(reference
, dx
, correctPBCimage
);
1924 /* Subtract old_com from correct image and add new_com */
1925 rvec_dec(correctPBCimage
, old_com
);
1926 rvec_inc(correctPBCimage
, new_com
);
1928 copy_rvec(correctPBCimage
, x
[i
]);
1933 /*! \brief Write back the the modified local positions from the collective array to the official positions. */
1934 static void apply_modified_positions(
1938 auto collectiveIndex
= g
->atomset
.collectiveIndex().begin();
1939 for (const auto localIndex
: g
->atomset
.localIndex())
1941 /* Copy the possibly modified position */
1942 copy_rvec(g
->xc
[*collectiveIndex
], x
[localIndex
]);
1948 gmx_bool
do_swapcoords(
1953 gmx_wallcycle
*wcycle
,
1961 int j
, ic
, ig
, nswaps
;
1962 int thisC
, otherC
; /* Index into this compartment and the other one */
1963 gmx_bool bSwap
= FALSE
;
1964 t_swapgrp
*g
, *gsol
;
1966 rvec com_solvent
, com_particle
; /* solvent and swap molecule's center of mass */
1969 wallcycle_start(wcycle
, ewcSWAP
);
1974 set_pbc(s
->pbc
, ir
->ePBC
, box
);
1976 /* Assemble the positions of the split groups, i.e. the channels.
1977 * Here we also pass a shifts array to communicate_group_positions(), so that it can make
1978 * the molecules whole even in cases where they span more than half of the box in
1980 for (ig
= eGrpSplit0
; ig
<= eGrpSplit1
; ig
++)
1982 g
= &(s
->group
[ig
]);
1983 communicate_group_positions(cr
, g
->xc
, g
->xc_shifts
, g
->xc_eshifts
, TRUE
,
1984 x
, g
->atomset
.numAtomsGlobal(), g
->atomset
.numAtomsLocal(), g
->atomset
.localIndex().data(), g
->atomset
.collectiveIndex().data(), g
->xc_old
, box
);
1986 get_center(g
->xc
, g
->m
, g
->atomset
.numAtomsGlobal(), g
->center
); /* center of split groups == channels */
1989 /* Assemble the positions of the ions (ig = 3, 4, ...). These molecules should
1990 * be small and we can always make them whole with a simple distance check.
1991 * Therefore we pass NULL as third argument. */
1992 for (ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
1994 g
= &(s
->group
[ig
]);
1995 communicate_group_positions(cr
, g
->xc
, nullptr, nullptr, FALSE
,
1996 x
, g
->atomset
.numAtomsGlobal(), g
->atomset
.numAtomsLocal(), g
->atomset
.localIndex().data(), g
->atomset
.collectiveIndex().data(), nullptr, nullptr);
1998 /* Determine how many ions of this type each compartment contains */
1999 sortMoleculesIntoCompartments(g
, cr
, sc
, box
, step
, s
->fpout
, bRerun
, FALSE
);
2002 /* Output how many ions are in the compartments */
2005 print_ionlist(s
, t
, "");
2008 /* If we are doing a rerun, we are finished here, since we cannot perform
2015 /* Do we have to perform a swap? */
2016 bSwap
= need_swap(sc
);
2019 /* Since we here know that we have to perform ion/water position exchanges,
2020 * we now assemble the solvent positions */
2021 g
= &(s
->group
[eGrpSolvent
]);
2022 communicate_group_positions(cr
, g
->xc
, nullptr, nullptr, FALSE
,
2023 x
, g
->atomset
.numAtomsGlobal(), g
->atomset
.numAtomsLocal(), g
->atomset
.localIndex().data(), g
->atomset
.collectiveIndex().data(), nullptr, nullptr);
2025 /* Determine how many molecules of solvent each compartment contains */
2026 sortMoleculesIntoCompartments(g
, cr
, sc
, box
, step
, s
->fpout
, bRerun
, TRUE
);
2028 /* Save number of solvent molecules per compartment prior to any swaps */
2029 g
->comp
[eCompA
].nMolBefore
= g
->comp
[eCompA
].nMol
;
2030 g
->comp
[eCompB
].nMolBefore
= g
->comp
[eCompB
].nMol
;
2032 for (ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
2034 g
= &(s
->group
[ig
]);
2036 for (ic
= 0; ic
< eCompNR
; ic
++)
2038 /* Determine in which compartment ions are missing and where they are too many */
2039 g
->vacancy
[ic
] = g
->comp
[ic
].nMolReq
- g
->comp
[ic
].nMolAv
;
2041 /* Save number of ions per compartment prior to swaps */
2042 g
->comp
[ic
].nMolBefore
= g
->comp
[ic
].nMol
;
2046 /* Now actually perform the particle exchanges, one swap group after another */
2047 gsol
= &s
->group
[eGrpSolvent
];
2048 for (ig
= eSwapFixedGrpNR
; ig
< s
->ngrp
; ig
++)
2052 for (thisC
= 0; thisC
< eCompNR
; thisC
++)
2054 /* Index to the other compartment */
2055 otherC
= (thisC
+1) % eCompNR
;
2057 while (g
->vacancy
[thisC
] >= sc
->threshold
)
2059 /* Swap in an ion */
2061 /* Get the xc-index of the first atom of a solvent molecule of this compartment */
2062 isol
= get_index_of_distant_atom(&gsol
->comp
[thisC
], gsol
->molname
);
2064 /* Get the xc-index of a particle from the other compartment */
2065 iion
= get_index_of_distant_atom(&g
->comp
[otherC
], g
->molname
);
2067 get_molecule_center(&gsol
->xc
[isol
], gsol
->apm
, gsol
->m
, com_solvent
, s
->pbc
);
2068 get_molecule_center(&g
->xc
[iion
], g
->apm
, g
->m
, com_particle
, s
->pbc
);
2070 /* Subtract solvent molecule's center of mass and add swap particle's center of mass */
2071 translate_positions(&gsol
->xc
[isol
], gsol
->apm
, com_solvent
, com_particle
, s
->pbc
);
2072 /* Similarly for the swap particle, subtract com_particle and add com_solvent */
2073 translate_positions(&g
->xc
[iion
], g
->apm
, com_particle
, com_solvent
, s
->pbc
);
2075 /* Keep track of the changes */
2076 g
->vacancy
[thisC
]--;
2077 g
->vacancy
[otherC
]++;
2078 g
->comp
[thisC
].nMol
++;
2079 g
->comp
[otherC
].nMol
--;
2080 g
->comp
[thisC
].inflow_net
++;
2081 g
->comp
[otherC
].inflow_net
--;
2082 /* Correct the past time window to still get the right averages from now on */
2083 g
->comp
[thisC
].nMolAv
++;
2084 g
->comp
[otherC
].nMolAv
--;
2085 for (j
= 0; j
< sc
->nAverage
; j
++)
2087 g
->comp
[thisC
].nMolPast
[j
]++;
2088 g
->comp
[otherC
].nMolPast
[j
]--;
2090 /* Clear ion history */
2093 int iMol
= iion
/ g
->apm
;
2094 g
->channel_label
[iMol
] = eChHistPassedNone
;
2095 g
->comp_from
[iMol
] = eDomainNotset
;
2097 /* That was the swap */
2102 if (nswaps
&& bVerbose
)
2104 fprintf(stderr
, "%s Performed %d swap%s in step %" PRId64
" for iontype %s.\n",
2105 SwS
, nswaps
, nswaps
> 1 ? "s" : "", step
, g
->molname
);
2109 if (s
->fpout
!= nullptr)
2111 print_ionlist(s
, t
, " # after swap");
2114 /* For the solvent and user-defined swap groups, each rank writes back its
2115 * (possibly modified) local positions to the official position array. */
2116 for (ig
= eGrpSolvent
; ig
< s
->ngrp
; ig
++)
2119 apply_modified_positions(g
, x
);
2122 } /* end of if(bSwap) */
2124 wallcycle_stop(wcycle
, ewcSWAP
);