forked from gfrd/egfrd
-
Notifications
You must be signed in to change notification settings - Fork 0
/
EGFRDSimulator.hpp
3944 lines (3475 loc) · 142 KB
/
EGFRDSimulator.hpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#ifndef EGFRDSIMULATOR_HPP
#define EGFRDSIMULATOR_HPP
#include <boost/bind.hpp>
#include <boost/array.hpp>
#include <boost/format.hpp>
#include <boost/optional.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/scoped_ptr.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/fusion/container/map.hpp>
#include <boost/fusion/algorithm/iteration/for_each.hpp>
#include <boost/fusion/sequence/intrinsic/at_key.hpp>
#include <boost/fusion/sequence/intrinsic/value_at_key.hpp>
#include <boost/fusion/include/at_key.hpp>
#include <boost/none_t.hpp>
#include <boost/variant.hpp>
#include "utils/array_helper.hpp"
#include "utils/get_mapper_mf.hpp"
#include "utils/fun_composition.hpp"
#include "utils/fun_wrappers.hpp"
#include "utils/pointer_as_ref.hpp"
#include "utils/pair.hpp"
#include "utils/math.hpp"
#include "utils/stringizer.hpp"
#include "ShellID.hpp"
#include "DomainID.hpp"
#include "Shell.hpp"
#include "EventScheduler.hpp"
#include "PairGreensFunction.hpp"
#include "ParticleSimulator.hpp"
#include "MatrixSpace.hpp"
#include "AnalyticalSingle.hpp"
#include "AnalyticalPair.hpp"
#include "Multi.hpp"
#include "GreensFunction3DRadAbs.hpp"
#include "GreensFunction3DRadInf.hpp"
#include "GreensFunction3DAbsSym.hpp"
#include "GreensFunction3DAbs.hpp"
#include "GreensFunction3D.hpp"
template<typename Tworld_>
struct EGFRDSimulatorTraitsBase: public ParticleSimulatorTraitsBase<Tworld_>
{
typedef ParticleSimulatorTraitsBase<Tworld_> base_type;
typedef Tworld_ world_type;
typedef ShellID shell_id_type;
typedef DomainID domain_id_type;
typedef SerialIDGenerator<shell_id_type> shell_id_generator;
typedef SerialIDGenerator<domain_id_type> domain_id_generator; typedef Domain<EGFRDSimulatorTraitsBase> domain_type;
typedef std::pair<const domain_id_type, boost::shared_ptr<domain_type> > domain_id_pair;
typedef EventScheduler<typename base_type::time_type> event_scheduler_type;
typedef typename event_scheduler_type::identifier_type event_id_type;
typedef typename event_scheduler_type::Event event_type;
typedef typename event_scheduler_type::value_type event_id_pair_type;
template<typename Tshape_>
struct shell_generator
{
typedef Shell<Tshape_, domain_id_type> type;
};
static const Real SAFETY = 1. + 1e-5;
static const Real SINGLE_SHELL_FACTOR = .1;
static const Real MULTI_SHELL_FACTOR = .05;
static const Real DEFAULT_DT_FACTOR = 1e-5;
static const Real CUTOFF_FACTOR = 5.6;
};
namespace detail {
template<typename T_>
struct get_greens_function {};
template<typename T_>
struct get_greens_function<Sphere<T_> >
{
typedef GreensFunction3DAbsSym type;
};
template<typename T_>
struct get_greens_function<Cylinder<T_> >
{
typedef GreensFunction3DAbsSym type;
};
template<typename T_>
struct get_pair_greens_function {};
template<typename T_>
struct get_pair_greens_function<Sphere<T_> >
{
typedef GreensFunction3DRadAbs iv_type;
typedef GreensFunction3DAbsSym com_type;
};
template<typename T_>
struct get_pair_greens_function<Cylinder<T_> >
{
typedef GreensFunction3DRadAbs iv_type;
typedef GreensFunction3DAbsSym com_type;
};
} // namespace detail
template<typename Ttraits_>
class EGFRDSimulator;
template<typename Ttraits_>
struct ImmutativeDomainVisitor
{
typedef typename EGFRDSimulator<Ttraits_>::multi_type multi_type;
typedef typename EGFRDSimulator<Ttraits_>::spherical_single_type spherical_single_type;
typedef typename EGFRDSimulator<Ttraits_>::cylindrical_single_type cylindrical_single_type;
typedef typename EGFRDSimulator<Ttraits_>::spherical_pair_type spherical_pair_type;
typedef typename EGFRDSimulator<Ttraits_>::cylindrical_pair_type cylindrical_pair_type;
virtual ~ImmutativeDomainVisitor() {}
virtual void operator()(multi_type const&) const = 0;
virtual void operator()(spherical_single_type const&) const = 0;
virtual void operator()(cylindrical_single_type const&) const = 0;
virtual void operator()(spherical_pair_type const&) const = 0;
virtual void operator()(cylindrical_pair_type const&) const = 0;
};
template<typename Ttraits_>
struct MutativeDomainVisitor
{
typedef typename EGFRDSimulator<Ttraits_>::multi_type multi_type;
typedef typename EGFRDSimulator<Ttraits_>::spherical_single_type spherical_single_type;
typedef typename EGFRDSimulator<Ttraits_>::cylindrical_single_type cylindrical_single_type;
typedef typename EGFRDSimulator<Ttraits_>::spherical_pair_type spherical_pair_type;
typedef typename EGFRDSimulator<Ttraits_>::cylindrical_pair_type cylindrical_pair_type;
virtual ~MutativeDomainVisitor() {}
virtual void operator()(multi_type&) const = 0;
virtual void operator()(spherical_single_type&) const = 0;
virtual void operator()(cylindrical_single_type&) const = 0;
virtual void operator()(spherical_pair_type&) const = 0;
virtual void operator()(cylindrical_pair_type&) const = 0;
};
#define CHECK(expr) \
do \
{ \
if (!(expr)) { retval = false; LOG_DEBUG(("checking [%s] failed", #expr)); } \
} while (0)
template<typename Ttraits_>
class EGFRDSimulator: public ParticleSimulator<Ttraits_>
{
public:
typedef Ttraits_ traits_type;
typedef ParticleSimulator<Ttraits_> base_type;
typedef typename base_type::sphere_type sphere_type;
typedef typename base_type::cylinder_type cylinder_type;
typedef typename base_type::disk_type disk_type;
typedef typename base_type::particle_simulation_structure_type particle_simulation_structure_type;
typedef typename base_type::spherical_surface_type spherical_surface_type;
typedef typename base_type::cylindrical_surface_type cylindrical_surface_type;
typedef typename base_type::disk_surface_type disk_surface_type;
typedef typename base_type::planar_surface_type planar_surface_type;
typedef typename base_type::cuboidal_region_type cuboidal_region_type;
typedef typename traits_type::world_type world_type;
typedef typename traits_type::domain_id_type domain_id_type;
typedef typename traits_type::shell_id_type shell_id_type;
typedef typename traits_type::template shell_generator<sphere_type>::type spherical_shell_type;
typedef typename traits_type::template shell_generator<cylinder_type>::type cylindrical_shell_type;
typedef std::pair<const shell_id_type, spherical_shell_type> spherical_shell_id_pair;
typedef std::pair<const shell_id_type, cylindrical_shell_type> cylindrical_shell_id_pair;
typedef typename traits_type::shell_id_generator shell_id_generator;
typedef typename traits_type::domain_id_generator domain_id_generator;
typedef typename traits_type::network_rules_type network_rules_type;
typedef typename world_type::traits_type::length_type length_type;
typedef typename world_type::traits_type::position_type position_type;
typedef typename world_type::traits_type::rng_type rng_type;
typedef typename world_type::traits_type::particle_type particle_type;
typedef typename world_type::traits_type::D_type D_type;
typedef typename world_type::traits_type::species_type species_type;
typedef typename world_type::traits_type::species_id_type species_id_type;
typedef typename world_type::traits_type::structure_type structure_type;
typedef typename world_type::particle_shape_type particle_shape_type;
typedef typename world_type::traits_type::particle_id_type particle_id_type;
typedef typename world_type::particle_id_pair particle_id_pair;
typedef typename world_type::particle_id_pair_and_distance particle_id_pair_and_distance;
typedef typename world_type::particle_id_pair_and_distance_list particle_id_pair_and_distance_list;
typedef typename traits_type::domain_type domain_type;
typedef typename traits_type::domain_id_pair domain_id_pair;
typedef typename traits_type::time_type time_type;
typedef Single<traits_type> single_type;
typedef Pair<traits_type> pair_type;
typedef Multi<EGFRDSimulator> multi_type;
typedef ShapedDomain<traits_type> shaped_domain_type;
typedef AnalyticalSingle<traits_type, spherical_shell_type> spherical_single_type;
typedef AnalyticalSingle<traits_type, cylindrical_shell_type> cylindrical_single_type;
typedef AnalyticalPair<traits_type, spherical_shell_type> spherical_pair_type;
typedef AnalyticalPair<traits_type, cylindrical_shell_type> cylindrical_pair_type;
typedef typename traits_type::reaction_record_type reaction_record_type;
typedef typename traits_type::reaction_recorder_type reaction_recorder_type;
typedef typename traits_type::event_scheduler_type event_scheduler_type;
typedef typename traits_type::event_type event_type;
typedef typename traits_type::event_id_type event_id_type;
typedef typename traits_type::event_id_pair_type event_id_pair_type;
typedef boost::variant<boost::none_t, spherical_shell_type, cylindrical_shell_type> shell_variant_type;
enum domain_kind
{
NONE = 0,
SPHERICAL_SINGLE,
CYLINDRICAL_SINGLE,
SPHERICAL_PAIR,
CYLINDRICAL_PAIR,
MULTI,
NUM_DOMAIN_KINDS
};
enum single_event_kind
{
SINGLE_EVENT_REACTION,
SINGLE_EVENT_ESCAPE,
NUM_SINGLE_EVENT_KINDS
};
enum pair_event_kind
{
PAIR_EVENT_SINGLE_REACTION_0,
PAIR_EVENT_SINGLE_REACTION_1,
PAIR_EVENT_COM_ESCAPE,
PAIR_EVENT_IV_UNDETERMINED,
PAIR_EVENT_IV_ESCAPE,
PAIR_EVENT_IV_REACTION,
NUM_PAIR_EVENT_KINDS
};
protected:
typedef boost::fusion::map<
boost::fusion::pair<spherical_shell_type,
MatrixSpace<spherical_shell_type,
shell_id_type, get_mapper_mf>&>,
boost::fusion::pair<cylindrical_shell_type, MatrixSpace<cylindrical_shell_type,
shell_id_type, get_mapper_mf>&> >
shell_matrix_map_type;
typedef typename boost::remove_reference<
typename boost::fusion::result_of::value_at_key<
shell_matrix_map_type,
spherical_shell_type>::type>::type
spherical_shell_matrix_type;
typedef typename boost::remove_reference<
typename boost::fusion::result_of::value_at_key<
shell_matrix_map_type,
cylindrical_shell_type>::type>::type
cylindrical_shell_matrix_type;
typedef typename get_mapper_mf<domain_id_type, boost::shared_ptr<domain_type> >::type domain_map;
typedef typename network_rules_type::reaction_rules reaction_rules;
typedef typename network_rules_type::reaction_rule_type reaction_rule_type;
typedef typename traits_type::rate_type rate_type;
struct domain_event_base: public event_type
{
domain_event_base(time_type time): event_type(time) {}
virtual domain_type& domain() const = 0;
};
template<typename Tdomain_, typename TeventKind_>
class domain_event: public domain_event_base
{
public:
typedef domain_event_base base_type;
typedef Tdomain_ domain_type;
typedef TeventKind_ event_kind_type;
public:
virtual domain_type& domain() const { return domain_; }
virtual ~domain_event() {}
event_kind_type kind() const { return kind_; }
domain_event(time_type time,
domain_type& domain,
event_kind_type kind)
: base_type(time), domain_(domain), kind_(kind) {}
private:
domain_type& domain_;
event_kind_type kind_;
};
typedef domain_event<single_type, single_event_kind> single_event;
typedef domain_event<pair_type, pair_event_kind> pair_event;
class multi_event: public domain_event_base
{
public:
typedef domain_event_base base_type;
typedef multi_type domain_type;
public:
virtual domain_type& domain() const { return domain_; }
virtual ~multi_event() {}
multi_event(time_type time,
domain_type& domain)
: base_type(time), domain_(domain) {}
private:
domain_type& domain_;
};
struct intruder_collector
{
intruder_collector(world_type const& world,
particle_shape_type const& cmp,
domain_id_type const& ignore)
: world(world), cmp(cmp), ignore(ignore),
closest(domain_id_type(),
std::numeric_limits<length_type>::infinity()) {}
template<typename Titer>
void operator()(Titer const& i, position_type const& off)
{
domain_id_type const& did((*i).second.did());
if (did == ignore)
return;
length_type const distance(
world.distance(
shape(offset((*i).second, off)), cmp.position()));
if (distance > cmp.radius())
{
if (distance < closest.second)
{
closest.first = did;
closest.second = distance;
}
}
else
{
if (!intruders.container())
{
intruders.container().set(new std::vector<domain_id_type>());
}
intruders.push_no_duplicate(did);
}
}
world_type const& world;
particle_shape_type cmp;
domain_id_type ignore;
std::pair<domain_id_type, length_type> closest;
sorted_list<std::vector<domain_id_type>,
std::less<domain_id_type>,
pointer_as_ref<std::vector<domain_id_type> > > intruders;
};
struct no_filter
{
bool operator()(domain_id_type const&) const { return true; }
};
struct one_id_filter
{
bool operator()(domain_id_type const& did) const { return did != ignore; }
one_id_filter(domain_id_type const& did): ignore(did) {}
domain_id_type const ignore;
};
template<typename TfilterFn_>
struct domain_collector
{
typedef TfilterFn_ filter_function;
domain_collector(world_type const& world,
particle_shape_type const& cmp,
filter_function const& filter)
: world(world), cmp(cmp), filter(filter) {}
template<typename Titer>
void operator()(Titer const& i, position_type const& off)
{
domain_id_type const& did((*i).second.did());
if (!filter(did))
return;
length_type const distance(world.distance(shape(offset((*i).second, off)), cmp.position()));
if (distance < cmp.radius())
{
if (!neighbors.container())
{
neighbors.container().set(new std::vector<domain_id_type>());
}
neighbors.push_no_duplicate(did);
}
}
world_type const& world;
particle_shape_type cmp;
filter_function const& filter;
std::pair<domain_id_type, length_type> closest;
sorted_list<std::vector<domain_id_type>,
std::less<domain_id_type>,
pointer_as_ref<std::vector<domain_id_type> > > neighbors;
};
template<typename TdidSet_>
struct closest_object_finder
{
typedef TdidSet_ domain_id_set;
closest_object_finder(world_type const& world,
position_type const& cmp,
domain_id_set const& ignore)
: world(world), cmp(cmp), ignore(ignore),
closest(domain_id_type(),
std::numeric_limits<length_type>::infinity()) {}
template<typename Titer>
void operator()(Titer const& i, position_type const& off)
{
domain_id_type const& did((*i).second.did());
if (contains(ignore, did))
return;
length_type const distance(world.distance(shape(offset((*i).second, off)), cmp));
if (distance < closest.second)
{
closest.first = did;
closest.second = distance;
}
}
world_type const& world;
position_type cmp;
domain_id_set const& ignore;
std::pair<domain_id_type, length_type> closest;
};
template<typename Tcol_>
struct shell_collector_applier
{
typedef Tcol_ collector_type;
shell_collector_applier(collector_type& col,
position_type const& pos)
: col_(col), pos_(pos) {}
template<typename T>
void operator()(T const& smat) const
{
world_type::traits_type::each_neighbor(smat.second, col_, pos_);
}
private:
collector_type& col_;
position_type pos_;
};
template<typename Tmap_>
struct domain_shell_map_builder
{
typedef Tmap_ domain_shell_association;
domain_shell_map_builder(world_type const& world,
domain_shell_association& did_map)
: world_(world), did_map_(did_map) {}
template<typename T>
void operator()(T const& smat) const
{
BOOST_ASSERT(world_.world_size() == smat.second.world_size());
BOOST_FOREACH (typename boost::remove_reference<typename T::second_type>::type::value_type pair, smat.second)
{
did_map_[pair.second.did()].insert(pair.first);
}
}
private:
world_type const& world_;
domain_shell_association& did_map_;
};
template<typename Tset_>
struct shell_id_collector
{
shell_id_collector(Tset_& shell_ids)
: shell_ids_(shell_ids) {}
template<typename T>
void operator()(T const& smat) const
{
std::for_each(
boost::begin(smat.second),
boost::end(smat.second),
compose_unary(
boost::bind(&insert<Tset_>,
boost::reference_wrapper<Tset_>(shell_ids_),
_1),
select_first<typename boost::remove_reference<
typename T::second_type>::type::value_type>()));
}
private:
Tset_& shell_ids_;
};
struct shell_finder
{
shell_finder(shell_id_type const& id, shell_variant_type& result)
: id(id), result(result) {}
template<typename T>
void operator()(T const& smat) const
{
typename boost::remove_reference<typename T::second_type>::type::const_iterator i(smat.second.find(id));
if (i != smat.second.end())
{
result = (*i).second;
}
}
shell_id_type id;
shell_variant_type& result;
};
struct draw_on_com_escape
{
position_type draw_com(spherical_pair_type const& domain,
time_type dt) const
{
return add(
domain.shell().second.position(),
normalize(
create_vector<position_type>(
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.)),
domain.a_R()));
}
position_type draw_iv(spherical_pair_type const& domain,
time_type dt, position_type const& old_iv) const
{
boost::scoped_ptr<PairGreensFunction> const gf(
choose_pair_greens_function(domain, dt));
length_type const r(draw_r(
rng_, *gf, dt, domain.a_r(), domain.sigma()));
length_type const theta(draw_theta(rng_, *gf, dt, r));
return adjust_iv_with_old_iv(
spherical_to_cartesian(
array_gen(r, theta, rng_.uniform(0., 1.) * 2 * M_PI)),
old_iv);
}
position_type draw_com(cylindrical_pair_type const& domain,
time_type dt) const
{
/* boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
world_.get_species(
domain.particles()[0].second.sid())
.structure_id()));
*/
boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
domain.particles()[0].second.structure_id()));
cylindrical_surface_type const* const structure(
dynamic_cast<cylindrical_surface_type*>(_structure.get()));
return add(
domain.shell().second.position(),
multiply(structure->shape().unit_z(), domain.a_R()));
}
position_type draw_iv(cylindrical_pair_type const& domain,
time_type dt, position_type const& old_iv) const
{
BOOST_ASSERT(::size(domain.reactions()) == 1);
length_type const r(
draw_r(rng_, GreensFunction3DRadAbs(domain.D_tot(),
domain.reactions()[0].k(), domain.r0(),
domain.sigma(), domain.a_r()),
dt, domain.a_r(), domain.sigma()));
return multiply(normalize(old_iv), r);
}
draw_on_com_escape(rng_type& rng, world_type const& world)
: rng_(rng), world_(world) {}
rng_type& rng_;
world_type const& world_;
};
struct draw_on_single_reaction
{
position_type draw_com(spherical_pair_type const& domain,
time_type dt) const
{
return add(
domain.shell().second.position(),
draw_r(rng_,
GreensFunction3DAbsSym(domain.D_R(), domain.a_R()),
dt, domain.a_R()));
}
position_type draw_iv(spherical_pair_type const& domain,
time_type dt, position_type const& old_iv) const
{
boost::scoped_ptr<PairGreensFunction> const gf(
choose_pair_greens_function(domain, dt));
length_type const r(draw_r(
rng_, *gf, dt, domain.a_r(), domain.sigma()));
length_type const theta(draw_theta(rng_, *gf, dt, r));
return adjust_iv_with_old_iv(
spherical_to_cartesian(
array_gen(r, theta, rng_.uniform(0., 1.) * 2 * M_PI)),
old_iv);
}
position_type draw_com(cylindrical_pair_type const& domain,
time_type dt) const
{
/* boost::shared_ptr<structure_type> const _structure(
world_.get_species(
domain.particles()[0].second.sid())
.structure_type_id());
*/
boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
domain.particles()[0].second.structure_id()));
cylindrical_surface_type const* const structure(
dynamic_cast<cylindrical_surface_type*>(_structure.get()));
BOOST_ASSERT(structure);
return add(
domain.shell().second.position(),
multiply(structure->shape().unit_z(), domain.a_R()));
}
position_type draw_iv(cylindrical_pair_type const& domain,
time_type dt, position_type const& old_iv) const
{
BOOST_ASSERT(::size(domain.reactions()) == 1);
length_type const r(
draw_r(rng_, GreensFunction3DRadAbs(domain.D_tot(),
domain.reactions()[0].k(), domain.r0(),
domain.sigma(), domain().a_r()),
dt, domain.a_r(), domain.sigma()));
BOOST_ASSERT(r > domain.sigma() && r <= domain.a_r());
return multiply(normalize(old_iv), r);
}
draw_on_single_reaction(rng_type& rng, world_type const& world)
: rng_(rng), world_(world) {}
rng_type& rng_;
world_type const& world_;
};
struct draw_on_iv_escape
{
position_type draw_com(spherical_pair_type const& domain,
time_type dt)
{
return add(
domain.shell().second.position(),
normalize(
create_vector<position_type>(
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.)),
draw_r(
rng_,
GreensFunction3DAbsSym(domain.D_R(), domain.a_R()),
dt, domain.a_R())));
}
position_type draw_iv(spherical_pair_type const& domain,
time_type dt, position_type const& old_iv)
{
boost::scoped_ptr<PairGreensFunction> const gf(
choose_pair_greens_function(domain, dt));
length_type const r(domain.a_r());
length_type const theta(draw_theta(rng_, *gf, dt, r));
return adjust_iv_with_old_iv(
spherical_to_cartesian(
array_gen(r, theta, rng_.uniform(0., 1.) * 2 * M_PI)),
old_iv);
}
position_type draw_com(cylindrical_pair_type const& domain,
time_type dt)
{
/* boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
world_.get_species(
domain.particles()[0].second.sid())
.structure_id()));
*/
boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
domain.particles()[0].second.structure_id()));
cylindrical_surface_type const* const structure(
dynamic_cast<cylindrical_surface_type*>(_structure.get()));
BOOST_ASSERT(structure);
length_type const r_R(draw_r(
rng_,
GreensFunction3DAbsSym(domain.D_R(), domain.a_R()),
dt, domain.a_R()));
return add(
domain.shell().second.position(),
multiply(structure->shape().unit_z(), r_R));
}
position_type draw_iv(cylindrical_pair_type const& domain,
time_type dt, position_type const& old_iv)
{
return multiply(normalize(old_iv), domain.a_r());
}
draw_on_iv_escape(rng_type& rng, world_type const& world)
: rng_(rng), world_(world) {}
rng_type& rng_;
world_type const& world_;
};
struct draw_on_iv_reaction
{
position_type draw_com(spherical_pair_type const& domain,
time_type dt)
{
return add(
domain.shell().second.position(),
normalize(
create_vector<position_type>(
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.)),
draw_r(
rng_,
GreensFunction3DAbsSym(domain.D_R(), domain.a_R()),
dt, domain.a_R())));
}
position_type draw_iv(spherical_pair_type const& domain,
time_type dt, position_type const& old_iv)
{
boost::scoped_ptr<PairGreensFunction> const gf(
choose_pair_greens_function(domain, dt));
length_type const r(domain.sigma());
length_type const theta(draw_theta(rng_, *gf, dt, r));
return adjust_iv_with_old_iv(
spherical_to_cartesian(
array_gen(r, theta, rng_.uniform(0., 1.) * 2 * M_PI)),
old_iv);
}
position_type draw_com(cylindrical_pair_type const& domain,
time_type dt)
{
boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
domain.particles()[0].second.structure_id()));
cylindrical_surface_type const* const structure(
dynamic_cast<cylindrical_surface_type*>(_structure.get()));
BOOST_ASSERT(structure);
length_type const r_R(draw_r(
rng_,
GreensFunction3DAbsSym(domain.D_R(), domain.a_R()),
dt, domain.a_R()));
return add(
domain.shell().second.position(),
multiply(structure->shape().unit_z(), r_R));
}
position_type draw_iv(cylindrical_pair_type const& domain,
time_type dt, position_type const& old_iv)
{
return multiply(domain.sigma(), normalize(old_iv));
}
draw_on_iv_reaction(rng_type& rng, world_type const& world)
: rng_(rng), world_(world) {}
rng_type& rng_;
world_type const& world_;
};
struct draw_on_burst
{
position_type draw_com(spherical_pair_type const& domain,
time_type dt)
{
return add(
domain.shell().second.position(),
normalize(
create_vector<position_type>(
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.),
rng_.uniform(-1., 1.)),
draw_r(
rng_,
GreensFunction3DAbsSym(domain.D_R(), domain.a_R()),
dt, domain.a_R())));
}
position_type draw_iv(spherical_pair_type const& domain,
time_type dt, position_type const& old_iv)
{
boost::scoped_ptr<PairGreensFunction> const gf(
choose_pair_greens_function(domain, dt));
length_type const r(draw_r(
rng_, *gf, dt, domain.a_r(), domain.sigma()));
length_type const theta(draw_theta(rng_, *gf, dt, r));
return adjust_iv_with_old_iv(
spherical_to_cartesian(
array_gen(r, theta, rng_.uniform(0., 1.) * 2 * M_PI)),
old_iv);
}
position_type draw_com(cylindrical_pair_type const& domain,
time_type dt)
{
/* boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
world_.get_species(
domain.particles()[0].second.sid())
.structure_id()));
*/
boost::shared_ptr<structure_type> const _structure(
world_.get_structure(
domain.particles()[0].second.structure_id()));
cylindrical_surface_type const* const structure(
dynamic_cast<cylindrical_surface_type*>(_structure.get()));
BOOST_ASSERT(structure);
length_type const r_R(draw_r(
rng_,
GreensFunction3DAbsSym(domain.D_R(), domain.a_R()),
dt, domain.a_R()));
return add(
domain.shell().second.position(),
multiply(structure->shape().unit_z(), r_R));
}
position_type draw_iv(cylindrical_pair_type const& domain,
time_type dt, position_type const& old_iv)
{
BOOST_ASSERT(::size(domain.reactions()) == 1);
length_type const r(
draw_r(rng_,
GreensFunction3DRadAbs(
domain.D_tot(),
domain.reactions()[0].k(), domain.r0(),
domain.sigma(), domain.a_r()),
dt, domain.a_r(), domain.sigma()));
return multiply(normalize(old_iv), r);
}
draw_on_burst(rng_type& rng, world_type const& world)
: rng_(rng), world_(world) {}
rng_type& rng_;
world_type const& world_;
};
public:
typedef abstract_limited_generator<domain_id_pair> domain_id_pair_generator;
public:
virtual ~EGFRDSimulator()
{
//std::for_each(domains_.begin(), domains_.end(),
// compose_unary(delete_ptr<domain_type>(),
// select_second<typename domain_map::value_type>()));
}
EGFRDSimulator(boost::shared_ptr<world_type> world,
boost::shared_ptr<network_rules_type const> network_rules,
rng_type& rng, int dissociation_retry_moves = 1,
Real bd_dt_factor = 1e-5,
length_type user_max_shell_size =
std::numeric_limits<length_type>::infinity())
: base_type(world, network_rules, rng),
num_retries_(dissociation_retry_moves),
bd_dt_factor_(bd_dt_factor),
user_max_shell_size_(user_max_shell_size),
ssmat_((*world).world_size(), (*world).matrix_size()),
csmat_((*world).world_size(), (*world).matrix_size()),
smatm_(boost::fusion::pair<spherical_shell_type,
spherical_shell_matrix_type&>(ssmat_),
boost::fusion::pair<cylindrical_shell_type,
cylindrical_shell_matrix_type&>(csmat_)),
single_shell_factor_(.1),
multi_shell_factor_(.05),
rejected_moves_(0), zero_step_count_(0), dirty_(true)
{
std::fill(domain_count_per_type_.begin(), domain_count_per_type_.end(), 0);
std::fill(single_step_count_.begin(), single_step_count_.end(), 0);
std::fill(pair_step_count_.begin(), pair_step_count_.end(), 0);
std::fill(multi_step_count_.begin(), multi_step_count_.end(), 0);
}
length_type user_max_shell_size() const
{
return user_max_shell_size_;
}
length_type max_shell_size() const
{
return std::min((*base_type::world_).cell_size() / 2 /
traits_type::SAFETY,
user_max_shell_size_);
}
template<typename Tshape>
std::pair<const shell_id_type,
typename traits_type::template shell_generator<Tshape>::type>
new_shell(domain_id_type const& did, Tshape const& shape)
{
typedef typename traits_type::template shell_generator<Tshape>::type shell_type;
std::pair<const shell_id_type, shell_type> const retval(shidgen_(), shell_type(did, shape));
boost::fusion::at_key<shell_type>(smatm_).update(retval);
return retval;
}
template<typename T>
std::pair<const shell_id_type, T> const& get_shell(shell_id_type const& id) const
{
typedef typename boost::remove_reference<
typename boost::fusion::result_of::value_at_key<
shell_matrix_map_type, T>::type>::type shell_matrix_type;
shell_matrix_type const& smat(boost::fusion::at_key<T>(smatm_));
typename shell_matrix_type::const_iterator i(smat.find(id));
if (i == smat.end())
{
throw not_found(
(boost::format("shell id #%s not found") % boost::lexical_cast<std::string>(id)).str());
}
return *i;
}
std::pair<shell_id_type, shell_variant_type> get_shell(shell_id_type const& id)
{
shell_variant_type result;
boost::fusion::for_each(smatm_, shell_finder(id, result));
return std::make_pair(id, result);
}
boost::shared_ptr<domain_type> get_domain(domain_id_type const& id) const
{
typename domain_map::const_iterator i(domains_.find(id));
if (i == domains_.end())
{
throw not_found(
(boost::format("domain id #%s not found") % boost::lexical_cast<std::string>(id)).str());
}
return (*i).second;
}
domain_id_pair_generator* get_domains() const
{
return make_range_generator<domain_id_pair>(domains_);
}