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nherringer
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Made suggested changes to use a struct for std::pair (AtomPair) and replaced instances of std::vector<std::vector<thing>> with std::vector<std::array<thing, fixed-Size>> where appropriate.
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‎src/pines/PINES.cpp‎

Lines changed: 77 additions & 89 deletions
Original file line numberDiff line numberDiff line change
@@ -54,6 +54,11 @@ struct AtomNumberLess {
5454
}
5555
};
5656

57+
struct AtomPair {
58+
AtomNumber alpha_group;
59+
AtomNumber beta_group;
60+
};
61+
5762
class PINES : public PLMD::colvar::Colvar {
5863
private:
5964
PLMD::Stopwatch timer;
@@ -81,27 +86,27 @@ class PINES : public PLMD::colvar::Colvar {
8186
std::vector<bool> stale_tolerance;
8287
PDB mypdb;
8388
std::vector<std::string> block_params;
84-
std::vector<std::vector<std::vector<AtomNumber> > > block_groups_atom_list;
89+
std::vector<std::array<std::vector<AtomNumber>,2> > block_groups_atom_list;
8590
std::vector<int> block_lengths;
8691
std::vector<int> Buffer_Pairs;
8792
std::vector<int> tot_num_pairs;
88-
std::vector<std::vector<std::vector<bool> > > input_filters;
93+
std::vector<std::array<std::array<bool,3>,2> > input_filters;
8994
std::vector<double> delta_pd;
9095
std::vector<double> r_tolerance;
9196
std::vector<std::vector<Vector> > PL_atoms_ref_coords;
92-
std::vector<std::vector<std::pair<AtomNumber,AtomNumber> > > Exclude_Pairs;
93-
std::vector<std::vector<std::vector<std::string> > > Name_list;
94-
std::vector<std::vector<std::vector<AtomNumber> > > ID_list;
95-
std::vector<std::vector<std::vector<int> > > ResID_list;
97+
std::vector<std::vector<AtomPair > > Exclude_Pairs;
98+
std::vector<std::array<std::vector<std::string> >,2> Name_list;
99+
std::vector<std::array<std::vector<AtomNumber> >,2> ID_list;
100+
std::vector<std::array<std::vector<int> >,2> ResID_list;
96101
std::vector<char> all_g1g2_pairs;
97-
std::vector<std::vector<std::pair<double, std::pair<AtomNumber,AtomNumber> > > > vecMaxHeapVecs;
98-
std::vector<std::vector<std::pair<AtomNumber,AtomNumber> > > latched_pairs;
99-
std::vector<char> preupdated_block;
102+
std::vector<std::vector<std::pair<double, AtomPair > > > vecMaxHeapVecs;
103+
std::vector<std::vector<AtomPair > > latched_pairs;
104+
std::vector<int> preupdated_block;
100105
std::vector<bool> isFirstBuild;
101106

102107
bool atomMatchesFilters(int n, int g, AtomNumber ind, int resid, const std::string& atom_name);
103-
void buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<double, std::pair<AtomNumber, AtomNumber>>>& heap);
104-
void updateBlockPairList(int n, std::vector<std::pair<double, std::pair<AtomNumber, AtomNumber>>>& heap);
108+
void buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<double, AtomPair>>& heap);
109+
void updateBlockPairList(int n, std::vector<std::pair<double, AtomPair>>& heap);
105110
double calculateDistance(int n, const AtomNumber& ind0, const AtomNumber& ind1, const PDB& mypdb);
106111
std::ofstream log;
107112
bool ensureBlockUpdated(int n);
@@ -116,12 +121,12 @@ class PINES : public PLMD::colvar::Colvar {
116121
//~PINES();
117122
// active methods:
118123
struct MinCompareDist {
119-
bool operator()(const std::pair<double, std::pair<AtomNumber, AtomNumber>>& p1, const std::pair<double, std::pair<AtomNumber, AtomNumber>>& p2) {
124+
bool operator()(const std::pair<double, AtomPair>& p1, const std::pair<double, AtomPair>& p2) {
120125
return p1.first < p2.first; // Min heap
121126
}
122127
};
123128
struct MaxCompareDist {
124-
bool operator()(const std::pair<double, std::pair<AtomNumber, AtomNumber>>& p1, const std::pair<double, std::pair<AtomNumber, AtomNumber>>& p2) {
129+
bool operator()(const std::pair<double, AtomPair>& p1, const std::pair<double, AtomPair>& p2) {
125130
return p1.first > p2.first; // Max heap
126131
}
127132
};
@@ -199,11 +204,11 @@ bool PINES::atomMatchesFilters(int n, int g, AtomNumber ind, int resid, const st
199204
return id_check && res_check && name_check;
200205
}
201206

202-
void PINES::buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<double, std::pair<AtomNumber, AtomNumber>>>& heap) {
207+
void PINES::buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<double, AtomPair>>& heap) {
203208
//logMsg("Building Pair List for block: " + std::to_string(n), "buildMaxHeapVecBlock");
204209

205210
int nthreads = omp_get_max_threads();
206-
std::vector<std::vector<std::pair<double, std::pair<AtomNumber, AtomNumber>>>> thread_heaps(nthreads);
211+
std::vector<std::vector<std::pair<double, AtomPair>>> thread_heaps(nthreads);
207212

208213
//logMsg("isFirstBuild[n]? " + std::to_string(isFirstBuild[n]), "buildMaxHeapVecBlock");
209214

@@ -221,7 +226,7 @@ void PINES::buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<
221226
Vector Pos0 = isFirstBuild[n] ? mypdb.getPosition(ind0) : getPosition(atom_ind_hashmap[ind0.index()]);
222227
int tid = omp_get_thread_num();
223228
auto& local_heap = thread_heaps[tid];
224-
std::unordered_set<std::pair<AtomNumber, AtomNumber>, pair_hash> local_unique_pairs;
229+
std::unordered_set<AtomPair, pair_hash> local_unique_pairs;
225230
// logMsg("ind0: " + std::to_string(ind0.index()), "buildMaxHeapVecBlock");
226231
// logMsg("Num pairs in heap: " + std::to_string(block_groups_atom_list[n][0].size()), "buildMaxHeapVecBlock");
227232
// logMsg(Pos0, "buildMaxHeapVecBlock");
@@ -255,7 +260,7 @@ void PINES::buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<
255260
}
256261

257262
// Flatten all thread-local heaps into one vector
258-
std::vector<std::pair<double, std::pair<AtomNumber, AtomNumber>>> all_pairs;
263+
std::vector<std::pair<double, AtomPair>> all_pairs;
259264
for (auto& th : thread_heaps) {
260265
all_pairs.insert(all_pairs.end(), th.begin(), th.end());
261266
}
@@ -276,8 +281,8 @@ void PINES::buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<
276281
listreduced[n].clear();
277282
std::set<AtomNumber, AtomNumberLess> uniqueAtoms;
278283
for (const auto& pair : heap) {
279-
uniqueAtoms.insert(pair.second.first); // Atom1
280-
uniqueAtoms.insert(pair.second.second); // Atom2
284+
uniqueAtoms.insert(pair.second.alpha_group); // Atom1
285+
uniqueAtoms.insert(pair.second.beta_group); // Atom2
281286
}
282287
for (const auto& atom : uniqueAtoms) {
283288
listreduced[n].push_back(atom);
@@ -299,7 +304,7 @@ void PINES::buildMaxHeapVecBlock(int n, const PDB& mypdb, std::vector<std::pair<
299304

300305
}
301306

302-
void PINES::updateBlockPairList(int n, std::vector<std::pair<double, std::pair<AtomNumber, AtomNumber>>>& heap) {
307+
void PINES::updateBlockPairList(int n, std::vector<std::pair<double, AtomPair>>& heap) {
303308
// This is separate from staleness, which triggers a refresh instead of an update.
304309
// This is simply to update the pair distances in the MaxHeap/Pairlist with the new atom positions
305310
// and rearrange the ordering in the MaxHeap/Pairlisat
@@ -309,8 +314,8 @@ void PINES::updateBlockPairList(int n, std::vector<std::pair<double, std::pair<A
309314

310315
#pragma omp parallel for
311316
for (int i = 0; i < tot_num_pairs[n]; i++) {
312-
AtomNumber ind0 = heap[i].second.first;
313-
AtomNumber ind1 = heap[i].second.second;
317+
AtomNumber ind0 = heap[i].second.alpha_group;
318+
AtomNumber ind1 = heap[i].second.beta_group;
314319
auto it0 = atom_ind_hashmap.find(ind0.index());
315320
auto it1 = atom_ind_hashmap.find(ind1.index());
316321
plumed_massert(it0 != atom_ind_hashmap.end() && it1 != atom_ind_hashmap.end(),"updateBlockPairList: atom index not requested");
@@ -335,38 +340,33 @@ void PINES::resizeAllContainers(int N) {
335340
nstride.assign(N,1);
336341
steps_since_update.assign(N, 0);
337342
block_params.resize(N);
338-
block_groups_atom_list.resize(N);
339-
block_lengths.resize(N);
340-
Buffer_Pairs.resize(N);
341-
tot_num_pairs.resize(N);
343+
block_groups_atom_list.assign(N, { {}, {} });
344+
block_lengths.assign(N, 0);
345+
Buffer_Pairs.assign(N, 0);
346+
tot_num_pairs.assign(N, 0);
342347
Exclude_Pairs.resize(N);
343-
all_g1g2_pairs.resize(N);
348+
all_g1g2_pairs.assign(N,false);
344349
vecMaxHeapVecs.resize(N);
345-
PIV.resize(N);
350+
PIV.assign(N, 0.0);
346351
listall.resize(N);
347352
listreduced.resize(N);
348-
stale_tolerance.resize(N);
349-
r00.resize(N);
353+
stale_tolerance.assign(N,false);
354+
r00.assign(N, 0.0);
350355
sw.resize(N);
351356
sfs.resize(N);
352357
delta_pd.assign(N, 0.0);
353358
r_tolerance.assign(N, 0.0);
354359
PL_atoms_ref_coords.resize(N);
355-
input_filters.resize(N);
356-
ID_list.resize(N);
357-
ResID_list.resize(N);
358-
Name_list.resize(N);
360+
input_filters.assign(N, { {}, {} });
361+
ID_list.assign(N, { {}, {} });
362+
ResID_list.assign(N, { {}, {} });
363+
Name_list.assign(N, { {}, {} });
359364
atom_ind_hashmap.clear();
360365
latched_pairs.resize(N);
361366
isFirstBuild.assign(N,true);
362367

363368
// Per-block inner structures
364369
for (int n = 0; n < N; n++) {
365-
block_groups_atom_list[n].resize(2);
366-
ID_list[n].resize(2);
367-
ResID_list[n].resize(2);
368-
Name_list[n].resize(2);
369-
input_filters[n].resize(2);
370370
PL_atoms_ref_coords[n].resize(0); // will be filled per atom if needed
371371
}
372372

@@ -431,53 +431,45 @@ void PINES::logMsg(const Vector& vec, const std::string& section) {
431431
}
432432

433433
PINES::PINES(const ActionOptions &ao) : PLUMED_COLVAR_INIT(ao),
434-
N_Blocks(1),
435-
total_PIV_length(1),
436-
driver_mode(false),
437-
freeze_selection(false),
438-
last_step_latched(-1),
434+
N_Blocks(),
435+
total_PIV_length(),
436+
driver_mode(),
437+
freeze_selection(),
438+
last_step_latched(),
439439
inited_step(-1),
440-
steps_since_update(std::vector<int>(1)),
441-
nstride(std::vector<int>(1,10)),
442-
ref_file(std::string()),
440+
steps_since_update(),
441+
nstride(),
442+
ref_file(),
443443
sfs(),
444-
sw(std::vector<string>(1)),
445-
r00(std::vector<double>(1)),
446-
PIV(std::vector<std::vector<double>>(1)),
447-
ann_deriv(std::vector<std::vector<Vector> >(1)),
448-
listall(std::vector<std::vector<AtomNumber> >()),
449-
listreduced(std::vector<std::vector<AtomNumber> >()),
450-
listreducedall(std::set<AtomNumber, AtomNumberLess>()),
451-
listreducedall_vec(std::vector<AtomNumber>()),
444+
sw(),
445+
r00(),
446+
PIV(),
447+
ann_deriv(),
448+
listall(),
449+
listreduced(),
450+
listreducedall(),
451+
listreducedall_vec(),
452452
atom_ind_hashmap(),
453-
stale_tolerance(std::vector<bool>(1,false)),
453+
stale_tolerance(),
454454
mypdb(),
455-
block_params(std::vector<string>(1)),
456-
block_groups_atom_list(std::vector<std::vector<std::vector<AtomNumber> > >()),
457-
block_lengths(std::vector<int>(1,1)),
458-
Buffer_Pairs(std::vector<int>(1,0)),
459-
tot_num_pairs(std::vector<int>(1,1)),
460-
input_filters(
461-
std::vector<std::vector<std::vector<bool> > >(
462-
1, // outermost dimension
463-
std::vector<std::vector<bool>>(
464-
1, // middle dimension
465-
std::vector<bool>(1, false) // innermost dimension with value `false`
466-
)
467-
)
468-
),
469-
delta_pd(std::vector<double>()),
470-
r_tolerance(std::vector<double>()),
455+
block_params(),
456+
block_groups_atom_list(),
457+
block_lengths(),
458+
Buffer_Pairs(),
459+
tot_num_pairs(),
460+
input_filters(),
461+
delta_pd(),
462+
r_tolerance(),
471463
PL_atoms_ref_coords(),
472-
Exclude_Pairs(std::vector<std::vector<std::pair<AtomNumber, AtomNumber> > >()),
473-
Name_list(std::vector<std::vector<std::vector<string> > >()),
474-
ID_list(std::vector<std::vector<std::vector<AtomNumber> > >()),
475-
ResID_list(std::vector<std::vector<std::vector<int> > >()),
476-
all_g1g2_pairs(std::vector<char>()),
464+
Exclude_Pairs(),
465+
Name_list(),
466+
ID_list(),
467+
ResID_list(),
468+
all_g1g2_pairs(),
477469
vecMaxHeapVecs(),
478-
latched_pairs(std::vector<std::vector<std::pair<AtomNumber,AtomNumber> > >()),
479-
preupdated_block(std::vector<char>()),
480-
isFirstBuild(std::vector<bool>()) {
470+
latched_pairs(),
471+
preupdated_block(),
472+
isFirstBuild() {
481473
log.open("pines_debug.log", std::ios::out);
482474
if (!log.is_open()) {
483475
error("Failed to open debug log file.");
@@ -572,7 +564,7 @@ PINES::PINES(const ActionOptions &ao) : PLUMED_COLVAR_INIT(ao),
572564
AtomNumber atom2;
573565
atom2.setIndex(std::stoi(ex_pairs_n[i+1]));
574566

575-
std::pair<AtomNumber, AtomNumber> excluded_pair;
567+
AtomPair excluded_pair;
576568
excluded_pair = {atom1, atom2};
577569
Exclude_Pairs[n].push_back(excluded_pair);
578570
}
@@ -654,10 +646,6 @@ PINES::PINES(const ActionOptions &ao) : PLUMED_COLVAR_INIT(ao),
654646
}
655647
}
656648

657-
r00.resize(N_Blocks);
658-
sw.resize(N_Blocks);
659-
sfs.resize(N_Blocks);
660-
661649
for (unsigned n = 0; n < N_Blocks; n++)
662650
if (!parseNumbered("SWITCH", n + 1, sw[n])) {
663651
break;
@@ -811,8 +799,8 @@ void PINES::calculate() {
811799
logMsg("***************N: "+std::to_string(n)+"***************\n","bigCalc");
812800
for (int i = 0; i < block_lengths[n]; ++i) {
813801
const auto& pr = latched_pairs[n][i];
814-
int a0 = atom_ind_hashmap[pr.first.index()];
815-
int a1 = atom_ind_hashmap[pr.second.index()];
802+
int a0 = atom_ind_hashmap[pr.alpha_group.index()];
803+
int a1 = atom_ind_hashmap[pr.beta_group.index()];
816804
Vector r0 = getPosition(a0);
817805
Vector r1 = getPosition(a1);
818806
double mod_dist = pbcDistance(r0, r1).modulo();
@@ -852,8 +840,8 @@ void PINES::calculate() {
852840
//timer.stop("sfs");
853841
//logMsg("PIV Values: PIV[" + std::to_string(n) + "][" + std::to_string(i) + "]= " + std::to_string(PIV[n][i]), "Calculate");
854842
//timer.start("distCalc");
855-
local_aid0 = atom_ind_hashmap[vecMaxHeapVecs[n][piv_ind].second.first.index()];
856-
local_aid1 = atom_ind_hashmap[vecMaxHeapVecs[n][piv_ind].second.second.index()];
843+
local_aid0 = atom_ind_hashmap[vecMaxHeapVecs[n][piv_ind].second.alpha_group.index()];
844+
local_aid1 = atom_ind_hashmap[vecMaxHeapVecs[n][piv_ind].second.beta_group.index()];
857845
Vector Pos0 = getPosition(local_aid0);
858846
Vector Pos1 = getPosition(local_aid1);
859847
Vector dr_dcoord = pbcDistance(Pos0, Pos1) / vecMaxHeapVecs[n][piv_ind].first;

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