Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2023 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed 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
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "NeighborList.h"
23 : #include "Vector.h"
24 : #include "Pbc.h"
25 : #include "AtomNumber.h"
26 : #include "Communicator.h"
27 : #include "OpenMP.h"
28 : #include "Tools.h"
29 : #include <vector>
30 : #include <algorithm>
31 : #include <numeric>
32 :
33 : namespace PLMD {
34 :
35 245 : NeighborList::NeighborList(const std::vector<AtomNumber>& list0, const std::vector<AtomNumber>& list1,
36 : const bool& serial, const bool& do_pair, const bool& do_pbc, const Pbc& pbc, Communicator& cm,
37 245 : const double& distance, const unsigned& stride): reduced(false),
38 245 : serial_(serial), do_pair_(do_pair), do_pbc_(do_pbc), pbc_(&pbc), comm(cm),
39 245 : distance_(distance), stride_(stride)
40 : {
41 : // store full list of atoms needed
42 245 : fullatomlist_=list0;
43 245 : fullatomlist_.insert(fullatomlist_.end(),list1.begin(),list1.end());
44 245 : nlist0_=list0.size();
45 245 : nlist1_=list1.size();
46 245 : twolists_=true;
47 245 : if(!do_pair) {
48 220 : nallpairs_=nlist0_*nlist1_;
49 : } else {
50 25 : plumed_assert(nlist0_==nlist1_) << "when using PAIR option, the two groups should have the same number of elements\n"
51 0 : << "the groups you specified have size "<<nlist0_<<" and "<<nlist1_;
52 25 : nallpairs_=nlist0_;
53 : }
54 245 : initialize();
55 245 : lastupdate_=0;
56 245 : }
57 :
58 39 : NeighborList::NeighborList(const std::vector<AtomNumber>& list0, const bool& serial, const bool& do_pbc,
59 : const Pbc& pbc, Communicator& cm, const double& distance,
60 39 : const unsigned& stride): reduced(false),
61 39 : serial_(serial), do_pbc_(do_pbc), pbc_(&pbc), comm(cm),
62 39 : distance_(distance), stride_(stride) {
63 39 : fullatomlist_=list0;
64 39 : nlist0_=list0.size();
65 39 : twolists_=false;
66 39 : nallpairs_=nlist0_*(nlist0_-1)/2;
67 39 : initialize();
68 39 : lastupdate_=0;
69 39 : }
70 :
71 284 : void NeighborList::initialize() {
72 284 : neighbors_.clear();
73 42954115 : for(unsigned int i=0; i<nallpairs_; ++i) {
74 85907662 : neighbors_.push_back(getIndexPair(i));
75 : }
76 284 : }
77 :
78 69974 : std::vector<AtomNumber>& NeighborList::getFullAtomList() {
79 69974 : return fullatomlist_;
80 : }
81 :
82 49191551 : std::pair<unsigned,unsigned> NeighborList::getIndexPair(unsigned ipair) {
83 : std::pair<unsigned,unsigned> index;
84 49191551 : if(twolists_ && do_pair_) {
85 636 : index=std::pair<unsigned,unsigned>(ipair,ipair+nlist0_);
86 49190915 : } else if (twolists_ && !do_pair_) {
87 8866469 : index=std::pair<unsigned,unsigned>(ipair/nlist1_,ipair%nlist1_+nlist0_);
88 40324446 : } else if (!twolists_) {
89 40324446 : unsigned ii = nallpairs_-1-ipair;
90 40324446 : unsigned K = unsigned(std::floor((std::sqrt(double(8*ii+1))+1)/2));
91 40324446 : unsigned jj = ii-K*(K-1)/2;
92 40324446 : index=std::pair<unsigned,unsigned>(nlist0_-1-K,nlist0_-1-jj);
93 : }
94 49191551 : return index;
95 : }
96 :
97 3138 : void NeighborList::update(const std::vector<Vector>& positions) {
98 3138 : neighbors_.clear();
99 3138 : const double d2=distance_*distance_;
100 : // check if positions array has the correct length
101 3138 : plumed_assert(positions.size()==fullatomlist_.size());
102 :
103 3138 : unsigned stride=comm.Get_size();
104 3138 : unsigned rank=comm.Get_rank();
105 3138 : unsigned nt=OpenMP::getNumThreads();
106 3138 : if(serial_) {
107 : stride=1;
108 : rank=0;
109 : nt=1;
110 : }
111 : std::vector<unsigned> local_flat_nl;
112 :
113 3138 : #pragma omp parallel num_threads(nt)
114 : {
115 : std::vector<unsigned> private_flat_nl;
116 : #pragma omp for nowait
117 : for(unsigned int i=rank; i<nallpairs_; i+=stride) {
118 : std::pair<unsigned,unsigned> index=getIndexPair(i);
119 : unsigned index0=index.first;
120 : unsigned index1=index.second;
121 : Vector distance;
122 : if(do_pbc_) {
123 : distance=pbc_->distance(positions[index0],positions[index1]);
124 : } else {
125 : distance=delta(positions[index0],positions[index1]);
126 : }
127 : double value=modulo2(distance);
128 : if(value<=d2) {
129 : private_flat_nl.push_back(index0);
130 : private_flat_nl.push_back(index1);
131 : }
132 : }
133 : #pragma omp critical
134 : local_flat_nl.insert(local_flat_nl.end(), private_flat_nl.begin(), private_flat_nl.end());
135 : }
136 :
137 : // find total dimension of neighborlist
138 3138 : std::vector <int> local_nl_size(stride, 0);
139 3138 : local_nl_size[rank] = local_flat_nl.size();
140 3138 : if(!serial_) comm.Sum(&local_nl_size[0], stride);
141 : int tot_size = std::accumulate(local_nl_size.begin(), local_nl_size.end(), 0);
142 3138 : if(tot_size==0) {setRequestList(); return;}
143 : // merge
144 3120 : std::vector<unsigned> merge_nl(tot_size, 0);
145 : // calculate vector of displacement
146 3120 : std::vector<int> disp(stride);
147 3120 : disp[0] = 0;
148 : int rank_size = 0;
149 9216 : for(unsigned i=0; i<stride-1; ++i) {
150 6096 : rank_size += local_nl_size[i];
151 6096 : disp[i+1] = rank_size;
152 : }
153 : // Allgather neighbor list
154 5197 : if(comm.initialized()&&!serial_) comm.Allgatherv((!local_flat_nl.empty()?&local_flat_nl[0]:NULL), local_nl_size[rank], &merge_nl[0], &local_nl_size[0], &disp[0]);
155 1016 : else merge_nl = local_flat_nl;
156 : // resize neighbor stuff
157 3120 : neighbors_.resize(tot_size/2);
158 6114036 : for(unsigned i=0; i<tot_size/2; i++) {
159 6110916 : unsigned j=2*i;
160 6110916 : neighbors_[i] = std::make_pair(merge_nl[j],merge_nl[j+1]);
161 : }
162 :
163 3120 : setRequestList();
164 : }
165 :
166 3138 : void NeighborList::setRequestList() {
167 3138 : requestlist_.clear();
168 6114054 : for(unsigned int i=0; i<size(); ++i) {
169 6110916 : requestlist_.push_back(fullatomlist_[neighbors_[i].first]);
170 6110916 : requestlist_.push_back(fullatomlist_[neighbors_[i].second]);
171 : }
172 3138 : Tools::removeDuplicates(requestlist_);
173 3138 : reduced=false;
174 3138 : }
175 :
176 240 : std::vector<AtomNumber>& NeighborList::getReducedAtomList() {
177 168359 : if(!reduced)for(unsigned int i=0; i<size(); ++i) {
178 : unsigned newindex0=0,newindex1=0;
179 168119 : AtomNumber index0=fullatomlist_[neighbors_[i].first];
180 168119 : AtomNumber index1=fullatomlist_[neighbors_[i].second];
181 : // I exploit the fact that requestlist_ is an ordered vector
182 168119 : auto p = std::find(requestlist_.begin(), requestlist_.end(), index0); plumed_dbg_assert(p!=requestlist_.end()); newindex0=p-requestlist_.begin();
183 168119 : p = std::find(requestlist_.begin(), requestlist_.end(), index1); plumed_dbg_assert(p!=requestlist_.end()); newindex1=p-requestlist_.begin();
184 : neighbors_[i]=std::pair<unsigned,unsigned>(newindex0,newindex1);
185 : }
186 240 : reduced=true;
187 240 : return requestlist_;
188 : }
189 :
190 13616 : unsigned NeighborList::getStride() const {
191 13616 : return stride_;
192 : }
193 :
194 0 : unsigned NeighborList::getLastUpdate() const {
195 0 : return lastupdate_;
196 : }
197 :
198 0 : void NeighborList::setLastUpdate(unsigned step) {
199 0 : lastupdate_=step;
200 0 : }
201 :
202 23715992 : unsigned NeighborList::size() const {
203 23715992 : return neighbors_.size();
204 : }
205 :
206 79830556 : std::pair<unsigned,unsigned> NeighborList::getClosePair(unsigned i) const {
207 79830556 : return neighbors_[i];
208 : }
209 :
210 34665936 : std::pair<AtomNumber,AtomNumber> NeighborList::getClosePairAtomNumber(unsigned i) const {
211 : std::pair<AtomNumber,AtomNumber> Aneigh;
212 34665936 : Aneigh=std::pair<AtomNumber,AtomNumber>(fullatomlist_[neighbors_[i].first],fullatomlist_[neighbors_[i].second]);
213 34665936 : return Aneigh;
214 : }
215 :
216 0 : std::vector<unsigned> NeighborList::getNeighbors(unsigned index) {
217 : std::vector<unsigned> neighbors;
218 0 : for(unsigned int i=0; i<size(); ++i) {
219 0 : if(neighbors_[i].first==index) neighbors.push_back(neighbors_[i].second);
220 0 : if(neighbors_[i].second==index) neighbors.push_back(neighbors_[i].first);
221 : }
222 0 : return neighbors;
223 : }
224 :
225 : }
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