Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2018 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 "LinkCells.h"
23 : #include "Communicator.h"
24 : #include "Tools.h"
25 :
26 : namespace PLMD {
27 :
28 530 : LinkCells::LinkCells( Communicator& cc ) :
29 : comm(cc),
30 : cutoffwasset(false),
31 : link_cutoff(0.0),
32 : ncells(3),
33 530 : nstride(3)
34 : {
35 530 : }
36 :
37 294 : void LinkCells::setCutoff( const double& lcut ) {
38 294 : cutoffwasset=true; link_cutoff=lcut;
39 294 : }
40 :
41 4 : double LinkCells::getCutoff() const {
42 4 : plumed_assert( cutoffwasset ); return link_cutoff;
43 : }
44 :
45 1520 : void LinkCells::buildCellLists( const std::vector<Vector>& pos, const std::vector<unsigned>& indices, const Pbc& pbc ) {
46 1520 : plumed_assert( cutoffwasset && pos.size()==indices.size() );
47 :
48 : // Must be able to check that pbcs are not nonsensical in some way?? -- GAT
49 :
50 : // Setup the pbc object by copying it from action
51 1520 : mypbc.setBox( pbc.getBox() );
52 :
53 : // Setup the lists
54 1520 : if( pos.size()!=allcells.size() ) {
55 385 : allcells.resize( pos.size() ); lcell_lists.resize( pos.size() );
56 : }
57 :
58 : {
59 : // This is the reciprocal lattice
60 : // notice that reciprocal.getRow(0) is a vector that is orthogonal to b and c
61 : // This allows to use linked cells in non orthorhomic boxes
62 1520 : Tensor reciprocal(transpose(mypbc.getInvBox()));
63 1520 : ncells[0] = std::floor( 1.0/ reciprocal.getRow(0).modulo() / link_cutoff );
64 1520 : if( ncells[0]==0 ) ncells[0]=1;
65 1520 : ncells[1] = std::floor( 1.0/ reciprocal.getRow(1).modulo() / link_cutoff );
66 1520 : if( ncells[1]==0 ) ncells[1]=1;
67 1520 : ncells[2] = std::floor( 1.0/ reciprocal.getRow(2).modulo() / link_cutoff );
68 1520 : if( ncells[2]==0 ) ncells[2]=1;
69 : }
70 : // Setup the strides
71 1520 : nstride[0]=1; nstride[1]=ncells[0]; nstride[2]=ncells[0]*ncells[1];
72 :
73 : // Setup the storage for link cells
74 1520 : unsigned ncellstot=ncells[0]*ncells[1]*ncells[2];
75 1520 : if( lcell_tots.size()!=ncellstot ) {
76 374 : lcell_tots.resize( ncellstot ); lcell_starts.resize( ncellstot );
77 : }
78 : // Clear nlcells
79 1520 : for(unsigned i=0; i<ncellstot; ++i) lcell_tots[i]=0;
80 : // Clear allcells
81 1520 : allcells.assign( allcells.size(), 0 );
82 :
83 : // Find out what cell everyone is in
84 1520 : unsigned rank=comm.Get_rank(), size=comm.Get_size();
85 220131 : for(unsigned i=rank; i<pos.size(); i+=size) {
86 218611 : allcells[i]=findCell( pos[i] );
87 218611 : lcell_tots[allcells[i]]++;
88 : }
89 : // And gather all this information on every node
90 1520 : comm.Sum( allcells ); comm.Sum( lcell_tots );
91 :
92 : // Now prepare the link cell lists
93 1520 : unsigned tot=0;
94 1520 : for(unsigned i=0; i<lcell_tots.size(); ++i) { lcell_starts[i]=tot; tot+=lcell_tots[i]; lcell_tots[i]=0; }
95 1520 : plumed_assert( tot==pos.size() );
96 :
97 : // And setup the link cells properly
98 227394 : for(unsigned j=0; j<pos.size(); ++j) {
99 225874 : unsigned myind = lcell_starts[ allcells[j] ] + lcell_tots[ allcells[j] ];
100 225874 : lcell_lists[ myind ] = indices[j];
101 225874 : lcell_tots[allcells[j]]++;
102 : }
103 1520 : }
104 :
105 : #define LINKC_MIN(n) ((n<2)? 0 : -1)
106 : #define LINKC_MAX(n) ((n<3)? 1 : 2)
107 : #define LINKC_PBC(n,num) ((n<0)? num-1 : n%num )
108 :
109 205779 : void LinkCells::retrieveNeighboringAtoms( const Vector& pos, unsigned& natomsper, std::vector<unsigned>& atoms ) const {
110 205779 : plumed_assert( natomsper==1 || natomsper==2 ); // This is really a bug. If you are trying to reuse this ask GAT for help
111 205779 : std::vector<unsigned> celn( findMyCell( pos ) );
112 :
113 555566 : for(int nx=LINKC_MIN(ncells[0]); nx<LINKC_MAX(ncells[0]); ++nx) {
114 349733 : int xval = celn[0] + nx;
115 349742 : xval=LINKC_PBC(xval,ncells[0])*nstride[0];
116 1127496 : for(int ny=LINKC_MIN(ncells[1]); ny<LINKC_MAX(ncells[1]); ++ny) {
117 777815 : int yval = celn[1] + ny;
118 777829 : yval=LINKC_PBC(yval,ncells[1])*nstride[1];
119 2829061 : for(int nz=LINKC_MIN(ncells[2]); nz<LINKC_MAX(ncells[2]); ++nz) {
120 2051739 : int zval = celn[2] + nz;
121 2051855 : zval=LINKC_PBC(zval,ncells[2])*nstride[2];
122 :
123 2051677 : unsigned mybox=xval+yval+zval;
124 15997870 : for(unsigned k=0; k<lcell_tots[mybox]; ++k) {
125 13969732 : unsigned myatom = lcell_lists[lcell_starts[mybox]+k];
126 13971573 : if( myatom!=atoms[0] ) { // Ideally would provide an option to not do this
127 13826416 : atoms[natomsper]=myatom;
128 13821400 : natomsper++;
129 : }
130 : }
131 : }
132 : }
133 205793 : }
134 205826 : }
135 :
136 424367 : std::vector<unsigned> LinkCells::findMyCell( const Vector& pos ) const {
137 424367 : Vector fpos=mypbc.realToScaled( pos ); std::vector<unsigned> celn(3);
138 1697576 : for(unsigned j=0; j<3; ++j) {
139 1273128 : celn[j] = std::floor( ( Tools::pbc(fpos[j]) + 0.5 ) * ncells[j] );
140 1273230 : plumed_assert( celn[j]>=0 && celn[j]<ncells[j] ); // Check that atom is in box
141 : }
142 424448 : return celn;
143 : }
144 :
145 218611 : unsigned LinkCells::findCell( const Vector& pos ) const {
146 218611 : std::vector<unsigned> celn( findMyCell(pos ) );
147 218611 : return celn[0]*nstride[0] + celn[1]*nstride[1] + celn[2]*nstride[2];
148 : }
149 :
150 :
151 2523 : }
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