Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2018 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 "MultiColvar.h"
23 : #include "tools/SwitchingFunction.h"
24 : #include "core/ActionRegister.h"
25 :
26 : #include <string>
27 : #include <cmath>
28 :
29 : using namespace std;
30 :
31 : namespace PLMD {
32 : namespace multicolvar {
33 :
34 : //+PLUMEDOC MCOLVAR BRIDGE
35 : /*
36 : Calculate the number of atoms that bridge two parts of a structure
37 :
38 : This quantity calculates:
39 :
40 : \f[
41 : f(x) = \sum_{ijk} s_A(r_{ij})s_B(r_{ik})
42 : \f]
43 :
44 : where the sum over \f$i\f$ is over all the ``bridging atoms" and
45 : \f$s_A\f$ and \f$s_B\f$ are \ref switchingfunction.
46 :
47 : \par Examples
48 :
49 : The following example instructs plumed to calculate the number of water molecules
50 : that are bridging betweeen atoms 1-10 and atoms 11-20 and to print the value
51 : to a file
52 :
53 : \verbatim
54 : BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 LABEL=w1
55 : PRINT ARG=a1.mean FILE=colvar
56 : \endverbatim
57 :
58 : */
59 : //+ENDPLUMEDOC
60 :
61 18 : class Bridge : public MultiColvar {
62 : private:
63 : Vector dij, dik;
64 : SwitchingFunction sf1;
65 : SwitchingFunction sf2;
66 : public:
67 : static void registerKeywords( Keywords& keys );
68 : explicit Bridge(const ActionOptions&);
69 : // active methods:
70 : virtual double compute( const unsigned& tindex, AtomValuePack& myatoms ) const ;
71 0 : bool isPeriodic() { return false; }
72 : };
73 :
74 2532 : PLUMED_REGISTER_ACTION(Bridge,"BRIDGE")
75 :
76 10 : void Bridge::registerKeywords( Keywords& keys ) {
77 10 : MultiColvar::registerKeywords( keys );
78 10 : keys.use("ATOMS");
79 : keys.add("atoms-2","BRIDGING_ATOMS","The list of atoms that can form the bridge between the two interesting parts "
80 10 : "of the structure.");
81 10 : keys.add("atoms-2","GROUPA","The list of atoms that are in the first interesting part of the structure");
82 10 : keys.add("atoms-2","GROUPB","The list of atoms that are in the second interesting part of the structure");
83 10 : keys.add("optional","SWITCH","The parameters of the two \\ref switchingfunction in the above formula");
84 : keys.add("optional","SWITCHA","The \\ref switchingfunction on the distance between bridging atoms and the atoms in "
85 10 : "group A");
86 : keys.add("optional","SWITCHB","The \\ref switchingfunction on the distance between the bridging atoms and the atoms in "
87 10 : "group B");
88 10 : }
89 :
90 9 : Bridge::Bridge(const ActionOptions&ao):
91 9 : PLUMED_MULTICOLVAR_INIT(ao)
92 : {
93 : // Read in the atoms
94 9 : std::vector<AtomNumber> all_atoms;
95 9 : readThreeGroups("GROUPA","GROUPB","BRIDGING_ATOMS",false,true,all_atoms);
96 : // Setup the multicolvar base
97 9 : setupMultiColvarBase( all_atoms );
98 : // Setup Central atom atoms
99 18 : std::vector<bool> catom_ind(3, false); catom_ind[0]=true;
100 9 : setAtomsForCentralAtom( catom_ind );
101 :
102 18 : std::string sfinput,errors; parse("SWITCH",sfinput);
103 9 : if( sfinput.length()>0 ) {
104 9 : sf1.set(sfinput,errors);
105 9 : if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors );
106 9 : sf2.set(sfinput,errors);
107 9 : if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors );
108 : } else {
109 0 : parse("SWITCHA",sfinput);
110 0 : if(sfinput.length()>0) {
111 0 : weightHasDerivatives=true;
112 0 : sf1.set(sfinput,errors);
113 0 : if( errors.length()!=0 ) error("problem reading SWITCHA keyword : " + errors );
114 0 : sfinput.clear(); parse("SWITCHB",sfinput);
115 0 : if(sfinput.length()==0) error("found SWITCHA keyword without SWITCHB");
116 0 : sf2.set(sfinput,errors);
117 0 : if( errors.length()!=0 ) error("problem reading SWITCHB keyword : " + errors );
118 : } else {
119 0 : error("missing definition of switching functions");
120 : }
121 : }
122 9 : log.printf(" distance between bridging atoms and atoms in GROUPA must be less than %s\n",sf1.description().c_str());
123 9 : log.printf(" distance between bridging atoms and atoms in GROUPB must be less than %s\n",sf2.description().c_str());
124 :
125 : // Setup link cells
126 9 : setLinkCellCutoff( sf1.get_dmax() + sf2.get_dmax() );
127 :
128 : // And setup the ActionWithVessel
129 9 : if( getNumberOfVessels()!=0 ) error("should not have vessels for this action");
130 18 : std::string fake_input;
131 9 : addVessel( "SUM", fake_input, -1 ); // -1 here means that this value will be named getLabel()
132 9 : readVesselKeywords();
133 : // And check everything has been read in correctly
134 18 : checkRead();
135 9 : }
136 :
137 50507 : double Bridge::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
138 50507 : double tot=0;
139 571240 : for(unsigned i=2; i<myatoms.getNumberOfAtoms(); ++i) {
140 520736 : Vector dij=getSeparation( myatoms.getPosition(i), myatoms.getPosition(0) );
141 520774 : double dw1, w1=sf1.calculateSqr( dij.modulo2(), dw1 );
142 520772 : Vector dik=getSeparation( myatoms.getPosition(i), myatoms.getPosition(1) );
143 520791 : double dw2, w2=sf2.calculateSqr( dik.modulo2(), dw2 );
144 :
145 520802 : tot += w1*w2;
146 : // And finish the calculation
147 520802 : addAtomDerivatives( 1, 0, w2*dw1*dij, myatoms );
148 520802 : addAtomDerivatives( 1, 1, w1*dw2*dik, myatoms );
149 520777 : addAtomDerivatives( 1, i, -w1*dw2*dik-w2*dw1*dij, myatoms );
150 520786 : myatoms.addBoxDerivatives( 1, w1*(-dw2)*Tensor(dik,dik)+w2*(-dw1)*Tensor(dij,dij) );
151 : }
152 50527 : return tot;
153 : }
154 :
155 : }
156 2523 : }
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