Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2020 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 "MetainferenceBase.h"
23 : #include "core/ActionRegister.h"
24 : #include "tools/NeighborList.h"
25 : #include "tools/Pbc.h"
26 :
27 : #include <string>
28 : #include <cmath>
29 : #include <memory>
30 :
31 : using namespace std;
32 :
33 : namespace PLMD {
34 : namespace isdb {
35 :
36 : //+PLUMEDOC ISDB_COLVAR NOE
37 : /*
38 : Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms
39 : or ambiguous NOE.
40 :
41 : Each NOE is defined by two groups containing the same number of atoms, distances are
42 : calculated in pairs, transformed in 1/r^6, summed and saved as components.
43 :
44 : \f[
45 : NOE() = (\frac{1}{N_{eq}}\sum_j^{N_{eq}} (\frac{1}{r_j^6}))
46 : \f]
47 :
48 : NOE can be used to calculate a Metainference score over one or more replicas using the intrinsic implementation
49 : of \ref METAINFERENCE that is activated by DOSCORE.
50 :
51 : \par Examples
52 : In the following examples three noes are defined, the first is calculated based on the distances
53 : of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances
54 : 4-15,4-16,8-15,8-16. \ref METAINFERENCE is activated using DOSCORE.
55 :
56 : \plumedfile
57 : NOE ...
58 : GROUPA1=1,3 GROUPB1=2,2
59 : GROUPA2=5 GROUPB2=7
60 : GROUPA3=4,4,8,8 GROUPB3=15,16,15,16
61 : DOSCORE
62 : LABEL=noes
63 : ... NOE
64 :
65 : PRINT ARG=noes.* FILE=colvar
66 : \endplumedfile
67 :
68 : */
69 : //+ENDPLUMEDOC
70 :
71 33 : class NOE :
72 : public MetainferenceBase
73 : {
74 : private:
75 : bool pbc;
76 : vector<unsigned> nga;
77 : std::unique_ptr<NeighborList> nl;
78 : unsigned tot_size;
79 : public:
80 : static void registerKeywords( Keywords& keys );
81 : explicit NOE(const ActionOptions&);
82 : virtual void calculate();
83 : void update();
84 : };
85 :
86 7378 : PLUMED_REGISTER_ACTION(NOE,"NOE")
87 :
88 12 : void NOE::registerKeywords( Keywords& keys ) {
89 12 : componentsAreNotOptional(keys);
90 12 : useCustomisableComponents(keys);
91 12 : MetainferenceBase::registerKeywords(keys);
92 36 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
93 48 : keys.add("numbered","GROUPA","the atoms involved in each of the contacts you wish to calculate. "
94 : "Keywords like GROUPA1, GROUPA2, GROUPA3,... should be listed and one contact will be "
95 : "calculated for each ATOM keyword you specify.");
96 48 : keys.add("numbered","GROUPB","the atoms involved in each of the contacts you wish to calculate. "
97 : "Keywords like GROUPB1, GROUPB2, GROUPB3,... should be listed and one contact will be "
98 : "calculated for each ATOM keyword you specify.");
99 36 : keys.reset_style("GROUPA","atoms");
100 36 : keys.reset_style("GROUPB","atoms");
101 36 : keys.addFlag("ADDEXP",false,"Set to TRUE if you want to have fixed components with the experimental reference values.");
102 48 : keys.add("numbered","NOEDIST","Add an experimental value for each NOE.");
103 48 : keys.addOutputComponent("noe","default","the # NOE");
104 48 : keys.addOutputComponent("exp","ADDEXP","the # NOE experimental distance");
105 12 : }
106 :
107 11 : NOE::NOE(const ActionOptions&ao):
108 : PLUMED_METAINF_INIT(ao),
109 22 : pbc(true)
110 : {
111 11 : bool nopbc=!pbc;
112 22 : parseFlag("NOPBC",nopbc);
113 11 : pbc=!nopbc;
114 :
115 : // Read in the atoms
116 : vector<AtomNumber> t, ga_lista, gb_lista;
117 22 : for(int i=1;; ++i ) {
118 66 : parseAtomList("GROUPA", i, t );
119 33 : if( t.empty() ) break;
120 143 : for(unsigned j=0; j<t.size(); j++) ga_lista.push_back(t[j]);
121 44 : nga.push_back(t.size());
122 22 : t.resize(0);
123 22 : }
124 : vector<unsigned> ngb;
125 22 : for(int i=1;; ++i ) {
126 66 : parseAtomList("GROUPB", i, t );
127 33 : if( t.empty() ) break;
128 143 : for(unsigned j=0; j<t.size(); j++) gb_lista.push_back(t[j]);
129 44 : ngb.push_back(t.size());
130 66 : if(ngb[i-1]!=nga[i-1]) error("The same number of atoms is expected for the same GROUPA-GROUPB couple");
131 22 : t.resize(0);
132 22 : }
133 11 : if(nga.size()!=ngb.size()) error("There should be the same number of GROUPA and GROUPB keywords");
134 : // Create neighbour lists
135 33 : nl.reset( new NeighborList(ga_lista,gb_lista,true,pbc,getPbc()) );
136 :
137 11 : bool addexp=false;
138 22 : parseFlag("ADDEXP",addexp);
139 11 : if(getDoScore()) addexp=true;
140 :
141 : vector<double> noedist;
142 11 : if(addexp) {
143 9 : noedist.resize( nga.size() );
144 : unsigned ntarget=0;
145 :
146 54 : for(unsigned i=0; i<nga.size(); ++i) {
147 36 : if( !parseNumbered( "NOEDIST", i+1, noedist[i] ) ) break;
148 : ntarget++;
149 : }
150 9 : if( ntarget!=nga.size() ) error("found wrong number of NOEDIST values");
151 : }
152 :
153 : // Ouput details of all contacts
154 : unsigned index=0;
155 88 : for(unsigned i=0; i<nga.size(); ++i) {
156 44 : log.printf(" The %uth NOE is calculated using %u equivalent couples of atoms\n", i, nga[i]);
157 88 : for(unsigned j=0; j<nga[i]; j++) {
158 66 : log.printf(" couple %u is %d %d.\n", j, ga_lista[index].serial(), gb_lista[index].serial() );
159 33 : index++;
160 : }
161 : }
162 11 : tot_size = index;
163 :
164 11 : if(pbc) log.printf(" using periodic boundary conditions\n");
165 0 : else log.printf(" without periodic boundary conditions\n");
166 :
167 33 : log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
168 :
169 11 : if(!getDoScore()) {
170 56 : for(unsigned i=0; i<nga.size(); i++) {
171 14 : string num; Tools::convert(i,num);
172 28 : addComponentWithDerivatives("noe_"+num);
173 28 : componentIsNotPeriodic("noe_"+num);
174 : }
175 7 : if(addexp) {
176 40 : for(unsigned i=0; i<nga.size(); i++) {
177 10 : string num; Tools::convert(i,num);
178 20 : addComponent("exp_"+num);
179 20 : componentIsNotPeriodic("exp_"+num);
180 20 : Value* comp=getPntrToComponent("exp_"+num);
181 10 : comp->set(noedist[i]);
182 : }
183 : }
184 : } else {
185 32 : for(unsigned i=0; i<nga.size(); i++) {
186 8 : string num; Tools::convert(i,num);
187 16 : addComponent("noe_"+num);
188 16 : componentIsNotPeriodic("noe_"+num);
189 : }
190 32 : for(unsigned i=0; i<nga.size(); i++) {
191 8 : string num; Tools::convert(i,num);
192 16 : addComponent("exp_"+num);
193 16 : componentIsNotPeriodic("exp_"+num);
194 16 : Value* comp=getPntrToComponent("exp_"+num);
195 8 : comp->set(noedist[i]);
196 : }
197 : }
198 :
199 11 : requestAtoms(nl->getFullAtomList(), false);
200 11 : if(getDoScore()) {
201 4 : setParameters(noedist);
202 4 : Initialise(nga.size());
203 : }
204 11 : setDerivatives();
205 11 : checkRead();
206 11 : }
207 :
208 456 : void NOE::calculate()
209 : {
210 456 : const unsigned ngasz=nga.size();
211 456 : vector<Vector> deriv(tot_size, Vector{0,0,0});
212 :
213 1368 : #pragma omp parallel for num_threads(OpenMP::getNumThreads())
214 : for(unsigned i=0; i<ngasz; i++) {
215 912 : Tensor dervir;
216 : double noe=0;
217 : unsigned index=0;
218 2280 : for(unsigned k=0; k<i; k++) index+=nga[k];
219 912 : string num; Tools::convert(i,num);
220 1824 : Value* val=getPntrToComponent("noe_"+num);
221 : // cycle over equivalent atoms
222 5928 : for(unsigned j=0; j<nga[i]; j++) {
223 1368 : const unsigned i0=nl->getClosePair(index+j).first;
224 1368 : const unsigned i1=nl->getClosePair(index+j).second;
225 :
226 1368 : Vector distance;
227 5472 : if(pbc) distance=pbcDistance(getPosition(i0),getPosition(i1));
228 0 : else distance=delta(getPosition(i0),getPosition(i1));
229 :
230 1368 : const double ir2=1./distance.modulo2();
231 1368 : const double ir6=ir2*ir2*ir2;
232 1368 : const double ir8=6*ir6*ir2;
233 :
234 1368 : noe += ir6;
235 2736 : deriv[index+j] = ir8*distance;
236 1368 : if(!getDoScore()) {
237 2448 : dervir += Tensor(distance, deriv[index+j]);
238 2448 : setAtomsDerivatives(val, i0, deriv[index+j]);
239 2448 : setAtomsDerivatives(val, i1, -deriv[index+j]);
240 : }
241 : }
242 : val->set(noe);
243 912 : if(!getDoScore()) {
244 816 : setBoxDerivatives(val, dervir);
245 : } else setCalcData(i, noe);
246 : }
247 :
248 456 : if(getDoScore()) {
249 : /* Metainference */
250 48 : Tensor dervir;
251 48 : double score = getScore();
252 : setScore(score);
253 :
254 : /* calculate final derivatives */
255 96 : Value* val=getPntrToComponent("score");
256 240 : for(unsigned i=0; i<ngasz; i++) {
257 : unsigned index=0;
258 192 : for(unsigned k=0; k<i; k++) index+=nga[k];
259 : // cycle over equivalent atoms
260 624 : for(unsigned j=0; j<nga[i]; j++) {
261 144 : const unsigned i0=nl->getClosePair(index+j).first;
262 144 : const unsigned i1=nl->getClosePair(index+j).second;
263 :
264 144 : Vector distance;
265 432 : if(pbc) distance=pbcDistance(getPosition(i0),getPosition(i1));
266 0 : else distance=delta(getPosition(i0),getPosition(i1));
267 :
268 288 : dervir += Tensor(distance,deriv[index+j]*getMetaDer(i));
269 144 : setAtomsDerivatives(val, i0, deriv[index+j]*getMetaDer(i));
270 144 : setAtomsDerivatives(val, i1, -deriv[index+j]*getMetaDer(i));
271 : }
272 : }
273 48 : setBoxDerivatives(val, dervir);
274 : }
275 456 : }
276 :
277 132 : void NOE::update() {
278 : // write status file
279 264 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) writeStatus();
280 132 : }
281 :
282 : }
283 5517 : }
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