Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2019 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 <cmath>
23 :
24 : #include "Function.h"
25 : #include "ActionRegister.h"
26 :
27 : #include <string>
28 : #include <cstring>
29 : #include <iostream>
30 :
31 : using namespace std;
32 :
33 : namespace PLMD {
34 : namespace function {
35 :
36 : //+PLUMEDOC FUNCTION FUNCPATHMSD
37 : /*
38 : This function calculates path collective variables.
39 :
40 : This is the Path Collective Variables implementation
41 : ( see \cite brand07 ).
42 : This variable computes the progress along a given set of frames that is provided
43 : in input ("s" component) and the distance from them ("z" component).
44 : It is a function of MSD that are obtained by the joint use of MSD variable and SQUARED flag
45 : (see below).
46 :
47 : \par Examples
48 :
49 : Here below is a case where you have defined three frames and you want to
50 : calculate the progress alng the path and the distance from it in p1
51 :
52 : \plumedfile
53 : t1: RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
54 : t2: RMSD REFERENCE=frame_21.dat TYPE=OPTIMAL SQUARED
55 : t3: RMSD REFERENCE=frame_42.dat TYPE=OPTIMAL SQUARED
56 : p1: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0
57 : PRINT ARG=t1,t2,t3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f
58 : \endplumedfile
59 :
60 : In this second example is shown how to define a PATH in the \ref CONTACTMAP space:
61 :
62 : \plumedfile
63 : CONTACTMAP ...
64 : ATOMS1=1,2 REFERENCE1=0.1
65 : ATOMS2=3,4 REFERENCE2=0.5
66 : ATOMS3=4,5 REFERENCE3=0.25
67 : ATOMS4=5,6 REFERENCE4=0.0
68 : SWITCH={RATIONAL R_0=1.5}
69 : LABEL=c1
70 : CMDIST
71 : ... CONTACTMAP
72 :
73 : CONTACTMAP ...
74 : ATOMS1=1,2 REFERENCE1=0.3
75 : ATOMS2=3,4 REFERENCE2=0.9
76 : ATOMS3=4,5 REFERENCE3=0.45
77 : ATOMS4=5,6 REFERENCE4=0.1
78 : SWITCH={RATIONAL R_0=1.5}
79 : LABEL=c2
80 : CMDIST
81 : ... CONTACTMAP
82 :
83 : CONTACTMAP ...
84 : ATOMS1=1,2 REFERENCE1=1.0
85 : ATOMS2=3,4 REFERENCE2=1.0
86 : ATOMS3=4,5 REFERENCE3=1.0
87 : ATOMS4=5,6 REFERENCE4=1.0
88 : SWITCH={RATIONAL R_0=1.5}
89 : LABEL=c3
90 : CMDIST
91 : ... CONTACTMAP
92 :
93 : p1: FUNCPATHMSD ARG=c1,c2,c3 LAMBDA=500.0
94 : PRINT ARG=c1,c2,c3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f
95 : \endplumedfile
96 :
97 : */
98 : //+ENDPLUMEDOC
99 :
100 6 : class FuncPathMSD : public Function {
101 : double lambda;
102 : int neigh_size;
103 : double neigh_stride;
104 : vector< pair<Value *,double> > neighpair;
105 : map<Value *,double > indexmap; // use double to allow isomaps
106 : vector <Value*> allArguments;
107 : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
108 : // this below is useful when one wants to sort a vector of double and have back the order
109 : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
110 : // create a custom sorter
111 : typedef vector<double>::const_iterator myiter;
112 : struct ordering {
113 : bool operator ()(pair<unsigned, myiter> const& a, pair<unsigned, myiter> const& b) {
114 : return *(a.second) < *(b.second);
115 : }
116 : };
117 : // sorting utility
118 : vector<int> increasingOrder( vector<double> &v) {
119 : // make a pair
120 : vector< pair<unsigned, myiter> > order(v.size());
121 : unsigned n = 0;
122 : for (myiter it = v.begin(); it != v.end(); ++it, ++n) {
123 : order[n] = make_pair(n, it); // note: heere i do not put the values but the addresses that point to the value
124 : }
125 : // now sort according the second value
126 : sort(order.begin(), order.end(), ordering());
127 : vector<int> vv(v.size()); n=0;
128 : for (const auto & it : order) {
129 : vv[n]=it.first; n++;
130 : }
131 : return vv;
132 : }
133 : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
134 : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
135 :
136 : struct pairordering {
137 : bool operator ()(pair<Value *, double> const& a, pair<Value*, double> const& b) {
138 437 : return (a).second > (b).second;
139 : }
140 : };
141 :
142 : public:
143 : explicit FuncPathMSD(const ActionOptions&);
144 : // active methods:
145 : virtual void calculate();
146 : virtual void prepare();
147 : static void registerKeywords(Keywords& keys);
148 : };
149 :
150 6454 : PLUMED_REGISTER_ACTION(FuncPathMSD,"FUNCPATHMSD")
151 :
152 3 : void FuncPathMSD::registerKeywords(Keywords& keys) {
153 3 : Function::registerKeywords(keys);
154 6 : keys.use("ARG");
155 12 : keys.add("compulsory","LAMBDA","the lambda parameter is needed for smoothing, is in the units of plumed");
156 12 : keys.add("optional","NEIGH_SIZE","size of the neighbor list");
157 12 : keys.add("optional","NEIGH_STRIDE","how often the neighbor list needs to be calculated in time units");
158 3 : componentsAreNotOptional(keys);
159 12 : keys.addOutputComponent("s","default","the position on the path");
160 12 : keys.addOutputComponent("z","default","the distance from the path");
161 3 : }
162 2 : FuncPathMSD::FuncPathMSD(const ActionOptions&ao):
163 : Action(ao),
164 : Function(ao),
165 : neigh_size(-1),
166 6 : neigh_stride(-1.)
167 : {
168 :
169 4 : parse("LAMBDA",lambda);
170 4 : parse("NEIGH_SIZE",neigh_size);
171 4 : parse("NEIGH_STRIDE",neigh_stride);
172 2 : checkRead();
173 2 : log.printf(" lambda is %f\n",lambda);
174 : // list the action involved and check the type
175 2 : std::string myname=getPntrToArgument(0)->getPntrToAction()->getName();
176 2 : if(myname!="RMSD"&&myname!="CONTACTMAP"&&myname!="DISTANCE") error("One or more of your arguments is not of RMSD/CONTACTMAP/DISTANCE type!!!");
177 10 : for(unsigned i=1; i<getNumberOfArguments(); i++) {
178 : // for each value get the name and the label of the corresponding action
179 8 : if( getPntrToArgument(i)->getPntrToAction()->getName()!=myname ) error("mismatch between the types of arguments");
180 : }
181 2 : log.printf(" Consistency check completed! Your path cvs look good!\n");
182 : // do some neighbor printout
183 2 : if(neigh_stride>0. || neigh_size>0) {
184 2 : if(neigh_size>getNumberOfArguments()) {
185 0 : log.printf(" List size required ( %d ) is too large: resizing to the maximum number of arg required: %d \n",neigh_size,getNumberOfArguments());
186 0 : neigh_size=getNumberOfArguments();
187 : }
188 1 : log.printf(" Neighbor list enabled: \n");
189 1 : log.printf(" size : %d elements\n",neigh_size);
190 1 : log.printf(" stride : %f time \n",neigh_stride);
191 : } else {
192 1 : log.printf(" Neighbor list NOT enabled \n");
193 : }
194 :
195 6 : addComponentWithDerivatives("s"); componentIsNotPeriodic("s");
196 6 : addComponentWithDerivatives("z"); componentIsNotPeriodic("z");
197 :
198 : // now backup the arguments
199 20 : for(unsigned i=0; i<getNumberOfArguments(); i++)allArguments.push_back(getPntrToArgument(i));
200 : double i=1.;
201 8 : for(const auto & it : allArguments) {
202 6 : indexmap[it]=i; i+=1.;
203 : }
204 :
205 2 : }
206 : // calculator
207 1092 : void FuncPathMSD::calculate() {
208 : // log.printf("NOW CALCULATE! \n");
209 : double s_path=0.;
210 : double partition=0.;
211 1092 : if(neighpair.empty()) { // at first step, resize it
212 0 : neighpair.resize(allArguments.size());
213 0 : for(unsigned i=0; i<allArguments.size(); i++)neighpair[i].first=allArguments[i];
214 : }
215 :
216 2184 : Value* val_s_path=getPntrToComponent("s");
217 2184 : Value* val_z_path=getPntrToComponent("z");
218 :
219 3959 : for(auto & it : neighpair) {
220 5734 : it.second=exp(-lambda*(it.first->get()));
221 2867 : s_path+=(indexmap[it.first])*it.second;
222 2867 : partition+=it.second;
223 : }
224 1092 : s_path/=partition;
225 : val_s_path->set(s_path);
226 1092 : val_z_path->set(-(1./lambda)*std::log(partition));
227 : int n=0;
228 3959 : for(const auto & it : neighpair) {
229 2867 : double expval=it.second;
230 2867 : double tmp=lambda*expval*(s_path-(indexmap[it.first]))/partition;
231 : setDerivative(val_s_path,n,tmp);
232 2867 : setDerivative(val_z_path,n,expval/partition);
233 2867 : n++;
234 : }
235 :
236 : // log.printf("CALCULATION DONE! \n");
237 1092 : }
238 : ///
239 : /// this function updates the needed argument list
240 : ///
241 1092 : void FuncPathMSD::prepare() {
242 :
243 : // neighbor list: rank and activate the chain for the next step
244 :
245 : // neighbor list: if neigh_size<0 never sort and keep the full vector
246 : // neighbor list: if neigh_size>0
247 : // if the size is full -> sort the vector and decide the dependencies for next step
248 : // if the size is not full -> check if next step will need the full dependency otherwise keep this dependencies
249 :
250 : // here just resize the neighpair. The real resizing of reinit will be done by the prepare stage that will modify the list of arguments
251 1092 : if (neigh_size>0) {
252 546 : if(neighpair.size()==allArguments.size()) { // I just did the complete round: need to sort, shorten and give it a go
253 : // sort the values
254 : sort(neighpair.begin(),neighpair.end(),pairordering());
255 : // resize the effective list
256 137 : neighpair.resize(neigh_size);
257 137 : log.printf(" NEIGH LIST NOW INCLUDE INDEXES: ");
258 685 : for(int i=0; i<neigh_size; ++i)log.printf(" %f ",indexmap[neighpair[i].first]); log.printf(" \n");
259 : } else {
260 409 : if( int(getStep())%int(neigh_stride/getTimeStep())==0 ) {
261 137 : log.printf(" Time %f : recalculating full neighlist \n",getStep()*getTimeStep());
262 274 : neighpair.resize(allArguments.size());
263 1507 : for(unsigned i=0; i<allArguments.size(); i++)neighpair[i].first=allArguments[i];
264 : }
265 : }
266 : } else {
267 546 : if( int(getStep())==0) {
268 2 : neighpair.resize(allArguments.size());
269 11 : for(unsigned i=0; i<allArguments.size(); i++)neighpair[i].first=allArguments[i];
270 : }
271 : }
272 : vector<Value*> argstocall;
273 : //log.printf("PREPARING \n");
274 : argstocall.clear();
275 1092 : if(!neighpair.empty()) {
276 3959 : for(const auto & it : neighpair) {
277 2867 : argstocall.push_back( it.first );
278 : // log.printf("CALLING %p %f ",(*it).first ,indexmap[(*it).first] );
279 : }
280 : } else {
281 0 : for(unsigned i=0; i<allArguments.size(); i++) {
282 0 : argstocall.push_back(allArguments[i]);
283 : }
284 : }
285 : // now the list of argument changes
286 1092 : requestArguments(argstocall);
287 : //now resize the derivatives as well
288 : //for each value in this action
289 5460 : for(int i=0; i< getNumberOfComponents(); i++) {
290 : //resize the derivative to the number the
291 2184 : getPntrToComponent(i)->clearDerivatives();
292 2184 : getPntrToComponent(i)->resizeDerivatives(getNumberOfArguments());
293 : }
294 : //log.printf("PREPARING DONE! \n");
295 1092 : }
296 :
297 : }
298 4839 : }
299 :
300 :
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