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 :
23 : #include "core/ActionPilot.h"
24 : #include "core/ActionWithArguments.h"
25 : #include "core/ActionRegister.h"
26 : #include "core/PlumedMain.h"
27 :
28 : namespace PLMD {
29 : namespace analysis {
30 :
31 : //+PLUMEDOC PRINTANALYSIS COMMITTOR
32 : /*
33 : Does a committor analysis.
34 :
35 : \par Examples
36 :
37 : The following input monitors two torsional angles during a simulation,
38 : defines two basins (A and B) as a function of the two torsions and
39 : stops the simulation when it falls in one of the two. In the log
40 : file will be shown the latest values for the CVs and the basin reached.
41 : \verbatim
42 : TORSION ATOMS=1,2,3,4 LABEL=r1
43 : TORSION ATOMS=2,3,4,5 LABEL=r2
44 : COMMITTOR ...
45 : ARG=r1,r2
46 : STRIDE=10
47 : BASIN_LL1=0.15,0.20
48 : BASIN_UL1=0.25,0.40
49 : BASIN_LL2=-0.25,-0.40
50 : BASIN_UL2=-0.15,-0.20
51 : ... COMMITTOR
52 : \endverbatim
53 :
54 : */
55 : //+ENDPLUMEDOC
56 :
57 2 : class Committor :
58 : public ActionPilot,
59 : public ActionWithArguments
60 : {
61 : private:
62 : std::string file;
63 : OFile ofile;
64 : std::string fmt;
65 : std::vector< std::vector<double> > lowerlimits;
66 : std::vector< std::vector<double> > upperlimits;
67 : unsigned nbasins;
68 : public:
69 : static void registerKeywords( Keywords& keys );
70 : explicit Committor(const ActionOptions&ao);
71 : void calculate();
72 12 : void apply() {}
73 : };
74 :
75 2524 : PLUMED_REGISTER_ACTION(Committor,"COMMITTOR")
76 :
77 2 : void Committor::registerKeywords( Keywords& keys ) {
78 2 : Action::registerKeywords(keys);
79 2 : ActionPilot::registerKeywords(keys);
80 2 : ActionWithArguments::registerKeywords(keys);
81 2 : keys.use("ARG");
82 2 : keys.add("numbered", "BASIN_LL","List of lower limits for basin #");
83 2 : keys.add("numbered", "BASIN_UL","List of upper limits for basin #");
84 2 : keys.reset_style("BASIN_LL","compulsory"); keys.reset_style("BASIN_UL","compulsory");
85 2 : keys.add("compulsory","STRIDE","1","the frequency with which the CVs are analysed");
86 2 : keys.add("optional","FILE","the name of the file on which to output the reached basin");
87 2 : keys.add("optional","FMT","the format that should be used to output real numbers");
88 2 : }
89 :
90 1 : Committor::Committor(const ActionOptions&ao):
91 : Action(ao),
92 : ActionPilot(ao),
93 : ActionWithArguments(ao),
94 1 : fmt("%f")
95 : {
96 1 : ofile.link(*this);
97 1 : parse("FILE",file);
98 1 : if(file.length()>0) {
99 1 : ofile.open(file);
100 1 : log.printf(" on file %s\n",file.c_str());
101 : } else {
102 0 : log.printf(" on plumed log file\n");
103 0 : ofile.link(log);
104 : }
105 1 : parse("FMT",fmt);
106 1 : fmt=" "+fmt;
107 1 : log.printf(" with format %s\n",fmt.c_str());
108 :
109 1 : for(unsigned i=0; i<getNumberOfArguments(); ++i) ofile.setupPrintValue( getPntrToArgument(i) );
110 :
111 4 : for(unsigned b=1;; ++b ) {
112 :
113 7 : std::vector<double> tmpl, tmpu;
114 4 : parseNumberedVector("BASIN_LL", b, tmpl );
115 4 : parseNumberedVector("BASIN_UL", b, tmpu );
116 4 : if( tmpl.empty() && tmpu.empty() ) break;
117 3 : if( tmpl.size()!=getNumberOfArguments()) error("Wrong number of values for BASIN_LL: they should be equal to the number of arguments");
118 3 : if( tmpu.size()!=getNumberOfArguments()) error("Wrong number of values for BASIN_UL: they should be equal to the number of arguments");
119 3 : lowerlimits.push_back(tmpl);
120 3 : upperlimits.push_back(tmpu);
121 3 : nbasins=b;
122 6 : }
123 1 : checkRead();
124 :
125 :
126 4 : for(unsigned b=0; b<nbasins; b++) {
127 3 : log.printf(" BASIN %u definition:\n", b+1);
128 9 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
129 6 : if(lowerlimits[b][i]>upperlimits[b][i]) error("COMMITTOR: UPPER bounds must always be greater than LOWER bounds");
130 6 : log.printf(" %f - %f\n", lowerlimits[b][i], upperlimits[b][i]);
131 : }
132 : }
133 1 : }
134 :
135 12 : void Committor::calculate() {
136 12 : std::vector<unsigned> inbasin;
137 12 : inbasin.assign (nbasins,1);
138 :
139 48 : for(unsigned b=0; b<nbasins; ++b) {
140 108 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
141 72 : if(getArgument(i)>lowerlimits[b][i]&&getArgument(i)<upperlimits[b][i]) inbasin[b]*=1; else inbasin[b]*=0;
142 : }
143 : }
144 :
145 48 : for(unsigned b=0; b<nbasins; ++b) {
146 36 : if(inbasin[b]==1) {
147 1 : ofile.fmtField(" %f");
148 1 : ofile.printField("time",getTime());
149 3 : for(unsigned i=0; i<getNumberOfArguments(); i++) {
150 2 : ofile.fmtField(fmt);
151 2 : ofile.printField( getPntrToArgument(i), getArgument(i) );
152 : }
153 1 : ofile.printField();
154 1 : std::string num; Tools::convert( b+1, num );
155 2 : std::string str = "COMMITED TO BASIN " + num;
156 1 : ofile.addConstantField(str);
157 1 : ofile.printField();
158 1 : ofile.flush();
159 2 : plumed.stop();
160 : }
161 12 : }
162 12 : }
163 :
164 : }
165 2523 : }
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