1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2017 of Haochuan Chen (excluding colvar_UIestimator.h)
3 Copyright (c) 2017 of Haohao Fu (colvar_UIestimator.h)
4
5 This program is free software: you can redistribute it and/or modify
6 it under the terms of the GNU Lesser General Public License as published
7 by the Free Software Foundation, either version 3 of the License, or
8 (at your option) any later version.
9
10 This program is distributed in the hope that it will be useful,
11 but WITHOUT ANY WARRANTY; without even the implied warranty of
12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 GNU Lesser General Public License for more details.
14
15 You should have received a copy of the GNU Lesser General Public License
16 along with this program. If not, see <http://www.gnu.org/licenses/>.
17 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
18 #ifdef __PLUMED_HAS_BOOST_SERIALIZATION
19 #include "cltools/CLTool.h"
20 #include "cltools/CLToolRegister.h"
21 #include "config/Config.h"
22 #include "core/ActionRegister.h"
23 #include "DRR.h"
24 #include "tools/Tools.h"
25 #include "tools/Units.h"
26 #include <boost/archive/binary_iarchive.hpp>
27 #include <boost/archive/binary_oarchive.hpp>
28 #include <boost/serialization/vector.hpp>
29 #include <cstdlib>
30 #include <fstream>
31 #include <iostream>
32 #include <string>
33
34 using namespace PLMD;
35 using namespace cltools;
36
37 namespace PLMD {
38 namespace drr {
39
40 //+PLUMEDOC EABFMOD_TOOLS drr_tool
41 /*
42 - Extract .grad and .count files from the binary output .drrstate
43 - Merge windows
44
45 \par Examples
46
47 The following command will extract .grad and .count files.
48 \verbatim
49 plumed drr_tool --extract eabf.drrstate
50 \endverbatim
51
52 The following command will merge windows of two .drrstate file, and output the
53 .grad and .count files.
54 \verbatim
55 plumed drr_tool --merge win1.drrstate,win2.drrstate
56 \endverbatim
57
58 After getting the .grad and .count file, you can do numerical integration by
59 using abf_integrate tool from
60 https://github.com/Colvars/colvars/tree/master/colvartools
61 \verbatim
62 abf_integrate eabf.czar.grad
63 \endverbatim
64 \note
65 The abf_integrate in colvartools is in kcal/mol, so it may be better to use --units kcal/mol when running drr_tool
66
67 */
68 //+ENDPLUMEDOC
69
70 using std::vector;
71 using std::string;
72
73 class drrtool : public CLTool {
74 public:
75 static void registerKeywords(Keywords &keys);
76 explicit drrtool(const CLToolOptions &co);
77 int main(FILE *in, FILE *out, Communicator &pc);
78 void extractdrr(const vector<string> &filename);
79 void mergewindows(const vector<string> &filename, string outputname);
80 void calcDivergence(const vector<string> &filename);
description() const81 string description() const { return "Extract or merge the drrstate files."; }
82
83 private:
84 bool verbosity;
85 Units units;
86 const string suffix{".drrstate"};
87 };
88
89 PLUMED_REGISTER_CLTOOL(drrtool, "drr_tool")
90
registerKeywords(Keywords & keys)91 void drrtool::registerKeywords(Keywords &keys) {
92 CLTool::registerKeywords(keys);
93 keys.add("optional", "--extract", "Extract drrstate file(s)");
94 keys.add("optional", "--merge", "Merge eABF windows");
95 keys.add("optional", "--merge_output", "The output filename of the merged result");
96 keys.add("optional", "--divergence", "Calculate divergence of gradient field (experimental)");
97 keys.add("compulsory","--units","kj/mol","the units of energy can be kj/mol, kcal/mol, j/mol, eV or the conversion factor from kj/mol");
98 keys.addFlag("-v", false, "Verbose output");
99 }
100
drrtool(const CLToolOptions & co)101 drrtool::drrtool(const CLToolOptions &co) : CLTool(co) {
102 inputdata = commandline;
103 verbosity = false;
104 }
105
main(FILE * in,FILE * out,Communicator & pc)106 int drrtool::main(FILE *in, FILE *out, Communicator &pc) {
107 parseFlag("-v", verbosity);
108 vector<string> stateFilesToExtract;
109 string unitname;
110 parse("--units",unitname);
111 units.setEnergy( unitname );
112 bool doextract = parseVector("--extract", stateFilesToExtract);
113 if (doextract) {
114 extractdrr(stateFilesToExtract);
115 }
116 vector<string> stateFilesToMerge;
117 bool domerge = parseVector("--merge", stateFilesToMerge);
118 if (domerge) {
119 string merge_outputname;
120 parse("--merge_output", merge_outputname);
121 mergewindows(stateFilesToMerge, merge_outputname);
122 }
123 vector<string> stateFilesToDivergence;
124 bool dodivergence = parseVector("--divergence", stateFilesToDivergence);
125 if (dodivergence) {
126 calcDivergence(stateFilesToDivergence);
127 }
128 return 0;
129 }
130
extractdrr(const vector<string> & filename)131 void drrtool::extractdrr(const vector<string> &filename) {
132 #pragma omp parallel for
133 for (size_t j = 0; j < filename.size(); ++j) {
134 std::ifstream in;
135 in.open(filename[j]);
136 boost::archive::binary_iarchive ia(in);
137 long long int step;
138 vector<double> fict;
139 vector<double> vfict;
140 vector<double> vfict_laststep;
141 vector<double> ffict;
142 ABF abfgrid;
143 CZAR czarestimator;
144 ia >> step >> fict >> vfict >> vfict_laststep >> ffict >> abfgrid >>
145 czarestimator;
146 in.close();
147 abfgrid.setOutputUnit(units.getEnergy());
148 czarestimator.setOutputUnit(units.getEnergy());
149 if (verbosity) {
150 std::cout << "Output units factor: " << units.getEnergy() << '\n';
151 std::cout << "Dumping information of extended variables..." << '\n';
152 std::cout << "Step: " << step << '\n';
153 for (size_t i = 0; i < fict.size(); ++i) {
154 std::cout << "Dimension[" << i + 1 << "]:\n"
155 << " Coordinate: " << fict[i] << '\n'
156 << " Velocity: " << vfict[i] << '\n'
157 << " Velocity(laststep): " << vfict_laststep[i] << '\n'
158 << " Force: " << ffict[i] << '\n';
159 }
160 std::cout << "Dumping counts and gradients from grids..." << '\n';
161 }
162 string outputname(filename[j]);
163 outputname = outputname.substr(0, outputname.length() - suffix.length());
164 if (verbosity)
165 std::cout << "Writing ABF(naive) estimator files..." << '\n';
166 abfgrid.writeAll(outputname);
167 if (verbosity)
168 std::cout << "Writing CZAR estimator files..." << '\n';
169 czarestimator.writeAll(outputname);
170 czarestimator.writeZCount(outputname);
171 }
172 }
173
mergewindows(const vector<string> & filename,string outputname)174 void drrtool::mergewindows(const vector<string> &filename, string outputname) {
175 if (filename.size() < 2) {
176 std::cerr << "ERROR! You need at least two .drrstate file to merge windows!" << std::endl;
177 std::abort();
178 }
179 // Read grid into abfs and czars;
180 vector<ABF> abfs;
181 vector<CZAR> czars;
182 for (auto it_fn = filename.begin(); it_fn != filename.end(); ++it_fn) {
183 std::ifstream in;
184 in.open((*it_fn));
185 boost::archive::binary_iarchive ia(in);
186 long long int step;
187 vector<double> fict;
188 vector<double> vfict;
189 vector<double> vfict_laststep;
190 vector<double> ffict;
191 ABF abfgrid;
192 CZAR czarestimator;
193 ia >> step >> fict >> vfict >> vfict_laststep >> ffict >> abfgrid >>
194 czarestimator;
195 abfgrid.setOutputUnit(units.getEnergy());
196 czarestimator.setOutputUnit(units.getEnergy());
197 abfs.push_back(abfgrid);
198 czars.push_back(czarestimator);
199 in.close();
200 }
201 CZAR cmerged = CZAR::mergewindow(czars[0], czars[1]);
202 ABF amerged = ABF::mergewindow(abfs[0], abfs[1]);
203 for (size_t i = 2; i < czars.size(); ++i) {
204 cmerged = CZAR::mergewindow(cmerged, czars[i]);
205 amerged = ABF::mergewindow(amerged, abfs[i]);
206 }
207 if (outputname.empty()) {
208 // Generate new file name for merged grad and count
209 vector<string> tmp_name = filename;
210 std::transform(std::begin(tmp_name), std::end(tmp_name), std::begin(tmp_name),
211 [&](string s) {return s.substr(0, s.find(suffix));});
212 outputname = std::accumulate(std::begin(tmp_name), std::end(tmp_name), string(""),
213 [](const string & a, const string & b) {return a + b + "+";});
214 outputname = outputname.substr(0, outputname.size() - 1);
215 std::cerr << "You have not specified an output filename for the merged"
216 << " result, so the default name \"" + outputname
217 << "\" is used here, which may yield unexpected behavior.\n";
218 }
219 cmerged.writeAll(outputname);
220 cmerged.writeZCount(outputname);
221 amerged.writeAll(outputname);
222 }
223
calcDivergence(const vector<string> & filename)224 void drrtool::calcDivergence(const vector<string> &filename) {
225 #pragma omp parallel for
226 for (size_t j = 0; j < filename.size(); ++j) {
227 std::ifstream in;
228 in.open(filename[j]);
229 boost::archive::binary_iarchive ia(in);
230 long long int step;
231 vector<double> fict;
232 vector<double> vfict;
233 vector<double> vfict_laststep;
234 vector<double> ffict;
235 ABF abfgrid;
236 CZAR czarestimator;
237 ia >> step >> fict >> vfict >> vfict_laststep >> ffict >> abfgrid >>
238 czarestimator;
239 in.close();
240 abfgrid.setOutputUnit(units.getEnergy());
241 czarestimator.setOutputUnit(units.getEnergy());
242 if (verbosity) {
243 std::cout << "Output units factor: " << units.getEnergy() << '\n';
244 std::cout << "Dumping information of extended variables..." << '\n';
245 std::cout << "Step: " << step << '\n';
246 for (size_t i = 0; i < fict.size(); ++i) {
247 std::cout << "Dimension[" << i + 1 << "]:\n"
248 << " Coordinate: " << fict[i] << '\n'
249 << " Velocity: " << vfict[i] << '\n'
250 << " Velocity(laststep): " << vfict_laststep[i] << '\n'
251 << " Force: " << ffict[i] << '\n';
252 }
253 std::cout << "Dumping counts and gradients from grids..." << '\n';
254 }
255 string outputname(filename[j]);
256 outputname = outputname.substr(0, outputname.length() - suffix.length());
257 abfgrid.writeDivergence(outputname);
258 czarestimator.writeDivergence(outputname);
259 }
260 }
261
262 } // End of namespace
263 }
264
265 #endif
266