Line data Source code
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 "core/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, const string &fmt);
81 5 : string description() const {
82 5 : return "Extract or merge the drrstate files.";
83 : }
84 :
85 : private:
86 : bool verbosity;
87 : Units units;
88 : const string suffix{".drrstate"};
89 : };
90 :
91 16264 : PLUMED_REGISTER_CLTOOL(drrtool, "drr_tool")
92 :
93 5418 : void drrtool::registerKeywords(Keywords &keys) {
94 5418 : CLTool::registerKeywords(keys);
95 5418 : keys.add("optional", "--extract", "Extract drrstate file(s)");
96 5418 : keys.add("optional", "--merge", "Merge eABF windows");
97 5418 : keys.add("optional", "--merge_output", "The output filename of the merged result");
98 5418 : keys.add("optional", "--divergence", "Calculate divergence of gradient field (experimental)");
99 5418 : keys.add("optional","--dump-fmt","( default=%%f ) the format to use to dump the output");
100 5418 : 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");
101 5418 : keys.addFlag("-v", false, "Verbose output");
102 5418 : }
103 :
104 10 : drrtool::drrtool(const CLToolOptions &co) : CLTool(co) {
105 10 : inputdata = commandline;
106 10 : verbosity = false;
107 10 : }
108 :
109 5 : int drrtool::main(FILE *in, FILE *out, Communicator &pc) {
110 10 : parseFlag("-v", verbosity);
111 : vector<string> stateFilesToExtract;
112 : string unitname;
113 5 : parse("--units",unitname);
114 5 : units.setEnergy( unitname );
115 5 : std::string dumpFmt("%.9f");;
116 5 : parse("--dump-fmt", dumpFmt);
117 5 : bool doextract = parseVector("--extract", stateFilesToExtract);
118 5 : if (doextract) {
119 2 : extractdrr(stateFilesToExtract);
120 : }
121 : vector<string> stateFilesToMerge;
122 5 : bool domerge = parseVector("--merge", stateFilesToMerge);
123 5 : if (domerge) {
124 : string merge_outputname;
125 2 : parse("--merge_output", merge_outputname);
126 4 : mergewindows(stateFilesToMerge, merge_outputname);
127 : }
128 : vector<string> stateFilesToDivergence;
129 5 : bool dodivergence = parseVector("--divergence", stateFilesToDivergence);
130 5 : if (dodivergence) {
131 1 : calcDivergence(stateFilesToDivergence, dumpFmt);
132 : }
133 5 : return 0;
134 10 : }
135 :
136 2 : void drrtool::extractdrr(const vector<string> &filename) {
137 2 : #pragma omp parallel for
138 : for (size_t j = 0; j < filename.size(); ++j) {
139 : std::ifstream in;
140 : in.open(filename[j]);
141 : boost::archive::binary_iarchive ia(in);
142 : long long int step;
143 : vector<double> fict;
144 : vector<double> vfict;
145 : vector<double> vfict_laststep;
146 : vector<double> ffict;
147 : ABF abfgrid;
148 : CZAR czarestimator;
149 : ia >> step >> fict >> vfict >> vfict_laststep >> ffict >> abfgrid >>
150 : czarestimator;
151 : in.close();
152 : abfgrid.setOutputUnit(units.getEnergy());
153 : czarestimator.setOutputUnit(units.getEnergy());
154 : if (verbosity) {
155 : std::cout << "Output units factor: " << units.getEnergy() << '\n';
156 : std::cout << "Dumping information of extended variables..." << '\n';
157 : std::cout << "Step: " << step << '\n';
158 : for (size_t i = 0; i < fict.size(); ++i) {
159 : std::cout << "Dimension[" << i + 1 << "]:\n"
160 : << " Coordinate: " << fict[i] << '\n'
161 : << " Velocity: " << vfict[i] << '\n'
162 : << " Velocity(laststep): " << vfict_laststep[i] << '\n'
163 : << " Force: " << ffict[i] << '\n';
164 : }
165 : std::cout << "Dumping counts and gradients from grids..." << '\n';
166 : }
167 : string outputname(filename[j]);
168 : outputname.resize(outputname.length() - suffix.length());
169 : if (verbosity) {
170 : std::cout << "Writing ABF(naive) estimator files..." << '\n';
171 : }
172 : abfgrid.writeAll(outputname);
173 : if (verbosity) {
174 : std::cout << "Writing CZAR estimator files..." << '\n';
175 : }
176 : czarestimator.writeAll(outputname);
177 : czarestimator.writeZCountZGrad(outputname);
178 : }
179 2 : }
180 :
181 2 : void drrtool::mergewindows(const vector<string> &filename, string outputname) {
182 2 : if (filename.size() < 2) {
183 0 : std::cerr << "ERROR! You need at least two .drrstate file to merge windows!" << std::endl;
184 0 : std::abort();
185 : }
186 : // Read grid into abfs and czars;
187 : vector<ABF> abfs;
188 : vector<CZAR> czars;
189 6 : for (auto it_fn = filename.begin(); it_fn != filename.end(); ++it_fn) {
190 4 : std::ifstream in;
191 4 : in.open((*it_fn));
192 4 : boost::archive::binary_iarchive ia(in);
193 : long long int step;
194 : vector<double> fict;
195 : vector<double> vfict;
196 : vector<double> vfict_laststep;
197 : vector<double> ffict;
198 : ABF abfgrid;
199 : CZAR czarestimator;
200 : ia >> step >> fict >> vfict >> vfict_laststep >> ffict >> abfgrid >>
201 : czarestimator;
202 4 : abfgrid.setOutputUnit(units.getEnergy());
203 : czarestimator.setOutputUnit(units.getEnergy());
204 4 : abfs.push_back(abfgrid);
205 4 : czars.push_back(czarestimator);
206 4 : in.close();
207 8 : }
208 2 : CZAR cmerged = CZAR::mergewindow(czars[0], czars[1]);
209 2 : ABF amerged = ABF::mergewindow(abfs[0], abfs[1]);
210 2 : for (size_t i = 2; i < czars.size(); ++i) {
211 0 : cmerged = CZAR::mergewindow(cmerged, czars[i]);
212 0 : amerged = ABF::mergewindow(amerged, abfs[i]);
213 : }
214 2 : if (outputname.empty()) {
215 : // Generate new file name for merged grad and count
216 1 : vector<string> tmp_name = filename;
217 1 : std::transform(std::begin(tmp_name), std::end(tmp_name), std::begin(tmp_name),
218 2 : [&](const string & s) {
219 2 : return s.substr(0, s.find(suffix));
220 : });
221 2 : outputname = std::accumulate(std::begin(tmp_name), std::end(tmp_name), string(""),
222 2 : [](const string & a, const string & b) {
223 4 : return a + b + "+";
224 1 : });
225 1 : outputname.resize(outputname.size() - 1);
226 : std::cerr << "You have not specified an output filename for the merged"
227 1 : << " result, so the default name \"" + outputname
228 2 : << "\" is used here, which may yield unexpected behavior.\n";
229 1 : }
230 2 : cmerged.writeAll(outputname);
231 2 : cmerged.writeZCountZGrad(outputname);
232 2 : amerged.writeAll(outputname);
233 4 : }
234 :
235 1 : void drrtool::calcDivergence(const vector<string> &filename, const string &dumpFmt) {
236 1 : #pragma omp parallel for
237 : for (size_t j = 0; j < filename.size(); ++j) {
238 : std::ifstream in;
239 : in.open(filename[j]);
240 : boost::archive::binary_iarchive ia(in);
241 : long long int step;
242 : vector<double> fict;
243 : vector<double> vfict;
244 : vector<double> vfict_laststep;
245 : vector<double> ffict;
246 : ABF abfgrid;
247 : CZAR czarestimator;
248 : ia >> step >> fict >> vfict >> vfict_laststep >> ffict >> abfgrid >>
249 : czarestimator;
250 : in.close();
251 : abfgrid.setOutputUnit(units.getEnergy());
252 : czarestimator.setOutputUnit(units.getEnergy());
253 : if (verbosity) {
254 : std::cout << "Output units factor: " << units.getEnergy() << '\n';
255 : std::cout << "Dumping information of extended variables..." << '\n';
256 : std::cout << "Step: " << step << '\n';
257 : for (size_t i = 0; i < fict.size(); ++i) {
258 : std::cout << "Dimension[" << i + 1 << "]:\n"
259 : << " Coordinate: " << fict[i] << '\n'
260 : << " Velocity: " << vfict[i] << '\n'
261 : << " Velocity(laststep): " << vfict_laststep[i] << '\n'
262 : << " Force: " << ffict[i] << '\n';
263 : }
264 : std::cout << "Dumping counts and gradients from grids..." << '\n';
265 : }
266 : string outputname(filename[j]);
267 : outputname.resize(outputname.length() - suffix.length());
268 : abfgrid.writeDivergence(outputname, dumpFmt);
269 : czarestimator.writeDivergence(outputname, dumpFmt);
270 : }
271 1 : }
272 :
273 : } // End of namespace
274 : }
275 :
276 : #endif
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