Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2021 The VES code team
3 : (see the PEOPLE-VES file at the root of this folder for a list of names)
4 :
5 : See http://www.ves-code.org for more information.
6 :
7 : This file is part of VES code module.
8 :
9 : The VES code module 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 : The VES code module 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 the VES code module. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 :
23 : #include "BasisFunctions.h"
24 : #include "TargetDistribution.h"
25 :
26 : #include "CoeffsVector.h"
27 : #include "VesTools.h"
28 :
29 : #include "core/ActionRegister.h"
30 : #include "core/ActionSet.h"
31 : #include "core/PlumedMain.h"
32 : #include "core/Value.h"
33 : #include "tools/File.h"
34 : #include "tools/Grid.h"
35 :
36 :
37 : namespace PLMD {
38 : namespace ves {
39 :
40 : //+PLUMEDOC VES_UTILS VES_OUTPUT_BASISFUNCTIONS
41 : /*
42 : Output basis functions to file.
43 :
44 : This action can be used to write out to a grid file the values and derivatives of
45 : given basis functions. This is normally used for debugging when programming new
46 : types of basis functions. For example, it is possible to calculate the
47 : derivatives numerically and compare to the analytically calculated
48 : derivatives.
49 :
50 : This action is normally used through the [driver](driver.md).
51 :
52 : ## Examples
53 :
54 : In the following input we define a Legendre polynomials basis functions
55 : of order 14 over the interval -4.0 to 4.0 and output their values
56 : and derivatives to files called bfL.values.data and bfL.derivs.data.
57 :
58 : ```plumed
59 : BF_LEGENDRE ...
60 : ORDER=14
61 : MINIMUM=-4.0
62 : MAXIMUM=4.0
63 : LABEL=bfL
64 : ... BF_LEGENDRE
65 :
66 : VES_OUTPUT_BASISFUNCTIONS ...
67 : BASIS_FUNCTIONS=bfL
68 : GRID_BINS=200
69 : FORMAT_VALUES_DERIVS=%13.6f
70 : ... VES_OUTPUT_BASISFUNCTIONS
71 : ```
72 :
73 : This input should be run through the driver by using a command similar to the
74 : following one where the trajectory/configuration file configuration.gro is needed to
75 : trick the code to exit correctly.
76 :
77 : ```plumed
78 : plumed driver --plumed plumed.dat --igro configuration.gro
79 : ```
80 :
81 : */
82 : //+ENDPLUMEDOC
83 :
84 :
85 : class OutputBasisFunctions :
86 : public Action {
87 : std::vector<BasisFunctions*> bf_pntrs;
88 : public:
89 : explicit OutputBasisFunctions(const ActionOptions&);
90 : TargetDistribution* setupTargetDistPntr(std::string keyword) const;
91 0 : void calculate() override {}
92 0 : void apply() override {}
93 : static void registerKeywords(Keywords& keys);
94 : };
95 :
96 :
97 : PLUMED_REGISTER_ACTION(OutputBasisFunctions,"VES_OUTPUT_BASISFUNCTIONS")
98 :
99 73 : void OutputBasisFunctions::registerKeywords(Keywords& keys) {
100 73 : Action::registerKeywords(keys);
101 73 : keys.add("compulsory","BASIS_FUNCTIONS","the label of the basis functions that you want to use");
102 73 : keys.add("optional","GRID_BINS","the number of bins used for the grid for writing the basis function values and derivatives. The default value is 1000.");
103 73 : keys.add("optional","GRID_MIN","the minimum of the grid for writing the basis function values and derivatives. By default it is the minimum of the interval on which the basis functions are defined.");
104 73 : keys.add("optional","GRID_MAX","the maximum of the grid for writing the basis function values and derivatives. By default it is the maximum of the interval on which the basis functions are defined.");
105 73 : keys.add("optional","FILE_VALUES","filename of the file on which the basis function values are written. By default it is BF_LABEL.values.data.");
106 73 : keys.add("optional","FILE_DERIVS","filename of the file on which the basis function derivatives are written. By default it is BF_LABEL.derivs.data.");
107 73 : keys.add("optional","FORMAT_VALUES_DERIVS","the numerical format of the basis function values and derivatives written to file. By default it is %15.8f.\n. You can also use FORMAT_VALUES and FORMAT_DERIVS to give the numerical formats separately.");
108 73 : keys.add("optional","FORMAT_VALUES","the numerical format of the basis function derivatives written to file. By default it is %15.8f.\n");
109 73 : keys.add("optional","FORMAT_DERIVS","the numerical format of the basis function values written to file. By default it is %15.8f.\n");
110 73 : keys.add("optional","FILE_TARGETDIST_AVERAGES","filename of the file on which the averages over the target distributions are written. By default it is BF_LABEL.targetdist-averages.data.");
111 73 : keys.add("optional","FORMAT_TARGETDIST_AVERAGES","the numerical format of the target distribution averages written to file. By default it is %15.8f.\n");
112 73 : keys.add("optional","FILE_TARGETDIST","filename of the files on which the target distributions are written. By default it is BF_LABEL.targetdist-#.data.");
113 73 : keys.add("numbered","TARGET_DISTRIBUTION","the target distribution to be used.");
114 73 : keys.addFlag("IGNORE_PERIODICITY",false,"if the periodicity of the basis functions should be ignored.");
115 73 : keys.addFlag("NUMERICAL_DERIVATIVES",false,"if the derivatives of the basis functions should be calculated numerically.");
116 73 : }
117 :
118 71 : OutputBasisFunctions::OutputBasisFunctions(const ActionOptions&ao):
119 : Action(ao),
120 71 : bf_pntrs(0) {
121 71 : std::vector<std::string> basisset_labels(0);
122 142 : parseVector("BASIS_FUNCTIONS",basisset_labels);
123 71 : if(basisset_labels.size()>1) {
124 0 : plumed_merror("Only one basis set label allowed in keyword BASIS_FUNCTIONS of "+getName());
125 : }
126 :
127 71 : std::string error_msg = "";
128 142 : bf_pntrs = VesTools::getPointersFromLabels<BasisFunctions*>(basisset_labels,plumed.getActionSet(),error_msg);
129 71 : if(error_msg.size()>0) {
130 0 : plumed_merror("Error in keyword BASIS_FUNCTIONS of "+getName()+": "+error_msg);
131 : }
132 :
133 71 : unsigned int nbins = 1000;
134 142 : parse("GRID_BINS",nbins);
135 :
136 71 : std::string min_str = bf_pntrs[0]->intervalMinStr();
137 71 : std::string max_str = bf_pntrs[0]->intervalMaxStr();
138 71 : parse("GRID_MIN",min_str);
139 142 : parse("GRID_MAX",max_str);
140 :
141 71 : std::string fname_values = bf_pntrs[0]->getLabel()+".values.data";
142 142 : parse("FILE_VALUES",fname_values);
143 71 : std::string fname_derives = bf_pntrs[0]->getLabel()+".derivs.data";
144 142 : parse("FILE_DERIVS",fname_derives);
145 71 : std::string fname_targetdist_aver = bf_pntrs[0]->getLabel()+".targetdist-averages.data";
146 142 : parse("FILE_TARGETDIST_AVERAGES",fname_targetdist_aver);
147 71 : std::string fname_targetdist = bf_pntrs[0]->getLabel()+".targetdist-.data";
148 71 : parse("FILE_TARGETDIST",fname_targetdist);
149 :
150 71 : std::string fmt_values_derivs = "%15.8f";
151 71 : parse("FORMAT_VALUES_DERIVS",fmt_values_derivs);
152 71 : std::string fmt_values = fmt_values_derivs;
153 71 : std::string fmt_derivs = fmt_values_derivs;
154 71 : parse("FORMAT_VALUES",fmt_values);
155 71 : parse("FORMAT_DERIVS",fmt_derivs);
156 :
157 71 : std::string fmt_targetdist_aver = "%15.8f";
158 71 : parse("FORMAT_TARGETDIST_AVERAGES",fmt_targetdist_aver);
159 :
160 71 : bool ignore_periodicity = false;
161 71 : parseFlag("IGNORE_PERIODICITY",ignore_periodicity);
162 :
163 71 : bool numerical_deriv = false;
164 142 : parseFlag("NUMERICAL_DERIVATIVES",numerical_deriv);
165 :
166 : std::vector<TargetDistribution*> targetdist_pntrs;
167 71 : targetdist_pntrs.push_back(NULL);
168 71 : std::string targetdist_label="";
169 176 : for(int i=1;; i++) {
170 494 : if(!parseNumbered("TARGET_DISTRIBUTION",i,targetdist_label)) {
171 : break;
172 : }
173 176 : std::string error_msg = "";
174 176 : TargetDistribution* pntr_tmp = VesTools::getPointerFromLabel<TargetDistribution*>(targetdist_label,plumed.getActionSet(),error_msg);
175 176 : if(error_msg.size()>0) {
176 0 : plumed_merror("Error in keyword TARGET_DISTRIBUTION of "+getName()+": "+error_msg);
177 : }
178 176 : targetdist_pntrs.push_back(pntr_tmp);
179 176 : }
180 71 : checkRead();
181 : //
182 71 : OFile ofile_values;
183 71 : ofile_values.link(*this);
184 71 : ofile_values.enforceBackup();
185 71 : ofile_values.open(fname_values);
186 71 : OFile ofile_derivs;
187 71 : ofile_derivs.link(*this);
188 71 : ofile_derivs.enforceBackup();
189 71 : ofile_derivs.open(fname_derives);
190 71 : bf_pntrs[0]->writeBasisFunctionsToFile(ofile_values,ofile_derivs,min_str,max_str,nbins,ignore_periodicity,fmt_values,fmt_derivs,numerical_deriv);
191 71 : ofile_values.close();
192 71 : ofile_derivs.close();
193 : //
194 71 : std::vector<std::string> grid_min(1);
195 71 : grid_min[0]=bf_pntrs[0]->intervalMinStr();
196 71 : std::vector<std::string> grid_max(1);
197 71 : grid_max[0]=bf_pntrs[0]->intervalMaxStr();
198 71 : std::vector<unsigned int> grid_bins(1);
199 71 : grid_bins[0]=nbins;
200 71 : std::vector<std::unique_ptr<Value>> arguments(1);
201 142 : arguments[0]= Tools::make_unique<Value>(nullptr,"arg",false);
202 71 : if(bf_pntrs[0]->arePeriodic() && !ignore_periodicity) {
203 46 : arguments[0]->setDomain(bf_pntrs[0]->intervalMinStr(),bf_pntrs[0]->intervalMaxStr());
204 : } else {
205 48 : arguments[0]->setNotPeriodic();
206 : }
207 :
208 71 : OFile ofile_targetdist_aver;
209 71 : ofile_targetdist_aver.link(*this);
210 71 : ofile_targetdist_aver.enforceBackup();
211 71 : ofile_targetdist_aver.open(fname_targetdist_aver);
212 :
213 318 : for(unsigned int i=0; i<targetdist_pntrs.size(); i++) {
214 : std::string is;
215 247 : Tools::convert(i,is);
216 : //
217 247 : if(targetdist_pntrs[i]!=NULL) {
218 352 : targetdist_pntrs[i]->setupGrids(Tools::unique2raw(arguments),grid_min,grid_max,grid_bins);
219 176 : plumed_massert(targetdist_pntrs[i]->getDimension()==1,"the target distribution must be one dimensional");
220 176 : targetdist_pntrs[i]->updateTargetDist();
221 : }
222 : //
223 247 : std::vector<double> bf_integrals = bf_pntrs[0]->getTargetDistributionIntegrals(targetdist_pntrs[i]);
224 494 : CoeffsVector targetdist_averages = CoeffsVector("aver.targetdist-"+is,Tools::unique2raw(arguments),bf_pntrs,comm,false);
225 247 : targetdist_averages.setValues(bf_integrals);
226 247 : if(fmt_targetdist_aver.size()>0) {
227 : targetdist_averages.setOutputFmt(fmt_targetdist_aver);
228 : }
229 247 : targetdist_averages.writeToFile(ofile_targetdist_aver,true);
230 247 : if(targetdist_pntrs[i]!=NULL) {
231 : Grid* targetdist_grid_pntr = targetdist_pntrs[i]->getTargetDistGridPntr();
232 176 : std::string fname = FileBase::appendSuffix(fname_targetdist,is);
233 176 : OFile ofile;
234 176 : ofile.link(*this);
235 176 : ofile.enforceBackup();
236 176 : ofile.open(fname);
237 176 : targetdist_grid_pntr->writeToFile(ofile);
238 176 : ofile.close();
239 176 : }
240 247 : }
241 71 : ofile_targetdist_aver.close();
242 :
243 :
244 213 : }
245 :
246 :
247 :
248 : }
249 : }
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