Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2018 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 "CoeffsVector.h"
24 : #include "VesTools.h"
25 : #include "VesBias.h"
26 :
27 :
28 : #include "tools/File.h"
29 : #include "core/ActionRegister.h"
30 : #include "core/PlumedMain.h"
31 :
32 :
33 : namespace PLMD {
34 : namespace ves {
35 :
36 : //+PLUMEDOC VES_UTILS VES_OUTPUT_FES
37 : /*
38 : Tool to output biases and FESs for VES biases from previously obtained coefficients.
39 :
40 : This action can be used to output to file biases and FESs for VES biases from
41 : previously obtained coefficients. It should be used through the \ref driver and
42 : can only be used in postprocessing. The VES bias needs to be defined in the
43 : exact same way as during the simulation. At the current moment this action does
44 : not support dynamic target distributions (e.g. well-tempered).
45 :
46 : \par Examples
47 :
48 : In the following input we define a VES bias and then read in the coefficient
49 : file coeffs.input.data and output the FES and bias every 500 iterations.
50 :
51 : \plumedfile
52 : phi: TORSION ATOMS=5,7,9,15
53 : psi: TORSION ATOMS=7,9,15,17
54 :
55 : bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
56 : bf2: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
57 :
58 : VES_LINEAR_EXPANSION ...
59 : ARG=phi,psi
60 : BASIS_FUNCTIONS=bf1,bf2
61 : LABEL=ves1
62 : GRID_BINS=100,100
63 : PROJ_ARG1=phi
64 : PROJ_ARG2=psi
65 : ... VES_LINEAR_EXPANSION
66 :
67 : VES_OUTPUT_FES ...
68 : BIAS=ves1
69 : FES_OUTPUT=500
70 : FES_PROJ_OUTPUT=500
71 : BIAS_OUTPUT=500
72 : COEFFS_INPUT=coeffs.input.data
73 : ... VES_OUTPUT_FES
74 : \endplumedfile
75 :
76 : This input should be run through the driver by using a command similar to the
77 : following one where the trajectory/configuration file conf.gro is needed to
78 : correctly define the CVs
79 : \verbatim
80 : plumed driver --plumed plumed.dat --igro conf.gro
81 : \endverbatim
82 :
83 : */
84 : //+ENDPLUMEDOC
85 :
86 3 : class OutputFesBias : public Action {
87 :
88 : public:
89 : static void registerKeywords(Keywords&);
90 : explicit OutputFesBias(const ActionOptions&);
91 0 : void update() {}
92 0 : void calculate() {}
93 0 : void apply() {}
94 : };
95 :
96 :
97 6455 : PLUMED_REGISTER_ACTION(OutputFesBias,"VES_OUTPUT_FES")
98 :
99 :
100 4 : void OutputFesBias::registerKeywords(Keywords& keys) {
101 16 : keys.add("compulsory","BIAS","the label of the VES bias for to output the FESs and the bias files");
102 16 : keys.add("compulsory","COEFFS_INPUT","the name of input coefficient file");
103 16 : keys.add("optional","BIAS_OUTPUT","how often the bias(es) should be written out to file. Note that the value is given in terms of coefficent iterations.");
104 16 : keys.add("optional","FES_OUTPUT","how often the FES(s) should be written out to file. Note that the value is given in terms of coefficent iterations.");
105 16 : keys.add("optional","FES_PROJ_OUTPUT","how often the projections of the FES(s) should be written out to file. Note that the value is given in terms of coefficent iterations.");
106 : //
107 4 : }
108 :
109 :
110 3 : OutputFesBias::OutputFesBias(const ActionOptions&ao):
111 3 : Action(ao)
112 : {
113 :
114 3 : std::vector<std::string> bias_labels;
115 6 : parseVector("BIAS",bias_labels);
116 3 : if(bias_labels.size()>1) {
117 0 : plumed_merror(getName()+" only support one VES bias");
118 : }
119 :
120 3 : std::string error_msg = "";
121 6 : std::vector<VesBias*> bias_pntrs = VesTools::getPointersFromLabels<VesBias*>(bias_labels,plumed.getActionSet(),error_msg);
122 3 : if(error_msg.size()>0) {plumed_merror("Error in keyword BIAS of "+getName()+": "+error_msg);}
123 :
124 15 : for(unsigned int i=0; i<bias_pntrs.size(); i++) {
125 6 : if(bias_pntrs[i]->numberOfCoeffsSets()>1) {
126 0 : plumed_merror(getName()+" at the moment supports only VES biases with a single coefficient set");
127 : }
128 : }
129 :
130 3 : std::vector<std::string> coeffs_fnames;
131 6 : parseVector("COEFFS_INPUT",coeffs_fnames);
132 3 : if(coeffs_fnames.size()!=bias_pntrs.size()) {
133 0 : plumed_merror(getName()+": there have to be as many coefficient file given in COEFFS_INPUT as VES biases given in BIAS");
134 : }
135 :
136 3 : unsigned int bias_output_stride = 0;
137 6 : parse("BIAS_OUTPUT",bias_output_stride);
138 :
139 3 : unsigned int fes_output_stride = 0;
140 6 : parse("FES_OUTPUT",fes_output_stride);
141 :
142 3 : unsigned int fesproj_output_stride = 0;
143 6 : parse("FES_PROJ_OUTPUT",fesproj_output_stride);
144 :
145 3 : if(bias_output_stride == 0 && fes_output_stride == 0 && fesproj_output_stride == 0) {
146 0 : plumed_merror(getName()+": you are not telling the action to do anything, you need to use one of the keywords BIAS_OUTPUT, FES_OUTPUT, or FES_PROJ_OUTPUT");
147 : }
148 :
149 3 : checkRead();
150 :
151 15 : for(unsigned int i=0; i<bias_pntrs.size(); i++) {
152 :
153 6 : if(bias_pntrs[i]->dynamicTargetDistribution()) {
154 0 : plumed_merror(getName()+" does not support dynamic target distributions at the moment");
155 : }
156 :
157 3 : if(bias_pntrs[i]->isStaticTargetDistFileOutputActive()) {
158 2 : bias_pntrs[i]->setupTargetDistFileOutput();
159 2 : bias_pntrs[i]->writeTargetDistToFile();
160 2 : bias_pntrs[i]->setupTargetDistProjFileOutput();
161 2 : bias_pntrs[i]->writeTargetDistProjToFile();
162 : }
163 :
164 :
165 3 : if(bias_output_stride>0) {
166 3 : bias_pntrs[i]->enableBiasFileOutput();
167 3 : bias_pntrs[i]->setupBiasFileOutput();
168 : }
169 :
170 3 : if(fes_output_stride>0) {
171 3 : bias_pntrs[i]->enableFesFileOutput();
172 3 : bias_pntrs[i]->setupFesFileOutput();
173 : }
174 :
175 3 : if(fesproj_output_stride>0) {
176 1 : bias_pntrs[i]->enableFesProjFileOutput();
177 1 : bias_pntrs[i]->setupFesProjFileOutput();
178 : }
179 :
180 3 : bias_pntrs[i]->enableIterationNumberInFilenames();
181 :
182 6 : IFile ifile;
183 3 : ifile.open(coeffs_fnames[i]);
184 :
185 39 : while(ifile) {
186 :
187 36 : bias_pntrs[i]->resetBiasFileOutput();
188 36 : bias_pntrs[i]->resetFesFileOutput();
189 :
190 108 : if(bias_pntrs[i]->getCoeffsPntrs()[0]->readOneSetFromFile(ifile)>0) {
191 99 : unsigned int iteration = bias_pntrs[i]->getCoeffsPntrs()[0]->getIterationCounter();
192 :
193 33 : if(bias_output_stride>0 && iteration%bias_output_stride==0) {
194 8 : bias_pntrs[i]->writeBiasToFile();
195 : }
196 :
197 33 : if(fes_output_stride>0 && iteration%fes_output_stride==0) {
198 8 : bias_pntrs[i]->writeFesToFile();
199 : }
200 :
201 33 : if(fesproj_output_stride>0 && iteration%fesproj_output_stride==0) {
202 3 : bias_pntrs[i]->writeFesProjToFile();
203 : }
204 :
205 : }
206 :
207 : }
208 :
209 : }
210 :
211 3 : log.printf("Stopping");
212 3 : plumed.stop();
213 3 : }
214 :
215 :
216 : }
217 4839 : }
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