Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2020-2021 of Michele Invernizzi.
3 :
4 : This file is part of the OPES plumed module.
5 :
6 : The OPES plumed module is free software: you can redistribute it and/or modify
7 : it under the terms of the GNU Lesser General Public License as published by
8 : the Free Software Foundation, either version 3 of the License, or
9 : (at your option) any later version.
10 :
11 : The OPES plumed module is distributed in the hope that it will be useful,
12 : but WITHOUT ANY WARRANTY; without even the implied warranty of
13 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 : GNU Lesser General Public License for more details.
15 :
16 : You should have received a copy of the GNU Lesser General Public License
17 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
18 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
19 : #include "ExpansionCVs.h"
20 : #include "core/ActionRegister.h"
21 :
22 : #include <algorithm>
23 :
24 : namespace PLMD {
25 : namespace opes {
26 :
27 : //+PLUMEDOC OPES_EXPANSION_CV ECV_CUSTOM
28 : /*
29 : Use some given CVs as a set of expansion collective variables (ECVs).
30 :
31 : This can be useful e.g. for quickly testing new ECVs, but from a performance point of view it is probably better to implement a new ECV class.
32 :
33 : By default the ARGs are expeted to be energies, $\Delta U_i$, and are then multiplied by the inverse temperature $\beta$
34 :
35 : $$
36 : \Delta u_i=\beta \Delta U_i\, .
37 : $$
38 :
39 : Use the DIMENSIONLESS flag to avoid this multiplication.
40 :
41 : The flag ADD_P0 adds also the unbiased distribution to the target.
42 : It is possible to specify a BARRIER as in [ECV_UMBRELLAS_LINE](ECV_UMBRELLAS_LINE.md), to avoid a too high initial bias.
43 :
44 : ## Examples
45 :
46 : ```plumed
47 : ene: ENERGY
48 : t1: CUSTOM PERIODIC=NO ARG=ene FUNC=(300/500-1)*x
49 : t2: CUSTOM PERIODIC=NO ARG=ene FUNC=(300/1000-1)*x
50 : ecv: ECV_CUSTOM ARG=t1,t2 TEMP=300 ADD_P0
51 : opes: OPES_EXPANDED ARG=ecv.* PACE=500
52 : ```
53 :
54 : It is equivalent to the following:
55 :
56 : ```plumed
57 : ene: ENERGY
58 : ecv: ECV_MULTITHERMAL ARG=ene TEMP=300 TEMP_SET_ALL=300,500,1000
59 : opes: OPES_EXPANDED ARG=ecv.* PACE=500
60 : ```
61 :
62 : */
63 : //+ENDPLUMEDOC
64 :
65 : class ECVcustom :
66 : public ExpansionCVs {
67 : private:
68 : unsigned P0_contribution_;
69 : double barrier_;
70 : double beta0_;
71 :
72 : std::vector< std::vector<double> > ECVs_;
73 : std::vector< std::vector<double> > derECVs_;
74 : void initECVs();
75 :
76 : public:
77 : explicit ECVcustom(const ActionOptions&);
78 : static void registerKeywords(Keywords& keys);
79 : void calculateECVs(const double *) override;
80 : const double * getPntrToECVs(unsigned) override;
81 : const double * getPntrToDerECVs(unsigned) override;
82 : std::vector<std::string> getLambdas() const override;
83 : void initECVs_observ(const std::vector<double>&,const unsigned,const unsigned) override;
84 : void initECVs_restart(const std::vector<std::string>&) override;
85 : };
86 :
87 : PLUMED_REGISTER_ACTION(ECVcustom,"ECV_CUSTOM")
88 :
89 10 : void ECVcustom::registerKeywords(Keywords& keys) {
90 10 : ExpansionCVs::registerKeywords(keys);
91 20 : keys.addInputKeyword("compulsory","ARG","scalar","the labels of the single ECVs. Delta U_i, in energy units");
92 10 : keys.addFlag("ADD_P0",false,"add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it");
93 10 : keys.addFlag("DIMENSIONLESS",false,"consider ARG as dimensionless rather than an energy, thus do not multiply it by beta");
94 10 : keys.add("optional","BARRIER","a guess of the free energy barrier to be overcome (better to stay higher than lower)");
95 10 : }
96 :
97 6 : ECVcustom::ECVcustom(const ActionOptions&ao)
98 : : Action(ao)
99 : , ExpansionCVs(ao)
100 6 : , beta0_(1./kbt_) {
101 : //set beta0_
102 : bool dimensionless;
103 6 : parseFlag("DIMENSIONLESS",dimensionless);
104 6 : if(dimensionless) {
105 0 : beta0_=1;
106 : }
107 :
108 : //set P0_contribution_
109 6 : bool add_P0=false;
110 6 : parseFlag("ADD_P0",add_P0);
111 6 : if(add_P0) {
112 2 : P0_contribution_=1;
113 : } else {
114 4 : P0_contribution_=0;
115 : }
116 :
117 : //set barrier_
118 6 : barrier_=std::numeric_limits<double>::infinity();
119 6 : parse("BARRIER",barrier_);
120 :
121 6 : checkRead();
122 :
123 : //set ECVs stuff
124 6 : totNumECVs_=getNumberOfArguments()+P0_contribution_;
125 6 : ECVs_.resize(getNumberOfArguments(),std::vector<double>(totNumECVs_));
126 6 : derECVs_.resize(getNumberOfArguments(),std::vector<double>(totNumECVs_));
127 18 : for(unsigned j=0; j<getNumberOfArguments(); j++) {
128 12 : derECVs_[j][j+P0_contribution_]=beta0_; //always constant
129 : }
130 :
131 : //print some info
132 6 : if(dimensionless) {
133 0 : log.printf(" -- DIMENSIONLESS: the ARG is not multiplied by beta\n");
134 : }
135 6 : if(barrier_!=std::numeric_limits<double>::infinity()) {
136 0 : log.printf(" guess for free energy BARRIER = %g\n",barrier_);
137 0 : if(dimensionless) {
138 0 : log.printf(" also the BARRIER is considered to be DIMENSIONLESS\n");
139 : }
140 : }
141 6 : if(P0_contribution_==1) {
142 2 : log.printf(" -- ADD_P0: the target includes also the unbiased probability itself\n");
143 : }
144 6 : }
145 :
146 273 : void ECVcustom::calculateECVs(const double * cv) {
147 819 : for(unsigned j=0; j<getNumberOfArguments(); j++) {
148 546 : ECVs_[j][j+P0_contribution_]=beta0_*cv[j];
149 : }
150 : //derivative is constant
151 273 : }
152 :
153 12 : const double * ECVcustom::getPntrToECVs(unsigned j) {
154 12 : plumed_massert(isReady_,"cannot access ECVs before initialization");
155 12 : plumed_massert(j<getNumberOfArguments(),getName()+" has fewer CVs");
156 12 : return &ECVs_[j][0];
157 : }
158 :
159 12 : const double * ECVcustom::getPntrToDerECVs(unsigned j) {
160 12 : plumed_massert(isReady_,"cannot access ECVs before initialization");
161 12 : plumed_massert(j<getNumberOfArguments(),getName()+" has fewer CVs");
162 12 : return &derECVs_[j][0];
163 : }
164 :
165 6 : std::vector<std::string> ECVcustom::getLambdas() const {
166 6 : std::vector<std::string> lambdas(totNumECVs_);
167 6 : if(P0_contribution_==1) {
168 2 : std::ostringstream subs;
169 2 : subs<<"P0";
170 4 : for(unsigned j=1; j<getNumberOfArguments(); j++) {
171 2 : subs<<"_P0";
172 : }
173 2 : lambdas[0]=subs.str();
174 2 : }
175 : //the lambdas are the ARG names, with '_' replaced, since it separates the lambdas of different CVs
176 : //the getLambdas method is const, so it complains if one tries to access a non-const pointer, hence the const_cast
177 12 : auto argName=[this](unsigned j) {
178 12 : std::string name=const_cast<ECVcustom *>(this)->getPntrToArgument(j)->getName();
179 : std::replace(name.begin(),name.end(),'_','-');
180 12 : return name;
181 6 : };
182 18 : for(unsigned k=P0_contribution_; k<totNumECVs_; k++) {
183 12 : const unsigned kk=k-P0_contribution_;
184 12 : std::ostringstream subs;
185 12 : if(kk==0) {
186 12 : subs<<argName(kk);
187 : } else {
188 6 : subs<<"NaN";
189 : }
190 24 : for(unsigned j=1; j<getNumberOfArguments(); j++) {
191 12 : if(kk==j) {
192 12 : subs<<"_"<<argName(kk);
193 : } else {
194 6 : subs<<"_NaN";
195 : }
196 : }
197 12 : lambdas[k]=subs.str();
198 12 : }
199 6 : return lambdas;
200 0 : }
201 :
202 6 : void ECVcustom::initECVs() {
203 6 : plumed_massert(!isReady_,"initialization should not be called twice");
204 6 : isReady_=true;
205 6 : log.printf(" *%4u ECVs for %s\n",totNumECVs_,getName().c_str());
206 6 : }
207 :
208 3 : void ECVcustom::initECVs_observ(const std::vector<double>& all_obs_cvs,const unsigned ncv,const unsigned index_j) {
209 3 : initECVs();
210 3 : calculateECVs(&all_obs_cvs[index_j]);
211 9 : for(unsigned j=0; j<getNumberOfArguments(); j++) {
212 12 : ECVs_[j][j+P0_contribution_]=std::min(barrier_*beta0_,ECVs_[j][j+P0_contribution_]);
213 : }
214 3 : }
215 :
216 3 : void ECVcustom::initECVs_restart(const std::vector<std::string>& lambdas) {
217 : std::size_t pos=0;
218 6 : for(unsigned j=0; j<getNumberOfArguments()-1; j++) {
219 3 : pos=lambdas[0].find("_",pos+1); //checking only lambdas[0] is hopefully enough
220 : }
221 3 : plumed_massert(pos<lambdas[0].length(),"this should not happen, fewer '_' than expected in "+getName());
222 3 : pos=lambdas[0].find("_",pos+1);
223 3 : plumed_massert(pos>lambdas[0].length(),"this should not happen, more '_' than expected in "+getName());
224 :
225 3 : std::vector<std::string> myLambdas=getLambdas();
226 3 : plumed_massert(myLambdas.size()==lambdas.size(),"RESTART - mismatch in number of "+getName());
227 3 : plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),"RESTART - mismatch in lambda values of "+getName());
228 :
229 3 : initECVs();
230 3 : }
231 :
232 : }
233 : }
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