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 : namespace PLMD {
23 : namespace opes {
24 :
25 : //+PLUMEDOC OPES_EXPANSION_CV ECV_CUSTOM
26 : /*
27 : Use some given CVs as a set of expansion collective variables (ECVs).
28 :
29 : 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.
30 :
31 : By default the ARGs are expeted to be energies, \f$\Delta U_i\f$, and are then multiplied by the inverse temperature \f$\beta\f$
32 : \f[
33 : \Delta u_i=\beta \Delta U_i\, .
34 : \f]
35 : Use the DIMENSIONLESS flag to avoid this multiplication.
36 :
37 : The flag ADD_P0 adds also the unbiased distribution to the target.
38 : It is possible to specify a BARRIER as in \ref ECV_UMBRELLAS_LINE, to avoid a too high initial bias.
39 :
40 : \par Examples
41 :
42 : \plumedfile
43 : ene: ENERGY
44 : t1: CUSTOM PERIODIC=NO ARG=ene FUNC=(300/500-1)*x
45 : t2: CUSTOM PERIODIC=NO ARG=ene FUNC=(300/1000-1)*x
46 : ecv: ECV_CUSTOM ARG=t1,t2 TEMP=300 ADD_P0
47 : opes: OPES_EXPANDED ARG=ecv.* PACE=500
48 : \endplumedfile
49 :
50 : It is equivalent to the following:
51 :
52 : \plumedfile
53 : ene: ENERGY
54 : ecv: ECV_MULTITHERMAL ARG=ene TEMP=300 TEMP_SET_ALL=300,500,1000
55 : opes: OPES_EXPANDED ARG=ecv.* PACE=500
56 : \endplumedfile
57 :
58 : */
59 : //+ENDPLUMEDOC
60 :
61 : class ECVcustom :
62 : public ExpansionCVs
63 : {
64 : private:
65 : unsigned P0_contribution_;
66 : double barrier_;
67 : double beta0_;
68 :
69 : std::vector< std::vector<double> > ECVs_;
70 : std::vector< std::vector<double> > derECVs_;
71 : void initECVs();
72 :
73 : public:
74 : explicit ECVcustom(const ActionOptions&);
75 : static void registerKeywords(Keywords& keys);
76 : void calculateECVs(const double *) override;
77 : const double * getPntrToECVs(unsigned) override;
78 : const double * getPntrToDerECVs(unsigned) override;
79 : std::vector< std::vector<unsigned> > getIndex_k() const override;
80 : std::vector<std::string> getLambdas() const override;
81 : void initECVs_observ(const std::vector<double>&,const unsigned,const unsigned) override;
82 : void initECVs_restart(const std::vector<std::string>&) override;
83 : };
84 :
85 10423 : PLUMED_REGISTER_ACTION(ECVcustom,"ECV_CUSTOM")
86 :
87 3 : void ECVcustom::registerKeywords(Keywords& keys)
88 : {
89 3 : ExpansionCVs::registerKeywords(keys);
90 3 : keys.remove("ARG");
91 6 : keys.add("compulsory","ARG","the labels of the single ECVs, \\f$\\Delta U_i\\f$, in energy units");
92 6 : keys.addFlag("ADD_P0",false,"add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it");
93 6 : keys.addFlag("DIMENSIONLESS",false,"consider ARG as dimensionless rather than an energy, thus do not multiply it by \\f$\\beta\\f$");
94 6 : keys.add("optional","BARRIER","a guess of the free energy barrier to be overcome (better to stay higher than lower)");
95 3 : }
96 :
97 2 : ECVcustom::ECVcustom(const ActionOptions&ao)
98 : : Action(ao)
99 : , ExpansionCVs(ao)
100 2 : , beta0_(1./kbt_)
101 : {
102 : //set beta0_
103 : bool dimensionless;
104 2 : parseFlag("DIMENSIONLESS",dimensionless);
105 2 : if(dimensionless)
106 0 : beta0_=1;
107 :
108 : //set P0_contribution_
109 2 : bool add_P0=false;
110 2 : parseFlag("ADD_P0",add_P0);
111 2 : if(add_P0)
112 2 : P0_contribution_=1;
113 : else
114 0 : P0_contribution_=0;
115 :
116 : //set barrier_
117 2 : barrier_=std::numeric_limits<double>::infinity();
118 2 : parse("BARRIER",barrier_);
119 :
120 2 : checkRead();
121 :
122 : //set ECVs stuff
123 2 : totNumECVs_=getNumberOfArguments()+P0_contribution_;
124 2 : ECVs_.resize(getNumberOfArguments(),std::vector<double>(totNumECVs_));
125 2 : derECVs_.resize(getNumberOfArguments(),std::vector<double>(totNumECVs_));
126 6 : for(unsigned j=0; j<getNumberOfArguments(); j++)
127 4 : derECVs_[j][j+P0_contribution_]=beta0_; //always constant
128 :
129 : //print some info
130 2 : if(dimensionless)
131 0 : log.printf(" -- DIMENSIONLESS: the ARG is not multiplied by beta\n");
132 2 : if(barrier_!=std::numeric_limits<double>::infinity())
133 : {
134 0 : log.printf(" guess for free energy BARRIER = %g\n",barrier_);
135 0 : if(dimensionless)
136 0 : log.printf(" also the BARRIER is considered to be DIMENSIONLESS\n");
137 : }
138 2 : if(P0_contribution_==1)
139 2 : log.printf(" -- ADD_P0: the target includes also the unbiased probability itself\n");
140 2 : }
141 :
142 91 : void ECVcustom::calculateECVs(const double * cv)
143 : {
144 273 : for(unsigned j=0; j<getNumberOfArguments(); j++)
145 182 : ECVs_[j][j+P0_contribution_]=beta0_*cv[j];
146 : //derivative is constant
147 91 : }
148 :
149 4 : const double * ECVcustom::getPntrToECVs(unsigned j)
150 : {
151 4 : plumed_massert(isReady_,"cannot access ECVs before initialization");
152 4 : plumed_massert(j<getNumberOfArguments(),getName()+" has fewer CVs");
153 4 : return &ECVs_[j][0];
154 : }
155 :
156 4 : const double * ECVcustom::getPntrToDerECVs(unsigned j)
157 : {
158 4 : plumed_massert(isReady_,"cannot access ECVs before initialization");
159 4 : plumed_massert(j<getNumberOfArguments(),getName()+" has fewer CVs");
160 4 : return &derECVs_[j][0];
161 : }
162 :
163 2 : std::vector< std::vector<unsigned> > ECVcustom::getIndex_k() const
164 : {
165 2 : plumed_massert(isReady_ && totNumECVs_>0,"cannot access getIndex_k() of ECV before initialization");
166 2 : std::vector< std::vector<unsigned> > index_k(totNumECVs_,std::vector<unsigned>(getNumberOfArguments()));
167 8 : for(unsigned k=0; k<totNumECVs_; k++)
168 18 : for(unsigned j=0; j<getNumberOfArguments(); j++)
169 12 : if(k==j+P0_contribution_)
170 4 : index_k[k][j]=k;
171 2 : return index_k;
172 0 : }
173 :
174 2 : std::vector<std::string> ECVcustom::getLambdas() const
175 : {
176 2 : std::vector<std::string> lambdas(totNumECVs_);
177 2 : if(P0_contribution_==1)
178 : {
179 2 : std::ostringstream subs;
180 2 : subs<<"P0";
181 4 : for(unsigned j=1; j<getNumberOfArguments(); j++)
182 2 : subs<<"_P0";
183 2 : lambdas[0]=subs.str();
184 2 : }
185 6 : for(unsigned k=P0_contribution_; k<totNumECVs_; k++)
186 : {
187 4 : const unsigned kk=k-P0_contribution_;
188 4 : std::ostringstream subs;
189 : //the getLambdas method is const, so it complains if one tries to access a non-const pointer, hence the const_cast
190 4 : if(kk==0)
191 : subs<<const_cast<ECVcustom *>(this)->getPntrToArgument(kk)->getName();
192 : else
193 2 : subs<<"NaN";
194 8 : for(unsigned j=1; j<getNumberOfArguments(); j++)
195 : {
196 4 : if(kk==j)
197 2 : subs<<"_"<<const_cast<ECVcustom *>(this)->getPntrToArgument(kk)->getName();
198 : else
199 2 : subs<<"_NaN";
200 : }
201 4 : lambdas[k]=subs.str();
202 4 : }
203 2 : return lambdas;
204 0 : }
205 :
206 2 : void ECVcustom::initECVs()
207 : {
208 2 : plumed_massert(!isReady_,"initialization should not be called twice");
209 2 : isReady_=true;
210 2 : log.printf(" *%4u ECVs for %s\n",totNumECVs_,getName().c_str());
211 2 : }
212 :
213 1 : void ECVcustom::initECVs_observ(const std::vector<double>& all_obs_cvs,const unsigned ncv,const unsigned index_j)
214 : {
215 1 : initECVs();
216 1 : calculateECVs(&all_obs_cvs[index_j]);
217 3 : for(unsigned j=0; j<getNumberOfArguments(); j++)
218 4 : ECVs_[j][j+P0_contribution_]=std::min(barrier_*beta0_,ECVs_[j][j+P0_contribution_]);
219 1 : }
220 :
221 1 : void ECVcustom::initECVs_restart(const std::vector<std::string>& lambdas)
222 : {
223 : std::size_t pos=0;
224 2 : for(unsigned j=0; j<getNumberOfArguments()-1; j++)
225 1 : pos=lambdas[0].find("_",pos+1); //checking only lambdas[0] is hopefully enough
226 1 : plumed_massert(pos<lambdas[0].length(),"this should not happen, fewer '_' than expected in "+getName());
227 1 : pos=lambdas[0].find("_",pos+1);
228 1 : plumed_massert(pos>lambdas[0].length(),"this should not happen, more '_' than expected in "+getName());
229 :
230 1 : std::vector<std::string> myLambdas=getLambdas();
231 1 : plumed_massert(myLambdas.size()==lambdas.size(),"RESTART - mismatch in number of "+getName());
232 1 : plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),"RESTART - mismatch in lambda values of "+getName());
233 :
234 1 : initECVs();
235 1 : }
236 :
237 : }
238 : }
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