Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2023 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed 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 : plumed 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 plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "Function.h"
23 : #include "tools/Communicator.h"
24 : #include "core/ActionRegister.h"
25 : #include "core/PlumedMain.h"
26 :
27 : namespace PLMD {
28 : namespace function {
29 :
30 : //+PLUMEDOC FUNCTION ENSEMBLE
31 : /*
32 : Calculates the replica averaging of a collective variable over multiple replicas.
33 :
34 : Each collective variable is averaged separately and stored in a component labelled <em>label</em>.cvlabel.
35 :
36 : \par Examples
37 :
38 : The following input tells plumed to calculate the distance between atoms 3 and 5
39 : and the average it over the available replicas.
40 : \plumedfile
41 : dist: DISTANCE ATOMS=3,5
42 : ens: ENSEMBLE ARG=dist
43 : PRINT ARG=dist,ens.dist
44 : \endplumedfile
45 :
46 : */
47 : //+ENDPLUMEDOC
48 :
49 :
50 : class Ensemble :
51 : public Function
52 : {
53 : unsigned ens_dim;
54 : unsigned my_repl;
55 : unsigned narg;
56 : bool master;
57 : bool do_reweight;
58 : bool do_moments;
59 : bool do_central;
60 : bool do_powers;
61 : double kbt;
62 : double moment;
63 : double power;
64 : public:
65 : explicit Ensemble(const ActionOptions&);
66 : std::string getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const override ;
67 : void calculate() override;
68 : static void registerKeywords(Keywords& keys);
69 : };
70 :
71 :
72 : PLUMED_REGISTER_ACTION(Ensemble,"ENSEMBLE")
73 :
74 29 : void Ensemble::registerKeywords(Keywords& keys) {
75 29 : Function::registerKeywords(keys);
76 29 : keys.use("ARG");
77 58 : keys.addFlag("REWEIGHT",false,"simple REWEIGHT using the latest ARG as energy");
78 58 : keys.addFlag("CENTRAL",false,"calculate a central moment instead of a standard moment");
79 58 : keys.add("optional","TEMP","the system temperature - this is only needed if you are reweighting");
80 58 : keys.add("optional","MOMENT","the moment you want to calculate in alternative to the mean or the variance");
81 58 : keys.add("optional","POWER","the power of the mean (and moment)");
82 29 : ActionWithValue::useCustomisableComponents(keys);
83 29 : }
84 :
85 27 : Ensemble::Ensemble(const ActionOptions&ao):
86 : Action(ao),
87 : Function(ao),
88 27 : do_reweight(false),
89 27 : do_moments(false),
90 27 : do_central(false),
91 27 : do_powers(false),
92 27 : kbt(-1.0),
93 27 : moment(0),
94 27 : power(0)
95 : {
96 27 : parseFlag("REWEIGHT", do_reweight);
97 27 : if(do_reweight) {
98 12 : kbt=getkBT();
99 12 : if(kbt==0.0) error("Unless the MD engine passes the temperature to plumed, with REWEIGHT you must specify TEMP");
100 30 : } else { double temp=0.0; parse("TEMP",temp); }
101 :
102 27 : parse("MOMENT",moment);
103 27 : if(moment==1) error("MOMENT can be any number but for 0 and 1");
104 27 : if(moment!=0) do_moments=true;
105 27 : parseFlag("CENTRAL", do_central);
106 27 : if(!do_moments&&do_central) error("To calculate a CENTRAL moment you need to define for which MOMENT");
107 :
108 27 : parse("POWER",power);
109 27 : if(power==1) error("POWER can be any number but for 0 and 1");
110 27 : if(power!=0) do_powers=true;
111 :
112 27 : checkRead();
113 :
114 27 : master = (comm.Get_rank()==0);
115 27 : ens_dim=0;
116 27 : my_repl=0;
117 27 : if(master) {
118 17 : ens_dim=multi_sim_comm.Get_size();
119 17 : my_repl=multi_sim_comm.Get_rank();
120 : }
121 27 : comm.Bcast(ens_dim,0);
122 27 : comm.Bcast(my_repl,0);
123 27 : if(ens_dim<2) log.printf("WARNING: ENSEMBLE with one replica is not doing any averaging!\n");
124 :
125 : // prepare output components, the number depending on reweighing or not
126 27 : narg = getNumberOfArguments();
127 27 : if(do_reweight) narg--;
128 :
129 : // these are the averages
130 3044 : for(unsigned i=0; i<narg; i++) {
131 3017 : std::string s=getPntrToArgument(i)->getName();
132 3017 : addComponentWithDerivatives(s);
133 3017 : getPntrToComponent(i)->setNotPeriodic();
134 : }
135 : // these are the moments
136 27 : if(do_moments) {
137 0 : for(unsigned i=0; i<narg; i++) {
138 0 : std::string s=getPntrToArgument(i)->getName()+"_m";
139 0 : addComponentWithDerivatives(s);
140 0 : getPntrToComponent(i+narg)->setNotPeriodic();
141 : }
142 : }
143 :
144 27 : log.printf(" averaging over %u replicas.\n", ens_dim);
145 27 : if(do_reweight) log.printf(" doing simple REWEIGHT using the latest ARGUMENT as energy.\n");
146 27 : if(do_moments&&!do_central) log.printf(" calculating also the %lf standard moment\n", moment);
147 27 : if(do_moments&&do_central) log.printf(" calculating also the %lf central moment\n", moment);
148 27 : if(do_powers) log.printf(" calculating the %lf power of the mean (and moment)\n", power);
149 27 : }
150 :
151 0 : std::string Ensemble::getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const {
152 0 : for(unsigned i=0; i<getNumberOfArguments(); ++i) {
153 0 : if( cname==getPntrToArgument(i)->getName() ) return "the average for argument " + cname;
154 0 : if( cname==getPntrToArgument(i)->getName() + "_m" ) return "the moment for argument " + cname;
155 : }
156 0 : plumed_error(); return "";
157 : }
158 :
159 :
160 125 : void Ensemble::calculate() {
161 : double norm = 0.0;
162 125 : double fact = 0.0;
163 :
164 : // calculate the weights either from BIAS
165 125 : if(do_reweight) {
166 : std::vector<double> bias;
167 0 : bias.resize(ens_dim);
168 0 : if(master) {
169 0 : bias[my_repl] = getArgument(narg);
170 0 : if(ens_dim>1) multi_sim_comm.Sum(&bias[0], ens_dim);
171 : }
172 0 : comm.Sum(&bias[0], ens_dim);
173 0 : const double maxbias = *(std::max_element(bias.begin(), bias.end()));
174 0 : for(unsigned i=0; i<ens_dim; ++i) {
175 0 : bias[i] = exp((bias[i]-maxbias)/kbt);
176 0 : norm += bias[i];
177 : }
178 0 : fact = bias[my_repl]/norm;
179 : // or arithmetic ones
180 : } else {
181 125 : norm = static_cast<double>(ens_dim);
182 125 : fact = 1.0/norm;
183 : }
184 :
185 125 : const double fact_kbt = fact/kbt;
186 :
187 125 : std::vector<double> mean(narg);
188 125 : std::vector<double> dmean(narg,fact);
189 : // calculate the mean
190 125 : if(master) {
191 2106 : for(unsigned i=0; i<narg; ++i) mean[i] = fact*getArgument(i);
192 99 : if(ens_dim>1) multi_sim_comm.Sum(&mean[0], narg);
193 : }
194 125 : comm.Sum(&mean[0], narg);
195 :
196 : std::vector<double> v_moment, dv_moment;
197 : // calculate other moments
198 125 : if(do_moments) {
199 0 : v_moment.resize(narg);
200 0 : dv_moment.resize(narg);
201 : // standard moment
202 0 : if(!do_central) {
203 0 : if(master) {
204 0 : for(unsigned i=0; i<narg; ++i) {
205 0 : const double tmp = fact*std::pow(getArgument(i),moment-1);
206 0 : v_moment[i] = tmp*getArgument(i);
207 0 : dv_moment[i] = moment*tmp;
208 : }
209 0 : if(ens_dim>1) multi_sim_comm.Sum(&v_moment[0], narg);
210 : } else {
211 0 : for(unsigned i=0; i<narg; ++i) {
212 0 : const double tmp = fact*std::pow(getArgument(i),moment-1);
213 0 : dv_moment[i] = moment*tmp;
214 : }
215 : }
216 : // central moment
217 : } else {
218 0 : if(master) {
219 0 : for(unsigned i=0; i<narg; ++i) {
220 0 : const double tmp = std::pow(getArgument(i)-mean[i],moment-1);
221 0 : v_moment[i] = fact*tmp*(getArgument(i)-mean[i]);
222 0 : dv_moment[i] = moment*tmp*(fact-fact/norm);
223 : }
224 0 : if(ens_dim>1) multi_sim_comm.Sum(&v_moment[0], narg);
225 : } else {
226 0 : for(unsigned i=0; i<narg; ++i) {
227 0 : const double tmp = std::pow(getArgument(i)-mean[i],moment-1);
228 0 : dv_moment[i] = moment*tmp*(fact-fact/norm);
229 : }
230 : }
231 : }
232 0 : comm.Sum(&v_moment[0], narg);
233 : }
234 :
235 : // calculate powers of moments
236 125 : if(do_powers) {
237 72 : for(unsigned i=0; i<narg; ++i) {
238 48 : const double tmp1 = std::pow(mean[i],power-1);
239 48 : mean[i] *= tmp1;
240 48 : dmean[i] *= power*tmp1;
241 48 : if(do_moments) {
242 0 : const double tmp2 = std::pow(v_moment[i],power-1);
243 0 : v_moment[i] *= tmp2;
244 0 : dv_moment[i] *= power*tmp2;
245 : }
246 : }
247 : }
248 :
249 : // set components
250 3358 : for(unsigned i=0; i<narg; ++i) {
251 : // set mean
252 3233 : Value* v=getPntrToComponent(i);
253 3233 : v->set(mean[i]);
254 3233 : setDerivative(v, i, dmean[i]);
255 3233 : if(do_reweight) {
256 0 : const double w_tmp = fact_kbt*(getArgument(i) - mean[i]);
257 0 : setDerivative(v, narg, w_tmp);
258 : }
259 3233 : if(do_moments) {
260 : // set moments
261 0 : Value* u=getPntrToComponent(i+narg);
262 0 : u->set(v_moment[i]);
263 0 : setDerivative(u, i, dv_moment[i]);
264 0 : if(do_reweight) {
265 0 : const double w_tmp = fact_kbt*(pow(getArgument(i),moment) - v_moment[i]);
266 0 : setDerivative(u, narg, w_tmp);
267 : }
268 : }
269 : }
270 125 : }
271 :
272 : }
273 : }
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