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 "ActionRegister.h"
24 : #include "core/PlumedMain.h"
25 : #include "core/Atoms.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 : void calculate() override;
67 : static void registerKeywords(Keywords& keys);
68 : };
69 :
70 :
71 10473 : PLUMED_REGISTER_ACTION(Ensemble,"ENSEMBLE")
72 :
73 28 : void Ensemble::registerKeywords(Keywords& keys) {
74 28 : Function::registerKeywords(keys);
75 28 : keys.use("ARG");
76 56 : keys.addFlag("REWEIGHT",false,"simple REWEIGHT using the latest ARG as energy");
77 56 : keys.addFlag("CENTRAL",false,"calculate a central moment instead of a standard moment");
78 56 : keys.add("optional","TEMP","the system temperature - this is only needed if you are reweighting");
79 56 : keys.add("optional","MOMENT","the moment you want to calculate in alternative to the mean or the variance");
80 56 : keys.add("optional","POWER","the power of the mean (and moment)");
81 28 : ActionWithValue::useCustomisableComponents(keys);
82 28 : }
83 :
84 27 : Ensemble::Ensemble(const ActionOptions&ao):
85 : Action(ao),
86 : Function(ao),
87 27 : do_reweight(false),
88 27 : do_moments(false),
89 27 : do_central(false),
90 27 : do_powers(false),
91 27 : kbt(-1.0),
92 27 : moment(0),
93 27 : power(0)
94 : {
95 27 : parseFlag("REWEIGHT", do_reweight);
96 27 : double temp=0.0;
97 27 : parse("TEMP",temp);
98 27 : if(do_reweight) {
99 12 : if(temp>0.0) kbt=plumed.getAtoms().getKBoltzmann()*temp;
100 0 : else kbt=plumed.getAtoms().getKbT();
101 12 : if(kbt==0.0) error("Unless the MD engine passes the temperature to plumed, with REWEIGHT you must specify TEMP");
102 : }
103 :
104 27 : parse("MOMENT",moment);
105 27 : if(moment==1) error("MOMENT can be any number but for 0 and 1");
106 27 : if(moment!=0) do_moments=true;
107 27 : parseFlag("CENTRAL", do_central);
108 27 : if(!do_moments&&do_central) error("To calculate a CENTRAL moment you need to define for which MOMENT");
109 :
110 27 : parse("POWER",power);
111 27 : if(power==1) error("POWER can be any number but for 0 and 1");
112 27 : if(power!=0) do_powers=true;
113 :
114 27 : checkRead();
115 :
116 27 : master = (comm.Get_rank()==0);
117 27 : ens_dim=0;
118 27 : my_repl=0;
119 27 : if(master) {
120 17 : ens_dim=multi_sim_comm.Get_size();
121 17 : my_repl=multi_sim_comm.Get_rank();
122 : }
123 27 : comm.Bcast(ens_dim,0);
124 27 : comm.Bcast(my_repl,0);
125 27 : if(ens_dim<2) log.printf("WARNING: ENSEMBLE with one replica is not doing any averaging!\n");
126 :
127 : // prepare output components, the number depending on reweighing or not
128 27 : narg = getNumberOfArguments();
129 27 : if(do_reweight) narg--;
130 :
131 : // these are the averages
132 3044 : for(unsigned i=0; i<narg; i++) {
133 3017 : std::string s=getPntrToArgument(i)->getName();
134 3017 : addComponentWithDerivatives(s);
135 3017 : getPntrToComponent(i)->setNotPeriodic();
136 : }
137 : // these are the moments
138 27 : if(do_moments) {
139 0 : for(unsigned i=0; i<narg; i++) {
140 0 : std::string s=getPntrToArgument(i)->getName()+"_m";
141 0 : addComponentWithDerivatives(s);
142 0 : getPntrToComponent(i+narg)->setNotPeriodic();
143 : }
144 : }
145 :
146 27 : log.printf(" averaging over %u replicas.\n", ens_dim);
147 27 : if(do_reweight) log.printf(" doing simple REWEIGHT using the latest ARGUMENT as energy.\n");
148 27 : if(do_moments&&!do_central) log.printf(" calculating also the %lf standard moment\n", moment);
149 27 : if(do_moments&&do_central) log.printf(" calculating also the %lf central moment\n", moment);
150 27 : if(do_powers) log.printf(" calculating the %lf power of the mean (and moment)\n", power);
151 27 : }
152 :
153 125 : void Ensemble::calculate() {
154 : double norm = 0.0;
155 125 : double fact = 0.0;
156 :
157 : // calculate the weights either from BIAS
158 125 : if(do_reweight) {
159 : std::vector<double> bias;
160 0 : bias.resize(ens_dim);
161 0 : if(master) {
162 0 : bias[my_repl] = getArgument(narg);
163 0 : if(ens_dim>1) multi_sim_comm.Sum(&bias[0], ens_dim);
164 : }
165 0 : comm.Sum(&bias[0], ens_dim);
166 0 : const double maxbias = *(std::max_element(bias.begin(), bias.end()));
167 0 : for(unsigned i=0; i<ens_dim; ++i) {
168 0 : bias[i] = exp((bias[i]-maxbias)/kbt);
169 0 : norm += bias[i];
170 : }
171 0 : fact = bias[my_repl]/norm;
172 : // or arithmetic ones
173 : } else {
174 125 : norm = static_cast<double>(ens_dim);
175 125 : fact = 1.0/norm;
176 : }
177 :
178 125 : const double fact_kbt = fact/kbt;
179 :
180 125 : std::vector<double> mean(narg);
181 125 : std::vector<double> dmean(narg,fact);
182 : // calculate the mean
183 125 : if(master) {
184 2106 : for(unsigned i=0; i<narg; ++i) mean[i] = fact*getArgument(i);
185 99 : if(ens_dim>1) multi_sim_comm.Sum(&mean[0], narg);
186 : }
187 125 : comm.Sum(&mean[0], narg);
188 :
189 : std::vector<double> v_moment, dv_moment;
190 : // calculate other moments
191 125 : if(do_moments) {
192 0 : v_moment.resize(narg);
193 0 : dv_moment.resize(narg);
194 : // standard moment
195 0 : if(!do_central) {
196 0 : if(master) {
197 0 : for(unsigned i=0; i<narg; ++i) {
198 0 : const double tmp = fact*std::pow(getArgument(i),moment-1);
199 0 : v_moment[i] = tmp*getArgument(i);
200 0 : dv_moment[i] = moment*tmp;
201 : }
202 0 : if(ens_dim>1) multi_sim_comm.Sum(&v_moment[0], narg);
203 : } else {
204 0 : for(unsigned i=0; i<narg; ++i) {
205 0 : const double tmp = fact*std::pow(getArgument(i),moment-1);
206 0 : dv_moment[i] = moment*tmp;
207 : }
208 : }
209 : // central moment
210 : } else {
211 0 : if(master) {
212 0 : for(unsigned i=0; i<narg; ++i) {
213 0 : const double tmp = std::pow(getArgument(i)-mean[i],moment-1);
214 0 : v_moment[i] = fact*tmp*(getArgument(i)-mean[i]);
215 0 : dv_moment[i] = moment*tmp*(fact-fact/norm);
216 : }
217 0 : if(ens_dim>1) multi_sim_comm.Sum(&v_moment[0], narg);
218 : } else {
219 0 : for(unsigned i=0; i<narg; ++i) {
220 0 : const double tmp = std::pow(getArgument(i)-mean[i],moment-1);
221 0 : dv_moment[i] = moment*tmp*(fact-fact/norm);
222 : }
223 : }
224 : }
225 0 : comm.Sum(&v_moment[0], narg);
226 : }
227 :
228 : // calculate powers of moments
229 125 : if(do_powers) {
230 72 : for(unsigned i=0; i<narg; ++i) {
231 48 : const double tmp1 = std::pow(mean[i],power-1);
232 48 : mean[i] *= tmp1;
233 48 : dmean[i] *= power*tmp1;
234 48 : if(do_moments) {
235 0 : const double tmp2 = std::pow(v_moment[i],power-1);
236 0 : v_moment[i] *= tmp2;
237 0 : dv_moment[i] *= power*tmp2;
238 : }
239 : }
240 : }
241 :
242 : // set components
243 3358 : for(unsigned i=0; i<narg; ++i) {
244 : // set mean
245 3233 : Value* v=getPntrToComponent(i);
246 3233 : v->set(mean[i]);
247 6466 : setDerivative(v, i, dmean[i]);
248 3233 : if(do_reweight) {
249 0 : const double w_tmp = fact_kbt*(getArgument(i) - mean[i]);
250 0 : setDerivative(v, narg, w_tmp);
251 : }
252 3233 : if(do_moments) {
253 : // set moments
254 0 : Value* u=getPntrToComponent(i+narg);
255 0 : u->set(v_moment[i]);
256 0 : setDerivative(u, i, dv_moment[i]);
257 0 : if(do_reweight) {
258 0 : const double w_tmp = fact_kbt*(pow(getArgument(i),moment) - v_moment[i]);
259 0 : setDerivative(u, narg, w_tmp);
260 : }
261 : }
262 : }
263 125 : }
264 :
265 : }
266 : }
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