Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2023 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 :
23 : /*
24 : This class was originally written by Marco Jacopo Ferrarotti
25 : (marco.ferrarotti@gmail.com) and Giovanni Bussi
26 : */
27 :
28 : #include "core/Action.h"
29 : #include "core/ActionPilot.h"
30 : #include "core/ActionWithValue.h"
31 : #include "core/ActionSet.h"
32 : #include "core/ActionRegister.h"
33 : #include "core/PlumedMain.h"
34 : #include "core/Atoms.h"
35 :
36 : #include "tools/File.h"
37 : #include "tools/Pbc.h"
38 :
39 : #include <algorithm>
40 :
41 : namespace PLMD {
42 : namespace generic {
43 :
44 : //+PLUMEDOC GENERIC EFFECTIVE_ENERGY_DRIFT
45 : /*
46 : Print the effective energy drift described in Ref \cite Ferrarotti2015
47 :
48 :
49 : \par Examples
50 :
51 :
52 : This is to monitor the effective energy drift for a metadynamics
53 : simulation on the Debye-Huckel energy. Since this variable is very expensive,
54 : it could be conveniently computed every second step.
55 : \plumedfile
56 : dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0
57 : METAD ARG=dh HEIGHT=0.5 SIGMA=0.1 PACE=500 STRIDE=2
58 : EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff
59 : \endplumedfile
60 :
61 : This is to monitor if a restraint is too stiff
62 : \plumedfile
63 : d: DISTANCE ATOMS=10,20
64 : RESTRAINT ARG=d KAPPA=100000 AT=0.6
65 : EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff
66 : \endplumedfile
67 :
68 : */
69 : //+ENDPLUMEDOC
70 :
71 :
72 : class EffectiveEnergyDrift:
73 : public ActionPilot {
74 : OFile output;
75 : long int printStride;
76 : std::string fmt;
77 :
78 : double eed;
79 :
80 : Atoms& atoms;
81 : std::vector<ActionWithValue*> biases;
82 :
83 : long int pDdStep;
84 : int nLocalAtoms;
85 : int pNLocalAtoms;
86 : std::vector<int> pGatindex;
87 : std::vector<Vector> positions;
88 : std::vector<Vector> pPositions;
89 : std::vector<Vector> forces;
90 : std::vector<Vector> pForces;
91 : Tensor box,pbox;
92 : Tensor fbox,pfbox;
93 :
94 : const int nProc;
95 : std::vector<int> indexCnt;
96 : std::vector<int> indexDsp;
97 : std::vector<int> dataCnt;
98 : std::vector<int> dataDsp;
99 : std::vector<int> indexS;
100 : std::vector<int> indexR;
101 : std::vector<double> dataS;
102 : std::vector<double> dataR;
103 : std::vector<int> backmap;
104 :
105 : double initialBias;
106 : bool isFirstStep;
107 :
108 : bool ensemble;
109 :
110 : public:
111 : explicit EffectiveEnergyDrift(const ActionOptions&);
112 : ~EffectiveEnergyDrift();
113 :
114 : static void registerKeywords( Keywords& keys );
115 :
116 450 : void calculate() override {};
117 450 : void apply() override {};
118 : void update() override;
119 : };
120 :
121 10437 : PLUMED_REGISTER_ACTION(EffectiveEnergyDrift,"EFFECTIVE_ENERGY_DRIFT")
122 :
123 10 : void EffectiveEnergyDrift::registerKeywords( Keywords& keys ) {
124 10 : Action::registerKeywords( keys );
125 10 : ActionPilot::registerKeywords( keys );
126 :
127 20 : keys.add("compulsory","STRIDE","1","should be set to 1. Effective energy drift computation has to be active at each step.");
128 20 : keys.add("compulsory", "FILE", "file on which to output the effective energy drift.");
129 20 : keys.add("compulsory", "PRINT_STRIDE", "frequency to which output the effective energy drift on FILE");
130 20 : keys.addFlag("ENSEMBLE",false,"Set to TRUE if you want to average over multiple replicas.");
131 20 : keys.add("optional","FMT","the format that should be used to output real numbers");
132 10 : keys.use("RESTART");
133 10 : keys.use("UPDATE_FROM");
134 10 : keys.use("UPDATE_UNTIL");
135 10 : }
136 :
137 9 : EffectiveEnergyDrift::EffectiveEnergyDrift(const ActionOptions&ao):
138 : Action(ao),
139 : ActionPilot(ao),
140 9 : fmt("%f"),
141 9 : eed(0.0),
142 9 : atoms(plumed.getAtoms()),
143 9 : nProc(plumed.comm.Get_size()),
144 9 : initialBias(0.0),
145 9 : isFirstStep(true),
146 27 : ensemble(false)
147 : {
148 : //stride must be == 1
149 9 : if(getStride()!=1) error("EFFECTIVE_ENERGY_DRIFT must have STRIDE=1 to work properly");
150 :
151 : //parse and open FILE
152 : std::string fileName;
153 18 : parse("FILE",fileName);
154 9 : if(fileName.length()==0) error("name out output file was not specified\n");
155 9 : output.link(*this);
156 9 : output.open(fileName);
157 :
158 : //parse PRINT_STRIDE
159 9 : parse("PRINT_STRIDE",printStride);
160 :
161 :
162 : //parse FMT
163 9 : parse("FMT",fmt);
164 9 : fmt=" "+fmt;
165 9 : log.printf(" with format %s\n",fmt.c_str());
166 :
167 : //parse ENSEMBLE
168 9 : ensemble=false;
169 9 : parseFlag("ENSEMBLE",ensemble);
170 9 : if(ensemble&&comm.Get_rank()==0) {
171 0 : if(multi_sim_comm.Get_size()<2) error("You CANNOT run Replica-Averaged simulations without running multiple replicas!\n");
172 : }
173 :
174 18 : log<<"Bibliography "<<cite("Ferrarotti, Bottaro, Perez-Villa, and Bussi, J. Chem. Theory Comput. 11, 139 (2015)")<<"\n";
175 :
176 : //construct biases from ActionWithValue with a component named bias
177 9 : std::vector<ActionWithValue*> tmpActions=plumed.getActionSet().select<ActionWithValue*>();
178 27 : for(unsigned i=0; i<tmpActions.size(); i++) if(tmpActions[i]->exists(tmpActions[i]->getLabel()+".bias")) biases.push_back(tmpActions[i]);
179 :
180 : //resize counters and displacements useful to communicate with MPI_Allgatherv
181 9 : indexCnt.resize(nProc);
182 9 : indexDsp.resize(nProc);
183 9 : dataCnt.resize(nProc);
184 9 : dataDsp.resize(nProc);
185 : //resize the received buffers
186 9 : indexR.resize(atoms.getNatoms());
187 9 : dataR.resize(atoms.getNatoms()*6);
188 9 : backmap.resize(atoms.getNatoms());
189 9 : }
190 :
191 18 : EffectiveEnergyDrift::~EffectiveEnergyDrift() {
192 :
193 18 : }
194 :
195 450 : void EffectiveEnergyDrift::update() {
196 450 : bool pbc=atoms.getPbc().isSet();
197 :
198 : //retrieve data of local atoms
199 : const std::vector<int>& gatindex = atoms.getGatindex();
200 450 : nLocalAtoms = gatindex.size();
201 450 : atoms.getLocalPositions(positions);
202 450 : atoms.getLocalForces(forces);
203 450 : if(pbc) {
204 450 : Tensor B=atoms.getPbc().getBox();
205 450 : Tensor IB=atoms.getPbc().getInvBox();
206 450 : #pragma omp parallel for
207 : for(unsigned i=0; i<positions.size(); ++i) {
208 : positions[i]=matmul(positions[i],IB);
209 : forces[i]=matmul(B,forces[i]);
210 : }
211 450 : box=B;
212 450 : fbox=matmul(transpose(inverse(box)),atoms.getVirial());
213 : }
214 :
215 : //init stored data at the first step
216 450 : if(isFirstStep) {
217 9 : pDdStep=0;
218 9 : pGatindex = atoms.getGatindex();
219 9 : pNLocalAtoms = pGatindex.size();
220 9 : pPositions=positions;
221 9 : pForces=forces;
222 9 : pbox=box;
223 9 : pfbox=fbox;
224 9 : initialBias=plumed.getBias();
225 :
226 9 : isFirstStep=false;
227 : }
228 :
229 : //if the dd has changed we have to reshare the stored data
230 450 : if(pDdStep<atoms.getDdStep() && nLocalAtoms<atoms.getNatoms()) {
231 : //prepare the data to be sent
232 204 : indexS.resize(pNLocalAtoms);
233 204 : dataS.resize(pNLocalAtoms*6);
234 :
235 5712 : for(int i=0; i<pNLocalAtoms; i++) {
236 5508 : indexS[i] = pGatindex[i];
237 5508 : dataS[i*6] = pPositions[i][0];
238 5508 : dataS[i*6+1] = pPositions[i][1];
239 5508 : dataS[i*6+2] = pPositions[i][2];
240 5508 : dataS[i*6+3] = pForces[i][0];
241 5508 : dataS[i*6+4] = pForces[i][1];
242 5508 : dataS[i*6+5] = pForces[i][2];
243 : }
244 :
245 : //setup the counters and displacements for the communication
246 204 : plumed.comm.Allgather(&pNLocalAtoms,1,&indexCnt[0],1);
247 204 : indexDsp[0] = 0;
248 1020 : for(int i=0; i<nProc; i++) {
249 816 : dataCnt[i] = indexCnt[i]*6;
250 :
251 816 : if(i+1<nProc) indexDsp[i+1] = indexDsp[i]+indexCnt[i];
252 816 : dataDsp[i] = indexDsp[i]*6;
253 : }
254 :
255 : //share stored data
256 402 : plumed.comm.Allgatherv((!indexS.empty()?&indexS[0]:NULL), pNLocalAtoms, &indexR[0], &indexCnt[0], &indexDsp[0]);
257 402 : plumed.comm.Allgatherv((!dataS.empty()?&dataS[0]:NULL), pNLocalAtoms*6, &dataR[0], &dataCnt[0], &dataDsp[0]);
258 :
259 : //resize vectors to store the proper amount of data
260 204 : pGatindex.resize(nLocalAtoms);
261 204 : pPositions.resize(nLocalAtoms);
262 204 : pForces.resize(nLocalAtoms);
263 :
264 : //compute backmap
265 22236 : for(unsigned j=0; j<indexR.size(); j++) backmap[indexR[j]]=j;
266 :
267 : //fill the vectors pGatindex, pPositions and pForces
268 5712 : for(int i=0; i<nLocalAtoms; i++) {
269 5508 : int glb=backmap[gatindex[i]];
270 5508 : pGatindex[i] = indexR[glb];
271 5508 : pPositions[i][0] = dataR[glb*6];
272 5508 : pPositions[i][1] = dataR[glb*6+1];
273 5508 : pPositions[i][2] = dataR[glb*6+2];
274 5508 : pForces[i][0] = dataR[glb*6+3];
275 5508 : pForces[i][1] = dataR[glb*6+4];
276 5508 : pForces[i][2] = dataR[glb*6+5];
277 : }
278 : }
279 :
280 : //compute the effective energy drift on local atoms
281 :
282 450 : double eed_tmp=eed;
283 450 : #pragma omp parallel for reduction(+:eed_tmp)
284 : for(int i=0; i<nLocalAtoms; i++) {
285 : Vector dst=delta(pPositions[i],positions[i]);
286 : if(pbc) for(unsigned k=0; k<3; k++) dst[k]=Tools::pbc(dst[k]);
287 : eed_tmp += dotProduct(dst, forces[i]+pForces[i])*0.5;
288 : }
289 :
290 450 : eed=eed_tmp;
291 :
292 450 : if(plumed.comm.Get_rank()==0) {
293 1950 : for(unsigned i=0; i<3; i++) for(unsigned j=0; j<3; j++)
294 1350 : eed-=0.5*(pfbox(i,j)+fbox(i,j))*(box(i,j)-pbox(i,j));
295 : }
296 :
297 :
298 : //print the effective energy drift on FILE with frequency PRINT_STRIDE
299 450 : if(plumed.getStep()%printStride==0) {
300 450 : double eedSum = eed;
301 : double bias = 0.0;
302 :
303 : //we cannot just use plumed.getBias() because it will be ==0.0 if PRINT_STRIDE
304 : //is not a multiple of the bias actions stride
305 900 : for(unsigned i=0; i<biases.size(); i++) bias+=biases[i]->getOutputQuantity("bias");
306 :
307 450 : plumed.comm.Sum(&eedSum,1);
308 :
309 450 : double effective = eedSum+bias-initialBias-plumed.getWork();
310 : // this is to take into account ensemble averaging
311 450 : if(ensemble) {
312 0 : if(plumed.comm.Get_rank()==0) plumed.multi_sim_comm.Sum(&effective,1);
313 0 : else effective=0.;
314 0 : plumed.comm.Sum(&effective,1);
315 : }
316 450 : output.fmtField(" %f");
317 450 : output.printField("time",getTime());
318 450 : output.fmtField(fmt);
319 450 : output.printField("effective-energy",effective);
320 450 : output.printField();
321 : }
322 :
323 : //store the data of the current step
324 450 : pDdStep = atoms.getDdStep();
325 450 : pNLocalAtoms = nLocalAtoms;
326 : pPositions.swap(positions);
327 : pForces.swap(forces);
328 450 : pbox=box;
329 450 : pfbox=fbox;
330 450 : }
331 :
332 : }
333 : }
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