Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2018 The VES code team
3 : (see the PEOPLE-VES file at the root of this folder for a list of names)
4 :
5 : See http://www.ves-code.org for more information.
6 :
7 : This file is part of VES code module.
8 :
9 : The VES code module 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 : The VES code module 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 the VES code module. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 :
23 : #include "BasisFunctions.h"
24 : #include "LinearBasisSetExpansion.h"
25 : #include "CoeffsVector.h"
26 : #include "GridIntegrationWeights.h"
27 :
28 : #include "cltools/CLTool.h"
29 : #include "cltools/CLToolRegister.h"
30 : #include "tools/Vector.h"
31 : #include "tools/Random.h"
32 : #include "tools/Grid.h"
33 : #include "tools/Communicator.h"
34 : #include "tools/FileBase.h"
35 : #include "core/PlumedMain.h"
36 : #include "core/ActionRegister.h"
37 : #include "core/ActionSet.h"
38 :
39 : #include <string>
40 : #include <cstdio>
41 : #include <cmath>
42 : #include <vector>
43 : #include <iostream>
44 :
45 : #ifdef __PLUMED_HAS_MPI
46 : #include <mpi.h>
47 : #endif
48 :
49 :
50 : namespace PLMD {
51 : namespace ves {
52 :
53 : //+PLUMEDOC VES_TOOLS ves_md_linearexpansion
54 : /*
55 : Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion.
56 :
57 : This is simple MD code that allows running dynamics of a single particle on a
58 : potential energy surface given by some linear basis set expansion in one to three
59 : dimensions.
60 :
61 : It is possible to run more than one replica of the system in parallel.
62 :
63 : \par Examples
64 :
65 : In the following example we perform dynamics on the
66 : Wolfe-Quapp potential that is defined as
67 : \f[
68 : U(x,y) = x^4 + y^4 - 2 x^2 - 4 y^2 + xy + 0.3 x + 0.1 y
69 : \f]
70 : To define the potential we employ polynomial power basis
71 : functions (\ref BF_POWERS). The input file is given as
72 : \verbatim
73 : nstep 10000
74 : tstep 0.005
75 : temperature 1.0
76 : friction 10.0
77 : random_seed 4525
78 : plumed_input plumed.dat
79 : dimension 2
80 : replicas 1
81 : basis_functions_1 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0
82 : basis_functions_2 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0
83 : input_coeffs pot_coeffs_input.data
84 : initial_position -1.174,+1.477
85 : output_potential potential.data
86 : output_potential_grid 150
87 : output_histogram histogram.data
88 :
89 : # Wolfe-Quapp potential given by the equation
90 : # U(x,y) = x**4 + y**4 - 2.0*x**2 - 4.0*y**2 + x*y + 0.3*x + 0.1*y
91 : # Minima around (-1.174,1.477); (-0.831,-1.366); (1.124,-1.486)
92 : # Maxima around (0.100,0.050)
93 : # Saddle points around (-1.013,-0.036); (0.093,0.174); (-0.208,-1.407)
94 : \endverbatim
95 :
96 : This input is then run by using the following command.
97 : \verbatim
98 : plumed ves_md_linearexpansion input
99 : \endverbatim
100 :
101 : The corresponding pot_coeffs_input.data file is
102 : \verbatim
103 : #! FIELDS idx_dim1 idx_dim2 pot.coeffs index description
104 : #! SET type LinearBasisSet
105 : #! SET ndimensions 2
106 : #! SET ncoeffs_total 25
107 : #! SET shape_dim1 5
108 : #! SET shape_dim2 5
109 : 0 0 0.0000000000000000e+00 0 1*1
110 : 1 0 0.3000000000000000e+00 1 s^1*1
111 : 2 0 -2.0000000000000000e+00 2 s^2*1
112 : 4 0 1.0000000000000000e+00 4 s^4*1
113 : 0 1 0.1000000000000000e+00 5 1*s^1
114 : 1 1 +1.0000000000000000e+00 6 s^1*s^1
115 : 0 2 -4.0000000000000000e+00 10 1*s^2
116 : 0 4 1.0000000000000000e+00 20 1*s^4
117 : #!-------------------
118 : \endverbatim
119 :
120 : One then uses the (x,y) postion of the particle as CVs by using the \ref POSITION
121 : action as shown in the following PLUMED input
122 : \plumedfile
123 : p: POSITION ATOM=1
124 : ene: ENERGY
125 : PRINT ARG=p.x,p.y,ene FILE=colvar.data FMT=%8.4f
126 : \endplumedfile
127 :
128 :
129 :
130 : */
131 : //+ENDPLUMEDOC
132 :
133 37 : class MD_LinearExpansionPES : public PLMD::CLTool {
134 : public:
135 0 : std::string description() const {return "MD of a one particle on a linear expansion PES";}
136 : static void registerKeywords( Keywords& keys );
137 : explicit MD_LinearExpansionPES( const CLToolOptions& co );
138 : int main( FILE* in, FILE* out, PLMD::Communicator& pc);
139 : private:
140 : unsigned int dim;
141 : LinearBasisSetExpansion* potential_expansion_pntr;
142 : //
143 : double calc_energy( const std::vector<Vector>&, std::vector<Vector>& );
144 : double calc_temp( const std::vector<Vector>& );
145 : };
146 :
147 6489 : PLUMED_REGISTER_CLTOOL(MD_LinearExpansionPES,"ves_md_linearexpansion")
148 :
149 1613 : void MD_LinearExpansionPES::registerKeywords( Keywords& keys ) {
150 1613 : CLTool::registerKeywords( keys );
151 8065 : keys.add("compulsory","nstep","10","The number of steps of dynamics you want to run.");
152 8065 : keys.add("compulsory","tstep","0.005","The integration timestep.");
153 8065 : keys.add("compulsory","temperature","1.0","The temperature to perform the simulation at. For multiple replica you can give a seperate value for each replica.");
154 8065 : keys.add("compulsory","friction","10.","The friction of the Langevin thermostat. For multiple replica you can give a seperate value for each replica.");
155 8065 : keys.add("compulsory","random_seed","5293818","Value of random number seed.");
156 8065 : keys.add("compulsory","plumed_input","plumed.dat","The name of the plumed input file(s). For multiple replica you can give a seperate value for each replica.");
157 8065 : keys.add("compulsory","dimension","1","Number of dimensions, supports 1 to 3.");
158 6452 : keys.add("compulsory","initial_position","Initial position of the particle. For multiple replica you can give a seperate value for each replica.");
159 8065 : keys.add("compulsory","replicas","1","Number of replicas.");
160 6452 : keys.add("compulsory","basis_functions_1","Basis functions for dimension 1.");
161 6452 : keys.add("optional","basis_functions_2","Basis functions for dimension 2 if needed.");
162 6452 : keys.add("optional","basis_functions_3","Basis functions for dimension 3 if needed.");
163 8065 : keys.add("compulsory","input_coeffs","potential-coeffs.in.data","Filename of the input coefficent file for the potential. For multiple replica you can give a seperate value for each replica.");
164 8065 : keys.add("compulsory","output_coeffs","potential-coeffs.out.data","Filename of the output coefficent file for the potential.");
165 8065 : keys.add("compulsory","output_coeffs_fmt","%30.16e","Format of the output coefficent file for the potential. Useful for regtests.");
166 6452 : keys.add("optional","coeffs_prefactor","prefactor for multiplying the coefficents with. For multiple replica you can give a seperate value for each replica.");
167 6452 : keys.add("optional","template_coeffs_file","only generate a template coefficent file with the filename given and exit.");
168 8065 : keys.add("compulsory","output_potential_grid","100","The number of grid points used for the potential and histogram output files.");
169 8065 : keys.add("compulsory","output_potential","potential.data","Filename of the potential output file.");
170 8065 : keys.add("compulsory","output_histogram","histogram.data","Filename of the histogram output file.");
171 1613 : }
172 :
173 :
174 37 : MD_LinearExpansionPES::MD_LinearExpansionPES( const CLToolOptions& co ):
175 : CLTool(co),
176 : dim(0),
177 37 : potential_expansion_pntr(NULL)
178 : {
179 37 : inputdata=ifile; //commandline;
180 37 : }
181 :
182 : inline
183 3737 : double MD_LinearExpansionPES::calc_energy( const std::vector<Vector>& pos, std::vector<Vector>& forces) {
184 3737 : std::vector<double> pos_tmp(dim);
185 3737 : std::vector<double> forces_tmp(dim,0.0);
186 12423 : for(unsigned int j=0; j<dim; ++j) {
187 8686 : pos_tmp[j]=pos[0][j];
188 : }
189 3737 : bool all_inside = true;
190 3737 : double potential = potential_expansion_pntr->getBiasAndForces(pos_tmp,all_inside,forces_tmp);
191 12423 : for(unsigned int j=0; j<dim; ++j) {
192 8686 : forces[0][j] = forces_tmp[j];
193 : }
194 3737 : return potential;
195 : }
196 :
197 :
198 : inline
199 3737 : double MD_LinearExpansionPES::calc_temp( const std::vector<Vector>& vel) {
200 : double total_KE=0.0;
201 : //! Double the total kinetic energy of the system
202 12423 : for(unsigned int j=0; j<dim; ++j) {
203 4343 : total_KE+=vel[0][j]*vel[0][j];
204 : }
205 3737 : return total_KE / (double) dim; // total_KE is actually 2*KE
206 : }
207 :
208 37 : int MD_LinearExpansionPES::main( FILE* in, FILE* out, PLMD::Communicator& pc) {
209 : int plumedWantsToStop;
210 37 : Random random;
211 : unsigned int stepWrite=1000;
212 :
213 : PLMD::PlumedMain* plumed=NULL;
214 : PLMD::PlumedMain* plumed_bf=NULL;
215 :
216 : unsigned int replicas;
217 : unsigned int coresPerReplica;
218 74 : parse("replicas",replicas);
219 37 : if(replicas==1) {
220 6 : coresPerReplica = pc.Get_size();
221 : } else {
222 31 : if(pc.Get_size()%replicas!=0) {
223 0 : error("the number of MPI processes is not a multiple of the number of replicas.");
224 : }
225 31 : coresPerReplica = pc.Get_size()/replicas;
226 : }
227 : // create intra and inter communicators
228 74 : Communicator intra, inter;
229 37 : if(Communicator::initialized()) {
230 33 : int iworld=(pc.Get_rank() / coresPerReplica);
231 33 : pc.Split(iworld,0,intra);
232 33 : pc.Split(intra.Get_rank(),0,inter);
233 : }
234 :
235 : unsigned int nsteps;
236 74 : parse("nstep",nsteps);
237 : double tstep;
238 74 : parse("tstep",tstep);
239 : // initialize to solve a cppcheck 1.86 warning
240 37 : double temp=0.0;
241 37 : std::vector<double> temps_vec(0);
242 74 : parseVector("temperature",temps_vec);
243 37 : if(temps_vec.size()==1) {
244 33 : temp = temps_vec[0];
245 : }
246 4 : else if(replicas > 1 && temps_vec.size()==replicas) {
247 12 : temp = temps_vec[inter.Get_rank()];
248 : }
249 : else {
250 0 : error("problem with temperature keyword, you need to give either one value or a value for each replica.");
251 : }
252 : //
253 : double friction;
254 37 : std::vector<double> frictions_vec(0);
255 74 : parseVector("friction",frictions_vec);
256 37 : if(frictions_vec.size()==1) {
257 33 : friction = frictions_vec[0];
258 : }
259 4 : else if(frictions_vec.size()==replicas) {
260 8 : friction = frictions_vec[inter.Get_rank()];
261 : }
262 : else {
263 0 : error("problem with friction keyword, you need to give either one value or a value for each replica.");
264 : }
265 : //
266 : int seed;
267 37 : std::vector<int> seeds_vec(0);
268 74 : parseVector("random_seed",seeds_vec);
269 221 : for(unsigned int i=0; i<seeds_vec.size(); i++) {
270 49 : if(seeds_vec[i]>0) {seeds_vec[i] = -seeds_vec[i];}
271 : }
272 37 : if(replicas==1) {
273 6 : if(seeds_vec.size()>1) {error("problem with random_seed keyword, for a single replica you should only give one value");}
274 6 : seed = seeds_vec[0];
275 : }
276 : else {
277 31 : if(seeds_vec.size()!=1 && seeds_vec.size()!=replicas) {
278 0 : error("problem with random_seed keyword, for multiple replicas you should give either one value or a seperate value for each replica");
279 : }
280 31 : if(seeds_vec.size()==1) {
281 27 : seeds_vec.resize(replicas);
282 300 : for(unsigned int i=1; i<seeds_vec.size(); i++) {seeds_vec[i] = seeds_vec[0] + i;}
283 : }
284 62 : seed = seeds_vec[inter.Get_rank()];
285 : }
286 :
287 : //
288 74 : parse("dimension",dim);
289 :
290 37 : std::vector<std::string> plumed_inputfiles;
291 74 : parseVector("plumed_input",plumed_inputfiles);
292 37 : if(plumed_inputfiles.size()!=1 && plumed_inputfiles.size()!=replicas) {
293 0 : error("in plumed_input you should either give one file or separate files for each replica.");
294 : }
295 :
296 37 : std::vector<Vector> initPos(replicas);
297 : std::vector<double> initPosTmp;
298 74 : parseVector("initial_position",initPosTmp);
299 37 : if(initPosTmp.size()==dim) {
300 73 : for(unsigned int i=0; i<replicas; i++) {
301 97 : for(unsigned int k=0; k<dim; k++) {
302 99 : initPos[i][k]=initPosTmp[k];
303 : }
304 : }
305 : }
306 26 : else if(initPosTmp.size()==dim*replicas) {
307 226 : for(unsigned int i=0; i<replicas; i++) {
308 332 : for(unsigned int k=0; k<dim; k++) {
309 348 : initPos[i][k]=initPosTmp[i*dim+k];
310 : }
311 : }
312 : }
313 : else {
314 0 : error("problem with initial_position keyword, you need to give either one value or a value for each replica.");
315 : }
316 :
317 :
318 37 : plumed_bf = new PLMD::PlumedMain;
319 37 : unsigned int nn=1;
320 37 : FILE* file_dummy = fopen("/dev/null","w+");
321 74 : plumed_bf->cmd("setNatoms",&nn);
322 74 : plumed_bf->cmd("setLog",file_dummy);
323 74 : plumed_bf->cmd("init",&nn);
324 37 : std::vector<BasisFunctions*> basisf_pntrs(dim);
325 74 : std::vector<std::string> basisf_keywords(dim);
326 37 : std::vector<Value*> args(dim);
327 74 : std::vector<bool> periodic(dim);
328 37 : std::vector<double> interval_min(dim);
329 37 : std::vector<double> interval_max(dim);
330 37 : std::vector<double> interval_range(dim);
331 123 : for(unsigned int i=0; i<dim; i++) {
332 : std::string bf_keyword;
333 43 : std::string is; Tools::convert(i+1,is);
334 86 : parse("basis_functions_"+is,bf_keyword);
335 43 : if(bf_keyword.size()==0) {
336 0 : error("basis_functions_"+is+" is needed");
337 : }
338 45 : if(bf_keyword.at(0)=='{' && bf_keyword.at(bf_keyword.size()-1)=='}') {
339 4 : bf_keyword = bf_keyword.substr(1,bf_keyword.size()-2);
340 : }
341 43 : basisf_keywords[i] = bf_keyword;
342 129 : plumed_bf->readInputLine(bf_keyword+" LABEL=dim"+is);
343 129 : basisf_pntrs[i] = plumed_bf->getActionSet().selectWithLabel<BasisFunctions*>("dim"+is);
344 129 : args[i] = new Value(NULL,"dim"+is,false);
345 43 : args[i]->setNotPeriodic();
346 43 : periodic[i] = basisf_pntrs[i]->arePeriodic();
347 86 : interval_min[i] = basisf_pntrs[i]->intervalMin();
348 86 : interval_max[i] = basisf_pntrs[i]->intervalMax();
349 86 : interval_range[i] = basisf_pntrs[i]->intervalMax()-basisf_pntrs[i]->intervalMin();
350 : }
351 74 : Communicator comm_dummy;
352 74 : CoeffsVector* coeffs_pntr = new CoeffsVector("pot.coeffs",args,basisf_pntrs,comm_dummy,false);
353 74 : potential_expansion_pntr = new LinearBasisSetExpansion("potential",1.0/temp,comm_dummy,args,basisf_pntrs,coeffs_pntr);
354 :
355 37 : std::string template_coeffs_fname="";
356 74 : parse("template_coeffs_file",template_coeffs_fname);
357 37 : if(template_coeffs_fname.size()>0) {
358 0 : OFile ofile_coeffstmpl;
359 0 : ofile_coeffstmpl.link(pc);
360 0 : ofile_coeffstmpl.open(template_coeffs_fname);
361 0 : coeffs_pntr->writeToFile(ofile_coeffstmpl,true);
362 0 : ofile_coeffstmpl.close();
363 0 : error("Only generating a template coefficent file - Should stop now.");
364 : }
365 :
366 74 : std::vector<std::string> input_coeffs_fnames(0);
367 74 : parseVector("input_coeffs",input_coeffs_fnames);
368 : std::string input_coeffs_fname;
369 : bool diff_input_coeffs = false;
370 37 : if(input_coeffs_fnames.size()==1) {
371 : input_coeffs_fname = input_coeffs_fnames[0];
372 : }
373 9 : else if(replicas > 1 && input_coeffs_fnames.size()==replicas) {
374 : diff_input_coeffs = true;
375 9 : input_coeffs_fname = input_coeffs_fnames[inter.Get_rank()];
376 : }
377 : else {
378 0 : error("problem with coeffs_file keyword, you need to give either one value or a value for each replica.");
379 : }
380 37 : coeffs_pntr->readFromFile(input_coeffs_fname,true,true);
381 37 : std::vector<double> coeffs_prefactors(0);
382 74 : parseVector("coeffs_prefactor",coeffs_prefactors);
383 37 : if(coeffs_prefactors.size()>0) {
384 : double coeffs_prefactor = 1.0;
385 6 : if(coeffs_prefactors.size()==1) {
386 2 : coeffs_prefactor = coeffs_prefactors[0];
387 : }
388 4 : else if(replicas > 1 && coeffs_prefactors.size()==replicas) {
389 : diff_input_coeffs = true;
390 8 : coeffs_prefactor = coeffs_prefactors[inter.Get_rank()];
391 : }
392 : else {
393 0 : error("problem with coeffs_prefactor keyword, you need to give either one value or a value for each replica.");
394 : }
395 6 : coeffs_pntr->scaleAllValues(coeffs_prefactor);
396 : }
397 : unsigned int pot_grid_bins;
398 74 : parse("output_potential_grid",pot_grid_bins);
399 37 : potential_expansion_pntr->setGridBins(pot_grid_bins);
400 37 : potential_expansion_pntr->setupBiasGrid(false);
401 37 : potential_expansion_pntr->updateBiasGrid();
402 37 : potential_expansion_pntr->setBiasMinimumToZero();
403 37 : potential_expansion_pntr->updateBiasGrid();
404 :
405 74 : OFile ofile_potential;
406 37 : ofile_potential.link(pc);
407 : std::string output_potential_fname;
408 74 : parse("output_potential",output_potential_fname);
409 37 : if(diff_input_coeffs) {
410 13 : ofile_potential.link(intra);
411 : std::string suffix;
412 13 : Tools::convert(inter.Get_rank(),suffix);
413 39 : output_potential_fname = FileBase::appendSuffix(output_potential_fname,"."+suffix);
414 : }
415 37 : ofile_potential.open(output_potential_fname);
416 37 : potential_expansion_pntr->writeBiasGridToFile(ofile_potential);
417 37 : ofile_potential.close();
418 :
419 111 : Grid histo_grid(*potential_expansion_pntr->getPntrToBiasGrid());
420 111 : std::vector<double> integration_weights = GridIntegrationWeights::getIntegrationWeights(&histo_grid);
421 : double norm=0.0;
422 292311 : for(Grid::index_t i=0; i<histo_grid.getSize(); i++) {
423 146137 : double value = integration_weights[i]*exp(-histo_grid.getValue(i)/temp);
424 146137 : norm += value;
425 146137 : histo_grid.setValue(i,value);
426 : }
427 37 : histo_grid.scaleAllValuesAndDerivatives(1.0/norm);
428 74 : OFile ofile_histogram;
429 37 : ofile_histogram.link(pc);
430 : std::string output_histogram_fname;
431 74 : parse("output_histogram",output_histogram_fname);
432 61 : if(diff_input_coeffs || temps_vec.size()>1) {
433 17 : ofile_histogram.link(intra);
434 : std::string suffix;
435 17 : Tools::convert(inter.Get_rank(),suffix);
436 51 : output_histogram_fname = FileBase::appendSuffix(output_histogram_fname,"."+suffix);
437 : }
438 37 : ofile_histogram.open(output_histogram_fname);
439 37 : histo_grid.writeToFile(ofile_histogram);
440 37 : ofile_histogram.close();
441 :
442 : std::string output_coeffs_fname;
443 74 : parse("output_coeffs",output_coeffs_fname);
444 : std::string output_coeffs_fmt;
445 74 : parse("output_coeffs_fmt",output_coeffs_fmt);
446 : coeffs_pntr->setOutputFmt(output_coeffs_fmt);
447 74 : OFile ofile_coeffsout;
448 37 : ofile_coeffsout.link(pc);
449 37 : if(diff_input_coeffs) {
450 13 : ofile_coeffsout.link(intra);
451 : std::string suffix;
452 13 : Tools::convert(inter.Get_rank(),suffix);
453 39 : output_coeffs_fname = FileBase::appendSuffix(output_coeffs_fname,"."+suffix);
454 : }
455 37 : ofile_coeffsout.open(output_coeffs_fname);
456 37 : coeffs_pntr->writeToFile(ofile_coeffsout,true);
457 37 : ofile_coeffsout.close();
458 :
459 37 : if(pc.Get_rank() == 0) {
460 13 : fprintf(out,"Replicas %u\n",replicas);
461 : fprintf(out,"Cores per replica %u\n",coresPerReplica);
462 13 : fprintf(out,"Number of steps %u\n",nsteps);
463 13 : fprintf(out,"Timestep %f\n",tstep);
464 13 : fprintf(out,"Temperature %f",temps_vec[0]);
465 38 : for(unsigned int i=1; i<temps_vec.size(); i++) {fprintf(out,",%f",temps_vec[i]);}
466 : fprintf(out,"\n");
467 13 : fprintf(out,"Friction %f",frictions_vec[0]);
468 38 : for(unsigned int i=1; i<frictions_vec.size(); i++) {fprintf(out,",%f",frictions_vec[i]);}
469 : fprintf(out,"\n");
470 13 : fprintf(out,"Random seed %d",seeds_vec[0]);
471 118 : for(unsigned int i=1; i<seeds_vec.size(); i++) {fprintf(out,",%d",seeds_vec[i]);}
472 : fprintf(out,"\n");
473 13 : fprintf(out,"Dimensions %u\n",dim);
474 29 : for(unsigned int i=0; i<dim; i++) {
475 32 : fprintf(out,"Basis Function %u %s\n",i+1,basisf_keywords[i].c_str());
476 : }
477 : fprintf(out,"PLUMED input %s",plumed_inputfiles[0].c_str());
478 29 : for(unsigned int i=1; i<plumed_inputfiles.size(); i++) {fprintf(out,",%s",plumed_inputfiles[i].c_str());}
479 : fprintf(out,"\n");
480 : fprintf(out,"kBoltzmann taken as 1, use NATURAL_UNITS in the plumed input\n");
481 13 : if(diff_input_coeffs) {fprintf(out,"using different coefficients for each replica\n");}
482 : }
483 :
484 :
485 37 : plumed=new PLMD::PlumedMain;
486 :
487 :
488 :
489 37 : if(plumed) {
490 37 : int s=sizeof(double);
491 74 : plumed->cmd("setRealPrecision",&s);
492 37 : if(replicas>1) {
493 31 : if (Communicator::initialized()) {
494 62 : plumed->cmd("GREX setMPIIntracomm",&intra.Get_comm());
495 31 : if (intra.Get_rank()==0) {
496 62 : plumed->cmd("GREX setMPIIntercomm",&inter.Get_comm());
497 : }
498 62 : plumed->cmd("GREX init");
499 62 : plumed->cmd("setMPIComm",&intra.Get_comm());
500 : } else {
501 0 : error("More than 1 replica but no MPI");
502 : }
503 : } else {
504 8 : if(Communicator::initialized()) plumed->cmd("setMPIComm",&pc.Get_comm());
505 : }
506 : }
507 :
508 37 : std::string plumed_logfile = "plumed.log";
509 37 : std::string stats_filename = "stats.out";
510 : std::string plumed_input = plumed_inputfiles[0];
511 37 : if(inter.Get_size()>1) {
512 : std::string suffix;
513 31 : Tools::convert(inter.Get_rank(),suffix);
514 93 : plumed_logfile = FileBase::appendSuffix(plumed_logfile,"."+suffix);
515 93 : stats_filename = FileBase::appendSuffix(stats_filename,"."+suffix);
516 31 : if(plumed_inputfiles.size()>1) {
517 2 : plumed_input = plumed_inputfiles[inter.Get_rank()];
518 : }
519 : }
520 :
521 37 : if(plumed) {
522 74 : plumed->cmd("setNoVirial");
523 37 : int natoms=1;
524 74 : plumed->cmd("setNatoms",&natoms);
525 74 : plumed->cmd("setMDEngine","mdrunner_linearexpansion");
526 74 : plumed->cmd("setTimestep",&tstep);
527 74 : plumed->cmd("setPlumedDat",plumed_input.c_str());
528 74 : plumed->cmd("setLogFile",plumed_logfile.c_str());
529 74 : plumed->cmd("setKbT",&temp);
530 37 : double energyunits=1.0;
531 74 : plumed->cmd("setMDEnergyUnits",&energyunits);
532 74 : plumed->cmd("init");
533 : }
534 :
535 : // Setup random number generator
536 37 : random.setSeed(seed);
537 :
538 37 : double potential, therm_eng=0; std::vector<double> masses(1,1);
539 37 : std::vector<Vector> positions(1), velocities(1), forces(1);
540 123 : for(unsigned int k=0; k<dim; k++) {
541 129 : positions[0][k] = initPos[inter.Get_rank()][k];
542 86 : if(periodic[k]) {
543 6 : positions[0][k] = positions[0][k] - floor(positions[0][k]/interval_range[k]+0.5)*interval_range[k];
544 : }
545 : else {
546 80 : if(positions[0][k]>interval_max[k]) {positions[0][k]=interval_max[k];}
547 80 : if(positions[0][k]<interval_min[k]) {positions[0][k]=interval_min[k];}
548 : }
549 : }
550 :
551 :
552 123 : for(unsigned k=0; k<dim; ++k) {
553 86 : velocities[0][k]=random.Gaussian() * sqrt( temp );
554 : }
555 :
556 37 : potential=calc_energy(positions,forces); double ttt=calc_temp(velocities);
557 :
558 37 : FILE* fp=fopen(stats_filename.c_str(),"w+");
559 37 : double conserved = potential+1.5*ttt+therm_eng;
560 : //fprintf(fp,"%d %f %f %f %f %f %f %f %f \n", 0, 0., positions[0][0], positions[0][1], positions[0][2], conserved, ttt, potential, therm_eng );
561 37 : if( intra.Get_rank()==0 ) {
562 72 : fprintf(fp,"%d %f %f %f %f %f %f %f %f \n", 0, 0., positions[0][0], positions[0][1], positions[0][2], conserved, ttt, potential, therm_eng );
563 : }
564 :
565 37 : if(plumed) {
566 37 : int step_tmp = 0;
567 74 : plumed->cmd("setStep",&step_tmp);
568 111 : plumed->cmd("setMasses",&masses[0]);
569 111 : plumed->cmd("setForces",&forces[0]);
570 74 : plumed->cmd("setEnergy",&potential);
571 111 : plumed->cmd("setPositions",&positions[0]);
572 74 : plumed->cmd("calc");
573 : }
574 :
575 7437 : for(unsigned int istep=0; istep<nsteps; ++istep) {
576 : //if( istep%20==0 && pc.Get_rank()==0 ) printf("Doing step %d\n",istep);
577 :
578 : // Langevin thermostat
579 3700 : double lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);
580 3700 : double lrand=sqrt((1.-lscale*lscale)*temp);
581 12300 : for(unsigned k=0; k<dim; ++k) {
582 4300 : therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];
583 8600 : velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();
584 4300 : therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];
585 : }
586 :
587 : // First step of velocity verlet
588 12300 : for(unsigned k=0; k<dim; ++k) {
589 8600 : velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];
590 8600 : positions[0][k] = positions[0][k] + tstep*velocities[0][k];
591 :
592 8600 : if(periodic[k]) {
593 600 : positions[0][k] = positions[0][k] - floor(positions[0][k]/interval_range[k]+0.5)*interval_range[k];
594 : }
595 : else {
596 8000 : if(positions[0][k]>interval_max[k]) {
597 7 : positions[0][k]=interval_max[k];
598 14 : velocities[0][k]=-std::abs(velocities[0][k]);
599 : }
600 8000 : if(positions[0][k]<interval_min[k]) {
601 2 : positions[0][k]=interval_min[k];
602 4 : velocities[0][k]=-std::abs(velocities[0][k]);
603 : }
604 : }
605 : }
606 :
607 3700 : potential=calc_energy(positions,forces);
608 :
609 3700 : if(plumed) {
610 3700 : int istepplusone=istep+1;
611 3700 : plumedWantsToStop=0;
612 7400 : plumed->cmd("setStep",&istepplusone);
613 11100 : plumed->cmd("setMasses",&masses[0]);
614 11100 : plumed->cmd("setForces",&forces[0]);
615 7400 : plumed->cmd("setEnergy",&potential);
616 11100 : plumed->cmd("setPositions",&positions[0]);
617 7400 : plumed->cmd("setStopFlag",&plumedWantsToStop);
618 7400 : plumed->cmd("calc");
619 : //if(istep%2000==0) plumed->cmd("writeCheckPointFile");
620 3700 : if(plumedWantsToStop) nsteps=istep;
621 : }
622 :
623 : // Second step of velocity verlet
624 12300 : for(unsigned k=0; k<dim; ++k) {
625 8600 : velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];
626 : }
627 :
628 : // Langevin thermostat
629 3700 : lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);
630 3700 : lrand=sqrt((1.-lscale*lscale)*temp);
631 12300 : for(unsigned k=0; k<dim; ++k) {
632 4300 : therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];
633 8600 : velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();
634 4300 : therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];
635 : }
636 :
637 : // Print everything
638 3700 : ttt = calc_temp( velocities );
639 3700 : conserved = potential+1.5*ttt+therm_eng;
640 3700 : if( (intra.Get_rank()==0) && ((istep % stepWrite)==0) ) {
641 72 : fprintf(fp,"%u %f %f %f %f %f %f %f %f \n", istep, istep*tstep, positions[0][0], positions[0][1], positions[0][2], conserved, ttt, potential, therm_eng );
642 : }
643 : }
644 :
645 37 : if(plumed) {delete plumed;}
646 37 : if(plumed_bf) {delete plumed_bf;}
647 37 : if(potential_expansion_pntr) {delete potential_expansion_pntr;}
648 37 : if(coeffs_pntr) {delete coeffs_pntr;}
649 203 : for(unsigned int i=0; i<args.size(); i++) {delete args[i];}
650 : args.clear();
651 : //printf("Rank: %d, Size: %d \n", pc.Get_rank(), pc.Get_size() );
652 : //printf("Rank: %d, Size: %d, MultiSimCommRank: %d, MultiSimCommSize: %d \n", pc.Get_rank(), pc.Get_size(), multi_sim_comm.Get_rank(), multi_sim_comm.Get_size() );
653 37 : fclose(fp);
654 37 : fclose(file_dummy);
655 :
656 37 : return 0;
657 : }
658 :
659 : }
660 4839 : }
|
