Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2016-2021 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 : #include "GridProjWeights.h"
28 :
29 : #include "cltools/CLTool.h"
30 : #include "cltools/CLToolRegister.h"
31 : #include "tools/Vector.h"
32 : #include "tools/Random.h"
33 : #include "tools/Grid.h"
34 : #include "tools/Communicator.h"
35 : #include "tools/FileBase.h"
36 : #include "core/PlumedMain.h"
37 : #include "core/ActionRegister.h"
38 : #include "core/ActionSet.h"
39 : #include "core/Value.h"
40 :
41 : #include <string>
42 : #include <cstdio>
43 : #include <cmath>
44 : #include <vector>
45 : #include <iostream>
46 :
47 : #ifdef __PLUMED_HAS_MPI
48 : #include <mpi.h>
49 : #endif
50 :
51 :
52 : namespace PLMD {
53 : namespace ves {
54 :
55 : //+PLUMEDOC VES_TOOLS ves_md_linearexpansion
56 : /*
57 : Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion.
58 :
59 : This is simple MD code that allows running dynamics of a single particle on a
60 : potential energy surface given by some linear basis set expansion in one to three
61 : dimensions.
62 :
63 : It is possible to run more than one replica of the system in parallel.
64 :
65 : \par Examples
66 :
67 : In the following example we perform dynamics on the
68 : Wolfe-Quapp potential that is defined as
69 : \f[
70 : U(x,y) = x^4 + y^4 - 2 x^2 - 4 y^2 + xy + 0.3 x + 0.1 y
71 : \f]
72 : To define the potential we employ polynomial power basis
73 : functions (\ref BF_POWERS). The input file is given as
74 : \verbatim
75 : nstep 10000
76 : tstep 0.005
77 : temperature 1.0
78 : friction 10.0
79 : random_seed 4525
80 : plumed_input plumed.dat
81 : dimension 2
82 : replicas 1
83 : basis_functions_1 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0
84 : basis_functions_2 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0
85 : input_coeffs pot_coeffs_input.data
86 : initial_position -1.174,+1.477
87 : output_potential potential.data
88 : output_potential_grid 150
89 : output_histogram histogram.data
90 :
91 : # Wolfe-Quapp potential given by the equation
92 : # U(x,y) = x**4 + y**4 - 2.0*x**2 - 4.0*y**2 + x*y + 0.3*x + 0.1*y
93 : # Minima around (-1.174,1.477); (-0.831,-1.366); (1.124,-1.486)
94 : # Maxima around (0.100,0.050)
95 : # Saddle points around (-1.013,-0.036); (0.093,0.174); (-0.208,-1.407)
96 : \endverbatim
97 :
98 : This input is then run by using the following command.
99 : \verbatim
100 : plumed ves_md_linearexpansion input
101 : \endverbatim
102 :
103 : The corresponding pot_coeffs_input.data file is
104 : \verbatim
105 : #! FIELDS idx_dim1 idx_dim2 pot.coeffs index description
106 : #! SET type LinearBasisSet
107 : #! SET ndimensions 2
108 : #! SET ncoeffs_total 25
109 : #! SET shape_dim1 5
110 : #! SET shape_dim2 5
111 : 0 0 0.0000000000000000e+00 0 1*1
112 : 1 0 0.3000000000000000e+00 1 s^1*1
113 : 2 0 -2.0000000000000000e+00 2 s^2*1
114 : 4 0 1.0000000000000000e+00 4 s^4*1
115 : 0 1 0.1000000000000000e+00 5 1*s^1
116 : 1 1 +1.0000000000000000e+00 6 s^1*s^1
117 : 0 2 -4.0000000000000000e+00 10 1*s^2
118 : 0 4 1.0000000000000000e+00 20 1*s^4
119 : #!-------------------
120 : \endverbatim
121 :
122 : One then uses the (x,y) position of the particle as CVs by using the \ref POSITION
123 : action as shown in the following PLUMED input
124 : \plumedfile
125 : p: POSITION ATOM=1
126 : ene: ENERGY
127 : PRINT ARG=p.x,p.y,ene FILE=colvar.data FMT=%8.4f
128 : \endplumedfile
129 :
130 :
131 :
132 : */
133 : //+ENDPLUMEDOC
134 :
135 : class MD_LinearExpansionPES : public PLMD::CLTool {
136 : public:
137 4 : std::string description() const override {return "MD of a one particle on a linear expansion PES";}
138 : static void registerKeywords( Keywords& keys );
139 : explicit MD_LinearExpansionPES( const CLToolOptions& co );
140 : int main( FILE* in, FILE* out, PLMD::Communicator& pc) override;
141 : private:
142 : size_t dim;
143 : std::string dim_string_prefix;
144 : std::unique_ptr<LinearBasisSetExpansion> potential_expansion_pntr;
145 : //
146 : double calc_energy( const std::vector<Vector>&, std::vector<Vector>& );
147 : double calc_temp( const std::vector<Vector>& );
148 : };
149 :
150 10463 : PLUMED_REGISTER_CLTOOL(MD_LinearExpansionPES,"ves_md_linearexpansion")
151 :
152 3473 : void MD_LinearExpansionPES::registerKeywords( Keywords& keys ) {
153 3473 : CLTool::registerKeywords( keys );
154 6946 : keys.add("compulsory","nstep","10","The number of steps of dynamics you want to run.");
155 6946 : keys.add("compulsory","tstep","0.005","The integration timestep.");
156 6946 : keys.add("compulsory","temperature","1.0","The temperature to perform the simulation at. For multiple replica you can give a separate value for each replica.");
157 6946 : keys.add("compulsory","friction","10.","The friction of the Langevin thermostat. For multiple replica you can give a separate value for each replica.");
158 6946 : keys.add("compulsory","random_seed","5293818","Value of random number seed.");
159 6946 : keys.add("compulsory","plumed_input","plumed.dat","The name of the plumed input file(s). For multiple replica you can give a separate value for each replica.");
160 6946 : keys.add("compulsory","dimension","1","Number of dimensions, supports 1 to 3.");
161 10419 : keys.add("compulsory","initial_position","Initial position of the particle. For multiple replica you can give a separate value for each replica.");
162 6946 : keys.add("compulsory","replicas","1","Number of replicas.");
163 10419 : keys.add("compulsory","basis_functions_1","Basis functions for dimension 1.");
164 10419 : keys.add("optional","basis_functions_2","Basis functions for dimension 2 if needed.");
165 10419 : keys.add("optional","basis_functions_3","Basis functions for dimension 3 if needed.");
166 10419 : keys.add("compulsory","input_coeffs","potential-coeffs.in.data","Filename of the input coefficient file for the potential. For multiple replica you can give a separate value for each replica.");
167 10419 : keys.add("compulsory","output_coeffs","potential-coeffs.out.data","Filename of the output coefficient file for the potential.");
168 10419 : keys.add("compulsory","output_coeffs_fmt","%30.16e","Format of the output coefficient file for the potential. Useful for regtests.");
169 10419 : keys.add("optional","coeffs_prefactor","prefactor for multiplying the coefficients with. For multiple replica you can give a separate value for each replica.");
170 10419 : keys.add("optional","template_coeffs_file","only generate a template coefficient file with the filename given and exit.");
171 10419 : keys.add("compulsory","output_potential_grid","100","The number of grid points used for the potential and histogram output files.");
172 10419 : keys.add("compulsory","output_potential","potential.data","Filename of the potential output file.");
173 10419 : keys.add("compulsory","output_histogram","histogram.data","Filename of the histogram output file.");
174 3473 : }
175 :
176 :
177 44 : MD_LinearExpansionPES::MD_LinearExpansionPES( const CLToolOptions& co ):
178 : CLTool(co),
179 44 : dim(0),
180 44 : dim_string_prefix("dim")
181 : {
182 44 : inputdata=ifile; //commandline;
183 44 : }
184 :
185 : inline
186 3939 : double MD_LinearExpansionPES::calc_energy( const std::vector<Vector>& pos, std::vector<Vector>& forces) {
187 3939 : std::vector<double> pos_tmp(dim);
188 3939 : std::vector<double> forces_tmp(dim,0.0);
189 8585 : for(unsigned int j=0; j<dim; ++j) {
190 4646 : pos_tmp[j]=pos[0][j];
191 : }
192 3939 : bool all_inside = true;
193 3939 : double potential = potential_expansion_pntr->getBiasAndForces(pos_tmp,all_inside,forces_tmp);
194 8585 : for(unsigned int j=0; j<dim; ++j) {
195 4646 : forces[0][j] = forces_tmp[j];
196 : }
197 3939 : return potential;
198 : }
199 :
200 :
201 : inline
202 3939 : double MD_LinearExpansionPES::calc_temp( const std::vector<Vector>& vel) {
203 : double total_KE=0.0;
204 : //! Double the total kinetic energy of the system
205 8585 : for(unsigned int j=0; j<dim; ++j) {
206 4646 : total_KE+=vel[0][j]*vel[0][j];
207 : }
208 3939 : return total_KE / (double) dim; // total_KE is actually 2*KE
209 : }
210 :
211 40 : int MD_LinearExpansionPES::main( FILE* in, FILE* out, PLMD::Communicator& pc) {
212 : int plumedWantsToStop;
213 40 : Random random;
214 : unsigned int stepWrite=1000;
215 :
216 40 : std::unique_ptr<PLMD::PlumedMain> plumed;
217 :
218 : size_t replicas;
219 : unsigned int coresPerReplica;
220 40 : parse("replicas",replicas);
221 40 : if(replicas==1) {
222 9 : coresPerReplica = pc.Get_size();
223 : } else {
224 31 : if(pc.Get_size()%replicas!=0) {
225 0 : error("the number of MPI processes is not a multiple of the number of replicas.");
226 : }
227 31 : coresPerReplica = pc.Get_size()/replicas;
228 : }
229 : // create intra and inter communicators
230 40 : Communicator intra, inter;
231 40 : if(Communicator::initialized()) {
232 33 : int iworld=(pc.Get_rank() / coresPerReplica);
233 33 : pc.Split(iworld,0,intra);
234 33 : pc.Split(intra.Get_rank(),0,inter);
235 : }
236 :
237 : unsigned int nsteps;
238 40 : parse("nstep",nsteps);
239 : double tstep;
240 40 : parse("tstep",tstep);
241 : // initialize to solve a cppcheck 1.86 warning
242 40 : double temp=0.0;
243 40 : std::vector<double> temps_vec(0);
244 80 : parseVector("temperature",temps_vec);
245 40 : if(temps_vec.size()==1) {
246 36 : temp = temps_vec[0];
247 : }
248 4 : else if(replicas > 1 && temps_vec.size()==replicas) {
249 4 : temp = temps_vec[inter.Get_rank()];
250 : }
251 : else {
252 0 : error("problem with temperature keyword, you need to give either one value or a value for each replica.");
253 : }
254 : //
255 : double friction;
256 40 : std::vector<double> frictions_vec(0);
257 80 : parseVector("friction",frictions_vec);
258 40 : if(frictions_vec.size()==1) {
259 36 : friction = frictions_vec[0];
260 : }
261 4 : else if(frictions_vec.size()==replicas) {
262 4 : friction = frictions_vec[inter.Get_rank()];
263 : }
264 : else {
265 0 : error("problem with friction keyword, you need to give either one value or a value for each replica.");
266 : }
267 : //
268 : int seed;
269 40 : std::vector<int> seeds_vec(0);
270 40 : parseVector("random_seed",seeds_vec);
271 92 : for(unsigned int i=0; i<seeds_vec.size(); i++) {
272 52 : if(seeds_vec[i]>0) {seeds_vec[i] = -seeds_vec[i];}
273 : }
274 40 : if(replicas==1) {
275 9 : if(seeds_vec.size()>1) {error("problem with random_seed keyword, for a single replica you should only give one value");}
276 9 : seed = seeds_vec[0];
277 : }
278 : else {
279 31 : if(seeds_vec.size()!=1 && seeds_vec.size()!=replicas) {
280 0 : error("problem with random_seed keyword, for multiple replicas you should give either one value or a separate value for each replica");
281 : }
282 31 : if(seeds_vec.size()==1) {
283 27 : seeds_vec.resize(replicas);
284 109 : for(unsigned int i=1; i<seeds_vec.size(); i++) {seeds_vec[i] = seeds_vec[0] + i;}
285 : }
286 31 : seed = seeds_vec[inter.Get_rank()];
287 : }
288 :
289 : //
290 80 : parse("dimension",dim);
291 :
292 : std::vector<std::string> plumed_inputfiles;
293 80 : parseVector("plumed_input",plumed_inputfiles);
294 40 : if(plumed_inputfiles.size()!=1 && plumed_inputfiles.size()!=replicas) {
295 0 : error("in plumed_input you should either give one file or separate files for each replica.");
296 : }
297 :
298 40 : std::vector<Vector> initPos(replicas);
299 : std::vector<double> initPosTmp;
300 80 : parseVector("initial_position",initPosTmp);
301 40 : if(initPosTmp.size()==dim) {
302 48 : for(unsigned int i=0; i<replicas; i++) {
303 72 : for(unsigned int k=0; k<dim; k++) {
304 38 : initPos[i][k]=initPosTmp[k];
305 : }
306 : }
307 : }
308 26 : else if(initPosTmp.size()==dim*replicas) {
309 126 : for(unsigned int i=0; i<replicas; i++) {
310 216 : for(unsigned int k=0; k<dim; k++) {
311 116 : initPos[i][k]=initPosTmp[i*dim+k];
312 : }
313 : }
314 : }
315 : else {
316 0 : error("problem with initial_position keyword, you need to give either one value or a value for each replica.");
317 : }
318 :
319 79 : auto deleter=[](FILE* f) { fclose(f); };
320 40 : FILE* file_dummy = fopen("/dev/null","w+");
321 40 : plumed_assert(file_dummy);
322 : // call fclose when file_dummy_deleter goes out of scope
323 : std::unique_ptr<FILE,decltype(deleter)> file_dummy_deleter(file_dummy,deleter);
324 : // Note: this should be declared before plumed_bf to make sure the file is closed after plumed_bf has been destroyed
325 :
326 40 : auto plumed_bf = Tools::make_unique<PLMD::PlumedMain>();
327 40 : unsigned int nn=1;
328 80 : plumed_bf->cmd("setNatoms",&nn);
329 80 : plumed_bf->cmd("setLog",file_dummy);
330 80 : plumed_bf->cmd("init",&nn);
331 40 : std::vector<BasisFunctions*> basisf_pntrs(dim);
332 40 : std::vector<std::string> basisf_keywords(dim);
333 40 : std::vector<std::unique_ptr<Value>> args(dim);
334 40 : std::vector<bool> periodic(dim);
335 40 : std::vector<double> interval_min(dim);
336 40 : std::vector<double> interval_max(dim);
337 40 : std::vector<double> interval_range(dim);
338 88 : for(unsigned int i=0; i<dim; i++) {
339 : std::string bf_keyword;
340 48 : std::string is; Tools::convert(i+1,is);
341 96 : parse("basis_functions_"+is,bf_keyword);
342 48 : if(bf_keyword.size()==0) {
343 0 : error("basis_functions_"+is+" is needed");
344 : }
345 48 : if(bf_keyword.at(0)=='{' && bf_keyword.at(bf_keyword.size()-1)=='}') {
346 4 : bf_keyword = bf_keyword.substr(1,bf_keyword.size()-2);
347 : }
348 : basisf_keywords[i] = bf_keyword;
349 96 : plumed_bf->readInputLine(bf_keyword+" LABEL="+dim_string_prefix+is);
350 48 : basisf_pntrs[i] = plumed_bf->getActionSet().selectWithLabel<BasisFunctions*>(dim_string_prefix+is);
351 96 : args[i] = Tools::make_unique<Value>(nullptr,dim_string_prefix+is,false);
352 48 : args[i]->setNotPeriodic();
353 48 : periodic[i] = basisf_pntrs[i]->arePeriodic();
354 48 : interval_min[i] = basisf_pntrs[i]->intervalMin();
355 48 : interval_max[i] = basisf_pntrs[i]->intervalMax();
356 48 : interval_range[i] = basisf_pntrs[i]->intervalMax()-basisf_pntrs[i]->intervalMin();
357 : }
358 40 : Communicator comm_dummy;
359 80 : auto coeffs_pntr = Tools::make_unique<CoeffsVector>("pot.coeffs",Tools::unique2raw(args),basisf_pntrs,comm_dummy,false);
360 80 : potential_expansion_pntr = Tools::make_unique<LinearBasisSetExpansion>("potential",1.0/temp,comm_dummy,Tools::unique2raw(args),basisf_pntrs,coeffs_pntr.get());
361 :
362 40 : std::string template_coeffs_fname="";
363 80 : parse("template_coeffs_file",template_coeffs_fname);
364 40 : if(template_coeffs_fname.size()>0) {
365 1 : OFile ofile_coeffstmpl;
366 1 : ofile_coeffstmpl.link(pc);
367 1 : ofile_coeffstmpl.open(template_coeffs_fname);
368 1 : coeffs_pntr->writeToFile(ofile_coeffstmpl,true);
369 1 : ofile_coeffstmpl.close();
370 : std::printf("Only generating a template coefficient file - Should stop now.");
371 : return 0;
372 1 : }
373 :
374 39 : std::vector<std::string> input_coeffs_fnames(0);
375 78 : parseVector("input_coeffs",input_coeffs_fnames);
376 : std::string input_coeffs_fname;
377 : bool diff_input_coeffs = false;
378 39 : if(input_coeffs_fnames.size()==1) {
379 : input_coeffs_fname = input_coeffs_fnames[0];
380 : }
381 9 : else if(replicas > 1 && input_coeffs_fnames.size()==replicas) {
382 : diff_input_coeffs = true;
383 9 : input_coeffs_fname = input_coeffs_fnames[inter.Get_rank()];
384 : }
385 : else {
386 0 : error("problem with coeffs_file keyword, you need to give either one value or a value for each replica.");
387 : }
388 39 : coeffs_pntr->readFromFile(input_coeffs_fname,true,true);
389 39 : std::vector<double> coeffs_prefactors(0);
390 78 : parseVector("coeffs_prefactor",coeffs_prefactors);
391 39 : if(coeffs_prefactors.size()>0) {
392 : double coeffs_prefactor = 1.0;
393 7 : if(coeffs_prefactors.size()==1) {
394 3 : coeffs_prefactor = coeffs_prefactors[0];
395 : }
396 4 : else if(replicas > 1 && coeffs_prefactors.size()==replicas) {
397 : diff_input_coeffs = true;
398 4 : coeffs_prefactor = coeffs_prefactors[inter.Get_rank()];
399 : }
400 : else {
401 0 : error("problem with coeffs_prefactor keyword, you need to give either one value or a value for each replica.");
402 : }
403 7 : coeffs_pntr->scaleAllValues(coeffs_prefactor);
404 : }
405 : unsigned int pot_grid_bins;
406 78 : parse("output_potential_grid",pot_grid_bins);
407 39 : potential_expansion_pntr->setGridBins(pot_grid_bins);
408 39 : potential_expansion_pntr->setupBiasGrid(false);
409 39 : potential_expansion_pntr->updateBiasGrid();
410 39 : potential_expansion_pntr->setBiasMinimumToZero();
411 39 : potential_expansion_pntr->updateBiasGrid();
412 :
413 39 : OFile ofile_potential;
414 39 : ofile_potential.link(pc);
415 : std::string output_potential_fname;
416 39 : parse("output_potential",output_potential_fname);
417 39 : if(diff_input_coeffs) {
418 13 : ofile_potential.link(intra);
419 : std::string suffix;
420 13 : Tools::convert(inter.Get_rank(),suffix);
421 26 : output_potential_fname = FileBase::appendSuffix(output_potential_fname,"."+suffix);
422 : }
423 39 : ofile_potential.open(output_potential_fname);
424 39 : potential_expansion_pntr->writeBiasGridToFile(ofile_potential);
425 39 : ofile_potential.close();
426 39 : if(dim>1) {
427 21 : for(unsigned int i=0; i<dim; i++) {
428 14 : std::string is; Tools::convert(i+1,is);
429 14 : std::vector<std::string> proj_arg(1);
430 14 : proj_arg[0] = dim_string_prefix+is;
431 14 : auto Fw = Tools::make_unique<FesWeight>(1/temp);
432 14 : Grid proj_grid = (potential_expansion_pntr->getPntrToBiasGrid())->project(proj_arg,Fw.get());
433 14 : proj_grid.setMinToZero();
434 :
435 28 : std::string output_potential_proj_fname = FileBase::appendSuffix(output_potential_fname,"."+dim_string_prefix+is);
436 14 : OFile ofile_potential_proj;
437 14 : ofile_potential_proj.link(pc);
438 14 : ofile_potential_proj.open(output_potential_proj_fname);
439 14 : proj_grid.writeToFile(ofile_potential_proj);
440 14 : ofile_potential_proj.close();
441 28 : }
442 : }
443 :
444 :
445 39 : Grid histo_grid(*potential_expansion_pntr->getPntrToBiasGrid());
446 78 : std::vector<double> integration_weights = GridIntegrationWeights::getIntegrationWeights(&histo_grid);
447 : double norm=0.0;
448 169278 : for(Grid::index_t i=0; i<histo_grid.getSize(); i++) {
449 169239 : double value = integration_weights[i]*exp(-histo_grid.getValue(i)/temp);
450 169239 : norm += value;
451 169239 : histo_grid.setValue(i,value);
452 : }
453 39 : histo_grid.scaleAllValuesAndDerivatives(1.0/norm);
454 39 : OFile ofile_histogram;
455 39 : ofile_histogram.link(pc);
456 : std::string output_histogram_fname;
457 39 : parse("output_histogram",output_histogram_fname);
458 39 : if(diff_input_coeffs || temps_vec.size()>1) {
459 17 : ofile_histogram.link(intra);
460 : std::string suffix;
461 17 : Tools::convert(inter.Get_rank(),suffix);
462 34 : output_histogram_fname = FileBase::appendSuffix(output_histogram_fname,"."+suffix);
463 : }
464 39 : ofile_histogram.open(output_histogram_fname);
465 39 : histo_grid.writeToFile(ofile_histogram);
466 39 : ofile_histogram.close();
467 :
468 : std::string output_coeffs_fname;
469 78 : parse("output_coeffs",output_coeffs_fname);
470 : std::string output_coeffs_fmt;
471 78 : parse("output_coeffs_fmt",output_coeffs_fmt);
472 : coeffs_pntr->setOutputFmt(output_coeffs_fmt);
473 39 : OFile ofile_coeffsout;
474 39 : ofile_coeffsout.link(pc);
475 39 : if(diff_input_coeffs) {
476 13 : ofile_coeffsout.link(intra);
477 : std::string suffix;
478 13 : Tools::convert(inter.Get_rank(),suffix);
479 26 : output_coeffs_fname = FileBase::appendSuffix(output_coeffs_fname,"."+suffix);
480 : }
481 39 : ofile_coeffsout.open(output_coeffs_fname);
482 39 : coeffs_pntr->writeToFile(ofile_coeffsout,true);
483 39 : ofile_coeffsout.close();
484 :
485 39 : if(pc.Get_rank() == 0) {
486 15 : std::fprintf(out,"Replicas %zu\n",replicas);
487 : std::fprintf(out,"Cores per replica %u\n",coresPerReplica);
488 15 : std::fprintf(out,"Number of steps %u\n",nsteps);
489 15 : std::fprintf(out,"Timestep %f\n",tstep);
490 15 : std::fprintf(out,"Temperature %f",temps_vec[0]);
491 18 : for(unsigned int i=1; i<temps_vec.size(); i++) {std::fprintf(out,",%f",temps_vec[i]);}
492 : std::fprintf(out,"\n");
493 15 : std::fprintf(out,"Friction %f",frictions_vec[0]);
494 18 : for(unsigned int i=1; i<frictions_vec.size(); i++) {std::fprintf(out,",%f",frictions_vec[i]);}
495 : std::fprintf(out,"\n");
496 15 : std::fprintf(out,"Random seed %d",seeds_vec[0]);
497 38 : for(unsigned int i=1; i<seeds_vec.size(); i++) {std::fprintf(out,",%d",seeds_vec[i]);}
498 : std::fprintf(out,"\n");
499 15 : std::fprintf(out,"Dimensions %zu\n",dim);
500 34 : for(unsigned int i=0; i<dim; i++) {
501 19 : std::fprintf(out,"Basis Function %u %s\n",i+1,basisf_keywords[i].c_str());
502 : }
503 : std::fprintf(out,"PLUMED input %s",plumed_inputfiles[0].c_str());
504 16 : for(unsigned int i=1; i<plumed_inputfiles.size(); i++) {std::fprintf(out,",%s",plumed_inputfiles[i].c_str());}
505 : std::fprintf(out,"\n");
506 : std::fprintf(out,"kBoltzmann taken as 1, use NATURAL_UNITS in the plumed input\n");
507 15 : if(diff_input_coeffs) {std::fprintf(out,"using different coefficients for each replica\n");}
508 : }
509 :
510 :
511 78 : plumed=Tools::make_unique<PLMD::PlumedMain>();
512 :
513 :
514 :
515 39 : if(plumed) {
516 39 : int s=sizeof(double);
517 78 : plumed->cmd("setRealPrecision",&s);
518 39 : if(replicas>1) {
519 31 : if (Communicator::initialized()) {
520 93 : plumed->cmd("GREX setMPIIntracomm",&intra.Get_comm());
521 31 : if (intra.Get_rank()==0) {
522 93 : plumed->cmd("GREX setMPIIntercomm",&inter.Get_comm());
523 : }
524 62 : plumed->cmd("GREX init");
525 93 : plumed->cmd("setMPIComm",&intra.Get_comm());
526 : } else {
527 0 : error("More than 1 replica but no MPI");
528 : }
529 : } else {
530 12 : if(Communicator::initialized()) plumed->cmd("setMPIComm",&pc.Get_comm());
531 : }
532 : }
533 :
534 39 : std::string plumed_logfile = "plumed.log";
535 39 : std::string stats_filename = "stats.out";
536 39 : std::string plumed_input = plumed_inputfiles[0];
537 39 : if(inter.Get_size()>1) {
538 : std::string suffix;
539 31 : Tools::convert(inter.Get_rank(),suffix);
540 62 : plumed_logfile = FileBase::appendSuffix(plumed_logfile,"."+suffix);
541 62 : stats_filename = FileBase::appendSuffix(stats_filename,"."+suffix);
542 31 : if(plumed_inputfiles.size()>1) {
543 2 : plumed_input = plumed_inputfiles[inter.Get_rank()];
544 : }
545 : }
546 :
547 39 : if(plumed) {
548 78 : plumed->cmd("setNoVirial");
549 39 : int natoms=1;
550 78 : plumed->cmd("setNatoms",&natoms);
551 78 : plumed->cmd("setMDEngine","mdrunner_linearexpansion");
552 78 : plumed->cmd("setTimestep",&tstep);
553 78 : plumed->cmd("setPlumedDat",plumed_input.c_str());
554 78 : plumed->cmd("setLogFile",plumed_logfile.c_str());
555 78 : plumed->cmd("setKbT",&temp);
556 39 : double energyunits=1.0;
557 78 : plumed->cmd("setMDEnergyUnits",&energyunits);
558 78 : plumed->cmd("init");
559 : }
560 :
561 : // Setup random number generator
562 39 : random.setSeed(seed);
563 :
564 39 : double potential, therm_eng=0; std::vector<double> masses(1,1);
565 39 : std::vector<Vector> positions(1), velocities(1), forces(1);
566 85 : for(unsigned int k=0; k<dim; k++) {
567 46 : positions[0][k] = initPos[inter.Get_rank()][k];
568 46 : if(periodic[k]) {
569 4 : positions[0][k] = positions[0][k] - floor((positions[0][k]-interval_min[k])/interval_range[k])*interval_range[k];
570 : }
571 : else {
572 42 : if(positions[0][k]>interval_max[k]) {positions[0][k]=interval_max[k];}
573 42 : if(positions[0][k]<interval_min[k]) {positions[0][k]=interval_min[k];}
574 : }
575 : }
576 :
577 :
578 85 : for(unsigned k=0; k<dim; ++k) {
579 46 : velocities[0][k]=random.Gaussian() * sqrt( temp );
580 : }
581 :
582 39 : potential=calc_energy(positions,forces); double ttt=calc_temp(velocities);
583 :
584 39 : FILE* fp=fopen(stats_filename.c_str(),"w+");
585 : // call fclose when fp_deleter goes out of scope
586 : std::unique_ptr<FILE,decltype(deleter)> fp_deleter(fp,deleter);
587 :
588 39 : double conserved = potential+1.5*ttt+therm_eng;
589 : //std::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 );
590 39 : if( intra.Get_rank()==0 ) {
591 38 : std::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 );
592 : }
593 :
594 39 : if(plumed) {
595 39 : int step_tmp = 0;
596 78 : plumed->cmd("setStep",&step_tmp);
597 78 : plumed->cmd("setMasses",&masses[0]);
598 78 : plumed->cmd("setForces",&forces[0][0]);
599 78 : plumed->cmd("setEnergy",&potential);
600 78 : plumed->cmd("setPositions",&positions[0][0]);
601 78 : plumed->cmd("calc");
602 : }
603 :
604 3939 : for(unsigned int istep=0; istep<nsteps; ++istep) {
605 : //if( istep%20==0 && pc.Get_rank()==0 ) printf("Doing step %d\n",istep);
606 :
607 : // Langevin thermostat
608 3900 : double lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);
609 3900 : double lrand=sqrt((1.-lscale*lscale)*temp);
610 8500 : for(unsigned k=0; k<dim; ++k) {
611 4600 : therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];
612 4600 : velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();
613 4600 : therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];
614 : }
615 :
616 : // First step of velocity verlet
617 8500 : for(unsigned k=0; k<dim; ++k) {
618 4600 : velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];
619 4600 : positions[0][k] = positions[0][k] + tstep*velocities[0][k];
620 :
621 4600 : if(periodic[k]) {
622 400 : positions[0][k] = positions[0][k] - floor((positions[0][k]-interval_min[k])/interval_range[k])*interval_range[k];
623 : }
624 : else {
625 4200 : if(positions[0][k]>interval_max[k]) {
626 7 : positions[0][k]=interval_max[k];
627 7 : velocities[0][k]=-std::abs(velocities[0][k]);
628 : }
629 4200 : if(positions[0][k]<interval_min[k]) {
630 2 : positions[0][k]=interval_min[k];
631 2 : velocities[0][k]=-std::abs(velocities[0][k]);
632 : }
633 : }
634 : }
635 :
636 3900 : potential=calc_energy(positions,forces);
637 :
638 3900 : if(plumed) {
639 3900 : int istepplusone=istep+1;
640 3900 : plumedWantsToStop=0;
641 7800 : plumed->cmd("setStep",&istepplusone);
642 7800 : plumed->cmd("setMasses",&masses[0]);
643 7800 : plumed->cmd("setForces",&forces[0][0]);
644 7800 : plumed->cmd("setEnergy",&potential);
645 7800 : plumed->cmd("setPositions",&positions[0][0]);
646 7800 : plumed->cmd("setStopFlag",&plumedWantsToStop);
647 7800 : plumed->cmd("calc");
648 : //if(istep%2000==0) plumed->cmd("writeCheckPointFile");
649 3900 : if(plumedWantsToStop) nsteps=istep;
650 : }
651 :
652 : // Second step of velocity verlet
653 8500 : for(unsigned k=0; k<dim; ++k) {
654 4600 : velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];
655 : }
656 :
657 : // Langevin thermostat
658 3900 : lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);
659 3900 : lrand=sqrt((1.-lscale*lscale)*temp);
660 8500 : for(unsigned k=0; k<dim; ++k) {
661 4600 : therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];
662 4600 : velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();
663 4600 : therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];
664 : }
665 :
666 : // Print everything
667 3900 : ttt = calc_temp( velocities );
668 3900 : conserved = potential+1.5*ttt+therm_eng;
669 3900 : if( (intra.Get_rank()==0) && ((istep % stepWrite)==0) ) {
670 38 : std::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 );
671 : }
672 : }
673 :
674 : //printf("Rank: %d, Size: %d \n", pc.Get_rank(), pc.Get_size() );
675 : //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() );
676 :
677 : return 0;
678 395 : }
679 :
680 : }
681 : }
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