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 "core/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 :
46 : #ifdef __PLUMED_HAS_MPI
47 : #include <mpi.h>
48 : #endif
49 :
50 :
51 : namespace PLMD {
52 : namespace ves {
53 :
54 : //+PLUMEDOC TOOLS ves_md_linearexpansion
55 : /*
56 : Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion.
57 :
58 : This is simple MD code that allows running dynamics of a single particle on a
59 : potential energy surface given by some linear basis set expansion in one to three
60 : dimensions.
61 :
62 : It is possible to run more than one replica of the system in parallel.
63 :
64 : ## Examples
65 :
66 : In the following example we perform dynamics on the
67 : Wolfe-Quapp potential that is defined as
68 :
69 : $$
70 : U(x,y) = x^4 + y^4 - 2 x^2 - 4 y^2 + xy + 0.3 x + 0.1 y
71 : $$
72 :
73 : This function has minima at (-1.174,1.477); (-0.831,-1.366); (1.124,-1.486),
74 : a maxima at (0.100,0.050) and saddle points around (-1.013,-0.036); (0.093,0.174); (-0.208,-1.407).
75 :
76 : To define the potential we employ polynomial power basis
77 : functions ([BF_POWERS](BF_POWERS.md)). The input file is given as
78 :
79 : ```plumed
80 : #TOOL=ves_md_linearexpansion
81 : nstep 10000
82 : tstep 0.005
83 : temperature 1.0
84 : friction 10.0
85 : random_seed 4525
86 : plumed_input plumed.dat
87 : dimension 2
88 : replicas 1
89 : basis_functions_1 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0
90 : basis_functions_2 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0
91 : input_coeffs pot_coeffs_input.data
92 : initial_position -1.174,+1.477
93 : output_potential potential.data
94 : output_potential_grid 150
95 : output_histogram histogram.data
96 : ```
97 :
98 : This input is then run by using the following command.
99 :
100 : ```plumed
101 : plumed ves_md_linearexpansion input
102 : ```
103 :
104 : The corresponding pot_coeffs_input.data file is
105 :
106 : ````
107 : #! FIELDS idx_dim1 idx_dim2 pot.coeffs index description
108 : #! SET type LinearBasisSet
109 : #! SET ndimensions 2
110 : #! SET ncoeffs_total 25
111 : #! SET shape_dim1 5
112 : #! SET shape_dim2 5
113 : 0 0 0.0000000000000000e+00 0 1*1
114 : 1 0 0.3000000000000000e+00 1 s^1*1
115 : 2 0 -2.0000000000000000e+00 2 s^2*1
116 : 4 0 1.0000000000000000e+00 4 s^4*1
117 : 0 1 0.1000000000000000e+00 5 1*s^1
118 : 1 1 +1.0000000000000000e+00 6 s^1*s^1
119 : 0 2 -4.0000000000000000e+00 10 1*s^2
120 : 0 4 1.0000000000000000e+00 20 1*s^4
121 : #!-------------------
122 : ````
123 :
124 : One then uses the (x,y) position of the particle as CVs by using the [POSITION](POSITION.md)
125 : action as shown in the following PLUMED input
126 :
127 : ```plumed
128 : p: POSITION ATOM=1
129 : ene: ENERGY
130 : PRINT ARG=p.x,p.y,ene FILE=colvar.data FMT=%8.4f
131 : ```
132 :
133 :
134 :
135 : */
136 : //+ENDPLUMEDOC
137 :
138 : class MD_LinearExpansionPES : public PLMD::CLTool {
139 : public:
140 5 : std::string description() const override {
141 5 : return "MD of a one particle on a linear expansion PES";
142 : }
143 : static void registerKeywords( Keywords& keys );
144 : explicit MD_LinearExpansionPES( const CLToolOptions& co );
145 : int main( FILE* in, FILE* out, PLMD::Communicator& pc) override;
146 : private:
147 : size_t dim;
148 : std::string dim_string_prefix;
149 : std::unique_ptr<LinearBasisSetExpansion> potential_expansion_pntr;
150 : //
151 : double calc_energy( const std::vector<Vector>&, std::vector<Vector>& );
152 : double calc_temp( const std::vector<Vector>& );
153 : };
154 :
155 17094 : PLUMED_REGISTER_CLTOOL(MD_LinearExpansionPES,"ves_md_linearexpansion")
156 :
157 5683 : void MD_LinearExpansionPES::registerKeywords( Keywords& keys ) {
158 5683 : CLTool::registerKeywords( keys );
159 5683 : keys.add("compulsory","nstep","10","The number of steps of dynamics you want to run.");
160 5683 : keys.add("compulsory","tstep","0.005","The integration timestep.");
161 5683 : 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.");
162 5683 : keys.add("compulsory","friction","10.","The friction of the Langevin thermostat. For multiple replica you can give a separate value for each replica.");
163 5683 : keys.add("compulsory","random_seed","5293818","Value of random number seed.");
164 5683 : 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.");
165 5683 : keys.add("compulsory","dimension","1","Number of dimensions, supports 1 to 3.");
166 5683 : keys.add("compulsory","initial_position","Initial position of the particle. For multiple replica you can give a separate value for each replica.");
167 5683 : keys.add("compulsory","replicas","1","Number of replicas.");
168 5683 : keys.add("compulsory","basis_functions_1","Basis functions for dimension 1.");
169 5683 : keys.add("optional","basis_functions_2","Basis functions for dimension 2 if needed.");
170 5683 : keys.add("optional","basis_functions_3","Basis functions for dimension 3 if needed.");
171 5683 : 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.");
172 5683 : keys.add("compulsory","output_coeffs","potential-coeffs.out.data","Filename of the output coefficient file for the potential.");
173 5683 : keys.add("compulsory","output_coeffs_fmt","%30.16e","Format of the output coefficient file for the potential. Useful for regtests.");
174 5683 : keys.add("optional","coeffs_prefactor","prefactor for multiplying the coefficients with. For multiple replica you can give a separate value for each replica.");
175 5683 : keys.add("optional","template_coeffs_file","only generate a template coefficient file with the filename given and exit.");
176 5683 : keys.add("compulsory","output_potential_grid","100","The number of grid points used for the potential and histogram output files.");
177 5683 : keys.add("compulsory","output_potential","potential.data","Filename of the potential output file.");
178 5683 : keys.add("compulsory","output_histogram","histogram.data","Filename of the histogram output file.");
179 5683 : }
180 :
181 :
182 45 : MD_LinearExpansionPES::MD_LinearExpansionPES( const CLToolOptions& co ):
183 : CLTool(co),
184 45 : dim(0),
185 45 : dim_string_prefix("dim") {
186 45 : inputdata=inputType::ifile; //inputType::commandline;
187 45 : }
188 :
189 : inline
190 3939 : double MD_LinearExpansionPES::calc_energy( const std::vector<Vector>& pos, std::vector<Vector>& forces) {
191 3939 : std::vector<double> pos_tmp(dim);
192 3939 : std::vector<double> forces_tmp(dim,0.0);
193 8585 : for(unsigned int j=0; j<dim; ++j) {
194 4646 : pos_tmp[j]=pos[0][j];
195 : }
196 3939 : bool all_inside = true;
197 3939 : double potential = potential_expansion_pntr->getBiasAndForces(pos_tmp,all_inside,forces_tmp);
198 8585 : for(unsigned int j=0; j<dim; ++j) {
199 4646 : forces[0][j] = forces_tmp[j];
200 : }
201 3939 : return potential;
202 : }
203 :
204 :
205 : inline
206 : double MD_LinearExpansionPES::calc_temp( const std::vector<Vector>& vel) {
207 : double total_KE=0.0;
208 : //! Double the total kinetic energy of the system
209 8585 : for(unsigned int j=0; j<dim; ++j) {
210 4646 : total_KE+=vel[0][j]*vel[0][j];
211 : }
212 39 : return total_KE / (double) dim; // total_KE is actually 2*KE
213 : }
214 :
215 40 : int MD_LinearExpansionPES::main( FILE* in, FILE* out, PLMD::Communicator& pc) {
216 : int plumedWantsToStop;
217 40 : Random random;
218 : unsigned int stepWrite=1000;
219 :
220 40 : std::unique_ptr<PLMD::PlumedMain> plumed;
221 :
222 : size_t replicas;
223 : unsigned int coresPerReplica;
224 40 : parse("replicas",replicas);
225 40 : if(replicas==1) {
226 9 : coresPerReplica = pc.Get_size();
227 : } else {
228 31 : if(pc.Get_size()%replicas!=0) {
229 0 : error("the number of MPI processes is not a multiple of the number of replicas.");
230 : }
231 31 : coresPerReplica = pc.Get_size()/replicas;
232 : }
233 : // create intra and inter communicators
234 40 : Communicator intra, inter;
235 40 : if(Communicator::initialized()) {
236 33 : int iworld=(pc.Get_rank() / coresPerReplica);
237 33 : pc.Split(iworld,0,intra);
238 33 : pc.Split(intra.Get_rank(),0,inter);
239 : }
240 :
241 : long long unsigned int nsteps;
242 40 : parse("nstep",nsteps);
243 : double tstep;
244 40 : parse("tstep",tstep);
245 : // initialize to solve a cppcheck 1.86 warning
246 40 : double temp=0.0;
247 40 : std::vector<double> temps_vec(0);
248 80 : parseVector("temperature",temps_vec);
249 40 : if(temps_vec.size()==1) {
250 36 : temp = temps_vec[0];
251 4 : } else if(replicas > 1 && temps_vec.size()==replicas) {
252 4 : temp = temps_vec[inter.Get_rank()];
253 : } else {
254 0 : error("problem with temperature keyword, you need to give either one value or a value for each replica.");
255 : }
256 : //
257 : double friction;
258 40 : std::vector<double> frictions_vec(0);
259 80 : parseVector("friction",frictions_vec);
260 40 : if(frictions_vec.size()==1) {
261 36 : friction = frictions_vec[0];
262 4 : } else if(frictions_vec.size()==replicas) {
263 4 : friction = frictions_vec[inter.Get_rank()];
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) {
273 44 : seeds_vec[i] = -seeds_vec[i];
274 : }
275 : }
276 40 : if(replicas==1) {
277 9 : if(seeds_vec.size()>1) {
278 0 : error("problem with random_seed keyword, for a single replica you should only give one value");
279 : }
280 9 : seed = seeds_vec[0];
281 : } else {
282 31 : if(seeds_vec.size()!=1 && seeds_vec.size()!=replicas) {
283 0 : error("problem with random_seed keyword, for multiple replicas you should give either one value or a separate value for each replica");
284 : }
285 31 : if(seeds_vec.size()==1) {
286 27 : seeds_vec.resize(replicas);
287 109 : for(unsigned int i=1; i<seeds_vec.size(); i++) {
288 82 : seeds_vec[i] = seeds_vec[0] + i;
289 : }
290 : }
291 31 : seed = seeds_vec[inter.Get_rank()];
292 : }
293 :
294 : //
295 80 : parse("dimension",dim);
296 :
297 : std::vector<std::string> plumed_inputfiles;
298 80 : parseVector("plumed_input",plumed_inputfiles);
299 40 : if(plumed_inputfiles.size()!=1 && plumed_inputfiles.size()!=replicas) {
300 0 : error("in plumed_input you should either give one file or separate files for each replica.");
301 : }
302 :
303 40 : std::vector<Vector> initPos(replicas);
304 : std::vector<double> initPosTmp;
305 80 : parseVector("initial_position",initPosTmp);
306 40 : if(initPosTmp.size()==dim) {
307 48 : for(unsigned int i=0; i<replicas; i++) {
308 72 : for(unsigned int k=0; k<dim; k++) {
309 38 : initPos[i][k]=initPosTmp[k];
310 : }
311 : }
312 26 : } else if(initPosTmp.size()==dim*replicas) {
313 126 : for(unsigned int i=0; i<replicas; i++) {
314 216 : for(unsigned int k=0; k<dim; k++) {
315 116 : initPos[i][k]=initPosTmp[i*dim+k];
316 : }
317 : }
318 : } else {
319 0 : error("problem with initial_position keyword, you need to give either one value or a value for each replica.");
320 : }
321 :
322 : auto deleter=[](FILE* f) {
323 79 : fclose(f);
324 39 : };
325 40 : FILE* file_dummy = fopen("/dev/null","w+");
326 40 : plumed_assert(file_dummy);
327 : // call fclose when file_dummy_deleter goes out of scope
328 : std::unique_ptr<FILE,decltype(deleter)> file_dummy_deleter(file_dummy,deleter);
329 : // Note: this should be declared before plumed_bf to make sure the file is closed after plumed_bf has been destroyed
330 :
331 : auto plumed_bf = Tools::make_unique<PLMD::PlumedMain>();
332 40 : unsigned int nn=1;
333 40 : plumed_bf->cmd("setNatoms",&nn);
334 40 : plumed_bf->cmd("setLog",file_dummy);
335 40 : plumed_bf->cmd("init",&nn);
336 40 : std::vector<BasisFunctions*> basisf_pntrs(dim);
337 40 : std::vector<std::string> basisf_keywords(dim);
338 40 : std::vector<std::unique_ptr<Value>> args(dim);
339 40 : std::vector<bool> periodic(dim);
340 40 : std::vector<double> interval_min(dim);
341 40 : std::vector<double> interval_max(dim);
342 40 : std::vector<double> interval_range(dim);
343 88 : for(unsigned int i=0; i<dim; i++) {
344 : std::string bf_keyword;
345 : std::string is;
346 48 : Tools::convert(i+1,is);
347 96 : parse("basis_functions_"+is,bf_keyword);
348 48 : if(bf_keyword.size()==0) {
349 0 : error("basis_functions_"+is+" is needed");
350 : }
351 48 : if(bf_keyword.at(0)=='{' && bf_keyword.at(bf_keyword.size()-1)=='}') {
352 4 : bf_keyword = bf_keyword.substr(1,bf_keyword.size()-2);
353 : }
354 : basisf_keywords[i] = bf_keyword;
355 96 : plumed_bf->readInputLine(bf_keyword+" LABEL="+dim_string_prefix+is);
356 48 : basisf_pntrs[i] = plumed_bf->getActionSet().selectWithLabel<BasisFunctions*>(dim_string_prefix+is);
357 96 : args[i] = Tools::make_unique<Value>(nullptr,dim_string_prefix+is,false);
358 48 : args[i]->setNotPeriodic();
359 48 : periodic[i] = basisf_pntrs[i]->arePeriodic();
360 48 : interval_min[i] = basisf_pntrs[i]->intervalMin();
361 48 : interval_max[i] = basisf_pntrs[i]->intervalMax();
362 48 : interval_range[i] = basisf_pntrs[i]->intervalMax()-basisf_pntrs[i]->intervalMin();
363 : }
364 40 : Communicator comm_dummy;
365 80 : auto coeffs_pntr = Tools::make_unique<CoeffsVector>("pot.coeffs",Tools::unique2raw(args),basisf_pntrs,comm_dummy,false);
366 80 : potential_expansion_pntr = Tools::make_unique<LinearBasisSetExpansion>("potential",1.0/temp,comm_dummy,Tools::unique2raw(args),basisf_pntrs,coeffs_pntr.get());
367 :
368 40 : std::string template_coeffs_fname="";
369 80 : parse("template_coeffs_file",template_coeffs_fname);
370 40 : if(template_coeffs_fname.size()>0) {
371 1 : OFile ofile_coeffstmpl;
372 1 : ofile_coeffstmpl.link(pc);
373 1 : ofile_coeffstmpl.open(template_coeffs_fname);
374 1 : coeffs_pntr->writeToFile(ofile_coeffstmpl,true);
375 1 : ofile_coeffstmpl.close();
376 : std::printf("Only generating a template coefficient file - Should stop now.");
377 : return 0;
378 1 : }
379 :
380 39 : std::vector<std::string> input_coeffs_fnames(0);
381 78 : parseVector("input_coeffs",input_coeffs_fnames);
382 : std::string input_coeffs_fname;
383 : bool diff_input_coeffs = false;
384 39 : if(input_coeffs_fnames.size()==1) {
385 : input_coeffs_fname = input_coeffs_fnames[0];
386 9 : } else if(replicas > 1 && input_coeffs_fnames.size()==replicas) {
387 : diff_input_coeffs = true;
388 9 : input_coeffs_fname = input_coeffs_fnames[inter.Get_rank()];
389 : } else {
390 0 : error("problem with coeffs_file keyword, you need to give either one value or a value for each replica.");
391 : }
392 39 : coeffs_pntr->readFromFile(input_coeffs_fname,true,true);
393 39 : std::vector<double> coeffs_prefactors(0);
394 78 : parseVector("coeffs_prefactor",coeffs_prefactors);
395 39 : if(coeffs_prefactors.size()>0) {
396 : double coeffs_prefactor = 1.0;
397 7 : if(coeffs_prefactors.size()==1) {
398 3 : coeffs_prefactor = coeffs_prefactors[0];
399 4 : } else if(replicas > 1 && coeffs_prefactors.size()==replicas) {
400 : diff_input_coeffs = true;
401 4 : coeffs_prefactor = coeffs_prefactors[inter.Get_rank()];
402 : } else {
403 0 : error("problem with coeffs_prefactor keyword, you need to give either one value or a value for each replica.");
404 : }
405 7 : coeffs_pntr->scaleAllValues(coeffs_prefactor);
406 : }
407 : unsigned int pot_grid_bins;
408 78 : parse("output_potential_grid",pot_grid_bins);
409 39 : potential_expansion_pntr->setGridBins(pot_grid_bins);
410 39 : potential_expansion_pntr->setupBiasGrid(false);
411 39 : potential_expansion_pntr->updateBiasGrid();
412 39 : potential_expansion_pntr->setBiasMinimumToZero();
413 39 : potential_expansion_pntr->updateBiasGrid();
414 :
415 39 : OFile ofile_potential;
416 39 : ofile_potential.link(pc);
417 : std::string output_potential_fname;
418 39 : parse("output_potential",output_potential_fname);
419 39 : if(diff_input_coeffs) {
420 13 : ofile_potential.link(intra);
421 : std::string suffix;
422 13 : Tools::convert(inter.Get_rank(),suffix);
423 26 : output_potential_fname = FileBase::appendSuffix(output_potential_fname,"."+suffix);
424 : }
425 39 : ofile_potential.open(output_potential_fname);
426 39 : potential_expansion_pntr->writeBiasGridToFile(ofile_potential);
427 39 : ofile_potential.close();
428 39 : if(dim>1) {
429 21 : for(unsigned int i=0; i<dim; i++) {
430 : std::string is;
431 14 : Tools::convert(i+1,is);
432 14 : std::vector<std::string> proj_arg(1);
433 14 : proj_arg[0] = dim_string_prefix+is;
434 14 : auto Fw = Tools::make_unique<FesWeight>(1/temp);
435 14 : Grid proj_grid = (potential_expansion_pntr->getPntrToBiasGrid())->project(proj_arg,Fw.get());
436 14 : proj_grid.setMinToZero();
437 :
438 28 : std::string output_potential_proj_fname = FileBase::appendSuffix(output_potential_fname,"."+dim_string_prefix+is);
439 14 : OFile ofile_potential_proj;
440 14 : ofile_potential_proj.link(pc);
441 14 : ofile_potential_proj.open(output_potential_proj_fname);
442 14 : proj_grid.writeToFile(ofile_potential_proj);
443 14 : ofile_potential_proj.close();
444 28 : }
445 : }
446 :
447 :
448 39 : Grid histo_grid(*potential_expansion_pntr->getPntrToBiasGrid());
449 78 : std::vector<double> integration_weights = GridIntegrationWeights::getIntegrationWeights(&histo_grid);
450 : double norm=0.0;
451 169278 : for(Grid::index_t i=0; i<histo_grid.getSize(); i++) {
452 169239 : double value = integration_weights[i]*exp(-histo_grid.getValue(i)/temp);
453 169239 : norm += value;
454 169239 : histo_grid.setValue(i,value);
455 : }
456 39 : histo_grid.scaleAllValuesAndDerivatives(1.0/norm);
457 39 : OFile ofile_histogram;
458 39 : ofile_histogram.link(pc);
459 : std::string output_histogram_fname;
460 39 : parse("output_histogram",output_histogram_fname);
461 39 : if(diff_input_coeffs || temps_vec.size()>1) {
462 17 : ofile_histogram.link(intra);
463 : std::string suffix;
464 17 : Tools::convert(inter.Get_rank(),suffix);
465 34 : output_histogram_fname = FileBase::appendSuffix(output_histogram_fname,"."+suffix);
466 : }
467 39 : ofile_histogram.open(output_histogram_fname);
468 39 : histo_grid.writeToFile(ofile_histogram);
469 39 : ofile_histogram.close();
470 :
471 : std::string output_coeffs_fname;
472 78 : parse("output_coeffs",output_coeffs_fname);
473 : std::string output_coeffs_fmt;
474 78 : parse("output_coeffs_fmt",output_coeffs_fmt);
475 : coeffs_pntr->setOutputFmt(output_coeffs_fmt);
476 39 : OFile ofile_coeffsout;
477 39 : ofile_coeffsout.link(pc);
478 39 : if(diff_input_coeffs) {
479 13 : ofile_coeffsout.link(intra);
480 : std::string suffix;
481 13 : Tools::convert(inter.Get_rank(),suffix);
482 26 : output_coeffs_fname = FileBase::appendSuffix(output_coeffs_fname,"."+suffix);
483 : }
484 39 : ofile_coeffsout.open(output_coeffs_fname);
485 39 : coeffs_pntr->writeToFile(ofile_coeffsout,true);
486 39 : ofile_coeffsout.close();
487 :
488 39 : if(pc.Get_rank() == 0) {
489 15 : std::fprintf(out,"Replicas %zu\n",replicas);
490 : std::fprintf(out,"Cores per replica %u\n",coresPerReplica);
491 15 : std::fprintf(out,"Number of steps %llu\n",nsteps);
492 15 : std::fprintf(out,"Timestep %f\n",tstep);
493 15 : std::fprintf(out,"Temperature %f",temps_vec[0]);
494 18 : for(unsigned int i=1; i<temps_vec.size(); i++) {
495 3 : std::fprintf(out,",%f",temps_vec[i]);
496 : }
497 : std::fprintf(out,"\n");
498 15 : std::fprintf(out,"Friction %f",frictions_vec[0]);
499 18 : for(unsigned int i=1; i<frictions_vec.size(); i++) {
500 3 : std::fprintf(out,",%f",frictions_vec[i]);
501 : }
502 : std::fprintf(out,"\n");
503 15 : std::fprintf(out,"Random seed %d",seeds_vec[0]);
504 38 : for(unsigned int i=1; i<seeds_vec.size(); i++) {
505 23 : std::fprintf(out,",%d",seeds_vec[i]);
506 : }
507 : std::fprintf(out,"\n");
508 15 : std::fprintf(out,"Dimensions %zu\n",dim);
509 34 : for(unsigned int i=0; i<dim; i++) {
510 19 : std::fprintf(out,"Basis Function %u %s\n",i+1,basisf_keywords[i].c_str());
511 : }
512 : std::fprintf(out,"PLUMED input %s",plumed_inputfiles[0].c_str());
513 16 : for(unsigned int i=1; i<plumed_inputfiles.size(); i++) {
514 : std::fprintf(out,",%s",plumed_inputfiles[i].c_str());
515 : }
516 : std::fprintf(out,"\n");
517 : std::fprintf(out,"kBoltzmann taken as 1, use NATURAL_UNITS in the plumed input\n");
518 15 : if(diff_input_coeffs) {
519 : std::fprintf(out,"using different coefficients for each replica\n");
520 : }
521 : }
522 :
523 :
524 39 : plumed=Tools::make_unique<PLMD::PlumedMain>();
525 :
526 :
527 :
528 39 : if(plumed) {
529 39 : int s=sizeof(double);
530 39 : plumed->cmd("setRealPrecision",&s);
531 39 : if(replicas>1) {
532 31 : if (Communicator::initialized()) {
533 62 : plumed->cmd("GREX setMPIIntracomm",&intra.Get_comm());
534 31 : if (intra.Get_rank()==0) {
535 62 : plumed->cmd("GREX setMPIIntercomm",&inter.Get_comm());
536 : }
537 31 : plumed->cmd("GREX init");
538 62 : plumed->cmd("setMPIComm",&intra.Get_comm());
539 : } else {
540 0 : error("More than 1 replica but no MPI");
541 : }
542 : } else {
543 8 : if(Communicator::initialized()) {
544 4 : plumed->cmd("setMPIComm",&pc.Get_comm());
545 : }
546 : }
547 : }
548 :
549 39 : std::string plumed_logfile = "plumed.log";
550 39 : std::string stats_filename = "stats.out";
551 39 : std::string plumed_input = plumed_inputfiles[0];
552 39 : if(inter.Get_size()>1) {
553 : std::string suffix;
554 31 : Tools::convert(inter.Get_rank(),suffix);
555 62 : plumed_logfile = FileBase::appendSuffix(plumed_logfile,"."+suffix);
556 62 : stats_filename = FileBase::appendSuffix(stats_filename,"."+suffix);
557 31 : if(plumed_inputfiles.size()>1) {
558 2 : plumed_input = plumed_inputfiles[inter.Get_rank()];
559 : }
560 : }
561 :
562 39 : if(plumed) {
563 39 : int natoms=1;
564 39 : plumed->cmd("setNatoms",&natoms);
565 39 : plumed->cmd("setNoVirial");
566 39 : plumed->cmd("setMDEngine","mdrunner_linearexpansion");
567 39 : plumed->cmd("setTimestep",&tstep);
568 39 : plumed->cmd("setPlumedDat",plumed_input.c_str());
569 39 : plumed->cmd("setLogFile",plumed_logfile.c_str());
570 39 : plumed->cmd("setKbT",&temp);
571 39 : double energyunits=1.0;
572 39 : plumed->cmd("setMDEnergyUnits",&energyunits);
573 39 : plumed->cmd("init");
574 : }
575 :
576 : // Setup random number generator
577 39 : random.setSeed(seed);
578 :
579 : double potential, therm_eng=0;
580 39 : std::vector<double> masses(1,1);
581 39 : std::vector<Vector> positions(1), velocities(1), forces(1);
582 85 : for(unsigned int k=0; k<dim; k++) {
583 46 : positions[0][k] = initPos[inter.Get_rank()][k];
584 46 : if(periodic[k]) {
585 4 : positions[0][k] = positions[0][k] - floor((positions[0][k]-interval_min[k])/interval_range[k])*interval_range[k];
586 : } else {
587 42 : if(positions[0][k]>interval_max[k]) {
588 7 : positions[0][k]=interval_max[k];
589 : }
590 42 : if(positions[0][k]<interval_min[k]) {
591 1 : positions[0][k]=interval_min[k];
592 : }
593 : }
594 : }
595 :
596 :
597 85 : for(unsigned k=0; k<dim; ++k) {
598 46 : velocities[0][k]=random.Gaussian() * sqrt( temp );
599 : }
600 :
601 39 : potential=calc_energy(positions,forces);
602 : double ttt=calc_temp(velocities);
603 :
604 39 : FILE* fp=fopen(stats_filename.c_str(),"w+");
605 : // call fclose when fp_deleter goes out of scope
606 : std::unique_ptr<FILE,decltype(deleter)> fp_deleter(fp,deleter);
607 :
608 39 : double conserved = potential+1.5*ttt+therm_eng;
609 : //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 );
610 39 : if( intra.Get_rank()==0 ) {
611 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 );
612 : }
613 :
614 39 : if(plumed) {
615 39 : long long unsigned int step_tmp = 0;
616 39 : plumed->cmd("setStepLongLong",&step_tmp);
617 39 : plumed->cmd("setMasses",&masses[0]);
618 39 : plumed->cmd("setForces",&forces[0][0]);
619 39 : plumed->cmd("setEnergy",&potential);
620 39 : plumed->cmd("setPositions",&positions[0][0]);
621 39 : plumed->cmd("calc");
622 : }
623 :
624 3939 : for(long long unsigned int istep=0; istep<nsteps; ++istep) {
625 : //if( istep%20==0 && pc.Get_rank()==0 ) printf("Doing step %llu\n",istep);
626 :
627 : // Langevin thermostat
628 3900 : double lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);
629 3900 : double lrand=sqrt((1.-lscale*lscale)*temp);
630 8500 : for(unsigned k=0; k<dim; ++k) {
631 4600 : therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];
632 4600 : velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();
633 4600 : therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];
634 : }
635 :
636 : // First step of velocity verlet
637 8500 : for(unsigned k=0; k<dim; ++k) {
638 4600 : velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];
639 4600 : positions[0][k] = positions[0][k] + tstep*velocities[0][k];
640 :
641 4600 : if(periodic[k]) {
642 400 : positions[0][k] = positions[0][k] - floor((positions[0][k]-interval_min[k])/interval_range[k])*interval_range[k];
643 : } else {
644 4200 : if(positions[0][k]>interval_max[k]) {
645 7 : positions[0][k]=interval_max[k];
646 7 : velocities[0][k]=-std::abs(velocities[0][k]);
647 : }
648 4200 : if(positions[0][k]<interval_min[k]) {
649 2 : positions[0][k]=interval_min[k];
650 2 : velocities[0][k]=-std::abs(velocities[0][k]);
651 : }
652 : }
653 : }
654 :
655 3900 : potential=calc_energy(positions,forces);
656 :
657 3900 : if(plumed) {
658 3900 : long long unsigned int istepplusone=istep+1;
659 3900 : plumedWantsToStop=0;
660 3900 : plumed->cmd("setStepLongLong",&istepplusone);
661 3900 : plumed->cmd("setMasses",&masses[0]);
662 3900 : plumed->cmd("setForces",&forces[0][0]);
663 3900 : plumed->cmd("setEnergy",&potential);
664 3900 : plumed->cmd("setPositions",&positions[0][0]);
665 3900 : plumed->cmd("setStopFlag",&plumedWantsToStop);
666 3900 : plumed->cmd("calc");
667 : //if(istep%2000==0) plumed->cmd("writeCheckPointFile");
668 3900 : if(plumedWantsToStop) {
669 0 : nsteps=istep;
670 : }
671 : }
672 :
673 : // Second step of velocity verlet
674 8500 : for(unsigned k=0; k<dim; ++k) {
675 4600 : velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];
676 : }
677 :
678 : // Langevin thermostat
679 3900 : lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);
680 3900 : lrand=sqrt((1.-lscale*lscale)*temp);
681 8500 : for(unsigned k=0; k<dim; ++k) {
682 4600 : therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];
683 4600 : velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();
684 4600 : therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];
685 : }
686 :
687 : // Print everything
688 : ttt = calc_temp( velocities );
689 3900 : conserved = potential+1.5*ttt+therm_eng;
690 3900 : if( (intra.Get_rank()==0) && ((istep % stepWrite)==0) ) {
691 38 : std::fprintf(fp,"%llu %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 );
692 : }
693 : }
694 :
695 : //printf("Rank: %d, Size: %d \n", pc.Get_rank(), pc.Get_size() );
696 : //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() );
697 :
698 : return 0;
699 395 : }
700 :
701 : }
702 : }
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