Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2017 of Haochuan Chen (excluding colvar_UIestimator.h)
3 : Copyright (c) 2017 of Haohao Fu (colvar_UIestimator.h)
4 :
5 : This program is free software: you can redistribute it and/or modify
6 : it under the terms of the GNU Lesser General Public License as published
7 : by the Free Software Foundation, either version 3 of the License, or
8 : (at your option) any later version.
9 :
10 : This program is distributed in the hope that it will be useful,
11 : but WITHOUT ANY WARRANTY; without even the implied warranty of
12 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 : GNU Lesser General Public License for more details.
14 :
15 : You should have received a copy of the GNU Lesser General Public License
16 : along with this program. If not, see <http://www.gnu.org/licenses/>.
17 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
18 : #ifdef __PLUMED_HAS_BOOST_SERIALIZATION
19 : #include "core/ActionRegister.h"
20 : #include "bias/Bias.h"
21 : #include "core/PlumedMain.h"
22 : #include "DRR.h"
23 : #include "tools/Random.h"
24 : #include "tools/Tools.h"
25 : #include "colvar_UIestimator.h"
26 :
27 : #include <boost/archive/binary_iarchive.hpp>
28 : #include <boost/archive/binary_oarchive.hpp>
29 : #include <boost/serialization/vector.hpp>
30 : #include <cmath>
31 : #include <fstream>
32 : #include <iomanip>
33 : #include <iostream>
34 : #include <limits>
35 : #include <random>
36 : #include <string>
37 :
38 : using namespace PLMD;
39 : using namespace bias;
40 : using namespace std;
41 :
42 : namespace PLMD {
43 : namespace drr {
44 :
45 : //+PLUMEDOC EABFMOD_BIAS DRR
46 : /*
47 : Used to performed extended-system adaptive biasing force(eABF)
48 :
49 : This method was introduced in \cite Lelievre2007. It is used
50 : on one or more collective variables. This method is also
51 : called dynamic reference restraining(DRR) \cite Zheng2012 . A detailed description
52 : of this module can be found at \cite Chen2018 .
53 :
54 : For each collective variable \f$\xi_i\f$, a fictitious variable \f$\lambda_i\f$
55 : is attached through a spring. The fictitious variable \f$\lambda_i\f$ undergoes
56 : overdamped Langevin dynamics just like \ref EXTENDED_LAGRANGIAN. The ABF
57 : algorithm applies bias force on \f$\lambda_i\f$. The bias force acts on
58 : \f$\lambda_i\f$ is the negative average spring force on \f$\lambda_i\f$, which
59 : enhances the sampling of \f$\lambda_i\f$.
60 :
61 : \f[
62 : F_{bias}(\lambda_i)=k(\lambda_i-\langle\xi_i\rangle_{\lambda_i})
63 : \f]
64 :
65 : If spring force constant k is large enough, then \f$\xi_i\f$ synchronizes with
66 : \f$\lambda_i\f$. The naive(ABF) estimator is just the negative
67 : average spring force of \f$\lambda_i\f$.
68 :
69 : The naive(ABF) estimator is biased. There are unbiased estimators such as
70 : CZAR(Corrected z-averaged restraint) \cite Lesage2016 and UI(Umbrella
71 : Integration).
72 : The CZAR estimates the gradients as:
73 :
74 : \f[
75 : \frac{\partial{A}}{\partial{\xi_i}}\left({\xi}\right)=-\frac{1}{\beta}\frac{\partial\ln\tilde{\rho}\left(\xi\right)}{\partial{\xi_i}}+k\left(\langle\lambda_i\rangle_\xi-\xi_i\right)
76 : \f]
77 :
78 : The UI estimates the gradients as:
79 : \f[
80 : A'(\xi^*)=\frac{{\sum_\lambda}N\left(\xi^*,\lambda\right)\left[\frac{\xi^*-\langle\xi\rangle_\lambda}{\beta\sigma_\lambda^2}-k(\xi^*-\lambda)\right]}{{\sum_\lambda}N\left(\xi^*,\lambda\right)}
81 : \f]
82 :
83 : The code performing UI(colvar_UIestimator.h) is contributed by Haohao Fu \cite Fu2016 .
84 : It may be slow. I only change the Boltzmann constant and output
85 : precision in it. For new version and issues, please see:
86 : https://github.com/fhh2626/colvars
87 :
88 : After running eABF/DRR, the \ref drr_tool utility can be used to extract the gradients and counts files from .drrstate. Naive(ABF) estimator's result is in .abf.grad and .abf.count files and CZAR estimator's result is in .czar.grad and .czar.count files. The additional .zcount and .zgrad files contain the number of samples of \f$\boldsymbol{\xi}\f$, and the negative of \f$\boldsymbol{\xi}\f$-averaged spring forces, respectively, which are mainly for inspecting and debugging purpose. To get PMF, the abf_integrate(https://github.com/Colvars/colvars/tree/master/colvartools) is useful for numerically integrating the .czar.grad file.
89 :
90 : \par Examples
91 :
92 : The following input tells plumed to perform a eABF/DRR simulation on two
93 : torsional angles.
94 : \plumedfile
95 : phi: TORSION ATOMS=5,7,9,15
96 : psi: TORSION ATOMS=7,9,15,17
97 :
98 : DRR ...
99 : LABEL=eabf
100 : ARG=phi,psi
101 : FULLSAMPLES=500
102 : GRID_MIN=-pi,-pi
103 : GRID_MAX=pi,pi
104 : GRID_BIN=180,180
105 : FRICTION=8.0,8.0
106 : TAU=0.5,0.5
107 : OUTPUTFREQ=50000
108 : HISTORYFREQ=500000
109 : ... DRR
110 :
111 : # monitor the two variables, their fictitious variables and applied forces.
112 : PRINT STRIDE=10 ARG=phi,psi,eabf.phi_fict,eabf.psi_fict,eabf.phi_biasforce,eabf.psi_biasforce FILE=COLVAR
113 : \endplumedfile
114 :
115 : The following input tells plumed to perform a eABF/DRR simulation on the
116 : distance of atom 10 and 92. The distance is restraint by \ref LOWER_WALLS and
117 : \ref UPPER_WALLS.
118 : \plumedfile
119 : dist1: DISTANCE ATOMS=10,92
120 : eabf_winall: DRR ARG=dist1 FULLSAMPLES=2000 GRID_MIN=1.20 GRID_MAX=3.20 GRID_BIN=200 FRICTION=8.0 TAU=0.5 OUTPUTFREQ=5000 HISTORYFREQ=500000
121 : uwall: UPPER_WALLS ARG=eabf_winall.dist1_fict AT=3.2 KAPPA=418.4
122 : lwall: LOWER_WALLS ARG=eabf_winall.dist1_fict AT=1.2 KAPPA=418.4
123 : PRINT STRIDE=10 ARG=dist1,eabf_winall.dist1_fict,eabf_winall.dist1_biasforce FILE=COLVAR
124 : \endplumedfile
125 :
126 : It's also possible to run extended generalized adaptive biasing force (egABF) described in \cite Zhao2017 .
127 : An egABF example:
128 : \plumedfile
129 : phi: TORSION ATOMS=5,7,9,15
130 : psi: TORSION ATOMS=7,9,15,17
131 :
132 : DRR ...
133 : LABEL=gabf_phi
134 : ARG=phi
135 : FULLSAMPLES=500
136 : GRID_MIN=-pi
137 : GRID_MAX=pi
138 : GRID_BIN=180
139 : FRICTION=8.0
140 : TAU=0.5
141 : OUTPUTFREQ=50000
142 : HISTORYFREQ=500000
143 : ... DRR
144 :
145 : DRR ...
146 : LABEL=gabf_psi
147 : ARG=psi
148 : FULLSAMPLES=500
149 : GRID_MIN=-pi
150 : GRID_MAX=pi
151 : GRID_BIN=180
152 : FRICTION=8.0
153 : TAU=0.5
154 : OUTPUTFREQ=50000
155 : HISTORYFREQ=500000
156 : ... DRR
157 :
158 : DRR ...
159 : LABEL=gabf_2d
160 : ARG=phi,psi
161 : EXTERNAL_FORCE=gabf_phi.phi_springforce,gabf_psi.psi_springforce
162 : EXTERNAL_FICT=gabf_phi.phi_fictNoPBC,gabf_psi.psi_fictNoPBC
163 : GRID_MIN=-pi,-pi
164 : GRID_MAX=pi,pi
165 : GRID_BIN=180,180
166 : NOBIAS
167 : OUTPUTFREQ=50000
168 : HISTORYFREQ=500000
169 : ... DRR
170 :
171 : PRINT STRIDE=10 ARG=phi,psi FILE=COLVAR
172 : \endplumedfile
173 :
174 : */
175 : //+ENDPLUMEDOC
176 :
177 : using std::vector;
178 : using std::string;
179 :
180 : class DynamicReferenceRestraining : public Bias {
181 : private:
182 : bool firsttime;
183 : bool nobias;
184 : vector<double> fictNoPBC;
185 : vector<double> real;
186 : vector<double> springlength; // spring lengths
187 : vector<double> fict; // coordinates of extended variables
188 : vector<double> vfict; // velocities of extended variables
189 : vector<double> vfict_laststep;
190 : vector<double> ffict; // forces exerted on extended variables
191 : vector<double> fbias; // bias forces from eABF
192 : vector<double> kappa;
193 : vector<double> tau;
194 : vector<double> friction;
195 : vector<double> etemp;
196 : vector<double> ffict_measured;
197 : vector<double> force_external;
198 : vector<double> fict_external;
199 : vector<Value *> biasforceValue;
200 : vector<Value *> springforceValue;
201 : vector<Value *> fictValue;
202 : vector<Value *> vfictValue;
203 : vector<Value *> fictNoPBCValue;
204 : vector<Value *> externalForceValue;
205 : vector<Value *> externalFictValue;
206 : vector<double> c1;
207 : vector<double> c2;
208 : vector<double> mass;
209 : vector<DRRAxis> delim;
210 : string outputname;
211 : string cptname;
212 : string outputprefix;
213 : string fmt_;
214 : const size_t ndims;
215 : double dt;
216 : double kbt;
217 : double outputfreq;
218 : double historyfreq;
219 : bool isRestart;
220 : bool useCZARestimator;
221 : bool useUIestimator;
222 : bool mergeHistoryFiles;
223 : bool textoutput;
224 : bool withExternalForce;
225 : bool withExternalFict;
226 : vector<unsigned> reflectingWall;
227 : ABF ABFGrid;
228 : CZAR CZARestimator;
229 : double fullsamples;
230 : vector<double> maxFactors;
231 : UIestimator::UIestimator eabf_UI;
232 : Random rand;
233 :
234 : public:
235 : explicit DynamicReferenceRestraining(const ActionOptions &);
236 : void calculate();
237 : void update();
238 : void save(const string &filename, long long int step);
239 : void load(const string &filename);
240 : void backupFile(const string &filename);
241 : static void registerKeywords(Keywords &keys);
242 : bool is_file_exist(const char *fileName);
243 : };
244 :
245 : PLUMED_REGISTER_ACTION(DynamicReferenceRestraining, "DRR")
246 :
247 14 : void DynamicReferenceRestraining::registerKeywords(Keywords &keys) {
248 14 : Bias::registerKeywords(keys);
249 14 : keys.use("ARG");
250 28 : keys.add("optional", "KAPPA", "specifies that the restraint is harmonic and "
251 : "what the values of the force constants on "
252 : "each of the variables are (default to "
253 : "k_BT/(GRID_SPACING)^2)");
254 28 : keys.add("compulsory", "TAU", "0.5", "specifies relaxation time on each of "
255 : "variables are, similar to "
256 : "extended Time Constant in Colvars");
257 28 : keys.add("compulsory", "FRICTION", "8.0",
258 : "add a friction to the variable, similar to extended Langevin Damping "
259 : "in Colvars");
260 28 : keys.add("compulsory", "GRID_MIN", "the lower bounds for the grid (GRID_BIN "
261 : "or GRID_SPACING should be specified)");
262 28 : keys.add("compulsory", "GRID_MAX", "the upper bounds for the grid (GRID_BIN "
263 : "or GRID_SPACING should be specified)");
264 28 : keys.add("compulsory", "REFLECTINGWALL", "0", "whether add reflecting walls "
265 : "for each CV at GRID_MIN and GRID_MAX. Setting non-zero values will "
266 : "enable this feature");
267 28 : keys.add("optional", "GRID_BIN", "the number of bins for the grid");
268 28 : keys.add("optional", "GRID_SPACING", "the approximate grid spacing (to be "
269 : "used as an alternative or together "
270 : "with GRID_BIN)");
271 28 : keys.add("optional", "ZGRID_MIN", "the lower bounds for the grid (ZGRID_BIN"
272 : " or ZGRID_SPACING should be specified)");
273 28 : keys.add("optional", "ZGRID_MAX", "the upper bounds for the grid (ZGRID_BIN"
274 : " or ZGRID_SPACING should be specified)");
275 28 : keys.add("optional", "ZGRID_BIN", "the number of bins for the grid");
276 28 : keys.add("optional", "ZGRID_SPACING", "the approximate grid spacing (to be "
277 : "used as an alternative or together "
278 : "with ZGRID_BIN)");
279 28 : keys.add("optional", "EXTERNAL_FORCE", "use forces from other action instead"
280 : " of internal spring force, this disable the extended system!");
281 28 : keys.add("optional", "EXTERNAL_FICT", "position of external fictitious "
282 : "particles, useful for UIESTIMATOR");
283 28 : keys.add("compulsory", "FULLSAMPLES", "500",
284 : "number of samples in a bin prior to application of the ABF");
285 28 : keys.add("compulsory", "MAXFACTOR", "1.0",
286 : "maximum scaling factor of biasing force");
287 28 : keys.add("compulsory", "OUTPUTFREQ", "write results to a file every N steps");
288 28 : keys.add("optional", "HISTORYFREQ", "save history to a file every N steps");
289 28 : keys.addFlag("NOCZAR", false, "disable the CZAR estimator");
290 28 : keys.addFlag("UI", false,
291 : "enable the umbrella integration estimator");
292 28 : keys.add("optional", "UIRESTARTPREFIX",
293 : "specify the restart files for umbrella integration");
294 28 : keys.add("optional", "OUTPUTPREFIX",
295 : "specify the output prefix (default to the label name)");
296 28 : keys.add("optional", "TEMP", "the system temperature - needed when FRICTION "
297 : "is present. If not provided will be taken from "
298 : "MD code (if available)");
299 28 : keys.add(
300 : "optional", "EXTTEMP",
301 : "the temperature of extended variables (default to system temperature)");
302 28 : keys.add("optional", "DRR_RFILE",
303 : "specifies the restart file (.drrstate file)");
304 28 : keys.addFlag("NOBIAS", false, "DO NOT apply bias forces.");
305 28 : keys.addFlag("TEXTOUTPUT", false, "use text output for grad and count files "
306 : "instead of boost::serialization binary "
307 : "output");
308 28 : keys.addFlag("MERGEHISTORYFILES", false, "output all historic results "
309 : "to a single file rather than multiple .drrstate files. "
310 : "This option is effective only when textOutput is on.");
311 28 : keys.add("optional","FMT","specify format for outfiles files (useful for decrease the number of digits in regtests)");
312 28 : keys.addOutputComponent(
313 : "_fict", "default",
314 : "one or multiple instances of this quantity can be referenced "
315 : "elsewhere in the input file. "
316 : "These quantities will named with the arguments of the bias followed by "
317 : "the character string _tilde. It is possible to add forces on these "
318 : "variable.");
319 28 : keys.addOutputComponent(
320 : "_vfict", "default",
321 : "one or multiple instances of this quantity can be referenced "
322 : "elsewhere in the input file. "
323 : "These quantities will named with the arguments of the bias followed by "
324 : "the character string _tilde. It is NOT possible to add forces on these "
325 : "variable.");
326 28 : keys.addOutputComponent(
327 : "_biasforce", "default",
328 : "The bias force from eABF/DRR of the fictitious particle.");
329 28 : keys.addOutputComponent("_springforce", "default", "Spring force between real CVs and extended CVs");
330 28 : keys.addOutputComponent("_fictNoPBC", "default",
331 : "the positions of fictitious particles (without PBC).");
332 14 : }
333 :
334 12 : DynamicReferenceRestraining::DynamicReferenceRestraining(
335 12 : const ActionOptions &ao)
336 12 : : PLUMED_BIAS_INIT(ao), firsttime(true), nobias(false),
337 12 : fictNoPBC(getNumberOfArguments(), 0.0), real(getNumberOfArguments(), 0.0),
338 12 : springlength(getNumberOfArguments(), 0.0),
339 12 : fict(getNumberOfArguments(), 0.0), vfict(getNumberOfArguments(), 0.0),
340 12 : vfict_laststep(getNumberOfArguments(), 0.0),
341 12 : ffict(getNumberOfArguments(), 0.0), fbias(getNumberOfArguments(), 0.0),
342 12 : kappa(getNumberOfArguments(), 0.0), tau(getNumberOfArguments(), 0.0),
343 12 : friction(getNumberOfArguments(), 0.0), etemp(getNumberOfArguments(), 0.0),
344 12 : ffict_measured(getNumberOfArguments(), 0.0),
345 12 : biasforceValue(getNumberOfArguments(), NULL),
346 12 : springforceValue(getNumberOfArguments(), NULL),
347 12 : fictValue(getNumberOfArguments(), NULL),
348 12 : vfictValue(getNumberOfArguments(), NULL),
349 12 : fictNoPBCValue(getNumberOfArguments(), NULL),
350 12 : externalForceValue(getNumberOfArguments(), NULL),
351 12 : externalFictValue(getNumberOfArguments(), NULL),
352 12 : c1(getNumberOfArguments(), 0.0),
353 12 : c2(getNumberOfArguments(), 0.0), mass(getNumberOfArguments(), 0.0),
354 12 : delim(getNumberOfArguments()), outputname(""), cptname(""),
355 12 : outputprefix(""), fmt_("%.9f"), ndims(getNumberOfArguments()), dt(0.0), kbt(0.0),
356 12 : outputfreq(0.0), historyfreq(-1.0), isRestart(false),
357 12 : useCZARestimator(true), useUIestimator(false), mergeHistoryFiles(false),
358 12 : textoutput(false), withExternalForce(false), withExternalFict(false),
359 12 : reflectingWall(getNumberOfArguments(), 0),
360 36 : maxFactors(getNumberOfArguments(), 1.0) {
361 12 : log << "eABF/DRR: You now are using the extended adaptive biasing "
362 : "force(eABF) method."
363 12 : << '\n';
364 12 : log << "eABF/DRR: Some people also refer to it as dynamic reference "
365 : "restraining(DRR) method."
366 12 : << '\n';
367 12 : log << "eABF/DRR: Currently the CZAR and naive(ABF on extended variables) "
368 : "estimator is enabled by default."
369 12 : << '\n';
370 12 : log << "eABF/DRR: For reasons of performance, the umbrella integration "
371 : "estimator is not enabled by default."
372 12 : << '\n';
373 12 : log << "eABF/DRR: This method is originally implemented in "
374 : "colvars(https://github.com/colvars/colvars)."
375 12 : << '\n';
376 12 : log << "eABF/DRR: The code in plumed is heavily modified from "
377 : "ExtendedLagrangian.cpp and doesn't implemented all variants of "
378 : "eABF/DRR."
379 12 : << '\n';
380 12 : log << "eABF/DRR: The thermostat used here may be different from Colvars."
381 12 : << '\n';
382 12 : log << "eABF/DRR: To integrate the gradients file, you can use abf_integrate "
383 : "from https://github.com/colvars/colvars/tree/master/colvartools."
384 12 : << '\n';
385 12 : log << "eABF/DRR: Please read relevant articles and use this biasing "
386 : "method carefully!"
387 12 : << '\n';
388 12 : parseFlag("NOBIAS", nobias);
389 12 : parseFlag("UI", useUIestimator);
390 12 : bool noCZAR = false;
391 12 : parseFlag("NOCZAR", noCZAR);
392 : // noCZAR == false ? useCZARestimator = true : useCZARestimator = false;
393 12 : parseFlag("TEXTOUTPUT", textoutput);
394 12 : parseFlag("MERGEHISTORYFILES", mergeHistoryFiles);
395 12 : parseVector("TAU", tau);
396 12 : parseVector("FRICTION", friction);
397 12 : parseVector("EXTTEMP", etemp);
398 12 : parseVector("KAPPA", kappa);
399 12 : parseVector("REFLECTINGWALL", reflectingWall);
400 12 : parse("FULLSAMPLES", fullsamples);
401 12 : parseVector("MAXFACTOR", maxFactors);
402 12 : parse("OUTPUTFREQ", outputfreq);
403 12 : parse("HISTORYFREQ", historyfreq);
404 24 : parse("OUTPUTPREFIX", outputprefix);
405 : string restart_prefix;
406 24 : parse("DRR_RFILE", restart_prefix);
407 : string uirprefix;
408 12 : parse("UIRESTARTPREFIX", uirprefix);
409 12 : parseArgumentList("EXTERNAL_FORCE", externalForceValue);
410 12 : parseArgumentList("EXTERNAL_FICT", externalFictValue);
411 24 : parse("FMT",fmt_);
412 12 : if (externalForceValue.empty()) {
413 11 : withExternalForce = false;
414 1 : } else if (externalForceValue.size() != ndims) {
415 0 : error("eABF/DRR: Number of forces doesn't match ARGS!");
416 : } else {
417 1 : withExternalForce = true;
418 : }
419 12 : if (withExternalForce && useUIestimator) {
420 1 : if (externalFictValue.empty()) {
421 0 : error("eABF/DRR: No external fictitious particles specified. UI estimator needs it.");
422 1 : } else if(externalFictValue.size() != ndims) {
423 0 : error("eABF/DRR: Number of fictitious particles doesn't match ARGS!");
424 : } else {
425 1 : withExternalFict = true;
426 : }
427 : }
428 12 : kbt = getkBT();
429 12 : if (kbt <= std::numeric_limits<double>::epsilon()) {
430 0 : error("eABF/DRR: It seems the MD engine does not setup the temperature correctly for PLUMED."
431 : "Please set it by the TEMP keyword manually.");
432 : }
433 12 : if (fullsamples < 0.5) {
434 0 : fullsamples = 500.0;
435 0 : log << "eABF/DRR: The fullsamples parametre is not set. Set it to "
436 : "500(default)."
437 0 : << '\n';
438 : }
439 12 : if (getRestart()) {
440 1 : if (restart_prefix.length() != 0) {
441 1 : isRestart = true;
442 1 : firsttime = false;
443 1 : load(restart_prefix);
444 : } else {
445 0 : log << "eABF/DRR: You don't specify the file for restarting." << '\n';
446 0 : log << "eABF/DRR: So I assume you are splitting windows." << '\n';
447 0 : isRestart = false;
448 0 : firsttime = true;
449 : }
450 : }
451 :
452 12 : vector<string> gmin(ndims);
453 12 : vector<string> zgmin(ndims);
454 12 : parseVector("GRID_MIN", gmin);
455 24 : parseVector("ZGRID_MIN", zgmin);
456 12 : if (gmin.size() != ndims) {
457 0 : error("eABF/DRR: not enough values for GRID_MIN");
458 : }
459 12 : if (zgmin.size() != ndims) {
460 33 : log << "eABF/DRR: You didn't specify ZGRID_MIN. " << '\n'
461 11 : << "eABF/DRR: The GRID_MIN will be used instead.";
462 11 : zgmin = gmin;
463 : }
464 12 : vector<string> gmax(ndims);
465 12 : vector<string> zgmax(ndims);
466 12 : parseVector("GRID_MAX", gmax);
467 24 : parseVector("ZGRID_MAX", zgmax);
468 12 : if (gmax.size() != ndims) {
469 0 : error("eABF/DRR: not enough values for GRID_MAX");
470 : }
471 12 : if (zgmax.size() != ndims) {
472 33 : log << "eABF/DRR: You didn't specify ZGRID_MAX. " << '\n'
473 11 : << "eABF/DRR: The GRID_MAX will be used instead.";
474 11 : zgmax = gmax;
475 : }
476 12 : vector<unsigned> gbin(ndims);
477 12 : vector<unsigned> zgbin(ndims);
478 12 : vector<double> gspacing(ndims);
479 12 : vector<double> zgspacing(ndims);
480 12 : parseVector("GRID_BIN", gbin);
481 12 : parseVector("ZGRID_BIN", zgbin);
482 12 : parseVector("GRID_SPACING", gspacing);
483 24 : parseVector("ZGRID_SPACING", zgspacing);
484 12 : if (gbin.size() != ndims) {
485 3 : log << "eABF/DRR: You didn't specify GRID_BIN. Trying to use GRID_SPACING "
486 : "instead."
487 3 : << '\n';
488 3 : if (gspacing.size() != ndims) {
489 0 : error("eABF/DRR: not enough values for GRID_BIN");
490 : } else {
491 3 : gbin.resize(ndims);
492 6 : for (size_t i = 0; i < ndims; ++i) {
493 : double l, h;
494 3 : PLMD::Tools::convert(gmin[i], l);
495 3 : PLMD::Tools::convert(gmax[i], h);
496 3 : gbin[i] = std::nearbyint((h - l) / gspacing[i]);
497 3 : gspacing[i] = (h - l) / gbin[i];
498 3 : log << "GRID_BIN[" << i << "] is " << gbin[i] << '\n';
499 : }
500 : }
501 : }
502 12 : if (zgbin.size() != ndims) {
503 11 : log << "eABF/DRR: You didn't specify ZGRID_BIN. Trying to use ZGRID_SPACING instead." << '\n';
504 11 : if (zgspacing.size() != ndims) {
505 11 : log << "eABF/DRR: You didn't specify ZGRID_SPACING. Trying to use GRID_SPACING or GRID_BIN instead." << '\n';
506 11 : zgbin = gbin;
507 11 : zgspacing = gspacing;
508 : } else {
509 0 : zgbin.resize(ndims);
510 0 : for (size_t i = 0; i < ndims; ++i) {
511 : double l, h;
512 0 : PLMD::Tools::convert(zgmin[i], l);
513 0 : PLMD::Tools::convert(zgmax[i], h);
514 0 : zgbin[i] = std::nearbyint((h - l) / zgspacing[i]);
515 0 : zgspacing[i] = (h - l) / zgbin[i];
516 0 : log << "ZGRID_BIN[" << i << "] is " << zgbin[i] << '\n';
517 : }
518 : }
519 : }
520 12 : checkRead();
521 :
522 : // Set up kbt for extended system
523 12 : log << "eABF/DRR: The fullsamples is " << fullsamples << '\n';
524 12 : log << "eABF/DRR: The kbt(real system) is " << kbt << '\n';
525 12 : dt = getTimeStep() * getStride();
526 12 : log << "eABF/DRR: timestep = " << getTimeStep() << " ps with stride = " << getStride() << " steps\n";
527 12 : vector<double> ekbt(ndims, 0.0);
528 12 : if (etemp.size() != ndims) {
529 12 : etemp.assign(ndims, kbt / getKBoltzmann());
530 : }
531 12 : if (tau.size() != ndims) {
532 0 : tau.assign(ndims, 0.5);
533 : }
534 12 : if (friction.size() != ndims) {
535 0 : friction.assign(ndims, 8.0);
536 : }
537 12 : if (maxFactors.size() != ndims) {
538 0 : maxFactors.assign(ndims, 1.0);
539 : }
540 31 : for (size_t i = 0; i < ndims; ++i) {
541 19 : log << "eABF/DRR: The maximum scaling factor [" << i << "] is " << maxFactors[i] << '\n';
542 19 : if (maxFactors[i] > 1.0) {
543 0 : log << "eABF/DRR: Warning! The maximum scaling factor larger than 1.0 is not recommended!" << '\n';
544 : }
545 : }
546 31 : for (size_t i = 0; i < ndims; ++i) {
547 19 : ekbt[i] = etemp[i] * getKBoltzmann();
548 19 : log << "eABF/DRR: The kbt(extended system) of [" << i << "] is " << ekbt[i]
549 19 : << '\n';
550 19 : log << "eABF/DRR: relaxation time tau [" << i << "] is " << tau[i] << '\n';
551 19 : log << "eABF/DRR: Extended variable [" << i << "] has friction: " << friction[i] << '\n';
552 : }
553 :
554 : // Set up the force grid
555 12 : vector<DRRAxis> zdelim(ndims);
556 31 : for (size_t i = 0; i < ndims; ++i) {
557 19 : log << "eABF/DRR: The " << i << " dimensional grid minimum is " << gmin[i]
558 19 : << '\n';
559 19 : log << "eABF/DRR: The " << i << " dimensional grid maximum is " << gmax[i]
560 19 : << '\n';
561 19 : log << "eABF/DRR: The " << i << " dimensional grid has " << gbin[i]
562 19 : << " bins" << '\n';
563 19 : log << "eABF/DRR: The " << i << " dimensional zgrid minimum is " << zgmin[i]
564 19 : << '\n';
565 19 : log << "eABF/DRR: The " << i << " dimensional zgrid maximum is " << zgmax[i]
566 19 : << '\n';
567 19 : log << "eABF/DRR: The " << i << " dimensional zgrid has " << zgbin[i]
568 19 : << " bins" << '\n';
569 : double l, h;
570 19 : PLMD::Tools::convert(gmin[i], l);
571 19 : PLMD::Tools::convert(gmax[i], h);
572 19 : delim[i].set(l, h, gbin[i]);
573 : double zl,zh;
574 19 : PLMD::Tools::convert(zgmin[i], zl);
575 19 : PLMD::Tools::convert(zgmax[i], zh);
576 19 : zdelim[i].set(zl, zh, zgbin[i]);
577 : }
578 12 : if (kappa.size() != ndims) {
579 9 : kappa.resize(ndims, 0.0);
580 25 : for (size_t i = 0; i < ndims; ++i) {
581 16 : if (kappa[i] <= 0) {
582 16 : log << "eABF/DRR: The spring force constant kappa[" << i
583 16 : << "] is not set." << '\n';
584 16 : kappa[i] = ekbt[i] / (delim[i].getWidth() * delim[i].getWidth());
585 16 : log << "eABF/DRR: set kappa[" << i
586 16 : << "] according to bin width(ekbt/(binWidth^2))." << '\n';
587 : }
588 16 : log << "eABF/DRR: The spring force constant kappa[" << i << "] is "
589 16 : << std::fixed << std::setprecision(10) << kappa[i] << '\n';
590 : }
591 : } else {
592 3 : log << "eABF/DRR: The kappa have been set manually." << '\n';
593 6 : for (size_t i = 0; i < ndims; ++i) {
594 3 : log << "eABF/DRR: The spring force constant kappa[" << i << "] is "
595 3 : << std::fixed << std::setprecision(10) << kappa[i] << '\n';
596 : }
597 : }
598 :
599 31 : for (size_t i = 0; i < ndims; ++i) {
600 19 : mass[i] = kappa[i] * tau[i] * tau[i] / (4 * pi * pi);
601 19 : log << "eABF/DRR: Fictitious mass[" << i << "] is " << mass[i] << '\n';
602 19 : c1[i] = exp(-0.5 * friction[i] * dt);
603 19 : c2[i] = sqrt(ekbt[i] * (1.0 - c1[i] * c1[i]) / mass[i]);
604 : }
605 :
606 31 : for (size_t i = 0; i < ndims; ++i) {
607 : // Position output
608 19 : string comp = getPntrToArgument(i)->getName() + "_fict";
609 38 : addComponentWithDerivatives(comp);
610 19 : if (getPntrToArgument(i)->isPeriodic()) {
611 : string a, b;
612 : double c, d;
613 16 : getPntrToArgument(i)->getDomain(a, b);
614 16 : getPntrToArgument(i)->getDomain(c, d);
615 16 : componentIsPeriodic(comp, a, b);
616 16 : delim[i].setPeriodicity(c, d);
617 : zdelim[i].setPeriodicity(c, d);
618 : } else {
619 3 : componentIsNotPeriodic(comp);
620 : }
621 19 : fictValue[i] = getPntrToComponent(comp);
622 : // Velocity output
623 38 : comp = getPntrToArgument(i)->getName() + "_vfict";
624 19 : addComponent(comp);
625 19 : componentIsNotPeriodic(comp);
626 19 : vfictValue[i] = getPntrToComponent(comp);
627 : // Bias force from eABF/DRR output
628 38 : comp = getPntrToArgument(i)->getName() + "_biasforce";
629 19 : addComponent(comp);
630 19 : componentIsNotPeriodic(comp);
631 19 : biasforceValue[i] = getPntrToComponent(comp);
632 : // Spring force output, useful for perform egABF and other analysis
633 38 : comp = getPntrToArgument(i)->getName() + "_springforce";
634 19 : addComponent(comp);
635 19 : componentIsNotPeriodic(comp);
636 19 : springforceValue[i] = getPntrToComponent(comp);
637 : // Position output, no pbc-aware
638 38 : comp = getPntrToArgument(i)->getName() + "_fictNoPBC";
639 19 : addComponent(comp);
640 19 : componentIsNotPeriodic(comp);
641 19 : fictNoPBCValue[i] = getPntrToComponent(comp);
642 : }
643 :
644 12 : if (outputprefix.length() == 0) {
645 0 : outputprefix = getLabel();
646 : }
647 : // Support multiple replica
648 12 : string replica_suffix = plumed.getSuffix();
649 12 : if (replica_suffix.empty() == false) {
650 4 : outputprefix = outputprefix + replica_suffix;
651 : }
652 12 : outputname = outputprefix + ".drrstate";
653 12 : cptname = outputprefix + ".cpt.drrstate";
654 :
655 12 : if (!isRestart) {
656 : // If you want to use on-the-fly text output for CZAR and naive estimator,
657 : // you should turn it to true first!
658 11 : ABFGrid = ABF(delim, ".abf", fullsamples, maxFactors, textoutput);
659 : // Just initialize it even useCZARestimator is off.
660 22 : CZARestimator = CZAR(zdelim, ".czar", kbt, textoutput);
661 11 : log << "eABF/DRR: The init function of the grid is finished." << '\n';
662 : } else {
663 : // ABF Parametres are not saved in binary files
664 : // So manully set them up
665 1 : ABFGrid.setParameters(fullsamples, maxFactors);
666 : }
667 12 : if (useCZARestimator) {
668 12 : log << "eABF/DRR: Using corrected z-average restraint estimator of gradients" << '\n';
669 24 : log << " Bibliography " << plumed.cite("Lesage, Lelièvre, Stoltz and Hénin, "
670 24 : "J. Phys. Chem. B 3676, 121 (2017)");
671 12 : log << plumed.cite("Darve and Pohorille, J. Chem. Phys. 9169, 115 (2001)") << '\n';
672 : }
673 12 : if (useUIestimator) {
674 9 : log << "eABF/DRR: Using umbrella integration(Zheng and Yang's) estimator "
675 : "of gradients."
676 9 : << '\n';
677 9 : log << "eABF/DRR: The UI estimator code is contributed by Haohao Fu."
678 9 : << '\n';
679 18 : log << " Bibliography " << plumed.cite(
680 18 : "Fu, Shao, Chipot and Cai, J. Chem. Theory Comput. 3506, 12 (2016)");
681 18 : log << plumed.cite("Zheng and Yang, J. Chem. Theory Comput. 810, 8 (2012)");
682 9 : log << plumed.cite("Darve and Pohorille, J. Chem. Phys. 9169, 115 (2001)") << '\n';
683 9 : vector<double> lowerboundary(zdelim.size(), 0);
684 9 : vector<double> upperboundary(zdelim.size(), 0);
685 9 : vector<double> width(zdelim.size(), 0);
686 24 : for (size_t i = 0; i < zdelim.size(); ++i) {
687 15 : lowerboundary[i] = zdelim[i].getMin();
688 15 : upperboundary[i] = zdelim[i].getMax();
689 15 : width[i] = zdelim[i].getWidth();
690 : }
691 : vector<string> input_filename;
692 : bool uirestart = false;
693 9 : if (isRestart && (uirprefix.length() != 0)) {
694 1 : input_filename.push_back(uirprefix);
695 : uirestart = true;
696 : }
697 9 : if (isRestart && (uirprefix.length() == 0)) {
698 0 : input_filename.push_back(outputprefix);
699 : }
700 9 : eabf_UI = UIestimator::UIestimator(
701 9 : lowerboundary, upperboundary, width, kappa, outputprefix, int(outputfreq),
702 18 : uirestart, input_filename, kbt / getKBoltzmann());
703 9 : }
704 24 : }
705 :
706 123 : void DynamicReferenceRestraining::calculate() {
707 123 : long long int step_now = getStep();
708 123 : if (firsttime) {
709 28 : for (size_t i = 0; i < ndims; ++i) {
710 17 : fict[i] = getArgument(i);
711 17 : if(reflectingWall[i] && (fict[i]>=delim[i].getMax() || fict[i]<=delim[i].getMin())) {
712 0 : error("eABF/DRR: initial position not in the range of [gmin, gmax]!");
713 : }
714 : }
715 11 : firsttime = false;
716 : }
717 123 : if (step_now != 0) {
718 111 : if ((step_now % int(outputfreq)) == 0) {
719 15 : save(outputname, step_now);
720 15 : if (textoutput) {
721 10 : ABFGrid.writeAll(outputprefix, fmt_);
722 10 : if (useCZARestimator) {
723 10 : CZARestimator.writeAll(outputprefix, fmt_);
724 10 : CZARestimator.writeZCountZGrad(outputprefix);
725 : }
726 : }
727 : }
728 111 : if (historyfreq > 0 && (step_now % int(historyfreq)) == 0) {
729 4 : if (textoutput) {
730 : const string filename =
731 4 : outputprefix + ".another.drrstate";
732 4 : save(filename, step_now);
733 : const string textfilename =
734 4 : mergeHistoryFiles ? (outputprefix + ".hist") : (outputprefix + "." + std::to_string(step_now));
735 4 : ABFGrid.writeAll(textfilename, fmt_, mergeHistoryFiles);
736 4 : if (useCZARestimator) {
737 4 : CZARestimator.writeAll(textfilename, fmt_, mergeHistoryFiles);
738 4 : CZARestimator.writeZCountZGrad(textfilename, mergeHistoryFiles);
739 : }
740 : } else {
741 : const string filename =
742 0 : outputprefix + "." + std::to_string(step_now) + ".drrstate";
743 0 : save(filename, step_now);
744 : }
745 : }
746 111 : if (getCPT()) {
747 0 : log << "eABF/DRR: The MD engine is writing checkpoint so we also write a "
748 : "DRR state file at step: "
749 0 : << step_now << ".\n";
750 0 : save(cptname, step_now);
751 : }
752 : }
753 123 : if (withExternalForce == false) {
754 : double ene = 0.0;
755 294 : for (size_t i = 0; i < ndims; ++i) {
756 183 : real[i] = getArgument(i);
757 183 : springlength[i] = difference(i, fict[i], real[i]);
758 183 : fictNoPBC[i] = real[i] - springlength[i];
759 183 : double f = -kappa[i] * springlength[i];
760 183 : ffict_measured[i] = -f;
761 183 : ene += 0.5 * kappa[i] * springlength[i] * springlength[i];
762 183 : setOutputForce(i, f);
763 183 : ffict[i] = -f;
764 183 : fict[i] = fictValue[i]->bringBackInPbc(fict[i]);
765 183 : fictValue[i]->set(fict[i]);
766 183 : vfictValue[i]->set(vfict_laststep[i]);
767 183 : springforceValue[i]->set(ffict_measured[i]);
768 183 : fictNoPBCValue[i]->set(fictNoPBC[i]);
769 : }
770 111 : setBias(ene);
771 111 : ABFGrid.store_getbias(fict, ffict_measured, fbias);
772 : } else {
773 36 : for (size_t i = 0; i < ndims; ++i) {
774 24 : real[i] = getArgument(i);
775 24 : ffict_measured[i] = externalForceValue[i]->get();
776 24 : if (withExternalFict) {
777 24 : fictNoPBC[i] = externalFictValue[i]->get();
778 : }
779 24 : springforceValue[i]->set(ffict_measured[i]);
780 24 : fictNoPBCValue[i]->set(fictNoPBC[i]);
781 : }
782 12 : ABFGrid.store_getbias(real, ffict_measured, fbias);
783 12 : if (!nobias) {
784 0 : for (size_t i = 0; i < ndims; ++i) {
785 0 : setOutputForce(i, fbias[i]);
786 : }
787 : }
788 : }
789 123 : if (useCZARestimator) {
790 123 : CZARestimator.store(real, ffict_measured);
791 : }
792 123 : if (useUIestimator) {
793 87 : eabf_UI.update_output_filename(outputprefix);
794 174 : eabf_UI.update(int(step_now), real, fictNoPBC);
795 : }
796 123 : }
797 :
798 123 : void DynamicReferenceRestraining::update() {
799 123 : if (withExternalForce == false) {
800 294 : for (size_t i = 0; i < ndims; ++i) {
801 : // consider additional forces on the fictitious particle
802 : // (e.g. MetaD stuff)
803 183 : ffict[i] += fictValue[i]->getForce();
804 183 : if (!nobias) {
805 183 : ffict[i] += fbias[i];
806 : }
807 183 : biasforceValue[i]->set(fbias[i]);
808 : // update velocity (half step)
809 183 : vfict[i] += ffict[i] * 0.5 * dt / mass[i];
810 : // thermostat (half step)
811 183 : vfict[i] = c1[i] * vfict[i] + c2[i] * rand.Gaussian();
812 : // save full step velocity to be dumped at next step
813 183 : vfict_laststep[i] = vfict[i];
814 : // thermostat (half step)
815 183 : vfict[i] = c1[i] * vfict[i] + c2[i] * rand.Gaussian();
816 : // update velocity (half step)
817 183 : vfict[i] += ffict[i] * 0.5 * dt / mass[i];
818 : // update position (full step)
819 183 : fict[i] += vfict[i] * dt;
820 : // reflecting boundary
821 183 : if (reflectingWall[i]) {
822 24 : if (fict[i]<delim[i].getMin()) {
823 1 : fict[i]=delim[i].getMin()+(delim[i].getMin()-fict[i]);
824 1 : vfict[i]*=-1.0;
825 23 : } else if (fict[i]>delim[i].getMax()) {
826 0 : fict[i]=delim[i].getMax()-(fict[i]-delim[i].getMax());
827 0 : vfict[i]*=-1.0;
828 : }
829 : }
830 : }
831 : }
832 123 : }
833 :
834 19 : void DynamicReferenceRestraining::save(const string &filename,
835 : long long int step) {
836 19 : std::ofstream out;
837 19 : out.open(filename.c_str(), std::ios::binary);
838 19 : boost::archive::binary_oarchive oa(out);
839 19 : oa << step << fict << vfict << vfict_laststep << ffict << ABFGrid
840 19 : << CZARestimator;
841 19 : out.close();
842 19 : }
843 :
844 1 : void DynamicReferenceRestraining::load(const string &rfile_prefix) {
845 1 : string replica_suffix = plumed.getSuffix();
846 : string filename;
847 1 : if (replica_suffix.empty() == true) {
848 2 : filename = rfile_prefix + ".drrstate";
849 : } else {
850 0 : filename = rfile_prefix + "." + replica_suffix + ".drrstate";
851 : }
852 1 : std::ifstream in;
853 : long long int step;
854 1 : in.open(filename.c_str(), std::ios::binary);
855 1 : log << "eABF/DRR: Read restart file: " << filename << '\n';
856 1 : boost::archive::binary_iarchive ia(in);
857 1 : ia >> step >> fict >> vfict >> vfict_laststep >> ffict >> ABFGrid >>
858 1 : CZARestimator;
859 1 : in.close();
860 1 : log << "eABF/DRR: Restart at step: " << step << '\n';
861 1 : backupFile(filename);
862 2 : }
863 :
864 1 : void DynamicReferenceRestraining::backupFile(const string &filename) {
865 : bool isSuccess = false;
866 : long int i = 0;
867 2 : while (!isSuccess) {
868 : // If libstdc++ support C++17 we can simplify following code.
869 2 : const string bckname = "bck." + filename + "." + std::to_string(i);
870 1 : if (is_file_exist(bckname.c_str())) {
871 0 : ++i;
872 : } else {
873 1 : log << "eABF/DRR: Backup original restart file to " << bckname << '\n';
874 1 : std::ifstream src(filename.c_str(), std::ios::binary);
875 1 : std::ofstream dst(bckname.c_str(), std::ios::binary);
876 1 : dst << src.rdbuf();
877 1 : src.close();
878 1 : dst.close();
879 : isSuccess = true;
880 1 : }
881 : }
882 1 : }
883 :
884 : // Copy from
885 : // stackoverflow(https://stackoverflow.com/questions/12774207/fastest-way-to-check-if-a-file-exist-using-standard-c-c11-c)
886 1 : bool DynamicReferenceRestraining::is_file_exist(const char *fileName) {
887 1 : std::ifstream infile(fileName);
888 1 : return infile.good();
889 1 : }
890 : }
891 : }
892 :
893 : #endif
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