Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2020-2021 of Michele Invernizzi.
3 :
4 : This file is part of the OPES plumed module.
5 :
6 : The OPES plumed module is free software: you can redistribute it and/or modify
7 : it under the terms of the GNU Lesser General Public License as published by
8 : the Free Software Foundation, either version 3 of the License, or
9 : (at your option) any later version.
10 :
11 : The OPES plumed module is distributed in the hope that it will be useful,
12 : but WITHOUT ANY WARRANTY; without even the implied warranty of
13 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 : GNU Lesser General Public License for more details.
15 :
16 : You should have received a copy of the GNU Lesser General Public License
17 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
18 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
19 : #include "ExpansionCVs.h"
20 : #include "core/ActionRegister.h"
21 :
22 : namespace PLMD {
23 : namespace opes {
24 :
25 : //+PLUMEDOC OPES_EXPANSION_CV ECV_MULTITHERMAL_MULTIBARIC
26 : /*
27 : Expand a simulation to sample multiple temperatures and pressures.
28 :
29 : The potential [ENERGY](ENERGY.md), $E$, and the [VOLUME](VOLUME.md), $V$, of the system should be used as ARG.
30 :
31 : $$
32 : \Delta u_{\beta',p'}=(\beta'-\beta) E + (\beta' p' -\beta p) V\, ,
33 : $$
34 :
35 : where $\beta', p'$ are the temperatures and pressures to be sampled, while $\beta, p$ is the temperature and pressure at which the simulation is conducted.
36 :
37 : If instead you wish to sample multiple temperatures and a single pressure, you should use [ECV_MULTITHERMAL](ECV_MULTITHERMAL.md) with as ARG the internal energy $U=E+pV$.
38 :
39 : The TEMP_STEPS and PRESSURE_STEPS are automatically guessed from the initial unbiased steps (see OBSERVATION_STEPS in [OPES_EXPANDED](OPES_EXPANDED.md)), unless explicitly set.
40 : The algorithm for this guess is described in the paper cited below should provide a rough estimate useful for most applications.
41 : The pressures are uniformely spaced, while the temperatures steps are geometrically spaced.
42 : Use instead the keyword NO_GEOM_SPACING for a linear spacing in inverse temperature (beta).
43 : For more detailed control you can use instead TEMP_SET_ALL and/or PRESSURE_SET_ALL to explicitly set all of them.
44 : The temperatures and pressures are then combined in a 2D grid.
45 :
46 : You can use CUT_CORNER to avoid a high-temperature/low-pressure region.
47 : This can be useful e.g. to increase the temperature for greater ergodicity, while avoiding water to vaporize, as in the paper cited below.
48 :
49 : You can reweight the resulting simulation at any temperature and pressure in chosen target, using e.g. [REWEIGHT_TEMP_PRESS](REWEIGHT_TEMP_PRESS.md).
50 : A similar target distribution can be sampled using TD_MULTITHERMAL_MULTIBARIC](TD_MULTITHERMAL_MULTIBARIC.md).
51 :
52 : ## Examples
53 :
54 : ```plumed
55 : ene: ENERGY
56 : vol: VOLUME
57 : ecv: ECV_MULTITHERMAL_MULTIBARIC ...
58 : ARG=ene,vol
59 : TEMP=500
60 : TEMP_MIN=270
61 : TEMP_MAX=800
62 : PRESSURE=0.06022140857*2000 #2 kbar
63 : PRESSURE_MIN=0.06022140857 #1 bar
64 : PRESSURE_MAX=0.06022140857*4000 #4 kbar
65 : CUT_CORNER=500,0.06022140857,800,0.06022140857*1000
66 : ...
67 : opes: OPES_EXPANDED ARG=ecv.* FILE=DeltaF.data PACE=500 WALKERS_MPI
68 : ```
69 :
70 : Notice that $p=0.06022140857$ corresponds to 1 bar only when using the default PLUMED units.
71 : If you modify them via the [UNITS](UNITS.md) command, then the pressure has to be rescaled accordingly.
72 :
73 : */
74 : //+ENDPLUMEDOC
75 :
76 : class ECVmultiThermalBaric :
77 : public ExpansionCVs {
78 : private:
79 : bool todoAutomatic_beta_;
80 : bool todoAutomatic_pres_;
81 : bool geom_spacing_;
82 : double pres0_;
83 : std::vector<double> pres_;
84 : std::vector<double> ECVs_beta_;
85 : std::vector<double> ECVs_pres_;
86 : std::vector<double> derECVs_beta_; //(beta_k-beta0) or (temp0/temp_k-1)/kbt
87 : std::vector<double> derECVs_pres_; //(beta_k*pres_kk-beta0*pres0) or (temp0/temp_k*pres_kk-pres0)/kbt
88 : void initECVs();
89 :
90 : //CUT_CORNER stuff
91 : double coeff_;
92 : double pres_low_;
93 : double kB_temp_low_;
94 : //SET_ALL_TEMP_PRESSURE stuff
95 : std::vector<std::string> custom_lambdas_;
96 :
97 : public:
98 : explicit ECVmultiThermalBaric(const ActionOptions&);
99 : static void registerKeywords(Keywords& keys);
100 : void calculateECVs(const double *) override;
101 : const double * getPntrToECVs(unsigned) override;
102 : const double * getPntrToDerECVs(unsigned) override;
103 : std::vector< std::vector<unsigned> > getIndex_k() const override;
104 : std::vector<std::string> getLambdas() const override;
105 : void initECVs_observ(const std::vector<double>&,const unsigned,const unsigned) override;
106 : void initECVs_restart(const std::vector<std::string>&) override;
107 : };
108 :
109 : PLUMED_REGISTER_ACTION(ECVmultiThermalBaric,"ECV_MULTITHERMAL_MULTIBARIC")
110 :
111 11 : void ECVmultiThermalBaric::registerKeywords(Keywords& keys) {
112 11 : ExpansionCVs::registerKeywords(keys);
113 22 : keys.addInputKeyword("compulsory","ARG","scalar","the labels of the potential energy and of the volume of the system. You can calculate them with ENERGY and VOLUME respectively");
114 : //temperature
115 11 : keys.add("optional","TEMP_MIN","the minimum of the temperature range");
116 11 : keys.add("optional","TEMP_MAX","the maximum of the temperature range");
117 11 : keys.add("optional","TEMP_STEPS","the number of steps in temperature");
118 11 : keys.add("optional","TEMP_SET_ALL","manually set all the temperatures");
119 11 : keys.addFlag("NO_GEOM_SPACING",false,"do not use geometrical spacing in temperature, but instead linear spacing in inverse temperature");
120 : //pressure
121 11 : keys.add("compulsory","PRESSURE","pressure. Use the proper units");
122 11 : keys.add("optional","PRESSURE_MIN","the minimum of the pressure range");
123 11 : keys.add("optional","PRESSURE_MAX","the maximum of the pressure range");
124 11 : keys.add("optional","PRESSURE_STEPS","the number of steps in pressure");
125 11 : keys.add("optional","PRESSURE_SET_ALL","manually set all the pressures");
126 : //other
127 11 : keys.add("optional","SET_ALL_TEMP_PRESSURE","manually set all the target temperature_pressure pairs. An underscore separates temperature and pressure, while different points are comma-separated, e.g.: temp1_pres1,temp1_pres2,...");
128 11 : keys.add("optional","CUT_CORNER","avoid region of high temperature and low pressure. Exclude all points below a line in the temperature-pressure plane, defined by two points: \\f$T_{\\text{low}},P_{\\text{low}},T_{\\text{high}},P_{\\text{high}}\\f$");
129 11 : keys.addDOI("10.1103/PhysRevX.10.041034");
130 11 : }
131 :
132 9 : ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&ao)
133 : : Action(ao)
134 : , ExpansionCVs(ao)
135 9 : , todoAutomatic_beta_(false)
136 9 : , todoAutomatic_pres_(false)
137 9 : , coeff_(0)
138 9 : , pres_low_(0)
139 9 : , kB_temp_low_(0) {
140 9 : plumed_massert(getNumberOfArguments()==2,"ENERGY and VOLUME should be given as ARG");
141 :
142 : //set temp0
143 9 : const double kB=getKBoltzmann();
144 9 : const double temp0=kbt_/kB;
145 :
146 : //parse temp range
147 9 : double temp_min=-1;
148 9 : double temp_max=-1;
149 9 : parse("TEMP_MIN",temp_min);
150 9 : parse("TEMP_MAX",temp_max);
151 9 : unsigned temp_steps=0;
152 18 : parse("TEMP_STEPS",temp_steps);
153 : std::vector<double> temps;
154 9 : parseVector("TEMP_SET_ALL",temps);
155 9 : parseFlag("NO_GEOM_SPACING",geom_spacing_);
156 9 : geom_spacing_=!geom_spacing_;
157 : //parse pressures
158 9 : parse("PRESSURE",pres0_);
159 : const double myNone=std::numeric_limits<double>::lowest(); //quiet_NaN is not supported by some intel compiler
160 9 : double pres_min=myNone; //-1 might be a meaningful pressure
161 9 : double pres_max=myNone;
162 9 : parse("PRESSURE_MIN",pres_min);
163 9 : parse("PRESSURE_MAX",pres_max);
164 9 : unsigned pres_steps=0;
165 9 : parse("PRESSURE_STEPS",pres_steps);
166 18 : parseVector("PRESSURE_SET_ALL",pres_);
167 : //other
168 : std::vector<double> cut_corner;
169 9 : parseVector("CUT_CORNER",cut_corner);
170 9 : parseVector("SET_ALL_TEMP_PRESSURE",custom_lambdas_);
171 :
172 9 : checkRead();
173 :
174 9 : if(custom_lambdas_.size()>0) {
175 : //make sure no incompatible options are used
176 2 : plumed_massert(temps.size()==0,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_SET_ALL");
177 2 : plumed_massert(pres_.size()==0,"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_SET_ALL");
178 2 : plumed_massert(temp_steps==0,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_STEPS");
179 2 : plumed_massert(pres_steps==0,"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_STEPS");
180 2 : plumed_massert(temp_min==-1 && temp_max==-1,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_MIN/MAX");
181 2 : plumed_massert(pres_min==myNone && pres_max==myNone,"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_MIN/MAX");
182 2 : plumed_massert(cut_corner.size()==0,"cannot set both SET_ALL_TEMP_PRESSURE and CUT_CORNER");
183 : //setup the target temperature-pressure grid
184 2 : derECVs_beta_.resize(custom_lambdas_.size());
185 2 : derECVs_pres_.resize(custom_lambdas_.size());
186 2 : const std::string error_msg="SET_ALL_TEMP_PRESSURE: two underscore-separated values are expected for each comma-separated point, cannot understand: ";
187 22 : for(unsigned i=0; i<custom_lambdas_.size(); i++) {
188 : try {
189 : std::size_t pos1;
190 : const double temp_i=std::stod(custom_lambdas_[i],&pos1);
191 20 : plumed_massert(pos1+1<custom_lambdas_[i].size(),error_msg+custom_lambdas_[i]);
192 20 : plumed_massert(custom_lambdas_[i][pos1]=='_',error_msg+custom_lambdas_[i]);
193 : std::size_t pos2;
194 20 : const double pres_i=std::stod(custom_lambdas_[i].substr(pos1+1),&pos2);
195 20 : plumed_massert(pos1+1+pos2==custom_lambdas_[i].size(),error_msg+custom_lambdas_[i]);
196 :
197 20 : derECVs_beta_[i]=(temp0/temp_i-1.)/kbt_;
198 20 : derECVs_pres_[i]=(temp0/temp_i*pres_i-pres0_)/kbt_;
199 0 : } catch (std::exception &ex) {
200 0 : plumed_merror(error_msg+custom_lambdas_[i]);
201 0 : }
202 : }
203 : } else {
204 : //set the intermediate temperatures
205 7 : if(temps.size()>0) {
206 1 : plumed_massert(temp_steps==0,"cannot set both TEMP_STEPS and TEMP_SET_ALL");
207 1 : plumed_massert(temp_min==-1 && temp_max==-1,"cannot set both TEMP_SET_ALL and TEMP_MIN/MAX");
208 1 : plumed_massert(temps.size()>=2,"set at least 2 temperatures");
209 1 : temp_min=temps[0];
210 1 : temp_max=temps[temps.size()-1];
211 1 : derECVs_beta_.resize(temps.size());
212 5 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
213 4 : derECVs_beta_[k]=(temp0/temps[k]-1.)/kbt_;
214 4 : if(k<derECVs_beta_.size()-1) {
215 3 : plumed_massert(temps[k]<=temps[k+1],"TEMP_SET_ALL must be properly ordered");
216 : }
217 : }
218 : } else {
219 : //get TEMP_MIN and TEMP_MAX
220 6 : if(temp_min==-1) {
221 0 : temp_min=temp0;
222 0 : log.printf(" no TEMP_MIN provided, using TEMP_MIN=TEMP\n");
223 : }
224 6 : if(temp_max==-1) {
225 1 : temp_max=temp0;
226 1 : log.printf(" no TEMP_MAX provided, using TEMP_MAX=TEMP\n");
227 : }
228 6 : plumed_massert(temp_max>=temp_min,"TEMP_MAX should be bigger than TEMP_MIN");
229 6 : derECVs_beta_.resize(2);
230 6 : derECVs_beta_[0]=(temp0/temp_min-1.)/kbt_;
231 6 : derECVs_beta_[1]=(temp0/temp_max-1.)/kbt_;
232 6 : if(temp_min==temp_max && temp_steps==0) {
233 0 : temp_steps=1;
234 : }
235 6 : if(temp_steps>0) {
236 4 : derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,"TEMP",geom_spacing_,1./kbt_);
237 : } else {
238 4 : todoAutomatic_beta_=true;
239 : }
240 : }
241 : const double tol=1e-3; //if temp is taken from MD engine it might be numerically slightly different
242 7 : if(temp0<(1-tol)*temp_min || temp0>(1+tol)*temp_max) {
243 1 : log.printf(" +++ WARNING +++ running at TEMP=%g which is outside the chosen temperature range\n",temp0);
244 : }
245 :
246 : //set the intermediate pressures
247 7 : if(pres_.size()>0) {
248 1 : plumed_massert(pres_steps==0,"cannot set both PRESSURE_STEPS and PRESSURE_SET_ALL");
249 1 : plumed_massert(pres_min==myNone && pres_max==myNone,"cannot set both PRESSURE_SET_ALL and PRESSURE_MIN/MAX");
250 1 : plumed_massert(pres_.size()>=2,"set at least 2 pressures");
251 6 : for(unsigned kk=0; kk<pres_.size()-1; kk++) {
252 5 : plumed_massert(pres_[kk]<=pres_[kk+1],"PRESSURE_SET_ALL must be properly ordered");
253 : }
254 1 : pres_min=pres_[0];
255 1 : pres_max=pres_[pres_.size()-1];
256 : } else {
257 : //get PRESSURE_MIN and PRESSURE_MAX
258 6 : if(pres_min==myNone) {
259 3 : pres_min=pres0_;
260 3 : log.printf(" no PRESSURE_MIN provided, using PRESSURE_MIN=PRESSURE\n");
261 : }
262 6 : if(pres_max==myNone) {
263 2 : pres_max=pres0_;
264 2 : log.printf(" no PRESSURE_MAX provided, using PRESSURE_MAX=PRESSURE\n");
265 : }
266 6 : plumed_massert(pres_max>=pres_min,"PRESSURE_MAX should be bigger than PRESSURE_MIN");
267 6 : if(pres_min==pres_max && pres_steps==0) {
268 0 : pres_steps=1;
269 : }
270 6 : if(pres_steps>0) {
271 4 : pres_=getSteps(pres_min,pres_max,pres_steps,"PRESSURE",false,0);
272 : } else {
273 4 : pres_.resize(2);
274 4 : pres_[0]=pres_min;
275 4 : pres_[1]=pres_max;
276 4 : todoAutomatic_pres_=true;
277 : }
278 : }
279 7 : if(pres0_<pres_min || pres0_>pres_max) {
280 0 : log.printf(" +++ WARNING +++ running at PRESSURE=%g which is outside the chosen pressure range\n",pres0_);
281 : }
282 :
283 : //set CUT_CORNER
284 7 : std::string cc_usage("CUT_CORNER=temp_low,pres_low,temp_high,pres_high");
285 7 : if(cut_corner.size()==4) {
286 6 : const double temp_low=cut_corner[0];
287 6 : const double pres_low=cut_corner[1];
288 6 : const double temp_high=cut_corner[2];
289 6 : const double pres_high=cut_corner[3];
290 6 : plumed_massert(temp_low<temp_high,"temp_low="+std::to_string(temp_low)+" should be smaller than temp_high="+std::to_string(temp_high)+", "+cc_usage);
291 6 : plumed_massert(temp_low>=temp_min && temp_low<=temp_max,"temp_low="+std::to_string(temp_low)+" is out of temperature range. "+cc_usage);
292 6 : plumed_massert(temp_high>=temp_min && temp_high<=temp_max,"temp_high="+std::to_string(temp_high)+" is out of temperature range. "+cc_usage);
293 6 : plumed_massert(pres_low<pres_high,"pres_low="+std::to_string(pres_low)+" should be smaller than pres_high="+std::to_string(pres_high)+", "+cc_usage);
294 6 : plumed_massert(pres_low>=pres_min && pres_low<=pres_max,"pres_low="+std::to_string(pres_low)+" is out of pressure range. "+cc_usage);
295 6 : plumed_massert(pres_high>=pres_min && pres_high<=pres_max,"pres_high="+std::to_string(pres_high)+" is out of pressure range. "+cc_usage);
296 6 : kB_temp_low_=kB*temp_low;
297 6 : coeff_=(pres_high-pres_low)/(temp_high-temp_low)/kB;
298 6 : plumed_massert(coeff_!=0,"this should not be possible");
299 6 : const double small_value=(temp_high-pres_low)/1e4;
300 6 : pres_low_=pres_low-small_value; //make sure pres_max is included
301 6 : plumed_massert(pres_max>=coeff_*(kB*temp_max-kB_temp_low_)+pres_low_,"please chose a pres_high slightly smaller than PRESSURE_MAX in "+cc_usage);
302 : } else {
303 1 : plumed_massert(cut_corner.size()==0,"expected 4 values: "+cc_usage);
304 : }
305 : }
306 :
307 : //print some info
308 9 : log.printf(" running at TEMP=%g and PRESSURE=%g\n",temp0,pres0_);
309 9 : log.printf(" targeting a temperature range from TEMP_MIN=%g to TEMP_MAX=%g\n",temp_min,temp_max);
310 9 : if(temp_min==temp_max) {
311 2 : log.printf(" +++ WARNING +++ if you only need a multibaric simulation it is more efficient to set it up with ECV_LINEAR\n");
312 : }
313 9 : log.printf(" and a pressure range from PRESSURE_MIN=%g to PRESSURE_MAX=%g\n",pres_min,pres_max);
314 9 : if(pres_min==pres_max) {
315 2 : log.printf(" +++ WARNING +++ if you only need a multithermal simulation it is more efficient to set it up with ECV_MULTITHERMAL\n");
316 : }
317 9 : if(!geom_spacing_) {
318 1 : log.printf(" -- NO_GEOM_SPACING: inverse temperatures will be linearly spaced\n");
319 : }
320 9 : if(coeff_!=0) {
321 6 : log.printf(" -- CUT_CORNER: ignoring some high temperature and low pressure values\n");
322 : }
323 9 : }
324 :
325 463 : void ECVmultiThermalBaric::calculateECVs(const double * ene_vol) {
326 5925 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
327 5462 : ECVs_beta_[k]=derECVs_beta_[k]*ene_vol[0];
328 : }
329 50075 : for(unsigned i=0; i<derECVs_pres_.size(); i++) {
330 49612 : ECVs_pres_[i]=derECVs_pres_[i]*ene_vol[1];
331 : }
332 : // derivatives are constant, as usual in linear expansions
333 463 : }
334 :
335 18 : const double * ECVmultiThermalBaric::getPntrToECVs(unsigned j) {
336 18 : plumed_massert(isReady_,"cannot access ECVs before initialization");
337 18 : plumed_massert(j==0 || j==1,getName()+" has only two CVs, the ENERGY and the VOLUME");
338 18 : if(j==0) {
339 9 : return &ECVs_beta_[0];
340 : } else { //if (j==1)
341 9 : return &ECVs_pres_[0];
342 : }
343 : }
344 :
345 18 : const double * ECVmultiThermalBaric::getPntrToDerECVs(unsigned j) {
346 18 : plumed_massert(isReady_,"cannot access ECVs before initialization");
347 18 : plumed_massert(j==0 || j==1,getName()+" has only two CVs, the ENERGY and the VOLUME");
348 18 : if(j==0) {
349 9 : return &derECVs_beta_[0];
350 : } else { //if (j==1)
351 9 : return &derECVs_pres_[0];
352 : }
353 : }
354 :
355 9 : std::vector< std::vector<unsigned> > ECVmultiThermalBaric::getIndex_k() const {
356 9 : plumed_massert(isReady_ && totNumECVs_>0,"cannot access getIndex_k() of ECV before initialization");
357 : std::vector< std::vector<unsigned> > index_k;
358 9 : if(custom_lambdas_.size()>0) {
359 : //same as default getIndex_k() function
360 2 : plumed_massert(totNumECVs_==custom_lambdas_.size(),"this should not happen");
361 22 : for(unsigned i=0; i<totNumECVs_; i++)
362 40 : index_k.emplace_back(std::vector<unsigned> {i,i});
363 : } else {
364 : unsigned i=0;
365 146 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
366 139 : const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);
367 139 : const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;
368 2594 : for(unsigned kk=0; kk<pres_.size(); kk++) {
369 2455 : if(coeff_==0 || pres_[kk]>=line_k) { //important to be inclusive, thus >=, not just >
370 2254 : index_k.emplace_back(std::vector<unsigned> {k,i});
371 2254 : i++;
372 : }
373 : }
374 : }
375 7 : plumed_massert(totNumECVs_==index_k.size(),"this should not happen, is something wrong with CUT_CORNER ?");
376 : }
377 9 : return index_k;
378 0 : }
379 :
380 18 : std::vector<std::string> ECVmultiThermalBaric::getLambdas() const {
381 18 : if(custom_lambdas_.size()>0) {
382 4 : return custom_lambdas_;
383 : }
384 :
385 14 : plumed_massert(!todoAutomatic_beta_ && !todoAutomatic_pres_,"cannot access lambdas before initializing them");
386 : std::vector<std::string> lambdas;
387 14 : const double kB=getKBoltzmann();
388 292 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
389 278 : const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);
390 278 : const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;
391 5188 : for(unsigned kk=0; kk<pres_.size(); kk++) {
392 4910 : if(coeff_==0 || pres_[kk]>=line_k) {
393 4508 : std::ostringstream subs;
394 4508 : subs<<kB_temp_k/kB<<"_"<<pres_[kk];
395 4508 : lambdas.emplace_back(subs.str());
396 4508 : }
397 : }
398 : }
399 : return lambdas;
400 14 : }
401 :
402 9 : void ECVmultiThermalBaric::initECVs() {
403 9 : plumed_massert(!isReady_,"initialization should not be called twice");
404 9 : plumed_massert(!todoAutomatic_beta_ && !todoAutomatic_pres_,"this should not happen");
405 9 : totNumECVs_=getLambdas().size(); //slow, but runs only once
406 9 : if(custom_lambdas_.size()>0) {
407 2 : log.printf(" *%4lu temperatures for %s\n",derECVs_beta_.size(),getName().c_str());
408 2 : log.printf(" *%4lu beta-pressures for %s\n",derECVs_pres_.size(),getName().c_str());
409 2 : log.printf(" -- SET_ALL_TEMP_PRESSURE: total number of temp-pres points is %u\n",totNumECVs_);
410 : } else {
411 7 : plumed_massert(derECVs_beta_.size()*pres_.size()>=totNumECVs_,"this should not happen, is something wrong with CUT_CORNER ?");
412 7 : derECVs_pres_.resize(totNumECVs_); //pres is mixed with temp (beta*p*V), thus we need to store all possible
413 : //initialize the derECVs.
414 : //this could be done before and one could avoid storing also beta0, beta_k, etc. but this way the code should be more readable
415 : unsigned i=0;
416 146 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
417 139 : const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);
418 139 : const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;
419 2594 : for(unsigned kk=0; kk<pres_.size(); kk++) {
420 2455 : if(coeff_==0 || pres_[kk]>=line_k) {
421 2254 : derECVs_pres_[i]=(pres_[kk]/kB_temp_k-pres0_/kbt_);
422 2254 : i++;
423 : }
424 : }
425 : }
426 7 : log.printf(" *%4lu temperatures for %s\n",derECVs_beta_.size(),getName().c_str());
427 7 : log.printf(" *%4lu pressures for %s\n",pres_.size(),getName().c_str());
428 7 : if(coeff_!=0) {
429 6 : log.printf(" -- CUT_CORNER: %lu temp-pres points were excluded, thus total is %u\n",derECVs_beta_.size()*pres_.size()-totNumECVs_,totNumECVs_);
430 : }
431 : }
432 9 : ECVs_beta_.resize(derECVs_beta_.size());
433 9 : ECVs_pres_.resize(derECVs_pres_.size());
434 9 : isReady_=true;
435 9 : }
436 :
437 6 : void ECVmultiThermalBaric::initECVs_observ(const std::vector<double>& all_obs_cvs,const unsigned ncv,const unsigned index_j) {
438 6 : if(todoAutomatic_beta_) { //estimate the steps in beta from observations
439 2 : plumed_massert(all_obs_cvs.size()%ncv==0 && index_j<ncv,"initECVs_observ parameters are inconsistent");
440 2 : std::vector<double> obs_ene(all_obs_cvs.size()/ncv); //copy only useful observations
441 17 : for(unsigned t=0; t<obs_ene.size(); t++) {
442 15 : obs_ene[t]=all_obs_cvs[t*ncv+index_j]+pres0_*all_obs_cvs[t*ncv+index_j+1]; //U=E+pV
443 : }
444 2 : const unsigned temp_steps=estimateNumSteps(derECVs_beta_[0],derECVs_beta_[1],obs_ene,"TEMP");
445 2 : log.printf(" (spacing is on beta, not on temperature)\n");
446 4 : derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,"TEMP",geom_spacing_,1./kbt_);
447 2 : todoAutomatic_beta_=false;
448 : }
449 6 : if(todoAutomatic_pres_) { //estimate the steps in pres from observations
450 2 : plumed_massert(all_obs_cvs.size()%ncv==0 && index_j+1<ncv,"initECVs_observ parameters are inconsistent");
451 2 : std::vector<double> obs_vol(all_obs_cvs.size()/ncv); //copy only useful observations
452 17 : for(unsigned t=0; t<obs_vol.size(); t++) {
453 15 : obs_vol[t]=all_obs_cvs[t*ncv+index_j+1];
454 : }
455 2 : const unsigned pres_steps=estimateNumSteps((pres_[0]-pres0_)/kbt_,(pres_[1]-pres0_)/kbt_,obs_vol,"PRESSURE");
456 2 : log.printf(" (spacing is in beta0 units)\n");
457 4 : pres_=getSteps(pres_[0],pres_[1],pres_steps,"PRESSURE",false,0);
458 2 : todoAutomatic_pres_=false;
459 : }
460 6 : initECVs();
461 6 : calculateECVs(&all_obs_cvs[index_j]);
462 6 : }
463 :
464 3 : void ECVmultiThermalBaric::initECVs_restart(const std::vector<std::string>& lambdas) {
465 3 : std::size_t pos=lambdas[0].find("_");
466 3 : plumed_massert(pos!=std::string::npos,"this should not happen, two CVs are used in "+getName()+", not less");
467 3 : pos=lambdas[0].find("_",pos+1);
468 3 : plumed_massert(pos==std::string::npos,"this should not happen, two CVs are used in "+getName()+", not more");
469 :
470 230 : auto getPres=[&lambdas](const unsigned i) {
471 230 : return lambdas[i].substr(lambdas[i].find("_")+1);
472 3 : };
473 3 : if(todoAutomatic_pres_) {
474 : unsigned pres_steps=1;
475 2 : std::string pres_min=getPres(0);
476 20 : for(unsigned i=1; i<lambdas.size(); i++) { //pres is second, thus increas by 1
477 20 : if(getPres(i)==pres_min) {
478 : break;
479 : }
480 18 : pres_steps++;
481 : }
482 4 : pres_=getSteps(pres_[0],pres_[1],pres_steps,"PRESSURE",false,0);
483 2 : todoAutomatic_pres_=false;
484 : }
485 3 : if(todoAutomatic_beta_) {
486 : unsigned temp_steps=1;
487 2 : std::string pres_max=getPres(pres_.size()-1);
488 208 : for(unsigned i=pres_.size(); i<lambdas.size(); i++) {
489 : //even if CUT_CORNER, the max pressures are all present, for each temp
490 206 : if(getPres(i)==pres_max) {
491 24 : temp_steps++;
492 : }
493 : }
494 4 : derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,"TEMP",geom_spacing_,1./kbt_);
495 2 : todoAutomatic_beta_=false;
496 : }
497 3 : std::vector<std::string> myLambdas=getLambdas();
498 3 : plumed_assert(myLambdas.size()==lambdas.size())<<"RESTART - mismatch in number of "<<getName()<<".\nFrom "<<lambdas.size()<<" labels "<<derECVs_beta_.size()<<" temperatures and "<<pres_.size()<<" pressures were found, for a total of "<<myLambdas.size()<<" estimated steps.\nCheck if the CUT_CORNER or the SET_ALL_TEMP_PRESSURE options are consistent\n";
499 3 : plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),"RESTART - mismatch in lambda values of "+getName());
500 :
501 3 : initECVs();
502 3 : }
503 :
504 : }
505 : }
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