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 \ref ENERGY, \f$E\f$, and the \ref VOLUME, \f$V\f$, of the system should be used as ARG.
30 : \f[
31 : \Delta u_{\beta',p'}=(\beta'-\beta) E + (\beta' p' -\beta p) V\, ,
32 : \f]
33 : where \f$\beta', p'\f$ are the temperatures and pressures to be sampled, while \f$\beta, p\f$ is the temperature and pressure at which the simulation is conducted.
34 :
35 : If instead you wish to sample multiple temperatures and a single pressure, you should use \ref ECV_MULTITHERMAL with as ARG the internal energy \f$U=E+pV\f$.
36 :
37 : The TEMP_STEPS and PRESSURE_STEPS are automatically guessed from the initial unbiased steps (see OBSERVATION_STEPS in \ref OPES_EXPANDED), unless explicitly set.
38 : The algorithm for this guess is described in \cite Invernizzi2020unified should provide a rough estimate useful for most applications.
39 : The pressures are uniformely spaced, while the temperatures steps are geometrically spaced.
40 : Use instead the keyword NO_GEOM_SPACING for a linear spacing in inverse temperature (beta).
41 : For more detailed control you can use instead TEMP_SET_ALL and/or PRESSURE_SET_ALL to explicitly set all of them.
42 : The temperatures and pressures are then combined in a 2D grid.
43 :
44 : You can use CUT_CORNER to avoid a high-temperature/low-pressure region.
45 : This can be useful e.g. to increase the temperature for greater ergodicity, while avoiding water to vaporize, as in Ref.\cite Invernizzi2020unified.
46 :
47 : You can reweight the resulting simulation at any temperature and pressure in chosen target, using e.g. \ref REWEIGHT_TEMP_PRESS.
48 : A similar target distribution can be sampled using \ref TD_MULTITHERMAL_MULTIBARIC.
49 :
50 : \par Examples
51 :
52 : \plumedfile
53 : ene: ENERGY
54 : vol: VOLUME
55 : ecv: ECV_MULTITHERMAL_MULTIBARIC ...
56 : ARG=ene,vol
57 : TEMP=500
58 : TEMP_MIN=270
59 : TEMP_MAX=800
60 : PRESSURE=0.06022140857*2000 #2 kbar
61 : PRESSURE_MIN=0.06022140857 #1 bar
62 : PRESSURE_MAX=0.06022140857*4000 #4 kbar
63 : CUT_CORNER=500,0.06022140857,800,0.06022140857*1000
64 : ...
65 : opes: OPES_EXPANDED ARG=ecv.* FILE=DeltaF.data PACE=500 WALKERS_MPI
66 : \endplumedfile
67 :
68 : Notice that \f$p=0.06022140857\f$ corresponds to 1 bar only when using the default PLUMED units.
69 : If you modify them via the \ref UNITS command, then the pressure has to be rescaled accordingly.
70 :
71 : */
72 : //+ENDPLUMEDOC
73 :
74 : class ECVmultiThermalBaric :
75 : public ExpansionCVs {
76 : private:
77 : bool todoAutomatic_beta_;
78 : bool todoAutomatic_pres_;
79 : bool geom_spacing_;
80 : double pres0_;
81 : std::vector<double> pres_;
82 : std::vector<double> ECVs_beta_;
83 : std::vector<double> ECVs_pres_;
84 : std::vector<double> derECVs_beta_; //(beta_k-beta0) or (temp0/temp_k-1)/kbt
85 : std::vector<double> derECVs_pres_; //(beta_k*pres_kk-beta0*pres0) or (temp0/temp_k*pres_kk-pres0)/kbt
86 : void initECVs();
87 :
88 : //CUT_CORNER stuff
89 : double coeff_;
90 : double pres_low_;
91 : double kB_temp_low_;
92 : //SET_ALL_TEMP_PRESSURE stuff
93 : std::vector<std::string> custom_lambdas_;
94 :
95 : public:
96 : explicit ECVmultiThermalBaric(const ActionOptions&);
97 : static void registerKeywords(Keywords& keys);
98 : void calculateECVs(const double *) override;
99 : const double * getPntrToECVs(unsigned) override;
100 : const double * getPntrToDerECVs(unsigned) override;
101 : std::vector< std::vector<unsigned> > getIndex_k() const override;
102 : std::vector<std::string> getLambdas() const override;
103 : void initECVs_observ(const std::vector<double>&,const unsigned,const unsigned) override;
104 : void initECVs_restart(const std::vector<std::string>&) override;
105 : };
106 :
107 : PLUMED_REGISTER_ACTION(ECVmultiThermalBaric,"ECV_MULTITHERMAL_MULTIBARIC")
108 :
109 11 : void ECVmultiThermalBaric::registerKeywords(Keywords& keys) {
110 11 : ExpansionCVs::registerKeywords(keys);
111 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");
112 : //temperature
113 11 : keys.add("optional","TEMP_MIN","the minimum of the temperature range");
114 11 : keys.add("optional","TEMP_MAX","the maximum of the temperature range");
115 11 : keys.add("optional","TEMP_STEPS","the number of steps in temperature");
116 11 : keys.add("optional","TEMP_SET_ALL","manually set all the temperatures");
117 11 : keys.addFlag("NO_GEOM_SPACING",false,"do not use geometrical spacing in temperature, but instead linear spacing in inverse temperature");
118 : //pressure
119 11 : keys.add("compulsory","PRESSURE","pressure. Use the proper units");
120 11 : keys.add("optional","PRESSURE_MIN","the minimum of the pressure range");
121 11 : keys.add("optional","PRESSURE_MAX","the maximum of the pressure range");
122 11 : keys.add("optional","PRESSURE_STEPS","the number of steps in pressure");
123 11 : keys.add("optional","PRESSURE_SET_ALL","manually set all the pressures");
124 : //other
125 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,...");
126 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$T_{\\text{low}},P_{\\text{low}},T_{\\text{high}},P_{\\text{high}}\\f$");
127 11 : }
128 :
129 9 : ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&ao)
130 : : Action(ao)
131 : , ExpansionCVs(ao)
132 9 : , todoAutomatic_beta_(false)
133 9 : , todoAutomatic_pres_(false)
134 9 : , coeff_(0)
135 9 : , pres_low_(0)
136 9 : , kB_temp_low_(0) {
137 9 : plumed_massert(getNumberOfArguments()==2,"ENERGY and VOLUME should be given as ARG");
138 :
139 : //set temp0
140 9 : const double kB=getKBoltzmann();
141 9 : const double temp0=kbt_/kB;
142 :
143 : //parse temp range
144 9 : double temp_min=-1;
145 9 : double temp_max=-1;
146 9 : parse("TEMP_MIN",temp_min);
147 9 : parse("TEMP_MAX",temp_max);
148 9 : unsigned temp_steps=0;
149 18 : parse("TEMP_STEPS",temp_steps);
150 : std::vector<double> temps;
151 9 : parseVector("TEMP_SET_ALL",temps);
152 9 : parseFlag("NO_GEOM_SPACING",geom_spacing_);
153 9 : geom_spacing_=!geom_spacing_;
154 : //parse pressures
155 9 : parse("PRESSURE",pres0_);
156 : const double myNone=std::numeric_limits<double>::lowest(); //quiet_NaN is not supported by some intel compiler
157 9 : double pres_min=myNone; //-1 might be a meaningful pressure
158 9 : double pres_max=myNone;
159 9 : parse("PRESSURE_MIN",pres_min);
160 9 : parse("PRESSURE_MAX",pres_max);
161 9 : unsigned pres_steps=0;
162 9 : parse("PRESSURE_STEPS",pres_steps);
163 18 : parseVector("PRESSURE_SET_ALL",pres_);
164 : //other
165 : std::vector<double> cut_corner;
166 9 : parseVector("CUT_CORNER",cut_corner);
167 9 : parseVector("SET_ALL_TEMP_PRESSURE",custom_lambdas_);
168 :
169 9 : checkRead();
170 :
171 9 : if(custom_lambdas_.size()>0) {
172 : //make sure no incompatible options are used
173 2 : plumed_massert(temps.size()==0,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_SET_ALL");
174 2 : plumed_massert(pres_.size()==0,"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_SET_ALL");
175 2 : plumed_massert(temp_steps==0,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_STEPS");
176 2 : plumed_massert(pres_steps==0,"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_STEPS");
177 2 : plumed_massert(temp_min==-1 && temp_max==-1,"cannot set both SET_ALL_TEMP_PRESSURE and TEMP_MIN/MAX");
178 2 : plumed_massert(pres_min==myNone && pres_max==myNone,"cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_MIN/MAX");
179 2 : plumed_massert(cut_corner.size()==0,"cannot set both SET_ALL_TEMP_PRESSURE and CUT_CORNER");
180 : //setup the target temperature-pressure grid
181 2 : derECVs_beta_.resize(custom_lambdas_.size());
182 2 : derECVs_pres_.resize(custom_lambdas_.size());
183 2 : const std::string error_msg="SET_ALL_TEMP_PRESSURE: two underscore-separated values are expected for each comma-separated point, cannot understand: ";
184 22 : for(unsigned i=0; i<custom_lambdas_.size(); i++) {
185 : try {
186 : std::size_t pos1;
187 : const double temp_i=std::stod(custom_lambdas_[i],&pos1);
188 20 : plumed_massert(pos1+1<custom_lambdas_[i].size(),error_msg+custom_lambdas_[i]);
189 20 : plumed_massert(custom_lambdas_[i][pos1]=='_',error_msg+custom_lambdas_[i]);
190 : std::size_t pos2;
191 20 : const double pres_i=std::stod(custom_lambdas_[i].substr(pos1+1),&pos2);
192 20 : plumed_massert(pos1+1+pos2==custom_lambdas_[i].size(),error_msg+custom_lambdas_[i]);
193 :
194 20 : derECVs_beta_[i]=(temp0/temp_i-1.)/kbt_;
195 20 : derECVs_pres_[i]=(temp0/temp_i*pres_i-pres0_)/kbt_;
196 0 : } catch (std::exception &ex) {
197 0 : plumed_merror(error_msg+custom_lambdas_[i]);
198 0 : }
199 : }
200 : } else {
201 : //set the intermediate temperatures
202 7 : if(temps.size()>0) {
203 1 : plumed_massert(temp_steps==0,"cannot set both TEMP_STEPS and TEMP_SET_ALL");
204 1 : plumed_massert(temp_min==-1 && temp_max==-1,"cannot set both TEMP_SET_ALL and TEMP_MIN/MAX");
205 1 : plumed_massert(temps.size()>=2,"set at least 2 temperatures");
206 1 : temp_min=temps[0];
207 1 : temp_max=temps[temps.size()-1];
208 1 : derECVs_beta_.resize(temps.size());
209 5 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
210 4 : derECVs_beta_[k]=(temp0/temps[k]-1.)/kbt_;
211 4 : if(k<derECVs_beta_.size()-1) {
212 3 : plumed_massert(temps[k]<=temps[k+1],"TEMP_SET_ALL must be properly ordered");
213 : }
214 : }
215 : } else {
216 : //get TEMP_MIN and TEMP_MAX
217 6 : if(temp_min==-1) {
218 0 : temp_min=temp0;
219 0 : log.printf(" no TEMP_MIN provided, using TEMP_MIN=TEMP\n");
220 : }
221 6 : if(temp_max==-1) {
222 1 : temp_max=temp0;
223 1 : log.printf(" no TEMP_MAX provided, using TEMP_MAX=TEMP\n");
224 : }
225 6 : plumed_massert(temp_max>=temp_min,"TEMP_MAX should be bigger than TEMP_MIN");
226 6 : derECVs_beta_.resize(2);
227 6 : derECVs_beta_[0]=(temp0/temp_min-1.)/kbt_;
228 6 : derECVs_beta_[1]=(temp0/temp_max-1.)/kbt_;
229 6 : if(temp_min==temp_max && temp_steps==0) {
230 0 : temp_steps=1;
231 : }
232 6 : if(temp_steps>0) {
233 4 : derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,"TEMP",geom_spacing_,1./kbt_);
234 : } else {
235 4 : todoAutomatic_beta_=true;
236 : }
237 : }
238 : const double tol=1e-3; //if temp is taken from MD engine it might be numerically slightly different
239 7 : if(temp0<(1-tol)*temp_min || temp0>(1+tol)*temp_max) {
240 1 : log.printf(" +++ WARNING +++ running at TEMP=%g which is outside the chosen temperature range\n",temp0);
241 : }
242 :
243 : //set the intermediate pressures
244 7 : if(pres_.size()>0) {
245 1 : plumed_massert(pres_steps==0,"cannot set both PRESSURE_STEPS and PRESSURE_SET_ALL");
246 1 : plumed_massert(pres_min==myNone && pres_max==myNone,"cannot set both PRESSURE_SET_ALL and PRESSURE_MIN/MAX");
247 1 : plumed_massert(pres_.size()>=2,"set at least 2 pressures");
248 6 : for(unsigned kk=0; kk<pres_.size()-1; kk++) {
249 5 : plumed_massert(pres_[kk]<=pres_[kk+1],"PRESSURE_SET_ALL must be properly ordered");
250 : }
251 1 : pres_min=pres_[0];
252 1 : pres_max=pres_[pres_.size()-1];
253 : } else {
254 : //get PRESSURE_MIN and PRESSURE_MAX
255 6 : if(pres_min==myNone) {
256 3 : pres_min=pres0_;
257 3 : log.printf(" no PRESSURE_MIN provided, using PRESSURE_MIN=PRESSURE\n");
258 : }
259 6 : if(pres_max==myNone) {
260 2 : pres_max=pres0_;
261 2 : log.printf(" no PRESSURE_MAX provided, using PRESSURE_MAX=PRESSURE\n");
262 : }
263 6 : plumed_massert(pres_max>=pres_min,"PRESSURE_MAX should be bigger than PRESSURE_MIN");
264 6 : if(pres_min==pres_max && pres_steps==0) {
265 0 : pres_steps=1;
266 : }
267 6 : if(pres_steps>0) {
268 4 : pres_=getSteps(pres_min,pres_max,pres_steps,"PRESSURE",false,0);
269 : } else {
270 4 : pres_.resize(2);
271 4 : pres_[0]=pres_min;
272 4 : pres_[1]=pres_max;
273 4 : todoAutomatic_pres_=true;
274 : }
275 : }
276 7 : if(pres0_<pres_min || pres0_>pres_max) {
277 0 : log.printf(" +++ WARNING +++ running at PRESSURE=%g which is outside the chosen pressure range\n",pres0_);
278 : }
279 :
280 : //set CUT_CORNER
281 7 : std::string cc_usage("CUT_CORNER=temp_low,pres_low,temp_high,pres_high");
282 7 : if(cut_corner.size()==4) {
283 6 : const double temp_low=cut_corner[0];
284 6 : const double pres_low=cut_corner[1];
285 6 : const double temp_high=cut_corner[2];
286 6 : const double pres_high=cut_corner[3];
287 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);
288 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);
289 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);
290 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);
291 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);
292 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);
293 6 : kB_temp_low_=kB*temp_low;
294 6 : coeff_=(pres_high-pres_low)/(temp_high-temp_low)/kB;
295 6 : plumed_massert(coeff_!=0,"this should not be possible");
296 6 : const double small_value=(temp_high-pres_low)/1e4;
297 6 : pres_low_=pres_low-small_value; //make sure pres_max is included
298 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);
299 : } else {
300 1 : plumed_massert(cut_corner.size()==0,"expected 4 values: "+cc_usage);
301 : }
302 : }
303 :
304 : //print some info
305 9 : log.printf(" running at TEMP=%g and PRESSURE=%g\n",temp0,pres0_);
306 9 : log.printf(" targeting a temperature range from TEMP_MIN=%g to TEMP_MAX=%g\n",temp_min,temp_max);
307 9 : if(temp_min==temp_max) {
308 2 : log.printf(" +++ WARNING +++ if you only need a multibaric simulation it is more efficient to set it up with ECV_LINEAR\n");
309 : }
310 9 : log.printf(" and a pressure range from PRESSURE_MIN=%g to PRESSURE_MAX=%g\n",pres_min,pres_max);
311 9 : if(pres_min==pres_max) {
312 2 : log.printf(" +++ WARNING +++ if you only need a multithermal simulation it is more efficient to set it up with ECV_MULTITHERMAL\n");
313 : }
314 9 : if(!geom_spacing_) {
315 1 : log.printf(" -- NO_GEOM_SPACING: inverse temperatures will be linearly spaced\n");
316 : }
317 9 : if(coeff_!=0) {
318 6 : log.printf(" -- CUT_CORNER: ignoring some high temperature and low pressure values\n");
319 : }
320 9 : }
321 :
322 463 : void ECVmultiThermalBaric::calculateECVs(const double * ene_vol) {
323 5925 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
324 5462 : ECVs_beta_[k]=derECVs_beta_[k]*ene_vol[0];
325 : }
326 50075 : for(unsigned i=0; i<derECVs_pres_.size(); i++) {
327 49612 : ECVs_pres_[i]=derECVs_pres_[i]*ene_vol[1];
328 : }
329 : // derivatives are constant, as usual in linear expansions
330 463 : }
331 :
332 18 : const double * ECVmultiThermalBaric::getPntrToECVs(unsigned j) {
333 18 : plumed_massert(isReady_,"cannot access ECVs before initialization");
334 18 : plumed_massert(j==0 || j==1,getName()+" has only two CVs, the ENERGY and the VOLUME");
335 18 : if(j==0) {
336 9 : return &ECVs_beta_[0];
337 : } else { //if (j==1)
338 9 : return &ECVs_pres_[0];
339 : }
340 : }
341 :
342 18 : const double * ECVmultiThermalBaric::getPntrToDerECVs(unsigned j) {
343 18 : plumed_massert(isReady_,"cannot access ECVs before initialization");
344 18 : plumed_massert(j==0 || j==1,getName()+" has only two CVs, the ENERGY and the VOLUME");
345 18 : if(j==0) {
346 9 : return &derECVs_beta_[0];
347 : } else { //if (j==1)
348 9 : return &derECVs_pres_[0];
349 : }
350 : }
351 :
352 9 : std::vector< std::vector<unsigned> > ECVmultiThermalBaric::getIndex_k() const {
353 9 : plumed_massert(isReady_ && totNumECVs_>0,"cannot access getIndex_k() of ECV before initialization");
354 : std::vector< std::vector<unsigned> > index_k;
355 9 : if(custom_lambdas_.size()>0) {
356 : //same as default getIndex_k() function
357 2 : plumed_massert(totNumECVs_==custom_lambdas_.size(),"this should not happen");
358 22 : for(unsigned i=0; i<totNumECVs_; i++)
359 40 : index_k.emplace_back(std::vector<unsigned> {i,i});
360 : } else {
361 : unsigned i=0;
362 146 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
363 139 : const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);
364 139 : const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;
365 2594 : for(unsigned kk=0; kk<pres_.size(); kk++) {
366 2455 : if(coeff_==0 || pres_[kk]>=line_k) { //important to be inclusive, thus >=, not just >
367 2254 : index_k.emplace_back(std::vector<unsigned> {k,i});
368 2254 : i++;
369 : }
370 : }
371 : }
372 7 : plumed_massert(totNumECVs_==index_k.size(),"this should not happen, is something wrong with CUT_CORNER ?");
373 : }
374 9 : return index_k;
375 0 : }
376 :
377 18 : std::vector<std::string> ECVmultiThermalBaric::getLambdas() const {
378 18 : if(custom_lambdas_.size()>0) {
379 4 : return custom_lambdas_;
380 : }
381 :
382 14 : plumed_massert(!todoAutomatic_beta_ && !todoAutomatic_pres_,"cannot access lambdas before initializing them");
383 : std::vector<std::string> lambdas;
384 14 : const double kB=getKBoltzmann();
385 292 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
386 278 : const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);
387 278 : const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;
388 5188 : for(unsigned kk=0; kk<pres_.size(); kk++) {
389 4910 : if(coeff_==0 || pres_[kk]>=line_k) {
390 4508 : std::ostringstream subs;
391 4508 : subs<<kB_temp_k/kB<<"_"<<pres_[kk];
392 4508 : lambdas.emplace_back(subs.str());
393 4508 : }
394 : }
395 : }
396 : return lambdas;
397 14 : }
398 :
399 9 : void ECVmultiThermalBaric::initECVs() {
400 9 : plumed_massert(!isReady_,"initialization should not be called twice");
401 9 : plumed_massert(!todoAutomatic_beta_ && !todoAutomatic_pres_,"this should not happen");
402 9 : totNumECVs_=getLambdas().size(); //slow, but runs only once
403 9 : if(custom_lambdas_.size()>0) {
404 2 : log.printf(" *%4lu temperatures for %s\n",derECVs_beta_.size(),getName().c_str());
405 2 : log.printf(" *%4lu beta-pressures for %s\n",derECVs_pres_.size(),getName().c_str());
406 2 : log.printf(" -- SET_ALL_TEMP_PRESSURE: total number of temp-pres points is %u\n",totNumECVs_);
407 : } else {
408 7 : plumed_massert(derECVs_beta_.size()*pres_.size()>=totNumECVs_,"this should not happen, is something wrong with CUT_CORNER ?");
409 7 : derECVs_pres_.resize(totNumECVs_); //pres is mixed with temp (beta*p*V), thus we need to store all possible
410 : //initialize the derECVs.
411 : //this could be done before and one could avoid storing also beta0, beta_k, etc. but this way the code should be more readable
412 : unsigned i=0;
413 146 : for(unsigned k=0; k<derECVs_beta_.size(); k++) {
414 139 : const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);
415 139 : const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;
416 2594 : for(unsigned kk=0; kk<pres_.size(); kk++) {
417 2455 : if(coeff_==0 || pres_[kk]>=line_k) {
418 2254 : derECVs_pres_[i]=(pres_[kk]/kB_temp_k-pres0_/kbt_);
419 2254 : i++;
420 : }
421 : }
422 : }
423 7 : log.printf(" *%4lu temperatures for %s\n",derECVs_beta_.size(),getName().c_str());
424 7 : log.printf(" *%4lu pressures for %s\n",pres_.size(),getName().c_str());
425 7 : if(coeff_!=0) {
426 6 : log.printf(" -- CUT_CORNER: %lu temp-pres points were excluded, thus total is %u\n",derECVs_beta_.size()*pres_.size()-totNumECVs_,totNumECVs_);
427 : }
428 : }
429 9 : ECVs_beta_.resize(derECVs_beta_.size());
430 9 : ECVs_pres_.resize(derECVs_pres_.size());
431 9 : isReady_=true;
432 9 : }
433 :
434 6 : void ECVmultiThermalBaric::initECVs_observ(const std::vector<double>& all_obs_cvs,const unsigned ncv,const unsigned index_j) {
435 6 : if(todoAutomatic_beta_) { //estimate the steps in beta from observations
436 2 : plumed_massert(all_obs_cvs.size()%ncv==0 && index_j<ncv,"initECVs_observ parameters are inconsistent");
437 2 : std::vector<double> obs_ene(all_obs_cvs.size()/ncv); //copy only useful observations
438 17 : for(unsigned t=0; t<obs_ene.size(); t++) {
439 15 : obs_ene[t]=all_obs_cvs[t*ncv+index_j]+pres0_*all_obs_cvs[t*ncv+index_j+1]; //U=E+pV
440 : }
441 2 : const unsigned temp_steps=estimateNumSteps(derECVs_beta_[0],derECVs_beta_[1],obs_ene,"TEMP");
442 2 : log.printf(" (spacing is on beta, not on temperature)\n");
443 4 : derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,"TEMP",geom_spacing_,1./kbt_);
444 2 : todoAutomatic_beta_=false;
445 : }
446 6 : if(todoAutomatic_pres_) { //estimate the steps in pres from observations
447 2 : plumed_massert(all_obs_cvs.size()%ncv==0 && index_j+1<ncv,"initECVs_observ parameters are inconsistent");
448 2 : std::vector<double> obs_vol(all_obs_cvs.size()/ncv); //copy only useful observations
449 17 : for(unsigned t=0; t<obs_vol.size(); t++) {
450 15 : obs_vol[t]=all_obs_cvs[t*ncv+index_j+1];
451 : }
452 2 : const unsigned pres_steps=estimateNumSteps((pres_[0]-pres0_)/kbt_,(pres_[1]-pres0_)/kbt_,obs_vol,"PRESSURE");
453 2 : log.printf(" (spacing is in beta0 units)\n");
454 4 : pres_=getSteps(pres_[0],pres_[1],pres_steps,"PRESSURE",false,0);
455 2 : todoAutomatic_pres_=false;
456 : }
457 6 : initECVs();
458 6 : calculateECVs(&all_obs_cvs[index_j]);
459 6 : }
460 :
461 3 : void ECVmultiThermalBaric::initECVs_restart(const std::vector<std::string>& lambdas) {
462 3 : std::size_t pos=lambdas[0].find("_");
463 3 : plumed_massert(pos!=std::string::npos,"this should not happen, two CVs are used in "+getName()+", not less");
464 3 : pos=lambdas[0].find("_",pos+1);
465 3 : plumed_massert(pos==std::string::npos,"this should not happen, two CVs are used in "+getName()+", not more");
466 :
467 230 : auto getPres=[&lambdas](const unsigned i) {
468 230 : return lambdas[i].substr(lambdas[i].find("_")+1);
469 3 : };
470 3 : if(todoAutomatic_pres_) {
471 : unsigned pres_steps=1;
472 2 : std::string pres_min=getPres(0);
473 20 : for(unsigned i=1; i<lambdas.size(); i++) { //pres is second, thus increas by 1
474 20 : if(getPres(i)==pres_min) {
475 : break;
476 : }
477 18 : pres_steps++;
478 : }
479 4 : pres_=getSteps(pres_[0],pres_[1],pres_steps,"PRESSURE",false,0);
480 2 : todoAutomatic_pres_=false;
481 : }
482 3 : if(todoAutomatic_beta_) {
483 : unsigned temp_steps=1;
484 2 : std::string pres_max=getPres(pres_.size()-1);
485 208 : for(unsigned i=pres_.size(); i<lambdas.size(); i++) {
486 : //even if CUT_CORNER, the max pressures are all present, for each temp
487 206 : if(getPres(i)==pres_max) {
488 24 : temp_steps++;
489 : }
490 : }
491 4 : derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,"TEMP",geom_spacing_,1./kbt_);
492 2 : todoAutomatic_beta_=false;
493 : }
494 3 : std::vector<std::string> myLambdas=getLambdas();
495 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";
496 3 : plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),"RESTART - mismatch in lambda values of "+getName());
497 :
498 3 : initECVs();
499 3 : }
500 :
501 : }
502 : }
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