Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2023 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed 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 : plumed 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 plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "PathMSDBase.h"
23 : #include "Colvar.h"
24 : #include "core/ActionRegister.h"
25 : #include "core/PlumedMain.h"
26 : #include "tools/Communicator.h"
27 : #include "tools/PDB.h"
28 : #include "tools/RMSD.h"
29 : #include "tools/Tools.h"
30 :
31 : namespace PLMD {
32 : namespace colvar {
33 :
34 29 : void PathMSDBase::registerKeywords(Keywords& keys) {
35 29 : Colvar::registerKeywords(keys);
36 29 : keys.add("compulsory","LAMBDA","the lambda parameter is needed for smoothing, is in the units of plumed");
37 29 : keys.add("compulsory","REFERENCE","the pdb is needed to provide the various milestones");
38 29 : keys.add("optional","NEIGH_SIZE","size of the neighbor list");
39 29 : keys.add("optional","NEIGH_STRIDE","how often the neighbor list needs to be calculated in time units");
40 29 : keys.add("optional", "EPSILON", "(default=-1) the maximum distance between the close and the current structure, the positive value turn on the close structure method");
41 29 : keys.add("optional", "LOG_CLOSE", "(default=0) value 1 enables logging regarding the close structure");
42 29 : keys.add("optional", "DEBUG_CLOSE", "(default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower");
43 29 : }
44 :
45 25 : PathMSDBase::PathMSDBase(const ActionOptions&ao):
46 : PLUMED_COLVAR_INIT(ao),
47 25 : nopbc(false),
48 25 : neigh_size(-1),
49 25 : neigh_stride(-1),
50 25 : epsilonClose(-1),
51 25 : debugClose(0),
52 25 : logClose(0),
53 25 : computeRefClose(false),
54 25 : nframes(0) {
55 25 : parse("LAMBDA",lambda);
56 25 : parse("NEIGH_SIZE",neigh_size);
57 25 : parse("NEIGH_STRIDE",neigh_stride);
58 25 : parse("REFERENCE",reference);
59 25 : parse("EPSILON", epsilonClose);
60 25 : parse("LOG_CLOSE", logClose);
61 25 : parse("DEBUG_CLOSE", debugClose);
62 25 : parseFlag("NOPBC",nopbc);
63 :
64 : // open the file
65 25 : if (FILE* fp=this->fopen(reference.c_str(),"r")) {
66 : // call fclose when exiting this block
67 25 : auto deleter=[this](FILE* f) {
68 25 : this->fclose(f);
69 25 : };
70 : std::unique_ptr<FILE,decltype(deleter)> fp_deleter(fp,deleter);
71 :
72 : std::vector<AtomNumber> aaa;
73 25 : log<<"Opening reference file "<<reference.c_str()<<"\n";
74 : bool do_read=true;
75 : unsigned nat=0;
76 1107 : while (do_read) {
77 1107 : PDB mypdb;
78 1107 : RMSD mymsd;
79 1107 : do_read=mypdb.readFromFilepointer(fp,usingNaturalUnits(),0.1/getUnits().getLength());
80 1107 : if(do_read) {
81 1082 : nframes++;
82 1082 : if(mypdb.getAtomNumbers().size()==0) {
83 0 : error("number of atoms in a frame should be more than zero");
84 : }
85 1082 : if(nat==0) {
86 25 : nat=mypdb.getAtomNumbers().size();
87 : }
88 1082 : if(nat!=mypdb.getAtomNumbers().size()) {
89 0 : error("frames should have the same number of atoms");
90 : }
91 1082 : if(aaa.empty()) {
92 25 : aaa=mypdb.getAtomNumbers();
93 25 : log.printf(" found %zu atoms in input \n",aaa.size());
94 25 : log.printf(" with indices : ");
95 346 : for(unsigned i=0; i<aaa.size(); ++i) {
96 321 : if(i%25==0) {
97 25 : log<<"\n";
98 : }
99 321 : log.printf("%d ",aaa[i].serial());
100 : }
101 25 : log.printf("\n");
102 : }
103 2164 : if(aaa!=mypdb.getAtomNumbers()) {
104 0 : error("frames should contain same atoms in same order");
105 : }
106 1082 : log<<"Found PDB: "<<nframes<<" containing "<<mypdb.getAtomNumbers().size()<<" atoms\n";
107 1082 : pdbv.push_back(mypdb);
108 1082 : derivs_s.resize(mypdb.getAtomNumbers().size());
109 1082 : derivs_z.resize(mypdb.getAtomNumbers().size());
110 1082 : mymsd.set(mypdb,"OPTIMAL");
111 1082 : msdv.push_back(mymsd); // the vector that stores the frames
112 : } else {
113 : break ;
114 : }
115 1107 : }
116 25 : log<<"Found TOTAL "<<nframes<< " PDB in the file "<<reference.c_str()<<" \n";
117 25 : if(nframes==0) {
118 0 : error("at least one frame expected");
119 : }
120 : //set up rmsdRefClose, initialize it to the first structure loaded from reference file
121 25 : rmsdPosClose.set(pdbv[0], "OPTIMAL");
122 25 : firstPosClose = true;
123 25 : }
124 25 : if(neigh_stride>0 || neigh_size>0) {
125 14 : if(neigh_size>int(nframes)) {
126 0 : log.printf(" List size required ( %d ) is too large: resizing to the maximum number of frames required: %u \n",neigh_size,nframes);
127 0 : neigh_size=nframes;
128 : }
129 14 : log.printf(" Neighbor list enabled: \n");
130 14 : log.printf(" size : %d elements\n",neigh_size);
131 14 : log.printf(" stride : %d timesteps \n",neigh_stride);
132 : } else {
133 11 : log.printf(" Neighbor list NOT enabled \n");
134 : }
135 25 : if (epsilonClose > 0) {
136 2 : log.printf(" Computing with the close structure, epsilon = %lf\n", epsilonClose);
137 4 : log << " Bibliography " << plumed.cite("Pazurikova J, Krenek A, Spiwok V, Simkova M J. Chem. Phys. 146, 115101 (2017)") << "\n";
138 : } else {
139 23 : debugClose = 0;
140 23 : logClose = 0;
141 : }
142 25 : if (debugClose) {
143 2 : log.printf(" Extensive debug info regarding close structure turned on\n");
144 : }
145 :
146 25 : rotationRefClose.resize(nframes);
147 25 : savedIndices = std::vector<unsigned>(nframes);
148 :
149 25 : if(nopbc) {
150 1 : log.printf(" without periodic boundary conditions\n");
151 : } else {
152 24 : log.printf(" using periodic boundary conditions\n");
153 : }
154 :
155 25 : }
156 :
157 25 : PathMSDBase::~PathMSDBase() {
158 75 : }
159 :
160 11179 : void PathMSDBase::calculate() {
161 :
162 11179 : if(neigh_size>0 && getExchangeStep()) {
163 0 : error("Neighbor lists for this collective variable are not compatible with replica exchange, sorry for that!");
164 : }
165 :
166 : //log.printf("NOW CALCULATE! \n");
167 :
168 11179 : if(!nopbc) {
169 11128 : makeWhole();
170 : }
171 :
172 :
173 : // resize the list to full
174 11179 : if(imgVec.empty()) { // this is the signal that means: recalculate all
175 7164 : imgVec.resize(nframes);
176 : #pragma omp simd
177 7164 : for(unsigned i=0; i<nframes; i++) {
178 300920 : imgVec[i].property=indexvec[i];
179 300920 : imgVec[i].index=i;
180 : }
181 : }
182 :
183 : // THIS IS THE HEAVY PART (RMSD STUFF)
184 11179 : unsigned stride=comm.Get_size();
185 11179 : unsigned rank=comm.Get_rank();
186 11179 : size_t nat=pdbv[0].size();
187 11179 : plumed_assert(nat>0);
188 11179 : plumed_assert(nframes>0);
189 11179 : plumed_assert(imgVec.size()>0);
190 :
191 11179 : std::vector<Tensor> tmp_rotationRefClose(nframes);
192 :
193 11179 : if (epsilonClose > 0) {
194 : //compute rmsd between positions and close structure, save rotation matrix, drotation_drr01
195 1092 : double posclose = rmsdPosClose.calc_Rot_DRotDRr01(getPositions(), rotationPosClose, drotationPosCloseDrr01, true);
196 : //if we compute for the first time or the existing close structure is too far from current structure
197 1092 : if (firstPosClose || (posclose > epsilonClose)) {
198 : //set the current structure as close one for a few next steps
199 16 : if (logClose) {
200 16 : log << "PLUMED_CLOSE: new close structure, rmsd pos close " << posclose << "\n";
201 : }
202 16 : rmsdPosClose.clear();
203 16 : rmsdPosClose.setReference(getPositions());
204 : //as this is a new close structure, we need to save the rotation matrices fitted to the reference structures
205 : // and we need to accurately recalculate for all reference structures
206 16 : computeRefClose = true;
207 16 : imgVec.resize(nframes);
208 688 : for(unsigned i=0; i<nframes; i++) {
209 672 : imgVec[i].property=indexvec[i];
210 672 : imgVec[i].index=i;
211 : }
212 16 : firstPosClose = false;
213 16 : } else {
214 : //the current structure is pretty close to the close structure, so we use saved rotation matrices to decrease the complexity of rmsd comuptation
215 1076 : if (debugClose) {
216 1076 : log << "PLUMED-CLOSE: old close structure, rmsd pos close " << posclose << "\n";
217 : }
218 1076 : computeRefClose = false;
219 : }
220 : }
221 :
222 11179 : std::vector<double> tmp_distances(imgVec.size(),0.0);
223 : std::vector<Vector> tmp_derivs;
224 : // this array is a merge of all tmp_derivs, so as to allow a single comm.Sum below
225 11179 : std::vector<Vector> tmp_derivs2(imgVec.size()*nat);
226 :
227 : // if imgVec.size() is less than nframes, it means that only some msd will be calculated
228 11179 : if (epsilonClose > 0) {
229 1092 : if (computeRefClose) {
230 : //recompute rotation matrices accurately
231 688 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
232 672 : tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);
233 672 : plumed_assert(tmp_derivs.size()==nat);
234 : #pragma omp simd
235 : for(unsigned j=0; j<nat; j++) {
236 8736 : tmp_derivs2[i*nat+j]=tmp_derivs[j];
237 : }
238 : }
239 : } else {
240 : //approximate distance with saved rotation matrices
241 46268 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
242 45192 : tmp_distances[i] = msdv[imgVec[i].index].calculateWithCloseStructure(getPositions(), tmp_derivs, rotationPosClose, rotationRefClose[imgVec[i].index], drotationPosCloseDrr01, true);
243 45192 : plumed_assert(tmp_derivs.size()==nat);
244 : #pragma omp simd
245 : for(unsigned j=0; j<nat; j++) {
246 587496 : tmp_derivs2[i*nat+j]=tmp_derivs[j];
247 : }
248 45192 : if (debugClose) {
249 45192 : double withclose = tmp_distances[i];
250 45192 : RMSD opt;
251 45192 : opt.setType("OPTIMAL");
252 45192 : opt.setReference(msdv[imgVec[i].index].getReference());
253 : std::vector<Vector> ders;
254 45192 : double withoutclose = opt.calculate(getPositions(), ders, true);
255 45192 : float difference = std::abs(withoutclose-withclose);
256 45192 : log<<"PLUMED-CLOSE: difference original "<<withoutclose;
257 45192 : log<<" - with close "<<withclose<<" = "<<difference<<", step "<<getStep()<<", i "<<i<<" imgVec[i].index "<<imgVec[i].index<<"\n";
258 45192 : }
259 : }
260 : }
261 : } else {
262 : // store temporary local results
263 297781 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
264 287694 : tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);
265 287694 : plumed_assert(tmp_derivs.size()==nat);
266 : #pragma omp simd
267 : for(unsigned j=0; j<nat; j++) {
268 3729822 : tmp_derivs2[i*nat+j]=tmp_derivs[j];
269 : }
270 : }
271 : }
272 :
273 : // reduce over all processors
274 11179 : comm.Sum(tmp_distances);
275 11179 : comm.Sum(tmp_derivs2);
276 11179 : if (epsilonClose > 0 && computeRefClose) {
277 16 : comm.Sum(tmp_rotationRefClose);
278 688 : for (unsigned i=0; i<nframes; i++) {
279 672 : rotationRefClose[i] = tmp_rotationRefClose[i];
280 : }
281 : }
282 : // assign imgVec[i].distance and imgVec[i].distder
283 482329 : for(size_t i=0; i<imgVec.size(); i++) {
284 471150 : imgVec[i].distance=tmp_distances[i];
285 471150 : imgVec[i].distder.assign(&tmp_derivs2[i*nat],nat+&tmp_derivs2[i*nat]);
286 : }
287 :
288 : // END OF THE HEAVY PART
289 :
290 : std::vector<Value*> val_s_path;
291 11179 : if(labels.size()>0) {
292 18018 : for(unsigned i=0; i<labels.size(); i++) {
293 12012 : val_s_path.push_back(getPntrToComponent(labels[i].c_str()));
294 : }
295 : } else {
296 5173 : val_s_path.push_back(getPntrToComponent("sss"));
297 : }
298 22358 : Value* val_z_path=getPntrToComponent("zzz");
299 :
300 11179 : std::vector<double> s_path(val_s_path.size());
301 28364 : for(unsigned i=0; i<s_path.size(); i++) {
302 17185 : s_path[i]=0.;
303 : }
304 : double min_distance=1e10;
305 482329 : for(auto & it : imgVec) {
306 471150 : if(it.distance < min_distance) {
307 : min_distance=it.distance;
308 : }
309 : }
310 :
311 : double partition=0.;
312 482329 : for(auto & it : imgVec) {
313 471150 : it.similarity=std::exp(-lambda*(it.distance - min_distance));
314 1194552 : for(unsigned i=0; i<s_path.size(); i++) {
315 723402 : s_path[i]+=(it.property[i])*it.similarity;
316 : }
317 471150 : partition+=it.similarity;
318 : }
319 28364 : for(unsigned i=0; i<s_path.size(); i++) {
320 17185 : s_path[i]/=partition;
321 17185 : val_s_path[i]->set(s_path[i]) ;
322 : }
323 11179 : val_z_path->set(-(1./lambda)*std::log(partition) + min_distance);
324 :
325 : // clean vector
326 11179 : Tools::set_to_zero(derivs_z);
327 : double tmp;
328 28364 : for(unsigned j=0; j<s_path.size(); j++) {
329 : // clean up
330 17185 : Tools::set_to_zero(derivs_s);
331 : // do the derivative
332 740587 : for(const auto & it : imgVec) {
333 723402 : double expval=it.similarity;
334 723402 : tmp=lambda*expval*(s_path[j]-it.property[j])/partition;
335 : #pragma omp simd
336 723402 : for(unsigned i=0; i< derivs_s.size(); i++) {
337 9394026 : derivs_s[i]+=tmp*it.distder[i] ;
338 : }
339 723402 : if(j==0) {
340 : #pragma omp simd
341 471150 : for(unsigned i=0; i< derivs_z.size(); i++) {
342 6114750 : derivs_z[i]+=it.distder[i]*expval/partition;
343 : }
344 : }
345 : }
346 240386 : for(unsigned i=0; i< derivs_s.size(); i++) {
347 223201 : setAtomsDerivatives (val_s_path[j],i,derivs_s[i]);
348 223201 : if(j==0) {
349 145123 : setAtomsDerivatives (val_z_path,i,derivs_z[i]);
350 : }
351 : }
352 : }
353 28364 : for(unsigned i=0; i<val_s_path.size(); ++i) {
354 17185 : setBoxDerivativesNoPbc(val_s_path[i]);
355 : }
356 11179 : setBoxDerivativesNoPbc(val_z_path);
357 : //
358 : // here set next round neighbors
359 : //
360 11179 : if (neigh_size>0) {
361 : //if( int(getStep())%int(neigh_stride/getTimeStep())==0 ){
362 : // enforce consistency: the stride is in time steps
363 7153 : if( int(getStep())%int(neigh_stride)==0 ) {
364 :
365 : // next round do it all:empty the vector
366 7153 : imgVec.clear();
367 : }
368 : // time to analyze the results:
369 7153 : if(imgVec.size()==nframes) {
370 : //sort by msd
371 0 : sort(imgVec.begin(), imgVec.end(), imgOrderByDist());
372 : //resize
373 0 : imgVec.resize(neigh_size);
374 : }
375 : }
376 : //log.printf("CALCULATION DONE! \n");
377 11179 : }
378 :
379 : }
380 :
381 : }
|
