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 : #include <algorithm>
32 :
33 : namespace PLMD {
34 : namespace colvar {
35 :
36 33 : void PathMSDBase::registerKeywords(Keywords& keys) {
37 33 : Colvar::registerKeywords(keys);
38 66 : keys.add("compulsory","LAMBDA","the lambda parameter is needed for smoothing, is in the units of plumed");
39 66 : keys.add("compulsory","REFERENCE","the pdb is needed to provide the various milestones");
40 66 : keys.add("optional","NEIGH_SIZE","size of the neighbor list");
41 66 : keys.add("optional","NEIGH_STRIDE","how often the neighbor list needs to be calculated in time units");
42 66 : 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");
43 66 : keys.add("optional", "LOG_CLOSE", "(default=0) value 1 enables logging regarding the close structure");
44 66 : keys.add("optional", "DEBUG_CLOSE", "(default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower");
45 33 : }
46 :
47 25 : PathMSDBase::PathMSDBase(const ActionOptions&ao):
48 : PLUMED_COLVAR_INIT(ao),
49 25 : nopbc(false),
50 25 : neigh_size(-1),
51 25 : neigh_stride(-1),
52 25 : epsilonClose(-1),
53 25 : debugClose(0),
54 25 : logClose(0),
55 25 : computeRefClose(false),
56 25 : nframes(0) {
57 25 : parse("LAMBDA",lambda);
58 25 : parse("NEIGH_SIZE",neigh_size);
59 25 : parse("NEIGH_STRIDE",neigh_stride);
60 25 : parse("REFERENCE",reference);
61 25 : parse("EPSILON", epsilonClose);
62 25 : parse("LOG_CLOSE", logClose);
63 25 : parse("DEBUG_CLOSE", debugClose);
64 25 : parseFlag("NOPBC",nopbc);
65 :
66 : // open the file
67 25 : if (FILE* fp=this->fopen(reference.c_str(),"r")) {
68 : // call fclose when exiting this block
69 25 : auto deleter=[this](FILE* f) {
70 25 : this->fclose(f);
71 25 : };
72 : std::unique_ptr<FILE,decltype(deleter)> fp_deleter(fp,deleter);
73 :
74 : std::vector<AtomNumber> aaa;
75 25 : log<<"Opening reference file "<<reference.c_str()<<"\n";
76 : bool do_read=true;
77 : unsigned nat=0;
78 1107 : while (do_read) {
79 1107 : PDB mypdb;
80 1107 : RMSD mymsd;
81 1107 : do_read=mypdb.readFromFilepointer(fp,usingNaturalUnits(),0.1/getUnits().getLength());
82 1107 : if(do_read) {
83 1082 : nframes++;
84 1082 : if(mypdb.getAtomNumbers().size()==0) {
85 0 : error("number of atoms in a frame should be more than zero");
86 : }
87 1082 : if(nat==0) {
88 25 : nat=mypdb.getAtomNumbers().size();
89 : }
90 1082 : if(nat!=mypdb.getAtomNumbers().size()) {
91 0 : error("frames should have the same number of atoms");
92 : }
93 1082 : if(aaa.empty()) {
94 25 : aaa=mypdb.getAtomNumbers();
95 25 : log.printf(" found %zu atoms in input \n",aaa.size());
96 25 : log.printf(" with indices : ");
97 346 : for(unsigned i=0; i<aaa.size(); ++i) {
98 321 : if(i%25==0) {
99 25 : log<<"\n";
100 : }
101 321 : log.printf("%d ",aaa[i].serial());
102 : }
103 25 : log.printf("\n");
104 : }
105 1082 : if(aaa!=mypdb.getAtomNumbers()) {
106 0 : error("frames should contain same atoms in same order");
107 : }
108 1082 : log<<"Found PDB: "<<nframes<<" containing "<<mypdb.getAtomNumbers().size()<<" atoms\n";
109 1082 : pdbv.push_back(mypdb);
110 1082 : derivs_s.resize(mypdb.getAtomNumbers().size());
111 1082 : derivs_z.resize(mypdb.getAtomNumbers().size());
112 1082 : mymsd.set(mypdb,"OPTIMAL");
113 1082 : msdv.push_back(mymsd); // the vector that stores the frames
114 : } else {
115 : break ;
116 : }
117 1107 : }
118 25 : log<<"Found TOTAL "<<nframes<< " PDB in the file "<<reference.c_str()<<" \n";
119 25 : if(nframes==0) {
120 0 : error("at least one frame expected");
121 : }
122 : //set up rmsdRefClose, initialize it to the first structure loaded from reference file
123 25 : rmsdPosClose.set(pdbv[0], "OPTIMAL");
124 25 : firstPosClose = true;
125 25 : }
126 25 : if(neigh_stride>0 || neigh_size>0) {
127 14 : if(neigh_size>int(nframes)) {
128 0 : log.printf(" List size required ( %d ) is too large: resizing to the maximum number of frames required: %u \n",neigh_size,nframes);
129 0 : neigh_size=nframes;
130 : }
131 14 : log.printf(" Neighbor list enabled: \n");
132 14 : log.printf(" size : %d elements\n",neigh_size);
133 14 : log.printf(" stride : %d timesteps \n",neigh_stride);
134 : } else {
135 11 : log.printf(" Neighbor list NOT enabled \n");
136 : }
137 25 : if (epsilonClose > 0) {
138 2 : log.printf(" Computing with the close structure, epsilon = %lf\n", epsilonClose);
139 4 : log << " Bibliography " << plumed.cite("Pazurikova J, Krenek A, Spiwok V, Simkova M J. Chem. Phys. 146, 115101 (2017)") << "\n";
140 : } else {
141 23 : debugClose = 0;
142 23 : logClose = 0;
143 : }
144 25 : if (debugClose) {
145 2 : log.printf(" Extensive debug info regarding close structure turned on\n");
146 : }
147 :
148 25 : rotationRefClose.resize(nframes);
149 25 : savedIndices = std::vector<unsigned>(nframes);
150 :
151 25 : if(nopbc) {
152 1 : log.printf(" without periodic boundary conditions\n");
153 : } else {
154 24 : log.printf(" using periodic boundary conditions\n");
155 : }
156 :
157 25 : }
158 :
159 25 : PathMSDBase::~PathMSDBase() {
160 75 : }
161 :
162 11179 : void PathMSDBase::calculate() {
163 :
164 11179 : if(neigh_size>0 && getExchangeStep()) {
165 0 : error("Neighbor lists for this collective variable are not compatible with replica exchange, sorry for that!");
166 : }
167 :
168 : //log.printf("NOW CALCULATE! \n");
169 :
170 11179 : if(!nopbc) {
171 11128 : makeWhole();
172 : }
173 :
174 :
175 : // resize the list to full
176 11179 : if(imgVec.empty()) { // this is the signal that means: recalculate all
177 7164 : imgVec.resize(nframes);
178 : // No `omp simd` here: ImagePath::property is a std::vector<double>, so this body performs a
179 : // vector copy-assignment, i.e. it allocates. There is nothing for a SIMD unit to do.
180 308084 : for(unsigned i=0; i<nframes; i++) {
181 300920 : imgVec[i].property=indexvec[i];
182 300920 : imgVec[i].index=i;
183 : }
184 : }
185 :
186 : // THIS IS THE HEAVY PART (RMSD STUFF)
187 11179 : unsigned stride=comm.Get_size();
188 11179 : unsigned rank=comm.Get_rank();
189 11179 : size_t nat=pdbv[0].size();
190 11179 : plumed_assert(nat>0);
191 11179 : plumed_assert(nframes>0);
192 11179 : plumed_assert(imgVec.size()>0);
193 :
194 11179 : std::vector<Tensor> tmp_rotationRefClose(nframes);
195 :
196 11179 : if (epsilonClose > 0) {
197 : //compute rmsd between positions and close structure, save rotation matrix, drotation_drr01
198 1092 : double posclose = rmsdPosClose.calc_Rot_DRotDRr01(getPositions(), rotationPosClose, drotationPosCloseDrr01, true);
199 : //if we compute for the first time or the existing close structure is too far from current structure
200 1092 : if (firstPosClose || (posclose > epsilonClose)) {
201 : //set the current structure as close one for a few next steps
202 16 : if (logClose) {
203 16 : log << "PLUMED_CLOSE: new close structure, rmsd pos close " << posclose << "\n";
204 : }
205 16 : rmsdPosClose.clear();
206 16 : rmsdPosClose.setReference(getPositions());
207 : //as this is a new close structure, we need to save the rotation matrices fitted to the reference structures
208 : // and we need to accurately recalculate for all reference structures
209 16 : computeRefClose = true;
210 16 : imgVec.resize(nframes);
211 688 : for(unsigned i=0; i<nframes; i++) {
212 672 : imgVec[i].property=indexvec[i];
213 672 : imgVec[i].index=i;
214 : }
215 16 : firstPosClose = false;
216 16 : } else {
217 : //the current structure is pretty close to the close structure, so we use saved rotation matrices to decrease the complexity of rmsd comuptation
218 1076 : if (debugClose) {
219 1076 : log << "PLUMED-CLOSE: old close structure, rmsd pos close " << posclose << "\n";
220 : }
221 1076 : computeRefClose = false;
222 : }
223 : }
224 :
225 11179 : std::vector<double> tmp_distances(imgVec.size(),0.0);
226 : std::vector<Vector> tmp_derivs;
227 : // this array is a merge of all tmp_derivs, so as to allow a single comm.Sum below
228 11179 : std::vector<Vector> tmp_derivs2(imgVec.size()*nat);
229 :
230 : // if imgVec.size() is less than nframes, it means that only some msd will be calculated
231 11179 : if (epsilonClose > 0) {
232 1092 : if (computeRefClose) {
233 : //recompute rotation matrices accurately
234 688 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
235 672 : tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);
236 672 : plumed_assert(tmp_derivs.size()==nat);
237 672 : std::copy_n(tmp_derivs.begin(), nat, tmp_derivs2.begin()+i*nat);
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 45192 : std::copy_n(tmp_derivs.begin(), nat, tmp_derivs2.begin()+i*nat);
245 45192 : if (debugClose) {
246 45192 : double withclose = tmp_distances[i];
247 45192 : RMSD opt;
248 45192 : opt.setType("OPTIMAL");
249 45192 : opt.setReference(msdv[imgVec[i].index].getReference());
250 : std::vector<Vector> ders;
251 45192 : double withoutclose = opt.calculate(getPositions(), ders, true);
252 45192 : float difference = std::abs(withoutclose-withclose);
253 45192 : log<<"PLUMED-CLOSE: difference original "<<withoutclose;
254 45192 : log<<" - with close "<<withclose<<" = "<<difference<<", step "<<getStep()<<", i "<<i<<" imgVec[i].index "<<imgVec[i].index<<"\n";
255 45192 : }
256 : }
257 : }
258 : } else {
259 : // store temporary local results
260 297781 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
261 287694 : tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);
262 287694 : plumed_assert(tmp_derivs.size()==nat);
263 287694 : std::copy_n(tmp_derivs.begin(), nat, tmp_derivs2.begin()+i*nat);
264 : }
265 : }
266 :
267 : // reduce over all processors
268 11179 : comm.Sum(tmp_distances);
269 11179 : comm.Sum(tmp_derivs2);
270 11179 : if (epsilonClose > 0 && computeRefClose) {
271 16 : comm.Sum(tmp_rotationRefClose);
272 688 : for (unsigned i=0; i<nframes; i++) {
273 672 : rotationRefClose[i] = tmp_rotationRefClose[i];
274 : }
275 : }
276 : // assign imgVec[i].distance and imgVec[i].distder
277 482329 : for(size_t i=0; i<imgVec.size(); i++) {
278 471150 : imgVec[i].distance=tmp_distances[i];
279 471150 : imgVec[i].distder.assign(&tmp_derivs2[i*nat],nat+&tmp_derivs2[i*nat]);
280 : }
281 :
282 : // END OF THE HEAVY PART
283 :
284 : std::vector<Value*> val_s_path;
285 11179 : if(labels.size()>0) {
286 18018 : for(unsigned i=0; i<labels.size(); i++) {
287 12012 : val_s_path.push_back(getPntrToComponent(labels[i].c_str()));
288 : }
289 : } else {
290 5173 : val_s_path.push_back(getPntrToComponent("sss"));
291 : }
292 22358 : Value* val_z_path=getPntrToComponent("zzz");
293 :
294 11179 : std::vector<double> s_path(val_s_path.size());
295 28364 : for(unsigned i=0; i<s_path.size(); i++) {
296 17185 : s_path[i]=0.;
297 : }
298 : double min_distance=1e10;
299 482329 : for(auto & it : imgVec) {
300 471150 : if(it.distance < min_distance) {
301 : min_distance=it.distance;
302 : }
303 : }
304 :
305 : double partition=0.;
306 482329 : for(auto & it : imgVec) {
307 471150 : it.similarity=std::exp(-lambda*(it.distance - min_distance));
308 1194552 : for(unsigned i=0; i<s_path.size(); i++) {
309 723402 : s_path[i]+=(it.property[i])*it.similarity;
310 : }
311 471150 : partition+=it.similarity;
312 : }
313 28364 : for(unsigned i=0; i<s_path.size(); i++) {
314 17185 : s_path[i]/=partition;
315 17185 : val_s_path[i]->set(s_path[i]) ;
316 : }
317 11179 : val_z_path->set(-(1./lambda)*std::log(partition) + min_distance);
318 :
319 : // clean vector
320 11179 : Tools::set_to_zero(derivs_z);
321 : double tmp;
322 28364 : for(unsigned j=0; j<s_path.size(); j++) {
323 : // clean up
324 17185 : Tools::set_to_zero(derivs_s);
325 : // do the derivative
326 740587 : for(const auto & it : imgVec) {
327 723402 : double expval=it.similarity;
328 723402 : tmp=lambda*expval*(s_path[j]-it.property[j])/partition;
329 : #pragma omp simd
330 723402 : for(unsigned i=0; i< derivs_s.size(); i++) {
331 9394026 : derivs_s[i]+=tmp*it.distder[i] ;
332 : }
333 723402 : if(j==0) {
334 : #pragma omp simd
335 471150 : for(unsigned i=0; i< derivs_z.size(); i++) {
336 6114750 : derivs_z[i]+=it.distder[i]*expval/partition;
337 : }
338 : }
339 : }
340 240386 : for(unsigned i=0; i< derivs_s.size(); i++) {
341 223201 : setAtomsDerivatives (val_s_path[j],i,derivs_s[i]);
342 223201 : if(j==0) {
343 145123 : setAtomsDerivatives (val_z_path,i,derivs_z[i]);
344 : }
345 : }
346 : }
347 28364 : for(unsigned i=0; i<val_s_path.size(); ++i) {
348 17185 : setBoxDerivativesNoPbc(val_s_path[i]);
349 : }
350 11179 : setBoxDerivativesNoPbc(val_z_path);
351 : //
352 : // here set next round neighbors
353 : //
354 11179 : if (neigh_size>0) {
355 : //if( int(getStep())%int(neigh_stride/getTimeStep())==0 ){
356 : // enforce consistency: the stride is in time steps
357 7153 : if( int(getStep())%int(neigh_stride)==0 ) {
358 :
359 : // next round do it all:empty the vector
360 7153 : imgVec.clear();
361 : }
362 : // time to analyze the results:
363 7153 : if(imgVec.size()==nframes) {
364 : //sort by msd
365 0 : sort(imgVec.begin(), imgVec.end(), imgOrderByDist());
366 : //resize
367 0 : imgVec.resize(neigh_size);
368 : }
369 : }
370 : //log.printf("CALCULATION DONE! \n");
371 11179 : }
372 :
373 : }
374 :
375 : }
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