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 58 : keys.add("compulsory","LAMBDA","the lambda parameter is needed for smoothing, is in the units of plumed");
37 58 : keys.add("compulsory","REFERENCE","the pdb is needed to provide the various milestones");
38 58 : keys.add("optional","NEIGH_SIZE","size of the neighbor list");
39 58 : keys.add("optional","NEIGH_STRIDE","how often the neighbor list needs to be calculated in time units");
40 58 : 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 58 : keys.add("optional", "LOG_CLOSE", "(default=0) value 1 enables logging regarding the close structure");
42 58 : 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 : {
56 25 : parse("LAMBDA",lambda);
57 25 : parse("NEIGH_SIZE",neigh_size);
58 25 : parse("NEIGH_STRIDE",neigh_stride);
59 25 : parse("REFERENCE",reference);
60 25 : parse("EPSILON", epsilonClose);
61 25 : parse("LOG_CLOSE", logClose);
62 25 : parse("DEBUG_CLOSE", debugClose);
63 25 : parseFlag("NOPBC",nopbc);
64 :
65 : // open the file
66 25 : if (FILE* fp=this->fopen(reference.c_str(),"r"))
67 : {
68 : // call fclose when exiting this block
69 25 : auto deleter=[this](FILE* f) { this->fclose(f); };
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) error("number of atoms in a frame should be more than zero");
83 1082 : if(nat==0) nat=mypdb.getAtomNumbers().size();
84 1082 : if(nat!=mypdb.getAtomNumbers().size()) error("frames should have the same number of atoms");
85 1082 : if(aaa.empty()) {
86 25 : aaa=mypdb.getAtomNumbers();
87 25 : log.printf(" found %zu atoms in input \n",aaa.size());
88 25 : log.printf(" with indices : ");
89 346 : for(unsigned i=0; i<aaa.size(); ++i) {
90 321 : if(i%25==0) log<<"\n";
91 321 : log.printf("%d ",aaa[i].serial());
92 : }
93 25 : log.printf("\n");
94 : }
95 2164 : if(aaa!=mypdb.getAtomNumbers()) error("frames should contain same atoms in same order");
96 1082 : log<<"Found PDB: "<<nframes<<" containing "<<mypdb.getAtomNumbers().size()<<" atoms\n";
97 1082 : pdbv.push_back(mypdb);
98 1082 : derivs_s.resize(mypdb.getAtomNumbers().size());
99 1082 : derivs_z.resize(mypdb.getAtomNumbers().size());
100 1082 : mymsd.set(mypdb,"OPTIMAL");
101 1082 : msdv.push_back(mymsd); // the vector that stores the frames
102 : } else {break ;}
103 1107 : }
104 25 : log<<"Found TOTAL "<<nframes<< " PDB in the file "<<reference.c_str()<<" \n";
105 25 : if(nframes==0) error("at least one frame expected");
106 : //set up rmsdRefClose, initialize it to the first structure loaded from reference file
107 25 : rmsdPosClose.set(pdbv[0], "OPTIMAL");
108 25 : firstPosClose = true;
109 25 : }
110 25 : if(neigh_stride>0 || neigh_size>0) {
111 14 : if(neigh_size>int(nframes)) {
112 0 : log.printf(" List size required ( %d ) is too large: resizing to the maximum number of frames required: %u \n",neigh_size,nframes);
113 0 : neigh_size=nframes;
114 : }
115 14 : log.printf(" Neighbor list enabled: \n");
116 14 : log.printf(" size : %d elements\n",neigh_size);
117 14 : log.printf(" stride : %d timesteps \n",neigh_stride);
118 : } else {
119 11 : log.printf(" Neighbor list NOT enabled \n");
120 : }
121 25 : if (epsilonClose > 0) {
122 2 : log.printf(" Computing with the close structure, epsilon = %lf\n", epsilonClose);
123 4 : log << " Bibliography " << plumed.cite("Pazurikova J, Krenek A, Spiwok V, Simkova M J. Chem. Phys. 146, 115101 (2017)") << "\n";
124 : }
125 : else {
126 23 : debugClose = 0;
127 23 : logClose = 0;
128 : }
129 25 : if (debugClose)
130 2 : log.printf(" Extensive debug info regarding close structure turned on\n");
131 :
132 25 : rotationRefClose.resize(nframes);
133 25 : savedIndices = std::vector<unsigned>(nframes);
134 :
135 25 : if(nopbc) log.printf(" without periodic boundary conditions\n");
136 24 : else log.printf(" using periodic boundary conditions\n");
137 :
138 25 : }
139 :
140 25 : PathMSDBase::~PathMSDBase() {
141 75 : }
142 :
143 11179 : void PathMSDBase::calculate() {
144 :
145 11179 : if(neigh_size>0 && getExchangeStep()) error("Neighbor lists for this collective variable are not compatible with replica exchange, sorry for that!");
146 :
147 : //log.printf("NOW CALCULATE! \n");
148 :
149 11179 : if(!nopbc) makeWhole();
150 :
151 :
152 : // resize the list to full
153 11179 : if(imgVec.empty()) { // this is the signal that means: recalculate all
154 7164 : imgVec.resize(nframes);
155 : #pragma omp simd
156 7164 : for(unsigned i=0; i<nframes; i++) {
157 300920 : imgVec[i].property=indexvec[i];
158 300920 : imgVec[i].index=i;
159 : }
160 : }
161 :
162 : // THIS IS THE HEAVY PART (RMSD STUFF)
163 11179 : unsigned stride=comm.Get_size();
164 11179 : unsigned rank=comm.Get_rank();
165 11179 : size_t nat=pdbv[0].size();
166 11179 : plumed_assert(nat>0);
167 11179 : plumed_assert(nframes>0);
168 11179 : plumed_assert(imgVec.size()>0);
169 :
170 11179 : std::vector<Tensor> tmp_rotationRefClose(nframes);
171 :
172 11179 : if (epsilonClose > 0) {
173 : //compute rmsd between positions and close structure, save rotation matrix, drotation_drr01
174 1092 : double posclose = rmsdPosClose.calc_Rot_DRotDRr01(getPositions(), rotationPosClose, drotationPosCloseDrr01, true);
175 : //if we compute for the first time or the existing close structure is too far from current structure
176 1092 : if (firstPosClose || (posclose > epsilonClose)) {
177 : //set the current structure as close one for a few next steps
178 16 : if (logClose)
179 16 : log << "PLUMED_CLOSE: new close structure, rmsd pos close " << posclose << "\n";
180 16 : rmsdPosClose.clear();
181 16 : rmsdPosClose.setReference(getPositions());
182 : //as this is a new close structure, we need to save the rotation matrices fitted to the reference structures
183 : // and we need to accurately recalculate for all reference structures
184 16 : computeRefClose = true;
185 16 : imgVec.resize(nframes);
186 688 : for(unsigned i=0; i<nframes; i++) {
187 672 : imgVec[i].property=indexvec[i];
188 672 : imgVec[i].index=i;
189 : }
190 16 : firstPosClose = false;
191 16 : }
192 : else {
193 : //the current structure is pretty close to the close structure, so we use saved rotation matrices to decrease the complexity of rmsd comuptation
194 1076 : if (debugClose)
195 1076 : log << "PLUMED-CLOSE: old close structure, rmsd pos close " << posclose << "\n";
196 1076 : computeRefClose = false;
197 : }
198 : }
199 :
200 11179 : std::vector<double> tmp_distances(imgVec.size(),0.0);
201 : std::vector<Vector> tmp_derivs;
202 : // this array is a merge of all tmp_derivs, so as to allow a single comm.Sum below
203 11179 : std::vector<Vector> tmp_derivs2(imgVec.size()*nat);
204 :
205 : // if imgVec.size() is less than nframes, it means that only some msd will be calculated
206 11179 : if (epsilonClose > 0) {
207 1092 : if (computeRefClose) {
208 : //recompute rotation matrices accurately
209 688 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
210 672 : tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);
211 672 : plumed_assert(tmp_derivs.size()==nat);
212 : #pragma omp simd
213 8736 : for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
214 : }
215 : }
216 : else {
217 : //approximate distance with saved rotation matrices
218 46268 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
219 45192 : tmp_distances[i] = msdv[imgVec[i].index].calculateWithCloseStructure(getPositions(), tmp_derivs, rotationPosClose, rotationRefClose[imgVec[i].index], drotationPosCloseDrr01, true);
220 45192 : plumed_assert(tmp_derivs.size()==nat);
221 : #pragma omp simd
222 587496 : for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
223 45192 : if (debugClose) {
224 45192 : double withclose = tmp_distances[i];
225 45192 : RMSD opt;
226 45192 : opt.setType("OPTIMAL");
227 45192 : opt.setReference(msdv[imgVec[i].index].getReference());
228 : std::vector<Vector> ders;
229 45192 : double withoutclose = opt.calculate(getPositions(), ders, true);
230 45192 : float difference = std::abs(withoutclose-withclose);
231 45192 : log<<"PLUMED-CLOSE: difference original "<<withoutclose;
232 45192 : log<<" - with close "<<withclose<<" = "<<difference<<", step "<<getStep()<<", i "<<i<<" imgVec[i].index "<<imgVec[i].index<<"\n";
233 45192 : }
234 : }
235 : }
236 : }
237 : else {
238 : // store temporary local results
239 297781 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
240 287694 : tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);
241 287694 : plumed_assert(tmp_derivs.size()==nat);
242 : #pragma omp simd
243 3729822 : for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
244 : }
245 : }
246 :
247 : // reduce over all processors
248 11179 : comm.Sum(tmp_distances);
249 11179 : comm.Sum(tmp_derivs2);
250 11179 : if (epsilonClose > 0 && computeRefClose) {
251 16 : comm.Sum(tmp_rotationRefClose);
252 688 : for (unsigned i=0; i<nframes; i++) {
253 672 : rotationRefClose[i] = tmp_rotationRefClose[i];
254 : }
255 : }
256 : // assign imgVec[i].distance and imgVec[i].distder
257 482329 : for(size_t i=0; i<imgVec.size(); i++) {
258 471150 : imgVec[i].distance=tmp_distances[i];
259 471150 : imgVec[i].distder.assign(&tmp_derivs2[i*nat],nat+&tmp_derivs2[i*nat]);
260 : }
261 :
262 : // END OF THE HEAVY PART
263 :
264 : std::vector<Value*> val_s_path;
265 11179 : if(labels.size()>0) {
266 18018 : for(unsigned i=0; i<labels.size(); i++) { val_s_path.push_back(getPntrToComponent(labels[i].c_str()));}
267 : } else {
268 5173 : val_s_path.push_back(getPntrToComponent("sss"));
269 : }
270 22358 : Value* val_z_path=getPntrToComponent("zzz");
271 :
272 28364 : std::vector<double> s_path(val_s_path.size()); for(unsigned i=0; i<s_path.size(); i++)s_path[i]=0.;
273 : double min_distance=1e10;
274 482329 : for(auto & it : imgVec) {
275 471150 : if(it.distance < min_distance) min_distance=it.distance;
276 : }
277 :
278 : double partition=0.;
279 482329 : for(auto & it : imgVec) {
280 471150 : it.similarity=std::exp(-lambda*(it.distance - min_distance));
281 1194552 : for(unsigned i=0; i<s_path.size(); i++) {
282 723402 : s_path[i]+=(it.property[i])*it.similarity;
283 : }
284 471150 : partition+=it.similarity;
285 : }
286 28364 : for(unsigned i=0; i<s_path.size(); i++) { s_path[i]/=partition; val_s_path[i]->set(s_path[i]) ;}
287 11179 : val_z_path->set(-(1./lambda)*std::log(partition) + min_distance);
288 :
289 : // clean vector
290 11179 : Tools::set_to_zero(derivs_z);
291 : double tmp;
292 28364 : for(unsigned j=0; j<s_path.size(); j++) {
293 : // clean up
294 17185 : Tools::set_to_zero(derivs_s);
295 : // do the derivative
296 740587 : for(const auto & it : imgVec) {
297 723402 : double expval=it.similarity;
298 723402 : tmp=lambda*expval*(s_path[j]-it.property[j])/partition;
299 : #pragma omp simd
300 10117428 : for(unsigned i=0; i< derivs_s.size(); i++) { derivs_s[i]+=tmp*it.distder[i] ;}
301 723402 : if(j==0) {
302 : #pragma omp simd
303 6585900 : for(unsigned i=0; i< derivs_z.size(); i++) { derivs_z[i]+=it.distder[i]*expval/partition;}
304 : }
305 : }
306 240386 : for(unsigned i=0; i< derivs_s.size(); i++) {
307 223201 : setAtomsDerivatives (val_s_path[j],i,derivs_s[i]);
308 223201 : if(j==0) {setAtomsDerivatives (val_z_path,i,derivs_z[i]);}
309 : }
310 : }
311 28364 : for(unsigned i=0; i<val_s_path.size(); ++i) setBoxDerivativesNoPbc(val_s_path[i]);
312 11179 : setBoxDerivativesNoPbc(val_z_path);
313 : //
314 : // here set next round neighbors
315 : //
316 11179 : if (neigh_size>0) {
317 : //if( int(getStep())%int(neigh_stride/getTimeStep())==0 ){
318 : // enforce consistency: the stride is in time steps
319 7153 : if( int(getStep())%int(neigh_stride)==0 ) {
320 :
321 : // next round do it all:empty the vector
322 7153 : imgVec.clear();
323 : }
324 : // time to analyze the results:
325 7153 : if(imgVec.size()==nframes) {
326 : //sort by msd
327 0 : sort(imgVec.begin(), imgVec.end(), imgOrderByDist());
328 : //resize
329 0 : imgVec.resize(neigh_size);
330 : }
331 : }
332 : //log.printf("CALCULATION DONE! \n");
333 11179 : }
334 :
335 : }
336 :
337 : }
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