Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2020 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 "ActionRegister.h"
25 : #include "core/PlumedMain.h"
26 : #include "core/Atoms.h"
27 : #include "tools/PDB.h"
28 : #include "tools/RMSD.h"
29 : #include "tools/Tools.h"
30 : #include <cmath>
31 :
32 : using namespace std;
33 :
34 : namespace PLMD {
35 : namespace colvar {
36 :
37 27 : void PathMSDBase::registerKeywords(Keywords& keys) {
38 27 : Colvar::registerKeywords(keys);
39 108 : keys.add("compulsory","LAMBDA","the lambda parameter is needed for smoothing, is in the units of plumed");
40 108 : keys.add("compulsory","REFERENCE","the pdb is needed to provide the various milestones");
41 108 : keys.add("optional","NEIGH_SIZE","size of the neighbor list");
42 108 : keys.add("optional","NEIGH_STRIDE","how often the neighbor list needs to be calculated in time units");
43 108 : 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");
44 108 : keys.add("optional", "LOG-CLOSE", "(default=0) value 1 enables logging regarding the close structure");
45 108 : keys.add("optional", "DEBUG-CLOSE", "(default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower");
46 108 : keys.add("optional", "LOG_CLOSE", "same as LOG-CLOSE");
47 108 : keys.add("optional", "DEBUG_CLOSE", "same as DEBUG-CLOSE");
48 27 : }
49 :
50 25 : PathMSDBase::PathMSDBase(const ActionOptions&ao):
51 : PLUMED_COLVAR_INIT(ao),
52 : nopbc(false),
53 : neigh_size(-1),
54 : neigh_stride(-1),
55 : epsilonClose(-1),
56 : debugClose(0),
57 : logClose(0),
58 : computeRefClose(false),
59 275 : nframes(0)
60 : {
61 50 : parse("LAMBDA",lambda);
62 50 : parse("NEIGH_SIZE",neigh_size);
63 50 : parse("NEIGH_STRIDE",neigh_stride);
64 50 : parse("REFERENCE",reference);
65 50 : parse("EPSILON", epsilonClose);
66 50 : parse("LOG-CLOSE", logClose);
67 49 : if(!logClose) parse("LOG_CLOSE", logClose);
68 50 : parse("DEBUG-CLOSE", debugClose);
69 49 : if(!debugClose) parse("DEBUG_CLOSE",debugClose);
70 50 : parseFlag("NOPBC",nopbc);
71 :
72 : // open the file
73 50 : FILE* fp=fopen(reference.c_str(),"r");
74 : std::vector<AtomNumber> aaa;
75 25 : if (fp!=NULL)
76 : {
77 50 : log<<"Opening reference file "<<reference.c_str()<<"\n";
78 : bool do_read=true;
79 1107 : while (do_read) {
80 2189 : PDB mypdb;
81 2189 : RMSD mymsd;
82 2214 : do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
83 1107 : if(do_read) {
84 1082 : nframes++;
85 2164 : if(mypdb.getAtomNumbers().size()==0) error("number of atoms in a frame should be more than zero");
86 1082 : unsigned nat=mypdb.getAtomNumbers().size();
87 2164 : if(nat!=mypdb.getAtomNumbers().size()) error("frames should have the same number of atoms");
88 1082 : if(aaa.empty()) {
89 25 : aaa=mypdb.getAtomNumbers();
90 50 : log.printf(" found %z atoms in input \n",aaa.size());
91 25 : log.printf(" with indices : ");
92 1013 : for(unsigned i=0; i<aaa.size(); ++i) {
93 321 : if(i%25==0) log<<"\n";
94 642 : log.printf("%d ",aaa[i].serial());
95 : }
96 25 : log.printf("\n");
97 : }
98 2164 : if(aaa!=mypdb.getAtomNumbers()) error("frames should contain same atoms in same order");
99 2164 : log<<"Found PDB: "<<nframes<<" containing "<<mypdb.getAtomNumbers().size()<<" atoms\n";
100 1082 : pdbv.push_back(mypdb);
101 2164 : derivs_s.resize(mypdb.getAtomNumbers().size());
102 2164 : derivs_z.resize(mypdb.getAtomNumbers().size());
103 2164 : mymsd.set(mypdb,"OPTIMAL");
104 1082 : msdv.push_back(mymsd); // the vector that stores the frames
105 : } else {break ;}
106 : }
107 25 : fclose (fp);
108 50 : log<<"Found TOTAL "<<nframes<< " PDB in the file "<<reference.c_str()<<" \n";
109 25 : if(nframes==0) error("at least one frame expected");
110 : //set up rmsdRefClose, initialize it to the first structure loaded from reference file
111 75 : rmsdPosClose.set(pdbv[0], "OPTIMAL");
112 25 : firstPosClose = true;
113 : }
114 25 : if(neigh_stride>0 || neigh_size>0) {
115 14 : if(neigh_size>int(nframes)) {
116 0 : log.printf(" List size required ( %d ) is too large: resizing to the maximum number of frames required: %u \n",neigh_size,nframes);
117 0 : neigh_size=nframes;
118 : }
119 14 : log.printf(" Neighbor list enabled: \n");
120 14 : log.printf(" size : %d elements\n",neigh_size);
121 14 : log.printf(" stride : %d timesteps \n",neigh_stride);
122 : } else {
123 11 : log.printf(" Neighbor list NOT enabled \n");
124 : }
125 25 : if (epsilonClose > 0) {
126 2 : log.printf(" Computing with the close structure, epsilon = %lf\n", epsilonClose);
127 6 : log << " Bibliography " << plumed.cite("Pazurikova J, Krenek A, Spiwok V, Simkova M J. Chem. Phys. 146, 115101 (2017)") << "\n";
128 : }
129 : else {
130 23 : debugClose = 0;
131 23 : logClose = 0;
132 : }
133 25 : if (debugClose)
134 2 : log.printf(" Extensive debug info regarding close structure turned on\n");
135 :
136 25 : rotationRefClose.resize(nframes);
137 50 : savedIndices = vector<unsigned>(nframes);
138 :
139 25 : if(nopbc) log.printf(" without periodic boundary conditions\n");
140 24 : else log.printf(" using periodic boundary conditions\n");
141 :
142 25 : }
143 :
144 75 : PathMSDBase::~PathMSDBase() {
145 25 : }
146 :
147 11179 : void PathMSDBase::calculate() {
148 :
149 11179 : if(neigh_size>0 && getExchangeStep()) error("Neighbor lists for this collective variable are not compatible with replica exchange, sorry for that!");
150 :
151 : //log.printf("NOW CALCULATE! \n");
152 :
153 11179 : if(!nopbc) makeWhole();
154 :
155 :
156 : // resize the list to full
157 11179 : if(imgVec.empty()) { // this is the signal that means: recalculate all
158 7164 : imgVec.resize(nframes);
159 : #pragma omp simd
160 7164 : for(unsigned i=0; i<nframes; i++) {
161 601840 : imgVec[i].property=indexvec[i];
162 300920 : imgVec[i].index=i;
163 : }
164 : }
165 :
166 : // THIS IS THE HEAVY PART (RMSD STUFF)
167 11179 : unsigned stride=comm.Get_size();
168 11179 : unsigned rank=comm.Get_rank();
169 11179 : unsigned nat=pdbv[0].size();
170 11179 : plumed_assert(nat>0);
171 11179 : plumed_assert(nframes>0);
172 11179 : plumed_assert(imgVec.size()>0);
173 :
174 11179 : std::vector<Tensor> tmp_rotationRefClose(nframes);
175 :
176 11179 : if (epsilonClose > 0) {
177 : //compute rmsd between positions and close structure, save rotation matrix, drotation_drr01
178 2184 : double posclose = rmsdPosClose.calc_Rot_DRotDRr01(getPositions(), rotationPosClose, drotationPosCloseDrr01, true);
179 : //if we compute for the first time or the existing close structure is too far from current structure
180 1092 : if (firstPosClose || (posclose > epsilonClose)) {
181 : //set the current structure as close one for a few next steps
182 16 : if (logClose)
183 16 : log << "PLUMED-CLOSE: new close structure, rmsd pos close " << posclose << "\n";
184 16 : rmsdPosClose.clear();
185 16 : rmsdPosClose.setReference(getPositions());
186 : //as this is a new close structure, we need to save the rotation matrices fitted to the reference structures
187 : // and we need to accurately recalculate for all reference structures
188 16 : computeRefClose = true;
189 16 : imgVec.resize(nframes);
190 1360 : for(unsigned i=0; i<nframes; i++) {
191 1344 : imgVec[i].property=indexvec[i];
192 672 : imgVec[i].index=i;
193 : }
194 16 : firstPosClose = false;
195 : }
196 : else {
197 : //the current structure is pretty close to the close structure, so we use saved rotation matrices to decrease the complexity of rmsd comuptation
198 1076 : if (debugClose)
199 1076 : log << "PLUMED-CLOSE: old close structure, rmsd pos close " << posclose << "\n";
200 1076 : computeRefClose = false;
201 : }
202 : }
203 :
204 22358 : std::vector<double> tmp_distances(imgVec.size(),0.0);
205 : std::vector<Vector> tmp_derivs;
206 : // this array is a merge of all tmp_derivs, so as to allow a single comm.Sum below
207 11179 : std::vector<Vector> tmp_derivs2(imgVec.size()*nat);
208 :
209 : // if imgVec.size() is less than nframes, it means that only some msd will be calculated
210 11179 : if (epsilonClose > 0) {
211 1092 : if (computeRefClose) {
212 : //recompute rotation matrices accurately
213 2048 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
214 1344 : tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);
215 672 : plumed_assert(tmp_derivs.size()==nat);
216 : #pragma omp simd
217 26208 : for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
218 : }
219 : }
220 : else {
221 : //approximate distance with saved rotation matrices
222 92536 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
223 180768 : tmp_distances[i] = msdv[imgVec[i].index].calculateWithCloseStructure(getPositions(), tmp_derivs, rotationPosClose, rotationRefClose[imgVec[i].index], drotationPosCloseDrr01, true);
224 45192 : plumed_assert(tmp_derivs.size()==nat);
225 : #pragma omp simd
226 1762488 : for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
227 45192 : if (debugClose) {
228 90384 : double withclose = tmp_distances[i];
229 90384 : RMSD opt;
230 90384 : opt.setType("OPTIMAL");
231 180768 : opt.setReference(msdv[imgVec[i].index].getReference());
232 : vector<Vector> ders;
233 45192 : double withoutclose = opt.calculate(getPositions(), ders, true);
234 45192 : float difference = fabs(withoutclose-withclose);
235 45192 : log<<"PLUMED-CLOSE: difference original "<<withoutclose;
236 90384 : log<<" - with close "<<withclose<<" = "<<difference<<", step "<<getStep()<<", i "<<i<<" imgVec[i].index "<<imgVec[i].index<<"\n";
237 : }
238 : }
239 : }
240 : }
241 : else {
242 : // store temporary local results
243 883256 : for(unsigned i=rank; i<imgVec.size(); i+=stride) {
244 575388 : tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);
245 287694 : plumed_assert(tmp_derivs.size()==nat);
246 : #pragma omp simd
247 11189466 : for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
248 : }
249 : }
250 :
251 : // reduce over all processors
252 11179 : comm.Sum(tmp_distances);
253 11179 : comm.Sum(tmp_derivs2);
254 11179 : if (epsilonClose > 0 && computeRefClose) {
255 16 : comm.Sum(tmp_rotationRefClose);
256 1360 : for (unsigned i=0; i<nframes; i++) {
257 1344 : rotationRefClose[i] = tmp_rotationRefClose[i];
258 : }
259 : }
260 : // assign imgVec[i].distance and imgVec[i].distder
261 1435808 : for(unsigned i=0; i<imgVec.size(); i++) {
262 471150 : imgVec[i].distance=tmp_distances[i];
263 942300 : imgVec[i].distder.assign(&tmp_derivs2[i*nat],nat+&tmp_derivs2[i*nat]);
264 : }
265 :
266 : // END OF THE HEAVY PART
267 :
268 : vector<Value*> val_s_path;
269 11179 : if(labels.size()>0) {
270 72072 : for(unsigned i=0; i<labels.size(); i++) { val_s_path.push_back(getPntrToComponent(labels[i].c_str()));}
271 : } else {
272 15519 : val_s_path.push_back(getPntrToComponent("sss"));
273 : }
274 22358 : Value* val_z_path=getPntrToComponent("zzz");
275 :
276 56728 : vector<double> s_path(val_s_path.size()); for(unsigned i=0; i<s_path.size(); i++)s_path[i]=0.;
277 : double partition=0.;
278 : double tmp;
279 :
280 : // clean vector
281 457727 : for(unsigned i=0; i< derivs_z.size(); i++) {derivs_z[i].zero();}
282 :
283 482329 : for(auto & it : imgVec) {
284 471150 : it.similarity=exp(-lambda*(it.distance));
285 : //log<<"DISTANCE "<<(*it).distance<<"\n";
286 3112506 : for(unsigned i=0; i<s_path.size(); i++) {
287 1446804 : s_path[i]+=(it.property[i])*it.similarity;
288 : }
289 471150 : partition+=it.similarity;
290 : }
291 125468 : for(unsigned i=0; i<s_path.size(); i++) { s_path[i]/=partition; val_s_path[i]->set(s_path[i]) ;}
292 11179 : val_z_path->set(-(1./lambda)*std::log(partition));
293 73913 : for(unsigned j=0; j<s_path.size(); j++) {
294 : // clean up
295 : #pragma omp simd
296 240386 : for(unsigned i=0; i< derivs_s.size(); i++) {derivs_s[i].zero();}
297 : // do the derivative
298 740587 : for(const auto & it : imgVec) {
299 723402 : double expval=it.similarity;
300 2170206 : tmp=lambda*expval*(s_path[j]-it.property[j])/partition;
301 : #pragma omp simd
302 19511454 : for(unsigned i=0; i< derivs_s.size(); i++) { derivs_s[i]+=tmp*it.distder[i] ;}
303 723402 : if(j==0) {
304 : #pragma omp simd
305 12700650 : for(unsigned i=0; i< derivs_z.size(); i++) { derivs_z[i]+=it.distder[i]*expval/partition;}
306 : }
307 : }
308 703973 : for(unsigned i=0; i< derivs_s.size(); i++) {
309 669603 : setAtomsDerivatives (val_s_path[j],i,derivs_s[i]);
310 368324 : if(j==0) {setAtomsDerivatives (val_z_path,i,derivs_z[i]);}
311 : }
312 : }
313 73913 : for(unsigned i=0; i<val_s_path.size(); ++i) setBoxDerivativesNoPbc(val_s_path[i]);
314 11179 : setBoxDerivativesNoPbc(val_z_path);
315 : //
316 : // here set next round neighbors
317 : //
318 11179 : if (neigh_size>0) {
319 : //if( int(getStep())%int(neigh_stride/getTimeStep())==0 ){
320 : // enforce consistency: the stride is in time steps
321 7153 : if( int(getStep())%int(neigh_stride)==0 ) {
322 :
323 : // next round do it all:empty the vector
324 : imgVec.clear();
325 : }
326 : // time to analyze the results:
327 7153 : if(imgVec.size()==nframes) {
328 : //sort by msd
329 : sort(imgVec.begin(), imgVec.end(), imgOrderByDist());
330 : //resize
331 0 : imgVec.resize(neigh_size);
332 : }
333 : }
334 : //log.printf("CALCULATION DONE! \n");
335 11179 : }
336 :
337 : }
338 :
339 5517 : }
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