Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2017 of Pipolo Silvio and Fabio Pietrucci.
3 :
4 : The piv module is free software: you can redistribute it and/or modify
5 : it under the terms of the GNU Lesser General Public License as published by
6 : the Free Software Foundation, either version 3 of the License, or
7 : (at your option) any later version.
8 :
9 : The piv module is distributed in the hope that it will be useful,
10 : but WITHOUT ANY WARRANTY; without even the implied warranty of
11 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 : GNU Lesser General Public License for more details.
13 :
14 : You should have received a copy of the GNU Lesser General Public License
15 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
16 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
17 : #include "colvar/Colvar.h"
18 : #include "core/ActionRegister.h"
19 : #include "core/PlumedMain.h"
20 : #include "core/ActionWithVirtualAtom.h"
21 : #include "tools/NeighborList.h"
22 : #include "tools/SwitchingFunction.h"
23 : #include "tools/PDB.h"
24 : #include "tools/Pbc.h"
25 : #include "tools/Communicator.h"
26 : #include "tools/Stopwatch.h"
27 : #include "core/ActionSet.h"
28 :
29 : #include <string>
30 : #include <cmath>
31 : #include <iostream>
32 :
33 : using namespace std;
34 :
35 : namespace PLMD {
36 : namespace piv {
37 :
38 : //+PLUMEDOC PIVMOD_COLVAR PIV
39 : /*
40 : Calculates the PIV-distance.
41 :
42 : PIV distance is the squared Cartesian distance between the PIV \cite gallet2013structural \cite pipolo2017navigating
43 : associated to the configuration of the system during the dynamics and a reference configuration provided
44 : as input (PDB file format).
45 : PIV can be used together with \ref FUNCPATHMSD to define a path in the PIV space.
46 :
47 : \par Examples
48 :
49 : The following example calculates PIV-distances from three reference configurations in Ref1.pdb, Ref2.pdb and Ref3.pdb
50 : and prints the results in a file named colvar.
51 : Three atoms (PIVATOMS=3) with names (pdb file) A B and C are used to construct the PIV and all PIV blocks (AA, BB, CC, AB, AC, BC) are considered.
52 : SFACTOR is a scaling factor that multiplies the contribution to the PIV-distance given by the single PIV block.
53 : NLIST sets the use of neighbor lists for calculating atom-atom distances.
54 : The SWITCH keyword specifies the parameters of the switching function that transforms atom-atom distances.
55 : SORT=1 means that the PIV block elements are sorted (SORT=0 no sorting.)
56 : Values for SORT, SFACTOR and the neighbor list parameters have to be specified for each block.
57 : The order is the following: AA,BB,CC,AB,AC,BC. If ONLYDIRECT (ONLYCROSS) is used the order is AA,BB,CC (AB,AC,BC).
58 : The sorting operation within each PIV block is performed using the counting sort algorithm, PRECISION specifies the size of the counting array.
59 :
60 : \plumedfile
61 : PIV ...
62 : LABEL=Pivd1
63 : PRECISION=1000
64 : NLIST
65 : REF_FILE=Ref1.pdb
66 : PIVATOMS=3
67 : ATOMTYPES=A,B,C
68 : SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2
69 : SORT=1,1,1,1,1,1
70 : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
71 : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
72 : SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}
73 : SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}
74 : SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}
75 : SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}
76 : NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7
77 : NL_STRIDE=10,10,10,10,10,10
78 : NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1
79 : ... PIV
80 : PIV ...
81 : LABEL=Pivd2
82 : PRECISION=1000
83 : NLIST
84 : REF_FILE=Ref2.pdb
85 : PIVATOMS=3
86 : ATOMTYPES=A,B,C
87 : SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2
88 : SORT=1,1,1,1,1,1
89 : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
90 : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
91 : SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}
92 : SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}
93 : SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}
94 : SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}
95 : NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7
96 : NL_STRIDE=10,10,10,10,10,10
97 : NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1
98 : ... PIV
99 : PIV ...
100 : LABEL=Pivd3
101 : PRECISION=1000
102 : NLIST
103 : REF_FILE=Ref3.pdb
104 : PIVATOMS=3
105 : ATOMTYPES=A,B,C
106 : SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2
107 : SORT=1,1,1,1,1,1
108 : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
109 : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
110 : SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}
111 : SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}
112 : SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}
113 : SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}
114 : NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7
115 : NL_STRIDE=10,10,10,10,10,10
116 : NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1
117 : ... PIV
118 :
119 : PRINT ARG=Pivd1,Pivd2,Pivd3 FILE=colvar
120 : \endplumedfile
121 :
122 : WARNING:
123 : Both the "CRYST" and "ATOM" lines of the PDB files must conform precisely to the official pdb format, including the width of each alphanumerical field:
124 :
125 : \verbatim
126 : CRYST1 31.028 36.957 23.143 89.93 92.31 89.99 P 1 1
127 : ATOM 1 OW1 wate 1 15.630 19.750 1.520 1.00 0.00
128 : \endverbatim
129 :
130 : In each pdb frame, atoms must be numbered in the same order and with the same element symbol as in the input of the MD program.
131 :
132 : The following example calculates the PIV-distances from two reference configurations Ref1.pdb and Ref2.pdb
133 : and uses PIV-distances to define a Path Collective Variable (\ref FUNCPATHMSD) with only two references (Ref1.pdb and Ref2.pdb).
134 : With the VOLUME keyword one scales the atom-atom distances by the cubic root of the ratio between the specified value and the box volume of the initial step of the trajectory file.
135 :
136 : \plumedfile
137 : PIV ...
138 : LABEL=c1
139 : PRECISION=1000
140 : VOLUME=12.15
141 : NLIST
142 : REF_FILE=Ref1.pdb
143 : PIVATOMS=2
144 : ATOMTYPES=A,B
145 : ONLYDIRECT
146 : SFACTOR=1.0,0.2
147 : SORT=1,1
148 : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
149 : SWITCH2={RATIONAL R_0=0.5 MM=10 NN=5}
150 : NL_CUTOFF=1.2,1.2
151 : NL_STRIDE=10,10
152 : NL_SKIN=0.1,0.1
153 : ... PIV
154 : PIV ...
155 : LABEL=c2
156 : PRECISION=1000
157 : VOLUME=12.15
158 : NLIST
159 : REF_FILE=Ref2.pdb
160 : PIVATOMS=2
161 : ATOMTYPES=A,B
162 : ONLYDIRECT
163 : SFACTOR=1.0,0.2
164 : SORT=1,1
165 : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
166 : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
167 : NL_CUTOFF=1.2,1.2
168 : NL_STRIDE=10,10
169 : NL_SKIN=0.1,0.1
170 : ... PIV
171 :
172 : p1: FUNCPATHMSD ARG=c1,c2 LAMBDA=0.180338
173 : METAD ARG=p1.s,p1.z SIGMA=0.01,0.2 HEIGHT=0.8 PACE=500 LABEL=res
174 : PRINT ARG=c1,c2,p1.s,p1.z,res.bias STRIDE=500 FILE=colvar FMT=%15.6f
175 : \endplumedfile
176 :
177 : When using PIV please cite \cite pipolo2017navigating .
178 :
179 : (See also \ref PRINT)
180 :
181 : */
182 : //+ENDPLUMEDOC
183 :
184 : class PIV : public Colvar {
185 : private:
186 : bool pbc, serial, timer;
187 : ForwardDecl<Stopwatch> stopwatch_fwd;
188 : Stopwatch& stopwatch=*stopwatch_fwd;
189 : int updatePIV;
190 : size_t Nprec;
191 : unsigned Natm,Nlist,NLsize;
192 : double Fvol,Vol0,m_PIVdistance;
193 : std::string ref_file;
194 : std::unique_ptr<NeighborList> nlall;
195 : std::vector<SwitchingFunction> sfs;
196 : std::vector<std:: vector<double> > rPIV;
197 : std::vector<double> scaling,r00;
198 : std::vector<double> nl_skin;
199 : std::vector<double> fmass;
200 : std::vector<bool> dosort;
201 : std::vector<Vector> compos;
202 : std::vector<string> sw;
203 : std::vector<std::unique_ptr<NeighborList>> nl;
204 : std::vector<std::unique_ptr<NeighborList>> nlcom;
205 : std::vector<Vector> m_deriv;
206 : Tensor m_virial;
207 : bool Svol,cross,direct,doneigh,test,CompDer,com;
208 :
209 : /// Local structure, used to store data that should be
210 : /// shared across multiple PIV instances
211 6 : struct SharedData {
212 : int prev_stp=-1;
213 : int init_stp=1;
214 : std:: vector<std:: vector<Vector> > prev_pos;
215 : std:: vector<std:: vector<double> > cPIV;
216 : std:: vector<std:: vector<int> > Atom0;
217 : std:: vector<std:: vector<int> > Atom1;
218 : };
219 : /// Owning pointer. Will only be allocated by the first PIV instance
220 : std::unique_ptr<SharedData> sharedData_unique;
221 : /// Raw pointer. Will have the same value for all PIV instances
222 : SharedData* sharedData=nullptr;
223 :
224 : public:
225 : static void registerKeywords( Keywords& keys );
226 : explicit PIV(const ActionOptions&);
227 : // active methods:
228 : virtual void calculate();
229 0 : void checkFieldsAllowed() {}
230 : };
231 :
232 : PLUMED_REGISTER_ACTION(PIV,"PIV")
233 :
234 14 : void PIV::registerKeywords( Keywords& keys ) {
235 14 : Colvar::registerKeywords( keys );
236 14 : keys.add("numbered","SWITCH","The switching functions parameter."
237 : "You should specify a Switching function for all PIV blocks."
238 : "Details of the various switching "
239 : "functions you can use are provided on switchingfunction.");
240 14 : keys.add("compulsory","PRECISION","the precision for approximating reals with integers in sorting.");
241 14 : keys.add("compulsory","REF_FILE","PDB file name that contains the ith reference structure.");
242 14 : keys.add("compulsory","PIVATOMS","Number of atoms to use for PIV.");
243 14 : keys.add("compulsory","SORT","Whether to sort or not the PIV block.");
244 14 : keys.add("compulsory","ATOMTYPES","The atom types to use for PIV.");
245 14 : keys.add("optional","SFACTOR","Scale the PIV-distance by such block-specific factor");
246 14 : keys.add("optional","VOLUME","Scale atom-atom distances by the cubic root of the cell volume. The input volume is used to scale the R_0 value of the switching function. ");
247 14 : keys.add("optional","UPDATEPIV","Frequency (in steps) at which the PIV is updated.");
248 14 : keys.addFlag("TEST",false,"Print the actual and reference PIV and exit");
249 14 : keys.addFlag("COM",false,"Use centers of mass of groups of atoms instead of atoms as specified in the Pdb file");
250 14 : keys.addFlag("ONLYCROSS",false,"Use only cross-terms (A-B, A-C, B-C, ...) in PIV");
251 14 : keys.addFlag("ONLYDIRECT",false,"Use only direct-terms (A-A, B-B, C-C, ...) in PIV");
252 14 : keys.addFlag("DERIVATIVES",false,"Activate the calculation of the PIV for every class (needed for numerical derivatives).");
253 14 : keys.addFlag("NLIST",false,"Use a neighbor list for distance calculations.");
254 14 : keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose");
255 14 : keys.addFlag("TIMER",false,"Perform timing analysis on heavy loops.");
256 14 : keys.add("optional","NL_CUTOFF","Neighbor lists cutoff.");
257 14 : keys.add("optional","NL_STRIDE","Update neighbor lists every NL_STRIDE steps.");
258 14 : keys.add("optional","NL_SKIN","The maximum atom displacement tolerated for the neighbor lists update.");
259 28 : keys.reset_style("SWITCH","compulsory");
260 28 : keys.setValueDescription("scalar","the PIV-distance");
261 14 : }
262 :
263 12 : PIV::PIV(const ActionOptions&ao):
264 : PLUMED_COLVAR_INIT(ao),
265 12 : pbc(true),
266 12 : serial(false),
267 12 : timer(false),
268 12 : updatePIV(1),
269 12 : Nprec(1000),
270 12 : Natm(1),
271 12 : Nlist(1),
272 12 : NLsize(1),
273 12 : Fvol(1.),
274 12 : Vol0(0.),
275 12 : m_PIVdistance(0.),
276 12 : rPIV(std:: vector<std:: vector<double> >(Nlist)),
277 12 : scaling(std:: vector<double>(Nlist)),
278 12 : r00(std:: vector<double>(Nlist)),
279 12 : nl_skin(std:: vector<double>(Nlist)),
280 12 : fmass(std:: vector<double>(Nlist)),
281 12 : dosort(std:: vector<bool>(Nlist)),
282 12 : compos(std:: vector<Vector>(NLsize)),
283 12 : sw(std:: vector<string>(Nlist)),
284 12 : nl(Nlist),
285 12 : nlcom(NLsize),
286 12 : m_deriv(std:: vector<Vector>(1)),
287 12 : Svol(false),
288 12 : cross(true),
289 12 : direct(true),
290 12 : doneigh(false),
291 12 : test(false),
292 12 : CompDer(false),
293 24 : com(false) {
294 12 : log << "Starting PIV Constructor\n";
295 :
296 : {
297 : // look for another PIV instance previously allocated
298 12 : auto* previous=plumed.getActionSet().selectLatest<PIV*>(this);
299 :
300 : // Uncommenting the following line, it is possible to force
301 : // a separate object per instance of the PIB object.
302 : // Results are unaffected, but performance is worse.
303 : // I think this is the expected behavior. GB
304 : // previous=nullptr;
305 :
306 12 : if(!previous) {
307 : // if not found, allocate the shared data struct
308 6 : sharedData_unique=Tools::make_unique<SharedData>();
309 : // then set the raw pointer
310 6 : sharedData=sharedData_unique.get();
311 : } else {
312 : // if found, use the previous raw pointer
313 6 : sharedData=previous->sharedData;
314 6 : log << "(a previous PIV action was found)\n";
315 : }
316 : }
317 :
318 : // Precision on the real-to-integer transformation for the sorting
319 12 : parse("PRECISION",Nprec);
320 12 : if(Nprec<2) {
321 0 : error("Precision must be => 2");
322 : }
323 :
324 : // PBC
325 12 : bool nopbc=!pbc;
326 12 : parseFlag("NOPBC",nopbc);
327 12 : pbc=!nopbc;
328 12 : if(pbc) {
329 12 : log << "Using Periodic Boundary Conditions\n";
330 : } else {
331 0 : log << "Isolated System (NO PBC)\n";
332 : }
333 :
334 : // SERIAL/PARALLEL
335 12 : parseFlag("SERIAL",serial);
336 12 : if(serial) {
337 0 : log << "Serial PIV construction\n";
338 : } else {
339 12 : log << "Parallel PIV construction\n";
340 : }
341 :
342 : // Derivatives
343 12 : parseFlag("DERIVATIVES",CompDer);
344 12 : if(CompDer) {
345 6 : log << "Computing Derivatives\n";
346 : }
347 :
348 : // Timing
349 12 : parseFlag("TIMER",timer);
350 12 : if(timer) {
351 1 : log << "Timing analysis\n";
352 1 : stopwatch.start();
353 1 : stopwatch.pause();
354 : }
355 :
356 : // Test
357 12 : parseFlag("TEST",test);
358 :
359 : // UPDATEPIV
360 12 : if(keywords.exists("UPDATEPIV")) {
361 24 : parse("UPDATEPIV",updatePIV);
362 : }
363 :
364 : // Test
365 12 : parseFlag("COM",com);
366 12 : if(com) {
367 0 : log << "Building PIV using COMs\n";
368 : }
369 :
370 : // Volume Scaling
371 12 : parse("VOLUME",Vol0);
372 12 : if (Vol0>0) {
373 12 : Svol=true;
374 : }
375 :
376 : // PIV direct and cross blocks
377 12 : bool oc=false,od=false;
378 12 : parseFlag("ONLYCROSS",oc);
379 12 : parseFlag("ONLYDIRECT",od);
380 12 : if (oc&&od) {
381 0 : error("ONLYCROSS and ONLYDIRECT are incompatible options!");
382 : }
383 12 : if(oc) {
384 4 : direct=false;
385 4 : log << "Using only CROSS-PIV blocks\n";
386 : }
387 12 : if(od) {
388 4 : cross=false;
389 4 : log << "Using only DIRECT-PIV blocks\n";
390 : }
391 :
392 : // Atoms for PIV
393 12 : parse("PIVATOMS",Natm);
394 12 : std:: vector<string> atype(Natm);
395 12 : parseVector("ATOMTYPES",atype);
396 : //if(atype.size()!=getNumberOfArguments() && atype.size()!=0) error("not enough values for ATOMTYPES");
397 :
398 : // Reference PDB file
399 12 : parse("REF_FILE",ref_file);
400 12 : PDB mypdb;
401 12 : FILE* fp=fopen(ref_file.c_str(),"r");
402 12 : if (fp!=NULL) {
403 12 : log<<"Opening PDB file with reference frame: "<<ref_file.c_str()<<"\n";
404 12 : mypdb.readFromFilepointer(fp,usingNaturalUnits(),0.1/getUnits().getLength());
405 12 : fclose (fp);
406 : } else {
407 0 : error("Error in reference PDB file");
408 : }
409 :
410 : // Build COM/Atom lists of AtomNumbers (this might be done in PBC.cpp)
411 : // Atomlist or Plist used to build pair lists
412 12 : std:: vector<std:: vector<AtomNumber> > Plist(Natm);
413 : // Atomlist used to build list of atoms for each COM
414 12 : std:: vector<std:: vector<AtomNumber> > comatm(1);
415 : // NLsize is the number of atoms in the pdb cell
416 12 : NLsize=mypdb.getAtomNumbers().size();
417 : // In the following P stands for Point (either an Atom or a COM)
418 : unsigned resnum=0;
419 : // Presind (array size: number of residues) contains the contains the residue number
420 : // this is because the residue numbers may not always be ordered from 1 to resnum
421 : std:: vector<unsigned> Presind;
422 : // Build Presind
423 19404 : for (unsigned i=0; i<mypdb.getAtomNumbers().size(); i++) {
424 19392 : unsigned rind=mypdb.getResidueNumber(mypdb.getAtomNumbers()[i]);
425 : bool oldres=false;
426 7705008 : for (unsigned j=0; j<Presind.size(); j++) {
427 7685616 : if(rind==Presind[j]) {
428 : oldres=true;
429 : }
430 : }
431 19392 : if(!oldres) {
432 4848 : Presind.push_back(rind);
433 : }
434 : }
435 12 : resnum=Presind.size();
436 :
437 : // Pind0 is the atom/COM used in Nlists (for COM Pind0 is the first atom in the pdb belonging to that COM)
438 : unsigned Pind0size;
439 12 : if(com) {
440 : Pind0size=resnum;
441 : } else {
442 12 : Pind0size=NLsize;
443 : }
444 12 : std:: vector<unsigned> Pind0(Pind0size);
445 : // If COM resize important arrays
446 12 : comatm.resize(NLsize);
447 12 : if(com) {
448 0 : nlcom.resize(NLsize);
449 0 : compos.resize(NLsize);
450 0 : fmass.resize(NLsize,0.);
451 : }
452 12 : log << "Total COM/Atoms: " << Natm*resnum << " \n";
453 : // Build lists of Atoms/COMs for NLists
454 : // comatm filled also for non_COM calculation for analysis purposes
455 36 : for (unsigned j=0; j<Natm; j++) {
456 : unsigned oind;
457 38808 : for (unsigned i=0; i<Pind0.size(); i++) {
458 38784 : Pind0[i]=0;
459 : }
460 38808 : for (unsigned i=0; i<mypdb.getAtomNumbers().size(); i++) {
461 : // Residue/Atom AtomNumber: used to build NL for COMS/Atoms pairs.
462 38784 : AtomNumber anum=mypdb.getAtomNumbers()[i];
463 : // ResidueName/Atomname associated to atom
464 38784 : string rname=mypdb.getResidueName(anum);
465 38784 : string aname=mypdb.getAtomName(anum);
466 : // Index associated to residue/atom: used to separate COM-lists
467 38784 : unsigned rind=mypdb.getResidueNumber(anum);
468 : unsigned aind=anum.index();
469 : // This builds lists for NL
470 : string Pname;
471 : unsigned Pind;
472 38784 : if(com) {
473 : Pname=rname;
474 0 : for(unsigned l=0; l<resnum; l++) {
475 0 : if(rind==Presind[l]) {
476 : Pind=l;
477 : }
478 : }
479 : } else {
480 : Pname=aname;
481 : Pind=aind;
482 : }
483 38784 : if(Pname==atype[j]) {
484 14544 : if(Pind0[Pind]==0) {
485 : // adding the atomnumber to the atom/COM list for pairs
486 14544 : Plist[j].push_back(anum);
487 14544 : Pind0[Pind]=aind+1;
488 : oind=Pind;
489 : }
490 : // adding the atomnumber to list of atoms for every COM/Atoms
491 14544 : comatm[Pind0[Pind]-1].push_back(anum);
492 : }
493 : }
494 : // Output Lists
495 24 : log << " Groups of type " << j << ": " << Plist[j].size() << " \n";
496 : string gname;
497 : unsigned gsize;
498 24 : if(com) {
499 0 : gname=mypdb.getResidueName(comatm[Pind0[oind]-1][0]);
500 0 : gsize=comatm[Pind0[oind]-1].size();
501 : } else {
502 48 : gname=mypdb.getAtomName(comatm[Pind0[oind]-1][0]);
503 : gsize=1;
504 : }
505 24 : log.printf(" %6s %3s %13s %10i %6s\n", "type ", gname.c_str()," containing ",gsize," atoms");
506 : }
507 :
508 : // This is to build the list with all the atoms
509 : std:: vector<AtomNumber> listall;
510 19404 : for (unsigned i=0; i<mypdb.getAtomNumbers().size(); i++) {
511 19392 : listall.push_back(mypdb.getAtomNumbers()[i]);
512 : }
513 :
514 : // PIV blocks and Neighbour Lists
515 12 : Nlist=0;
516 : // Direct adds the A-A ad B-B blocks (N)
517 12 : if(direct) {
518 8 : Nlist=Nlist+unsigned(Natm);
519 : }
520 : // Cross adds the A-B blocks (N*(N-1)/2)
521 12 : if(cross) {
522 8 : Nlist=Nlist+unsigned(double(Natm*(Natm-1))/2.);
523 : }
524 : // Resize vectors according to Nlist
525 12 : rPIV.resize(Nlist);
526 :
527 : // PIV scaled option
528 12 : scaling.resize(Nlist);
529 36 : for(unsigned j=0; j<Nlist; j++) {
530 24 : scaling[j]=1.;
531 : }
532 12 : if(keywords.exists("SFACTOR")) {
533 24 : parseVector("SFACTOR",scaling);
534 : //if(scaling.size()!=getNumberOfArguments() && scaling.size()!=0) error("not enough values for SFACTOR");
535 : }
536 : // Neighbour Lists option
537 12 : parseFlag("NLIST",doneigh);
538 12 : nl.resize(Nlist);
539 12 : nl_skin.resize(Nlist);
540 12 : if(doneigh) {
541 12 : std:: vector<double> nl_cut(Nlist,0.);
542 12 : std:: vector<int> nl_st(Nlist,0);
543 12 : parseVector("NL_CUTOFF",nl_cut);
544 : //if(nl_cut.size()!=getNumberOfArguments() && nl_cut.size()!=0) error("not enough values for NL_CUTOFF");
545 12 : parseVector("NL_STRIDE",nl_st);
546 : //if(nl_st.size()!=getNumberOfArguments() && nl_st.size()!=0) error("not enough values for NL_STRIDE");
547 12 : parseVector("NL_SKIN",nl_skin);
548 : //if(nl_skin.size()!=getNumberOfArguments() && nl_skin.size()!=0) error("not enough values for NL_SKIN");
549 36 : for (unsigned j=0; j<Nlist; j++) {
550 24 : if(nl_cut[j]<=0.0) {
551 0 : error("NL_CUTOFF should be explicitly specified and positive");
552 : }
553 24 : if(nl_st[j]<=0) {
554 0 : error("NL_STRIDE should be explicitly specified and positive");
555 : }
556 24 : if(nl_skin[j]<=0.) {
557 0 : error("NL_SKIN should be explicitly specified and positive");
558 : }
559 24 : nl_cut[j]=nl_cut[j]+nl_skin[j];
560 : }
561 12 : log << "Creating Neighbor Lists \n";
562 : // WARNING: is nl_cut meaningful here?
563 24 : nlall= Tools::make_unique<NeighborList>(listall,true,pbc,getPbc(),comm,nl_cut[0],nl_st[0]);
564 12 : if(com) {
565 : //Build lists of Atoms for every COM
566 0 : for (unsigned i=0; i<compos.size(); i++) {
567 : // WARNING: is nl_cut meaningful here?
568 0 : nlcom[i] = Tools::make_unique<NeighborList>(comatm[i],true,pbc,getPbc(),comm,nl_cut[0],nl_st[0]);
569 : }
570 : }
571 : unsigned ncnt=0;
572 : // Direct blocks AA, BB, CC, ...
573 12 : if(direct) {
574 24 : for (unsigned j=0; j<Natm; j++) {
575 16 : nl[ncnt]= Tools::make_unique<NeighborList>(Plist[j],true,pbc,getPbc(),comm,nl_cut[j],nl_st[j]);
576 16 : ncnt+=1;
577 : }
578 : }
579 : // Cross blocks AB, AC, BC, ...
580 12 : if(cross) {
581 24 : for (unsigned j=0; j<Natm; j++) {
582 24 : for (unsigned i=j+1; i<Natm; i++) {
583 16 : nl[ncnt]= Tools::make_unique<NeighborList>(Plist[i],Plist[j],true,false,pbc,getPbc(),comm,nl_cut[ncnt],nl_st[ncnt]);
584 8 : ncnt+=1;
585 : }
586 : }
587 : }
588 : } else {
589 0 : log << "WARNING: Neighbor List not activated this has not been tested!! \n";
590 0 : nlall= Tools::make_unique<NeighborList>(listall,true,pbc,getPbc(),comm);
591 0 : for (unsigned j=0; j<Nlist; j++) {
592 0 : nl[j]= Tools::make_unique<NeighborList>(Plist[j],Plist[j],true,true,pbc,getPbc(),comm);
593 : }
594 : }
595 : // Output Nlist
596 12 : log << "Total Nlists: " << Nlist << " \n";
597 36 : for (unsigned j=0; j<Nlist; j++) {
598 24 : log << " list " << j+1 << " size " << nl[j]->size() << " \n";
599 : }
600 : // Calculate COM masses once and for all from lists
601 12 : if(com) {
602 0 : for(unsigned j=0; j<compos.size(); j++) {
603 : double commass=0.;
604 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
605 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
606 0 : commass+=mypdb.getOccupancy()[andx];
607 : }
608 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
609 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
610 0 : if(commass>0.) {
611 0 : fmass[andx]=mypdb.getOccupancy()[andx]/commass;
612 : } else {
613 0 : fmass[andx]=1.;
614 : }
615 : }
616 : }
617 : }
618 :
619 : // Sorting
620 12 : dosort.resize(Nlist);
621 12 : std:: vector<int> ynsort(Nlist);
622 12 : parseVector("SORT",ynsort);
623 36 : for (unsigned i=0; i<Nlist; i++) {
624 24 : if(ynsort[i]==0||CompDer) {
625 : dosort[i]=false;
626 : } else {
627 : dosort[i]=true;
628 : }
629 : }
630 :
631 : //build box vectors and correct for pbc
632 12 : log << "Building the box from PDB data ... \n";
633 12 : Tensor Box=mypdb.getBoxVec();
634 12 : log << " Done! A,B,C vectors in Cartesian space: \n";
635 12 : log.printf(" A: %12.6f%12.6f%12.6f\n", Box[0][0],Box[0][1],Box[0][2]);
636 12 : log.printf(" B: %12.6f%12.6f%12.6f\n", Box[1][0],Box[1][1],Box[1][2]);
637 12 : log.printf(" C: %12.6f%12.6f%12.6f\n", Box[2][0],Box[2][1],Box[2][2]);
638 12 : log << "Changing the PBC according to the new box \n";
639 12 : Pbc mypbc;
640 12 : mypbc.setBox(Box);
641 12 : log << "The box volume is " << mypbc.getBox().determinant() << " \n";
642 :
643 : //Compute scaling factor
644 12 : if(Svol) {
645 12 : Fvol=cbrt(Vol0/mypbc.getBox().determinant());
646 12 : log << "Scaling atom distances by " << Fvol << " \n";
647 : } else {
648 0 : log << "Using unscaled atom distances \n";
649 : }
650 :
651 12 : r00.resize(Nlist);
652 12 : sw.resize(Nlist);
653 36 : for (unsigned j=0; j<Nlist; j++) {
654 48 : if( !parseNumbered( "SWITCH", j+1, sw[j] ) ) {
655 : break;
656 : }
657 : }
658 12 : if(CompDer) {
659 : // Set switching function parameters here only if computing derivatives
660 : // now set at the beginning of the dynamics to solve the r0 issue
661 6 : log << "Switching Function Parameters \n";
662 6 : sfs.resize(Nlist);
663 : std::string errors;
664 18 : for (unsigned j=0; j<Nlist; j++) {
665 12 : if(Svol) {
666 : double r0;
667 : std::string old_r0;
668 12 : vector<string> data=Tools::getWords(sw[j]);
669 : data.erase(data.begin());
670 12 : Tools::parse(data,"R_0",old_r0);
671 12 : Tools::convert(old_r0,r0);
672 12 : r0*=Fvol;
673 : std::string new_r0;
674 12 : Tools::convert(r0,new_r0);
675 12 : std::size_t pos = sw[j].find("R_0");
676 12 : sw[j].replace(pos+4,old_r0.size(),new_r0);
677 12 : }
678 12 : sfs[j].set(sw[j],errors);
679 : std::string num;
680 12 : Tools::convert(j+1, num);
681 12 : if( errors.length()!=0 ) {
682 0 : error("problem reading SWITCH" + num + " keyword : " + errors );
683 : }
684 12 : r00[j]=sfs[j].get_r0();
685 12 : log << " Swf: " << j << " r0=" << (sfs[j].description()).c_str() << " \n";
686 : }
687 : }
688 :
689 : // build COMs from positions if requested
690 12 : if(com) {
691 0 : for(unsigned j=0; j<compos.size(); j++) {
692 0 : compos[j][0]=0.;
693 0 : compos[j][1]=0.;
694 0 : compos[j][2]=0.;
695 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
696 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
697 0 : compos[j]+=fmass[andx]*mypdb.getPositions()[andx];
698 : }
699 : }
700 : }
701 : // build the rPIV distances (transformation and sorting is done afterwards)
702 12 : if(CompDer) {
703 6 : log << " PIV | block | Size | Zeros | Ones |" << " \n";
704 : }
705 36 : for(unsigned j=0; j<Nlist; j++) {
706 11516328 : for(unsigned i=0; i<nl[j]->size(); i++) {
707 11516304 : unsigned i0=(nl[j]->getClosePairAtomNumber(i).first).index();
708 11516304 : unsigned i1=(nl[j]->getClosePairAtomNumber(i).second).index();
709 : //calculate/get COM position of centers i0 and i1
710 11516304 : Vector Pos0,Pos1;
711 11516304 : if(com) {
712 : //if(pbc) makeWhole();
713 0 : Pos0=compos[i0];
714 0 : Pos1=compos[i1];
715 : } else {
716 11516304 : Pos0=mypdb.getPositions()[i0];
717 11516304 : Pos1=mypdb.getPositions()[i1];
718 : }
719 11516304 : Vector ddist;
720 11516304 : if(pbc) {
721 11516304 : ddist=mypbc.distance(Pos0,Pos1);
722 : } else {
723 0 : ddist=delta(Pos0,Pos1);
724 : }
725 11516304 : double df=0.;
726 : // Transformation and sorting done at the first timestep to solve the r0 definition issue
727 11516304 : if(CompDer) {
728 1104 : rPIV[j].push_back(sfs[j].calculate(ddist.modulo()*Fvol, df));
729 : } else {
730 11515200 : rPIV[j].push_back(ddist.modulo()*Fvol);
731 : }
732 : }
733 24 : if(CompDer) {
734 12 : if(dosort[j]) {
735 0 : std::sort(rPIV[j].begin(),rPIV[j].end());
736 : }
737 : int lmt0=0;
738 : int lmt1=0;
739 1116 : for(unsigned i=0; i<rPIV[j].size(); i++) {
740 1104 : if(int(rPIV[j][i]*double(Nprec-1))==0) {
741 0 : lmt0+=1;
742 : }
743 1104 : if(int(rPIV[j][i]*double(Nprec-1))==1) {
744 0 : lmt1+=1;
745 : }
746 : }
747 12 : log.printf(" |%10i|%15zu|%15i|%15i|\n", j, rPIV[j].size(), lmt0, lmt1);
748 : }
749 : }
750 :
751 12 : checkRead();
752 : // From the plumed manual on how to build-up a new Colvar
753 24 : addValueWithDerivatives();
754 12 : requestAtoms(nlall->getFullAtomList());
755 12 : setNotPeriodic();
756 : // getValue()->setPeridodicity(false);
757 : // set size of derivative vector
758 12 : m_deriv.resize(getNumberOfAtoms());
759 12 : }
760 :
761 327 : void PIV::calculate() {
762 :
763 : // Local variables
764 :
765 327 : if(sharedData_unique) {
766 : // This is executed by the first PIV instance.
767 : // We initialize variables with the correct Nlist.
768 321 : sharedData_unique->prev_pos.resize(Nlist);
769 321 : sharedData_unique->cPIV.resize(Nlist);
770 321 : sharedData_unique->Atom0.resize(Nlist);
771 321 : sharedData_unique->Atom1.resize(Nlist);
772 : }
773 :
774 : // create references to minimize the impact of the code below
775 327 : auto & prev_stp(sharedData->prev_stp);
776 : auto & init_stp(sharedData->init_stp);
777 : auto & prev_pos(sharedData->prev_pos);
778 : auto & cPIV(sharedData->cPIV);
779 : auto & Atom0(sharedData->Atom0);
780 : auto & Atom1(sharedData->Atom1);
781 :
782 327 : std:: vector<std:: vector<int> > A0(Nprec);
783 327 : std:: vector<std:: vector<int> > A1(Nprec);
784 : size_t stride=1;
785 : unsigned rank=0;
786 :
787 327 : if(!serial) {
788 327 : stride=comm.Get_size();
789 327 : rank=comm.Get_rank();
790 : } else {
791 : stride=1;
792 : rank=0;
793 : }
794 :
795 : // Transform (and sort) the rPIV before starting the dynamics
796 327 : if (((prev_stp==-1) || (init_stp==1)) &&!CompDer) {
797 6 : if(prev_stp!=-1) {
798 3 : init_stp=0;
799 : }
800 : // Calculate the volume scaling factor
801 6 : if(Svol) {
802 6 : Fvol=cbrt(Vol0/getBox().determinant());
803 : }
804 : //Set switching function parameters
805 6 : log << "\n";
806 6 : log << "REFERENCE PDB # " << prev_stp+2 << " \n";
807 : // Set switching function parameters here only if computing derivatives
808 : // now set at the beginning of the dynamics to solve the r0 issue
809 6 : log << "Switching Function Parameters \n";
810 6 : sfs.resize(Nlist);
811 : std::string errors;
812 18 : for (unsigned j=0; j<Nlist; j++) {
813 12 : if(Svol) {
814 : double r0;
815 : std::string old_r0;
816 12 : vector<string> data=Tools::getWords(sw[j]);
817 : data.erase(data.begin());
818 12 : Tools::parse(data,"R_0",old_r0);
819 12 : Tools::convert(old_r0,r0);
820 12 : r0*=Fvol;
821 : std::string new_r0;
822 12 : Tools::convert(r0,new_r0);
823 12 : std::size_t pos = sw[j].find("R_0");
824 12 : sw[j].replace(pos+4,old_r0.size(),new_r0);
825 12 : }
826 12 : sfs[j].set(sw[j],errors);
827 : std::string num;
828 12 : Tools::convert(j+1, num);
829 12 : if( errors.length()!=0 ) {
830 0 : error("problem reading SWITCH" + num + " keyword : " + errors );
831 : }
832 12 : r00[j]=sfs[j].get_r0();
833 12 : log << " Swf: " << j << " r0=" << (sfs[j].description()).c_str() << " \n";
834 : }
835 : //Transform and sort
836 6 : log << "Building Reference PIV Vector \n";
837 6 : log << " PIV | block | Size | Zeros | Ones |" << " \n";
838 6 : double df=0.;
839 18 : for (unsigned j=0; j<Nlist; j++) {
840 11515212 : for (unsigned i=0; i<rPIV[j].size(); i++) {
841 11515200 : rPIV[j][i]=sfs[j].calculate(rPIV[j][i], df);
842 : }
843 12 : if(dosort[j]) {
844 12 : std::sort(rPIV[j].begin(),rPIV[j].end());
845 : }
846 : int lmt0=0;
847 : int lmt1=0;
848 11515212 : for(unsigned i=0; i<rPIV[j].size(); i++) {
849 11515200 : if(int(rPIV[j][i]*double(Nprec-1))==0) {
850 26 : lmt0+=1;
851 : }
852 11515200 : if(int(rPIV[j][i]*double(Nprec-1))==1) {
853 63358 : lmt1+=1;
854 : }
855 : }
856 12 : log.printf(" |%10i|%15zu|%15i|%15i|\n", j, rPIV[j].size(), lmt0, lmt1);
857 : }
858 6 : log << "\n";
859 : }
860 : // Do the sorting only once per timestep to avoid building the PIV N times for N rPIV PDB structures!
861 327 : if ((getStep()>prev_stp&&getStep()%updatePIV==0)||CompDer) {
862 324 : if (CompDer) {
863 321 : log << " Step " << getStep() << " Computing Derivatives NON-SORTED PIV \n";
864 : }
865 : //
866 : // build COMs from positions if requested
867 324 : if(com) {
868 0 : if(pbc) {
869 0 : makeWhole();
870 : }
871 0 : for(unsigned j=0; j<compos.size(); j++) {
872 0 : compos[j][0]=0.;
873 0 : compos[j][1]=0.;
874 0 : compos[j][2]=0.;
875 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
876 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
877 0 : compos[j]+=fmass[andx]*getPosition(andx);
878 : }
879 : }
880 : }
881 : // update neighbor lists when an atom moves out of the Neighbor list skin
882 324 : if (doneigh) {
883 : bool doupdate=false;
884 : // For the first step build previous positions = actual positions
885 324 : if (prev_stp==-1) {
886 6 : bool docom=com;
887 18 : for (unsigned j=0; j<Nlist; j++) {
888 9708 : for (unsigned i=0; i<nl[j]->getFullAtomList().size(); i++) {
889 9696 : Vector Pos;
890 9696 : if(docom) {
891 0 : Pos=compos[i];
892 : } else {
893 9696 : Pos=getPosition(nl[j]->getFullAtomList()[i].index());
894 : }
895 9696 : prev_pos[j].push_back(Pos);
896 : }
897 : }
898 : doupdate=true;
899 : }
900 : // Decide whether to update lists based on atom displacement, every stride
901 324 : std:: vector<std:: vector<Vector> > tmp_pos(Nlist);
902 324 : if (getStep() % nlall->getStride() ==0) {
903 324 : bool docom=com;
904 972 : for (unsigned j=0; j<Nlist; j++) {
905 20520 : for (unsigned i=0; i<nl[j]->getFullAtomList().size(); i++) {
906 19872 : Vector Pos;
907 19872 : if(docom) {
908 0 : Pos=compos[i];
909 : } else {
910 19872 : Pos=getPosition(nl[j]->getFullAtomList()[i].index());
911 : }
912 19872 : tmp_pos[j].push_back(Pos);
913 19872 : if (pbcDistance(tmp_pos[j][i],prev_pos[j][i]).modulo()>=nl_skin[j]) {
914 : doupdate=true;
915 : }
916 : }
917 : }
918 : }
919 : // Update Nlists if needed
920 324 : if (doupdate==true) {
921 18 : for (unsigned j=0; j<Nlist; j++) {
922 9708 : for (unsigned i=0; i<nl[j]->getFullAtomList().size(); i++) {
923 9696 : prev_pos[j][i]=tmp_pos[j][i];
924 : }
925 12 : nl[j]->update(prev_pos[j]);
926 12 : log << " Step " << getStep() << " Neighbour lists updated " << nl[j]->size() << " \n";
927 : }
928 : }
929 324 : }
930 : // Calculate the volume scaling factor
931 324 : if(Svol) {
932 324 : Fvol=cbrt(Vol0/getBox().determinant());
933 : }
934 324 : Vector ddist;
935 : // Global to local variables
936 324 : bool doserial=serial;
937 : // Build "Nlist" PIV blocks
938 972 : for(unsigned j=0; j<Nlist; j++) {
939 648 : if(dosort[j]) {
940 : // from global to local variables to speedup the for loop with if statements
941 6 : bool docom=com;
942 6 : bool dopbc=pbc;
943 : // Vectors collecting occupancies: OrdVec one rank, OrdVecAll all ranks
944 6 : std:: vector<int> OrdVec(Nprec,0);
945 6 : cPIV[j].resize(0);
946 6 : Atom0[j].resize(0);
947 6 : Atom1[j].resize(0);
948 : // Building distances for the PIV vector at time t
949 6 : if(timer) {
950 3 : stopwatch.start("1 Build cPIV");
951 : }
952 5757606 : for(unsigned i=rank; i<nl[j]->size(); i+=stride) {
953 5757600 : unsigned i0=(nl[j]->getClosePairAtomNumber(i).first).index();
954 5757600 : unsigned i1=(nl[j]->getClosePairAtomNumber(i).second).index();
955 5757600 : Vector Pos0,Pos1;
956 5757600 : if(docom) {
957 0 : Pos0=compos[i0];
958 0 : Pos1=compos[i1];
959 : } else {
960 5757600 : Pos0=getPosition(i0);
961 5757600 : Pos1=getPosition(i1);
962 : }
963 5757600 : if(dopbc) {
964 5757600 : ddist=pbcDistance(Pos0,Pos1);
965 : } else {
966 0 : ddist=delta(Pos0,Pos1);
967 : }
968 5757600 : double df=0.;
969 : //Integer sorting ... faster!
970 : //Transforming distances with the Switching function + real to integer transformation
971 5757600 : int Vint=int(sfs[j].calculate(ddist.modulo()*Fvol, df)*double(Nprec-1)+0.5);
972 : //Integer transformed distance values as index of the Ordering Vector OrdVec
973 5757600 : OrdVec[Vint]+=1;
974 : //Keeps track of atom indices for force and virial calculations
975 5757600 : A0[Vint].push_back(i0);
976 5757600 : A1[Vint].push_back(i1);
977 : }
978 6 : if(timer) {
979 3 : stopwatch.stop("1 Build cPIV");
980 : }
981 6 : if(timer) {
982 3 : stopwatch.start("2 Sort cPIV");
983 : }
984 6 : if(!doserial && comm.initialized()) {
985 : // Vectors keeping track of the dimension and the starting-position of the rank-specific pair vector in the big pair vector.
986 0 : std:: vector<int> Vdim(stride,0);
987 0 : std:: vector<int> Vpos(stride,0);
988 : // Vectors collecting occupancies: OrdVec one rank, OrdVecAll all ranks
989 0 : std:: vector<int> OrdVecAll(stride*Nprec);
990 : // Big vectors containing all Atom indexes for every occupancy (Atom0O(Nprec,n) and Atom1O(Nprec,n) matrices in one vector)
991 : std:: vector<int> Atom0F;
992 : std:: vector<int> Atom1F;
993 : // Vector used to reconstruct arrays
994 0 : std:: vector<unsigned> k(stride,0);
995 : // Zeros might be many, this slows down a lot due to MPI communication
996 : // Avoid passing the zeros (i=1) for atom indices
997 0 : for(unsigned i=1; i<Nprec; i++) {
998 : // Building long vectors with all atom indexes for occupancies ordered from i=1 to i=Nprec-1
999 : // Can this be avoided ???
1000 0 : Atom0F.insert(Atom0F.end(),A0[i].begin(),A0[i].end());
1001 0 : Atom1F.insert(Atom1F.end(),A1[i].begin(),A1[i].end());
1002 0 : A0[i].resize(0);
1003 0 : A1[i].resize(0);
1004 : }
1005 : // Resize partial arrays to fill up for the next PIV block
1006 0 : A0[0].resize(0);
1007 0 : A1[0].resize(0);
1008 0 : A0[Nprec-1].resize(0);
1009 0 : A1[Nprec-1].resize(0);
1010 : // Avoid passing the zeros (i=1) for atom indices
1011 0 : OrdVec[0]=0;
1012 0 : OrdVec[Nprec-1]=0;
1013 :
1014 : // Wait for all ranks before communication of Vectors
1015 0 : comm.Barrier();
1016 :
1017 : // pass the array sizes before passing the arrays
1018 0 : int dim=Atom0F.size();
1019 : // Vdim and Vpos keep track of the dimension and the starting-position of the rank-specific pair vector in the big pair vector.
1020 0 : comm.Allgather(&dim,1,&Vdim[0],1);
1021 :
1022 : // TO BE IMPROVED: the following may be done by the rank 0 (now every rank does it)
1023 : int Fdim=0;
1024 0 : for(unsigned i=1; i<stride; i++) {
1025 0 : Vpos[i]=Vpos[i-1]+Vdim[i-1];
1026 0 : Fdim+=Vdim[i];
1027 : }
1028 0 : Fdim+=Vdim[0];
1029 : // build big vectors for atom pairs on all ranks for all ranks
1030 0 : std:: vector<int> Atom0FAll(Fdim);
1031 0 : std:: vector<int> Atom1FAll(Fdim);
1032 : // TO BE IMPROVED: Allgathers may be substituted by gathers by proc 0
1033 : // Moreover vectors are gathered head-to-tail and assembled later-on in a serial step.
1034 : // Gather the full Ordering Vector (occupancies). This is what we need to build the PIV
1035 0 : comm.Allgather(&OrdVec[0],Nprec,&OrdVecAll[0],Nprec);
1036 : // Gather the vectors of atom pairs to keep track of the idexes for the forces
1037 0 : comm.Allgatherv(Atom0F.data(),Atom0F.size(),&Atom0FAll[0],&Vdim[0],&Vpos[0]);
1038 0 : comm.Allgatherv(Atom1F.data(),Atom1F.size(),&Atom1FAll[0],&Vdim[0],&Vpos[0]);
1039 :
1040 : // Reconstruct the full vectors from collections of Allgathered parts (this is a serial step)
1041 : // This is the tricky serial step, to assemble together PIV and atom-pair info from head-tail big vectors
1042 : // Loop before on l and then on i would be better but the allgather should be modified
1043 : // Loop on blocks
1044 : //for(unsigned m=0;m<Nlist;m++) {
1045 : // Loop on Ordering Vector size excluding zeros (i=1)
1046 0 : if(timer) {
1047 0 : stopwatch.stop("2 Sort cPIV");
1048 : }
1049 0 : if(timer) {
1050 0 : stopwatch.start("3 Reconstruct cPIV");
1051 : }
1052 0 : for(unsigned i=1; i<Nprec; i++) {
1053 : // Loop on the ranks
1054 0 : for(unsigned l=0; l<stride; l++) {
1055 : // Loop on the number of head-to-tail pieces
1056 0 : for(unsigned m=0; m<OrdVecAll[i+l*Nprec]; m++) {
1057 : // cPIV is the current PIV at time t
1058 0 : cPIV[j].push_back(double(i)/double(Nprec-1));
1059 0 : Atom0[j].push_back(Atom0FAll[k[l]+Vpos[l]]);
1060 0 : Atom1[j].push_back(Atom1FAll[k[l]+Vpos[l]]);
1061 0 : k[l]+=1;
1062 : }
1063 : }
1064 : }
1065 0 : if(timer) {
1066 0 : stopwatch.stop("3 Reconstruct cPIV");
1067 : }
1068 : } else {
1069 6000000 : for(unsigned i=1; i<Nprec; i++) {
1070 11757594 : for(unsigned m=0; m<OrdVec[i]; m++) {
1071 5757600 : cPIV[j].push_back(double(i)/double(Nprec-1));
1072 5757600 : Atom0[j].push_back(A0[i][m]);
1073 5757600 : Atom1[j].push_back(A1[i][m]);
1074 : }
1075 : }
1076 : }
1077 : }
1078 : }
1079 : }
1080 327 : Vector distance;
1081 327 : double dfunc=0.;
1082 : // Calculate volume scaling factor
1083 327 : if(Svol) {
1084 327 : Fvol=cbrt(Vol0/getBox().determinant());
1085 : }
1086 :
1087 : // This test may be run by specifying the TEST keyword as input, it pritnts rPIV and cPIV and quits
1088 327 : if(test) {
1089 : unsigned limit=0;
1090 0 : for(unsigned j=0; j<Nlist; j++) {
1091 0 : if(dosort[j]) {
1092 0 : limit = cPIV[j].size();
1093 : } else {
1094 0 : limit = rPIV[j].size();
1095 : }
1096 0 : log.printf("PIV Block: %6i %12s %6i \n", j, " Size:", limit);
1097 0 : log.printf("%6s%6s%12s%12s%36s\n"," i"," j", " c-PIV "," r-PIV "," i-j distance vector ");
1098 0 : for(unsigned i=0; i<limit; i++) {
1099 : unsigned i0=0;
1100 : unsigned i1=0;
1101 0 : if(dosort[j]) {
1102 0 : i0=Atom0[j][i];
1103 0 : i1=Atom1[j][i];
1104 : } else {
1105 0 : i0=(nl[j]->getClosePairAtomNumber(i).first).index();
1106 0 : i1=(nl[j]->getClosePairAtomNumber(i).second).index();
1107 : }
1108 0 : Vector Pos0,Pos1;
1109 0 : if(com) {
1110 0 : Pos0=compos[i0];
1111 0 : Pos1=compos[i1];
1112 : } else {
1113 0 : Pos0=getPosition(i0);
1114 0 : Pos1=getPosition(i1);
1115 : }
1116 0 : if(pbc) {
1117 0 : distance=pbcDistance(Pos0,Pos1);
1118 : } else {
1119 0 : distance=delta(Pos0,Pos1);
1120 : }
1121 0 : dfunc=0.;
1122 : double cP,rP;
1123 0 : if(dosort[j]) {
1124 0 : cP = cPIV[j][i];
1125 0 : rP = rPIV[j][rPIV[j].size()-cPIV[j].size()+i];
1126 : } else {
1127 0 : double dm=distance.modulo();
1128 0 : cP = sfs[j].calculate(dm*Fvol, dfunc);
1129 0 : rP = rPIV[j][i];
1130 : }
1131 0 : log.printf("%6i%6i%12.6f%12.6f%12.6f%12.6f%12.6f\n",i0,i1,cP,rP,distance[0],distance[1],distance[2]);
1132 : }
1133 : }
1134 0 : log.printf("This was a test, now exit \n");
1135 0 : exit();
1136 : }
1137 :
1138 327 : if(timer) {
1139 1 : stopwatch.start("4 Build For Derivatives");
1140 : }
1141 : // non-global variables Nder and Scalevol defined to speedup if structures in cycles
1142 327 : bool Nder=CompDer;
1143 327 : bool Scalevol=Svol;
1144 327 : if(getStep()%updatePIV==0) {
1145 : // set to zero PIVdistance, derivatives and virial when they are calculated
1146 29799 : for(unsigned j=0; j<m_deriv.size(); j++) {
1147 117888 : for(unsigned k=0; k<3; k++) {
1148 88416 : m_deriv[j][k]=0.;
1149 : }
1150 : }
1151 1308 : for(unsigned j=0; j<3; j++) {
1152 3924 : for(unsigned k=0; k<3; k++) {
1153 2943 : m_virial[j][k]=0.;
1154 : }
1155 : }
1156 327 : m_PIVdistance=0.;
1157 : // Re-compute atomic distances for derivatives and compute PIV-PIV distance
1158 981 : for(unsigned j=0; j<Nlist; j++) {
1159 : unsigned limit=0;
1160 : // dosorting definition is to speedup if structure in cycles with non-global variables
1161 654 : bool dosorting=dosort[j];
1162 654 : bool docom=com;
1163 654 : bool dopbc=pbc;
1164 654 : if(dosorting) {
1165 12 : limit = cPIV[j].size();
1166 : } else {
1167 642 : limit = rPIV[j].size();
1168 : }
1169 11574918 : for(unsigned i=rank; i<limit; i+=stride) {
1170 : unsigned i0=0;
1171 : unsigned i1=0;
1172 11574264 : if(dosorting) {
1173 11515200 : i0=Atom0[j][i];
1174 11515200 : i1=Atom1[j][i];
1175 : } else {
1176 59064 : i0=(nl[j]->getClosePairAtomNumber(i).first).index();
1177 59064 : i1=(nl[j]->getClosePairAtomNumber(i).second).index();
1178 : }
1179 11574264 : Vector Pos0,Pos1;
1180 11574264 : if(docom) {
1181 0 : Pos0=compos[i0];
1182 0 : Pos1=compos[i1];
1183 : } else {
1184 11574264 : Pos0=getPosition(i0);
1185 11574264 : Pos1=getPosition(i1);
1186 : }
1187 11574264 : if(dopbc) {
1188 11574264 : distance=pbcDistance(Pos0,Pos1);
1189 : } else {
1190 0 : distance=delta(Pos0,Pos1);
1191 : }
1192 11574264 : dfunc=0.;
1193 : // this is needed for dfunc and dervatives
1194 11574264 : double dm=distance.modulo();
1195 11574264 : double tPIV = sfs[j].calculate(dm*Fvol, dfunc);
1196 : // PIV distance
1197 : double coord=0.;
1198 11574264 : if(!dosorting||Nder) {
1199 59064 : coord = tPIV - rPIV[j][i];
1200 : } else {
1201 11515200 : coord = cPIV[j][i] - rPIV[j][rPIV[j].size()-cPIV[j].size()+i];
1202 : }
1203 : // Calculate derivatives, virial, and variable=sum_j (scaling[j] *(cPIV-rPIV)_j^2)
1204 : // WARNING: dfunc=dswf/(Fvol*dm) (this may change in future Plumed versions)
1205 11574264 : double tmp = 2.*scaling[j]*coord*Fvol*Fvol*dfunc;
1206 11574264 : Vector tmpder = tmp*distance;
1207 : // 0.5*(x_i-x_k)*f_ik (force on atom k due to atom i)
1208 11574264 : if(docom) {
1209 0 : Vector dist;
1210 0 : for(unsigned k=0; k<nlcom[i0]->getFullAtomList().size(); k++) {
1211 0 : unsigned x0=nlcom[i0]->getFullAtomList()[k].index();
1212 0 : m_deriv[x0] -= tmpder*fmass[x0];
1213 0 : for(unsigned l=0; l<3; l++) {
1214 0 : dist[l]=0.;
1215 : }
1216 0 : Vector P0=getPosition(x0);
1217 0 : for(unsigned l=0; l<nlcom[i0]->getFullAtomList().size(); l++) {
1218 0 : unsigned x1=nlcom[i0]->getFullAtomList()[l].index();
1219 0 : Vector P1=getPosition(x1);
1220 0 : if(dopbc) {
1221 0 : dist+=pbcDistance(P0,P1);
1222 : } else {
1223 0 : dist+=delta(P0,P1);
1224 : }
1225 : }
1226 0 : for(unsigned l=0; l<nlcom[i1]->getFullAtomList().size(); l++) {
1227 0 : unsigned x1=nlcom[i1]->getFullAtomList()[l].index();
1228 0 : Vector P1=getPosition(x1);
1229 0 : if(dopbc) {
1230 0 : dist+=pbcDistance(P0,P1);
1231 : } else {
1232 0 : dist+=delta(P0,P1);
1233 : }
1234 : }
1235 0 : m_virial -= 0.25*fmass[x0]*Tensor(dist,tmpder);
1236 : }
1237 0 : for(unsigned k=0; k<nlcom[i1]->getFullAtomList().size(); k++) {
1238 0 : unsigned x1=nlcom[i1]->getFullAtomList()[k].index();
1239 0 : m_deriv[x1] += tmpder*fmass[x1];
1240 0 : for(unsigned l=0; l<3; l++) {
1241 0 : dist[l]=0.;
1242 : }
1243 0 : Vector P1=getPosition(x1);
1244 0 : for(unsigned l=0; l<nlcom[i1]->getFullAtomList().size(); l++) {
1245 0 : unsigned x0=nlcom[i1]->getFullAtomList()[l].index();
1246 0 : Vector P0=getPosition(x0);
1247 0 : if(dopbc) {
1248 0 : dist+=pbcDistance(P1,P0);
1249 : } else {
1250 0 : dist+=delta(P1,P0);
1251 : }
1252 : }
1253 0 : for(unsigned l=0; l<nlcom[i0]->getFullAtomList().size(); l++) {
1254 0 : unsigned x0=nlcom[i0]->getFullAtomList()[l].index();
1255 0 : Vector P0=getPosition(x0);
1256 0 : if(dopbc) {
1257 0 : dist+=pbcDistance(P1,P0);
1258 : } else {
1259 0 : dist+=delta(P1,P0);
1260 : }
1261 : }
1262 0 : m_virial += 0.25*fmass[x1]*Tensor(dist,tmpder);
1263 : }
1264 : } else {
1265 11574264 : m_deriv[i0] -= tmpder;
1266 11574264 : m_deriv[i1] += tmpder;
1267 11574264 : m_virial -= tmp*Tensor(distance,distance);
1268 : }
1269 11574264 : if(Scalevol) {
1270 11574264 : m_virial+=1./3.*tmp*dm*dm*Tensor::identity();
1271 : }
1272 11574264 : m_PIVdistance += scaling[j]*coord*coord;
1273 : }
1274 : }
1275 :
1276 327 : if (!serial && comm.initialized()) {
1277 0 : comm.Barrier();
1278 0 : comm.Sum(&m_PIVdistance,1);
1279 0 : if(!m_deriv.empty()) {
1280 0 : comm.Sum(&m_deriv[0][0],3*m_deriv.size());
1281 : }
1282 0 : comm.Sum(&m_virial[0][0],9);
1283 : }
1284 : }
1285 327 : prev_stp=getStep();
1286 :
1287 : //Timing
1288 327 : if(timer) {
1289 1 : stopwatch.stop("4 Build For Derivatives");
1290 : }
1291 327 : if(timer) {
1292 1 : log.printf("Timings for action %s with label %s \n", getName().c_str(), getLabel().c_str() );
1293 1 : log<<stopwatch;
1294 : }
1295 :
1296 : // Update derivatives, virial, and variable (PIV-distance^2)
1297 29799 : for(unsigned i=0; i<m_deriv.size(); ++i) {
1298 29472 : setAtomsDerivatives(i,m_deriv[i]);
1299 : }
1300 327 : setValue (m_PIVdistance);
1301 327 : setBoxDerivatives (m_virial);
1302 327 : }
1303 : //Close Namespaces at the very beginning
1304 : }
1305 : }
1306 :
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