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 "colvar/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/Stopwatch.h"
26 :
27 : #include <string>
28 : #include <cmath>
29 : #include <iostream>
30 :
31 : using namespace std;
32 :
33 : namespace PLMD
34 : {
35 : namespace piv
36 : {
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 : {
186 : private:
187 : bool pbc, serial, timer;
188 : ForwardDecl<Stopwatch> stopwatch_fwd;
189 : Stopwatch& stopwatch=*stopwatch_fwd;
190 : int updatePIV;
191 : size_t Nprec;
192 : unsigned Natm,Nlist,NLsize;
193 : double Fvol,Vol0,m_PIVdistance;
194 : std::string ref_file;
195 : NeighborList *nlall;
196 : std::vector<SwitchingFunction> sfs;
197 : std::vector<std:: vector<double> > rPIV;
198 : std::vector<double> scaling,r00;
199 : std::vector<double> nl_skin;
200 : std::vector<double> fmass;
201 : std::vector<bool> dosort;
202 : std::vector<Vector> compos;
203 : std::vector<string> sw;
204 : std::vector<NeighborList *> nl;
205 : std::vector<NeighborList *> nlcom;
206 : std::vector<Vector> m_deriv;
207 : Tensor m_virial;
208 : bool Svol,cross,direct,doneigh,test,CompDer,com;
209 : public:
210 : static void registerKeywords( Keywords& keys );
211 : explicit PIV(const ActionOptions&);
212 : ~PIV();
213 : // active methods:
214 : virtual void calculate();
215 0 : void checkFieldsAllowed() {}
216 : };
217 :
218 10443 : PLUMED_REGISTER_ACTION(PIV,"PIV")
219 :
220 13 : void PIV::registerKeywords( Keywords& keys )
221 : {
222 13 : Colvar::registerKeywords( keys );
223 26 : keys.add("numbered","SWITCH","The switching functions parameter."
224 : "You should specify a Switching function for all PIV blocks."
225 : "Details of the various switching "
226 : "functions you can use are provided on \\ref switchingfunction.");
227 26 : keys.add("compulsory","PRECISION","the precision for approximating reals with integers in sorting.");
228 26 : keys.add("compulsory","REF_FILE","PDB file name that contains the \\f$i\\f$th reference structure.");
229 26 : keys.add("compulsory","PIVATOMS","Number of atoms to use for PIV.");
230 26 : keys.add("compulsory","SORT","Whether to sort or not the PIV block.");
231 26 : keys.add("compulsory","ATOMTYPES","The atom types to use for PIV.");
232 26 : keys.add("optional","SFACTOR","Scale the PIV-distance by such block-specific factor");
233 26 : 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. ");
234 26 : keys.add("optional","UPDATEPIV","Frequency (in steps) at which the PIV is updated.");
235 26 : keys.addFlag("TEST",false,"Print the actual and reference PIV and exit");
236 26 : keys.addFlag("COM",false,"Use centers of mass of groups of atoms instead of atoms as specified in the Pdb file");
237 26 : keys.addFlag("ONLYCROSS",false,"Use only cross-terms (A-B, A-C, B-C, ...) in PIV");
238 26 : keys.addFlag("ONLYDIRECT",false,"Use only direct-terms (A-A, B-B, C-C, ...) in PIV");
239 26 : keys.addFlag("DERIVATIVES",false,"Activate the calculation of the PIV for every class (needed for numerical derivatives).");
240 26 : keys.addFlag("NLIST",false,"Use a neighbor list for distance calculations.");
241 26 : keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose");
242 26 : keys.addFlag("TIMER",false,"Perform timing analysis on heavy loops.");
243 26 : keys.add("optional","NL_CUTOFF","Neighbor lists cutoff.");
244 26 : keys.add("optional","NL_STRIDE","Update neighbor lists every NL_STRIDE steps.");
245 26 : keys.add("optional","NL_SKIN","The maximum atom displacement tolerated for the neighbor lists update.");
246 26 : keys.reset_style("SWITCH","compulsory");
247 13 : }
248 :
249 12 : PIV::PIV(const ActionOptions&ao):
250 : PLUMED_COLVAR_INIT(ao),
251 12 : pbc(true),
252 12 : serial(false),
253 12 : timer(false),
254 12 : updatePIV(1),
255 12 : Nprec(1000),
256 12 : Natm(1),
257 12 : Nlist(1),
258 12 : NLsize(1),
259 12 : Fvol(1.),
260 12 : Vol0(0.),
261 12 : m_PIVdistance(0.),
262 12 : rPIV(std:: vector<std:: vector<double> >(Nlist)),
263 12 : scaling(std:: vector<double>(Nlist)),
264 12 : r00(std:: vector<double>(Nlist)),
265 12 : nl_skin(std:: vector<double>(Nlist)),
266 12 : fmass(std:: vector<double>(Nlist)),
267 12 : dosort(std:: vector<bool>(Nlist)),
268 12 : compos(std:: vector<Vector>(NLsize)),
269 12 : sw(std:: vector<string>(Nlist)),
270 12 : nl(std:: vector<NeighborList *>(Nlist)),
271 12 : nlcom(std:: vector<NeighborList *>(NLsize)),
272 12 : m_deriv(std:: vector<Vector>(1)),
273 12 : Svol(false),
274 12 : cross(true),
275 12 : direct(true),
276 12 : doneigh(false),
277 12 : test(false),
278 12 : CompDer(false),
279 24 : com(false)
280 : {
281 12 : log << "Starting PIV Constructor\n";
282 :
283 : // Precision on the real-to-integer transformation for the sorting
284 12 : parse("PRECISION",Nprec);
285 12 : if(Nprec<2) error("Precision must be => 2");
286 :
287 : // PBC
288 12 : bool nopbc=!pbc;
289 12 : parseFlag("NOPBC",nopbc);
290 12 : pbc=!nopbc;
291 12 : if(pbc) {
292 12 : log << "Using Periodic Boundary Conditions\n";
293 : } else {
294 0 : log << "Isolated System (NO PBC)\n";
295 : }
296 :
297 : // SERIAL/PARALLEL
298 12 : parseFlag("SERIAL",serial);
299 12 : if(serial) {
300 0 : log << "Serial PIV construction\n";
301 : } else {
302 12 : log << "Parallel PIV construction\n";
303 : }
304 :
305 : // Derivatives
306 12 : parseFlag("DERIVATIVES",CompDer);
307 12 : if(CompDer) log << "Computing Derivatives\n";
308 :
309 : // Timing
310 12 : parseFlag("TIMER",timer);
311 12 : if(timer) {
312 1 : log << "Timing analysis\n";
313 1 : stopwatch.start();
314 1 : stopwatch.pause();
315 : }
316 :
317 : // Test
318 12 : parseFlag("TEST",test);
319 :
320 : // UPDATEPIV
321 24 : if(keywords.exists("UPDATEPIV")) {
322 24 : parse("UPDATEPIV",updatePIV);
323 : }
324 :
325 : // Test
326 12 : parseFlag("COM",com);
327 12 : if(com) log << "Building PIV using COMs\n";
328 :
329 : // Volume Scaling
330 12 : parse("VOLUME",Vol0);
331 12 : if (Vol0>0) {
332 12 : Svol=true;
333 : }
334 :
335 : // PIV direct and cross blocks
336 12 : bool oc=false,od=false;
337 12 : parseFlag("ONLYCROSS",oc);
338 12 : parseFlag("ONLYDIRECT",od);
339 12 : if (oc&&od) {
340 0 : error("ONLYCROSS and ONLYDIRECT are incompatible options!");
341 : }
342 12 : if(oc) {
343 4 : direct=false;
344 4 : log << "Using only CROSS-PIV blocks\n";
345 : }
346 12 : if(od) {
347 4 : cross=false;
348 4 : log << "Using only DIRECT-PIV blocks\n";
349 : }
350 :
351 : // Atoms for PIV
352 12 : parse("PIVATOMS",Natm);
353 12 : std:: vector<string> atype(Natm);
354 12 : parseVector("ATOMTYPES",atype);
355 : //if(atype.size()!=getNumberOfArguments() && atype.size()!=0) error("not enough values for ATOMTYPES");
356 :
357 : // Reference PDB file
358 12 : parse("REF_FILE",ref_file);
359 12 : PDB mypdb;
360 12 : FILE* fp=fopen(ref_file.c_str(),"r");
361 12 : if (fp!=NULL) {
362 12 : log<<"Opening PDB file with reference frame: "<<ref_file.c_str()<<"\n";
363 24 : mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
364 12 : fclose (fp);
365 : } else {
366 0 : error("Error in reference PDB file");
367 : }
368 :
369 : // Build COM/Atom lists of AtomNumbers (this might be done in PBC.cpp)
370 : // Atomlist or Plist used to build pair lists
371 12 : std:: vector<std:: vector<AtomNumber> > Plist(Natm);
372 : // Atomlist used to build list of atoms for each COM
373 12 : std:: vector<std:: vector<AtomNumber> > comatm(1);
374 : // NLsize is the number of atoms in the pdb cell
375 12 : NLsize=mypdb.getAtomNumbers().size();
376 : // In the following P stands for Point (either an Atom or a COM)
377 : unsigned resnum=0;
378 : // Presind (array size: number of residues) contains the contains the residue number
379 : // this is because the residue numbers may not always be ordered from 1 to resnum
380 : std:: vector<unsigned> Presind;
381 : // Build Presind
382 19404 : for (unsigned i=0; i<mypdb.getAtomNumbers().size(); i++) {
383 19392 : unsigned rind=mypdb.getResidueNumber(mypdb.getAtomNumbers()[i]);
384 : bool oldres=false;
385 7705008 : for (unsigned j=0; j<Presind.size(); j++) {
386 7685616 : if(rind==Presind[j]) {
387 : oldres=true;
388 : }
389 : }
390 19392 : if(!oldres) {
391 4848 : Presind.push_back(rind);
392 : }
393 : }
394 12 : resnum=Presind.size();
395 :
396 : // Pind0 is the atom/COM used in Nlists (for COM Pind0 is the first atom in the pdb belonging to that COM)
397 : unsigned Pind0size;
398 12 : if(com) {
399 : Pind0size=resnum;
400 : } else {
401 12 : Pind0size=NLsize;
402 : }
403 12 : std:: vector<unsigned> Pind0(Pind0size);
404 : // If COM resize important arrays
405 12 : comatm.resize(NLsize);
406 12 : if(com) {
407 0 : nlcom.resize(NLsize);
408 0 : compos.resize(NLsize);
409 0 : fmass.resize(NLsize,0.);
410 : }
411 12 : log << "Total COM/Atoms: " << Natm*resnum << " \n";
412 : // Build lists of Atoms/COMs for NLists
413 : // comatm filled also for non_COM calculation for analysis purposes
414 36 : for (unsigned j=0; j<Natm; j++) {
415 : unsigned oind;
416 38808 : for (unsigned i=0; i<Pind0.size(); i++) {
417 38784 : Pind0[i]=0;
418 : }
419 38808 : for (unsigned i=0; i<mypdb.getAtomNumbers().size(); i++) {
420 : // Residue/Atom AtomNumber: used to build NL for COMS/Atoms pairs.
421 38784 : AtomNumber anum=mypdb.getAtomNumbers()[i];
422 : // ResidueName/Atomname associated to atom
423 38784 : string rname=mypdb.getResidueName(anum);
424 38784 : string aname=mypdb.getAtomName(anum);
425 : // Index associated to residue/atom: used to separate COM-lists
426 38784 : unsigned rind=mypdb.getResidueNumber(anum);
427 : unsigned aind=anum.index();
428 : // This builds lists for NL
429 : string Pname;
430 : unsigned Pind;
431 38784 : if(com) {
432 : Pname=rname;
433 0 : for(unsigned l=0; l<resnum; l++) {
434 0 : if(rind==Presind[l]) {
435 : Pind=l;
436 : }
437 : }
438 : } else {
439 : Pname=aname;
440 : Pind=aind;
441 : }
442 38784 : if(Pname==atype[j]) {
443 14544 : if(Pind0[Pind]==0) {
444 : // adding the atomnumber to the atom/COM list for pairs
445 14544 : Plist[j].push_back(anum);
446 14544 : Pind0[Pind]=aind+1;
447 : oind=Pind;
448 : }
449 : // adding the atomnumber to list of atoms for every COM/Atoms
450 14544 : comatm[Pind0[Pind]-1].push_back(anum);
451 : }
452 : }
453 : // Output Lists
454 24 : log << " Groups of type " << j << ": " << Plist[j].size() << " \n";
455 : string gname;
456 : unsigned gsize;
457 24 : if(com) {
458 0 : gname=mypdb.getResidueName(comatm[Pind0[oind]-1][0]);
459 0 : gsize=comatm[Pind0[oind]-1].size();
460 : } else {
461 48 : gname=mypdb.getAtomName(comatm[Pind0[oind]-1][0]);
462 : gsize=1;
463 : }
464 24 : log.printf(" %6s %3s %13s %10i %6s\n", "type ", gname.c_str()," containing ",gsize," atoms");
465 : }
466 :
467 : // This is to build the list with all the atoms
468 : std:: vector<AtomNumber> listall;
469 19404 : for (unsigned i=0; i<mypdb.getAtomNumbers().size(); i++) {
470 19392 : listall.push_back(mypdb.getAtomNumbers()[i]);
471 : }
472 :
473 : // PIV blocks and Neighbour Lists
474 12 : Nlist=0;
475 : // Direct adds the A-A ad B-B blocks (N)
476 12 : if(direct) {
477 8 : Nlist=Nlist+unsigned(Natm);
478 : }
479 : // Cross adds the A-B blocks (N*(N-1)/2)
480 12 : if(cross) {
481 8 : Nlist=Nlist+unsigned(double(Natm*(Natm-1))/2.);
482 : }
483 : // Resize vectors according to Nlist
484 12 : rPIV.resize(Nlist);
485 :
486 : // PIV scaled option
487 12 : scaling.resize(Nlist);
488 36 : for(unsigned j=0; j<Nlist; j++) {
489 24 : scaling[j]=1.;
490 : }
491 24 : if(keywords.exists("SFACTOR")) {
492 24 : parseVector("SFACTOR",scaling);
493 : //if(scaling.size()!=getNumberOfArguments() && scaling.size()!=0) error("not enough values for SFACTOR");
494 : }
495 : // Neighbour Lists option
496 12 : parseFlag("NLIST",doneigh);
497 12 : nl.resize(Nlist);
498 12 : nl_skin.resize(Nlist);
499 12 : if(doneigh) {
500 12 : std:: vector<double> nl_cut(Nlist,0.);
501 12 : std:: vector<int> nl_st(Nlist,0);
502 12 : parseVector("NL_CUTOFF",nl_cut);
503 : //if(nl_cut.size()!=getNumberOfArguments() && nl_cut.size()!=0) error("not enough values for NL_CUTOFF");
504 12 : parseVector("NL_STRIDE",nl_st);
505 : //if(nl_st.size()!=getNumberOfArguments() && nl_st.size()!=0) error("not enough values for NL_STRIDE");
506 12 : parseVector("NL_SKIN",nl_skin);
507 : //if(nl_skin.size()!=getNumberOfArguments() && nl_skin.size()!=0) error("not enough values for NL_SKIN");
508 36 : for (unsigned j=0; j<Nlist; j++) {
509 24 : if(nl_cut[j]<=0.0) error("NL_CUTOFF should be explicitly specified and positive");
510 24 : if(nl_st[j]<=0) error("NL_STRIDE should be explicitly specified and positive");
511 24 : if(nl_skin[j]<=0.) error("NL_SKIN should be explicitly specified and positive");
512 24 : nl_cut[j]=nl_cut[j]+nl_skin[j];
513 : }
514 12 : log << "Creating Neighbor Lists \n";
515 : // WARNING: is nl_cut meaningful here?
516 12 : nlall= new NeighborList(listall,true,pbc,getPbc(),comm,nl_cut[0],nl_st[0]);
517 12 : if(com) {
518 : //Build lists of Atoms for every COM
519 0 : for (unsigned i=0; i<compos.size(); i++) {
520 : // WARNING: is nl_cut meaningful here?
521 0 : nlcom[i]= new NeighborList(comatm[i],true,pbc,getPbc(),comm,nl_cut[0],nl_st[0]);
522 : }
523 : }
524 : unsigned ncnt=0;
525 : // Direct blocks AA, BB, CC, ...
526 12 : if(direct) {
527 24 : for (unsigned j=0; j<Natm; j++) {
528 16 : nl[ncnt]= new NeighborList(Plist[j],true,pbc,getPbc(),comm,nl_cut[j],nl_st[j]);
529 16 : ncnt+=1;
530 : }
531 : }
532 : // Cross blocks AB, AC, BC, ...
533 12 : if(cross) {
534 24 : for (unsigned j=0; j<Natm; j++) {
535 24 : for (unsigned i=j+1; i<Natm; i++) {
536 8 : nl[ncnt]= new NeighborList(Plist[i],Plist[j],true,false,pbc,getPbc(),comm,nl_cut[ncnt],nl_st[ncnt]);
537 8 : ncnt+=1;
538 : }
539 : }
540 : }
541 : } else {
542 0 : log << "WARNING: Neighbor List not activated this has not been tested!! \n";
543 0 : nlall= new NeighborList(listall,true,pbc,getPbc(),comm);
544 0 : for (unsigned j=0; j<Nlist; j++) {
545 0 : nl[j]= new NeighborList(Plist[j],Plist[j],true,true,pbc,getPbc(),comm);
546 : }
547 : }
548 : // Output Nlist
549 12 : log << "Total Nlists: " << Nlist << " \n";
550 36 : for (unsigned j=0; j<Nlist; j++) {
551 24 : log << " list " << j+1 << " size " << nl[j]->size() << " \n";
552 : }
553 : // Calculate COM masses once and for all from lists
554 12 : if(com) {
555 0 : for(unsigned j=0; j<compos.size(); j++) {
556 : double commass=0.;
557 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
558 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
559 0 : commass+=mypdb.getOccupancy()[andx];
560 : }
561 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
562 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
563 0 : if(commass>0.) {
564 0 : fmass[andx]=mypdb.getOccupancy()[andx]/commass;
565 : } else {
566 0 : fmass[andx]=1.;
567 : }
568 : }
569 : }
570 : }
571 :
572 : // Sorting
573 12 : dosort.resize(Nlist);
574 12 : std:: vector<int> ynsort(Nlist);
575 12 : parseVector("SORT",ynsort);
576 36 : for (unsigned i=0; i<Nlist; i++) {
577 24 : if(ynsort[i]==0||CompDer) {
578 : dosort[i]=false;
579 : } else {
580 : dosort[i]=true;
581 : }
582 : }
583 :
584 : //build box vectors and correct for pbc
585 12 : log << "Building the box from PDB data ... \n";
586 12 : Tensor Box=mypdb.getBoxVec();
587 12 : log << " Done! A,B,C vectors in Cartesian space: \n";
588 12 : log.printf(" A: %12.6f%12.6f%12.6f\n", Box[0][0],Box[0][1],Box[0][2]);
589 12 : log.printf(" B: %12.6f%12.6f%12.6f\n", Box[1][0],Box[1][1],Box[1][2]);
590 12 : log.printf(" C: %12.6f%12.6f%12.6f\n", Box[2][0],Box[2][1],Box[2][2]);
591 12 : log << "Changing the PBC according to the new box \n";
592 12 : Pbc mypbc;
593 12 : mypbc.setBox(Box);
594 12 : log << "The box volume is " << mypbc.getBox().determinant() << " \n";
595 :
596 : //Compute scaling factor
597 12 : if(Svol) {
598 12 : Fvol=cbrt(Vol0/mypbc.getBox().determinant());
599 12 : log << "Scaling atom distances by " << Fvol << " \n";
600 : } else {
601 0 : log << "Using unscaled atom distances \n";
602 : }
603 :
604 12 : r00.resize(Nlist);
605 12 : sw.resize(Nlist);
606 36 : for (unsigned j=0; j<Nlist; j++) {
607 48 : if( !parseNumbered( "SWITCH", j+1, sw[j] ) ) break;
608 : }
609 12 : if(CompDer) {
610 : // Set switching function parameters here only if computing derivatives
611 : // now set at the beginning of the dynamics to solve the r0 issue
612 6 : log << "Switching Function Parameters \n";
613 6 : sfs.resize(Nlist);
614 : std::string errors;
615 18 : for (unsigned j=0; j<Nlist; j++) {
616 12 : if(Svol) {
617 : double r0;
618 : std::string old_r0;
619 12 : vector<string> data=Tools::getWords(sw[j]);
620 : data.erase(data.begin());
621 12 : Tools::parse(data,"R_0",old_r0);
622 12 : Tools::convert(old_r0,r0);
623 12 : r0*=Fvol;
624 12 : std::string new_r0; Tools::convert(r0,new_r0);
625 12 : std::size_t pos = sw[j].find("R_0");
626 12 : sw[j].replace(pos+4,old_r0.size(),new_r0);
627 12 : }
628 12 : sfs[j].set(sw[j],errors);
629 : std::string num;
630 12 : Tools::convert(j+1, num);
631 12 : if( errors.length()!=0 ) error("problem reading SWITCH" + num + " keyword : " + errors );
632 12 : r00[j]=sfs[j].get_r0();
633 24 : log << " Swf: " << j << " r0=" << (sfs[j].description()).c_str() << " \n";
634 : }
635 : }
636 :
637 : // build COMs from positions if requested
638 12 : if(com) {
639 0 : for(unsigned j=0; j<compos.size(); j++) {
640 0 : compos[j][0]=0.;
641 0 : compos[j][1]=0.;
642 0 : compos[j][2]=0.;
643 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
644 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
645 0 : compos[j]+=fmass[andx]*mypdb.getPositions()[andx];
646 : }
647 : }
648 : }
649 : // build the rPIV distances (transformation and sorting is done afterwards)
650 12 : if(CompDer) {
651 6 : log << " PIV | block | Size | Zeros | Ones |" << " \n";
652 : }
653 36 : for(unsigned j=0; j<Nlist; j++) {
654 11516328 : for(unsigned i=0; i<nl[j]->size(); i++) {
655 11516304 : unsigned i0=(nl[j]->getClosePairAtomNumber(i).first).index();
656 11516304 : unsigned i1=(nl[j]->getClosePairAtomNumber(i).second).index();
657 : //calculate/get COM position of centers i0 and i1
658 11516304 : Vector Pos0,Pos1;
659 11516304 : if(com) {
660 : //if(pbc) makeWhole();
661 0 : Pos0=compos[i0];
662 0 : Pos1=compos[i1];
663 : } else {
664 11516304 : Pos0=mypdb.getPositions()[i0];
665 11516304 : Pos1=mypdb.getPositions()[i1];
666 : }
667 11516304 : Vector ddist;
668 11516304 : if(pbc) {
669 11516304 : ddist=mypbc.distance(Pos0,Pos1);
670 : } else {
671 0 : ddist=delta(Pos0,Pos1);
672 : }
673 11516304 : double df=0.;
674 : // Transformation and sorting done at the first timestep to solve the r0 definition issue
675 11516304 : if(CompDer) {
676 1104 : rPIV[j].push_back(sfs[j].calculate(ddist.modulo()*Fvol, df));
677 : } else {
678 11515200 : rPIV[j].push_back(ddist.modulo()*Fvol);
679 : }
680 : }
681 24 : if(CompDer) {
682 12 : if(dosort[j]) {
683 0 : std::sort(rPIV[j].begin(),rPIV[j].end());
684 : }
685 : int lmt0=0;
686 : int lmt1=0;
687 1116 : for(unsigned i=0; i<rPIV[j].size(); i++) {
688 1104 : if(int(rPIV[j][i]*double(Nprec-1))==0) {
689 0 : lmt0+=1;
690 : }
691 1104 : if(int(rPIV[j][i]*double(Nprec-1))==1) {
692 0 : lmt1+=1;
693 : }
694 : }
695 12 : log.printf(" |%10i|%15zu|%15i|%15i|\n", j, rPIV[j].size(), lmt0, lmt1);
696 : }
697 : }
698 :
699 12 : checkRead();
700 : // From the plumed manual on how to build-up a new Colvar
701 12 : addValueWithDerivatives();
702 12 : requestAtoms(nlall->getFullAtomList());
703 12 : setNotPeriodic();
704 : // getValue()->setPeridodicity(false);
705 : // set size of derivative vector
706 12 : m_deriv.resize(getNumberOfAtoms());
707 24 : }
708 :
709 : // The following deallocates pointers
710 24 : PIV::~PIV()
711 : {
712 36 : for (unsigned j=0; j<Nlist; j++) {
713 24 : delete nl[j];
714 : }
715 12 : if(com) {
716 0 : for (unsigned j=0; j<NLsize; j++) {
717 0 : delete nlcom[j];
718 : }
719 : }
720 12 : delete nlall;
721 48 : }
722 :
723 327 : void PIV::calculate()
724 : {
725 :
726 : // Local variables
727 : // The following are probably needed as static arrays
728 : static int prev_stp=-1;
729 : static int init_stp=1;
730 327 : static std:: vector<std:: vector<Vector> > prev_pos(Nlist);
731 327 : static std:: vector<std:: vector<double> > cPIV(Nlist);
732 327 : static std:: vector<std:: vector<int> > Atom0(Nlist);
733 327 : static std:: vector<std:: vector<int> > Atom1(Nlist);
734 327 : std:: vector<std:: vector<int> > A0(Nprec);
735 327 : std:: vector<std:: vector<int> > A1(Nprec);
736 : size_t stride=1;
737 : unsigned rank=0;
738 :
739 327 : if(!serial) {
740 327 : stride=comm.Get_size();
741 327 : rank=comm.Get_rank();
742 : } else {
743 : stride=1;
744 : rank=0;
745 : }
746 :
747 : // Transform (and sort) the rPIV before starting the dynamics
748 327 : if (((prev_stp==-1) || (init_stp==1)) &&!CompDer) {
749 6 : if(prev_stp!=-1) {init_stp=0;}
750 : // Calculate the volume scaling factor
751 6 : if(Svol) {
752 6 : Fvol=cbrt(Vol0/getBox().determinant());
753 : }
754 : //Set switching function parameters
755 6 : log << "\n";
756 6 : log << "REFERENCE PDB # " << prev_stp+2 << " \n";
757 : // Set switching function parameters here only if computing derivatives
758 : // now set at the beginning of the dynamics to solve the r0 issue
759 6 : log << "Switching Function Parameters \n";
760 6 : sfs.resize(Nlist);
761 : std::string errors;
762 18 : for (unsigned j=0; j<Nlist; j++) {
763 12 : if(Svol) {
764 : double r0;
765 : std::string old_r0;
766 12 : vector<string> data=Tools::getWords(sw[j]);
767 : data.erase(data.begin());
768 12 : Tools::parse(data,"R_0",old_r0);
769 12 : Tools::convert(old_r0,r0);
770 12 : r0*=Fvol;
771 12 : std::string new_r0; Tools::convert(r0,new_r0);
772 12 : std::size_t pos = sw[j].find("R_0");
773 12 : sw[j].replace(pos+4,old_r0.size(),new_r0);
774 12 : }
775 12 : sfs[j].set(sw[j],errors);
776 : std::string num;
777 12 : Tools::convert(j+1, num);
778 12 : if( errors.length()!=0 ) error("problem reading SWITCH" + num + " keyword : " + errors );
779 12 : r00[j]=sfs[j].get_r0();
780 24 : log << " Swf: " << j << " r0=" << (sfs[j].description()).c_str() << " \n";
781 : }
782 : //Transform and sort
783 6 : log << "Building Reference PIV Vector \n";
784 6 : log << " PIV | block | Size | Zeros | Ones |" << " \n";
785 6 : double df=0.;
786 18 : for (unsigned j=0; j<Nlist; j++) {
787 11515212 : for (unsigned i=0; i<rPIV[j].size(); i++) {
788 11515200 : rPIV[j][i]=sfs[j].calculate(rPIV[j][i], df);
789 : }
790 12 : if(dosort[j]) {
791 12 : std::sort(rPIV[j].begin(),rPIV[j].end());
792 : }
793 : int lmt0=0;
794 : int lmt1=0;
795 11515212 : for(unsigned i=0; i<rPIV[j].size(); i++) {
796 11515200 : if(int(rPIV[j][i]*double(Nprec-1))==0) {
797 26 : lmt0+=1;
798 : }
799 11515200 : if(int(rPIV[j][i]*double(Nprec-1))==1) {
800 63358 : lmt1+=1;
801 : }
802 : }
803 12 : log.printf(" |%10i|%15zu|%15i|%15i|\n", j, rPIV[j].size(), lmt0, lmt1);
804 : }
805 6 : log << "\n";
806 : }
807 : // Do the sorting only once per timestep to avoid building the PIV N times for N rPIV PDB structures!
808 327 : if ((getStep()>prev_stp&&getStep()%updatePIV==0)||CompDer) {
809 324 : if (CompDer) log << " Step " << getStep() << " Computing Derivatives NON-SORTED PIV \n";
810 : //
811 : // build COMs from positions if requested
812 324 : if(com) {
813 0 : if(pbc) makeWhole();
814 0 : for(unsigned j=0; j<compos.size(); j++) {
815 0 : compos[j][0]=0.;
816 0 : compos[j][1]=0.;
817 0 : compos[j][2]=0.;
818 0 : for(unsigned i=0; i<nlcom[j]->getFullAtomList().size(); i++) {
819 0 : unsigned andx=nlcom[j]->getFullAtomList()[i].index();
820 0 : compos[j]+=fmass[andx]*getPosition(andx);
821 : }
822 : }
823 : }
824 : // update neighbor lists when an atom moves out of the Neighbor list skin
825 324 : if (doneigh) {
826 : bool doupdate=false;
827 : // For the first step build previous positions = actual positions
828 324 : if (prev_stp==-1) {
829 6 : bool docom=com;
830 18 : for (unsigned j=0; j<Nlist; j++) {
831 9708 : for (unsigned i=0; i<nl[j]->getFullAtomList().size(); i++) {
832 9696 : Vector Pos;
833 9696 : if(docom) {
834 0 : Pos=compos[i];
835 : } else {
836 9696 : Pos=getPosition(nl[j]->getFullAtomList()[i].index());
837 : }
838 9696 : prev_pos[j].push_back(Pos);
839 : }
840 : }
841 : doupdate=true;
842 : }
843 : // Decide whether to update lists based on atom displacement, every stride
844 324 : std:: vector<std:: vector<Vector> > tmp_pos(Nlist);
845 324 : if (getStep() % nlall->getStride() ==0) {
846 324 : bool docom=com;
847 972 : for (unsigned j=0; j<Nlist; j++) {
848 20520 : for (unsigned i=0; i<nl[j]->getFullAtomList().size(); i++) {
849 19872 : Vector Pos;
850 19872 : if(docom) {
851 0 : Pos=compos[i];
852 : } else {
853 19872 : Pos=getPosition(nl[j]->getFullAtomList()[i].index());
854 : }
855 19872 : tmp_pos[j].push_back(Pos);
856 19872 : if (pbcDistance(tmp_pos[j][i],prev_pos[j][i]).modulo()>=nl_skin[j]) {
857 : doupdate=true;
858 : }
859 : }
860 : }
861 : }
862 : // Update Nlists if needed
863 324 : if (doupdate==true) {
864 18 : for (unsigned j=0; j<Nlist; j++) {
865 9708 : for (unsigned i=0; i<nl[j]->getFullAtomList().size(); i++) {
866 9696 : prev_pos[j][i]=tmp_pos[j][i];
867 : }
868 12 : nl[j]->update(prev_pos[j]);
869 12 : log << " Step " << getStep() << " Neighbour lists updated " << nl[j]->size() << " \n";
870 : }
871 : }
872 324 : }
873 : // Calculate the volume scaling factor
874 324 : if(Svol) {
875 324 : Fvol=cbrt(Vol0/getBox().determinant());
876 : }
877 324 : Vector ddist;
878 : // Global to local variables
879 324 : bool doserial=serial;
880 : // Build "Nlist" PIV blocks
881 972 : for(unsigned j=0; j<Nlist; j++) {
882 648 : if(dosort[j]) {
883 : // from global to local variables to speedup the for loop with if statements
884 6 : bool docom=com;
885 6 : bool dopbc=pbc;
886 : // Vectors collecting occupancies: OrdVec one rank, OrdVecAll all ranks
887 6 : std:: vector<int> OrdVec(Nprec,0);
888 6 : cPIV[j].resize(0);
889 6 : Atom0[j].resize(0);
890 6 : Atom1[j].resize(0);
891 : // Building distances for the PIV vector at time t
892 9 : if(timer) stopwatch.start("1 Build cPIV");
893 5757606 : for(unsigned i=rank; i<nl[j]->size(); i+=stride) {
894 5757600 : unsigned i0=(nl[j]->getClosePairAtomNumber(i).first).index();
895 5757600 : unsigned i1=(nl[j]->getClosePairAtomNumber(i).second).index();
896 5757600 : Vector Pos0,Pos1;
897 5757600 : if(docom) {
898 0 : Pos0=compos[i0];
899 0 : Pos1=compos[i1];
900 : } else {
901 5757600 : Pos0=getPosition(i0);
902 5757600 : Pos1=getPosition(i1);
903 : }
904 5757600 : if(dopbc) {
905 5757600 : ddist=pbcDistance(Pos0,Pos1);
906 : } else {
907 0 : ddist=delta(Pos0,Pos1);
908 : }
909 5757600 : double df=0.;
910 : //Integer sorting ... faster!
911 : //Transforming distances with the Switching function + real to integer transformation
912 5757600 : int Vint=int(sfs[j].calculate(ddist.modulo()*Fvol, df)*double(Nprec-1)+0.5);
913 : //Integer transformed distance values as index of the Ordering Vector OrdVec
914 5757600 : OrdVec[Vint]+=1;
915 : //Keeps track of atom indices for force and virial calculations
916 5757600 : A0[Vint].push_back(i0);
917 5757600 : A1[Vint].push_back(i1);
918 : }
919 9 : if(timer) stopwatch.stop("1 Build cPIV");
920 9 : if(timer) stopwatch.start("2 Sort cPIV");
921 6 : if(!doserial && comm.initialized()) {
922 : // Vectors keeping track of the dimension and the starting-position of the rank-specific pair vector in the big pair vector.
923 0 : std:: vector<int> Vdim(stride,0);
924 0 : std:: vector<int> Vpos(stride,0);
925 : // Vectors collecting occupancies: OrdVec one rank, OrdVecAll all ranks
926 0 : std:: vector<int> OrdVecAll(stride*Nprec);
927 : // Big vectors containing all Atom indexes for every occupancy (Atom0O(Nprec,n) and Atom1O(Nprec,n) matrices in one vector)
928 : std:: vector<int> Atom0F;
929 : std:: vector<int> Atom1F;
930 : // Vector used to reconstruct arrays
931 0 : std:: vector<unsigned> k(stride,0);
932 : // Zeros might be many, this slows down a lot due to MPI communication
933 : // Avoid passing the zeros (i=1) for atom indices
934 0 : for(unsigned i=1; i<Nprec; i++) {
935 : // Building long vectors with all atom indexes for occupancies ordered from i=1 to i=Nprec-1
936 : // Can this be avoided ???
937 0 : Atom0F.insert(Atom0F.end(),A0[i].begin(),A0[i].end());
938 0 : Atom1F.insert(Atom1F.end(),A1[i].begin(),A1[i].end());
939 0 : A0[i].resize(0);
940 0 : A1[i].resize(0);
941 : }
942 : // Resize partial arrays to fill up for the next PIV block
943 0 : A0[0].resize(0);
944 0 : A1[0].resize(0);
945 0 : A0[Nprec-1].resize(0);
946 0 : A1[Nprec-1].resize(0);
947 : // Avoid passing the zeros (i=1) for atom indices
948 0 : OrdVec[0]=0;
949 0 : OrdVec[Nprec-1]=0;
950 :
951 : // Wait for all ranks before communication of Vectors
952 0 : comm.Barrier();
953 :
954 : // pass the array sizes before passing the arrays
955 0 : int dim=Atom0F.size();
956 : // Vdim and Vpos keep track of the dimension and the starting-position of the rank-specific pair vector in the big pair vector.
957 0 : comm.Allgather(&dim,1,&Vdim[0],1);
958 :
959 : // TO BE IMPROVED: the following may be done by the rank 0 (now every rank does it)
960 : int Fdim=0;
961 0 : for(unsigned i=1; i<stride; i++) {
962 0 : Vpos[i]=Vpos[i-1]+Vdim[i-1];
963 0 : Fdim+=Vdim[i];
964 : }
965 0 : Fdim+=Vdim[0];
966 : // build big vectors for atom pairs on all ranks for all ranks
967 0 : std:: vector<int> Atom0FAll(Fdim);
968 0 : std:: vector<int> Atom1FAll(Fdim);
969 : // TO BE IMPROVED: Allgathers may be substituted by gathers by proc 0
970 : // Moreover vectors are gathered head-to-tail and assembled later-on in a serial step.
971 : // Gather the full Ordering Vector (occupancies). This is what we need to build the PIV
972 0 : comm.Allgather(&OrdVec[0],Nprec,&OrdVecAll[0],Nprec);
973 : // Gather the vectors of atom pairs to keep track of the idexes for the forces
974 0 : comm.Allgatherv(Atom0F.data(),Atom0F.size(),&Atom0FAll[0],&Vdim[0],&Vpos[0]);
975 0 : comm.Allgatherv(Atom1F.data(),Atom1F.size(),&Atom1FAll[0],&Vdim[0],&Vpos[0]);
976 :
977 : // Reconstruct the full vectors from collections of Allgathered parts (this is a serial step)
978 : // This is the tricky serial step, to assemble together PIV and atom-pair info from head-tail big vectors
979 : // Loop before on l and then on i would be better but the allgather should be modified
980 : // Loop on blocks
981 : //for(unsigned m=0;m<Nlist;m++) {
982 : // Loop on Ordering Vector size excluding zeros (i=1)
983 0 : if(timer) stopwatch.stop("2 Sort cPIV");
984 0 : if(timer) stopwatch.start("3 Reconstruct cPIV");
985 0 : for(unsigned i=1; i<Nprec; i++) {
986 : // Loop on the ranks
987 0 : for(unsigned l=0; l<stride; l++) {
988 : // Loop on the number of head-to-tail pieces
989 0 : for(unsigned m=0; m<OrdVecAll[i+l*Nprec]; m++) {
990 : // cPIV is the current PIV at time t
991 0 : cPIV[j].push_back(double(i)/double(Nprec-1));
992 0 : Atom0[j].push_back(Atom0FAll[k[l]+Vpos[l]]);
993 0 : Atom1[j].push_back(Atom1FAll[k[l]+Vpos[l]]);
994 0 : k[l]+=1;
995 : }
996 : }
997 : }
998 0 : if(timer) stopwatch.stop("3 Reconstruct cPIV");
999 : } else {
1000 6000000 : for(unsigned i=1; i<Nprec; i++) {
1001 11757594 : for(unsigned m=0; m<OrdVec[i]; m++) {
1002 5757600 : cPIV[j].push_back(double(i)/double(Nprec-1));
1003 5757600 : Atom0[j].push_back(A0[i][m]);
1004 5757600 : Atom1[j].push_back(A1[i][m]);
1005 : }
1006 : }
1007 : }
1008 : }
1009 : }
1010 : }
1011 327 : Vector distance;
1012 327 : double dfunc=0.;
1013 : // Calculate volume scaling factor
1014 327 : if(Svol) {
1015 327 : Fvol=cbrt(Vol0/getBox().determinant());
1016 : }
1017 :
1018 : // This test may be run by specifying the TEST keyword as input, it pritnts rPIV and cPIV and quits
1019 327 : if(test) {
1020 : unsigned limit=0;
1021 0 : for(unsigned j=0; j<Nlist; j++) {
1022 0 : if(dosort[j]) {
1023 0 : limit = cPIV[j].size();
1024 : } else {
1025 0 : limit = rPIV[j].size();
1026 : }
1027 0 : log.printf("PIV Block: %6i %12s %6i \n", j, " Size:", limit);
1028 0 : log.printf("%6s%6s%12s%12s%36s\n"," i"," j", " c-PIV "," r-PIV "," i-j distance vector ");
1029 0 : for(unsigned i=0; i<limit; i++) {
1030 : unsigned i0=0;
1031 : unsigned i1=0;
1032 0 : if(dosort[j]) {
1033 0 : i0=Atom0[j][i];
1034 0 : i1=Atom1[j][i];
1035 : } else {
1036 0 : i0=(nl[j]->getClosePairAtomNumber(i).first).index();
1037 0 : i1=(nl[j]->getClosePairAtomNumber(i).second).index();
1038 : }
1039 0 : Vector Pos0,Pos1;
1040 0 : if(com) {
1041 0 : Pos0=compos[i0];
1042 0 : Pos1=compos[i1];
1043 : } else {
1044 0 : Pos0=getPosition(i0);
1045 0 : Pos1=getPosition(i1);
1046 : }
1047 0 : if(pbc) {
1048 0 : distance=pbcDistance(Pos0,Pos1);
1049 : } else {
1050 0 : distance=delta(Pos0,Pos1);
1051 : }
1052 0 : dfunc=0.;
1053 : double cP,rP;
1054 0 : if(dosort[j]) {
1055 0 : cP = cPIV[j][i];
1056 0 : rP = rPIV[j][rPIV[j].size()-cPIV[j].size()+i];
1057 : } else {
1058 0 : double dm=distance.modulo();
1059 0 : cP = sfs[j].calculate(dm*Fvol, dfunc);
1060 0 : rP = rPIV[j][i];
1061 : }
1062 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]);
1063 : }
1064 : }
1065 0 : log.printf("This was a test, now exit \n");
1066 0 : exit();
1067 : }
1068 :
1069 328 : if(timer) stopwatch.start("4 Build For Derivatives");
1070 : // non-global variables Nder and Scalevol defined to speedup if structures in cycles
1071 327 : bool Nder=CompDer;
1072 327 : bool Scalevol=Svol;
1073 327 : if(getStep()%updatePIV==0) {
1074 : // set to zero PIVdistance, derivatives and virial when they are calculated
1075 29799 : for(unsigned j=0; j<m_deriv.size(); j++) {
1076 117888 : for(unsigned k=0; k<3; k++) {m_deriv[j][k]=0.;}
1077 : }
1078 1308 : for(unsigned j=0; j<3; j++) {
1079 3924 : for(unsigned k=0; k<3; k++) {
1080 2943 : m_virial[j][k]=0.;
1081 : }
1082 : }
1083 327 : m_PIVdistance=0.;
1084 : // Re-compute atomic distances for derivatives and compute PIV-PIV distance
1085 981 : for(unsigned j=0; j<Nlist; j++) {
1086 : unsigned limit=0;
1087 : // dosorting definition is to speedup if structure in cycles with non-global variables
1088 654 : bool dosorting=dosort[j];
1089 654 : bool docom=com;
1090 654 : bool dopbc=pbc;
1091 654 : if(dosorting) {
1092 12 : limit = cPIV[j].size();
1093 : } else {
1094 642 : limit = rPIV[j].size();
1095 : }
1096 11574918 : for(unsigned i=rank; i<limit; i+=stride) {
1097 : unsigned i0=0;
1098 : unsigned i1=0;
1099 11574264 : if(dosorting) {
1100 11515200 : i0=Atom0[j][i];
1101 11515200 : i1=Atom1[j][i];
1102 : } else {
1103 59064 : i0=(nl[j]->getClosePairAtomNumber(i).first).index();
1104 59064 : i1=(nl[j]->getClosePairAtomNumber(i).second).index();
1105 : }
1106 11574264 : Vector Pos0,Pos1;
1107 11574264 : if(docom) {
1108 0 : Pos0=compos[i0];
1109 0 : Pos1=compos[i1];
1110 : } else {
1111 11574264 : Pos0=getPosition(i0);
1112 11574264 : Pos1=getPosition(i1);
1113 : }
1114 11574264 : if(dopbc) {
1115 11574264 : distance=pbcDistance(Pos0,Pos1);
1116 : } else {
1117 0 : distance=delta(Pos0,Pos1);
1118 : }
1119 11574264 : dfunc=0.;
1120 : // this is needed for dfunc and dervatives
1121 11574264 : double dm=distance.modulo();
1122 11574264 : double tPIV = sfs[j].calculate(dm*Fvol, dfunc);
1123 : // PIV distance
1124 : double coord=0.;
1125 11574264 : if(!dosorting||Nder) {
1126 59064 : coord = tPIV - rPIV[j][i];
1127 : } else {
1128 11515200 : coord = cPIV[j][i] - rPIV[j][rPIV[j].size()-cPIV[j].size()+i];
1129 : }
1130 : // Calculate derivatives, virial, and variable=sum_j (scaling[j] *(cPIV-rPIV)_j^2)
1131 : // WARNING: dfunc=dswf/(Fvol*dm) (this may change in future Plumed versions)
1132 11574264 : double tmp = 2.*scaling[j]*coord*Fvol*Fvol*dfunc;
1133 11574264 : Vector tmpder = tmp*distance;
1134 : // 0.5*(x_i-x_k)*f_ik (force on atom k due to atom i)
1135 11574264 : if(docom) {
1136 0 : Vector dist;
1137 0 : for(unsigned k=0; k<nlcom[i0]->getFullAtomList().size(); k++) {
1138 0 : unsigned x0=nlcom[i0]->getFullAtomList()[k].index();
1139 0 : m_deriv[x0] -= tmpder*fmass[x0];
1140 0 : for(unsigned l=0; l<3; l++) {
1141 0 : dist[l]=0.;
1142 : }
1143 0 : Vector P0=getPosition(x0);
1144 0 : for(unsigned l=0; l<nlcom[i0]->getFullAtomList().size(); l++) {
1145 0 : unsigned x1=nlcom[i0]->getFullAtomList()[l].index();
1146 0 : Vector P1=getPosition(x1);
1147 0 : if(dopbc) {
1148 0 : dist+=pbcDistance(P0,P1);
1149 : } else {
1150 0 : dist+=delta(P0,P1);
1151 : }
1152 : }
1153 0 : for(unsigned l=0; l<nlcom[i1]->getFullAtomList().size(); l++) {
1154 0 : unsigned x1=nlcom[i1]->getFullAtomList()[l].index();
1155 0 : Vector P1=getPosition(x1);
1156 0 : if(dopbc) {
1157 0 : dist+=pbcDistance(P0,P1);
1158 : } else {
1159 0 : dist+=delta(P0,P1);
1160 : }
1161 : }
1162 0 : m_virial -= 0.25*fmass[x0]*Tensor(dist,tmpder);
1163 : }
1164 0 : for(unsigned k=0; k<nlcom[i1]->getFullAtomList().size(); k++) {
1165 0 : unsigned x1=nlcom[i1]->getFullAtomList()[k].index();
1166 0 : m_deriv[x1] += tmpder*fmass[x1];
1167 0 : for(unsigned l=0; l<3; l++) {
1168 0 : dist[l]=0.;
1169 : }
1170 0 : Vector P1=getPosition(x1);
1171 0 : for(unsigned l=0; l<nlcom[i1]->getFullAtomList().size(); l++) {
1172 0 : unsigned x0=nlcom[i1]->getFullAtomList()[l].index();
1173 0 : Vector P0=getPosition(x0);
1174 0 : if(dopbc) {
1175 0 : dist+=pbcDistance(P1,P0);
1176 : } else {
1177 0 : dist+=delta(P1,P0);
1178 : }
1179 : }
1180 0 : for(unsigned l=0; l<nlcom[i0]->getFullAtomList().size(); l++) {
1181 0 : unsigned x0=nlcom[i0]->getFullAtomList()[l].index();
1182 0 : Vector P0=getPosition(x0);
1183 0 : if(dopbc) {
1184 0 : dist+=pbcDistance(P1,P0);
1185 : } else {
1186 0 : dist+=delta(P1,P0);
1187 : }
1188 : }
1189 0 : m_virial += 0.25*fmass[x1]*Tensor(dist,tmpder);
1190 : }
1191 : } else {
1192 11574264 : m_deriv[i0] -= tmpder;
1193 11574264 : m_deriv[i1] += tmpder;
1194 11574264 : m_virial -= tmp*Tensor(distance,distance);
1195 : }
1196 11574264 : if(Scalevol) {
1197 11574264 : m_virial+=1./3.*tmp*dm*dm*Tensor::identity();
1198 : }
1199 11574264 : m_PIVdistance += scaling[j]*coord*coord;
1200 : }
1201 : }
1202 :
1203 327 : if (!serial && comm.initialized()) {
1204 0 : comm.Barrier();
1205 0 : comm.Sum(&m_PIVdistance,1);
1206 0 : if(!m_deriv.empty()) comm.Sum(&m_deriv[0][0],3*m_deriv.size());
1207 0 : comm.Sum(&m_virial[0][0],9);
1208 : }
1209 : }
1210 327 : prev_stp=getStep();
1211 :
1212 : //Timing
1213 328 : if(timer) stopwatch.stop("4 Build For Derivatives");
1214 327 : if(timer) {
1215 1 : log.printf("Timings for action %s with label %s \n", getName().c_str(), getLabel().c_str() );
1216 1 : log<<stopwatch;
1217 : }
1218 :
1219 : // Update derivatives, virial, and variable (PIV-distance^2)
1220 29799 : for(unsigned i=0; i<m_deriv.size(); ++i) setAtomsDerivatives(i,m_deriv[i]);
1221 327 : setValue (m_PIVdistance);
1222 327 : setBoxDerivatives (m_virial);
1223 327 : }
1224 : //Close Namespaces at the very beginning
1225 : }
1226 : }
1227 :
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