1 /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 Copyright (c) 2011-2021 The plumed team
3 (see the PEOPLE file at the root of the distribution for a list of names)
4
5 See http://www.plumed.org for more information.
6
7 This file is part of plumed, version 2.
8
9 plumed is free software: you can redistribute it and/or modify
10 it under the terms of the GNU Lesser General Public License as published by
11 the Free Software Foundation, either version 3 of the License, or
12 (at your option) any later version.
13
14 plumed is distributed in the hope that it will be useful,
15 but WITHOUT ANY WARRANTY; without even the implied warranty of
16 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 GNU Lesser General Public License for more details.
18
19 You should have received a copy of the GNU Lesser General Public License
20 along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 #include "Atoms.h"
23 #include "ActionAtomistic.h"
24 #include "MDAtoms.h"
25 #include "PlumedMain.h"
26 #include "tools/Pbc.h"
27 #include <algorithm>
28 #include <iostream>
29 #include <string>
30 #include <cmath>
31
32 using namespace std;
33
34 namespace PLMD {
35
36 /// We assume that charges and masses are constant along the simulation
37 /// Set this to false if you want to revert to the original (expensive) behavior
38 static const bool shareMassAndChargeOnlyAtFirstStep=true;
39
40 class PlumedMain;
41
Atoms(PlumedMain & plumed)42 Atoms::Atoms(PlumedMain&plumed):
43 natoms(0),
44 md_energy(0.0),
45 energy(0.0),
46 dataCanBeSet(false),
47 collectEnergy(false),
48 energyHasBeenSet(false),
49 positionsHaveBeenSet(0),
50 massesHaveBeenSet(false),
51 chargesHaveBeenSet(false),
52 boxHasBeenSet(false),
53 forcesHaveBeenSet(0),
54 virialHasBeenSet(false),
55 massAndChargeOK(false),
56 shuffledAtoms(0),
57 mdatoms(MDAtomsBase::create(sizeof(double))),
58 plumed(plumed),
59 naturalUnits(false),
60 MDnaturalUnits(false),
61 timestep(0.0),
62 forceOnEnergy(0.0),
63 zeroallforces(false),
64 kbT(0.0),
65 asyncSent(false),
66 atomsNeeded(false),
67 ddStep(0)
68 {
69 }
70
~Atoms()71 Atoms::~Atoms() {
72 if(actions.size()>0) {
73 std::cerr<<"WARNING: there is some inconsistency in action added to atoms, as some of them were not properly destroyed. This might indicate an internal bug!!\n";
74 }
75 }
76
startStep()77 void Atoms::startStep() {
78 collectEnergy=false; energyHasBeenSet=false; positionsHaveBeenSet=0;
79 massesHaveBeenSet=false; chargesHaveBeenSet=false; boxHasBeenSet=false;
80 forcesHaveBeenSet=0; virialHasBeenSet=false; dataCanBeSet=true;
81 }
82
setBox(void * p)83 void Atoms::setBox(void*p) {
84 mdatoms->setBox(p);
85 Tensor b; mdatoms->getBox(b); boxHasBeenSet=true;
86 }
87
setPositions(void * p)88 void Atoms::setPositions(void*p) {
89 plumed_massert( dataCanBeSet,"setPositions must be called after setStep in MD code interface");
90 plumed_massert( p || gatindex.size()==0, "NULL position pointer with non-zero local atoms");
91 mdatoms->setp(p); positionsHaveBeenSet=3;
92 }
93
setMasses(void * p)94 void Atoms::setMasses(void*p) {
95 plumed_massert( dataCanBeSet,"setMasses must be called after setStep in MD code interface");
96 plumed_massert( p || gatindex.size()==0, "NULL mass pointer with non-zero local atoms");
97 mdatoms->setm(p); massesHaveBeenSet=true;
98
99 }
100
setCharges(void * p)101 void Atoms::setCharges(void*p) {
102 plumed_massert( dataCanBeSet, "setCharges must be called after setStep in MD code interface");
103 plumed_massert( p || gatindex.size()==0, "NULL charges pointer with non-zero local atoms");
104 mdatoms->setc(p); chargesHaveBeenSet=true;
105 }
106
setVirial(void * p)107 void Atoms::setVirial(void*p) {
108 plumed_massert( dataCanBeSet,"setVirial must be called after setStep in MD code interface");
109 mdatoms->setVirial(p); virialHasBeenSet=true;
110 }
111
setEnergy(void * p)112 void Atoms::setEnergy(void*p) {
113 plumed_massert( dataCanBeSet,"setEnergy must be called after setStep in MD code interface");
114 MD2double(p,md_energy);
115 md_energy*=MDUnits.getEnergy()/units.getEnergy();
116 energyHasBeenSet=true;
117 }
118
setForces(void * p)119 void Atoms::setForces(void*p) {
120 plumed_massert( dataCanBeSet,"setForces must be called after setStep in MD code interface");
121 plumed_massert( p || gatindex.size()==0, "NULL force pointer with non-zero local atoms");
122 forcesHaveBeenSet=3;
123 mdatoms->setf(p);
124 }
125
setPositions(void * p,int i)126 void Atoms::setPositions(void*p,int i) {
127 plumed_massert( dataCanBeSet,"setPositions must be called after setStep in MD code interface");
128 plumed_massert( p || gatindex.size()==0, "NULL positions pointer with non-zero local atoms");
129 mdatoms->setp(p,i); positionsHaveBeenSet++;
130 }
131
setForces(void * p,int i)132 void Atoms::setForces(void*p,int i) {
133 plumed_massert( dataCanBeSet,"setForces must be called after setStep in MD code interface");
134 plumed_massert( p || gatindex.size()==0, "NULL force pointer with non-zero local atoms");
135 mdatoms->setf(p,i); forcesHaveBeenSet++;
136 }
137
share()138 void Atoms::share() {
139 // At first step I scatter all the atoms so as to store their mass and charge
140 // Notice that this works with the assumption that charges and masses are
141 // not changing during the simulation!
142 if(!massAndChargeOK && shareMassAndChargeOnlyAtFirstStep) {
143 shareAll();
144 return;
145 }
146
147 if(!(int(gatindex.size())==natoms && shuffledAtoms==0)) {
148 for(unsigned i=0; i<actions.size(); i++) {
149 if(actions[i]->isActive()) {
150 if(!actions[i]->getUnique().empty()) {
151 atomsNeeded=true;
152 // unique are the local atoms
153 unique.insert(actions[i]->getUniqueLocal().begin(),actions[i]->getUniqueLocal().end());
154 }
155 }
156 }
157 } else {
158 for(unsigned i=0; i<actions.size(); i++) {
159 if(actions[i]->isActive()) {
160 if(!actions[i]->getUnique().empty()) {
161 atomsNeeded=true;
162 }
163 }
164 }
165
166 }
167
168 share(unique);
169 }
170
shareAll()171 void Atoms::shareAll() {
172 unique.clear();
173 // keep in unique only those atoms that are local
174 if(dd && shuffledAtoms>0) {
175 for(int i=0; i<natoms; i++) if(g2l[i]>=0) unique.insert(AtomNumber::index(i));
176 } else {
177 for(int i=0; i<natoms; i++) unique.insert(AtomNumber::index(i));
178 }
179 atomsNeeded=true;
180 share(unique);
181 }
182
share(const std::set<AtomNumber> & unique)183 void Atoms::share(const std::set<AtomNumber>& unique) {
184 plumed_assert( positionsHaveBeenSet==3 && massesHaveBeenSet );
185
186 virial.zero();
187 if(zeroallforces || int(gatindex.size())==natoms) {
188 for(int i=0; i<natoms; i++) forces[i].zero();
189 } else {
190 for(const auto & p : unique) forces[p.index()].zero();
191 }
192 for(unsigned i=getNatoms(); i<positions.size(); i++) forces[i].zero(); // virtual atoms
193 forceOnEnergy=0.0;
194 mdatoms->getBox(box);
195
196 if(!atomsNeeded) return;
197 atomsNeeded=false;
198
199 if(int(gatindex.size())==natoms && shuffledAtoms==0) {
200 // faster version, which retrieves all atoms
201 mdatoms->getPositions(0,natoms,positions);
202 } else {
203 uniq_index.clear();
204 uniq_index.reserve(unique.size());
205 if(shuffledAtoms>0) {
206 for(const auto & p : unique) uniq_index.push_back(g2l[p.index()]);
207 }
208 mdatoms->getPositions(unique,uniq_index,positions);
209 }
210
211
212 // how many double per atom should be scattered:
213 int ndata=3;
214 if(!massAndChargeOK) {
215 ndata=5;
216 masses.assign(masses.size(),std::numeric_limits<double>::quiet_NaN());
217 charges.assign(charges.size(),std::numeric_limits<double>::quiet_NaN());
218 mdatoms->getCharges(gatindex,charges);
219 mdatoms->getMasses(gatindex,masses);
220 }
221
222 if(dd && shuffledAtoms>0) {
223 if(dd.async) {
224 for(unsigned i=0; i<dd.mpi_request_positions.size(); i++) dd.mpi_request_positions[i].wait();
225 for(unsigned i=0; i<dd.mpi_request_index.size(); i++) dd.mpi_request_index[i].wait();
226 }
227 int count=0;
228 for(const auto & p : unique) {
229 dd.indexToBeSent[count]=p.index();
230 dd.positionsToBeSent[ndata*count+0]=positions[p.index()][0];
231 dd.positionsToBeSent[ndata*count+1]=positions[p.index()][1];
232 dd.positionsToBeSent[ndata*count+2]=positions[p.index()][2];
233 if(!massAndChargeOK) {
234 dd.positionsToBeSent[ndata*count+3]=masses[p.index()];
235 dd.positionsToBeSent[ndata*count+4]=charges[p.index()];
236 }
237 count++;
238 }
239 if(dd.async) {
240 asyncSent=true;
241 dd.mpi_request_positions.resize(dd.Get_size());
242 dd.mpi_request_index.resize(dd.Get_size());
243 for(int i=0; i<dd.Get_size(); i++) {
244 dd.mpi_request_index[i]=dd.Isend(&dd.indexToBeSent[0],count,i,666);
245 dd.mpi_request_positions[i]=dd.Isend(&dd.positionsToBeSent[0],ndata*count,i,667);
246 }
247 } else {
248 const int n=(dd.Get_size());
249 vector<int> counts(n);
250 vector<int> displ(n);
251 vector<int> counts5(n);
252 vector<int> displ5(n);
253 dd.Allgather(count,counts);
254 displ[0]=0;
255 for(int i=1; i<n; ++i) displ[i]=displ[i-1]+counts[i-1];
256 for(int i=0; i<n; ++i) counts5[i]=counts[i]*ndata;
257 for(int i=0; i<n; ++i) displ5[i]=displ[i]*ndata;
258 dd.Allgatherv(&dd.indexToBeSent[0],count,&dd.indexToBeReceived[0],&counts[0],&displ[0]);
259 dd.Allgatherv(&dd.positionsToBeSent[0],ndata*count,&dd.positionsToBeReceived[0],&counts5[0],&displ5[0]);
260 int tot=displ[n-1]+counts[n-1];
261 for(int i=0; i<tot; i++) {
262 positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];
263 positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];
264 positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];
265 if(!massAndChargeOK) {
266 masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+3];
267 charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+4];
268 }
269 }
270 }
271 }
272 }
273
wait()274 void Atoms::wait() {
275 dataCanBeSet=false; // Everything should be set by this stage
276 // How many double per atom should be scattered
277 int ndata=3;
278 if(!massAndChargeOK)ndata=5;
279
280 if(dd) {
281 dd.Bcast(box,0);
282 }
283 pbc.setBox(box);
284
285 if(collectEnergy) energy=md_energy;
286
287 if(dd && shuffledAtoms>0) {
288 // receive toBeReceived
289 if(asyncSent) {
290 Communicator::Status status;
291 int count=0;
292 for(int i=0; i<dd.Get_size(); i++) {
293 dd.Recv(&dd.indexToBeReceived[count],dd.indexToBeReceived.size()-count,i,666,status);
294 int c=status.Get_count<int>();
295 dd.Recv(&dd.positionsToBeReceived[ndata*count],dd.positionsToBeReceived.size()-ndata*count,i,667);
296 count+=c;
297 }
298 for(int i=0; i<count; i++) {
299 positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];
300 positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];
301 positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];
302 if(!massAndChargeOK) {
303 masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+3];
304 charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[ndata*i+4];
305 }
306 }
307 asyncSent=false;
308 }
309 if(collectEnergy) dd.Sum(energy);
310 }
311 // I take note that masses and charges have been set once for all
312 // at the beginning of the simulation.
313 if(shareMassAndChargeOnlyAtFirstStep) massAndChargeOK=true;
314 }
315
updateForces()316 void Atoms::updateForces() {
317 plumed_assert( forcesHaveBeenSet==3 );
318 if(forceOnEnergy*forceOnEnergy>epsilon) {
319 double alpha=1.0-forceOnEnergy;
320 mdatoms->rescaleForces(gatindex,alpha);
321 mdatoms->updateForces(gatindex,forces);
322 } else {
323 if(int(gatindex.size())==natoms && shuffledAtoms==0) mdatoms->updateForces(gatindex,forces);
324 else mdatoms->updateForces(unique,uniq_index,forces);
325 }
326 if( !plumed.novirial && dd.Get_rank()==0 ) {
327 plumed_assert( virialHasBeenSet );
328 mdatoms->updateVirial(virial);
329 }
330 }
331
setNatoms(int n)332 void Atoms::setNatoms(int n) {
333 natoms=n;
334 positions.resize(n);
335 forces.resize(n);
336 masses.resize(n);
337 charges.resize(n);
338 gatindex.resize(n);
339 for(unsigned i=0; i<gatindex.size(); i++) gatindex[i]=i;
340 }
341
342
add(ActionAtomistic * a)343 void Atoms::add(ActionAtomistic*a) {
344 actions.push_back(a);
345 }
346
remove(ActionAtomistic * a)347 void Atoms::remove(ActionAtomistic*a) {
348 auto f=find(actions.begin(),actions.end(),a);
349 plumed_massert(f!=actions.end(),"cannot remove an action registered to atoms");
350 actions.erase(f);
351 }
352
353
enable(Communicator & c)354 void Atoms::DomainDecomposition::enable(Communicator& c) {
355 on=true;
356 Set_comm(c.Get_comm());
357 async=Get_size()<10;
358 if(std::getenv("PLUMED_ASYNC_SHARE")) {
359 std::string s(std::getenv("PLUMED_ASYNC_SHARE"));
360 if(s=="yes") async=true;
361 else if(s=="no") async=false;
362 else plumed_merror("PLUMED_ASYNC_SHARE variable is set to " + s + "; should be yes or no");
363 }
364 }
365
setAtomsNlocal(int n)366 void Atoms::setAtomsNlocal(int n) {
367 gatindex.resize(n);
368 g2l.resize(natoms,-1);
369 if(dd) {
370 // Since these vectors are sent with MPI by using e.g.
371 // &dd.positionsToBeSent[0]
372 // we make sure they are non-zero-sized so as to
373 // avoid errors when doing boundary check
374 if(n==0) n++;
375 dd.positionsToBeSent.resize(n*5,0.0);
376 dd.positionsToBeReceived.resize(natoms*5,0.0);
377 dd.indexToBeSent.resize(n,0);
378 dd.indexToBeReceived.resize(natoms,0);
379 }
380 }
381
setAtomsGatindex(int * g,bool fortran)382 void Atoms::setAtomsGatindex(int*g,bool fortran) {
383 plumed_massert( g || gatindex.size()==0, "NULL gatindex pointer with non-zero local atoms");
384 ddStep=plumed.getStep();
385 if(fortran) {
386 for(unsigned i=0; i<gatindex.size(); i++) gatindex[i]=g[i]-1;
387 } else {
388 for(unsigned i=0; i<gatindex.size(); i++) gatindex[i]=g[i];
389 }
390 for(unsigned i=0; i<g2l.size(); i++) g2l[i]=-1;
391 if( gatindex.size()==natoms ) {
392 shuffledAtoms=0;
393 for(unsigned i=0; i<gatindex.size(); i++) {
394 if( gatindex[i]!=i ) { shuffledAtoms=1; break; }
395 }
396 } else {
397 shuffledAtoms=1;
398 }
399 if(dd) {
400 dd.Sum(shuffledAtoms);
401 }
402 for(unsigned i=0; i<gatindex.size(); i++) g2l[gatindex[i]]=i;
403
404 for(unsigned i=0; i<actions.size(); i++) {
405 // keep in unique only those atoms that are local
406 actions[i]->updateUniqueLocal();
407 }
408 unique.clear();
409 }
410
setAtomsContiguous(int start)411 void Atoms::setAtomsContiguous(int start) {
412 ddStep=plumed.getStep();
413 for(unsigned i=0; i<gatindex.size(); i++) gatindex[i]=start+i;
414 for(unsigned i=0; i<g2l.size(); i++) g2l[i]=-1;
415 for(unsigned i=0; i<gatindex.size(); i++) g2l[gatindex[i]]=i;
416 if(gatindex.size()<natoms) shuffledAtoms=1;
417 for(unsigned i=0; i<actions.size(); i++) {
418 // keep in unique only those atoms that are local
419 actions[i]->updateUniqueLocal();
420 }
421 unique.clear();
422 }
423
setRealPrecision(int p)424 void Atoms::setRealPrecision(int p) {
425 mdatoms=MDAtomsBase::create(p);
426 }
427
getRealPrecision() const428 int Atoms::getRealPrecision()const {
429 return mdatoms->getRealPrecision();
430 }
431
MD2double(const void * m,double & d) const432 void Atoms::MD2double(const void*m,double&d)const {
433 plumed_assert(mdatoms); mdatoms->MD2double(m,d);
434 }
double2MD(const double & d,void * m) const435 void Atoms::double2MD(const double&d,void*m)const {
436 plumed_assert(mdatoms); mdatoms->double2MD(d,m);
437 }
438
updateUnits()439 void Atoms::updateUnits() {
440 mdatoms->setUnits(units,MDUnits);
441 }
442
setTimeStep(void * p)443 void Atoms::setTimeStep(void*p) {
444 MD2double(p,timestep);
445 // The following is to avoid extra digits in case the MD code uses floats
446 // e.g.: float f=0.002 when converted to double becomes 0.002000000094995
447 // To avoid this, we keep only up to 6 significant digits after first one
448 double magnitude=std::pow(10,std::floor(std::log10(timestep)));
449 timestep=std::floor(timestep/magnitude*1e6)/1e6*magnitude;
450 }
451
getTimeStep() const452 double Atoms::getTimeStep()const {
453 return timestep/units.getTime()*MDUnits.getTime();
454 }
455
setKbT(void * p)456 void Atoms::setKbT(void*p) {
457 MD2double(p,kbT);
458 }
459
getKbT() const460 double Atoms::getKbT()const {
461 return kbT/units.getEnergy()*MDUnits.getEnergy();
462 }
463
464
createFullList(int * n)465 void Atoms::createFullList(int*n) {
466 if(!massAndChargeOK && shareMassAndChargeOnlyAtFirstStep) {
467 *n=natoms;
468 fullList.resize(natoms);
469 for(unsigned i=0; i<natoms; i++) fullList[i]=i;
470 } else {
471 // We update here the unique list defined at Atoms::unique.
472 // This is not very clear, and probably should be coded differently.
473 // Hopefully this fix the longstanding issue with NAMD.
474 unique.clear();
475 for(unsigned i=0; i<actions.size(); i++) {
476 if(actions[i]->isActive()) {
477 if(!actions[i]->getUnique().empty()) {
478 atomsNeeded=true;
479 // unique are the local atoms
480 unique.insert(actions[i]->getUnique().begin(),actions[i]->getUnique().end());
481 }
482 }
483 }
484 fullList.resize(0);
485 fullList.reserve(unique.size());
486 for(const auto & p : unique) fullList.push_back(p.index());
487 *n=fullList.size();
488 }
489 }
490
getFullList(int ** x)491 void Atoms::getFullList(int**x) {
492 if(!fullList.empty()) *x=&fullList[0];
493 else *x=NULL;
494 }
495
clearFullList()496 void Atoms::clearFullList() {
497 fullList.resize(0);
498 }
499
init()500 void Atoms::init() {
501 // Default: set domain decomposition to NO-decomposition, waiting for
502 // further instruction
503 if(dd) {
504 setAtomsNlocal(natoms);
505 setAtomsContiguous(0);
506 }
507 }
508
setDomainDecomposition(Communicator & comm)509 void Atoms::setDomainDecomposition(Communicator& comm) {
510 dd.enable(comm);
511 }
512
resizeVectors(unsigned n)513 void Atoms::resizeVectors(unsigned n) {
514 positions.resize(n);
515 forces.resize(n);
516 masses.resize(n);
517 charges.resize(n);
518 }
519
addVirtualAtom(ActionWithVirtualAtom * a)520 AtomNumber Atoms::addVirtualAtom(ActionWithVirtualAtom*a) {
521 unsigned n=positions.size();
522 resizeVectors(n+1);
523 virtualAtomsActions.push_back(a);
524 return AtomNumber::index(n);
525 }
526
removeVirtualAtom(ActionWithVirtualAtom * a)527 void Atoms::removeVirtualAtom(ActionWithVirtualAtom*a) {
528 unsigned n=positions.size();
529 plumed_massert(a==virtualAtomsActions[virtualAtomsActions.size()-1],"virtual atoms should be destroyed in reverse creation order");
530 resizeVectors(n-1);
531 virtualAtomsActions.pop_back();
532 }
533
insertGroup(const std::string & name,const std::vector<AtomNumber> & a)534 void Atoms::insertGroup(const std::string&name,const std::vector<AtomNumber>&a) {
535 plumed_massert(groups.count(name)==0,"group named "+name+" already exists");
536 groups[name]=a;
537 }
538
removeGroup(const std::string & name)539 void Atoms::removeGroup(const std::string&name) {
540 plumed_massert(groups.count(name)==1,"cannot remove group named "+name);
541 groups.erase(name);
542 }
543
writeBinary(std::ostream & o) const544 void Atoms::writeBinary(std::ostream&o)const {
545 o.write(reinterpret_cast<const char*>(&positions[0][0]),natoms*3*sizeof(double));
546 o.write(reinterpret_cast<const char*>(&box(0,0)),9*sizeof(double));
547 o.write(reinterpret_cast<const char*>(&energy),sizeof(double));
548 }
549
readBinary(std::istream & i)550 void Atoms::readBinary(std::istream&i) {
551 i.read(reinterpret_cast<char*>(&positions[0][0]),natoms*3*sizeof(double));
552 i.read(reinterpret_cast<char*>(&box(0,0)),9*sizeof(double));
553 i.read(reinterpret_cast<char*>(&energy),sizeof(double));
554 pbc.setBox(box);
555 }
556
getKBoltzmann() const557 double Atoms::getKBoltzmann()const {
558 if(naturalUnits || MDnaturalUnits) return 1.0;
559 else return kBoltzmann/units.getEnergy();
560 }
561
getMDKBoltzmann() const562 double Atoms::getMDKBoltzmann()const {
563 if(naturalUnits || MDnaturalUnits) return 1.0;
564 else return kBoltzmann/MDUnits.getEnergy();
565 }
566
getLocalMasses(std::vector<double> & localMasses)567 void Atoms::getLocalMasses(std::vector<double>& localMasses) {
568 localMasses.resize(gatindex.size());
569 for(unsigned i=0; i<gatindex.size(); i++) localMasses[i] = masses[gatindex[i]];
570 }
571
getLocalPositions(std::vector<Vector> & localPositions)572 void Atoms::getLocalPositions(std::vector<Vector>& localPositions) {
573 localPositions.resize(gatindex.size());
574 mdatoms->getLocalPositions(localPositions);
575 }
576
getLocalForces(std::vector<Vector> & localForces)577 void Atoms::getLocalForces(std::vector<Vector>& localForces) {
578 localForces.resize(gatindex.size());
579 for(unsigned i=0; i<gatindex.size(); i++) localForces[i] = forces[gatindex[i]];
580 }
581
getLocalMDForces(std::vector<Vector> & localForces)582 void Atoms::getLocalMDForces(std::vector<Vector>& localForces) {
583 localForces.resize(gatindex.size());
584 for(unsigned i=0; i<gatindex.size(); i++) {
585 localForces[i] = mdatoms->getMDforces(i);
586 }
587 }
588
setExtraCV(const std::string & name,void * p)589 void Atoms::setExtraCV(const std::string &name,void*p) {
590 mdatoms->setExtraCV(name,p);
591 }
592
setExtraCVForce(const std::string & name,void * p)593 void Atoms::setExtraCVForce(const std::string &name,void*p) {
594 mdatoms->setExtraCVForce(name,p);
595 }
596
getExtraCV(const std::string & name)597 double Atoms::getExtraCV(const std::string &name) {
598 return mdatoms->getExtraCV(name);
599 }
600
updateExtraCVForce(const std::string & name,double f)601 void Atoms::updateExtraCVForce(const std::string &name,double f) {
602 mdatoms->updateExtraCVForce(name,f);
603 }
604
605 }
606