| 56 |
|
#include "UseTheForce/notifyCutoffs_interface.h" |
| 57 |
|
#include "utils/MemoryUtils.hpp" |
| 58 |
|
#include "utils/simError.h" |
| 59 |
+ |
#include "selection/SelectionManager.hpp" |
| 60 |
|
|
| 61 |
|
#ifdef IS_MPI |
| 62 |
|
#include "UseTheForce/mpiComponentPlan.h" |
| 109 |
|
|
| 110 |
|
//calculate atoms in rigid bodies |
| 111 |
|
int nAtomsInRigidBodies = 0; |
| 112 |
< |
int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
| 112 |
> |
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
| 113 |
|
|
| 114 |
|
for (int j=0; j < nRigidBodiesInStamp; j++) { |
| 115 |
|
rbStamp = molStamp->getRigidBody(j); |
| 138 |
|
#ifdef IS_MPI |
| 139 |
|
molToProcMap_.resize(nGlobalMols_); |
| 140 |
|
#endif |
| 141 |
< |
|
| 141 |
> |
|
| 142 |
|
} |
| 143 |
|
|
| 144 |
|
SimInfo::~SimInfo() { |
| 145 |
< |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
| 146 |
< |
|
| 147 |
< |
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
| 145 |
> |
std::map<int, Molecule*>::iterator i; |
| 146 |
> |
for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
| 147 |
> |
delete i->second; |
| 148 |
> |
} |
| 149 |
> |
molecules_.clear(); |
| 150 |
|
|
| 151 |
+ |
MemoryUtils::deletePointers(moleculeStamps_); |
| 152 |
+ |
|
| 153 |
|
delete sman_; |
| 154 |
|
delete simParams_; |
| 155 |
|
delete forceField_; |
| 151 |
– |
|
| 156 |
|
} |
| 157 |
|
|
| 158 |
|
int SimInfo::getNGlobalConstraints() { |
| 367 |
|
exclude_.addPair(c, d); |
| 368 |
|
} |
| 369 |
|
|
| 370 |
< |
|
| 370 |
> |
Molecule::RigidBodyIterator rbIter; |
| 371 |
> |
RigidBody* rb; |
| 372 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 373 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
| 374 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 375 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 376 |
> |
a = atoms[i]->getGlobalIndex(); |
| 377 |
> |
b = atoms[j]->getGlobalIndex(); |
| 378 |
> |
exclude_.addPair(a, b); |
| 379 |
> |
} |
| 380 |
> |
} |
| 381 |
> |
} |
| 382 |
> |
|
| 383 |
|
} |
| 384 |
|
|
| 385 |
|
void SimInfo::removeExcludePairs(Molecule* mol) { |
| 424 |
|
exclude_.removePair(c, d); |
| 425 |
|
} |
| 426 |
|
|
| 427 |
+ |
Molecule::RigidBodyIterator rbIter; |
| 428 |
+ |
RigidBody* rb; |
| 429 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 430 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
| 431 |
+ |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
| 432 |
+ |
for (int j = i + 1; j < atoms.size(); ++j) { |
| 433 |
+ |
a = atoms[i]->getGlobalIndex(); |
| 434 |
+ |
b = atoms[j]->getGlobalIndex(); |
| 435 |
+ |
exclude_.removePair(a, b); |
| 436 |
+ |
} |
| 437 |
+ |
} |
| 438 |
+ |
} |
| 439 |
+ |
|
| 440 |
|
} |
| 441 |
|
|
| 442 |
|
|
| 671 |
|
} |
| 672 |
|
|
| 673 |
|
//setup fortran simulation |
| 645 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
| 646 |
– |
//why the hell fortran need to know molecule? |
| 647 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
| 674 |
|
int nGlobalExcludes = 0; |
| 675 |
|
int* globalExcludes = NULL; |
| 676 |
|
int* excludeList = exclude_.getExcludeList(); |
| 777 |
|
return maxCutoffRadius; |
| 778 |
|
} |
| 779 |
|
|
| 780 |
< |
void SimInfo::setupCutoff() { |
| 755 |
< |
double rcut_; //cutoff radius |
| 756 |
< |
double rsw_; //switching radius |
| 780 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
| 781 |
|
|
| 782 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
| 783 |
|
|
| 788 |
|
"\tfor the cutoffRadius.\n"); |
| 789 |
|
painCave.isFatal = 0; |
| 790 |
|
simError(); |
| 791 |
< |
rcut_ = 15.0; |
| 791 |
> |
rcut = 15.0; |
| 792 |
|
} else{ |
| 793 |
< |
rcut_ = simParams_->getRcut(); |
| 793 |
> |
rcut = simParams_->getRcut(); |
| 794 |
|
} |
| 795 |
|
|
| 796 |
|
if (!simParams_->haveRsw()){ |
| 800 |
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
| 801 |
|
painCave.isFatal = 0; |
| 802 |
|
simError(); |
| 803 |
< |
rsw_ = 0.95 * rcut_; |
| 803 |
> |
rsw = 0.95 * rcut; |
| 804 |
|
} else{ |
| 805 |
< |
rsw_ = simParams_->getRsw(); |
| 805 |
> |
rsw = simParams_->getRsw(); |
| 806 |
|
} |
| 807 |
|
|
| 808 |
|
} else { |
| 810 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 811 |
|
|
| 812 |
|
if (simParams_->haveRcut()) { |
| 813 |
< |
rcut_ = simParams_->getRcut(); |
| 813 |
> |
rcut = simParams_->getRcut(); |
| 814 |
|
} else { |
| 815 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
| 816 |
< |
rcut_ = calcMaxCutoffRadius(); |
| 816 |
> |
rcut = calcMaxCutoffRadius(); |
| 817 |
|
} |
| 818 |
|
|
| 819 |
|
if (simParams_->haveRsw()) { |
| 820 |
< |
rsw_ = simParams_->getRsw(); |
| 820 |
> |
rsw = simParams_->getRsw(); |
| 821 |
|
} else { |
| 822 |
< |
rsw_ = rcut_; |
| 822 |
> |
rsw = rcut; |
| 823 |
|
} |
| 824 |
|
|
| 825 |
|
} |
| 826 |
< |
|
| 826 |
> |
} |
| 827 |
> |
|
| 828 |
> |
void SimInfo::setupCutoff() { |
| 829 |
> |
getCutoff(rcut_, rsw_); |
| 830 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
| 831 |
|
|
| 832 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 858 |
|
} |
| 859 |
|
|
| 860 |
|
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
| 861 |
+ |
if (sman_ == sman) { |
| 862 |
+ |
return; |
| 863 |
+ |
} |
| 864 |
+ |
delete sman_; |
| 865 |
|
sman_ = sman; |
| 866 |
|
|
| 867 |
|
Molecule* mol; |
