144 |
|
} |
145 |
|
|
146 |
|
SimInfo::~SimInfo() { |
147 |
< |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
148 |
< |
|
149 |
< |
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
147 |
> |
std::map<int, Molecule*>::iterator i; |
148 |
> |
for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
149 |
> |
delete i->second; |
150 |
> |
} |
151 |
> |
molecules_.clear(); |
152 |
|
|
153 |
+ |
MemoryUtils::deletePointers(moleculeStamps_); |
154 |
+ |
|
155 |
|
delete sman_; |
156 |
|
delete simParams_; |
157 |
|
delete forceField_; |
758 |
|
return maxCutoffRadius; |
759 |
|
} |
760 |
|
|
761 |
< |
void SimInfo::setupCutoff() { |
758 |
< |
double rcut_; //cutoff radius |
759 |
< |
double rsw_; //switching radius |
761 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
762 |
|
|
763 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
764 |
|
|
769 |
|
"\tfor the cutoffRadius.\n"); |
770 |
|
painCave.isFatal = 0; |
771 |
|
simError(); |
772 |
< |
rcut_ = 15.0; |
772 |
> |
rcut = 15.0; |
773 |
|
} else{ |
774 |
< |
rcut_ = simParams_->getRcut(); |
774 |
> |
rcut = simParams_->getRcut(); |
775 |
|
} |
776 |
|
|
777 |
|
if (!simParams_->haveRsw()){ |
781 |
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
782 |
|
painCave.isFatal = 0; |
783 |
|
simError(); |
784 |
< |
rsw_ = 0.95 * rcut_; |
784 |
> |
rsw = 0.95 * rcut; |
785 |
|
} else{ |
786 |
< |
rsw_ = simParams_->getRsw(); |
786 |
> |
rsw = simParams_->getRsw(); |
787 |
|
} |
788 |
|
|
789 |
|
} else { |
791 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
792 |
|
|
793 |
|
if (simParams_->haveRcut()) { |
794 |
< |
rcut_ = simParams_->getRcut(); |
794 |
> |
rcut = simParams_->getRcut(); |
795 |
|
} else { |
796 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
797 |
< |
rcut_ = calcMaxCutoffRadius(); |
797 |
> |
rcut = calcMaxCutoffRadius(); |
798 |
|
} |
799 |
|
|
800 |
|
if (simParams_->haveRsw()) { |
801 |
< |
rsw_ = simParams_->getRsw(); |
801 |
> |
rsw = simParams_->getRsw(); |
802 |
|
} else { |
803 |
< |
rsw_ = rcut_; |
803 |
> |
rsw = rcut; |
804 |
|
} |
805 |
|
|
806 |
|
} |
807 |
< |
|
807 |
> |
} |
808 |
> |
|
809 |
> |
void SimInfo::setupCutoff() { |
810 |
> |
getCutoff(rcut_, rsw_); |
811 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
812 |
|
|
813 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
839 |
|
} |
840 |
|
|
841 |
|
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
842 |
+ |
//if (sman_ == sman_) { |
843 |
+ |
// return; |
844 |
+ |
//} |
845 |
+ |
|
846 |
+ |
//delete sman_; |
847 |
|
sman_ = sman; |
848 |
|
|
849 |
|
Molecule* mol; |