| 54 |
|
#include "math/Vector3.hpp" |
| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
|
#include "primitives/StuntDouble.hpp" |
| 57 |
– |
#include "UseTheForce/fCutoffPolicy.h" |
| 57 |
|
#include "UseTheForce/doForces_interface.h" |
| 58 |
|
#include "UseTheForce/DarkSide/neighborLists_interface.h" |
| 59 |
|
#include "utils/MemoryUtils.hpp" |
| 63 |
|
#include "UseTheForce/ForceField.hpp" |
| 64 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 65 |
|
|
| 67 |
– |
|
| 66 |
|
#ifdef IS_MPI |
| 67 |
|
#include "UseTheForce/mpiComponentPlan.h" |
| 68 |
|
#include "UseTheForce/DarkSide/simParallel_interface.h" |
| 743 |
|
simError(); |
| 744 |
|
} |
| 745 |
|
} |
| 748 |
– |
|
| 749 |
– |
InteractionManager::Instance()->setCutoffRadius(cutoffRadius_); |
| 746 |
|
|
| 747 |
|
map<string, CutoffMethod> stringToCutoffMethod; |
| 748 |
|
stringToCutoffMethod["HARD"] = HARD; |
| 775 |
|
simError(); |
| 776 |
|
cutoffMethod_ = SHIFTED_FORCE; |
| 777 |
|
} |
| 782 |
– |
|
| 783 |
– |
InteractionManager::Instance()->setCutoffMethod(cutoffMethod_); |
| 778 |
|
} |
| 779 |
|
|
| 780 |
|
/** |
| 806 |
|
painCave.severity = OPENMD_WARNING; |
| 807 |
|
simError(); |
| 808 |
|
} |
| 815 |
– |
|
| 816 |
– |
InteractionManager::Instance()->setSwitchingRadius(switchingRadius_); |
| 817 |
– |
|
| 818 |
– |
SwitchingFunctionType ft; |
| 809 |
|
|
| 810 |
|
if (simParams_->haveSwitchingFunctionType()) { |
| 811 |
|
string funcType = simParams_->getSwitchingFunctionType(); |
| 812 |
|
toUpper(funcType); |
| 813 |
|
if (funcType == "CUBIC") { |
| 814 |
< |
ft = cubic; |
| 814 |
> |
sft_ = cubic; |
| 815 |
|
} else { |
| 816 |
|
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
| 817 |
< |
ft = fifth_order_poly; |
| 817 |
> |
sft_ = fifth_order_poly; |
| 818 |
|
} else { |
| 819 |
|
// throw error |
| 820 |
|
sprintf( painCave.errMsg, |
| 828 |
|
} |
| 829 |
|
} |
| 830 |
|
} |
| 841 |
– |
|
| 842 |
– |
InteractionManager::Instance()->setSwitchingFunctionType(ft); |
| 831 |
|
} |
| 832 |
|
|
| 833 |
|
/** |
| 834 |
< |
* setupSkinThickness |
| 834 |
> |
* setupNeighborlists |
| 835 |
|
* |
| 836 |
|
* If the skinThickness was explicitly set, use that value (but check it) |
| 837 |
|
* If the skinThickness was not explicitly set: use 1.0 angstroms |
| 838 |
|
*/ |
| 839 |
< |
void SimInfo::setupSkinThickness() { |
| 839 |
> |
void SimInfo::setupNeighborlists() { |
| 840 |
|
if (simParams_->haveSkinThickness()) { |
| 841 |
|
skinThickness_ = simParams_->getSkinThickness(); |
| 842 |
|
} else { |
| 843 |
|
skinThickness_ = 1.0; |
| 844 |
|
sprintf(painCave.errMsg, |
| 845 |
< |
"SimInfo Warning: No value was set for the skinThickness.\n" |
| 845 |
> |
"SimInfo: No value was set for the skinThickness.\n" |
| 846 |
|
"\tOpenMD will use a default value of %f Angstroms\n" |
| 847 |
|
"\tfor this simulation\n", skinThickness_); |
| 848 |
+ |
painCave.severity = OPENMD_INFO; |
| 849 |
|
painCave.isFatal = 0; |
| 850 |
|
simError(); |
| 851 |
|
} |
| 852 |
|
} |
| 853 |
|
|
| 854 |
< |
void SimInfo::setupSimType() { |
| 866 |
< |
set<AtomType*>::iterator i; |
| 867 |
< |
set<AtomType*> atomTypes; |
| 868 |
< |
atomTypes = getSimulatedAtomTypes(); |
| 869 |
< |
|
| 854 |
> |
void SimInfo::setupSimVariables() { |
| 855 |
|
useAtomicVirial_ = simParams_->getUseAtomicVirial(); |
| 856 |
+ |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true |
| 857 |
+ |
calcBoxDipole_ = false; |
| 858 |
+ |
if ( simParams_->haveAccumulateBoxDipole() ) |
| 859 |
+ |
if ( simParams_->getAccumulateBoxDipole() ) { |
| 860 |
+ |
calcBoxDipole_ = true; |
| 861 |
+ |
} |
| 862 |
|
|
| 863 |
+ |
set<AtomType*>::iterator i; |
| 864 |
+ |
set<AtomType*> atomTypes; |
| 865 |
+ |
atomTypes = getSimulatedAtomTypes(); |
| 866 |
|
int usesElectrostatic = 0; |
| 867 |
|
int usesMetallic = 0; |
| 868 |
|
int usesDirectional = 0; |
| 1058 |
|
} |
| 1059 |
|
|
| 1060 |
|
|
| 1067 |
– |
void SimInfo::setupSwitchingFunction() { |
| 1068 |
– |
|
| 1069 |
– |
} |
| 1070 |
– |
|
| 1061 |
|
void SimInfo::setupAccumulateBoxDipole() { |
| 1062 |
|
|
| 1073 |
– |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true |
| 1074 |
– |
if ( simParams_->haveAccumulateBoxDipole() ) |
| 1075 |
– |
if ( simParams_->getAccumulateBoxDipole() ) { |
| 1076 |
– |
calcBoxDipole_ = true; |
| 1077 |
– |
} |
| 1063 |
|
|
| 1064 |
|
} |
| 1065 |
|
|
