| 54 |
|
#include "math/Vector3.hpp" |
| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
|
#include "primitives/StuntDouble.hpp" |
| 57 |
– |
#include "UseTheForce/doForces_interface.h" |
| 58 |
– |
#include "UseTheForce/DarkSide/neighborLists_interface.h" |
| 57 |
|
#include "utils/MemoryUtils.hpp" |
| 58 |
|
#include "utils/simError.h" |
| 59 |
|
#include "selection/SelectionManager.hpp" |
| 61 |
|
#include "UseTheForce/ForceField.hpp" |
| 62 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 63 |
|
|
| 66 |
– |
|
| 67 |
– |
#ifdef IS_MPI |
| 68 |
– |
#include "UseTheForce/mpiComponentPlan.h" |
| 69 |
– |
#include "UseTheForce/DarkSide/simParallel_interface.h" |
| 70 |
– |
#endif |
| 71 |
– |
|
| 64 |
|
using namespace std; |
| 65 |
|
namespace OpenMD { |
| 66 |
|
|
| 71 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 72 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), |
| 73 |
|
nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), |
| 74 |
< |
nConstraints_(0), sman_(NULL), fortranInitialized_(false), |
| 74 |
> |
nConstraints_(0), sman_(NULL), topologyDone_(false), |
| 75 |
|
calcBoxDipole_(false), useAtomicVirial_(true) { |
| 76 |
|
|
| 77 |
|
MoleculeStamp* molStamp; |
| 125 |
|
//equal to the total number of atoms minus number of atoms belong to |
| 126 |
|
//cutoff group defined in meta-data file plus the number of cutoff |
| 127 |
|
//groups defined in meta-data file |
| 128 |
+ |
std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
| 129 |
+ |
std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
| 130 |
+ |
std::cerr << "nG = " << nGroups << "\n"; |
| 131 |
+ |
|
| 132 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 133 |
+ |
|
| 134 |
+ |
std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; |
| 135 |
|
|
| 136 |
|
//every free atom (atom does not belong to rigid bodies) is an |
| 137 |
|
//integrable object therefore the total number of integrable objects |
| 655 |
|
/** |
| 656 |
|
* update |
| 657 |
|
* |
| 658 |
< |
* Performs the global checks and variable settings after the objects have been |
| 659 |
< |
* created. |
| 658 |
> |
* Performs the global checks and variable settings after the |
| 659 |
> |
* objects have been created. |
| 660 |
|
* |
| 661 |
|
*/ |
| 662 |
< |
void SimInfo::update() { |
| 665 |
< |
|
| 662 |
> |
void SimInfo::update() { |
| 663 |
|
setupSimVariables(); |
| 667 |
– |
setupCutoffs(); |
| 668 |
– |
setupSwitching(); |
| 669 |
– |
setupElectrostatics(); |
| 670 |
– |
setupNeighborlists(); |
| 671 |
– |
|
| 672 |
– |
#ifdef IS_MPI |
| 673 |
– |
setupFortranParallel(); |
| 674 |
– |
#endif |
| 675 |
– |
setupFortranSim(); |
| 676 |
– |
fortranInitialized_ = true; |
| 677 |
– |
|
| 664 |
|
calcNdf(); |
| 665 |
|
calcNdfRaw(); |
| 666 |
|
calcNdfTrans(); |
| 667 |
|
} |
| 668 |
|
|
| 669 |
+ |
/** |
| 670 |
+ |
* getSimulatedAtomTypes |
| 671 |
+ |
* |
| 672 |
+ |
* Returns an STL set of AtomType* that are actually present in this |
| 673 |
+ |
* simulation. Must query all processors to assemble this information. |
| 674 |
+ |
* |
| 675 |
+ |
*/ |
| 676 |
|
set<AtomType*> SimInfo::getSimulatedAtomTypes() { |
| 677 |
|
SimInfo::MoleculeIterator mi; |
| 678 |
|
Molecule* mol; |
| 685 |
|
atomTypes.insert(atom->getAtomType()); |
| 686 |
|
} |
| 687 |
|
} |
| 695 |
– |
return atomTypes; |
| 696 |
– |
} |
| 688 |
|
|
| 689 |
< |
/** |
| 699 |
< |
* setupCutoffs |
| 700 |
< |
* |
| 701 |
< |
* Sets the values of cutoffRadius and cutoffMethod |
| 702 |
< |
* |
| 703 |
< |
* cutoffRadius : realType |
| 704 |
< |
* If the cutoffRadius was explicitly set, use that value. |
| 705 |
< |
* If the cutoffRadius was not explicitly set: |
| 706 |
< |
* Are there electrostatic atoms? Use 12.0 Angstroms. |
| 707 |
< |
* No electrostatic atoms? Poll the atom types present in the |
| 708 |
< |
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 709 |
< |
* Use the maximum suggested value that was found. |
| 710 |
< |
* |
| 711 |
< |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) |
| 712 |
< |
* If cutoffMethod was explicitly set, use that choice. |
| 713 |
< |
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 714 |
< |
*/ |
| 715 |
< |
void SimInfo::setupCutoffs() { |
| 716 |
< |
|
| 717 |
< |
if (simParams_->haveCutoffRadius()) { |
| 718 |
< |
cutoffRadius_ = simParams_->getCutoffRadius(); |
| 719 |
< |
} else { |
| 720 |
< |
if (usesElectrostaticAtoms_) { |
| 721 |
< |
sprintf(painCave.errMsg, |
| 722 |
< |
"SimInfo: No value was set for the cutoffRadius.\n" |
| 723 |
< |
"\tOpenMD will use a default value of 12.0 angstroms" |
| 724 |
< |
"\tfor the cutoffRadius.\n"); |
| 725 |
< |
painCave.isFatal = 0; |
| 726 |
< |
painCave.severity = OPENMD_INFO; |
| 727 |
< |
simError(); |
| 728 |
< |
cutoffRadius_ = 12.0; |
| 729 |
< |
} else { |
| 730 |
< |
RealType thisCut; |
| 731 |
< |
set<AtomType*>::iterator i; |
| 732 |
< |
set<AtomType*> atomTypes; |
| 733 |
< |
atomTypes = getSimulatedAtomTypes(); |
| 734 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 735 |
< |
thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i)); |
| 736 |
< |
cutoffRadius_ = max(thisCut, cutoffRadius_); |
| 737 |
< |
} |
| 738 |
< |
sprintf(painCave.errMsg, |
| 739 |
< |
"SimInfo: No value was set for the cutoffRadius.\n" |
| 740 |
< |
"\tOpenMD will use %lf angstroms.\n", |
| 741 |
< |
cutoffRadius_); |
| 742 |
< |
painCave.isFatal = 0; |
| 743 |
< |
painCave.severity = OPENMD_INFO; |
| 744 |
< |
simError(); |
| 745 |
< |
} |
| 746 |
< |
} |
| 689 |
> |
#ifdef IS_MPI |
| 690 |
|
|
| 691 |
< |
InteractionManager::Instance()->setCutoffRadius(cutoffRadius_); |
| 691 |
> |
// loop over the found atom types on this processor, and add their |
| 692 |
> |
// numerical idents to a vector: |
| 693 |
|
|
| 694 |
< |
map<string, CutoffMethod> stringToCutoffMethod; |
| 695 |
< |
stringToCutoffMethod["HARD"] = HARD; |
| 696 |
< |
stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION; |
| 697 |
< |
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
| 754 |
< |
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
| 755 |
< |
|
| 756 |
< |
if (simParams_->haveCutoffMethod()) { |
| 757 |
< |
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 758 |
< |
map<string, CutoffMethod>::iterator i; |
| 759 |
< |
i = stringToCutoffMethod.find(cutMeth); |
| 760 |
< |
if (i == stringToCutoffMethod.end()) { |
| 761 |
< |
sprintf(painCave.errMsg, |
| 762 |
< |
"SimInfo: Could not find chosen cutoffMethod %s\n" |
| 763 |
< |
"\tShould be one of: " |
| 764 |
< |
"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 765 |
< |
cutMeth.c_str()); |
| 766 |
< |
painCave.isFatal = 1; |
| 767 |
< |
painCave.severity = OPENMD_ERROR; |
| 768 |
< |
simError(); |
| 769 |
< |
} else { |
| 770 |
< |
cutoffMethod_ = i->second; |
| 771 |
< |
} |
| 772 |
< |
} else { |
| 773 |
< |
sprintf(painCave.errMsg, |
| 774 |
< |
"SimInfo: No value was set for the cutoffMethod.\n" |
| 775 |
< |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 776 |
< |
painCave.isFatal = 0; |
| 777 |
< |
painCave.severity = OPENMD_INFO; |
| 778 |
< |
simError(); |
| 779 |
< |
cutoffMethod_ = SHIFTED_FORCE; |
| 780 |
< |
} |
| 694 |
> |
vector<int> foundTypes; |
| 695 |
> |
set<AtomType*>::iterator i; |
| 696 |
> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) |
| 697 |
> |
foundTypes.push_back( (*i)->getIdent() ); |
| 698 |
|
|
| 699 |
< |
InteractionManager::Instance()->setCutoffMethod(cutoffMethod_); |
| 700 |
< |
} |
| 784 |
< |
|
| 785 |
< |
/** |
| 786 |
< |
* setupSwitching |
| 787 |
< |
* |
| 788 |
< |
* Sets the values of switchingRadius and |
| 789 |
< |
* If the switchingRadius was explicitly set, use that value (but check it) |
| 790 |
< |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 791 |
< |
*/ |
| 792 |
< |
void SimInfo::setupSwitching() { |
| 793 |
< |
|
| 794 |
< |
if (simParams_->haveSwitchingRadius()) { |
| 795 |
< |
switchingRadius_ = simParams_->getSwitchingRadius(); |
| 796 |
< |
if (switchingRadius_ > cutoffRadius_) { |
| 797 |
< |
sprintf(painCave.errMsg, |
| 798 |
< |
"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n", |
| 799 |
< |
switchingRadius_, cutoffRadius_); |
| 800 |
< |
painCave.isFatal = 1; |
| 801 |
< |
painCave.severity = OPENMD_ERROR; |
| 802 |
< |
simError(); |
| 803 |
< |
} |
| 804 |
< |
} else { |
| 805 |
< |
switchingRadius_ = 0.85 * cutoffRadius_; |
| 806 |
< |
sprintf(painCave.errMsg, |
| 807 |
< |
"SimInfo: No value was set for the switchingRadius.\n" |
| 808 |
< |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 809 |
< |
"\tswitchingRadius = %f. for this simulation\n", switchingRadius_); |
| 810 |
< |
painCave.isFatal = 0; |
| 811 |
< |
painCave.severity = OPENMD_WARNING; |
| 812 |
< |
simError(); |
| 813 |
< |
} |
| 814 |
< |
|
| 815 |
< |
InteractionManager::Instance()->setSwitchingRadius(switchingRadius_); |
| 699 |
> |
// count_local holds the number of found types on this processor |
| 700 |
> |
int count_local = foundTypes.size(); |
| 701 |
|
|
| 702 |
< |
SwitchingFunctionType ft; |
| 702 |
> |
// count holds the total number of found types on all processors |
| 703 |
> |
// (some will be redundant with the ones found locally): |
| 704 |
> |
int count; |
| 705 |
> |
MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM); |
| 706 |
> |
|
| 707 |
> |
// create a vector to hold the globally found types, and resize it: |
| 708 |
> |
vector<int> ftGlobal; |
| 709 |
> |
ftGlobal.resize(count); |
| 710 |
> |
vector<int> counts; |
| 711 |
> |
|
| 712 |
> |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 713 |
> |
counts.resize(nproc); |
| 714 |
> |
vector<int> disps; |
| 715 |
> |
disps.resize(nproc); |
| 716 |
> |
|
| 717 |
> |
// now spray out the foundTypes to all the other processors: |
| 718 |
|
|
| 719 |
< |
if (simParams_->haveSwitchingFunctionType()) { |
| 720 |
< |
string funcType = simParams_->getSwitchingFunctionType(); |
| 821 |
< |
toUpper(funcType); |
| 822 |
< |
if (funcType == "CUBIC") { |
| 823 |
< |
ft = cubic; |
| 824 |
< |
} else { |
| 825 |
< |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
| 826 |
< |
ft = fifth_order_poly; |
| 827 |
< |
} else { |
| 828 |
< |
// throw error |
| 829 |
< |
sprintf( painCave.errMsg, |
| 830 |
< |
"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n" |
| 831 |
< |
"\tswitchingFunctionType must be one of: " |
| 832 |
< |
"\"cubic\" or \"fifth_order_polynomial\".", |
| 833 |
< |
funcType.c_str() ); |
| 834 |
< |
painCave.isFatal = 1; |
| 835 |
< |
painCave.severity = OPENMD_ERROR; |
| 836 |
< |
simError(); |
| 837 |
< |
} |
| 838 |
< |
} |
| 839 |
< |
} |
| 719 |
> |
MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT, |
| 720 |
> |
&ftGlobal[0], &counts[0], &disps[0], MPI::INT); |
| 721 |
|
|
| 722 |
< |
InteractionManager::Instance()->setSwitchingFunctionType(ft); |
| 722 |
> |
// foundIdents is a stl set, so inserting an already found ident |
| 723 |
> |
// will have no effect. |
| 724 |
> |
set<int> foundIdents; |
| 725 |
> |
vector<int>::iterator j; |
| 726 |
> |
for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) |
| 727 |
> |
foundIdents.insert((*j)); |
| 728 |
> |
|
| 729 |
> |
// now iterate over the foundIdents and get the actual atom types |
| 730 |
> |
// that correspond to these: |
| 731 |
> |
set<int>::iterator it; |
| 732 |
> |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 733 |
> |
atomTypes.insert( forceField_->getAtomType((*it)) ); |
| 734 |
> |
|
| 735 |
> |
#endif |
| 736 |
> |
|
| 737 |
> |
return atomTypes; |
| 738 |
|
} |
| 739 |
|
|
| 740 |
< |
/** |
| 741 |
< |
* setupSkinThickness |
| 742 |
< |
* |
| 743 |
< |
* If the skinThickness was explicitly set, use that value (but check it) |
| 744 |
< |
* If the skinThickness was not explicitly set: use 1.0 angstroms |
| 745 |
< |
*/ |
| 746 |
< |
void SimInfo::setupSkinThickness() { |
| 747 |
< |
if (simParams_->haveSkinThickness()) { |
| 852 |
< |
skinThickness_ = simParams_->getSkinThickness(); |
| 853 |
< |
} else { |
| 854 |
< |
skinThickness_ = 1.0; |
| 855 |
< |
sprintf(painCave.errMsg, |
| 856 |
< |
"SimInfo Warning: No value was set for the skinThickness.\n" |
| 857 |
< |
"\tOpenMD will use a default value of %f Angstroms\n" |
| 858 |
< |
"\tfor this simulation\n", skinThickness_); |
| 859 |
< |
painCave.isFatal = 0; |
| 860 |
< |
simError(); |
| 861 |
< |
} |
| 862 |
< |
} |
| 740 |
> |
void SimInfo::setupSimVariables() { |
| 741 |
> |
useAtomicVirial_ = simParams_->getUseAtomicVirial(); |
| 742 |
> |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true |
| 743 |
> |
calcBoxDipole_ = false; |
| 744 |
> |
if ( simParams_->haveAccumulateBoxDipole() ) |
| 745 |
> |
if ( simParams_->getAccumulateBoxDipole() ) { |
| 746 |
> |
calcBoxDipole_ = true; |
| 747 |
> |
} |
| 748 |
|
|
| 864 |
– |
void SimInfo::setupSimType() { |
| 749 |
|
set<AtomType*>::iterator i; |
| 750 |
|
set<AtomType*> atomTypes; |
| 751 |
< |
atomTypes = getSimulatedAtomTypes(); |
| 868 |
< |
|
| 869 |
< |
useAtomicVirial_ = simParams_->getUseAtomicVirial(); |
| 870 |
< |
|
| 751 |
> |
atomTypes = getSimulatedAtomTypes(); |
| 752 |
|
int usesElectrostatic = 0; |
| 753 |
|
int usesMetallic = 0; |
| 754 |
|
int usesDirectional = 0; |
| 770 |
|
temp = usesElectrostatic; |
| 771 |
|
MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 772 |
|
#endif |
| 892 |
– |
fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_; |
| 893 |
– |
fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_; |
| 894 |
– |
fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_; |
| 895 |
– |
fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_; |
| 896 |
– |
fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; |
| 897 |
– |
fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; |
| 773 |
|
} |
| 774 |
|
|
| 775 |
< |
void SimInfo::setupFortranSim() { |
| 776 |
< |
int isError; |
| 777 |
< |
int nExclude, nOneTwo, nOneThree, nOneFour; |
| 778 |
< |
vector<int> fortranGlobalGroupMembership; |
| 775 |
> |
|
| 776 |
> |
vector<int> SimInfo::getGlobalAtomIndices() { |
| 777 |
> |
SimInfo::MoleculeIterator mi; |
| 778 |
> |
Molecule* mol; |
| 779 |
> |
Molecule::AtomIterator ai; |
| 780 |
> |
Atom* atom; |
| 781 |
> |
|
| 782 |
> |
vector<int> GlobalAtomIndices(getNAtoms(), 0); |
| 783 |
|
|
| 784 |
< |
notifyFortranSkinThickness(&skinThickness_); |
| 784 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 785 |
> |
|
| 786 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 787 |
> |
GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex(); |
| 788 |
> |
} |
| 789 |
> |
} |
| 790 |
> |
return GlobalAtomIndices; |
| 791 |
> |
} |
| 792 |
|
|
| 907 |
– |
int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0; |
| 908 |
– |
int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0; |
| 909 |
– |
notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf); |
| 793 |
|
|
| 794 |
< |
isError = 0; |
| 794 |
> |
vector<int> SimInfo::getGlobalGroupIndices() { |
| 795 |
> |
SimInfo::MoleculeIterator mi; |
| 796 |
> |
Molecule* mol; |
| 797 |
> |
Molecule::CutoffGroupIterator ci; |
| 798 |
> |
CutoffGroup* cg; |
| 799 |
|
|
| 800 |
< |
//globalGroupMembership_ is filled by SimCreator |
| 801 |
< |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 802 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
| 800 |
> |
vector<int> GlobalGroupIndices; |
| 801 |
> |
|
| 802 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 803 |
> |
|
| 804 |
> |
//local index of cutoff group is trivial, it only depends on the |
| 805 |
> |
//order of travesing |
| 806 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 807 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 808 |
> |
GlobalGroupIndices.push_back(cg->getGlobalIndex()); |
| 809 |
> |
} |
| 810 |
|
} |
| 811 |
+ |
return GlobalGroupIndices; |
| 812 |
+ |
} |
| 813 |
|
|
| 814 |
+ |
|
| 815 |
+ |
void SimInfo::prepareTopology() { |
| 816 |
+ |
int nExclude, nOneTwo, nOneThree, nOneFour; |
| 817 |
+ |
|
| 818 |
|
//calculate mass ratio of cutoff group |
| 919 |
– |
vector<RealType> mfact; |
| 819 |
|
SimInfo::MoleculeIterator mi; |
| 820 |
|
Molecule* mol; |
| 821 |
|
Molecule::CutoffGroupIterator ci; |
| 824 |
|
Atom* atom; |
| 825 |
|
RealType totalMass; |
| 826 |
|
|
| 827 |
< |
//to avoid memory reallocation, reserve enough space for mfact |
| 828 |
< |
mfact.reserve(getNCutoffGroups()); |
| 827 |
> |
//to avoid memory reallocation, reserve enough space for massFactors_ |
| 828 |
> |
massFactors_.clear(); |
| 829 |
> |
massFactors_.reserve(getNCutoffGroups()); |
| 830 |
|
|
| 831 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 832 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 832 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 833 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 834 |
|
|
| 835 |
|
totalMass = cg->getMass(); |
| 836 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 837 |
|
// Check for massless groups - set mfact to 1 if true |
| 838 |
|
if (totalMass != 0) |
| 839 |
< |
mfact.push_back(atom->getMass()/totalMass); |
| 839 |
> |
massFactors_.push_back(atom->getMass()/totalMass); |
| 840 |
|
else |
| 841 |
< |
mfact.push_back( 1.0 ); |
| 841 |
> |
massFactors_.push_back( 1.0 ); |
| 842 |
|
} |
| 843 |
|
} |
| 844 |
|
} |
| 845 |
|
|
| 846 |
< |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
| 946 |
< |
vector<int> identArray; |
| 846 |
> |
// Build the identArray_ |
| 847 |
|
|
| 848 |
< |
//to avoid memory reallocation, reserve enough space identArray |
| 849 |
< |
identArray.reserve(getNAtoms()); |
| 950 |
< |
|
| 848 |
> |
identArray_.clear(); |
| 849 |
> |
identArray_.reserve(getNAtoms()); |
| 850 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 851 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 852 |
< |
identArray.push_back(atom->getIdent()); |
| 852 |
> |
identArray_.push_back(atom->getIdent()); |
| 853 |
|
} |
| 854 |
|
} |
| 956 |
– |
|
| 957 |
– |
//fill molMembershipArray |
| 958 |
– |
//molMembershipArray is filled by SimCreator |
| 959 |
– |
vector<int> molMembershipArray(nGlobalAtoms_); |
| 960 |
– |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 961 |
– |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
| 962 |
– |
} |
| 855 |
|
|
| 856 |
< |
//setup fortran simulation |
| 856 |
> |
//scan topology |
| 857 |
|
|
| 858 |
|
nExclude = excludedInteractions_.getSize(); |
| 859 |
|
nOneTwo = oneTwoInteractions_.getSize(); |
| 865 |
|
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 866 |
|
int* oneFourList = oneFourInteractions_.getPairList(); |
| 867 |
|
|
| 868 |
< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], |
| 869 |
< |
&nExclude, excludeList, |
| 870 |
< |
&nOneTwo, oneTwoList, |
| 871 |
< |
&nOneThree, oneThreeList, |
| 872 |
< |
&nOneFour, oneFourList, |
| 873 |
< |
&molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 874 |
< |
&fortranGlobalGroupMembership[0], &isError); |
| 868 |
> |
//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], |
| 869 |
> |
// &nExclude, excludeList, |
| 870 |
> |
// &nOneTwo, oneTwoList, |
| 871 |
> |
// &nOneThree, oneThreeList, |
| 872 |
> |
// &nOneFour, oneFourList, |
| 873 |
> |
// &molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 874 |
> |
// &fortranGlobalGroupMembership[0], &isError); |
| 875 |
|
|
| 876 |
< |
if( isError ){ |
| 985 |
< |
|
| 986 |
< |
sprintf( painCave.errMsg, |
| 987 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
| 988 |
< |
painCave.isFatal = 1; |
| 989 |
< |
painCave.severity = OPENMD_ERROR; |
| 990 |
< |
simError(); |
| 991 |
< |
} |
| 992 |
< |
|
| 993 |
< |
|
| 994 |
< |
sprintf( checkPointMsg, |
| 995 |
< |
"succesfully sent the simulation information to fortran.\n"); |
| 996 |
< |
|
| 997 |
< |
errorCheckPoint(); |
| 998 |
< |
|
| 999 |
< |
// Setup number of neighbors in neighbor list if present |
| 1000 |
< |
if (simParams_->haveNeighborListNeighbors()) { |
| 1001 |
< |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 1002 |
< |
setNeighbors(&nlistNeighbors); |
| 1003 |
< |
} |
| 1004 |
< |
|
| 1005 |
< |
|
| 1006 |
< |
} |
| 1007 |
< |
|
| 1008 |
< |
|
| 1009 |
< |
void SimInfo::setupFortranParallel() { |
| 1010 |
< |
#ifdef IS_MPI |
| 1011 |
< |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
| 1012 |
< |
vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
| 1013 |
< |
vector<int> localToGlobalCutoffGroupIndex; |
| 1014 |
< |
SimInfo::MoleculeIterator mi; |
| 1015 |
< |
Molecule::AtomIterator ai; |
| 1016 |
< |
Molecule::CutoffGroupIterator ci; |
| 1017 |
< |
Molecule* mol; |
| 1018 |
< |
Atom* atom; |
| 1019 |
< |
CutoffGroup* cg; |
| 1020 |
< |
mpiSimData parallelData; |
| 1021 |
< |
int isError; |
| 1022 |
< |
|
| 1023 |
< |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 1024 |
< |
|
| 1025 |
< |
//local index(index in DataStorge) of atom is important |
| 1026 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 1027 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
| 1028 |
< |
} |
| 1029 |
< |
|
| 1030 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 1031 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 1032 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
| 1033 |
< |
} |
| 1034 |
< |
|
| 1035 |
< |
} |
| 1036 |
< |
|
| 1037 |
< |
//fill up mpiSimData struct |
| 1038 |
< |
parallelData.nMolGlobal = getNGlobalMolecules(); |
| 1039 |
< |
parallelData.nMolLocal = getNMolecules(); |
| 1040 |
< |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 1041 |
< |
parallelData.nAtomsLocal = getNAtoms(); |
| 1042 |
< |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 1043 |
< |
parallelData.nGroupsLocal = getNCutoffGroups(); |
| 1044 |
< |
parallelData.myNode = worldRank; |
| 1045 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
| 1046 |
< |
|
| 1047 |
< |
//pass mpiSimData struct and index arrays to fortran |
| 1048 |
< |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
| 1049 |
< |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
| 1050 |
< |
&localToGlobalCutoffGroupIndex[0], &isError); |
| 1051 |
< |
|
| 1052 |
< |
if (isError) { |
| 1053 |
< |
sprintf(painCave.errMsg, |
| 1054 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 1055 |
< |
painCave.isFatal = 1; |
| 1056 |
< |
simError(); |
| 1057 |
< |
} |
| 1058 |
< |
|
| 1059 |
< |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 1060 |
< |
errorCheckPoint(); |
| 1061 |
< |
|
| 1062 |
< |
#endif |
| 1063 |
< |
} |
| 1064 |
< |
|
| 1065 |
< |
|
| 1066 |
< |
void SimInfo::setupSwitchingFunction() { |
| 1067 |
< |
|
| 1068 |
< |
} |
| 1069 |
< |
|
| 1070 |
< |
void SimInfo::setupAccumulateBoxDipole() { |
| 1071 |
< |
|
| 1072 |
< |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true |
| 1073 |
< |
if ( simParams_->haveAccumulateBoxDipole() ) |
| 1074 |
< |
if ( simParams_->getAccumulateBoxDipole() ) { |
| 1075 |
< |
calcBoxDipole_ = true; |
| 1076 |
< |
} |
| 1077 |
< |
|
| 876 |
> |
topologyDone_ = true; |
| 877 |
|
} |
| 878 |
|
|
| 879 |
|
void SimInfo::addProperty(GenericData* genData) { |
| 910 |
|
Molecule* mol; |
| 911 |
|
RigidBody* rb; |
| 912 |
|
Atom* atom; |
| 913 |
+ |
CutoffGroup* cg; |
| 914 |
|
SimInfo::MoleculeIterator mi; |
| 915 |
|
Molecule::RigidBodyIterator rbIter; |
| 916 |
< |
Molecule::AtomIterator atomIter;; |
| 916 |
> |
Molecule::AtomIterator atomIter; |
| 917 |
> |
Molecule::CutoffGroupIterator cgIter; |
| 918 |
|
|
| 919 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 920 |
|
|
| 925 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 926 |
|
rb->setSnapshotManager(sman_); |
| 927 |
|
} |
| 928 |
+ |
|
| 929 |
+ |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
| 930 |
+ |
cg->setSnapshotManager(sman_); |
| 931 |
+ |
} |
| 932 |
|
} |
| 933 |
|
|
| 934 |
|
} |
