| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 55 |
|
#include "math/Vector3.hpp" |
| 56 |
|
#include "primitives/Molecule.hpp" |
| 57 |
|
#include "primitives/StuntDouble.hpp" |
| 57 |
– |
#include "UseTheForce/DarkSide/neighborLists_interface.h" |
| 58 |
– |
#include "UseTheForce/doForces_interface.h" |
| 58 |
|
#include "utils/MemoryUtils.hpp" |
| 59 |
|
#include "utils/simError.h" |
| 60 |
|
#include "selection/SelectionManager.hpp" |
| 61 |
|
#include "io/ForceFieldOptions.hpp" |
| 62 |
|
#include "UseTheForce/ForceField.hpp" |
| 63 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 65 |
– |
|
| 64 |
|
#ifdef IS_MPI |
| 65 |
< |
#include "UseTheForce/mpiComponentPlan.h" |
| 66 |
< |
#include "UseTheForce/DarkSide/simParallel_interface.h" |
| 69 |
< |
#endif |
| 65 |
> |
#include <mpi.h> |
| 66 |
> |
#endif |
| 67 |
|
|
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD { |
| 75 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
| 76 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), |
| 77 |
|
nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), |
| 78 |
< |
nConstraints_(0), sman_(NULL), fortranInitialized_(false), |
| 78 |
> |
nConstraints_(0), sman_(NULL), topologyDone_(false), |
| 79 |
|
calcBoxDipole_(false), useAtomicVirial_(true) { |
| 80 |
|
|
| 81 |
|
MoleculeStamp* molStamp; |
| 129 |
|
//equal to the total number of atoms minus number of atoms belong to |
| 130 |
|
//cutoff group defined in meta-data file plus the number of cutoff |
| 131 |
|
//groups defined in meta-data file |
| 135 |
– |
std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; |
| 136 |
– |
std::cerr << "nCA = " << nCutoffAtoms << "\n"; |
| 137 |
– |
std::cerr << "nG = " << nGroups << "\n"; |
| 132 |
|
|
| 133 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 140 |
– |
|
| 141 |
– |
std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; |
| 134 |
|
|
| 135 |
|
//every free atom (atom does not belong to rigid bodies) is an |
| 136 |
|
//integrable object therefore the total number of integrable objects |
| 272 |
|
fdf_ = fdf_local; |
| 273 |
|
#endif |
| 274 |
|
return fdf_; |
| 275 |
+ |
} |
| 276 |
+ |
|
| 277 |
+ |
unsigned int SimInfo::getNLocalCutoffGroups(){ |
| 278 |
+ |
int nLocalCutoffAtoms = 0; |
| 279 |
+ |
Molecule* mol; |
| 280 |
+ |
MoleculeIterator mi; |
| 281 |
+ |
CutoffGroup* cg; |
| 282 |
+ |
Molecule::CutoffGroupIterator ci; |
| 283 |
+ |
|
| 284 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 285 |
+ |
|
| 286 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 287 |
+ |
cg = mol->nextCutoffGroup(ci)) { |
| 288 |
+ |
nLocalCutoffAtoms += cg->getNumAtom(); |
| 289 |
+ |
|
| 290 |
+ |
} |
| 291 |
+ |
} |
| 292 |
+ |
|
| 293 |
+ |
return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_; |
| 294 |
|
} |
| 295 |
|
|
| 296 |
|
void SimInfo::calcNdfRaw() { |
| 698 |
|
Atom* atom; |
| 699 |
|
set<AtomType*> atomTypes; |
| 700 |
|
|
| 701 |
< |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 702 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 701 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 702 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 703 |
> |
atom = mol->nextAtom(ai)) { |
| 704 |
|
atomTypes.insert(atom->getAtomType()); |
| 705 |
|
} |
| 706 |
|
} |
| 707 |
< |
|
| 707 |
> |
|
| 708 |
|
#ifdef IS_MPI |
| 709 |
|
|
| 710 |
|
// loop over the found atom types on this processor, and add their |
| 711 |
|
// numerical idents to a vector: |
| 712 |
< |
|
| 712 |
> |
|
| 713 |
|
vector<int> foundTypes; |
| 714 |
|
set<AtomType*>::iterator i; |
| 715 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) |
| 718 |
|
// count_local holds the number of found types on this processor |
| 719 |
|
int count_local = foundTypes.size(); |
| 720 |
|
|
| 721 |
< |
// count holds the total number of found types on all processors |
| 710 |
< |
// (some will be redundant with the ones found locally): |
| 711 |
< |
int count; |
| 712 |
< |
MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM); |
| 721 |
> |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 722 |
|
|
| 723 |
< |
// create a vector to hold the globally found types, and resize it: |
| 724 |
< |
vector<int> ftGlobal; |
| 725 |
< |
ftGlobal.resize(count); |
| 726 |
< |
vector<int> counts; |
| 723 |
> |
// we need arrays to hold the counts and displacement vectors for |
| 724 |
> |
// all processors |
| 725 |
> |
vector<int> counts(nproc, 0); |
| 726 |
> |
vector<int> disps(nproc, 0); |
| 727 |
|
|
| 728 |
< |
int nproc = MPI::COMM_WORLD.Get_size(); |
| 729 |
< |
counts.resize(nproc); |
| 730 |
< |
vector<int> disps; |
| 731 |
< |
disps.resize(nproc); |
| 728 |
> |
// fill the counts array |
| 729 |
> |
MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0], |
| 730 |
> |
1, MPI::INT); |
| 731 |
> |
|
| 732 |
> |
// use the processor counts to compute the displacement array |
| 733 |
> |
disps[0] = 0; |
| 734 |
> |
int totalCount = counts[0]; |
| 735 |
> |
for (int iproc = 1; iproc < nproc; iproc++) { |
| 736 |
> |
disps[iproc] = disps[iproc-1] + counts[iproc-1]; |
| 737 |
> |
totalCount += counts[iproc]; |
| 738 |
> |
} |
| 739 |
|
|
| 740 |
< |
// now spray out the foundTypes to all the other processors: |
| 740 |
> |
// we need a (possibly redundant) set of all found types: |
| 741 |
> |
vector<int> ftGlobal(totalCount); |
| 742 |
|
|
| 743 |
+ |
// now spray out the foundTypes to all the other processors: |
| 744 |
|
MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT, |
| 745 |
< |
&ftGlobal[0], &counts[0], &disps[0], MPI::INT); |
| 745 |
> |
&ftGlobal[0], &counts[0], &disps[0], |
| 746 |
> |
MPI::INT); |
| 747 |
|
|
| 748 |
+ |
vector<int>::iterator j; |
| 749 |
+ |
|
| 750 |
|
// foundIdents is a stl set, so inserting an already found ident |
| 751 |
|
// will have no effect. |
| 752 |
|
set<int> foundIdents; |
| 753 |
< |
vector<int>::iterator j; |
| 753 |
> |
|
| 754 |
|
for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) |
| 755 |
|
foundIdents.insert((*j)); |
| 756 |
|
|
| 757 |
|
// now iterate over the foundIdents and get the actual atom types |
| 758 |
|
// that correspond to these: |
| 759 |
|
set<int>::iterator it; |
| 760 |
< |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 760 |
> |
for (it = foundIdents.begin(); it != foundIdents.end(); ++it) |
| 761 |
|
atomTypes.insert( forceField_->getAtomType((*it)) ); |
| 762 |
|
|
| 763 |
|
#endif |
| 764 |
< |
|
| 764 |
> |
|
| 765 |
|
return atomTypes; |
| 766 |
|
} |
| 767 |
|
|
| 773 |
|
if ( simParams_->getAccumulateBoxDipole() ) { |
| 774 |
|
calcBoxDipole_ = true; |
| 775 |
|
} |
| 776 |
< |
|
| 776 |
> |
|
| 777 |
|
set<AtomType*>::iterator i; |
| 778 |
|
set<AtomType*> atomTypes; |
| 779 |
|
atomTypes = getSimulatedAtomTypes(); |
| 786 |
|
usesMetallic |= (*i)->isMetal(); |
| 787 |
|
usesDirectional |= (*i)->isDirectional(); |
| 788 |
|
} |
| 789 |
< |
|
| 789 |
> |
|
| 790 |
|
#ifdef IS_MPI |
| 791 |
|
int temp; |
| 792 |
|
temp = usesDirectional; |
| 793 |
|
MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 794 |
< |
|
| 794 |
> |
|
| 795 |
|
temp = usesMetallic; |
| 796 |
|
MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 797 |
< |
|
| 797 |
> |
|
| 798 |
|
temp = usesElectrostatic; |
| 799 |
|
MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 800 |
+ |
#else |
| 801 |
+ |
|
| 802 |
+ |
usesDirectionalAtoms_ = usesDirectional; |
| 803 |
+ |
usesMetallicAtoms_ = usesMetallic; |
| 804 |
+ |
usesElectrostaticAtoms_ = usesElectrostatic; |
| 805 |
+ |
|
| 806 |
|
#endif |
| 807 |
< |
fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_; |
| 808 |
< |
fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_; |
| 809 |
< |
fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_; |
| 810 |
< |
fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_; |
| 784 |
< |
fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; |
| 785 |
< |
fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; |
| 807 |
> |
|
| 808 |
> |
requiresPrepair_ = usesMetallicAtoms_ ? true : false; |
| 809 |
> |
requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; |
| 810 |
> |
requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; |
| 811 |
|
} |
| 812 |
|
|
| 813 |
< |
void SimInfo::setupFortran() { |
| 814 |
< |
int isError; |
| 815 |
< |
int nExclude, nOneTwo, nOneThree, nOneFour; |
| 816 |
< |
vector<int> fortranGlobalGroupMembership; |
| 813 |
> |
|
| 814 |
> |
vector<int> SimInfo::getGlobalAtomIndices() { |
| 815 |
> |
SimInfo::MoleculeIterator mi; |
| 816 |
> |
Molecule* mol; |
| 817 |
> |
Molecule::AtomIterator ai; |
| 818 |
> |
Atom* atom; |
| 819 |
> |
|
| 820 |
> |
vector<int> GlobalAtomIndices(getNAtoms(), 0); |
| 821 |
|
|
| 822 |
< |
isError = 0; |
| 822 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 823 |
> |
|
| 824 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 825 |
> |
GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex(); |
| 826 |
> |
} |
| 827 |
> |
} |
| 828 |
> |
return GlobalAtomIndices; |
| 829 |
> |
} |
| 830 |
|
|
| 831 |
< |
//globalGroupMembership_ is filled by SimCreator |
| 832 |
< |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 833 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
| 831 |
> |
|
| 832 |
> |
vector<int> SimInfo::getGlobalGroupIndices() { |
| 833 |
> |
SimInfo::MoleculeIterator mi; |
| 834 |
> |
Molecule* mol; |
| 835 |
> |
Molecule::CutoffGroupIterator ci; |
| 836 |
> |
CutoffGroup* cg; |
| 837 |
> |
|
| 838 |
> |
vector<int> GlobalGroupIndices; |
| 839 |
> |
|
| 840 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 841 |
> |
|
| 842 |
> |
//local index of cutoff group is trivial, it only depends on the |
| 843 |
> |
//order of travesing |
| 844 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 845 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 846 |
> |
GlobalGroupIndices.push_back(cg->getGlobalIndex()); |
| 847 |
> |
} |
| 848 |
|
} |
| 849 |
+ |
return GlobalGroupIndices; |
| 850 |
+ |
} |
| 851 |
|
|
| 852 |
+ |
|
| 853 |
+ |
void SimInfo::prepareTopology() { |
| 854 |
+ |
int nExclude, nOneTwo, nOneThree, nOneFour; |
| 855 |
+ |
|
| 856 |
|
//calculate mass ratio of cutoff group |
| 801 |
– |
vector<RealType> mfact; |
| 857 |
|
SimInfo::MoleculeIterator mi; |
| 858 |
|
Molecule* mol; |
| 859 |
|
Molecule::CutoffGroupIterator ci; |
| 862 |
|
Atom* atom; |
| 863 |
|
RealType totalMass; |
| 864 |
|
|
| 865 |
< |
//to avoid memory reallocation, reserve enough space for mfact |
| 866 |
< |
mfact.reserve(getNCutoffGroups()); |
| 865 |
> |
/** |
| 866 |
> |
* The mass factor is the relative mass of an atom to the total |
| 867 |
> |
* mass of the cutoff group it belongs to. By default, all atoms |
| 868 |
> |
* are their own cutoff groups, and therefore have mass factors of |
| 869 |
> |
* 1. We need some special handling for massless atoms, which |
| 870 |
> |
* will be treated as carrying the entire mass of the cutoff |
| 871 |
> |
* group. |
| 872 |
> |
*/ |
| 873 |
> |
massFactors_.clear(); |
| 874 |
> |
massFactors_.resize(getNAtoms(), 1.0); |
| 875 |
|
|
| 876 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 877 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 877 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 878 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 879 |
|
|
| 880 |
|
totalMass = cg->getMass(); |
| 881 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 882 |
|
// Check for massless groups - set mfact to 1 if true |
| 883 |
< |
if (totalMass != 0) |
| 884 |
< |
mfact.push_back(atom->getMass()/totalMass); |
| 883 |
> |
if (totalMass != 0) |
| 884 |
> |
massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; |
| 885 |
|
else |
| 886 |
< |
mfact.push_back( 1.0 ); |
| 886 |
> |
massFactors_[atom->getLocalIndex()] = 1.0; |
| 887 |
|
} |
| 888 |
|
} |
| 889 |
|
} |
| 897 |
|
identArray_.push_back(atom->getIdent()); |
| 898 |
|
} |
| 899 |
|
} |
| 836 |
– |
|
| 837 |
– |
//fill molMembershipArray |
| 838 |
– |
//molMembershipArray is filled by SimCreator |
| 839 |
– |
vector<int> molMembershipArray(nGlobalAtoms_); |
| 840 |
– |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 841 |
– |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
| 842 |
– |
} |
| 900 |
|
|
| 901 |
< |
//setup fortran simulation |
| 901 |
> |
//scan topology |
| 902 |
|
|
| 903 |
|
nExclude = excludedInteractions_.getSize(); |
| 904 |
|
nOneTwo = oneTwoInteractions_.getSize(); |
| 910 |
|
int* oneThreeList = oneThreeInteractions_.getPairList(); |
| 911 |
|
int* oneFourList = oneFourInteractions_.getPairList(); |
| 912 |
|
|
| 913 |
< |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], |
| 857 |
< |
&nExclude, excludeList, |
| 858 |
< |
&nOneTwo, oneTwoList, |
| 859 |
< |
&nOneThree, oneThreeList, |
| 860 |
< |
&nOneFour, oneFourList, |
| 861 |
< |
&molMembershipArray[0], &mfact[0], &nCutoffGroups_, |
| 862 |
< |
&fortranGlobalGroupMembership[0], &isError); |
| 863 |
< |
|
| 864 |
< |
if( isError ){ |
| 865 |
< |
|
| 866 |
< |
sprintf( painCave.errMsg, |
| 867 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
| 868 |
< |
painCave.isFatal = 1; |
| 869 |
< |
painCave.severity = OPENMD_ERROR; |
| 870 |
< |
simError(); |
| 871 |
< |
} |
| 872 |
< |
|
| 873 |
< |
|
| 874 |
< |
sprintf( checkPointMsg, |
| 875 |
< |
"succesfully sent the simulation information to fortran.\n"); |
| 876 |
< |
|
| 877 |
< |
errorCheckPoint(); |
| 878 |
< |
|
| 879 |
< |
// Setup number of neighbors in neighbor list if present |
| 880 |
< |
if (simParams_->haveNeighborListNeighbors()) { |
| 881 |
< |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 882 |
< |
setNeighbors(&nlistNeighbors); |
| 883 |
< |
} |
| 884 |
< |
|
| 885 |
< |
#ifdef IS_MPI |
| 886 |
< |
//SimInfo is responsible for creating localToGlobalAtomIndex and |
| 887 |
< |
//localToGlobalGroupIndex |
| 888 |
< |
vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
| 889 |
< |
vector<int> localToGlobalCutoffGroupIndex; |
| 890 |
< |
mpiSimData parallelData; |
| 891 |
< |
|
| 892 |
< |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 893 |
< |
|
| 894 |
< |
//local index(index in DataStorge) of atom is important |
| 895 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 896 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
| 897 |
< |
} |
| 898 |
< |
|
| 899 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 900 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 901 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
| 902 |
< |
} |
| 903 |
< |
|
| 904 |
< |
} |
| 905 |
< |
|
| 906 |
< |
//fill up mpiSimData struct |
| 907 |
< |
parallelData.nMolGlobal = getNGlobalMolecules(); |
| 908 |
< |
parallelData.nMolLocal = getNMolecules(); |
| 909 |
< |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 910 |
< |
parallelData.nAtomsLocal = getNAtoms(); |
| 911 |
< |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 912 |
< |
parallelData.nGroupsLocal = getNCutoffGroups(); |
| 913 |
< |
parallelData.myNode = worldRank; |
| 914 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
| 915 |
< |
|
| 916 |
< |
//pass mpiSimData struct and index arrays to fortran |
| 917 |
< |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
| 918 |
< |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
| 919 |
< |
&localToGlobalCutoffGroupIndex[0], &isError); |
| 920 |
< |
|
| 921 |
< |
if (isError) { |
| 922 |
< |
sprintf(painCave.errMsg, |
| 923 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 924 |
< |
painCave.isFatal = 1; |
| 925 |
< |
simError(); |
| 926 |
< |
} |
| 927 |
< |
|
| 928 |
< |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 929 |
< |
errorCheckPoint(); |
| 930 |
< |
#endif |
| 931 |
< |
|
| 932 |
< |
initFortranFF(&isError); |
| 933 |
< |
if (isError) { |
| 934 |
< |
sprintf(painCave.errMsg, |
| 935 |
< |
"initFortranFF errror: fortran didn't like something we gave it.\n"); |
| 936 |
< |
painCave.isFatal = 1; |
| 937 |
< |
simError(); |
| 938 |
< |
} |
| 939 |
< |
fortranInitialized_ = true; |
| 913 |
> |
topologyDone_ = true; |
| 914 |
|
} |
| 915 |
|
|
| 916 |
|
void SimInfo::addProperty(GenericData* genData) { |
