59 |
|
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
60 |
|
#include "UseTheForce/doForces_interface.h" |
61 |
|
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
62 |
– |
#include "UseTheForce/notifyCutoffs_interface.h" |
62 |
|
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
63 |
|
#include "utils/MemoryUtils.hpp" |
64 |
|
#include "utils/simError.h" |
65 |
|
#include "selection/SelectionManager.hpp" |
66 |
+ |
#include "io/ForceFieldOptions.hpp" |
67 |
+ |
#include "UseTheForce/ForceField.hpp" |
68 |
|
|
69 |
|
#ifdef IS_MPI |
70 |
|
#include "UseTheForce/mpiComponentPlan.h" |
82 |
|
return result; |
83 |
|
} |
84 |
|
|
85 |
< |
SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
86 |
< |
ForceField* ff, Globals* simParams) : |
87 |
< |
stamps_(stamps), forceField_(ff), simParams_(simParams), |
87 |
< |
ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
85 |
> |
SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
86 |
> |
forceField_(ff), simParams_(simParams), |
87 |
> |
ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
88 |
|
nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
89 |
|
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
90 |
|
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
91 |
|
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
92 |
|
sman_(NULL), fortranInitialized_(false) { |
93 |
|
|
94 |
– |
|
95 |
– |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
94 |
|
MoleculeStamp* molStamp; |
95 |
|
int nMolWithSameStamp; |
96 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
98 |
|
CutoffGroupStamp* cgStamp; |
99 |
|
RigidBodyStamp* rbStamp; |
100 |
|
int nRigidAtoms = 0; |
101 |
< |
|
102 |
< |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
103 |
< |
molStamp = i->first; |
104 |
< |
nMolWithSameStamp = i->second; |
101 |
> |
std::vector<Component*> components = simParams->getComponents(); |
102 |
> |
|
103 |
> |
for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
104 |
> |
molStamp = (*i)->getMoleculeStamp(); |
105 |
> |
nMolWithSameStamp = (*i)->getNMol(); |
106 |
|
|
107 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
108 |
|
|
109 |
|
//calculate atoms in molecules |
110 |
|
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
111 |
|
|
113 |
– |
|
112 |
|
//calculate atoms in cutoff groups |
113 |
|
int nAtomsInGroups = 0; |
114 |
|
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
115 |
|
|
116 |
|
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
117 |
< |
cgStamp = molStamp->getCutoffGroup(j); |
117 |
> |
cgStamp = molStamp->getCutoffGroupStamp(j); |
118 |
|
nAtomsInGroups += cgStamp->getNMembers(); |
119 |
|
} |
120 |
|
|
127 |
|
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
128 |
|
|
129 |
|
for (int j=0; j < nRigidBodiesInStamp; j++) { |
130 |
< |
rbStamp = molStamp->getRigidBody(j); |
130 |
> |
rbStamp = molStamp->getRigidBodyStamp(j); |
131 |
|
nAtomsInRigidBodies += rbStamp->getNMembers(); |
132 |
|
} |
133 |
|
|
166 |
|
} |
167 |
|
molecules_.clear(); |
168 |
|
|
171 |
– |
delete stamps_; |
169 |
|
delete sman_; |
170 |
|
delete simParams_; |
171 |
|
delete forceField_; |
272 |
|
} |
273 |
|
} |
274 |
|
|
275 |
< |
}//end for (integrableObject) |
276 |
< |
}// end for (mol) |
275 |
> |
} |
276 |
> |
} |
277 |
|
|
278 |
|
// n_constraints is local, so subtract them on each processor |
279 |
|
ndf_local -= nConstraints_; |
290 |
|
|
291 |
|
} |
292 |
|
|
293 |
+ |
int SimInfo::getFdf() { |
294 |
+ |
#ifdef IS_MPI |
295 |
+ |
MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
296 |
+ |
#else |
297 |
+ |
fdf_ = fdf_local; |
298 |
+ |
#endif |
299 |
+ |
return fdf_; |
300 |
+ |
} |
301 |
+ |
|
302 |
|
void SimInfo::calcNdfRaw() { |
303 |
|
int ndfRaw_local; |
304 |
|
|
799 |
|
} |
800 |
|
|
801 |
|
//calculate mass ratio of cutoff group |
802 |
< |
std::vector<double> mfact; |
802 |
> |
std::vector<RealType> mfact; |
803 |
|
SimInfo::MoleculeIterator mi; |
804 |
|
Molecule* mol; |
805 |
|
Molecule::CutoffGroupIterator ci; |
806 |
|
CutoffGroup* cg; |
807 |
|
Molecule::AtomIterator ai; |
808 |
|
Atom* atom; |
809 |
< |
double totalMass; |
809 |
> |
RealType totalMass; |
810 |
|
|
811 |
|
//to avoid memory reallocation, reserve enough space for mfact |
812 |
|
mfact.reserve(getNCutoffGroups()); |
929 |
|
|
930 |
|
#endif |
931 |
|
|
932 |
< |
double SimInfo::calcMaxCutoffRadius() { |
932 |
> |
void SimInfo::setupCutoff() { |
933 |
> |
|
934 |
> |
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
935 |
|
|
936 |
+ |
// Check the cutoff policy |
937 |
+ |
int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default |
938 |
|
|
939 |
< |
std::set<AtomType*> atomTypes; |
940 |
< |
std::set<AtomType*>::iterator i; |
941 |
< |
std::vector<double> cutoffRadius; |
942 |
< |
|
943 |
< |
//get the unique atom types |
934 |
< |
atomTypes = getUniqueAtomTypes(); |
935 |
< |
|
936 |
< |
//query the max cutoff radius among these atom types |
937 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
938 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
939 |
> |
std::string myPolicy; |
940 |
> |
if (forceFieldOptions_.haveCutoffPolicy()){ |
941 |
> |
myPolicy = forceFieldOptions_.getCutoffPolicy(); |
942 |
> |
}else if (simParams_->haveCutoffPolicy()) { |
943 |
> |
myPolicy = simParams_->getCutoffPolicy(); |
944 |
|
} |
945 |
|
|
946 |
< |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
942 |
< |
#ifdef IS_MPI |
943 |
< |
//pick the max cutoff radius among the processors |
944 |
< |
#endif |
945 |
< |
|
946 |
< |
return maxCutoffRadius; |
947 |
< |
} |
948 |
< |
|
949 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
950 |
< |
|
951 |
< |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
952 |
< |
|
953 |
< |
if (!simParams_->haveCutoffRadius()){ |
954 |
< |
sprintf(painCave.errMsg, |
955 |
< |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
956 |
< |
"\tOOPSE will use a default value of 15.0 angstroms" |
957 |
< |
"\tfor the cutoffRadius.\n"); |
958 |
< |
painCave.isFatal = 0; |
959 |
< |
simError(); |
960 |
< |
rcut = 15.0; |
961 |
< |
} else{ |
962 |
< |
rcut = simParams_->getCutoffRadius(); |
963 |
< |
} |
964 |
< |
|
965 |
< |
if (!simParams_->haveSwitchingRadius()){ |
966 |
< |
sprintf(painCave.errMsg, |
967 |
< |
"SimCreator Warning: No value was set for switchingRadius.\n" |
968 |
< |
"\tOOPSE will use a default value of\n" |
969 |
< |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
970 |
< |
painCave.isFatal = 0; |
971 |
< |
simError(); |
972 |
< |
rsw = 0.85 * rcut; |
973 |
< |
} else{ |
974 |
< |
rsw = simParams_->getSwitchingRadius(); |
975 |
< |
} |
976 |
< |
|
977 |
< |
} else { |
978 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
979 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
980 |
< |
|
981 |
< |
if (simParams_->haveCutoffRadius()) { |
982 |
< |
rcut = simParams_->getCutoffRadius(); |
983 |
< |
} else { |
984 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
985 |
< |
rcut = calcMaxCutoffRadius(); |
986 |
< |
} |
987 |
< |
|
988 |
< |
if (simParams_->haveSwitchingRadius()) { |
989 |
< |
rsw = simParams_->getSwitchingRadius(); |
990 |
< |
} else { |
991 |
< |
rsw = rcut; |
992 |
< |
} |
993 |
< |
|
994 |
< |
} |
995 |
< |
} |
996 |
< |
|
997 |
< |
void SimInfo::setupCutoff() { |
998 |
< |
getCutoff(rcut_, rsw_); |
999 |
< |
double rnblist = rcut_ + 1; // skin of neighbor list |
1000 |
< |
|
1001 |
< |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
1002 |
< |
|
1003 |
< |
int cp = TRADITIONAL_CUTOFF_POLICY; |
1004 |
< |
if (simParams_->haveCutoffPolicy()) { |
1005 |
< |
std::string myPolicy = simParams_->getCutoffPolicy(); |
946 |
> |
if (!myPolicy.empty()){ |
947 |
|
toUpper(myPolicy); |
948 |
|
if (myPolicy == "MIX") { |
949 |
|
cp = MIX_CUTOFF_POLICY; |
962 |
|
} |
963 |
|
} |
964 |
|
} |
965 |
< |
} |
965 |
> |
} |
966 |
> |
notifyFortranCutoffPolicy(&cp); |
967 |
|
|
968 |
< |
|
968 |
> |
// Check the Skin Thickness for neighborlists |
969 |
> |
RealType skin; |
970 |
|
if (simParams_->haveSkinThickness()) { |
971 |
< |
double skinThickness = simParams_->getSkinThickness(); |
972 |
< |
} |
971 |
> |
skin = simParams_->getSkinThickness(); |
972 |
> |
notifyFortranSkinThickness(&skin); |
973 |
> |
} |
974 |
> |
|
975 |
> |
// Check if the cutoff was set explicitly: |
976 |
> |
if (simParams_->haveCutoffRadius()) { |
977 |
> |
rcut_ = simParams_->getCutoffRadius(); |
978 |
> |
if (simParams_->haveSwitchingRadius()) { |
979 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
980 |
> |
} else { |
981 |
> |
if (fInfo_.SIM_uses_Charges | |
982 |
> |
fInfo_.SIM_uses_Dipoles | |
983 |
> |
fInfo_.SIM_uses_RF) { |
984 |
> |
|
985 |
> |
rsw_ = 0.85 * rcut_; |
986 |
> |
sprintf(painCave.errMsg, |
987 |
> |
"SimCreator Warning: No value was set for the switchingRadius.\n" |
988 |
> |
"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n" |
989 |
> |
"\tswitchingRadius = %f. for this simulation\n", rsw_); |
990 |
> |
painCave.isFatal = 0; |
991 |
> |
simError(); |
992 |
> |
} else { |
993 |
> |
rsw_ = rcut_; |
994 |
> |
sprintf(painCave.errMsg, |
995 |
> |
"SimCreator Warning: No value was set for the switchingRadius.\n" |
996 |
> |
"\tOOPSE will use the same value as the cutoffRadius.\n" |
997 |
> |
"\tswitchingRadius = %f. for this simulation\n", rsw_); |
998 |
> |
painCave.isFatal = 0; |
999 |
> |
simError(); |
1000 |
> |
} |
1001 |
> |
} |
1002 |
> |
|
1003 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
1004 |
> |
|
1005 |
> |
} else { |
1006 |
> |
|
1007 |
> |
// For electrostatic atoms, we'll assume a large safe value: |
1008 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
1009 |
> |
sprintf(painCave.errMsg, |
1010 |
> |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
1011 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
1012 |
> |
"\tfor the cutoffRadius.\n"); |
1013 |
> |
painCave.isFatal = 0; |
1014 |
> |
simError(); |
1015 |
> |
rcut_ = 15.0; |
1016 |
> |
|
1017 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
1018 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
1019 |
> |
toUpper(myMethod); |
1020 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
1021 |
> |
if (simParams_->haveSwitchingRadius()){ |
1022 |
> |
sprintf(painCave.errMsg, |
1023 |
> |
"SimInfo Warning: A value was set for the switchingRadius\n" |
1024 |
> |
"\teven though the electrostaticSummationMethod was\n" |
1025 |
> |
"\tset to %s\n", myMethod.c_str()); |
1026 |
> |
painCave.isFatal = 1; |
1027 |
> |
simError(); |
1028 |
> |
} |
1029 |
> |
} |
1030 |
> |
} |
1031 |
> |
|
1032 |
> |
if (simParams_->haveSwitchingRadius()){ |
1033 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
1034 |
> |
} else { |
1035 |
> |
sprintf(painCave.errMsg, |
1036 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
1037 |
> |
"\tOOPSE will use a default value of\n" |
1038 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
1039 |
> |
painCave.isFatal = 0; |
1040 |
> |
simError(); |
1041 |
> |
rsw_ = 0.85 * rcut_; |
1042 |
> |
} |
1043 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
1044 |
> |
} else { |
1045 |
> |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
1046 |
> |
// We'll punt and let fortran figure out the cutoffs later. |
1047 |
> |
|
1048 |
> |
notifyFortranYouAreOnYourOwn(); |
1049 |
|
|
1050 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
1051 |
< |
// also send cutoff notification to electrostatics |
1033 |
< |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
1050 |
> |
} |
1051 |
> |
} |
1052 |
|
} |
1053 |
|
|
1054 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1056 |
|
int errorOut; |
1057 |
|
int esm = NONE; |
1058 |
|
int sm = UNDAMPED; |
1059 |
< |
double alphaVal; |
1060 |
< |
double dielectric; |
1059 |
> |
RealType alphaVal; |
1060 |
> |
RealType dielectric; |
1061 |
|
|
1062 |
|
errorOut = isError; |
1063 |
|
alphaVal = simParams_->getDampingAlpha(); |
1083 |
|
} else { |
1084 |
|
// throw error |
1085 |
|
sprintf( painCave.errMsg, |
1086 |
< |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() ); |
1086 |
> |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
1087 |
> |
"\t(Input file specified %s .)\n" |
1088 |
> |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
1089 |
> |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
1090 |
> |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
1091 |
|
painCave.isFatal = 1; |
1092 |
|
simError(); |
1093 |
|
} |
1108 |
|
if (!simParams_->haveDampingAlpha()) { |
1109 |
|
//throw error |
1110 |
|
sprintf( painCave.errMsg, |
1111 |
< |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
1111 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
1112 |
> |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1113 |
|
painCave.isFatal = 0; |
1114 |
|
simError(); |
1115 |
|
} |
1116 |
|
} else { |
1117 |
|
// throw error |
1118 |
|
sprintf( painCave.errMsg, |
1119 |
< |
"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
1119 |
> |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
1120 |
> |
"\t(Input file specified %s .)\n" |
1121 |
> |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
1122 |
> |
"or \"damped\".\n", myScreen.c_str() ); |
1123 |
|
painCave.isFatal = 1; |
1124 |
|
simError(); |
1125 |
|
} |
1128 |
|
|
1129 |
|
// let's pass some summation method variables to fortran |
1130 |
|
setElectrostaticSummationMethod( &esm ); |
1131 |
+ |
setFortranElectrostaticMethod( &esm ); |
1132 |
|
setScreeningMethod( &sm ); |
1133 |
|
setDampingAlpha( &alphaVal ); |
1134 |
|
setReactionFieldDielectric( &dielectric ); |
1135 |
< |
initFortranFF( &esm, &errorOut ); |
1135 |
> |
initFortranFF( &errorOut ); |
1136 |
|
} |
1137 |
|
|
1138 |
|
void SimInfo::setupSwitchingFunction() { |
1217 |
|
Molecule* mol; |
1218 |
|
|
1219 |
|
Vector3d comVel(0.0); |
1220 |
< |
double totalMass = 0.0; |
1220 |
> |
RealType totalMass = 0.0; |
1221 |
|
|
1222 |
|
|
1223 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1224 |
< |
double mass = mol->getMass(); |
1224 |
> |
RealType mass = mol->getMass(); |
1225 |
|
totalMass += mass; |
1226 |
|
comVel += mass * mol->getComVel(); |
1227 |
|
} |
1228 |
|
|
1229 |
|
#ifdef IS_MPI |
1230 |
< |
double tmpMass = totalMass; |
1230 |
> |
RealType tmpMass = totalMass; |
1231 |
|
Vector3d tmpComVel(comVel); |
1232 |
< |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1233 |
< |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1232 |
> |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1233 |
> |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1234 |
|
#endif |
1235 |
|
|
1236 |
|
comVel /= totalMass; |
1243 |
|
Molecule* mol; |
1244 |
|
|
1245 |
|
Vector3d com(0.0); |
1246 |
< |
double totalMass = 0.0; |
1246 |
> |
RealType totalMass = 0.0; |
1247 |
|
|
1248 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1249 |
< |
double mass = mol->getMass(); |
1249 |
> |
RealType mass = mol->getMass(); |
1250 |
|
totalMass += mass; |
1251 |
|
com += mass * mol->getCom(); |
1252 |
|
} |
1253 |
|
|
1254 |
|
#ifdef IS_MPI |
1255 |
< |
double tmpMass = totalMass; |
1255 |
> |
RealType tmpMass = totalMass; |
1256 |
|
Vector3d tmpCom(com); |
1257 |
< |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1258 |
< |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1257 |
> |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1258 |
> |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1259 |
|
#endif |
1260 |
|
|
1261 |
|
com /= totalMass; |
1279 |
|
Molecule* mol; |
1280 |
|
|
1281 |
|
|
1282 |
< |
double totalMass = 0.0; |
1282 |
> |
RealType totalMass = 0.0; |
1283 |
|
|
1284 |
|
|
1285 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1286 |
< |
double mass = mol->getMass(); |
1286 |
> |
RealType mass = mol->getMass(); |
1287 |
|
totalMass += mass; |
1288 |
|
com += mass * mol->getCom(); |
1289 |
|
comVel += mass * mol->getComVel(); |
1290 |
|
} |
1291 |
|
|
1292 |
|
#ifdef IS_MPI |
1293 |
< |
double tmpMass = totalMass; |
1293 |
> |
RealType tmpMass = totalMass; |
1294 |
|
Vector3d tmpCom(com); |
1295 |
|
Vector3d tmpComVel(comVel); |
1296 |
< |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1297 |
< |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1298 |
< |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1296 |
> |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1297 |
> |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1298 |
> |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1299 |
|
#endif |
1300 |
|
|
1301 |
|
com /= totalMass; |
1314 |
|
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1315 |
|
|
1316 |
|
|
1317 |
< |
double xx = 0.0; |
1318 |
< |
double yy = 0.0; |
1319 |
< |
double zz = 0.0; |
1320 |
< |
double xy = 0.0; |
1321 |
< |
double xz = 0.0; |
1322 |
< |
double yz = 0.0; |
1317 |
> |
RealType xx = 0.0; |
1318 |
> |
RealType yy = 0.0; |
1319 |
> |
RealType zz = 0.0; |
1320 |
> |
RealType xy = 0.0; |
1321 |
> |
RealType xz = 0.0; |
1322 |
> |
RealType yz = 0.0; |
1323 |
|
Vector3d com(0.0); |
1324 |
|
Vector3d comVel(0.0); |
1325 |
|
|
1331 |
|
Vector3d thisq(0.0); |
1332 |
|
Vector3d thisv(0.0); |
1333 |
|
|
1334 |
< |
double thisMass = 0.0; |
1334 |
> |
RealType thisMass = 0.0; |
1335 |
|
|
1336 |
|
|
1337 |
|
|
1369 |
|
#ifdef IS_MPI |
1370 |
|
Mat3x3d tmpI(inertiaTensor); |
1371 |
|
Vector3d tmpAngMom; |
1372 |
< |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1373 |
< |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1372 |
> |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1373 |
> |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1374 |
|
#endif |
1375 |
|
|
1376 |
|
return; |
1391 |
|
Vector3d thisr(0.0); |
1392 |
|
Vector3d thisp(0.0); |
1393 |
|
|
1394 |
< |
double thisMass; |
1394 |
> |
RealType thisMass; |
1395 |
|
|
1396 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1397 |
|
thisMass = mol->getMass(); |
1404 |
|
|
1405 |
|
#ifdef IS_MPI |
1406 |
|
Vector3d tmpAngMom; |
1407 |
< |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1407 |
> |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1408 |
|
#endif |
1409 |
|
|
1410 |
|
return angularMomentum; |