# | Line 59 | Line 59 | |
---|---|---|
59 | #include "utils/simError.h" | |
60 | #include "selection/SelectionManager.hpp" | |
61 | #include "io/ForceFieldOptions.hpp" | |
62 | < | #include "UseTheForce/ForceField.hpp" |
62 | > | #include "brains/ForceField.hpp" |
63 | #include "nonbonded/SwitchingFunction.hpp" | |
64 | #ifdef IS_MPI | |
65 | #include <mpi.h> | |
# | Line 72 | Line 72 | namespace OpenMD { | |
72 | forceField_(ff), simParams_(simParams), | |
73 | ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), | |
74 | nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), | |
75 | < | nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
75 | > | nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0), |
76 | nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), | |
77 | nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), | |
78 | < | nConstraints_(0), sman_(NULL), topologyDone_(false), |
78 | > | nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false), |
79 | calcBoxDipole_(false), useAtomicVirial_(true) { | |
80 | ||
81 | MoleculeStamp* molStamp; | |
# | Line 225 | Line 225 | namespace OpenMD { | |
225 | ||
226 | ||
227 | void SimInfo::calcNdf() { | |
228 | < | int ndf_local; |
228 | > | int ndf_local, nfq_local; |
229 | MoleculeIterator i; | |
230 | vector<StuntDouble*>::iterator j; | |
231 | + | vector<Atom*>::iterator k; |
232 | + | |
233 | Molecule* mol; | |
234 | < | StuntDouble* integrableObject; |
234 | > | StuntDouble* sd; |
235 | > | Atom* atom; |
236 | ||
237 | ndf_local = 0; | |
238 | + | nfq_local = 0; |
239 | ||
240 | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { | |
237 | – | for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
238 | – | integrableObject = mol->nextIntegrableObject(j)) { |
241 | ||
242 | + | for (sd = mol->beginIntegrableObject(j); sd != NULL; |
243 | + | sd = mol->nextIntegrableObject(j)) { |
244 | + | |
245 | ndf_local += 3; | |
246 | ||
247 | < | if (integrableObject->isDirectional()) { |
248 | < | if (integrableObject->isLinear()) { |
247 | > | if (sd->isDirectional()) { |
248 | > | if (sd->isLinear()) { |
249 | ndf_local += 2; | |
250 | } else { | |
251 | ndf_local += 3; | |
252 | } | |
253 | } | |
249 | – | |
254 | } | |
255 | + | |
256 | + | for (atom = mol->beginFluctuatingCharge(k); atom != NULL; |
257 | + | atom = mol->nextFluctuatingCharge(k)) { |
258 | + | if (atom->isFluctuatingCharge()) { |
259 | + | nfq_local++; |
260 | + | } |
261 | + | } |
262 | } | |
263 | ||
264 | + | ndfLocal_ = ndf_local; |
265 | + | |
266 | // n_constraints is local, so subtract them on each processor | |
267 | ndf_local -= nConstraints_; | |
268 | ||
269 | #ifdef IS_MPI | |
270 | MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
271 | + | MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
272 | #else | |
273 | ndf_ = ndf_local; | |
274 | + | nGlobalFluctuatingCharges_ = nfq_local; |
275 | #endif | |
276 | ||
277 | // nZconstraints_ is global, as are the 3 COM translations for the | |
# | Line 299 | Line 314 | namespace OpenMD { | |
314 | MoleculeIterator i; | |
315 | vector<StuntDouble*>::iterator j; | |
316 | Molecule* mol; | |
317 | < | StuntDouble* integrableObject; |
317 | > | StuntDouble* sd; |
318 | ||
319 | // Raw degrees of freedom that we have to set | |
320 | ndfRaw_local = 0; | |
321 | ||
322 | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { | |
308 | – | for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
309 | – | integrableObject = mol->nextIntegrableObject(j)) { |
323 | ||
324 | + | for (sd = mol->beginIntegrableObject(j); sd != NULL; |
325 | + | sd = mol->nextIntegrableObject(j)) { |
326 | + | |
327 | ndfRaw_local += 3; | |
328 | ||
329 | < | if (integrableObject->isDirectional()) { |
330 | < | if (integrableObject->isLinear()) { |
329 | > | if (sd->isDirectional()) { |
330 | > | if (sd->isLinear()) { |
331 | ndfRaw_local += 2; | |
332 | } else { | |
333 | ndfRaw_local += 3; | |
# | Line 371 | Line 387 | namespace OpenMD { | |
387 | Molecule::RigidBodyIterator rbIter; | |
388 | RigidBody* rb; | |
389 | Molecule::IntegrableObjectIterator ii; | |
390 | < | StuntDouble* integrableObject; |
390 | > | StuntDouble* sd; |
391 | ||
392 | < | for (integrableObject = mol->beginIntegrableObject(ii); |
393 | < | integrableObject != NULL; |
378 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
392 | > | for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
393 | > | sd = mol->nextIntegrableObject(ii)) { |
394 | ||
395 | < | if (integrableObject->isRigidBody()) { |
396 | < | rb = static_cast<RigidBody*>(integrableObject); |
395 | > | if (sd->isRigidBody()) { |
396 | > | rb = static_cast<RigidBody*>(sd); |
397 | vector<Atom*> atoms = rb->getAtoms(); | |
398 | set<int> rigidAtoms; | |
399 | for (int i = 0; i < static_cast<int>(atoms.size()); ++i) { | |
# | Line 389 | Line 404 | namespace OpenMD { | |
404 | } | |
405 | } else { | |
406 | set<int> oneAtomSet; | |
407 | < | oneAtomSet.insert(integrableObject->getGlobalIndex()); |
408 | < | atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
407 | > | oneAtomSet.insert(sd->getGlobalIndex()); |
408 | > | atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
409 | } | |
410 | } | |
411 | ||
# | Line 524 | Line 539 | namespace OpenMD { | |
539 | Molecule::RigidBodyIterator rbIter; | |
540 | RigidBody* rb; | |
541 | Molecule::IntegrableObjectIterator ii; | |
542 | < | StuntDouble* integrableObject; |
542 | > | StuntDouble* sd; |
543 | ||
544 | < | for (integrableObject = mol->beginIntegrableObject(ii); |
545 | < | integrableObject != NULL; |
531 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
544 | > | for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
545 | > | sd = mol->nextIntegrableObject(ii)) { |
546 | ||
547 | < | if (integrableObject->isRigidBody()) { |
548 | < | rb = static_cast<RigidBody*>(integrableObject); |
547 | > | if (sd->isRigidBody()) { |
548 | > | rb = static_cast<RigidBody*>(sd); |
549 | vector<Atom*> atoms = rb->getAtoms(); | |
550 | set<int> rigidAtoms; | |
551 | for (int i = 0; i < static_cast<int>(atoms.size()); ++i) { | |
# | Line 542 | Line 556 | namespace OpenMD { | |
556 | } | |
557 | } else { | |
558 | set<int> oneAtomSet; | |
559 | < | oneAtomSet.insert(integrableObject->getGlobalIndex()); |
560 | < | atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
559 | > | oneAtomSet.insert(sd->getGlobalIndex()); |
560 | > | atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
561 | } | |
562 | } | |
563 | ||
# | Line 777 | Line 791 | namespace OpenMD { | |
791 | set<AtomType*>::iterator i; | |
792 | set<AtomType*> atomTypes; | |
793 | atomTypes = getSimulatedAtomTypes(); | |
794 | < | int usesElectrostatic = 0; |
795 | < | int usesMetallic = 0; |
796 | < | int usesDirectional = 0; |
794 | > | bool usesElectrostatic = false; |
795 | > | bool usesMetallic = false; |
796 | > | bool usesDirectional = false; |
797 | > | bool usesFluctuatingCharges = false; |
798 | //loop over all of the atom types | |
799 | for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { | |
800 | usesElectrostatic |= (*i)->isElectrostatic(); | |
801 | usesMetallic |= (*i)->isMetal(); | |
802 | usesDirectional |= (*i)->isDirectional(); | |
803 | + | usesFluctuatingCharges |= (*i)->isFluctuatingCharge(); |
804 | } | |
805 | < | |
806 | < | #ifdef IS_MPI |
807 | < | int temp; |
805 | > | |
806 | > | #ifdef IS_MPI |
807 | > | bool temp; |
808 | temp = usesDirectional; | |
809 | < | MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
810 | < | |
809 | > | MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL, |
810 | > | MPI::LOR); |
811 | > | |
812 | temp = usesMetallic; | |
813 | < | MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
813 | > | MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL, |
814 | > | MPI::LOR); |
815 | ||
816 | temp = usesElectrostatic; | |
817 | < | MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
817 | > | MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL, |
818 | > | MPI::LOR); |
819 | > | |
820 | > | temp = usesFluctuatingCharges; |
821 | > | MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL, |
822 | > | MPI::LOR); |
823 | #else | |
824 | ||
825 | usesDirectionalAtoms_ = usesDirectional; | |
826 | usesMetallicAtoms_ = usesMetallic; | |
827 | usesElectrostaticAtoms_ = usesElectrostatic; | |
828 | + | usesFluctuatingCharges_ = usesFluctuatingCharges; |
829 | ||
830 | #endif | |
831 | ||
# | Line 970 | Line 994 | namespace OpenMD { | |
994 | ||
995 | } | |
996 | ||
973 | – | Vector3d SimInfo::getComVel(){ |
974 | – | SimInfo::MoleculeIterator i; |
975 | – | Molecule* mol; |
997 | ||
977 | – | Vector3d comVel(0.0); |
978 | – | RealType totalMass = 0.0; |
979 | – | |
980 | – | |
981 | – | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
982 | – | RealType mass = mol->getMass(); |
983 | – | totalMass += mass; |
984 | – | comVel += mass * mol->getComVel(); |
985 | – | } |
986 | – | |
987 | – | #ifdef IS_MPI |
988 | – | RealType tmpMass = totalMass; |
989 | – | Vector3d tmpComVel(comVel); |
990 | – | MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
991 | – | MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
992 | – | #endif |
993 | – | |
994 | – | comVel /= totalMass; |
995 | – | |
996 | – | return comVel; |
997 | – | } |
998 | – | |
999 | – | Vector3d SimInfo::getCom(){ |
1000 | – | SimInfo::MoleculeIterator i; |
1001 | – | Molecule* mol; |
1002 | – | |
1003 | – | Vector3d com(0.0); |
1004 | – | RealType totalMass = 0.0; |
1005 | – | |
1006 | – | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1007 | – | RealType mass = mol->getMass(); |
1008 | – | totalMass += mass; |
1009 | – | com += mass * mol->getCom(); |
1010 | – | } |
1011 | – | |
1012 | – | #ifdef IS_MPI |
1013 | – | RealType tmpMass = totalMass; |
1014 | – | Vector3d tmpCom(com); |
1015 | – | MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1016 | – | MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1017 | – | #endif |
1018 | – | |
1019 | – | com /= totalMass; |
1020 | – | |
1021 | – | return com; |
1022 | – | |
1023 | – | } |
1024 | – | |
998 | ostream& operator <<(ostream& o, SimInfo& info) { | |
999 | ||
1000 | return o; | |
1001 | } | |
1002 | ||
1003 | < | |
1031 | < | /* |
1032 | < | Returns center of mass and center of mass velocity in one function call. |
1033 | < | */ |
1034 | < | |
1035 | < | void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1036 | < | SimInfo::MoleculeIterator i; |
1037 | < | Molecule* mol; |
1038 | < | |
1039 | < | |
1040 | < | RealType totalMass = 0.0; |
1041 | < | |
1042 | < | |
1043 | < | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1044 | < | RealType mass = mol->getMass(); |
1045 | < | totalMass += mass; |
1046 | < | com += mass * mol->getCom(); |
1047 | < | comVel += mass * mol->getComVel(); |
1048 | < | } |
1049 | < | |
1050 | < | #ifdef IS_MPI |
1051 | < | RealType tmpMass = totalMass; |
1052 | < | Vector3d tmpCom(com); |
1053 | < | Vector3d tmpComVel(comVel); |
1054 | < | MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1055 | < | MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1056 | < | MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1057 | < | #endif |
1058 | < | |
1059 | < | com /= totalMass; |
1060 | < | comVel /= totalMass; |
1061 | < | } |
1062 | < | |
1063 | < | /* |
1064 | < | Return intertia tensor for entire system and angular momentum Vector. |
1065 | < | |
1066 | < | |
1067 | < | [ Ixx -Ixy -Ixz ] |
1068 | < | J =| -Iyx Iyy -Iyz | |
1069 | < | [ -Izx -Iyz Izz ] |
1070 | < | */ |
1071 | < | |
1072 | < | void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1073 | < | |
1074 | < | |
1075 | < | RealType xx = 0.0; |
1076 | < | RealType yy = 0.0; |
1077 | < | RealType zz = 0.0; |
1078 | < | RealType xy = 0.0; |
1079 | < | RealType xz = 0.0; |
1080 | < | RealType yz = 0.0; |
1081 | < | Vector3d com(0.0); |
1082 | < | Vector3d comVel(0.0); |
1083 | < | |
1084 | < | getComAll(com, comVel); |
1085 | < | |
1086 | < | SimInfo::MoleculeIterator i; |
1087 | < | Molecule* mol; |
1088 | < | |
1089 | < | Vector3d thisq(0.0); |
1090 | < | Vector3d thisv(0.0); |
1091 | < | |
1092 | < | RealType thisMass = 0.0; |
1093 | < | |
1094 | < | |
1095 | < | |
1096 | < | |
1097 | < | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1098 | < | |
1099 | < | thisq = mol->getCom()-com; |
1100 | < | thisv = mol->getComVel()-comVel; |
1101 | < | thisMass = mol->getMass(); |
1102 | < | // Compute moment of intertia coefficients. |
1103 | < | xx += thisq[0]*thisq[0]*thisMass; |
1104 | < | yy += thisq[1]*thisq[1]*thisMass; |
1105 | < | zz += thisq[2]*thisq[2]*thisMass; |
1106 | < | |
1107 | < | // compute products of intertia |
1108 | < | xy += thisq[0]*thisq[1]*thisMass; |
1109 | < | xz += thisq[0]*thisq[2]*thisMass; |
1110 | < | yz += thisq[1]*thisq[2]*thisMass; |
1111 | < | |
1112 | < | angularMomentum += cross( thisq, thisv ) * thisMass; |
1113 | < | |
1114 | < | } |
1115 | < | |
1116 | < | |
1117 | < | inertiaTensor(0,0) = yy + zz; |
1118 | < | inertiaTensor(0,1) = -xy; |
1119 | < | inertiaTensor(0,2) = -xz; |
1120 | < | inertiaTensor(1,0) = -xy; |
1121 | < | inertiaTensor(1,1) = xx + zz; |
1122 | < | inertiaTensor(1,2) = -yz; |
1123 | < | inertiaTensor(2,0) = -xz; |
1124 | < | inertiaTensor(2,1) = -yz; |
1125 | < | inertiaTensor(2,2) = xx + yy; |
1126 | < | |
1127 | < | #ifdef IS_MPI |
1128 | < | Mat3x3d tmpI(inertiaTensor); |
1129 | < | Vector3d tmpAngMom; |
1130 | < | MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1131 | < | MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1132 | < | #endif |
1133 | < | |
1134 | < | return; |
1135 | < | } |
1136 | < | |
1137 | < | //Returns the angular momentum of the system |
1138 | < | Vector3d SimInfo::getAngularMomentum(){ |
1139 | < | |
1140 | < | Vector3d com(0.0); |
1141 | < | Vector3d comVel(0.0); |
1142 | < | Vector3d angularMomentum(0.0); |
1143 | < | |
1144 | < | getComAll(com,comVel); |
1145 | < | |
1146 | < | SimInfo::MoleculeIterator i; |
1147 | < | Molecule* mol; |
1148 | < | |
1149 | < | Vector3d thisr(0.0); |
1150 | < | Vector3d thisp(0.0); |
1151 | < | |
1152 | < | RealType thisMass; |
1153 | < | |
1154 | < | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1155 | < | thisMass = mol->getMass(); |
1156 | < | thisr = mol->getCom()-com; |
1157 | < | thisp = (mol->getComVel()-comVel)*thisMass; |
1158 | < | |
1159 | < | angularMomentum += cross( thisr, thisp ); |
1160 | < | |
1161 | < | } |
1162 | < | |
1163 | < | #ifdef IS_MPI |
1164 | < | Vector3d tmpAngMom; |
1165 | < | MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); |
1166 | < | #endif |
1167 | < | |
1168 | < | return angularMomentum; |
1169 | < | } |
1170 | < | |
1003 | > | |
1004 | StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { | |
1005 | return IOIndexToIntegrableObject.at(index); | |
1006 | } | |
# | Line 1175 | Line 1008 | namespace OpenMD { | |
1008 | void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) { | |
1009 | IOIndexToIntegrableObject= v; | |
1010 | } | |
1178 | – | |
1179 | – | /* Returns the Volume of the simulation based on a ellipsoid with semi-axes |
1180 | – | based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
1181 | – | where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to |
1182 | – | V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
1183 | – | */ |
1184 | – | void SimInfo::getGyrationalVolume(RealType &volume){ |
1185 | – | Mat3x3d intTensor; |
1186 | – | RealType det; |
1187 | – | Vector3d dummyAngMom; |
1188 | – | RealType sysconstants; |
1189 | – | RealType geomCnst; |
1190 | – | |
1191 | – | geomCnst = 3.0/2.0; |
1192 | – | /* Get the inertial tensor and angular momentum for free*/ |
1193 | – | getInertiaTensor(intTensor,dummyAngMom); |
1194 | – | |
1195 | – | det = intTensor.determinant(); |
1196 | – | sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
1197 | – | volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
1198 | – | return; |
1199 | – | } |
1200 | – | |
1201 | – | void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ |
1202 | – | Mat3x3d intTensor; |
1203 | – | Vector3d dummyAngMom; |
1204 | – | RealType sysconstants; |
1205 | – | RealType geomCnst; |
1206 | – | |
1207 | – | geomCnst = 3.0/2.0; |
1208 | – | /* Get the inertial tensor and angular momentum for free*/ |
1209 | – | getInertiaTensor(intTensor,dummyAngMom); |
1210 | – | |
1211 | – | detI = intTensor.determinant(); |
1212 | – | sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
1213 | – | volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
1214 | – | return; |
1215 | – | } |
1011 | /* | |
1012 | void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) { | |
1013 | assert( v.size() == nAtoms_ + nRigidBodies_); |
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