# | Line 1 | Line 1 | |
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1 | #include "Integrator.hpp" | |
2 | #include "simError.h" | |
3 | < | #include <cmath> |
3 | > | #include <math.h> |
4 | template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) | |
5 | < | : T(theInfo, the_ff), fz(NULL), curZPos(NULL), fzOut(NULL), |
6 | < | indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
5 | > | : T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL), |
6 | > | fzOut(NULL), curZconsTime(0), forcePolicy(NULL) |
7 | { | |
8 | ||
9 | //get properties from SimInfo | |
# | Line 213 | Line 213 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
213 | ||
214 | //if user does not specify the zpos for the zconstraint molecule | |
215 | //its initial z coordinate will be used as default | |
216 | < | for(int i = 0; i < parameters->size(); i++){ |
216 | > | for(int i = 0; i < (int)(parameters->size()); i++){ |
217 | ||
218 | if(!(*parameters)[i].havingZPos){ | |
219 | #ifndef IS_MPI | |
# | Line 227 | Line 227 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
227 | //query which processor current zconstraint molecule belongs to | |
228 | int *MolToProcMap; | |
229 | int whichNode; | |
230 | < | double initZPos; |
230 | > | |
231 | MolToProcMap = mpiSim->getMolToProcMap(); | |
232 | whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; | |
233 | ||
# | Line 244 | Line 244 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
244 | ||
245 | } | |
246 | ||
247 | < | MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
247 | > | MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, MPI_COMM_WORLD); |
248 | #endif | |
249 | ||
250 | (*parameters)[i].zPos = COM[whichDirection]; | |
# | Line 304 | Line 304 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
304 | } | |
305 | ||
306 | //determine the states of z-constraint molecules | |
307 | < | for(int i = 0; i < zconsMols.size(); i++){ |
307 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
308 | indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); | |
309 | ||
310 | zconsMols[i]->getCOM(COM); | |
# | Line 320 | Line 320 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
320 | double totalMassOfUncons_local; | |
321 | totalMassOfUncons_local = 0; | |
322 | ||
323 | < | for(int i = 0; i < unconsMols.size(); i++) |
323 | > | for(int i = 0; i < (int)(unconsMols.size()); i++) |
324 | totalMassOfUncons_local += unconsMols[i]->getTotalMass(); | |
325 | ||
326 | #ifndef IS_MPI | |
# | Line 333 | Line 333 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
333 | //get total number of unconstrained atoms | |
334 | int nUnconsAtoms_local; | |
335 | nUnconsAtoms_local = 0; | |
336 | < | for(int i = 0; i < unconsMols.size(); i++) |
336 | > | for(int i = 0; i < (int)(unconsMols.size()); i++) |
337 | nUnconsAtoms_local += unconsMols[i]->getNAtoms(); | |
338 | ||
339 | #ifndef IS_MPI | |
# | Line 408 | Line 408 | template<typename T> void ZConstraint<T>::update() | |
408 | } | |
409 | ||
410 | //determine the states of z-constraint molecules | |
411 | < | for(int i = 0; i < zconsMols.size(); i++){ |
411 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
412 | zconsMols[i]->getCOM(COM); | |
413 | if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) | |
414 | states.push_back(zcsFixed); | |
# | Line 440 | Line 440 | template<typename T> void ZConstraint<T>::update() | |
440 | simError(); | |
441 | } | |
442 | ||
443 | < | for(int i = 0; i < zconsMols.size(); i++){ |
443 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
444 | indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); | |
445 | } | |
446 | ||
# | Line 559 | Line 559 | template<typename T> void ZConstraint<T>::calcForce(in | |
559 | ||
560 | //write out forces and current positions of z-constraint molecules | |
561 | if(info->getTime() >= curZconsTime){ | |
562 | < | for(int i = 0; i < zconsMols.size(); i++){ |
562 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
563 | zconsMols[i]->getCOM(COM); | |
564 | curZPos[i] = COM[whichDirection]; | |
565 | ||
# | Line 654 | Line 654 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
654 | ||
655 | //zero out the velocities of center of mass of fixed z-constrained molecules | |
656 | ||
657 | < | for(int i = 0; i < zconsMols.size(); i++){ |
657 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
658 | ||
659 | if (states[i] == zcsFixed){ | |
660 | ||
# | Line 695 | Line 695 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
695 | MVzOfMovingMols_local = 0; | |
696 | totalMassOfMovingZMols_local = 0; | |
697 | ||
698 | < | for(int i =0; i < unconsMols.size(); i++){ |
698 | > | for(int i =0; i < (int)(unconsMols.size()); i++){ |
699 | unconsMols[i]->getCOMvel(COMvel); | |
700 | MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; | |
701 | } | |
702 | ||
703 | < | for(int i = 0; i < zconsMols.size(); i++){ |
703 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
704 | if (states[i] == zcsMoving){ | |
705 | zconsMols[i]->getCOMvel(COMvel); | |
706 | MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; | |
# | Line 722 | Line 722 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
722 | ||
723 | //modify the velocites of unconstrained molecules | |
724 | Atom** unconsAtoms; | |
725 | < | for(int i = 0; i < unconsMols.size(); i++){ |
725 | > | for(int i = 0; i < (int)(unconsMols.size()); i++){ |
726 | ||
727 | unconsAtoms = unconsMols[i]->getMyAtoms(); | |
728 | for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ | |
# | Line 735 | Line 735 | template<typename T> void ZConstraint<T>::zeroOutVel() | |
735 | ||
736 | //modify the velocities of moving z-constrained molecuels | |
737 | Atom** movingZAtoms; | |
738 | < | for(int i = 0; i < zconsMols.size(); i++){ |
738 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
739 | ||
740 | if (states[i] ==zcsMoving){ | |
741 | ||
# | Line 771 | Line 771 | template<typename T> void ZConstraint<T>::doZconstrain | |
771 | Atom** zconsAtoms; | |
772 | double totalFZ; | |
773 | double totalFZ_local; | |
774 | – | double COMvel[3]; |
774 | double COM[3]; | |
775 | double force[3]; | |
776 | ||
# | Line 785 | Line 784 | template<typename T> void ZConstraint<T>::doZconstrain | |
784 | //cout << "before zero out z-constraint force on fixed z-constraint molecuels " | |
785 | // << "total force is " << calcTotalForce() << endl; | |
786 | ||
787 | < | for(int i = 0; i < zconsMols.size(); i++){ |
787 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
788 | ||
789 | if (states[i] == zcsFixed){ | |
790 | ||
# | Line 821 | Line 820 | template<typename T> void ZConstraint<T>::doZconstrain | |
820 | force[1]= 0; | |
821 | force[2]= 0; | |
822 | ||
823 | < | for(int i = 0; i < zconsMols.size(); i++){ |
823 | > | for(int i = 0; i < (int)(zconsMols.size()); i++){ |
824 | ||
825 | if (states[i] == zcsFixed){ | |
826 | ||
# | Line 847 | Line 846 | template<typename T> void ZConstraint<T>::doZconstrain | |
846 | force[2]= 0; | |
847 | ||
848 | //modify the forces of unconstrained molecules | |
849 | < | for(int i = 0; i < unconsMols.size(); i++){ |
849 | > | for(int i = 0; i < (int)(unconsMols.size()); i++){ |
850 | ||
851 | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); | |
852 | ||
# | Line 860 | Line 859 | template<typename T> void ZConstraint<T>::doZconstrain | |
859 | } | |
860 | ||
861 | //modify the forces of moving z-constrained molecules | |
862 | < | for(int i = 0; i < zconsMols.size(); i++) { |
862 | > | for(int i = 0; i < (int)(zconsMols.size()); i++) { |
863 | if (states[i] == zcsMoving){ | |
864 | ||
865 | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); | |
# | Line 897 | Line 896 | template<typename T> void ZConstraint<T>::doHarmonic() | |
896 | ||
897 | totalFZ_local = 0; | |
898 | ||
899 | < | for(int i = 0; i < zconsMols.size(); i++) { |
899 | > | for(int i = 0; i < (int)(zconsMols.size()); i++) { |
900 | ||
901 | if (states[i] == zcsMoving){ | |
902 | zconsMols[i]->getCOM(COM); | |
# | Line 939 | Line 938 | template<typename T> void ZConstraint<T>::doHarmonic() | |
938 | force[2]= 0; | |
939 | ||
940 | //modify the forces of unconstrained molecules | |
941 | < | for(int i = 0; i < unconsMols.size(); i++){ |
941 | > | for(int i = 0; i < (int)(unconsMols.size()); i++){ |
942 | ||
943 | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); | |
944 | ||
# | Line 968 | Line 967 | template<typename T> bool ZConstraint<T>::checkZConsSt | |
967 | ||
968 | changed_local = 0; | |
969 | ||
970 | < | for(int i =0; i < zconsMols.size(); i++){ |
970 | > | for(int i =0; i < (int)(zconsMols.size()); i++){ |
971 | ||
972 | zconsMols[i]->getCOM(COM); | |
973 | diff = fabs(COM[whichDirection] - zPos[i]); | |
# | Line 1000 | Line 999 | template<typename T> bool ZConstraint<T>::haveFixedZMo | |
999 | ||
1000 | havingFixed_local = 0; | |
1001 | ||
1002 | < | for(int i = 0; i < zconsMols.size(); i++) |
1002 | > | for(int i = 0; i < (int)(zconsMols.size()); i++) |
1003 | if (states[i] == zcsFixed){ | |
1004 | havingFixed_local = 1; | |
1005 | break; | |
# | Line 1026 | Line 1025 | template<typename T> bool ZConstraint<T>::haveMovingZM | |
1025 | ||
1026 | havingMoving_local = 0; | |
1027 | ||
1028 | < | for(int i = 0; i < zconsMols.size(); i++) |
1028 | > | for(int i = 0; i < (int)(zconsMols.size()); i++) |
1029 | if (states[i] == zcsMoving){ | |
1030 | havingMoving_local = 1; | |
1031 | break; | |
# | Line 1108 | Line 1107 | template<typename T> double ZConstraint<T>::calcSysCOM | |
1107 | ||
1108 | massOfZCons_local = 0; | |
1109 | ||
1110 | < | for(int i = 0; i < massOfZConsMols.size(); i++){ |
1110 | > | for(int i = 0; i < (int)(massOfZConsMols.size()); i++){ |
1111 | massOfZCons_local += massOfZConsMols[i]; | |
1112 | } | |
1113 | #ifndef IS_MPI | |
# | Line 1159 | Line 1158 | template<typename T> void ZConstraint<T>::PolicyByNumb | |
1158 | int nMovingZAtoms; | |
1159 | ||
1160 | nMovingZAtoms_local = 0; | |
1161 | < | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1161 | > | for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1162 | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) | |
1163 | nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); | |
1164 | ||
# | Line 1197 | Line 1196 | template<typename T> void ZConstraint<T>::PolicyByMass | |
1196 | double massOfMovingZAtoms; | |
1197 | ||
1198 | massOfMovingZAtoms_local = 0; | |
1199 | < | for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1199 | > | for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1200 | if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) | |
1201 | massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); | |
1202 |
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