# | Line 32 | Line 32 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
---|---|---|
32 | if(!data){ | |
33 | sprintf( painCave.errMsg, | |
34 | "ZConstraint Warning: User does not set force substraction policy, " | |
35 | < | "average force substraction policy is used\n"); |
35 | > | "PolicyByMass is used\n"); |
36 | painCave.isFatal = 0; | |
37 | simError(); | |
38 | ||
39 | < | forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
39 | > | forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
40 | } | |
41 | else{ | |
42 | policy = dynamic_cast<StringData*>(data); | |
# | Line 44 | Line 44 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
44 | if(!policy){ | |
45 | sprintf( painCave.errMsg, | |
46 | "ZConstraint Error: Convertion from GenericData to StringData failure, " | |
47 | < | "average force substraction policy is used\n"); |
47 | > | "PolicyByMass is used\n"); |
48 | painCave.isFatal = 0; | |
49 | simError(); | |
50 | ||
51 | < | forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
51 | > | forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
52 | } | |
53 | else{ | |
54 | if(policy->getData() == "BYNUMBER") | |
# | Line 58 | Line 58 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
58 | else{ | |
59 | sprintf( painCave.errMsg, | |
60 | "ZConstraint Warning: unknown force substraction policy, " | |
61 | < | "average force substraction policy is used\n"); |
61 | > | "PolicyByMass is used\n"); |
62 | painCave.isFatal = 0; | |
63 | simError(); | |
64 | + | forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
65 | } | |
66 | } | |
67 | } | |
# | Line 249 | Line 250 | template<typename T> ZConstraint<T>::ZConstraint(SimIn | |
250 | (*parameters)[i].zPos = COM[whichDirection]; | |
251 | ||
252 | sprintf( painCave.errMsg, | |
253 | < | "ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
253 | > | "ZConstraint warning: Does not specify zpos for z-constraint molecule " |
254 | "initial z coornidate will be used \n"); | |
255 | painCave.isFatal = 0; | |
256 | simError(); | |
# | Line 578 | Line 579 | template<typename T> void ZConstraint<T>::calcForce(in | |
579 | //do zconstraint force; | |
580 | if (haveFixedZMols()) | |
581 | this->doZconstraintForce(); | |
582 | < | |
582 | > | |
583 | //use harmonical poteintial to move the molecules to the specified positions | |
584 | if (haveMovingZMols()) | |
585 | this->doHarmonic(); | |
# | Line 612 | Line 613 | template<typename T> void ZConstraint<T>::calcForce(in | |
613 | #ifdef IS_MPI | |
614 | } | |
615 | #endif | |
615 | – | |
616 | } | |
617 | ||
618 | ||
# | Line 802 | Line 802 | template<typename T> void ZConstraint<T>::doZconstrain | |
802 | double COM[3]; | |
803 | double force[3]; | |
804 | ||
805 | – | |
806 | – | |
805 | //constrain the molecules which do not reach the specified positions | |
806 | ||
807 | //Zero Out the force of z-contrained molecules | |
# | Line 825 | Line 823 | template<typename T> void ZConstraint<T>::doZconstrain | |
823 | } | |
824 | totalFZ_local += fz[i]; | |
825 | ||
826 | < | // cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
827 | < | // <<"\tcurrent zpos: " << COM[whichDirection] |
828 | < | // << "\tcurrent fz: " <<fz[i] << endl; |
826 | > | //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
827 | > | // <<"\tcurrent zpos: " << COM[whichDirection] |
828 | > | // << "\tcurrent fz: " <<fz[i] << endl; |
829 | ||
830 | + | |
831 | } | |
832 | ||
833 | } | |
# | Line 854 | Line 853 | template<typename T> void ZConstraint<T>::doZconstrain | |
853 | zconsAtoms = zconsMols[i]->getMyAtoms(); | |
854 | ||
855 | for(int j =0; j < nAtomOfCurZConsMol; j++) { | |
856 | < | force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
857 | < | //force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
856 | > | //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
857 | > | force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
858 | zconsAtoms[j]->addFrc(force); | |
859 | } | |
860 | ||
# | Line 865 | Line 864 | template<typename T> void ZConstraint<T>::doZconstrain | |
864 | ||
865 | // cout << "after zero out z-constraint force on fixed z-constraint molecuels " | |
866 | // << "total force is " << calcTotalForce() << endl; | |
868 | – | |
869 | – | //calculate the number of atoms of moving z-constrained molecules |
870 | – | int nMovingZAtoms_local; |
871 | – | int nMovingZAtoms; |
872 | – | |
873 | – | nMovingZAtoms_local = 0; |
874 | – | for(int i = 0; i < zconsMols.size(); i++) |
875 | – | if(states[i] == zcsMoving) |
876 | – | nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
877 | – | |
878 | – | #ifdef IS_MPI |
879 | – | MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, |
880 | – | MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
881 | – | #else |
882 | – | nMovingZAtoms = nMovingZAtoms_local; |
883 | – | #endif |
867 | ||
868 | force[0]= 0; | |
869 | force[1]= 0; | |
# | Line 892 | Line 875 | template<typename T> void ZConstraint<T>::doZconstrain | |
875 | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); | |
876 | ||
877 | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ | |
878 | < | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
879 | < | //force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
878 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
879 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
880 | unconsAtoms[j]->addFrc(force); | |
881 | } | |
882 | ||
# | Line 906 | Line 889 | template<typename T> void ZConstraint<T>::doZconstrain | |
889 | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); | |
890 | ||
891 | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ | |
892 | < | force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
893 | < | //force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
892 | > | //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
893 | > | force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
894 | movingZAtoms[j]->addFrc(force); | |
895 | } | |
896 | } | |
# | Line 944 | Line 927 | template<typename T> void ZConstraint<T>::doHarmonic() | |
927 | zconsMols[i]->getCOM(COM); | |
928 | // cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] | |
929 | // << "\tcurrent zpos: " << COM[whichDirection] << endl; | |
930 | + | |
931 | + | diff = COM[whichDirection] -zPos[i]; |
932 | ||
948 | – | diff = COM[whichDirection] -zPos[i]; |
949 | – | |
933 | harmonicU = 0.5 * kz[i] * diff * diff; | |
934 | < | info->lrPot += harmonicU; |
934 | > | info->lrPot += harmonicU; |
935 | ||
936 | harmonicF = - kz[i] * diff; | |
937 | totalFZ_local += harmonicF; | |
# | Line 958 | Line 941 | template<typename T> void ZConstraint<T>::doHarmonic() | |
941 | Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); | |
942 | ||
943 | for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ | |
944 | < | force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
945 | < | //force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
944 | > | //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
945 | > | force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
946 | movingZAtoms[j]->addFrc(force); | |
947 | } | |
948 | } | |
# | Line 982 | Line 965 | template<typename T> void ZConstraint<T>::doHarmonic() | |
965 | Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); | |
966 | ||
967 | for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ | |
968 | < | force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
969 | < | //force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
968 | > | //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
969 | > | force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
970 | unconsAtoms[j]->addFrc(force); | |
971 | } | |
972 | } | |
# | Line 1023 | Line 1006 | template<typename T> bool ZConstraint<T>::checkZConsSt | |
1006 | #else | |
1007 | MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
1008 | #endif | |
1009 | < | |
1009 | > | |
1010 | return (changed > 0); | |
1011 | + | |
1012 | } | |
1013 | ||
1014 | template<typename T> bool ZConstraint<T>::haveFixedZMols(){ | |
# | Line 1046 | Line 1030 | template<typename T> bool ZConstraint<T>::haveFixedZMo | |
1030 | MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
1031 | #endif | |
1032 | ||
1033 | < | return havingFixed > 0 ? true : false; |
1033 | > | return (havingFixed > 0); |
1034 | } | |
1035 | ||
1036 | ||
# | Line 1072 | Line 1056 | template<typename T> bool ZConstraint<T>::haveMovingZM | |
1056 | MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); | |
1057 | #endif | |
1058 | ||
1059 | < | return havingMoving > 0 ? true : false; |
1059 | > | return (havingMoving > 0); |
1060 | ||
1061 | } | |
1062 |
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