# | Line 54 | Line 54 | |
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54 | #include "primitives/Molecule.hpp" | |
55 | #include "UseTheForce/fCutoffPolicy.h" | |
56 | #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" | |
57 | + | #include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
58 | + | #include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
59 | #include "UseTheForce/doForces_interface.h" | |
60 | #include "UseTheForce/DarkSide/electrostatic_interface.h" | |
61 | #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" | |
# | Line 83 | Line 86 | namespace oopse { | |
86 | MoleculeStamp* molStamp; | |
87 | int nMolWithSameStamp; | |
88 | int nCutoffAtoms = 0; // number of atoms belong to cutoff groups | |
89 | < | int nGroups = 0; //total cutoff groups defined in meta-data file |
89 | > | int nGroups = 0; //total cutoff groups defined in meta-data file |
90 | CutoffGroupStamp* cgStamp; | |
91 | RigidBodyStamp* rbStamp; | |
92 | int nRigidAtoms = 0; | |
# | Line 108 | Line 111 | namespace oopse { | |
111 | } | |
112 | ||
113 | nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; | |
114 | + | |
115 | nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; | |
116 | ||
117 | //calculate atoms in rigid bodies | |
# | Line 124 | Line 128 | namespace oopse { | |
128 | ||
129 | } | |
130 | ||
131 | < | //every free atom (atom does not belong to cutoff groups) is a cutoff group |
132 | < | //therefore the total number of cutoff groups in the system is equal to |
133 | < | //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
134 | < | //file plus the number of cutoff groups defined in meta-data file |
131 | > | //every free atom (atom does not belong to cutoff groups) is a cutoff |
132 | > | //group therefore the total number of cutoff groups in the system is |
133 | > | //equal to the total number of atoms minus number of atoms belong to |
134 | > | //cutoff group defined in meta-data file plus the number of cutoff |
135 | > | //groups defined in meta-data file |
136 | nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; | |
137 | ||
138 | < | //every free atom (atom does not belong to rigid bodies) is an integrable object |
139 | < | //therefore the total number of integrable objects in the system is equal to |
140 | < | //the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
141 | < | //file plus the number of rigid bodies defined in meta-data file |
142 | < | nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
143 | < | |
138 | > | //every free atom (atom does not belong to rigid bodies) is an |
139 | > | //integrable object therefore the total number of integrable objects |
140 | > | //in the system is equal to the total number of atoms minus number of |
141 | > | //atoms belong to rigid body defined in meta-data file plus the number |
142 | > | //of rigid bodies defined in meta-data file |
143 | > | nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
144 | > | + nGlobalRigidBodies_; |
145 | > | |
146 | nGlobalMols_ = molStampIds_.size(); | |
147 | ||
148 | #ifdef IS_MPI | |
# | Line 467 | Line 474 | namespace oopse { | |
474 | int isError = 0; | |
475 | ||
476 | setupElectrostaticSummationMethod( isError ); | |
477 | + | setupSwitchingFunction(); |
478 | ||
479 | if(isError){ | |
480 | sprintf( painCave.errMsg, | |
# | Line 522 | Line 530 | namespace oopse { | |
530 | int useDirectionalAtom = 0; | |
531 | int useElectrostatics = 0; | |
532 | //usePBC and useRF are from simParams | |
533 | < | int usePBC = simParams_->getPBC(); |
533 | > | int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
534 | > | int useRF; |
535 | > | int useSF; |
536 | > | std::string myMethod; |
537 | > | |
538 | > | // set the useRF logical |
539 | > | useRF = 0; |
540 | > | useSF = 0; |
541 | > | |
542 | > | |
543 | > | if (simParams_->haveElectrostaticSummationMethod()) { |
544 | > | std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
545 | > | toUpper(myMethod); |
546 | > | if (myMethod == "REACTION_FIELD") { |
547 | > | useRF=1; |
548 | > | } else { |
549 | > | if (myMethod == "SHIFTED_FORCE") { |
550 | > | useSF = 1; |
551 | > | } |
552 | > | } |
553 | > | } |
554 | ||
555 | //loop over all of the atom types | |
556 | for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { | |
# | Line 585 | Line 613 | namespace oopse { | |
613 | temp = useFLARB; | |
614 | MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
615 | ||
616 | + | temp = useRF; |
617 | + | MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
618 | + | |
619 | + | temp = useSF; |
620 | + | MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
621 | + | |
622 | #endif | |
623 | ||
624 | fInfo_.SIM_uses_PBC = usePBC; | |
# | Line 599 | Line 633 | namespace oopse { | |
633 | fInfo_.SIM_uses_EAM = useEAM; | |
634 | fInfo_.SIM_uses_Shapes = useShape; | |
635 | fInfo_.SIM_uses_FLARB = useFLARB; | |
636 | + | fInfo_.SIM_uses_RF = useRF; |
637 | + | fInfo_.SIM_uses_SF = useSF; |
638 | ||
639 | < | if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
640 | < | |
639 | > | if( myMethod == "REACTION_FIELD") { |
640 | > | |
641 | if (simParams_->haveDielectric()) { | |
642 | fInfo_.dielect = simParams_->getDielectric(); | |
643 | } else { | |
# | Line 611 | Line 647 | namespace oopse { | |
647 | "\tsetting a dielectric constant!\n"); | |
648 | painCave.isFatal = 1; | |
649 | simError(); | |
650 | < | } |
615 | < | |
616 | < | } else { |
617 | < | fInfo_.dielect = 0.0; |
650 | > | } |
651 | } | |
652 | ||
653 | } | |
# | Line 650 | Line 683 | namespace oopse { | |
683 | ||
684 | totalMass = cg->getMass(); | |
685 | for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { | |
686 | < | mfact.push_back(atom->getMass()/totalMass); |
686 | > | // Check for massless groups - set mfact to 1 if true |
687 | > | if (totalMass != 0) |
688 | > | mfact.push_back(atom->getMass()/totalMass); |
689 | > | else |
690 | > | mfact.push_back( 1.0 ); |
691 | } | |
692 | ||
693 | } | |
# | Line 786 | Line 823 | namespace oopse { | |
823 | ||
824 | if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { | |
825 | ||
826 | < | if (!simParams_->haveRcut()){ |
826 | > | if (!simParams_->haveCutoffRadius()){ |
827 | sprintf(painCave.errMsg, | |
828 | "SimCreator Warning: No value was set for the cutoffRadius.\n" | |
829 | "\tOOPSE will use a default value of 15.0 angstroms" | |
# | Line 795 | Line 832 | namespace oopse { | |
832 | simError(); | |
833 | rcut = 15.0; | |
834 | } else{ | |
835 | < | rcut = simParams_->getRcut(); |
835 | > | rcut = simParams_->getCutoffRadius(); |
836 | } | |
837 | ||
838 | < | if (!simParams_->haveRsw()){ |
838 | > | if (!simParams_->haveSwitchingRadius()){ |
839 | sprintf(painCave.errMsg, | |
840 | "SimCreator Warning: No value was set for switchingRadius.\n" | |
841 | "\tOOPSE will use a default value of\n" | |
842 | < | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
842 | > | "\t0.85 * cutoffRadius for the switchingRadius\n"); |
843 | painCave.isFatal = 0; | |
844 | simError(); | |
845 | < | rsw = 0.95 * rcut; |
845 | > | rsw = 0.85 * rcut; |
846 | } else{ | |
847 | < | rsw = simParams_->getRsw(); |
847 | > | rsw = simParams_->getSwitchingRadius(); |
848 | } | |
849 | ||
850 | } else { | |
851 | // if charge, dipole or reaction field is not used and the cutofff radius is not specified in | |
852 | //meta-data file, the maximum cutoff radius calculated from forcefiled will be used | |
853 | ||
854 | < | if (simParams_->haveRcut()) { |
855 | < | rcut = simParams_->getRcut(); |
854 | > | if (simParams_->haveCutoffRadius()) { |
855 | > | rcut = simParams_->getCutoffRadius(); |
856 | } else { | |
857 | //set cutoff radius to the maximum cutoff radius based on atom types in the whole system | |
858 | rcut = calcMaxCutoffRadius(); | |
859 | } | |
860 | ||
861 | < | if (simParams_->haveRsw()) { |
862 | < | rsw = simParams_->getRsw(); |
861 | > | if (simParams_->haveSwitchingRadius()) { |
862 | > | rsw = simParams_->getSwitchingRadius(); |
863 | } else { | |
864 | rsw = rcut; | |
865 | } | |
# | Line 839 | Line 876 | namespace oopse { | |
876 | int cp = TRADITIONAL_CUTOFF_POLICY; | |
877 | if (simParams_->haveCutoffPolicy()) { | |
878 | std::string myPolicy = simParams_->getCutoffPolicy(); | |
879 | + | toUpper(myPolicy); |
880 | if (myPolicy == "MIX") { | |
881 | cp = MIX_CUTOFF_POLICY; | |
882 | } else { | |
# | Line 857 | Line 895 | namespace oopse { | |
895 | } | |
896 | } | |
897 | } | |
898 | + | |
899 | + | |
900 | + | if (simParams_->haveSkinThickness()) { |
901 | + | double skinThickness = simParams_->getSkinThickness(); |
902 | + | } |
903 | + | |
904 | notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); | |
905 | // also send cutoff notification to electrostatics | |
906 | < | setElectrostaticCutoffRadius(&rcut_); |
906 | > | setElectrostaticCutoffRadius(&rcut_, &rsw_); |
907 | } | |
908 | ||
909 | void SimInfo::setupElectrostaticSummationMethod( int isError ) { | |
910 | ||
911 | int errorOut; | |
912 | int esm = NONE; | |
913 | + | int sm = UNDAMPED; |
914 | double alphaVal; | |
915 | double dielectric; | |
916 | ||
# | Line 875 | Line 920 | namespace oopse { | |
920 | ||
921 | if (simParams_->haveElectrostaticSummationMethod()) { | |
922 | std::string myMethod = simParams_->getElectrostaticSummationMethod(); | |
923 | + | toUpper(myMethod); |
924 | if (myMethod == "NONE") { | |
925 | esm = NONE; | |
926 | } else { | |
927 | < | if (myMethod == "UNDAMPED_WOLF") { |
928 | < | esm = UNDAMPED_WOLF; |
927 | > | if (myMethod == "SWITCHING_FUNCTION") { |
928 | > | esm = SWITCHING_FUNCTION; |
929 | } else { | |
930 | < | if (myMethod == "DAMPED_WOLF") { |
931 | < | esm = DAMPED_WOLF; |
932 | < | if (!simParams_->haveDampingAlpha()) { |
933 | < | //throw error |
934 | < | sprintf( painCave.errMsg, |
889 | < | "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal); |
890 | < | painCave.isFatal = 0; |
891 | < | simError(); |
892 | < | } |
893 | < | } else { |
894 | < | if (myMethod == "REACTION_FIELD") { |
895 | < | esm = REACTION_FIELD; |
930 | > | if (myMethod == "SHIFTED_POTENTIAL") { |
931 | > | esm = SHIFTED_POTENTIAL; |
932 | > | } else { |
933 | > | if (myMethod == "SHIFTED_FORCE") { |
934 | > | esm = SHIFTED_FORCE; |
935 | } else { | |
936 | < | // throw error |
937 | < | sprintf( painCave.errMsg, |
938 | < | "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() ); |
939 | < | painCave.isFatal = 1; |
940 | < | simError(); |
941 | < | } |
942 | < | } |
936 | > | if (myMethod == "REACTION_FIELD") { |
937 | > | esm = REACTION_FIELD; |
938 | > | } else { |
939 | > | // throw error |
940 | > | sprintf( painCave.errMsg, |
941 | > | "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() ); |
942 | > | painCave.isFatal = 1; |
943 | > | simError(); |
944 | > | } |
945 | > | } |
946 | > | } |
947 | > | } |
948 | > | } |
949 | > | } |
950 | > | |
951 | > | if (simParams_->haveElectrostaticScreeningMethod()) { |
952 | > | std::string myScreen = simParams_->getElectrostaticScreeningMethod(); |
953 | > | toUpper(myScreen); |
954 | > | if (myScreen == "UNDAMPED") { |
955 | > | sm = UNDAMPED; |
956 | > | } else { |
957 | > | if (myScreen == "DAMPED") { |
958 | > | sm = DAMPED; |
959 | > | if (!simParams_->haveDampingAlpha()) { |
960 | > | //throw error |
961 | > | sprintf( painCave.errMsg, |
962 | > | "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
963 | > | painCave.isFatal = 0; |
964 | > | simError(); |
965 | > | } |
966 | > | } else { |
967 | > | // throw error |
968 | > | sprintf( painCave.errMsg, |
969 | > | "SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
970 | > | painCave.isFatal = 1; |
971 | > | simError(); |
972 | } | |
973 | } | |
974 | } | |
975 | + | |
976 | // let's pass some summation method variables to fortran | |
977 | setElectrostaticSummationMethod( &esm ); | |
978 | < | setDampedWolfAlpha( &alphaVal ); |
978 | > | setScreeningMethod( &sm ); |
979 | > | setDampingAlpha( &alphaVal ); |
980 | setReactionFieldDielectric( &dielectric ); | |
981 | initFortranFF( &esm, &errorOut ); | |
982 | + | } |
983 | + | |
984 | + | void SimInfo::setupSwitchingFunction() { |
985 | + | int ft = CUBIC; |
986 | + | |
987 | + | if (simParams_->haveSwitchingFunctionType()) { |
988 | + | std::string funcType = simParams_->getSwitchingFunctionType(); |
989 | + | toUpper(funcType); |
990 | + | if (funcType == "CUBIC") { |
991 | + | ft = CUBIC; |
992 | + | } else { |
993 | + | if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
994 | + | ft = FIFTH_ORDER_POLY; |
995 | + | } else { |
996 | + | // throw error |
997 | + | sprintf( painCave.errMsg, |
998 | + | "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); |
999 | + | painCave.isFatal = 1; |
1000 | + | simError(); |
1001 | + | } |
1002 | + | } |
1003 | + | } |
1004 | + | |
1005 | + | // send switching function notification to switcheroo |
1006 | + | setFunctionType(&ft); |
1007 | + | |
1008 | } | |
1009 | ||
1010 | void SimInfo::addProperty(GenericData* genData) { |
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