54 |
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#include "primitives/Molecule.hpp" |
55 |
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#include "UseTheForce/fCutoffPolicy.h" |
56 |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
57 |
+ |
#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
58 |
+ |
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
59 |
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#include "UseTheForce/doForces_interface.h" |
60 |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
61 |
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#include "UseTheForce/notifyCutoffs_interface.h" |
62 |
+ |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
63 |
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#include "utils/MemoryUtils.hpp" |
64 |
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#include "utils/simError.h" |
65 |
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#include "selection/SelectionManager.hpp" |
86 |
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MoleculeStamp* molStamp; |
87 |
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int nMolWithSameStamp; |
88 |
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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 |
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CutoffGroupStamp* cgStamp; |
91 |
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RigidBodyStamp* rbStamp; |
92 |
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int nRigidAtoms = 0; |
111 |
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} |
112 |
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|
113 |
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
114 |
+ |
|
115 |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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|
|
117 |
|
//calculate atoms in rigid bodies |
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 |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
137 |
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|
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 |
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> |
+ nGlobalRigidBodies_; |
145 |
> |
|
146 |
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nGlobalMols_ = molStampIds_.size(); |
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|
148 |
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#ifdef IS_MPI |
474 |
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int isError = 0; |
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|
|
476 |
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setupElectrostaticSummationMethod( isError ); |
477 |
+ |
setupSwitchingFunction(); |
478 |
|
|
479 |
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if(isError){ |
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sprintf( painCave.errMsg, |
519 |
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int useLennardJones = 0; |
520 |
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int useElectrostatic = 0; |
521 |
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int useEAM = 0; |
522 |
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int useSC = 0; |
523 |
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int useCharge = 0; |
524 |
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int useDirectional = 0; |
525 |
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int useDipole = 0; |
531 |
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int useDirectionalAtom = 0; |
532 |
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int useElectrostatics = 0; |
533 |
|
//usePBC and useRF are from simParams |
534 |
< |
int usePBC = simParams_->getPBC(); |
534 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
535 |
> |
int useRF; |
536 |
> |
int useSF; |
537 |
> |
std::string myMethod; |
538 |
> |
|
539 |
> |
// set the useRF logical |
540 |
> |
useRF = 0; |
541 |
> |
useSF = 0; |
542 |
> |
|
543 |
> |
|
544 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
545 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
546 |
> |
toUpper(myMethod); |
547 |
> |
if (myMethod == "REACTION_FIELD") { |
548 |
> |
useRF=1; |
549 |
> |
} else { |
550 |
> |
if (myMethod == "SHIFTED_FORCE") { |
551 |
> |
useSF = 1; |
552 |
> |
} |
553 |
> |
} |
554 |
> |
} |
555 |
|
|
556 |
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//loop over all of the atom types |
557 |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
558 |
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useLennardJones |= (*i)->isLennardJones(); |
559 |
|
useElectrostatic |= (*i)->isElectrostatic(); |
560 |
|
useEAM |= (*i)->isEAM(); |
561 |
+ |
useSC |= (*i)->isSC(); |
562 |
|
useCharge |= (*i)->isCharge(); |
563 |
|
useDirectional |= (*i)->isDirectional(); |
564 |
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useDipole |= (*i)->isDipole(); |
609 |
|
temp = useEAM; |
610 |
|
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
611 |
|
|
612 |
+ |
temp = useSC; |
613 |
+ |
MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
614 |
+ |
|
615 |
|
temp = useShape; |
616 |
|
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
617 |
|
|
618 |
|
temp = useFLARB; |
619 |
|
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
620 |
|
|
621 |
+ |
temp = useRF; |
622 |
+ |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
623 |
+ |
|
624 |
+ |
temp = useSF; |
625 |
+ |
MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
626 |
+ |
|
627 |
|
#endif |
628 |
|
|
629 |
|
fInfo_.SIM_uses_PBC = usePBC; |
636 |
|
fInfo_.SIM_uses_StickyPower = useStickyPower; |
637 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
638 |
|
fInfo_.SIM_uses_EAM = useEAM; |
639 |
+ |
fInfo_.SIM_uses_SC = useSC; |
640 |
|
fInfo_.SIM_uses_Shapes = useShape; |
641 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
642 |
+ |
fInfo_.SIM_uses_RF = useRF; |
643 |
+ |
fInfo_.SIM_uses_SF = useSF; |
644 |
|
|
645 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
646 |
< |
|
645 |
> |
if( myMethod == "REACTION_FIELD") { |
646 |
> |
|
647 |
|
if (simParams_->haveDielectric()) { |
648 |
|
fInfo_.dielect = simParams_->getDielectric(); |
649 |
|
} else { |
653 |
|
"\tsetting a dielectric constant!\n"); |
654 |
|
painCave.isFatal = 1; |
655 |
|
simError(); |
656 |
< |
} |
615 |
< |
|
616 |
< |
} else { |
617 |
< |
fInfo_.dielect = 0.0; |
656 |
> |
} |
657 |
|
} |
658 |
|
|
659 |
|
} |
689 |
|
|
690 |
|
totalMass = cg->getMass(); |
691 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
692 |
< |
mfact.push_back(atom->getMass()/totalMass); |
692 |
> |
// Check for massless groups - set mfact to 1 if true |
693 |
> |
if (totalMass != 0) |
694 |
> |
mfact.push_back(atom->getMass()/totalMass); |
695 |
> |
else |
696 |
> |
mfact.push_back( 1.0 ); |
697 |
|
} |
698 |
|
|
699 |
|
} |
829 |
|
|
830 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
831 |
|
|
832 |
< |
if (!simParams_->haveRcut()){ |
832 |
> |
if (!simParams_->haveCutoffRadius()){ |
833 |
|
sprintf(painCave.errMsg, |
834 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
835 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
838 |
|
simError(); |
839 |
|
rcut = 15.0; |
840 |
|
} else{ |
841 |
< |
rcut = simParams_->getRcut(); |
841 |
> |
rcut = simParams_->getCutoffRadius(); |
842 |
|
} |
843 |
|
|
844 |
< |
if (!simParams_->haveRsw()){ |
844 |
> |
if (!simParams_->haveSwitchingRadius()){ |
845 |
|
sprintf(painCave.errMsg, |
846 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
847 |
|
"\tOOPSE will use a default value of\n" |
848 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
848 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
849 |
|
painCave.isFatal = 0; |
850 |
|
simError(); |
851 |
< |
rsw = 0.95 * rcut; |
851 |
> |
rsw = 0.85 * rcut; |
852 |
|
} else{ |
853 |
< |
rsw = simParams_->getRsw(); |
853 |
> |
rsw = simParams_->getSwitchingRadius(); |
854 |
|
} |
855 |
|
|
856 |
|
} else { |
857 |
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
858 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
859 |
|
|
860 |
< |
if (simParams_->haveRcut()) { |
861 |
< |
rcut = simParams_->getRcut(); |
860 |
> |
if (simParams_->haveCutoffRadius()) { |
861 |
> |
rcut = simParams_->getCutoffRadius(); |
862 |
|
} else { |
863 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
864 |
|
rcut = calcMaxCutoffRadius(); |
865 |
|
} |
866 |
|
|
867 |
< |
if (simParams_->haveRsw()) { |
868 |
< |
rsw = simParams_->getRsw(); |
867 |
> |
if (simParams_->haveSwitchingRadius()) { |
868 |
> |
rsw = simParams_->getSwitchingRadius(); |
869 |
|
} else { |
870 |
|
rsw = rcut; |
871 |
|
} |
882 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
883 |
|
if (simParams_->haveCutoffPolicy()) { |
884 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
885 |
+ |
toUpper(myPolicy); |
886 |
|
if (myPolicy == "MIX") { |
887 |
|
cp = MIX_CUTOFF_POLICY; |
888 |
|
} else { |
900 |
|
} |
901 |
|
} |
902 |
|
} |
903 |
+ |
} |
904 |
+ |
|
905 |
+ |
|
906 |
+ |
if (simParams_->haveSkinThickness()) { |
907 |
+ |
double skinThickness = simParams_->getSkinThickness(); |
908 |
|
} |
909 |
+ |
|
910 |
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
911 |
|
// also send cutoff notification to electrostatics |
912 |
< |
setElectrostaticCutoffRadius(&rcut_); |
912 |
> |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
913 |
|
} |
914 |
|
|
915 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
916 |
|
|
917 |
|
int errorOut; |
918 |
|
int esm = NONE; |
919 |
+ |
int sm = UNDAMPED; |
920 |
|
double alphaVal; |
921 |
|
double dielectric; |
922 |
|
|
926 |
|
|
927 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
928 |
|
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
929 |
+ |
toUpper(myMethod); |
930 |
|
if (myMethod == "NONE") { |
931 |
|
esm = NONE; |
932 |
|
} else { |
933 |
< |
if (myMethod == "UNDAMPED_WOLF") { |
934 |
< |
esm = UNDAMPED_WOLF; |
933 |
> |
if (myMethod == "SWITCHING_FUNCTION") { |
934 |
> |
esm = SWITCHING_FUNCTION; |
935 |
|
} else { |
936 |
< |
if (myMethod == "DAMPED_WOLF") { |
937 |
< |
esm = DAMPED_WOLF; |
938 |
< |
if (!simParams_->haveDampingAlpha()) { |
939 |
< |
//throw error |
940 |
< |
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; |
936 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
937 |
> |
esm = SHIFTED_POTENTIAL; |
938 |
> |
} else { |
939 |
> |
if (myMethod == "SHIFTED_FORCE") { |
940 |
> |
esm = SHIFTED_FORCE; |
941 |
|
} else { |
942 |
< |
// throw error |
943 |
< |
sprintf( painCave.errMsg, |
944 |
< |
"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() ); |
945 |
< |
painCave.isFatal = 1; |
946 |
< |
simError(); |
947 |
< |
} |
948 |
< |
} |
942 |
> |
if (myMethod == "REACTION_FIELD") { |
943 |
> |
esm = REACTION_FIELD; |
944 |
> |
} else { |
945 |
> |
// throw error |
946 |
> |
sprintf( painCave.errMsg, |
947 |
> |
"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() ); |
948 |
> |
painCave.isFatal = 1; |
949 |
> |
simError(); |
950 |
> |
} |
951 |
> |
} |
952 |
> |
} |
953 |
> |
} |
954 |
> |
} |
955 |
> |
} |
956 |
> |
|
957 |
> |
if (simParams_->haveElectrostaticScreeningMethod()) { |
958 |
> |
std::string myScreen = simParams_->getElectrostaticScreeningMethod(); |
959 |
> |
toUpper(myScreen); |
960 |
> |
if (myScreen == "UNDAMPED") { |
961 |
> |
sm = UNDAMPED; |
962 |
> |
} else { |
963 |
> |
if (myScreen == "DAMPED") { |
964 |
> |
sm = DAMPED; |
965 |
> |
if (!simParams_->haveDampingAlpha()) { |
966 |
> |
//throw error |
967 |
> |
sprintf( painCave.errMsg, |
968 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
969 |
> |
painCave.isFatal = 0; |
970 |
> |
simError(); |
971 |
> |
} |
972 |
> |
} else { |
973 |
> |
// throw error |
974 |
> |
sprintf( painCave.errMsg, |
975 |
> |
"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
976 |
> |
painCave.isFatal = 1; |
977 |
> |
simError(); |
978 |
|
} |
979 |
|
} |
980 |
|
} |
981 |
+ |
|
982 |
|
// let's pass some summation method variables to fortran |
983 |
|
setElectrostaticSummationMethod( &esm ); |
984 |
< |
setDampedWolfAlpha( &alphaVal ); |
984 |
> |
setScreeningMethod( &sm ); |
985 |
> |
setDampingAlpha( &alphaVal ); |
986 |
|
setReactionFieldDielectric( &dielectric ); |
987 |
|
initFortranFF( &esm, &errorOut ); |
988 |
|
} |
989 |
|
|
990 |
+ |
void SimInfo::setupSwitchingFunction() { |
991 |
+ |
int ft = CUBIC; |
992 |
+ |
|
993 |
+ |
if (simParams_->haveSwitchingFunctionType()) { |
994 |
+ |
std::string funcType = simParams_->getSwitchingFunctionType(); |
995 |
+ |
toUpper(funcType); |
996 |
+ |
if (funcType == "CUBIC") { |
997 |
+ |
ft = CUBIC; |
998 |
+ |
} else { |
999 |
+ |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
1000 |
+ |
ft = FIFTH_ORDER_POLY; |
1001 |
+ |
} else { |
1002 |
+ |
// throw error |
1003 |
+ |
sprintf( painCave.errMsg, |
1004 |
+ |
"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); |
1005 |
+ |
painCave.isFatal = 1; |
1006 |
+ |
simError(); |
1007 |
+ |
} |
1008 |
+ |
} |
1009 |
+ |
} |
1010 |
+ |
|
1011 |
+ |
// send switching function notification to switcheroo |
1012 |
+ |
setFunctionType(&ft); |
1013 |
+ |
|
1014 |
+ |
} |
1015 |
+ |
|
1016 |
|
void SimInfo::addProperty(GenericData* genData) { |
1017 |
|
properties_.addProperty(genData); |
1018 |
|
} |