53 |
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#include "math/Vector3.hpp" |
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/fCoulombicCorrection.h" |
56 |
> |
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
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> |
#include "UseTheForce/DarkSide/fScreeningMethod.h" |
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#include "UseTheForce/doForces_interface.h" |
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+ |
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
84 |
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MoleculeStamp* molStamp; |
85 |
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int nMolWithSameStamp; |
86 |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
87 |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
87 |
> |
int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
89 |
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RigidBodyStamp* rbStamp; |
90 |
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int nRigidAtoms = 0; |
109 |
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} |
110 |
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|
111 |
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
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|
113 |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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|
115 |
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//calculate atoms in rigid bodies |
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|
127 |
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} |
128 |
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|
129 |
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//every free atom (atom does not belong to cutoff groups) is a cutoff group |
130 |
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//therefore the total number of cutoff groups in the system is equal to |
131 |
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//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
132 |
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//file plus the number of cutoff groups defined in meta-data file |
129 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff |
130 |
> |
//group therefore the total number of cutoff groups in the system is |
131 |
> |
//equal to the total number of atoms minus number of atoms belong to |
132 |
> |
//cutoff group defined in meta-data file plus the number of cutoff |
133 |
> |
//groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
135 |
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|
136 |
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//every free atom (atom does not belong to rigid bodies) is an integrable object |
137 |
< |
//therefore the total number of integrable objects in the system is equal to |
138 |
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//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
139 |
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//file plus the number of rigid bodies defined in meta-data file |
140 |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
141 |
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|
136 |
> |
//every free atom (atom does not belong to rigid bodies) is an |
137 |
> |
//integrable object therefore the total number of integrable objects |
138 |
> |
//in the system is equal to the total number of atoms minus number of |
139 |
> |
//atoms belong to rigid body defined in meta-data file plus the number |
140 |
> |
//of rigid bodies defined in meta-data file |
141 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
142 |
> |
+ nGlobalRigidBodies_; |
143 |
> |
|
144 |
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nGlobalMols_ = molStampIds_.size(); |
145 |
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|
146 |
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#ifdef IS_MPI |
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/** @deprecate */ |
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int isError = 0; |
473 |
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|
474 |
< |
setupCoulombicCorrection( isError ); |
474 |
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setupElectrostaticSummationMethod( isError ); |
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|
476 |
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if(isError){ |
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sprintf( painCave.errMsg, |
527 |
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int useDirectionalAtom = 0; |
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int useElectrostatics = 0; |
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//usePBC and useRF are from simParams |
530 |
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int usePBC = simParams_->getPBC(); |
531 |
< |
int useRF = simParams_->getUseRF(); |
530 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
531 |
> |
int useRF; |
532 |
> |
int useDW; |
533 |
> |
std::string myMethod; |
534 |
> |
|
535 |
> |
// set the useRF logical |
536 |
> |
useRF = 0; |
537 |
> |
useDW = 0; |
538 |
> |
|
539 |
> |
|
540 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
541 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
542 |
> |
toUpper(myMethod); |
543 |
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if (myMethod == "REACTION_FIELD") { |
544 |
> |
useRF=1; |
545 |
> |
} else { |
546 |
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if (myMethod == "SHIFTED_POTENTIAL") { |
547 |
> |
useDW = 1; |
548 |
> |
} |
549 |
> |
} |
550 |
> |
} |
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|
552 |
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//loop over all of the atom types |
553 |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
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temp = useRF; |
614 |
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MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
615 |
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|
591 |
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temp = useUW; |
592 |
– |
MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
593 |
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|
616 |
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temp = useDW; |
617 |
< |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
618 |
< |
|
617 |
> |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
618 |
> |
|
619 |
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#endif |
620 |
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|
621 |
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fInfo_.SIM_uses_PBC = usePBC; |
631 |
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fInfo_.SIM_uses_Shapes = useShape; |
632 |
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fInfo_.SIM_uses_FLARB = useFLARB; |
633 |
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fInfo_.SIM_uses_RF = useRF; |
634 |
+ |
fInfo_.SIM_uses_DampedWolf = useDW; |
635 |
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|
636 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
637 |
< |
|
636 |
> |
if( myMethod == "REACTION_FIELD") { |
637 |
> |
|
638 |
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if (simParams_->haveDielectric()) { |
639 |
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fInfo_.dielect = simParams_->getDielectric(); |
640 |
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} else { |
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"\tsetting a dielectric constant!\n"); |
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painCave.isFatal = 1; |
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simError(); |
647 |
< |
} |
625 |
< |
|
626 |
< |
} else { |
627 |
< |
fInfo_.dielect = 0.0; |
647 |
> |
} |
648 |
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} |
649 |
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|
650 |
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} |
680 |
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|
681 |
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totalMass = cg->getMass(); |
682 |
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for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
683 |
< |
mfact.push_back(atom->getMass()/totalMass); |
683 |
> |
// Check for massless groups - set mfact to 1 if true |
684 |
> |
if (totalMass != 0) |
685 |
> |
mfact.push_back(atom->getMass()/totalMass); |
686 |
> |
else |
687 |
> |
mfact.push_back( 1.0 ); |
688 |
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} |
689 |
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|
690 |
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} |
820 |
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|
821 |
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if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
822 |
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|
823 |
< |
if (!simParams_->haveRcut()){ |
823 |
> |
if (!simParams_->haveCutoffRadius()){ |
824 |
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sprintf(painCave.errMsg, |
825 |
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"SimCreator Warning: No value was set for the cutoffRadius.\n" |
826 |
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"\tOOPSE will use a default value of 15.0 angstroms" |
829 |
|
simError(); |
830 |
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rcut = 15.0; |
831 |
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} else{ |
832 |
< |
rcut = simParams_->getRcut(); |
832 |
> |
rcut = simParams_->getCutoffRadius(); |
833 |
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} |
834 |
|
|
835 |
< |
if (!simParams_->haveRsw()){ |
835 |
> |
if (!simParams_->haveSwitchingRadius()){ |
836 |
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sprintf(painCave.errMsg, |
837 |
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"SimCreator Warning: No value was set for switchingRadius.\n" |
838 |
|
"\tOOPSE will use a default value of\n" |
839 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
839 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
840 |
|
painCave.isFatal = 0; |
841 |
|
simError(); |
842 |
< |
rsw = 0.95 * rcut; |
842 |
> |
rsw = 0.85 * rcut; |
843 |
|
} else{ |
844 |
< |
rsw = simParams_->getRsw(); |
844 |
> |
rsw = simParams_->getSwitchingRadius(); |
845 |
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} |
846 |
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|
847 |
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} else { |
848 |
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// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
849 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
850 |
|
|
851 |
< |
if (simParams_->haveRcut()) { |
852 |
< |
rcut = simParams_->getRcut(); |
851 |
> |
if (simParams_->haveCutoffRadius()) { |
852 |
> |
rcut = simParams_->getCutoffRadius(); |
853 |
|
} else { |
854 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
855 |
|
rcut = calcMaxCutoffRadius(); |
856 |
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} |
857 |
|
|
858 |
< |
if (simParams_->haveRsw()) { |
859 |
< |
rsw = simParams_->getRsw(); |
858 |
> |
if (simParams_->haveSwitchingRadius()) { |
859 |
> |
rsw = simParams_->getSwitchingRadius(); |
860 |
|
} else { |
861 |
|
rsw = rcut; |
862 |
|
} |
873 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
874 |
|
if (simParams_->haveCutoffPolicy()) { |
875 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
876 |
+ |
toUpper(myPolicy); |
877 |
|
if (myPolicy == "MIX") { |
878 |
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cp = MIX_CUTOFF_POLICY; |
879 |
|
} else { |
891 |
|
} |
892 |
|
} |
893 |
|
} |
894 |
+ |
} |
895 |
+ |
|
896 |
+ |
|
897 |
+ |
if (simParams_->haveSkinThickness()) { |
898 |
+ |
double skinThickness = simParams_->getSkinThickness(); |
899 |
|
} |
900 |
+ |
|
901 |
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
902 |
+ |
// also send cutoff notification to electrostatics |
903 |
+ |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
904 |
|
} |
905 |
|
|
906 |
< |
void SimInfo::setupCoulombicCorrection( int isError ) { |
906 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
907 |
|
|
908 |
|
int errorOut; |
909 |
< |
int cc = NONE; |
909 |
> |
int esm = NONE; |
910 |
> |
int sm = UNDAMPED; |
911 |
|
double alphaVal; |
912 |
+ |
double dielectric; |
913 |
|
|
914 |
|
errorOut = isError; |
915 |
+ |
alphaVal = simParams_->getDampingAlpha(); |
916 |
+ |
dielectric = simParams_->getDielectric(); |
917 |
|
|
918 |
< |
if (simParams_->haveCoulombicCorrection()) { |
919 |
< |
std::string myCorrection = simParams_->getCoulombicCorrection(); |
920 |
< |
if (myCorrection == "NONE") { |
921 |
< |
cc = NONE; |
918 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
919 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
920 |
> |
toUpper(myMethod); |
921 |
> |
if (myMethod == "NONE") { |
922 |
> |
esm = NONE; |
923 |
|
} else { |
924 |
< |
if (myCorrection == "UNDAMPED_WOLF") { |
925 |
< |
cc = UNDAMPED_WOLF; |
924 |
> |
if (myMethod == "SWITCHING_FUNCTION") { |
925 |
> |
esm = SWITCHING_FUNCTION; |
926 |
|
} else { |
927 |
< |
if (myCorrection == "WOLF") { |
928 |
< |
cc = WOLF; |
929 |
< |
if (!simParams_->haveDampingAlpha()) { |
930 |
< |
//throw error |
931 |
< |
sprintf( painCave.errMsg, |
894 |
< |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha()); |
895 |
< |
painCave.isFatal = 0; |
896 |
< |
simError(); |
897 |
< |
} |
898 |
< |
alphaVal = simParams_->getDampingAlpha(); |
899 |
< |
} else { |
900 |
< |
if (myCorrection == "REACTION_FIELD") { |
901 |
< |
cc = REACTION_FIELD; |
927 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
928 |
> |
esm = SHIFTED_POTENTIAL; |
929 |
> |
} else { |
930 |
> |
if (myMethod == "SHIFTED_FORCE") { |
931 |
> |
esm = SHIFTED_FORCE; |
932 |
|
} else { |
933 |
< |
// throw error |
934 |
< |
sprintf( painCave.errMsg, |
935 |
< |
"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() ); |
936 |
< |
painCave.isFatal = 1; |
937 |
< |
simError(); |
938 |
< |
} |
939 |
< |
} |
933 |
> |
if (myMethod == "REACTION_FIELD") { |
934 |
> |
esm = REACTION_FIELD; |
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\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() ); |
939 |
> |
painCave.isFatal = 1; |
940 |
> |
simError(); |
941 |
> |
} |
942 |
> |
} |
943 |
> |
} |
944 |
|
} |
945 |
|
} |
946 |
|
} |
947 |
< |
initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut ); |
947 |
> |
|
948 |
> |
if (simParams_->haveScreeningMethod()) { |
949 |
> |
std::string myScreen = simParams_->getScreeningMethod(); |
950 |
> |
toUpper(myScreen); |
951 |
> |
if (myScreen == "UNDAMPED") { |
952 |
> |
sm = UNDAMPED; |
953 |
> |
} else { |
954 |
> |
if (myScreen == "DAMPED") { |
955 |
> |
sm = DAMPED; |
956 |
> |
if (!simParams_->haveDampingAlpha()) { |
957 |
> |
//throw error |
958 |
> |
sprintf( painCave.errMsg, |
959 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
960 |
> |
painCave.isFatal = 0; |
961 |
> |
simError(); |
962 |
> |
} else { |
963 |
> |
// throw error |
964 |
> |
sprintf( painCave.errMsg, |
965 |
> |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
966 |
> |
painCave.isFatal = 1; |
967 |
> |
simError(); |
968 |
> |
} |
969 |
> |
} |
970 |
> |
} |
971 |
> |
} |
972 |
> |
// let's pass some summation method variables to fortran |
973 |
> |
setElectrostaticSummationMethod( &esm ); |
974 |
> |
setScreeningMethod( &sm ); |
975 |
> |
setDampingAlpha( &alphaVal ); |
976 |
> |
setReactionFieldDielectric( &dielectric ); |
977 |
> |
initFortranFF( &esm, &errorOut ); |
978 |
|
} |
979 |
|
|
980 |
|
void SimInfo::addProperty(GenericData* genData) { |