53 |
|
#include "math/Vector3.hpp" |
54 |
|
#include "primitives/Molecule.hpp" |
55 |
|
#include "UseTheForce/fCutoffPolicy.h" |
56 |
< |
#include "UseTheForce/fCoulombicCorrection.h" |
56 |
> |
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
57 |
|
#include "UseTheForce/doForces_interface.h" |
58 |
+ |
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
59 |
|
#include "UseTheForce/notifyCutoffs_interface.h" |
60 |
|
#include "utils/MemoryUtils.hpp" |
61 |
|
#include "utils/simError.h" |
83 |
|
MoleculeStamp* molStamp; |
84 |
|
int nMolWithSameStamp; |
85 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
86 |
< |
int nGroups = 0; //total cutoff groups defined in meta-data file |
86 |
> |
int nGroups = 0; //total cutoff groups defined in meta-data file |
87 |
|
CutoffGroupStamp* cgStamp; |
88 |
|
RigidBodyStamp* rbStamp; |
89 |
|
int nRigidAtoms = 0; |
108 |
|
} |
109 |
|
|
110 |
|
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
111 |
+ |
|
112 |
|
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
113 |
|
|
114 |
|
//calculate atoms in rigid bodies |
125 |
|
|
126 |
|
} |
127 |
|
|
128 |
< |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
129 |
< |
//therefore the total number of cutoff groups in the system is equal to |
130 |
< |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
131 |
< |
//file plus the number of cutoff groups defined in meta-data file |
128 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff |
129 |
> |
//group therefore the total number of cutoff groups in the system is |
130 |
> |
//equal to the total number of atoms minus number of atoms belong to |
131 |
> |
//cutoff group defined in meta-data file plus the number of cutoff |
132 |
> |
//groups defined in meta-data file |
133 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
134 |
|
|
135 |
< |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
136 |
< |
//therefore the total number of integrable objects in the system is equal to |
137 |
< |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
138 |
< |
//file plus the number of rigid bodies defined in meta-data file |
139 |
< |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
140 |
< |
|
135 |
> |
//every free atom (atom does not belong to rigid bodies) is an |
136 |
> |
//integrable object therefore the total number of integrable objects |
137 |
> |
//in the system is equal to the total number of atoms minus number of |
138 |
> |
//atoms belong to rigid body defined in meta-data file plus the number |
139 |
> |
//of rigid bodies defined in meta-data file |
140 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
141 |
> |
+ nGlobalRigidBodies_; |
142 |
> |
|
143 |
|
nGlobalMols_ = molStampIds_.size(); |
144 |
|
|
145 |
|
#ifdef IS_MPI |
470 |
|
/** @deprecate */ |
471 |
|
int isError = 0; |
472 |
|
|
473 |
< |
setupCoulombicCorrection( isError ); |
473 |
> |
setupElectrostaticSummationMethod( isError ); |
474 |
|
|
475 |
|
if(isError){ |
476 |
|
sprintf( painCave.errMsg, |
526 |
|
int useDirectionalAtom = 0; |
527 |
|
int useElectrostatics = 0; |
528 |
|
//usePBC and useRF are from simParams |
529 |
< |
int usePBC = simParams_->getPBC(); |
530 |
< |
int useRF = simParams_->getUseRF(); |
529 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
530 |
> |
int useRF; |
531 |
> |
int useDW; |
532 |
> |
std::string myMethod; |
533 |
|
|
534 |
+ |
// set the useRF logical |
535 |
+ |
useRF = 0; |
536 |
+ |
useDW = 0; |
537 |
+ |
|
538 |
+ |
|
539 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
540 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
541 |
+ |
toUpper(myMethod); |
542 |
+ |
if (myMethod == "REACTION_FIELD") { |
543 |
+ |
useRF=1; |
544 |
+ |
} else { |
545 |
+ |
if (myMethod == "DAMPED_WOLF") { |
546 |
+ |
useDW = 1; |
547 |
+ |
} |
548 |
+ |
} |
549 |
+ |
} |
550 |
+ |
|
551 |
|
//loop over all of the atom types |
552 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
553 |
|
useLennardJones |= (*i)->isLennardJones(); |
612 |
|
temp = useRF; |
613 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
614 |
|
|
591 |
– |
temp = useUW; |
592 |
– |
MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
593 |
– |
|
615 |
|
temp = useDW; |
616 |
< |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
617 |
< |
|
616 |
> |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
617 |
> |
|
618 |
|
#endif |
619 |
|
|
620 |
|
fInfo_.SIM_uses_PBC = usePBC; |
630 |
|
fInfo_.SIM_uses_Shapes = useShape; |
631 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
632 |
|
fInfo_.SIM_uses_RF = useRF; |
633 |
+ |
fInfo_.SIM_uses_DampedWolf = useDW; |
634 |
|
|
635 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
636 |
< |
|
635 |
> |
if( myMethod == "REACTION_FIELD") { |
636 |
> |
|
637 |
|
if (simParams_->haveDielectric()) { |
638 |
|
fInfo_.dielect = simParams_->getDielectric(); |
639 |
|
} else { |
643 |
|
"\tsetting a dielectric constant!\n"); |
644 |
|
painCave.isFatal = 1; |
645 |
|
simError(); |
646 |
< |
} |
625 |
< |
|
626 |
< |
} else { |
627 |
< |
fInfo_.dielect = 0.0; |
646 |
> |
} |
647 |
|
} |
648 |
|
|
649 |
|
} |
679 |
|
|
680 |
|
totalMass = cg->getMass(); |
681 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
682 |
< |
mfact.push_back(atom->getMass()/totalMass); |
682 |
> |
// Check for massless groups - set mfact to 1 if true |
683 |
> |
if (totalMass != 0) |
684 |
> |
mfact.push_back(atom->getMass()/totalMass); |
685 |
> |
else |
686 |
> |
mfact.push_back( 1.0 ); |
687 |
|
} |
688 |
|
|
689 |
|
} |
819 |
|
|
820 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
821 |
|
|
822 |
< |
if (!simParams_->haveRcut()){ |
822 |
> |
if (!simParams_->haveCutoffRadius()){ |
823 |
|
sprintf(painCave.errMsg, |
824 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
825 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
828 |
|
simError(); |
829 |
|
rcut = 15.0; |
830 |
|
} else{ |
831 |
< |
rcut = simParams_->getRcut(); |
831 |
> |
rcut = simParams_->getCutoffRadius(); |
832 |
|
} |
833 |
|
|
834 |
< |
if (!simParams_->haveRsw()){ |
834 |
> |
if (!simParams_->haveSwitchingRadius()){ |
835 |
|
sprintf(painCave.errMsg, |
836 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
837 |
|
"\tOOPSE will use a default value of\n" |
838 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
838 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
839 |
|
painCave.isFatal = 0; |
840 |
|
simError(); |
841 |
< |
rsw = 0.95 * rcut; |
841 |
> |
rsw = 0.85 * rcut; |
842 |
|
} else{ |
843 |
< |
rsw = simParams_->getRsw(); |
843 |
> |
rsw = simParams_->getSwitchingRadius(); |
844 |
|
} |
845 |
|
|
846 |
|
} else { |
847 |
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
848 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
849 |
|
|
850 |
< |
if (simParams_->haveRcut()) { |
851 |
< |
rcut = simParams_->getRcut(); |
850 |
> |
if (simParams_->haveCutoffRadius()) { |
851 |
> |
rcut = simParams_->getCutoffRadius(); |
852 |
|
} else { |
853 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
854 |
|
rcut = calcMaxCutoffRadius(); |
855 |
|
} |
856 |
|
|
857 |
< |
if (simParams_->haveRsw()) { |
858 |
< |
rsw = simParams_->getRsw(); |
857 |
> |
if (simParams_->haveSwitchingRadius()) { |
858 |
> |
rsw = simParams_->getSwitchingRadius(); |
859 |
|
} else { |
860 |
|
rsw = rcut; |
861 |
|
} |
872 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
873 |
|
if (simParams_->haveCutoffPolicy()) { |
874 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
875 |
+ |
toUpper(myPolicy); |
876 |
|
if (myPolicy == "MIX") { |
877 |
|
cp = MIX_CUTOFF_POLICY; |
878 |
|
} else { |
891 |
|
} |
892 |
|
} |
893 |
|
} |
894 |
+ |
|
895 |
+ |
|
896 |
+ |
if (simParams_->haveSkinThickness()) { |
897 |
+ |
double skinThickness = simParams_->getSkinThickness(); |
898 |
+ |
} |
899 |
+ |
|
900 |
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
901 |
+ |
// also send cutoff notification to electrostatics |
902 |
+ |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
903 |
|
} |
904 |
|
|
905 |
< |
void SimInfo::setupCoulombicCorrection( int isError ) { |
905 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
906 |
|
|
907 |
|
int errorOut; |
908 |
< |
int cc = NONE; |
908 |
> |
int esm = NONE; |
909 |
|
double alphaVal; |
910 |
+ |
double dielectric; |
911 |
|
|
912 |
|
errorOut = isError; |
913 |
+ |
alphaVal = simParams_->getDampingAlpha(); |
914 |
+ |
dielectric = simParams_->getDielectric(); |
915 |
|
|
916 |
< |
if (simParams_->haveCoulombicCorrection()) { |
917 |
< |
std::string myCorrection = simParams_->getCoulombicCorrection(); |
918 |
< |
if (myCorrection == "NONE") { |
919 |
< |
cc = NONE; |
916 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
917 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
918 |
> |
toUpper(myMethod); |
919 |
> |
if (myMethod == "NONE") { |
920 |
> |
esm = NONE; |
921 |
|
} else { |
922 |
< |
if (myCorrection == "UNDAMPED_WOLF") { |
923 |
< |
cc = UNDAMPED_WOLF; |
922 |
> |
if (myMethod == "UNDAMPED_WOLF") { |
923 |
> |
esm = UNDAMPED_WOLF; |
924 |
|
} else { |
925 |
< |
if (myCorrection == "WOLF") { |
926 |
< |
cc = WOLF; |
925 |
> |
if (myMethod == "DAMPED_WOLF") { |
926 |
> |
esm = DAMPED_WOLF; |
927 |
|
if (!simParams_->haveDampingAlpha()) { |
928 |
|
//throw error |
929 |
|
sprintf( painCave.errMsg, |
930 |
< |
"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()); |
930 |
> |
"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); |
931 |
|
painCave.isFatal = 0; |
932 |
|
simError(); |
933 |
|
} |
898 |
– |
alphaVal = simParams_->getDampingAlpha(); |
934 |
|
} else { |
935 |
< |
if (myCorrection == "REACTION_FIELD") { |
936 |
< |
cc = REACTION_FIELD; |
935 |
> |
if (myMethod == "REACTION_FIELD") { |
936 |
> |
esm = REACTION_FIELD; |
937 |
|
} else { |
938 |
|
// throw error |
939 |
|
sprintf( painCave.errMsg, |
940 |
< |
"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() ); |
940 |
> |
"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() ); |
941 |
|
painCave.isFatal = 1; |
942 |
|
simError(); |
943 |
|
} |
945 |
|
} |
946 |
|
} |
947 |
|
} |
948 |
< |
initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut ); |
948 |
> |
// let's pass some summation method variables to fortran |
949 |
> |
setElectrostaticSummationMethod( &esm ); |
950 |
> |
setDampedWolfAlpha( &alphaVal ); |
951 |
> |
setReactionFieldDielectric( &dielectric ); |
952 |
> |
initFortranFF( &esm, &errorOut ); |
953 |
|
} |
954 |
|
|
955 |
|
void SimInfo::addProperty(GenericData* genData) { |