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 |
526 |
|
int useDirectionalAtom = 0; |
527 |
|
int useElectrostatics = 0; |
528 |
|
//usePBC and useRF are from simParams |
529 |
< |
int usePBC = simParams_->getPBC(); |
529 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
530 |
|
int useRF; |
531 |
+ |
std::string myMethod; |
532 |
|
|
533 |
|
// set the useRF logical |
534 |
< |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
535 |
< |
if (myMethod == "REACTION_FIELD") |
536 |
< |
useRF = 1; |
537 |
< |
else |
538 |
< |
useRF = 0; |
534 |
> |
useRF = 0; |
535 |
> |
|
536 |
> |
|
537 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
538 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
539 |
> |
toUpper(myMethod); |
540 |
> |
if (myMethod == "REACTION_FIELD") { |
541 |
> |
useRF=1; |
542 |
> |
} |
543 |
> |
} |
544 |
|
|
545 |
|
//loop over all of the atom types |
546 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
622 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
623 |
|
fInfo_.SIM_uses_RF = useRF; |
624 |
|
|
625 |
< |
if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") { |
626 |
< |
|
625 |
> |
if( myMethod == "REACTION_FIELD") { |
626 |
> |
|
627 |
|
if (simParams_->haveDielectric()) { |
628 |
|
fInfo_.dielect = simParams_->getDielectric(); |
629 |
|
} else { |
633 |
|
"\tsetting a dielectric constant!\n"); |
634 |
|
painCave.isFatal = 1; |
635 |
|
simError(); |
636 |
< |
} |
627 |
< |
|
628 |
< |
} else { |
629 |
< |
fInfo_.dielect = 0.0; |
636 |
> |
} |
637 |
|
} |
631 |
– |
|
638 |
|
} |
639 |
|
|
640 |
|
void SimInfo::setupFortranSim() { |
668 |
|
|
669 |
|
totalMass = cg->getMass(); |
670 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
671 |
< |
mfact.push_back(atom->getMass()/totalMass); |
671 |
> |
// Check for massless groups - set mfact to 1 if true |
672 |
> |
if (totalMass != 0) |
673 |
> |
mfact.push_back(atom->getMass()/totalMass); |
674 |
> |
else |
675 |
> |
mfact.push_back( 1.0 ); |
676 |
|
} |
677 |
|
|
678 |
|
} |
808 |
|
|
809 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
810 |
|
|
811 |
< |
if (!simParams_->haveRcut()){ |
811 |
> |
if (!simParams_->haveCutoffRadius()){ |
812 |
|
sprintf(painCave.errMsg, |
813 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
814 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
817 |
|
simError(); |
818 |
|
rcut = 15.0; |
819 |
|
} else{ |
820 |
< |
rcut = simParams_->getRcut(); |
820 |
> |
rcut = simParams_->getCutoffRadius(); |
821 |
|
} |
822 |
|
|
823 |
< |
if (!simParams_->haveRsw()){ |
823 |
> |
if (!simParams_->haveSwitchingRadius()){ |
824 |
|
sprintf(painCave.errMsg, |
825 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
826 |
|
"\tOOPSE will use a default value of\n" |
829 |
|
simError(); |
830 |
|
rsw = 0.95 * rcut; |
831 |
|
} else{ |
832 |
< |
rsw = simParams_->getRsw(); |
832 |
> |
rsw = simParams_->getSwitchingRadius(); |
833 |
|
} |
834 |
|
|
835 |
|
} else { |
836 |
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
837 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
838 |
|
|
839 |
< |
if (simParams_->haveRcut()) { |
840 |
< |
rcut = simParams_->getRcut(); |
839 |
> |
if (simParams_->haveCutoffRadius()) { |
840 |
> |
rcut = simParams_->getCutoffRadius(); |
841 |
|
} else { |
842 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
843 |
|
rcut = calcMaxCutoffRadius(); |
844 |
|
} |
845 |
|
|
846 |
< |
if (simParams_->haveRsw()) { |
847 |
< |
rsw = simParams_->getRsw(); |
846 |
> |
if (simParams_->haveSwitchingRadius()) { |
847 |
> |
rsw = simParams_->getSwitchingRadius(); |
848 |
|
} else { |
849 |
|
rsw = rcut; |
850 |
|
} |
861 |
|
int cp = TRADITIONAL_CUTOFF_POLICY; |
862 |
|
if (simParams_->haveCutoffPolicy()) { |
863 |
|
std::string myPolicy = simParams_->getCutoffPolicy(); |
864 |
+ |
toUpper(myPolicy); |
865 |
|
if (myPolicy == "MIX") { |
866 |
|
cp = MIX_CUTOFF_POLICY; |
867 |
|
} else { |
880 |
|
} |
881 |
|
} |
882 |
|
} |
883 |
+ |
|
884 |
+ |
|
885 |
+ |
if (simParams_->haveSkinThickness()) { |
886 |
+ |
double skinThickness = simParams_->getSkinThickness(); |
887 |
+ |
} |
888 |
+ |
|
889 |
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
890 |
|
// also send cutoff notification to electrostatics |
891 |
< |
setElectrostaticCutoffRadius(&rcut_); |
891 |
> |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
892 |
|
} |
893 |
|
|
894 |
|
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
904 |
|
|
905 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
906 |
|
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
907 |
+ |
toUpper(myMethod); |
908 |
|
if (myMethod == "NONE") { |
909 |
|
esm = NONE; |
910 |
|
} else { |
921 |
|
simError(); |
922 |
|
} |
923 |
|
} else { |
924 |
< |
if (myMethod == "REACTION_FIELD") { |
924 |
> |
if (myMethod == "REACTION_FIELD") { |
925 |
|
esm = REACTION_FIELD; |
926 |
|
} else { |
927 |
|
// throw error |