52 |
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#include "brains/SimInfo.hpp" |
53 |
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#include "math/Vector3.hpp" |
54 |
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#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 |
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#include "UseTheForce/doForces_interface.h" |
60 |
+ |
#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 |
|
CutoffGroupStamp* cgStamp; |
91 |
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RigidBodyStamp* rbStamp; |
92 |
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int nRigidAtoms = 0; |
111 |
|
} |
112 |
|
|
113 |
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
114 |
+ |
|
115 |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
116 |
|
|
117 |
|
//calculate atoms in rigid bodies |
128 |
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|
129 |
|
} |
130 |
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|
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 |
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nGlobalMols_ = molStampIds_.size(); |
147 |
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|
148 |
|
#ifdef IS_MPI |
472 |
|
//setup fortran force field |
473 |
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/** @deprecate */ |
474 |
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int isError = 0; |
475 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
475 |
> |
|
476 |
> |
setupElectrostaticSummationMethod( isError ); |
477 |
> |
setupSwitchingFunction(); |
478 |
> |
|
479 |
|
if(isError){ |
480 |
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sprintf( painCave.errMsg, |
481 |
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"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
530 |
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int useDirectionalAtom = 0; |
531 |
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int useElectrostatics = 0; |
532 |
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//usePBC and useRF are from simParams |
533 |
< |
int usePBC = simParams_->getPBC(); |
534 |
< |
int useRF = simParams_->getUseRF(); |
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 |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
557 |
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useLennardJones |= (*i)->isLennardJones(); |
615 |
|
|
616 |
|
temp = useRF; |
617 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
618 |
< |
|
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; |
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 { |
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 |
|
} |
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 |
|
} |
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" |
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 |
|
} |
867 |
|
} |
868 |
|
} |
869 |
|
|
870 |
< |
void SimInfo::setupCutoff() { |
870 |
> |
void SimInfo::setupCutoff() { |
871 |
|
getCutoff(rcut_, rsw_); |
872 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
873 |
|
|
874 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
875 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
875 |
> |
|
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 { |
883 |
> |
if (myPolicy == "MAX") { |
884 |
> |
cp = MAX_CUTOFF_POLICY; |
885 |
> |
} else { |
886 |
> |
if (myPolicy == "TRADITIONAL") { |
887 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
888 |
> |
} else { |
889 |
> |
// throw error |
890 |
> |
sprintf( painCave.errMsg, |
891 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
892 |
> |
painCave.isFatal = 1; |
893 |
> |
simError(); |
894 |
> |
} |
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_, &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 |
> |
|
917 |
> |
errorOut = isError; |
918 |
> |
alphaVal = simParams_->getDampingAlpha(); |
919 |
> |
dielectric = simParams_->getDielectric(); |
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 == "SWITCHING_FUNCTION") { |
928 |
> |
esm = SWITCHING_FUNCTION; |
929 |
> |
} else { |
930 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
931 |
> |
esm = SHIFTED_POTENTIAL; |
932 |
> |
} else { |
933 |
> |
if (myMethod == "SHIFTED_FORCE") { |
934 |
> |
esm = SHIFTED_FORCE; |
935 |
> |
} else { |
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 |
> |
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) { |
1150 |
|
|
1151 |
|
/* |
1152 |
|
Return intertia tensor for entire system and angular momentum Vector. |
1153 |
+ |
|
1154 |
+ |
|
1155 |
+ |
[ Ixx -Ixy -Ixz ] |
1156 |
+ |
J =| -Iyx Iyy -Iyz | |
1157 |
+ |
[ -Izx -Iyz Izz ] |
1158 |
|
*/ |
1159 |
|
|
1160 |
|
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1206 |
|
inertiaTensor(0,1) = -xy; |
1207 |
|
inertiaTensor(0,2) = -xz; |
1208 |
|
inertiaTensor(1,0) = -xy; |
1209 |
< |
inertiaTensor(2,0) = xx + zz; |
1209 |
> |
inertiaTensor(1,1) = xx + zz; |
1210 |
|
inertiaTensor(1,2) = -yz; |
1211 |
|
inertiaTensor(2,0) = -xz; |
1212 |
|
inertiaTensor(2,1) = -yz; |
1234 |
|
SimInfo::MoleculeIterator i; |
1235 |
|
Molecule* mol; |
1236 |
|
|
1237 |
< |
Vector3d thisq(0.0); |
1238 |
< |
Vector3d thisv(0.0); |
1237 |
> |
Vector3d thisr(0.0); |
1238 |
> |
Vector3d thisp(0.0); |
1239 |
|
|
1240 |
< |
double thisMass = 0.0; |
1240 |
> |
double thisMass; |
1241 |
|
|
1242 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1243 |
< |
thisq = mol->getCom()-com; |
1244 |
< |
thisv = mol->getComVel()-comVel; |
1245 |
< |
thisMass = mol->getMass(); |
1072 |
< |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1243 |
> |
thisMass = mol->getMass(); |
1244 |
> |
thisr = mol->getCom()-com; |
1245 |
> |
thisp = (mol->getComVel()-comVel)*thisMass; |
1246 |
|
|
1247 |
+ |
angularMomentum += cross( thisr, thisp ); |
1248 |
+ |
|
1249 |
|
} |
1250 |
|
|
1251 |
|
#ifdef IS_MPI |