| 52 |
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#include "brains/SimInfo.hpp" |
| 53 |
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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+ |
#include "UseTheForce/fCutoffPolicy.h" |
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+ |
#include "UseTheForce/fCoulombicCorrection.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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//setup fortran force field |
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/** @deprecate */ |
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int isError = 0; |
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< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
| 467 |
> |
|
| 468 |
> |
setupCoulombicCorrection( isError ); |
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> |
|
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if(isError){ |
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sprintf( painCave.errMsg, |
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"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
| 587 |
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|
| 588 |
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temp = useRF; |
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MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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|
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+ |
temp = useUW; |
| 592 |
+ |
MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 593 |
+ |
|
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+ |
temp = useDW; |
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+ |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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|
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#endif |
| 598 |
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|
| 840 |
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} |
| 841 |
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} |
| 842 |
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|
| 843 |
< |
void SimInfo::setupCutoff() { |
| 843 |
> |
void SimInfo::setupCutoff() { |
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getCutoff(rcut_, rsw_); |
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double rnblist = rcut_ + 1; // skin of neighbor list |
| 846 |
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|
| 847 |
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//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 848 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
| 848 |
> |
|
| 849 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
| 850 |
> |
if (simParams_->haveCutoffPolicy()) { |
| 851 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
| 852 |
> |
if (myPolicy == "MIX") { |
| 853 |
> |
cp = MIX_CUTOFF_POLICY; |
| 854 |
> |
} else { |
| 855 |
> |
if (myPolicy == "MAX") { |
| 856 |
> |
cp = MAX_CUTOFF_POLICY; |
| 857 |
> |
} else { |
| 858 |
> |
if (myPolicy == "TRADITIONAL") { |
| 859 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
| 860 |
> |
} else { |
| 861 |
> |
// throw error |
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> |
sprintf( painCave.errMsg, |
| 863 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
| 864 |
> |
painCave.isFatal = 1; |
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> |
simError(); |
| 866 |
> |
} |
| 867 |
> |
} |
| 868 |
> |
} |
| 869 |
> |
} |
| 870 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
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|
} |
| 872 |
|
|
| 873 |
+ |
void SimInfo::setupCoulombicCorrection( int isError ) { |
| 874 |
+ |
|
| 875 |
+ |
int errorOut; |
| 876 |
+ |
int cc = NONE; |
| 877 |
+ |
double alphaVal; |
| 878 |
+ |
|
| 879 |
+ |
errorOut = isError; |
| 880 |
+ |
|
| 881 |
+ |
if (simParams_->haveCoulombicCorrection()) { |
| 882 |
+ |
std::string myCorrection = simParams_->getCoulombicCorrection(); |
| 883 |
+ |
if (myCorrection == "NONE") { |
| 884 |
+ |
cc = NONE; |
| 885 |
+ |
} else { |
| 886 |
+ |
if (myCorrection == "UNDAMPED_WOLF") { |
| 887 |
+ |
cc = UNDAMPED_WOLF; |
| 888 |
+ |
} else { |
| 889 |
+ |
if (myCorrection == "WOLF") { |
| 890 |
+ |
cc = WOLF; |
| 891 |
+ |
if (!simParams_->haveDampingAlpha()) { |
| 892 |
+ |
//throw error |
| 893 |
+ |
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; |
| 902 |
+ |
} else { |
| 903 |
+ |
// throw error |
| 904 |
+ |
sprintf( painCave.errMsg, |
| 905 |
+ |
"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() ); |
| 906 |
+ |
painCave.isFatal = 1; |
| 907 |
+ |
simError(); |
| 908 |
+ |
} |
| 909 |
+ |
} |
| 910 |
+ |
} |
| 911 |
+ |
} |
| 912 |
+ |
} |
| 913 |
+ |
initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut ); |
| 914 |
+ |
} |
| 915 |
+ |
|
| 916 |
|
void SimInfo::addProperty(GenericData* genData) { |
| 917 |
|
properties_.addProperty(genData); |
| 918 |
|
} |
| 1056 |
|
|
| 1057 |
|
/* |
| 1058 |
|
Return intertia tensor for entire system and angular momentum Vector. |
| 1059 |
+ |
|
| 1060 |
+ |
|
| 1061 |
+ |
[ Ixx -Ixy -Ixz ] |
| 1062 |
+ |
J =| -Iyx Iyy -Iyz | |
| 1063 |
+ |
[ -Izx -Iyz Izz ] |
| 1064 |
|
*/ |
| 1065 |
|
|
| 1066 |
|
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
| 1112 |
|
inertiaTensor(0,1) = -xy; |
| 1113 |
|
inertiaTensor(0,2) = -xz; |
| 1114 |
|
inertiaTensor(1,0) = -xy; |
| 1115 |
< |
inertiaTensor(2,0) = xx + zz; |
| 1115 |
> |
inertiaTensor(1,1) = xx + zz; |
| 1116 |
|
inertiaTensor(1,2) = -yz; |
| 1117 |
|
inertiaTensor(2,0) = -xz; |
| 1118 |
|
inertiaTensor(2,1) = -yz; |
| 1140 |
|
SimInfo::MoleculeIterator i; |
| 1141 |
|
Molecule* mol; |
| 1142 |
|
|
| 1143 |
< |
Vector3d thisq(0.0); |
| 1144 |
< |
Vector3d thisv(0.0); |
| 1143 |
> |
Vector3d thisr(0.0); |
| 1144 |
> |
Vector3d thisp(0.0); |
| 1145 |
|
|
| 1146 |
< |
double thisMass = 0.0; |
| 1146 |
> |
double thisMass; |
| 1147 |
|
|
| 1148 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 1149 |
< |
thisq = mol->getCom()-com; |
| 1150 |
< |
thisv = mol->getComVel()-comVel; |
| 1151 |
< |
thisMass = mol->getMass(); |
| 1072 |
< |
angularMomentum += cross( thisq, thisv ) * thisMass; |
| 1149 |
> |
thisMass = mol->getMass(); |
| 1150 |
> |
thisr = mol->getCom()-com; |
| 1151 |
> |
thisp = (mol->getComVel()-comVel)*thisMass; |
| 1152 |
|
|
| 1153 |
+ |
angularMomentum += cross( thisr, thisp ); |
| 1154 |
+ |
|
| 1155 |
|
} |
| 1156 |
|
|
| 1157 |
|
#ifdef IS_MPI |
