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Commit 9b6e8314 authored by Peter Eastman's avatar Peter Eastman
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Renamed a misnamed method in AmoebaMultipoleForce

parent dcc334a9
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plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 9b6e8314
......@@ -191,7 +191,7 @@ public:
*
* @return the index of the particle that was added
*/
int addParticle(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int addMultipole(double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity);
/**
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 9b6e8314
......@@ -127,7 +127,7 @@ void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
ewaldErrorTol = tol;
}
int AmoebaMultipoleForce::addParticle( double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int AmoebaMultipoleForce::addMultipole( double charge, const std::vector<double>& molecularDipole, const std::vector<double>& molecularQuadrupole, int axisType,
int multipoleAtomZ, int multipoleAtomX, int multipoleAtomY, double thole, double dampingFactor, double polarity) {
multipoles.push_back(MultipoleInfo( charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY, thole, dampingFactor, polarity));
return multipoles.size()-1;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp
View file @ 9b6e8314
......@@ -89,7 +89,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
// first N
 
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
 
// 3 H attached to first N
 
......@@ -112,23 +112,23 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
 
// second N
 
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
 
// 3 H attached to second N
 
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
 
// covalent maps
 
......@@ -943,7 +943,7 @@ static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::Polari
quadrupole[7] = data[quadrupoleIndex + 7];
quadrupole[8] = data[quadrupoleIndex + 8];
 
amoebaMultipoleForce->addParticle( data[chargeIndex], dipole, quadrupole, static_cast<int>(data[axisTypeIndex]),
amoebaMultipoleForce->addMultipole( data[chargeIndex], dipole, quadrupole, static_cast<int>(data[axisTypeIndex]),
static_cast<int>(data[multipoleAtomZIndex]), static_cast<int>(data[multipoleAtomXIndex]), static_cast<int>(data[multipoleAtomYIndex]),
data[tholeIndex], data[dampingFactorIndex], data[polarityIndex] );
data += entriesPerParticle;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ 9b6e8314
......@@ -102,7 +102,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaMultipoleForce* amoebaMu
// first N
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
// 3 H attached to first N
......@@ -125,23 +125,23 @@ static void setupMultipoleAmmonia(System& system, AmoebaMultipoleForce* amoebaMu
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9e-01, 2.8135002e-01, 4.96e-04 );
// second N
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.796e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9e-01, 3.1996314e-01, 1.073e-03 );
amoebaMultipoleForce->addMultipole( -5.796e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9e-01, 3.1996314e-01, 1.073e-03 );
// 3 H attached to second N
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9e-01, 2.8135002e-01, 4.96e-04 );
// covalent maps
......@@ -584,11 +584,11 @@ static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::Nonbond
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......@@ -811,11 +811,11 @@ static void testQuadrupoleValidation( FILE* log ){
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......@@ -1009,8 +1009,8 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
ionQuadrupole[6] = 0.0000000e+00;
ionQuadrupole[7] = 0.0000000e+00;
ionQuadrupole[8] = 0.0000000e+00;
amoebaMultipoleForce->addParticle( -1.0000000e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.9000000e-01, 3.9842202e-01, 4.0000000e-03 );
amoebaMultipoleForce->addParticle( 1.0000000e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.9000000e-01, 2.2209062e-01, 1.2000000e-04 );
amoebaMultipoleForce->addMultipole( -1.0000000e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.9000000e-01, 3.9842202e-01, 4.0000000e-03 );
amoebaMultipoleForce->addMultipole( 1.0000000e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.9000000e-01, 2.2209062e-01, 1.2000000e-04 );
// waters
......@@ -1054,11 +1054,11 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 2; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......@@ -1293,11 +1293,11 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::No
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp
View file @ 9b6e8314
......@@ -87,7 +87,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
// first N
 
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
 
// 3 H attached to first N
 
......@@ -110,23 +110,23 @@ static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
 
// second N
 
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
 
// 3 H attached to second N
 
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addMultipole( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
 
// covalent maps
 
......@@ -942,7 +942,7 @@ static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::Polari
quadrupole[7] = data[quadrupoleIndex + 7];
quadrupole[8] = data[quadrupoleIndex + 8];
 
amoebaMultipoleForce->addParticle( data[chargeIndex], dipole, quadrupole, static_cast<int>(data[axisTypeIndex]),
amoebaMultipoleForce->addMultipole( data[chargeIndex], dipole, quadrupole, static_cast<int>(data[axisTypeIndex]),
static_cast<int>(data[multipoleAtomZIndex]), static_cast<int>(data[multipoleAtomXIndex]), static_cast<int>(data[multipoleAtomYIndex]),
data[tholeIndex], data[dampingFactorIndex], data[polarityIndex] );
data += entriesPerParticle;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp
View file @ 9b6e8314
......@@ -100,7 +100,7 @@ static void setupMultipoleAmmonia(System& system, AmoebaMultipoleForce* amoebaMu
// first N
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
amoebaMultipoleForce->addMultipole( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
// 3 H attached to first N
......@@ -123,23 +123,23 @@ static void setupMultipoleAmmonia(System& system, AmoebaMultipoleForce* amoebaMu
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9e-01, 2.8135002e-01, 4.96e-04 );
// second N
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.796e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9e-01, 3.1996314e-01, 1.073e-03 );
amoebaMultipoleForce->addMultipole( -5.796e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9e-01, 3.1996314e-01, 1.073e-03 );
// 3 H attached to second N
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addParticle( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9e-01, 2.8135002e-01, 4.96e-04 );
amoebaMultipoleForce->addMultipole( 1.932e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9e-01, 2.8135002e-01, 4.96e-04 );
// covalent maps
......@@ -580,11 +580,11 @@ static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::Nonbond
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......@@ -792,11 +792,11 @@ static void testQuadrupoleValidation( FILE* log ){
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......@@ -945,8 +945,8 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
ionQuadrupole[6] = 0.0000000e+00;
ionQuadrupole[7] = 0.0000000e+00;
ionQuadrupole[8] = 0.0000000e+00;
amoebaMultipoleForce->addParticle( -1.0e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.90e-01, 3.9842202e-01, 4.00e-03 );
amoebaMultipoleForce->addParticle( 1.0e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.90e-01, 2.2209062e-01, 1.20e-04 );
amoebaMultipoleForce->addMultipole( -1.0e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.90e-01, 3.9842202e-01, 4.00e-03 );
amoebaMultipoleForce->addMultipole( 1.0e+00, ionDipole, ionQuadrupole, 5, -1, -1, -1, 3.90e-01, 2.2209062e-01, 1.20e-04 );
// waters
......@@ -990,11 +990,11 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 2; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......@@ -1214,11 +1214,11 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::No
hydrogenMolecularQuadrupole[8] = 1.3452570e-04;
for( unsigned int jj = 0; jj < numberOfParticles; jj += 3 ){
amoebaMultipoleForce->addParticle( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
amoebaMultipoleForce->addMultipole( -5.1966000e-01, oxygenMolecularDipole, oxygenMolecularQuadrupole, 1, jj+1, jj+2, -1,
3.9000000e-01, 3.0698765e-01, 8.3700000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+2, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
amoebaMultipoleForce->addMultipole( 2.5983000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 0, jj, jj+1, -1,
3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
}
......
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ 9b6e8314
......@@ -177,7 +177,7 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q7" ) );
molecularQuadrupole.push_back( quadrupole.getDoubleProperty( "q8" ) );
force->addParticle( particle.getDoubleProperty("charge"), molecularDipole, molecularQuadrupole,
force->addMultipole( particle.getDoubleProperty("charge"), molecularDipole, molecularQuadrupole,
particle.getIntProperty("axisType"),
particle.getIntProperty("multipoleAtomZ"),
particle.getIntProperty("multipoleAtomX"),
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp
View file @ 9b6e8314
......@@ -83,7 +83,7 @@ void testSerialization() {
for( unsigned int jj = 0; jj < 9; jj++ ){
molecularQuadrupole.push_back( static_cast<double>(rand()) );
}
force1.addParticle( static_cast<double>(ii+1), molecularDipole, molecularQuadrupole, AmoebaMultipoleForce::Bisector,
force1.addMultipole( static_cast<double>(ii+1), molecularDipole, molecularQuadrupole, AmoebaMultipoleForce::Bisector,
ii+1, ii+2, ii+3, static_cast<double>(rand()), static_cast<double>(rand()), static_cast<double>(rand()) );
for( unsigned int jj = 0; jj < covalentTypes.size(); jj++ ){
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 9b6e8314
......@@ -3463,7 +3463,7 @@ class AmoebaMultipoleGenerator:
atom.multipoleDict = savedMultipoleDict
atom.polarizationGroups = dict()
newIndex = force.addParticle(savedMultipoleDict['charge'], savedMultipoleDict['dipole'], savedMultipoleDict['quadrupole'], savedMultipoleDict['axisType'],
newIndex = force.addMultipole(savedMultipoleDict['charge'], savedMultipoleDict['dipole'], savedMultipoleDict['quadrupole'], savedMultipoleDict['axisType'],
zaxis, xaxis, yaxis, savedMultipoleDict['thole'], savedMultipoleDict['pdamp'], savedMultipoleDict['polarizability'])
if (atomIndex == newIndex):
force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.Covalent12, bonded12ParticleSets[atomIndex])
......
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