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Commit 0671c7b0 authored by peastman's avatar peastman
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Elimininated obsolete SimTKOpenMMCommon files

parent 7fb10336
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Showing with 55 additions and 118 deletions
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceLJCoulomb14.h"
#include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @ 0671c7b0
......@@ -27,7 +27,6 @@
#include <complex>
#include <algorithm>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceLJCoulombIxn.h"
#include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
View file @ 0671c7b0
......@@ -24,7 +24,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceLincsAlgorithm.h"
#include "ReferenceDynamics.h"
......@@ -213,12 +212,9 @@ void ReferenceLincsAlgorithm::updateAtomPositions(int numberOfAtoms, vector<Real
@param atomCoordinatesP atom coordinates prime
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
int ReferenceLincsAlgorithm::apply(int numberOfAtoms, vector<RealVec>& atomCoordinates,
void ReferenceLincsAlgorithm::apply(int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses) {
......@@ -233,7 +229,7 @@ int ReferenceLincsAlgorithm::apply(int numberOfAtoms, vector<RealVec>& atomCoord
// ---------------------------------------------------------------------------------------
if (_numberOfConstraints == 0)
return SimTKOpenMMCommon::DefaultReturn;
return;
if (!_hasInitialized)
initialize(numberOfAtoms, inverseMasses);
......@@ -287,9 +283,6 @@ int ReferenceLincsAlgorithm::apply(int numberOfAtoms, vector<RealVec>& atomCoord
}
solveMatrix();
updateAtomPositions(numberOfAtoms, atomCoordinatesP, inverseMasses);
return SimTKOpenMMCommon::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
......@@ -301,12 +294,9 @@ int ReferenceLincsAlgorithm::apply(int numberOfAtoms, vector<RealVec>& atomCoord
@param velocities atom velocities
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
int ReferenceLincsAlgorithm::applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
void ReferenceLincsAlgorithm::applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses) {
throw OpenMM::OpenMMException("applyToVelocities is not implemented");
}
platforms/reference/src/SimTKReference/ReferencePairIxn.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "ReferencePairIxn.h"
......
platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceProperDihedralBond.h"
#include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceRbDihedralBond.h"
#include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <cstring>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceStochasticDynamics.h"
#include "ReferenceVirtualSites.h"
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 0671c7b0
......@@ -26,7 +26,6 @@
#include <sstream>
#include <algorithm>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceVariableStochasticDynamics.h"
#include "ReferenceVirtualSites.h"
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp
View file @ 0671c7b0
......@@ -26,7 +26,6 @@
#include <sstream>
#include <algorithm>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceVariableVerletDynamics.h"
#include "ReferenceVirtualSites.h"
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <cstring>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceVerletDynamics.h"
#include "ReferenceVirtualSites.h"
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMCommon.cpp deleted 100644 → 0
View file @ 7fb10336
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
using namespace OpenMM;
// static settings
// initialization of static data members
const std::string SimTKOpenMMCommon::NotSet = std::string("NotSet");
const std::string SimTKOpenMMCommon::Comment = std::string("#");
const std::string SimTKOpenMMCommon::Tab = std::string("\t");
const int SimTKOpenMMCommon::DefaultReturn = 0;
const int SimTKOpenMMCommon::ErrorReturn = -1;
const RealOpenMM SimTKOpenMMCommon::BigCutoffValue = 1.0e+05;
platforms/reference/src/gbsa/CpuGBVI.cpp
View file @ 0671c7b0
......@@ -26,7 +26,6 @@
#include <sstream>
#include <stdio.h>
#include "SimTKOpenMMCommon.h"
#include "ReferenceForce.h"
#include "CpuGBVI.h"
......@@ -86,7 +85,7 @@ void CpuGBVI::setGBVIParameters(GBVIParameters* gbviParameters) {
--------------------------------------------------------------------------------------- */
RealOpenMMVector& CpuGBVI::getSwitchDeriviative() {
vector<RealOpenMM>& CpuGBVI::getSwitchDeriviative() {
return _switchDeriviative;
}
......@@ -203,7 +202,7 @@ void CpuGBVI::computeBornRadiiUsingQuinticSpline(RealOpenMM atomicRadius3, RealO
--------------------------------------------------------------------------------------- */
void CpuGBVI::computeBornRadii(const vector<RealVec>& atomCoordinates, RealOpenMMVector& bornRadii) {
void CpuGBVI::computeBornRadii(const vector<RealVec>& atomCoordinates, vector<RealOpenMM>& bornRadii) {
// ---------------------------------------------------------------------------------------
......@@ -218,10 +217,10 @@ void CpuGBVI::computeBornRadii(const vector<RealVec>& atomCoordinates, RealOpenM
GBVIParameters* gbviParameters = getGBVIParameters();
int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
const vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii();
const vector<RealOpenMM>& scaledRadii = gbviParameters->getScaledRadii();
RealOpenMMVector& switchDeriviatives = getSwitchDeriviative();
vector<RealOpenMM>& switchDeriviatives = getSwitchDeriviative();
// ---------------------------------------------------------------------------------------
......@@ -448,7 +447,7 @@ RealOpenMM CpuGBVI::Sgb(RealOpenMM t) {
--------------------------------------------------------------------------------------- */
RealOpenMM CpuGBVI::computeBornEnergy(const vector<RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges) {
RealOpenMM CpuGBVI::computeBornEnergy(const vector<RealVec>& atomCoordinates, const vector<RealOpenMM>& partialCharges) {
// ---------------------------------------------------------------------------------------
......@@ -466,12 +465,12 @@ RealOpenMM CpuGBVI::computeBornEnergy(const vector<RealVec>& atomCoordinates, co
const GBVIParameters* gbviParameters = getGBVIParameters();
const RealOpenMM preFactor = gbviParameters->getElectricConstant();
const int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const RealOpenMMVector& gammaParameters = gbviParameters->getGammaParameters();
const vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii();
const vector<RealOpenMM>& gammaParameters = gbviParameters->getGammaParameters();
// compute Born radii
RealOpenMMVector bornRadii(numberOfAtoms);
vector<RealOpenMM> bornRadii(numberOfAtoms);
computeBornRadii(atomCoordinates, bornRadii);
// ---------------------------------------------------------------------------------------
......@@ -532,7 +531,7 @@ RealOpenMM CpuGBVI::computeBornEnergy(const vector<RealVec>& atomCoordinates, co
--------------------------------------------------------------------------------------- */
void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const vector<RealOpenMM>& partialCharges,
std::vector<OpenMM::RealVec>& inputForces) {
// ---------------------------------------------------------------------------------------
......@@ -551,8 +550,8 @@ void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const Rea
const GBVIParameters* gbviParameters = getGBVIParameters();
const int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const RealOpenMMVector& gammaParameters = gbviParameters->getGammaParameters();
const vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii();
const vector<RealOpenMM>& gammaParameters = gbviParameters->getGammaParameters();
// ---------------------------------------------------------------------------------------
......@@ -564,7 +563,7 @@ void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const Rea
// compute Born radii
RealOpenMMVector bornRadii(numberOfAtoms);
vector<RealOpenMM> bornRadii(numberOfAtoms);
computeBornRadii(atomCoordinates, bornRadii);
// set energy/forces to zero
......@@ -576,7 +575,7 @@ void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const Rea
forces[ii][2] = zero;
}
RealOpenMMVector bornForces(numberOfAtoms, 0.0);
vector<RealOpenMM> bornForces(numberOfAtoms, 0.0);
// ---------------------------------------------------------------------------------------
......@@ -645,8 +644,8 @@ void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const Rea
// dGpol/dBornRadius) = bornForces[]
// dBornRadius/dr = (1/3)*(bR**4)*(dV/dr)
const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
const RealOpenMMVector& switchDeriviative = getSwitchDeriviative();
const vector<RealOpenMM>& scaledRadii = gbviParameters->getScaledRadii();
const vector<RealOpenMM>& switchDeriviative = getSwitchDeriviative();
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
RealOpenMM R = atomicRadii[atomI];
......@@ -748,9 +747,9 @@ void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const Rea
--------------------------------------------------------------------------------------- */
void CpuGBVI::printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
void CpuGBVI::printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const vector<RealOpenMM>& partialCharges,
const vector<RealOpenMM>& bornRadii,
const vector<RealOpenMM>& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log) {
......@@ -758,8 +757,8 @@ void CpuGBVI::printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, con
const GBVIParameters* gbviParameters = getGBVIParameters();
const int numberOfAtoms = gbviParameters->getNumberOfAtoms();
const RealOpenMMVector& atomicRadii = gbviParameters->getAtomicRadii();
const RealOpenMMVector& gammaParameters = gbviParameters->getGammaParameters();
const vector<RealOpenMM>& atomicRadii = gbviParameters->getAtomicRadii();
const vector<RealOpenMM>& gammaParameters = gbviParameters->getGammaParameters();
// ---------------------------------------------------------------------------------------
......@@ -769,8 +768,8 @@ void CpuGBVI::printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, con
// ---------------------------------------------------------------------------------------
const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
const RealOpenMMVector& switchDeriviative = getSwitchDeriviative();
const vector<RealOpenMM>& scaledRadii = gbviParameters->getScaledRadii();
const vector<RealOpenMM>& switchDeriviative = getSwitchDeriviative();
RealOpenMM tau = static_cast<RealOpenMM>(gbviParameters->getTau());
int useComparisonFormat = 1;
......
platforms/reference/src/gbsa/CpuObc.cpp
View file @ 0671c7b0
......@@ -28,7 +28,6 @@
#include <cmath>
#include <cstdio>
#include "SimTKOpenMMCommon.h"
#include "ReferenceForce.h"
#include "CpuObc.h"
......@@ -144,9 +143,9 @@ void CpuObc::computeBornRadii(const vector<RealVec>& atomCoordinates, vector<Rea
ObcParameters* obcParameters = getObcParameters();
int numberOfAtoms = obcParameters->getNumberOfAtoms();
const RealOpenMMVector& atomicRadii = obcParameters->getAtomicRadii();
const RealOpenMMVector& scaledRadiusFactor = obcParameters->getScaledRadiusFactors();
RealOpenMMVector& obcChain = getObcChain();
const vector<RealOpenMM>& atomicRadii = obcParameters->getAtomicRadii();
const vector<RealOpenMM>& scaledRadiusFactor = obcParameters->getScaledRadiusFactors();
vector<RealOpenMM>& obcChain = getObcChain();
RealOpenMM dielectricOffset = obcParameters->getDielectricOffset();
RealOpenMM alphaObc = obcParameters->getAlphaObc();
......@@ -237,9 +236,9 @@ void CpuObc::computeBornRadii(const vector<RealVec>& atomCoordinates, vector<Rea
--------------------------------------------------------------------------------------- */
void CpuObc::computeAceNonPolarForce(const ObcParameters* obcParameters,
const RealOpenMMVector& bornRadii,
const vector<RealOpenMM>& bornRadii,
RealOpenMM* energy,
RealOpenMMVector& forces) const {
vector<RealOpenMM>& forces) const {
// ---------------------------------------------------------------------------------------
......@@ -254,7 +253,7 @@ void CpuObc::computeAceNonPolarForce(const ObcParameters* obcParameters,
const RealOpenMM probeRadius = obcParameters->getProbeRadius();
const RealOpenMM surfaceAreaFactor = obcParameters->getPi4Asolv();
const RealOpenMMVector& atomicRadii = obcParameters->getAtomicRadii();
const vector<RealOpenMM>& atomicRadii = obcParameters->getAtomicRadii();
int numberOfAtoms = obcParameters->getNumberOfAtoms();
// the original ACE equation is based on Eq.2 of
......@@ -295,7 +294,7 @@ void CpuObc::computeAceNonPolarForce(const ObcParameters* obcParameters,
--------------------------------------------------------------------------------------- */
RealOpenMM CpuObc::computeBornEnergyForces(const vector<RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, vector<RealVec>& inputForces) {
const vector<RealOpenMM>& partialCharges, vector<RealVec>& inputForces) {
// ---------------------------------------------------------------------------------------
......@@ -325,13 +324,13 @@ RealOpenMM CpuObc::computeBornEnergyForces(const vector<RealVec>& atomCoordinate
// compute Born radii
RealOpenMMVector bornRadii(numberOfAtoms);
vector<RealOpenMM> bornRadii(numberOfAtoms);
computeBornRadii(atomCoordinates, bornRadii);
// set energy/forces to zero
RealOpenMM obcEnergy = zero;
RealOpenMMVector bornForces(numberOfAtoms, 0.0);
vector<RealOpenMM> bornForces(numberOfAtoms, 0.0);
// ---------------------------------------------------------------------------------------
......@@ -410,13 +409,13 @@ RealOpenMM CpuObc::computeBornEnergyForces(const vector<RealVec>& atomCoordinate
// second main loop
const RealOpenMMVector& obcChain = getObcChain();
const RealOpenMMVector& atomicRadii = _obcParameters->getAtomicRadii();
const vector<RealOpenMM>& obcChain = getObcChain();
const vector<RealOpenMM>& atomicRadii = _obcParameters->getAtomicRadii();
const RealOpenMM alphaObc = _obcParameters->getAlphaObc();
const RealOpenMM betaObc = _obcParameters->getBetaObc();
const RealOpenMM gammaObc = _obcParameters->getGammaObc();
const RealOpenMMVector& scaledRadiusFactor = _obcParameters->getScaledRadiusFactors();
const vector<RealOpenMM>& scaledRadiusFactor = _obcParameters->getScaledRadiusFactors();
// compute factor that depends only on the outer loop index
......@@ -515,9 +514,9 @@ RealOpenMM CpuObc::computeBornEnergyForces(const vector<RealVec>& atomCoordinate
--------------------------------------------------------------------------------------- */
void CpuObc::printObc(const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const vector<RealOpenMM>& partialCharges,
const vector<RealOpenMM>& bornRadii,
const vector<RealOpenMM>& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log) {
......@@ -525,10 +524,10 @@ void CpuObc::printObc(const std::vector<OpenMM::RealVec>& atomCoordinates,
const ObcParameters* obcParameters = getObcParameters();
const int numberOfAtoms = obcParameters->getNumberOfAtoms();
const RealOpenMMVector& atomicRadii = obcParameters->getAtomicRadii();
const vector<RealOpenMM>& atomicRadii = obcParameters->getAtomicRadii();
const RealOpenMM preFactor = 2.0*obcParameters->getElectricConstant();
const RealOpenMMVector& obcChain = getObcChain();
const RealOpenMMVector& scaledRadiusFactor = obcParameters->getScaledRadiusFactors();
const vector<RealOpenMM>& obcChain = getObcChain();
const vector<RealOpenMM>& scaledRadiusFactor = obcParameters->getScaledRadiusFactors();
const RealOpenMM alphaObc = obcParameters->getAlphaObc();
const RealOpenMM betaObc = obcParameters->getBetaObc();
......
platforms/reference/src/gbsa/GBVIParameters.cpp
View file @ 0671c7b0
......@@ -28,7 +28,6 @@
#include "openmm/OpenMMException.h"
#include "GBVIParameters.h"
#include "SimTKOpenMMCommon.h"
using std::vector;
using namespace OpenMM;
......@@ -146,7 +145,7 @@ void GBVIParameters::setSoluteDielectric(RealOpenMM soluteDielectric) {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& GBVIParameters::getAtomicRadii() const {
const vector<RealOpenMM>& GBVIParameters::getAtomicRadii() const {
return _atomicRadii;
}
......@@ -158,7 +157,7 @@ const RealOpenMMVector& GBVIParameters::getAtomicRadii() const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setAtomicRadii(const RealOpenMMVector& atomicRadii) {
void GBVIParameters::setAtomicRadii(const vector<RealOpenMM>& atomicRadii) {
if (atomicRadii.size() == _atomicRadii.size()) {
for (unsigned int ii = 0; ii < atomicRadii.size(); ii++) {
......@@ -170,7 +169,7 @@ void GBVIParameters::setAtomicRadii(const RealOpenMMVector& atomicRadii) {
msg << atomicRadii.size();
msg << " current size=" << _atomicRadii.size();
throw OpenMM::OpenMMException(msg.str());
}
}
}
......@@ -181,7 +180,7 @@ void GBVIParameters::setAtomicRadii(const RealOpenMMVector& atomicRadii) {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& GBVIParameters::getScaledRadii() const {
const vector<RealOpenMM>& GBVIParameters::getScaledRadii() const {
return _scaledRadii;
}
......@@ -193,7 +192,7 @@ const RealOpenMMVector& GBVIParameters::getScaledRadii() const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setScaledRadii(const RealOpenMMVector& scaledRadii) {
void GBVIParameters::setScaledRadii(const vector<RealOpenMM>& scaledRadii) {
if (scaledRadii.size() == _scaledRadii.size()) {
for (unsigned int ii = 0; ii < scaledRadii.size(); ii++) {
......@@ -218,7 +217,7 @@ void GBVIParameters::setScaledRadii(const RealOpenMMVector& scaledRadii) {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& GBVIParameters::getGammaParameters() const {
const vector<RealOpenMM>& GBVIParameters::getGammaParameters() const {
return _gammaParameters;
}
......@@ -230,7 +229,7 @@ const RealOpenMMVector& GBVIParameters::getGammaParameters() const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setGammaParameters(const RealOpenMMVector& gammas) {
void GBVIParameters::setGammaParameters(const vector<RealOpenMM>& gammas) {
if (gammas.size() == _gammaParameters.size()) {
for (unsigned int ii = 0; ii < gammas.size(); ii++) {
......
platforms/reference/src/gbsa/ObcParameters.cpp
View file @ 0671c7b0
......@@ -28,7 +28,6 @@
#include "openmm/OpenMMException.h"
#include "ObcParameters.h"
#include "SimTKOpenMMCommon.h"
using std::vector;
using namespace OpenMM;
......@@ -271,7 +270,7 @@ void ObcParameters::setPi4Asolv(RealOpenMM pi4Asolv) {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& ObcParameters::getAtomicRadii() const {
const vector<RealOpenMM>& ObcParameters::getAtomicRadii() const {
return _atomicRadii;
}
......@@ -283,7 +282,7 @@ const RealOpenMMVector& ObcParameters::getAtomicRadii() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setAtomicRadii(const RealOpenMMVector& atomicRadii) {
void ObcParameters::setAtomicRadii(const vector<RealOpenMM>& atomicRadii) {
if (atomicRadii.size() == _atomicRadii.size()) {
for (unsigned int ii = 0; ii < atomicRadii.size(); ii++) {
......@@ -307,7 +306,7 @@ void ObcParameters::setAtomicRadii(const RealOpenMMVector& atomicRadii) {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& ObcParameters::getScaledRadiusFactors() const {
const vector<RealOpenMM>& ObcParameters::getScaledRadiusFactors() const {
return _scaledRadiusFactors;
}
......@@ -319,7 +318,7 @@ const RealOpenMMVector& ObcParameters::getScaledRadiusFactors() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setScaledRadiusFactors(const RealOpenMMVector& scaledRadiusFactors) {
void ObcParameters::setScaledRadiusFactors(const vector<RealOpenMM>& scaledRadiusFactors) {
if (scaledRadiusFactors.size() == _scaledRadiusFactors.size()) {
for (unsigned int ii = 0; ii < scaledRadiusFactors.size(); ii++) {
......
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