Skip to content

GitLab

Commit 0671c7b0 authored by peastman's avatar peastman
Browse files

Elimininated obsolete SimTKOpenMMCommon files

parent 7fb10336
Show whitespace changes
Inline Side-by-side
Showing with 42 additions and 115 deletions
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomGBForce.h"
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ 0671c7b0
......@@ -26,7 +26,6 @@
#include <sstream>
#include <utility>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomManyParticleForce.h"
......
platforms/cpu/src/CpuCustomNonbondedForce.cpp
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomNonbondedForce.h"
......
platforms/cpu/src/CpuLangevinDynamics.cpp
View file @ 0671c7b0
......@@ -23,7 +23,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuLangevinDynamics.h"
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ 0671c7b0
......@@ -24,7 +24,6 @@
#include <complex>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForce.h"
#include "ReferenceForce.h"
......
platforms/cpu/src/CpuNonbondedForceVec4.cpp
View file @ 0671c7b0
......@@ -22,7 +22,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec4.h"
......
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ 0671c7b0
......@@ -22,7 +22,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec8.h"
#include "openmm/OpenMMException.h"
......
platforms/reference/include/CpuGBVI.h
View file @ 0671c7b0
......@@ -39,7 +39,7 @@ class CpuGBVI {
// GB/VI parameters
GBVIParameters* _gbviParameters;
RealOpenMMVector _switchDeriviative;
std::vector<RealOpenMM> _switchDeriviative;
public:
......@@ -93,7 +93,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii);
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
/**---------------------------------------------------------------------------------------
......@@ -174,7 +174,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges);
RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<RealOpenMM>& partialCharges);
/**---------------------------------------------------------------------------------------
......@@ -187,7 +187,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void computeBornForces(std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
/**---------------------------------------------------------------------------------------
......@@ -254,7 +254,7 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
RealOpenMMVector& getSwitchDeriviative();
std::vector<RealOpenMM>& getSwitchDeriviative();
/**---------------------------------------------------------------------------------------
......@@ -303,9 +303,9 @@ class CpuGBVI {
--------------------------------------------------------------------------------------- */
void printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
void printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<RealOpenMM>& partialCharges,
const std::vector<RealOpenMM>& bornRadii,
const std::vector<RealOpenMM>& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log);
......
platforms/reference/include/CpuObc.h
View file @ 0671c7b0
......@@ -39,7 +39,7 @@ class CpuObc {
// arrays containing OBC chain derivative
RealOpenMMVector _obcChain;
std::vector<RealOpenMM> _obcChain;
// flag to signal whether ACE approximation
// is to be included
......@@ -117,7 +117,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
RealOpenMMVector& getObcChain();
std::vector<RealOpenMM>& getObcChain();
/**---------------------------------------------------------------------------------------
......@@ -128,7 +128,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii);
void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
/**---------------------------------------------------------------------------------------
......@@ -142,8 +142,8 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void computeAceNonPolarForce(const ObcParameters* obcParameters, const RealOpenMMVector& bornRadii,
RealOpenMM* energy, RealOpenMMVector& forces) const;
void computeAceNonPolarForce(const ObcParameters* obcParameters, const std::vector<RealOpenMM>& bornRadii,
RealOpenMM* energy, std::vector<RealOpenMM>& forces) const;
/**---------------------------------------------------------------------------------------
......@@ -156,7 +156,7 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
RealOpenMM computeBornEnergyForces(const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& forces);
const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& forces);
/**---------------------------------------------------------------------------------------
......@@ -173,9 +173,9 @@ class CpuObc {
--------------------------------------------------------------------------------------- */
void printObc(const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<RealOpenMM>& partialCharges,
const std::vector<RealOpenMM>& bornRadii,
const std::vector<RealOpenMM>& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log);
......
platforms/reference/include/GBVIParameters.h
View file @ 0671c7b0
......@@ -25,7 +25,8 @@
#ifndef __GBVIParameters_H__
#define __GBVIParameters_H__
#include "SimTKOpenMMCommon.h"
#include "RealVec.h"
#include <vector>
namespace OpenMM {
......@@ -57,9 +58,9 @@ class GBVIParameters {
// parameter vectors
RealOpenMMVector _atomicRadii;
RealOpenMMVector _scaledRadii;
RealOpenMMVector _gammaParameters;
std::vector<RealOpenMM> _atomicRadii;
std::vector<RealOpenMM> _scaledRadii;
std::vector<RealOpenMM> _gammaParameters;
// cutoff and periodic boundary conditions
......@@ -160,7 +161,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getScaledRadii() const;
const std::vector<RealOpenMM>& getScaledRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -170,7 +171,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setScaledRadii(const RealOpenMMVector& scaledRadii);
void setScaledRadii(const std::vector<RealOpenMM>& scaledRadii);
/**---------------------------------------------------------------------------------------
......@@ -180,7 +181,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getAtomicRadii() const;
const std::vector<RealOpenMM>& getAtomicRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -190,7 +191,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setAtomicRadii(const RealOpenMMVector& atomicRadii);
void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
/**---------------------------------------------------------------------------------------
......@@ -200,7 +201,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getGammaParameters() const;
const std::vector<RealOpenMM>& getGammaParameters() const;
/**---------------------------------------------------------------------------------------
......@@ -210,7 +211,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setGammaParameters(const RealOpenMMVector& gammaParameters);
void setGammaParameters(const std::vector<RealOpenMM>& gammaParameters);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ObcParameters.h
View file @ 0671c7b0
......@@ -25,7 +25,8 @@
#ifndef __ObcParameters_H__
#define __ObcParameters_H__
#include "SimTKOpenMMCommon.h"
#include "RealVec.h"
#include <vector>
namespace OpenMM {
......@@ -57,8 +58,8 @@ class ObcParameters {
// scaled radius factors (S_kk in HCT paper)
RealOpenMMVector _atomicRadii;
RealOpenMMVector _scaledRadiusFactors;
std::vector<RealOpenMM> _atomicRadii;
std::vector<RealOpenMM> _scaledRadiusFactors;
// cutoff and periodic boundary conditions
......@@ -264,7 +265,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getScaledRadiusFactors() const;
const std::vector<RealOpenMM>& getScaledRadiusFactors() const;
/**---------------------------------------------------------------------------------------
......@@ -274,7 +275,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setScaledRadiusFactors(const RealOpenMMVector& scaledRadiusFactors);
void setScaledRadiusFactors(const std::vector<RealOpenMM>& scaledRadiusFactors);
/**---------------------------------------------------------------------------------------
......@@ -284,7 +285,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getAtomicRadii() const;
const std::vector<RealOpenMM>& getAtomicRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -294,7 +295,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setAtomicRadii(const RealOpenMMVector& atomicRadii);
void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceAndersenThermostat.h
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#ifndef __ReferenceAndersenThermostat_H__
#define __ReferenceAndersenThermostat_H__
#include "SimTKOpenMMCommon.h"
#include <vector>
namespace OpenMM {
......
platforms/reference/include/ReferenceCMAPTorsionIxn.h
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#ifndef __ReferenceCMAPTorsionIxn_H__
#define __ReferenceCMAPTorsionIxn_H__
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceBondIxn.h"
#include <vector>
......
platforms/reference/include/ReferenceConstraintAlgorithm.h
View file @ 0671c7b0
......@@ -25,8 +25,9 @@
#ifndef __ReferenceConstraintAlgorithm_H__
#define __ReferenceConstraintAlgorithm_H__
#include "SimTKOpenMMCommon.h"
#include "RealVec.h"
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......
platforms/reference/include/ReferenceDynamics.h
View file @ 0671c7b0
......@@ -26,7 +26,6 @@
#define __ReferenceDynamics_H__
#include "ReferenceConstraintAlgorithm.h"
#include "SimTKOpenMMCommon.h"
#include "openmm/System.h"
#include <cstddef>
#include <vector>
......
platforms/reference/include/ReferenceLincsAlgorithm.h
View file @ 0671c7b0
......@@ -131,12 +131,9 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
@param atomCoordinatesP atom coordinates prime
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
int apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
void apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses);
/**---------------------------------------------------------------------------------------
......@@ -148,12 +145,9 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
@param velocities atom velocities
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
int applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
void applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses);
};
......
platforms/reference/include/ReferenceMonteCarloBarostat.h
View file @ 0671c7b0
......@@ -25,7 +25,6 @@
#ifndef __ReferenceMonteCarloBarostat_H__
#define __ReferenceMonteCarloBarostat_H__
#include "SimTKOpenMMCommon.h"
#include <utility>
#include <vector>
......
platforms/reference/include/ReferencePME.h
View file @ 0671c7b0
......@@ -32,7 +32,7 @@
#ifndef __ReferencePME_H__
#define __ReferencePME_H__
#include "SimTKOpenMMCommon.h"
#include "RealVec.h"
#include "openmm/internal/windowsExport.h"
#include <vector>
......
platforms/reference/include/ReferencePairIxn.h
View file @ 0671c7b0
......@@ -27,6 +27,7 @@
#include "RealVec.h"
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......
platforms/reference/include/SimTKOpenMMCommon.h 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.
*/
#ifndef __SimTKOpenMMCommon_H__
#define __SimTKOpenMMCommon_H__
#include <vector>
#include <string>
#include "RealVec.h"
namespace OpenMM {
typedef std::vector<RealOpenMM> RealOpenMMVector;
typedef RealOpenMMVector::iterator RealOpenMMVectorI;
typedef RealOpenMMVector::const_iterator RealOpenMMVectorCI;
// ---------------------------------------------------------------------------------------
class SimTKOpenMMCommon {
public:
static const std::string NotSet;
static const RealOpenMM BigCutoffValue;
static const std::string Comment;
static const std::string Tab;
static const std::string YesU;
static const std::string YesUl;
static const std::string YesL;
// subroutine returns
static const int DefaultReturn;
static const int ErrorReturn;
};
} // namespace OpenMM
#endif // __SimTKOpenMMCommon_H__
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment