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Commit 0534520e authored by Peter's avatar Peter
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Merge branch 'headers' of https://github.com/peastman/openmm into headers

parents b8b00973 300758a5
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Showing with 79 additions and 79 deletions
platforms/reference/src/SimTKReference/fftpack.h → platforms/reference/include/fftpack.h
View file @ 0534520e
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
* drop a line to lindahl@cbr.su.se and let me know about it! * drop a line to lindahl@cbr.su.se and let me know about it!
*/ */
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#ifndef _FFTPACK_H_ #ifndef _FFTPACK_H_
#define _FFTPACK_H_ #define _FFTPACK_H_
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 0534520e
...@@ -30,34 +30,34 @@ ...@@ -30,34 +30,34 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "ReferenceKernels.h" #include "ReferenceKernels.h"
#include "gbsa/CpuObc.h" #include "CpuObc.h"
#include "gbsa/CpuGBVI.h" #include "CpuGBVI.h"
#include "SimTKReference/ReferenceAndersenThermostat.h" #include "ReferenceAndersenThermostat.h"
#include "SimTKReference/ReferenceAngleBondIxn.h" #include "ReferenceAngleBondIxn.h"
#include "SimTKReference/ReferenceBondForce.h" #include "ReferenceBondForce.h"
#include "SimTKReference/ReferenceBrownianDynamics.h" #include "ReferenceBrownianDynamics.h"
#include "SimTKReference/ReferenceCCMAAlgorithm.h" #include "ReferenceCCMAAlgorithm.h"
#include "SimTKReference/ReferenceCMAPTorsionIxn.h" #include "ReferenceCMAPTorsionIxn.h"
#include "SimTKReference/ReferenceCustomAngleIxn.h" #include "ReferenceCustomAngleIxn.h"
#include "SimTKReference/ReferenceCustomBondIxn.h" #include "ReferenceCustomBondIxn.h"
#include "SimTKReference/ReferenceCustomCompoundBondIxn.h" #include "ReferenceCustomCompoundBondIxn.h"
#include "SimTKReference/ReferenceCustomDynamics.h" #include "ReferenceCustomDynamics.h"
#include "SimTKReference/ReferenceCustomExternalIxn.h" #include "ReferenceCustomExternalIxn.h"
#include "SimTKReference/ReferenceCustomGBIxn.h" #include "ReferenceCustomGBIxn.h"
#include "SimTKReference/ReferenceCustomHbondIxn.h" #include "ReferenceCustomHbondIxn.h"
#include "SimTKReference/ReferenceCustomNonbondedIxn.h" #include "ReferenceCustomNonbondedIxn.h"
#include "SimTKReference/ReferenceCustomTorsionIxn.h" #include "ReferenceCustomTorsionIxn.h"
#include "SimTKReference/ReferenceHarmonicBondIxn.h" #include "ReferenceHarmonicBondIxn.h"
#include "SimTKReference/ReferenceLJCoulomb14.h" #include "ReferenceLJCoulomb14.h"
#include "SimTKReference/ReferenceLJCoulombIxn.h" #include "ReferenceLJCoulombIxn.h"
#include "SimTKReference/ReferenceMonteCarloBarostat.h" #include "ReferenceMonteCarloBarostat.h"
#include "SimTKReference/ReferenceProperDihedralBond.h" #include "ReferenceProperDihedralBond.h"
#include "SimTKReference/ReferenceRbDihedralBond.h" #include "ReferenceRbDihedralBond.h"
#include "SimTKReference/ReferenceStochasticDynamics.h" #include "ReferenceStochasticDynamics.h"
#include "SimTKReference/ReferenceVariableStochasticDynamics.h" #include "ReferenceVariableStochasticDynamics.h"
#include "SimTKReference/ReferenceVariableVerletDynamics.h" #include "ReferenceVariableVerletDynamics.h"
#include "SimTKReference/ReferenceVerletDynamics.h" #include "ReferenceVerletDynamics.h"
#include "SimTKReference/ReferenceVirtualSites.h" #include "ReferenceVirtualSites.h"
#include "openmm/CMMotionRemover.h" #include "openmm/CMMotionRemover.h"
#include "openmm/Context.h" #include "openmm/Context.h"
#include "openmm/System.h" #include "openmm/System.h"
...@@ -71,7 +71,7 @@ ...@@ -71,7 +71,7 @@
#include "openmm/internal/SplineFitter.h" #include "openmm/internal/SplineFitter.h"
#include "openmm/Integrator.h" #include "openmm/Integrator.h"
#include "openmm/OpenMMException.h" #include "openmm/OpenMMException.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "lepton/CustomFunction.h" #include "lepton/CustomFunction.h"
#include "lepton/Parser.h" #include "lepton/Parser.h"
#include "lepton/ParsedExpression.h" #include "lepton/ParsedExpression.h"
......
platforms/reference/src/ReferencePlatform.cpp
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...@@ -33,8 +33,8 @@ ...@@ -33,8 +33,8 @@
#include "ReferenceKernelFactory.h" #include "ReferenceKernelFactory.h"
#include "ReferenceKernels.h" #include "ReferenceKernels.h"
#include "openmm/internal/ContextImpl.h" #include "openmm/internal/ContextImpl.h"
#include "SimTKUtilities/SimTKOpenMMRealType.h" #include "SimTKOpenMMRealType.h"
#include "SimTKUtilities/RealVec.h" #include "RealVec.h"
#include <vector> #include <vector>
using namespace OpenMM; using namespace OpenMM;
......
platforms/reference/src/SimTKReference/PME.h
View file @ 0534520e
...@@ -29,7 +29,7 @@ ...@@ -29,7 +29,7 @@
* POSSIBILITY OF SUCH DAMAGE. * POSSIBILITY OF SUCH DAMAGE.
*/ */
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include <vector> #include <vector>
typedef RealOpenMM rvec[3]; typedef RealOpenMM rvec[3];
......
platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp
View file @ 0534520e
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceAndersenThermostat.h" #include "ReferenceAndersenThermostat.h"
using std::vector; using std::vector;
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ 0534520e
...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceAngleBondIxn.h" #include "ReferenceAngleBondIxn.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceBondForce.cpp
View file @ 0534520e
...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceBondForce.h" #include "ReferenceBondForce.h"
using std::vector; using std::vector;
......
platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @ 0534520e
...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
#include "ReferenceBondIxn.h" #include "ReferenceBondIxn.h"
......
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
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...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <cstring> #include <cstring>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceBrownianDynamics.h" #include "ReferenceBrownianDynamics.h"
#include "ReferenceVirtualSites.h" #include "ReferenceVirtualSites.h"
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
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...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "ReferenceCCMAAlgorithm.h" #include "ReferenceCCMAAlgorithm.h"
#include "ReferenceDynamics.h" #include "ReferenceDynamics.h"
#include "quern.h" #include "quern.h"
......
platforms/reference/src/SimTKReference/ReferenceConstraint.cpp
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...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceConstraint.h" #include "ReferenceConstraint.h"
#include "ReferenceDynamics.h" #include "ReferenceDynamics.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ 0534520e
...@@ -24,9 +24,9 @@ ...@@ -24,9 +24,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceCustomAngleIxn.h" #include "ReferenceCustomAngleIxn.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
View file @ 0534520e
...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceCustomBondIxn.h" #include "ReferenceCustomBondIxn.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
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...@@ -26,9 +26,9 @@ ...@@ -26,9 +26,9 @@
#include <sstream> #include <sstream>
#include <utility> #include <utility>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
#include "ReferenceCustomCompoundBondIxn.h" #include "ReferenceCustomCompoundBondIxn.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
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...@@ -22,9 +22,9 @@ ...@@ -22,9 +22,9 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceVirtualSites.h" #include "ReferenceVirtualSites.h"
#include "ReferenceCustomDynamics.h" #include "ReferenceCustomDynamics.h"
#include "openmm/OpenMMException.h" #include "openmm/OpenMMException.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
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...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceCustomExternalIxn.h" #include "ReferenceCustomExternalIxn.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
View file @ 0534520e
...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
#include "ReferenceCustomGBIxn.h" #include "ReferenceCustomGBIxn.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
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...@@ -26,9 +26,9 @@ ...@@ -26,9 +26,9 @@
#include <sstream> #include <sstream>
#include <utility> #include <utility>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
#include "ReferenceCustomHbondIxn.h" #include "ReferenceCustomHbondIxn.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
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...@@ -25,9 +25,9 @@ ...@@ -25,9 +25,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
#include "ReferenceCustomNonbondedIxn.h" #include "ReferenceCustomNonbondedIxn.h"
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
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...@@ -24,9 +24,9 @@ ...@@ -24,9 +24,9 @@
#include <string.h> #include <string.h>
#include <sstream> #include <sstream>
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "SimTKOpenMMUtilities.h"
#include "ReferenceCustomTorsionIxn.h" #include "ReferenceCustomTorsionIxn.h"
#include "ReferenceForce.h" #include "ReferenceForce.h"
......
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