Merge branch 'headers' of https://github.com/peastman/openmm into headers

platforms/reference/src/SimTKReference/fftpack.h → platforms/reference/include/fftpack.h

@@ -14,7 +14,7 @@
 * drop a line to lindahl@cbr.su.se and let me know about it!
 */
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "SimTKOpenMMCommon.h"
 
 #ifndef _FFTPACK_H_
 #define _FFTPACK_H_

platforms/reference/src/ReferenceKernels.cpp

@@ -30,34 +30,34 @@
  * -------------------------------------------------------------------------- */
 
 #include "ReferenceKernels.h"
-#include "gbsa/CpuObc.h"
-#include "gbsa/CpuGBVI.h"
-#include "SimTKReference/ReferenceAndersenThermostat.h"
-#include "SimTKReference/ReferenceAngleBondIxn.h"
-#include "SimTKReference/ReferenceBondForce.h"
-#include "SimTKReference/ReferenceBrownianDynamics.h"
-#include "SimTKReference/ReferenceCCMAAlgorithm.h"
-#include "SimTKReference/ReferenceCMAPTorsionIxn.h"
-#include "SimTKReference/ReferenceCustomAngleIxn.h"
-#include "SimTKReference/ReferenceCustomBondIxn.h"
-#include "SimTKReference/ReferenceCustomCompoundBondIxn.h"
-#include "SimTKReference/ReferenceCustomDynamics.h"
-#include "SimTKReference/ReferenceCustomExternalIxn.h"
-#include "SimTKReference/ReferenceCustomGBIxn.h"
-#include "SimTKReference/ReferenceCustomHbondIxn.h"
-#include "SimTKReference/ReferenceCustomNonbondedIxn.h"
-#include "SimTKReference/ReferenceCustomTorsionIxn.h"
-#include "SimTKReference/ReferenceHarmonicBondIxn.h"
-#include "SimTKReference/ReferenceLJCoulomb14.h"
-#include "SimTKReference/ReferenceLJCoulombIxn.h"
-#include "SimTKReference/ReferenceMonteCarloBarostat.h"
-#include "SimTKReference/ReferenceProperDihedralBond.h"
-#include "SimTKReference/ReferenceRbDihedralBond.h"
-#include "SimTKReference/ReferenceStochasticDynamics.h"
-#include "SimTKReference/ReferenceVariableStochasticDynamics.h"
-#include "SimTKReference/ReferenceVariableVerletDynamics.h"
-#include "SimTKReference/ReferenceVerletDynamics.h"
-#include "SimTKReference/ReferenceVirtualSites.h"
+#include "CpuObc.h"
+#include "CpuGBVI.h"
+#include "ReferenceAndersenThermostat.h"
+#include "ReferenceAngleBondIxn.h"
+#include "ReferenceBondForce.h"
+#include "ReferenceBrownianDynamics.h"
+#include "ReferenceCCMAAlgorithm.h"
+#include "ReferenceCMAPTorsionIxn.h"
+#include "ReferenceCustomAngleIxn.h"
+#include "ReferenceCustomBondIxn.h"
+#include "ReferenceCustomCompoundBondIxn.h"
+#include "ReferenceCustomDynamics.h"
+#include "ReferenceCustomExternalIxn.h"
+#include "ReferenceCustomGBIxn.h"
+#include "ReferenceCustomHbondIxn.h"
+#include "ReferenceCustomNonbondedIxn.h"
+#include "ReferenceCustomTorsionIxn.h"
+#include "ReferenceHarmonicBondIxn.h"
+#include "ReferenceLJCoulomb14.h"
+#include "ReferenceLJCoulombIxn.h"
+#include "ReferenceMonteCarloBarostat.h"
+#include "ReferenceProperDihedralBond.h"
+#include "ReferenceRbDihedralBond.h"
+#include "ReferenceStochasticDynamics.h"
+#include "ReferenceVariableStochasticDynamics.h"
+#include "ReferenceVariableVerletDynamics.h"
+#include "ReferenceVerletDynamics.h"
+#include "ReferenceVirtualSites.h"
 #include "openmm/CMMotionRemover.h"
 #include "openmm/Context.h"
 #include "openmm/System.h"
@@ -71,7 +71,7 @@
 #include "openmm/internal/SplineFitter.h"
 #include "openmm/Integrator.h"
 #include "openmm/OpenMMException.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "lepton/CustomFunction.h"
 #include "lepton/Parser.h"
 #include "lepton/ParsedExpression.h"

platforms/reference/src/ReferencePlatform.cpp

@@ -33,8 +33,8 @@
 #include "ReferenceKernelFactory.h"
 #include "ReferenceKernels.h"
 #include "openmm/internal/ContextImpl.h"
-#include "SimTKUtilities/SimTKOpenMMRealType.h"
-#include "SimTKUtilities/RealVec.h"
+#include "SimTKOpenMMRealType.h"
+#include "RealVec.h"
 #include <vector>
 
 using namespace OpenMM;

platforms/reference/src/SimTKReference/PME.h

@@ -29,7 +29,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "SimTKOpenMMCommon.h"
 #include <vector>
 
 typedef RealOpenMM rvec[3];

platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp

@@ -25,7 +25,7 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceAndersenThermostat.h"
 
 using std::vector;

platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceAngleBondIxn.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceBondForce.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceBondForce.h"
 
 using std::vector;

platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "ReferenceBondIxn.h"
 

platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp

@@ -25,9 +25,9 @@
 #include <cstring>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceBrownianDynamics.h"
 #include "ReferenceVirtualSites.h"
 

platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMLog.h"
 #include "ReferenceCCMAAlgorithm.h"
 #include "ReferenceDynamics.h"
 #include "quern.h"

platforms/reference/src/SimTKReference/ReferenceConstraint.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceConstraint.h"
 #include "ReferenceDynamics.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp

@@ -24,9 +24,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceCustomAngleIxn.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceCustomBondIxn.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp

@@ -26,9 +26,9 @@
 #include <sstream>
 #include <utility>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "ReferenceCustomCompoundBondIxn.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp

@@ -22,9 +22,9 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceVirtualSites.h"
 #include "ReferenceCustomDynamics.h"
 #include "openmm/OpenMMException.h"

platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceCustomExternalIxn.h"
 #include "ReferenceForce.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "ReferenceCustomGBIxn.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp

@@ -26,9 +26,9 @@
 #include <sstream>
 #include <utility>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "ReferenceCustomHbondIxn.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp

@@ -25,9 +25,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "ReferenceCustomNonbondedIxn.h"
 

platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp

@@ -24,9 +24,9 @@
 #include <string.h>
 #include <sstream>
 
-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceCustomTorsionIxn.h"
 #include "ReferenceForce.h"