Merge github.com:leeping/openmm

e3b25204 · leeping · 41e9a095 · 74415dd9 · e3b25204 · e3b25204
Commit e3b25204 authored Jul 15, 2013 by leeping
20 changed files
--- a/platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
+++ b/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"

--- a/platforms/reference/src/SimTKReference/ReferenceConstraint.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
+++ b/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"

--- a/platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
+++ b/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"


--- a/platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceDynamics.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 "ReferenceDynamics.h"

 #include <cstdio>

--- a/platforms/reference/src/SimTKReference/ReferenceForce.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceForce.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 "ReferenceForce.h"

 #include <cstdio>

--- a/platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.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 "ReferenceHarmonicBondIxn.h"
 #include "ReferenceForce.h"


--- a/platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.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 "ReferenceLJCoulomb14.h"
 #include "ReferenceForce.h"


--- a/platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
@@ -26,9 +26,9 @@
 #include <sstream>
 #include <complex>

-#include "../SimTKUtilities/SimTKOpenMMCommon.h"
-#include "../SimTKUtilities/SimTKOpenMMLog.h"
-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceLJCoulombIxn.h"
 #include "ReferenceForce.h"
 #include "PME.h"

--- a/platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
@@ -24,9 +24,9 @@
 #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 "ReferenceLincsAlgorithm.h"
 #include "ReferenceDynamics.h"
 #include "openmm/OpenMMException.h"

--- a/platforms/reference/src/SimTKReference/ReferenceMonteCarloBarostat.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceMonteCarloBarostat.cpp
@@ -25,7 +25,7 @@
 #include <string.h>
 #include <sstream>

-#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "ReferenceMonteCarloBarostat.h"

 using namespace std;

--- a/platforms/reference/src/SimTKReference/ReferencePairIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferencePairIxn.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 "ReferencePairIxn.h"


--- a/platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.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 "ReferenceProperDihedralBond.h"
 #include "ReferenceForce.h"