Fixed some compilation errors

CMakeLists.txt

@@ -296,7 +296,9 @@ SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM librar
 
 SET(EXTRA_LINK_FLAGS ${EXTRA_COMPILE_FLAGS})
 IF (CMAKE_SYSTEM_NAME MATCHES "Linux")
+    IF (NOT ANDROID)
         SET(EXTRA_LINK_FLAGS "${EXTRA_LINK_FLAGS} -Wl,--no-as-needed -lrt")
+    ENDIF (NOT ANDROID)
 ENDIF (CMAKE_SYSTEM_NAME MATCHES "Linux")
 
 IF(OPENMM_BUILD_SHARED_LIB)

platforms/cpu/src/CpuCustomManyParticleForce.cpp

@@ -199,7 +199,7 @@ void CpuCustomManyParticleForce::setUseCutoff(RealOpenMM distance) {
 }
 
 void CpuCustomManyParticleForce::setPeriodic(RealVec* periodicBoxVectors) {
-    assert(cutoff);
+    assert(useCutoff);
     assert(periodicBoxVectors[0][0] >= 2.0*cutoffDistance);
     assert(periodicBoxVectors[1][1] >= 2.0*cutoffDistance);
     assert(periodicBoxVectors[2][2] >= 2.0*cutoffDistance);

platforms/reference/src/SimTKReference/ObcParameters.cpp

@@ -382,9 +382,9 @@ void ObcParameters::setPeriodic(OpenMM::RealVec* vectors) {
 
     assert(_cutoff);
 
-    assert(boxSize[0][0] >= 2.0*_cutoffDistance);
-    assert(boxSize[1][1] >= 2.0*_cutoffDistance);
-    assert(boxSize[2][2] >= 2.0*_cutoffDistance);
+    assert(vectors[0][0] >= 2.0*_cutoffDistance);
+    assert(vectors[1][1] >= 2.0*_cutoffDistance);
+    assert(vectors[2][2] >= 2.0*_cutoffDistance);
 
     _periodic           = true;
     _periodicBoxVectors[0] = vectors[0];