Fixed problems related to RMSDForce

openmmapi/include/OpenMM.h

@@ -65,6 +65,7 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/RBTorsionForce.h"
+#include "openmm/RMSDForce.h"
 #include "openmm/State.h"
 #include "openmm/System.h"
 #include "openmm/TabulatedFunction.h"

platforms/opencl/src/kernels/rmsd.cl

@@ -78,9 +78,9 @@ __kernel void computeRMSDForces(int numParticles, __global const real4* restrict
         int index = particles[i];
         real3 pos = posq[index].xyz - center;
         real3 refPos = referencePos[index].xyz;
-        real3 rotatedRef = (real3) (buffer[0]*refPos[0] + buffer[3]*refPos[1] + buffer[6]*refPos[2],
-                                    buffer[1]*refPos[0] + buffer[4]*refPos[1] + buffer[7]*refPos[2],
-                                    buffer[2]*refPos[0] + buffer[5]*refPos[1] + buffer[8]*refPos[2]);
+        real3 rotatedRef = (real3) (buffer[0]*refPos.x + buffer[3]*refPos.y + buffer[6]*refPos.z,
+                                    buffer[1]*refPos.x + buffer[4]*refPos.y + buffer[7]*refPos.z,
+                                    buffer[2]*refPos.x + buffer[5]*refPos.y + buffer[8]*refPos.z);
         forceBuffers[index].xyz -= (pos-rotatedRef)*scale;
     }
 }

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -453,5 +453,7 @@ UNITS = {
 ("DrudeSCFIntegrator", "getMinimizationErrorTolerance") : ("unit.kilojoules_per_mole/unit.nanometer", ()),
 ("RPMDIntegrator", "getContractions") : (None, ()),
 ("RPMDIntegrator", "getTotalEnergy") : ("unit.kilojoules_per_mole", ()),
+("RMSDForce", "getReferencePositions") : ("unit.nanometer", ()),
+("RMSDForce", "getParticles") : (None, ()),
 }
 

wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i

@@ -415,11 +415,14 @@ int Py_SequenceToVecVecVecDouble(PyObject* obj, std::vector<std::vector<std::vec
     $1 = &v;
 }
 %typemap(typecheck, precedence=SWIG_TYPECHECK_DOUBLE_ARRAY, fragment="Py_SequenceToVecVec3") const std::vector<Vec3>& {
-    std::vector<double> v;
+    std::vector<Vec3> v;
     int res=0;
     res = Py_SequenceToVecVec3($input, v);
     $1 = SWIG_IsOK(res);
 }
+%typemap(out) const std::vector<Vec3>& {
+    $result = copyVVec3ToList(*$1);
+}
 
 
 // typemap for const vector<double>