Merge remote-tracking branch 'upstream/master'

CMakeLists.txt

@@ -296,7 +296,9 @@ SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM librar
 
 SET(EXTRA_LINK_FLAGS ${EXTRA_COMPILE_FLAGS})
 IF (CMAKE_SYSTEM_NAME MATCHES "Linux")
-    SET(EXTRA_LINK_FLAGS "${EXTRA_LINK_FLAGS} -Wl,--no-as-needed -lrt")
+    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)
@@ -403,11 +405,11 @@ MARK_AS_ADVANCED(CUDA_BUILD_CUBIN)
 MARK_AS_ADVANCED(CUDA_BUILD_EMULATION)
 
 FIND_PACKAGE(OpenCL QUIET)
-IF(OPENCL_FOUND AND NOT APPLE)
+IF(OPENCL_FOUND)
     SET(OPENMM_BUILD_OPENCL_LIB ON CACHE BOOL "Build OpenMMOpenCL library")
-ELSE(OPENCL_FOUND AND NOT APPLE)
+ELSE(OPENCL_FOUND)
     SET(OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL "Build OpenMMOpenCL library")
-ENDIF(OPENCL_FOUND AND NOT APPLE)
+ENDIF(OPENCL_FOUND)
 IF(OPENMM_BUILD_OPENCL_LIB)
     ADD_SUBDIRECTORY(platforms/opencl)
 ENDIF(OPENMM_BUILD_OPENCL_LIB)

olla/include/openmm/kernels.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -494,6 +494,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CMAPTorsionForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) = 0;
 };
 
 /**

openmmapi/include/openmm/CMAPTorsionForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -148,6 +148,17 @@ public:
      * @param b4    the index of the fourth particle forming the second torsion
      */
     void setTorsionParameters(int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4);
+    /**
+     * Update the map and torsion parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setMapParameters() and setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
+     * to copy them over to the Context.
+     *
+     * The only information that can be updated with this method is the energy values for a map, and the map index
+     * for a torsion.  The size of a map and the set of particles involved in a torsion cannot be changed.  Also,
+     * new bonds and torsions cannot be added.
+     */
+    void updateParametersInContext(Context& context);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.

openmmapi/include/openmm/CustomAngleForce.h

@@ -194,7 +194,7 @@ public:
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-angle parameters.

openmmapi/include/openmm/CustomBondForce.h

@@ -191,7 +191,7 @@ public:
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-bond parameters.

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -289,7 +289,7 @@ public:
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-bond parameters.

openmmapi/include/openmm/CustomExternalForce.h

@@ -191,7 +191,7 @@ public:
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-particle parameters.

openmmapi/include/openmm/CustomGBForce.h

@@ -515,7 +515,7 @@ public:
     /**
      * Update the per-particle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-particle parameters.

openmmapi/include/openmm/CustomHbondForce.h

@@ -435,7 +435,7 @@ public:
      * Update the per-donor and per-acceptor parameters in a Context to match those stored in this Force object.  This method
      * provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
      * Simply call setDonorParameters() and setAcceptorParameters() to modify this object's parameters, then call
-     * updateParametersInState() to copy them over to the Context.
+     * updateParametersInContext() to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-donor and per-acceptor parameters.
      * All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can only

openmmapi/include/openmm/CustomTorsionForce.h

@@ -197,7 +197,7 @@ public:
     /**
      * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the values of per-torsion parameters.

openmmapi/include/openmm/GBSAOBCForce.h

@@ -176,7 +176,7 @@ public:
      * Update the particle parameters in a Context to match those stored in this Force object.  This method
      * provides an efficient method to update certain parameters in an existing Context without needing to
      * reinitialize it.  Simply call setParticleParameters() to modify this object's parameters, then call
-     * updateParametersInState() to copy them over to the Context.
+     * updateParametersInContext() to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-particle parameters.  All other aspects
      * of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed

openmmapi/include/openmm/HarmonicAngleForce.h

@@ -95,7 +95,7 @@ public:
     /**
      * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-angle parameters.  The set of particles involved

openmmapi/include/openmm/HarmonicBondForce.h

@@ -92,7 +92,7 @@ public:
     /**
      * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-bond parameters.  The set of particles involved

openmmapi/include/openmm/NonbondedForce.h

@@ -343,7 +343,7 @@ public:
      * Update the particle and exception parameters in a Context to match those stored in this Force object.  This method
      * provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
      * Simply call setParticleParameters() and setExceptionParameters() to modify this object's parameters, then call
-     * updateParametersInState() to copy them over to the Context.
+     * updateParametersInContext() to copy them over to the Context.
      * 
      * This method has several limitations.  The only information it updates is the parameters of particles and exceptions.
      * All other aspects of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be

openmmapi/include/openmm/PeriodicTorsionForce.h

@@ -101,7 +101,7 @@ public:
     /**
      * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-torsion parameters.  The set of particles involved

openmmapi/include/openmm/RBTorsionForce.h

@@ -110,7 +110,7 @@ public:
     /**
      * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
      * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
-     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
      * to copy them over to the Context.
      * 
      * The only information this method updates is the values of per-torsion parameters.  The set of particles involved

openmmapi/include/openmm/internal/CMAPTorsionForceImpl.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -60,6 +60,7 @@ public:
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }
     std::vector<std::string> getKernelNames();
+    void updateParametersInContext(ContextImpl& context);
     /**
      * Given the energy values for a map, compute the spline coefficients at each point of the map.
      */

openmmapi/include/openmm/internal/vectorize8.h

@@ -191,6 +191,18 @@ static inline fvec8 sqrt(const fvec8& v) {
     return fvec8(_mm256_sqrt_ps(v.val));
 }
 
+static inline fvec8 rsqrt(const fvec8& v) {
+    // Initial estimate of rsqrt().
+
+    fvec8 y(_mm256_rsqrt_ps(v.val));
+
+    // Perform an iteration of Newton refinement.
+
+    fvec8 x2 = v*0.5f;
+    y *= fvec8(1.5f)-x2*y*y;
+    return y;
+}
+
 static inline float dot8(const fvec8& v1, const fvec8& v2) {
     fvec8 result = _mm256_dp_ps(v1, v2, 0xF1);
     return _mm_cvtss_f32(result.lowerVec())+_mm_cvtss_f32(result.upperVec());

openmmapi/include/openmm/internal/vectorize_neon.h

@@ -251,11 +251,15 @@ static inline fvec4 abs(const fvec4& v) {
     return vabsq_f32(v);
 }
 
-static inline fvec4 sqrt(const fvec4& v) {
+static inline fvec4 rsqrt(const fvec4& v) {
     float32x4_t recipSqrt = vrsqrteq_f32(v);
     recipSqrt = vmulq_f32(recipSqrt, vrsqrtsq_f32(vmulq_f32(recipSqrt, v), recipSqrt));
     recipSqrt = vmulq_f32(recipSqrt, vrsqrtsq_f32(vmulq_f32(recipSqrt, v), recipSqrt));
-    return vmulq_f32(v, recipSqrt);
+    return recipSqrt;
+}
+
+static inline fvec4 sqrt(const fvec4& v) {
+    return rsqrt(v)*v;
 }
 
 static inline float dot3(const fvec4& v1, const fvec4& v2) {

openmmapi/include/openmm/internal/vectorize_pnacl.h

@@ -330,7 +330,7 @@ static inline fvec4 ceil(const fvec4& v) {
     return truncated + blend(0.0f, 1.0f, truncated<v);
 }
 
-static inline fvec4 sqrt(const fvec4& v) {
+static inline fvec4 rsqrt(const fvec4& v) {
     // Initial estimate of rsqrt().
 
     ivec4 i = (__m128i) v;
@@ -343,7 +343,11 @@ static inline fvec4 sqrt(const fvec4& v) {
     y *= 1.5f-x2*y*y;
     y *= 1.5f-x2*y*y;
     y *= 1.5f-x2*y*y;
-    return y*v;
+    return y;
+}
+
+static inline fvec4 sqrt(const fvec4& v) {
+    return rsqrt(v)*v;
 }
 
 #endif /*OPENMM_VECTORIZE_PNACL_H_*/