Merge branch 'master' of http://github.com/SimTk/openmm

README.md

@@ -13,6 +13,6 @@ Getting Help
 
 Need Help? Check out the [documentation](https://simtk.org/docman/?group_id=161) and [discussion forums](https://simtk.org/forums/viewforum.php?f=161).
 
-[C++ API Reference](https://simtk.org/api_docs/openmm/api5_0/c++/)
+[C++ API Reference](https://simtk.org/api_docs/openmm/api6_0/c++/)
 
-[Python API Reference](https://simtk.org/api_docs/openmm/api5_0/python/)
+[Python API Reference](https://simtk.org/api_docs/openmm/api6_0/python/)

platforms/opencl/include/OpenCLPlatform.h

@@ -48,6 +48,7 @@ public:
     }
     double getSpeed() const;
     bool supportsDoublePrecision() const;
+    static bool isPlatformSupported();
     const std::string& getPropertyValue(const Context& context, const std::string& property) const;
     void setPropertyValue(Context& context, const std::string& property, const std::string& value) const;
     void contextCreated(ContextImpl& context, const std::map<std::string, std::string>& properties) const;

platforms/opencl/src/OpenCLPlatform.cpp

@@ -33,6 +33,10 @@
 #include "openmm/System.h"
 #include <algorithm>
 #include <sstream>
+#ifdef __APPLE__
+#include "sys/sysctl.h"
+#endif
+
 
 using namespace OpenMM;
 using std::map;
@@ -42,11 +46,13 @@ using std::vector;
 
 #ifdef OPENMM_OPENCL_BUILDING_STATIC_LIBRARY
 extern "C" void registerOpenCLPlatform() {
-    Platform::registerPlatform(new OpenCLPlatform());
+    if (OpenCLPlatform::isPlatformSupported())
+        Platform::registerPlatform(new OpenCLPlatform());
 }
 #else
 extern "C" OPENMM_EXPORT_OPENCL void registerPlatforms() {
-    Platform::registerPlatform(new OpenCLPlatform());
+    if (OpenCLPlatform::isPlatformSupported())
+        Platform::registerPlatform(new OpenCLPlatform());
 }
 #endif
 
@@ -102,6 +108,33 @@ bool OpenCLPlatform::supportsDoublePrecision() const {
     return true;
 }
 
+bool OpenCLPlatform::isPlatformSupported() {
+    // Return false for OpenCL implementations that are known
+    // to be buggy (Apple OSX since 10.7.5)
+
+#ifdef __APPLE__
+    char str[256];
+    size_t size = sizeof(str);
+    int ret = sysctlbyname("kern.osrelease", str, &size, NULL, 0);
+    if (ret != 0)
+        return false;
+
+    int major, minor, micro;
+    if (sscanf(str, "%d.%d.%d", &major, &minor, &micro) != 3)
+        return false;
+
+    if ((major > 11) || (major == 11 && minor > 4) || (major == 11 && minor == 4 && micro >= 2))
+        // 11.4.2 is the darwin release corresponding to OSX 10.7.5, which is the
+        // point at which a number of serious bugs were introduced into the
+        // Apple OpenCL libraries, resulting in catistrophically incorrect MD simulations
+        // (see https://github.com/SimTk/openmm/issues/395 for example). Once a fix is released,
+        // this version check should be updated.
+        return false;
+#endif
+
+    return true;
+}
+
 const string& OpenCLPlatform::getPropertyValue(const Context& context, const string& property) const {
     const ContextImpl& impl = getContextImpl(context);
     const PlatformData* data = reinterpret_cast<const PlatformData*>(impl.getPlatformData());

wrappers/python/simtk/openmm/app/element.py

@@ -42,22 +42,34 @@ class Element(object):
 
     The simtk.openmm.app.element module contains objects for all the standard chemical elements,
     such as element.hydrogen or element.carbon.  You can also call the static method Element.getBySymbol() to
-    look up the Element with a particular chemical symbol."""
+    look up the Element with a particular chemical symbol.
+
+    Element objects should be considered immutable
+    """
 
     _elements_by_symbol = {}
     _elements_by_atomic_number = {}
 
     def __init__(self, number, name, symbol, mass):
+        """Create a new element
+
+        Parameters:
+        number (int) The atomic number of the element
+        name (string) The name of the element
+        symbol (string) The chemical symbol of the element
+        mass (float) The atomic mass of the element
+        """
         ## The atomic number of the element
-        self.atomic_number = number
+        self._atomic_number = number
         ## The name of the element
-        self.name = name
+        self._name = name
         ## The chemical symbol of the element
-        self.symbol = symbol
+        self._symbol = symbol
         ## The atomic mass of the element
-        self.mass = mass
+        self._mass = mass
         # Index this element in a global table
         s = symbol.strip().upper()
+
         assert s not in Element._elements_by_symbol
         Element._elements_by_symbol[s] = self
         if number in Element._elements_by_atomic_number:
@@ -81,6 +93,28 @@ class Element(object):
     def getByAtomicNumber(atomic_number):
         return Element._elements_by_atomic_number[atomic_number]
 
+    @property
+    def atomic_number(self):
+        return self._atomic_number
+
+    @property
+    def name(self):
+        return self._name
+
+    @property
+    def symbol(self):
+        return self._symbol
+
+    @property
+    def mass(self):
+        return self._mass
+
+    def __str__(self):
+        return '<Element %s>' % self.name
+
+    def __repr__(self):
+        return '<Element %s>' % self.name
+
 # This is for backward compatibility.
 def get_by_symbol(symbol):
     s = symbol.strip().upper()

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -399,6 +399,7 @@ UNITS = {
            'unit.kilojoule_per_mole/(unit.nanometer*unit.nanometer)')),
 ("MonteCarloBarostat", "getFrequency") : (None, ()),
 ("MonteCarloAnisotropicBarostat", "getFrequency") : (None, ()),
+("NonbondedForce", "getPMEParameters") : (None, ('1/unit.nanometer', None, None, None)),
 ("NonbondedForce", "getExceptionParameters")
  : (None, (None, None,
            'unit.elementary_charge*unit.elementary_charge',

wrappers/python/tests/TestElement.py

+import pickle
+import unittest
+from simtk.unit import dalton
+from simtk.openmm.app import element
+
+class TestElement(unittest.TestCase):
+    def test_immutable(self):
+        def modifyElement():
+            # this should not be allowed
+            element.sulfur.mass = 100*dalton
+        self.assertRaises(AttributeError, modifyElement)
+    
+    def test_pickleable(self):
+        newsulfur = pickle.loads(pickle.dumps(element.sulfur))
+        # make sure that a new object is not created during the pickle/unpickle
+        # cycle
+        assert element.sulfur == newsulfur
+        assert element.sulfur is newsulfur
+        assert id(element.sulfur) == id(newsulfur)
+    
+    def test_attributes(self):
+        assert element.hydrogen.atomic_number == 1
+        assert element.hydrogen.symbol == 'H'
+        assert element.hydrogen.name == 'hydrogen'
+        assert element.hydrogen.mass == 1.007947 * dalton
+
+
+if __name__ == '__main__':
+    unittest.main()
+
+        
\ No newline at end of file