Merged changes from main branch

openmmapi/include/OpenMM.h

@@ -62,6 +62,7 @@
 #include "openmm/RBTorsionForce.h"
 #include "openmm/State.h"
 #include "openmm/System.h"
+#include "openmm/TabulatedFunction.h"
 #include "openmm/Units.h"
 #include "openmm/VariableLangevinIntegrator.h"
 #include "openmm/VariableVerletIntegrator.h"

openmmapi/include/openmm/AndersenThermostat.h

@@ -74,6 +74,15 @@ public:
     double getDefaultTemperature() const {
         return defaultTemp;
     }
+    /**
+     * Set the default temperature of the heat bath.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param temperature         the default temperature of the heat bath (in Kelvin)
+     */
+    void setDefaultTemperature(double temperature) {
+        defaultTemp = temperature;
+    }
     /**
      * Get the default collision frequency (in 1/ps).
      *
@@ -82,6 +91,15 @@ public:
     double getDefaultCollisionFrequency() const {
         return defaultFreq;
     }
+    /**
+     * Set the default collision frequency.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param frequency         the default collision frequency (in 1/ps)
+     */
+    void setDefaultCollisionFrequency(double frequency) {
+        defaultFreq = frequency;
+    }
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */

openmmapi/include/openmm/CustomExternalForce.h

@@ -61,7 +61,7 @@ namespace OpenMM {
  * This force depends on four parameters: the spring constant k and equilibrium coordinates x0, y0, and z0.  The following code defines these parameters:
  *
  * <tt><pre>
- * force->addGlobalParameter("k");
+ * force->addGlobalParameter("k", 100.0);
  * force->addPerParticleParameter("x0");
  * force->addPerParticleParameter("y0");
  * force->addPerParticleParameter("z0");

openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h

@@ -100,6 +100,15 @@ public:
     const Vec3& getDefaultPressure() const {
         return defaultPressure;
     }
+    /**
+     * Set the default pressure acting on the system.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param pressure   the default pressure acting on the system, measured in bar.
+     */
+    void setDefaultPressure(const Vec3& pressure) {
+        defaultPressure = pressure;
+    }
     /**
      * Get whether to allow the X dimension of the periodic box to change size.
      */

openmmapi/include/openmm/MonteCarloBarostat.h

@@ -74,6 +74,15 @@ public:
     double getDefaultPressure() const {
         return defaultPressure;
     }
+    /**
+     * Set the default pressure acting on the system.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param pressure   the default pressure acting on the system, measured in bar.
+     */
+    void setDefaultPressure(double pressure) {
+        defaultPressure = pressure;
+    }
     /**
      * Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
      * 0, the barostat is disabled.

openmmapi/include/openmm/internal/ThreadPool.h

@@ -53,7 +53,13 @@ class OPENMM_EXPORT ThreadPool {
 public:
     class Task;
     class ThreadData;
-    ThreadPool();
+    /**
+     * Create a ThreadPool.
+     *
+     * @param numThreads  the number of worker threads to create.  If this is 0 (the default), the
+     *                    number of threads is set equal to the number of logical CPU cores available
+     */
+    ThreadPool(int numThreads=0);
     ~ThreadPool();
     /**
      * Get the number of worker threads in the pool.

openmmapi/src/CustomCompoundBondForceImpl.cpp

@@ -147,7 +147,7 @@ ParsedExpression CustomCompoundBondForceImpl::prepareExpression(const CustomComp
 ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
         map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
     const Operation& op = node.getOperation();
-    if (op.getId() != Operation::CUSTOM || op.getNumArguments() < 2)
+    if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
     {
         // This is not an angle or dihedral, so process its children.