Merge pull request #903 from peastman/minimize

Fixed failing test cases.  Increased default minimizer tolerance to 10.

docs-source/usersguide/application.rst

@@ -1222,9 +1222,9 @@ specify if you want further control over the minimization.  First, you can
 specify a tolerance for when the energy should be considered to have converged:
 ::
 
-    simulation.minimizeEnergy(tolerance=10*kilojoule/mole)
+    simulation.minimizeEnergy(tolerance=5*kilojoule/mole)
 
-If you do not specify this parameter, a default tolerance of 1 kJ/mole is used.
+If you do not specify this parameter, a default tolerance of 10 kJ/mole is used.
 
 Second, you can specify a maximum number of iterations:
 ::

openmmapi/include/openmm/LocalEnergyMinimizer.h

@@ -54,12 +54,12 @@ public:
      * @param context        a Context specifying the System to minimize and the initial particle positions
      * @param tolerance      this specifies how precisely the energy minimum must be located.  Minimization
      *                       will be halted once the root-mean-square value of all force components reaches
-     *                       this tolerance.  The default value is 1.
+     *                       this tolerance.  The default value is 10.
      * @param maxIterations  the maximum number of iterations to perform.  If this is 0, minimation is continued
      *                       until the results converge without regard to how many iterations it takes.  The
      *                       default value is 0.
      */
-    static void minimize(Context& context, double tolerance = 1, int maxIterations = 0);
+    static void minimize(Context& context, double tolerance = 10, int maxIterations = 0);
 };
 
 } // namespace OpenMM

platforms/cuda/tests/TestCudaLocalEnergyMinimizer.cpp

@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -81,7 +81,7 @@ void testLargeSystem() {
     const int numParticles = numMolecules*2;
     const double cutoff = 2.0;
     const double boxSize = 4.0;
-    const double tolerance = 5;
+    const double tolerance = 10;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nonbonded = new NonbondedForce();
@@ -114,7 +114,7 @@ void testLargeSystem() {
     State finalState = context.getState(State::Forces | State::Energy | State::Positions);
     ASSERT(finalState.getPotentialEnergy() < initialState.getPotentialEnergy());
 
-    // Compute the force magnitude, substracting off any component parallel to a constraint, and
+    // Compute the force magnitude, subtracting off any component parallel to a constraint, and
     // check that it satisfies the requested tolerance.
 
     double forceNorm = 0.0;
@@ -129,8 +129,8 @@ void testLargeSystem() {
         f -= dir*dir.dot(f);
         forceNorm += f.dot(f);
     }
-    forceNorm = sqrt(forceNorm/(4*numMolecules));
-    ASSERT(forceNorm < 3*tolerance);
+    forceNorm = sqrt(forceNorm/(5*numMolecules));
+    ASSERT(forceNorm < 2*tolerance);
 }
 
 void testVirtualSites() {
@@ -138,7 +138,7 @@ void testVirtualSites() {
     const int numParticles = numMolecules*3;
     const double cutoff = 2.0;
     const double boxSize = 4.0;
-    const double tolerance = 5;
+    const double tolerance = 10;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nonbonded = new NonbondedForce();
@@ -195,8 +195,8 @@ void testVirtualSites() {
         
         ASSERT_EQUAL_VEC((finalState.getPositions()[i+1]+finalState.getPositions()[i])*0.5, finalState.getPositions()[i+2], 1e-5);
     }
-    forceNorm = sqrt(forceNorm/(4*numMolecules));
-    ASSERT(forceNorm < 3*tolerance);
+    forceNorm = sqrt(forceNorm/(5*numMolecules));
+    ASSERT(forceNorm < 2*tolerance);
 }
 
 int main(int argc, char* argv[]) {

platforms/opencl/tests/TestOpenCLLocalEnergyMinimizer.cpp

@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -81,7 +81,7 @@ void testLargeSystem() {
     const int numParticles = numMolecules*2;
     const double cutoff = 2.0;
     const double boxSize = 4.0;
-    const double tolerance = 5;
+    const double tolerance = 10;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nonbonded = new NonbondedForce();
@@ -114,7 +114,7 @@ void testLargeSystem() {
     State finalState = context.getState(State::Forces | State::Energy | State::Positions);
     ASSERT(finalState.getPotentialEnergy() < initialState.getPotentialEnergy());
 
-    // Compute the force magnitude, substracting off any component parallel to a constraint, and
+    // Compute the force magnitude, subtracting off any component parallel to a constraint, and
     // check that it satisfies the requested tolerance.
 
     double forceNorm = 0.0;
@@ -129,8 +129,8 @@ void testLargeSystem() {
         f -= dir*dir.dot(f);
         forceNorm += f.dot(f);
     }
-    forceNorm = sqrt(forceNorm/(4*numMolecules));
-    ASSERT(forceNorm < 3*tolerance);
+    forceNorm = sqrt(forceNorm/(5*numMolecules));
+    ASSERT(forceNorm < 2*tolerance);
 }
 
 void testVirtualSites() {
@@ -138,7 +138,7 @@ void testVirtualSites() {
     const int numParticles = numMolecules*3;
     const double cutoff = 2.0;
     const double boxSize = 4.0;
-    const double tolerance = 5;
+    const double tolerance = 10;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nonbonded = new NonbondedForce();
@@ -195,8 +195,8 @@ void testVirtualSites() {
         
         ASSERT_EQUAL_VEC((finalState.getPositions()[i+1]+finalState.getPositions()[i])*0.5, finalState.getPositions()[i+2], 1e-5);
     }
-    forceNorm = sqrt(forceNorm/(4*numMolecules));
-    ASSERT(forceNorm < 3*tolerance);
+    forceNorm = sqrt(forceNorm/(5*numMolecules));
+    ASSERT(forceNorm < 2*tolerance);
 }
 
 int main(int argc, char* argv[]) {

platforms/reference/tests/TestReferenceLocalEnergyMinimizer.cpp

@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -129,8 +129,8 @@ void testLargeSystem() {
         f -= dir*dir.dot(f);
         forceNorm += f.dot(f);
     }
-    forceNorm = sqrt(forceNorm/(4*numMolecules));
-    ASSERT(forceNorm < 3*tolerance);
+    forceNorm = sqrt(forceNorm/(5*numMolecules));
+    ASSERT(forceNorm < 2*tolerance);
 }
 
 void testVirtualSites() {
@@ -195,8 +195,8 @@ void testVirtualSites() {
         
         ASSERT_EQUAL_VEC((finalState.getPositions()[i+1]+finalState.getPositions()[i])*0.5, finalState.getPositions()[i+2], 1e-5);
     }
-    forceNorm = sqrt(forceNorm/(4*numMolecules));
-    ASSERT(forceNorm < 3*tolerance);
+    forceNorm = sqrt(forceNorm/(5*numMolecules));
+    ASSERT(forceNorm < 2*tolerance);
 }
 
 int main() {

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

@@ -78,11 +78,11 @@ class Simulation(object):
         else:
             self.context = mm.Context(system, integrator, platform, platformProperties)
 
-    def minimizeEnergy(self, tolerance=1*unit.kilojoule/unit.mole, maxIterations=0):
+    def minimizeEnergy(self, tolerance=10*unit.kilojoule/unit.mole, maxIterations=0):
         """Perform a local energy minimization on the system.
 
         Parameters:
-         - tolerance (energy=1*kilojoule/mole) The energy tolerance to which the system should be minimized
+         - tolerance (energy=10*kilojoules/mole) The energy tolerance to which the system should be minimized
          - maxIterations (int=0) The maximum number of iterations to perform.  If this is 0, minimization is continued
            until the results converge without regard to how many iterations it takes.
         """