Merge pull request #33 from jchodera/segfault-workaround

[WIP] Segfault workaround

openmmtools/tests/test_integrators.py

@@ -67,12 +67,6 @@ def check_stability(integrator, test, platform=None, nsteps=100, temperature=300
 #=============================================================================================
 # TESTS
 #=============================================================================================
-def test_doctest():
-    """Performing integrators doctests.
-    """
-    from openmmtools import integrators
-    import doctest
-    doctest.testmod(integrators)
 
 def test_stabilities_harmonic_oscillator():
    """

tests/test_integrators_and_testsystems.py → openmmtools/tests/test_integrators_and_testsystems.py

@@ -67,7 +67,12 @@ def test_integrators_and_testsystems():
 
    # Create lists of integrator and testsystem names.
    integrator_names = [ methodname for methodname in dir(integrators) if re.match('.*Integrator$', methodname) ]
-   testsystem_names = [ testsystem_class.__name__ for testsystem_class in testsystems.TestSystem.__subclasses__() ]
+
+   def all_subclasses(cls):
+       """Return list of all subclasses and subsubclasses for a given class."""
+       return cls.__subclasses__() + [s for s in cls.__subclasses__()]
+   testsystem_classes = all_subclasses(testsystems.TestSystem)
+   testsystem_names = [ cls.__name__ for cls in testsystem_classes ]
 
    # Use Reference platform.
    platform = openmm.Platform.getPlatformByName('Reference')

openmmtools/tests/test_testsystems.py

@@ -10,12 +10,6 @@
 
 from functools import partial
 
-def test_doctest():
-    """Performing testsystems doctests.
-    """
-    import doctest
-    doctest.testmod(testsystems)
-
 def test_get_data_filename():
     """Testing retrieval of data files shipped with distro.
     """
@@ -39,22 +33,28 @@ def test_subrandom_particle_positions():
     box_vectors = openmm.System().getDefaultPeriodicBoxVectors()
     positions = testsystems.subrandom_particle_positions(nparticles, box_vectors)
 
+def check_properties(testsystem):
+    class_name = testsystem.__class__.__name__
+    property_list = testsystem.analytical_properties
+    state = testsystems.ThermodynamicState(temperature=300.0*unit.kelvin, pressure=1.0*unit.atmosphere)
+    if len(property_list) > 0:
+        for property_name in property_list:
+            method = getattr(testsystem, 'get_' + property_name)
+            logging.info("%32s . %32s : %32s" % (class_name, property_name, str(method(state))))
+    return
+
 def test_properties_all_testsystems():
     """Testing computation of analytic properties for all systems.
     """
     testsystem_classes = testsystems.TestSystem.__subclasses__()
     logging.info("Testing analytical property computation:")
     for testsystem_class in testsystem_classes:
         class_name = testsystem_class.__name__
-        logging.info(class_name)
-        print(class_name) # DEBUG
         testsystem = testsystem_class()
-        property_list = testsystem.analytical_properties
-        state = testsystems.ThermodynamicState(temperature=300.0*unit.kelvin, pressure=1.0*unit.atmosphere)
-        if len(property_list) > 0:
-            for property_name in property_list:
-                method = getattr(testsystem, 'get_' + property_name)
-                logging.info("%32s . %32s : %32s" % (class_name, property_name, str(method(state))))
+        f = partial(check_properties, testsystem)
+        f.description = "Testing properties for testsystem %s" % class_name
+        logging.info(f.description)
+        yield f
 
 fast_testsystems = [
     "HarmonicOscillator",
@@ -111,7 +111,10 @@ def check_potential_energy(system, positions):
 def test_energy_all_testsystems(skip_slow_tests=False):
     """Testing computation of potential energy for all systems.
     """
-    testsystem_classes = testsystems.TestSystem.__subclasses__()
+    def all_subclasses(cls):
+        """Return list of all subclasses and subsubclasses for a given class."""
+        return cls.__subclasses__() + [s for s in cls.__subclasses__()]
+    testsystem_classes = all_subclasses(testsystems.TestSystem)
 
     for testsystem_class in testsystem_classes:
         class_name = testsystem_class.__name__

openmmtools/testsystems.py

@@ -1343,12 +1343,16 @@ class LennardJonesFluid(TestSystem):
     """Create a periodic fluid of Lennard-Jones particles.
     Initial positions are assigned using a subrandom grid to minimize steric interactions.
 
+    Note
+    ----
+    The default reduced_density is set to 0.05 (gas) so that no minimization is needed to simulate the default system.
+
     Parameters
     ----------
     nparticles : int, optional, default=500
         Number of Lennard-Jones particles.
-    reduced_density : float, optional, default=0.86
-        Reduced density (density * sigma**3); default is appropriate for liquid argon.
+    reduced_density : float, optional, default=0.05
+        Reduced density (density * sigma**3); default is appropriate for gas
     mass : simtk.unit.Quantity, optional, default=39.9 * unit.amu
         mass of each particle; default is appropriate for argon
     sigma : simtk.unit.Quantity, optional, default=3.4 * unit.angstrom
@@ -1385,7 +1389,7 @@ class LennardJonesFluid(TestSystem):
 
     def __init__(self,
         nparticles=500,
-        reduced_density=0.86, # liquid
+        reduced_density=0.05, # liquid
         mass=39.9 * unit.amu, # argon
         sigma=3.4 * unit.angstrom, # argon,
         epsilon=0.238 * unit.kilocalories_per_mole, # argon,
@@ -1405,8 +1409,8 @@ def __init__(self,
         system = openmm.System()
 
         # Determine volume and periodic box vectors.
-        density = reduced_density / sigma**3
-        volume = nparticles * (density ** -1)
+        number_density = reduced_density / sigma**3
+        volume = nparticles * (number_density ** -1)
         box_edge = volume ** (1./3.)
         a = unit.Quantity((box_edge,        0*unit.angstrom, 0*unit.angstrom))
         b = unit.Quantity((0*unit.angstrom, box_edge,        0*unit.angstrom))