Merge pull request #2411 from peastman/units

Add ability to enforce units on input arguments

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -446,6 +446,7 @@ class SwigInputBuilder:
 
         #write only non Constructor and Destructor methods and python mods
         self.fOut.write("\n")
+        methodsWithOutputArgs = set()
         for items in methodList:
             clearOutput=""
             (shortClassName, memberNode,
@@ -479,6 +480,7 @@ class SwigInputBuilder:
                                         (INDENT, simpleType, pType, pName))
                         clearOutput = "%s%s%%clear %s %s;\n" \
                                      % (clearOutput, INDENT, pType, pName)
+                        methodsWithOutputArgs.add((shortClassName, methName))
 
             mArgsstring = getText("argsstring", memberNode)
             try:
@@ -503,6 +505,9 @@ class SwigInputBuilder:
             paramList = findNodes(memberNode, 'param')
 
             # write pythonprepend blocks
+            if isConstructors:
+                mArgsstring = '' # specifying args to constructors seems to prevent append and prepend from working
+            else:
                 mArgsstring = getText("argsstring", memberNode)
             if self.fOutPythonprepend and \
                len(paramList) and \
@@ -523,6 +528,28 @@ class SwigInputBuilder:
         s = ("the %s object does not own its corresponding OpenMM object"
              % self.__class__.__name__)
         raise Exception(s)'''.format(argName=argName)
+
+                # Convert input arguments to the proper units, if specified.
+                if key not in methodsWithOutputArgs:
+                    if key in self.configModule.UNITS:
+                        argUnits=self.configModule.UNITS[key][1]
+                    elif ("*", methName) in self.configModule.UNITS:
+                        argUnits=self.configModule.UNITS[("*", methName)][1]
+                    else:
+                        argUnits = ()
+                    if len(argUnits) > 0 and (self.SWIG_COMPACT_ARGUMENTS or isConstructors):
+                        textInside += '''
+    args = list(args)'''
+                    for i, units in enumerate(argUnits):
+                        if units is not None:
+                            if self.SWIG_COMPACT_ARGUMENTS or isConstructors:
+                                argName = 'args[%s]' % i
+                            else:
+                                argName = getText('declname', paramList[i])
+                            textInside += '''
+    if unit.is_quantity({argName}):
+        {argName} = {argName}.value_in_unit({units})'''.format(argName=argName, units=units)
+
                 for argNum in self.configModule.REQUIRE_ORDERED_SET.get(key, []):
                     if self.SWIG_COMPACT_ARGUMENTS:
                         argName = 'args[%s]' % argNum
@@ -568,7 +595,7 @@ class SwigInputBuilder:
                                  % (addText, INDENT, valueUnits[0])
 
                 for vUnit in valueUnits[1]:
-                    if vUnit is not None:
+                    if vUnit is not None and key in methodsWithOutputArgs:
                         addText = "%s%sval[%s]=unit.Quantity(val[%s], %s)\n" \
                                      % (addText, INDENT, index, index, vUnit)
                     index+=1

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -117,9 +117,6 @@ SKIP_METHODS = [('State', 'getPositions'),
 # The build script assumes method args that are non-const references are
 # used to output values. This list gives excpetions to this rule.
 NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
-                  ('System', 'getDefaultPeriodicBoxVectors', 'a'),
-                  ('System', 'getDefaultPeriodicBoxVectors', 'b'),
-                  ('System', 'getDefaultPeriodicBoxVectors', 'c'),
                   ('Platform', 'setPropertyValue', 'context'),
                   ('AmoebaTorsionTorsionForce', 'setTorsionTorsionGrid', 'grid'),
                   ('AmoebaVdwForce', 'setParticleExclusions', 'exclusions'),
@@ -175,8 +172,14 @@ UNITS = {
 ("*", "getDefaultPressureX") : ("unit.bar", ()),
 ("*", "getDefaultPressureY") : ("unit.bar", ()),
 ("*", "getDefaultPressureZ") : ("unit.bar", ()),
+("*", "setDefaultPressure") : (None, ("unit.bar",)),
+("*", "setDefaultPressureX") : (None, ("unit.bar",)),
+("*", "setDefaultPressureY") : (None, ("unit.bar",)),
+("*", "setDefaultPressureZ") : (None, ("unit.bar",)),
 ("*", "getDefaultSurfaceTension") : ("unit.bar*unit.nanometer", ()),
+("*", "setDefaultSurfaceTension") : (None, ("unit.bar*unit.nanometer",)),
 ("*", "getDefaultTemperature") : ("unit.kelvin", ()),
+("*", "setDefaultTemperature") : (None, ("unit.kelvin",)),
 ("*", "getErrorTolerance") : (None, ()),
 ("*", "getEwaldErrorTolerance") : (None, ()),
 ("*", "getFriction") : ("1/unit.picosecond", ()),
@@ -459,6 +462,7 @@ UNITS = {
 ("System", "getVirtualSite") : (None, ()),
 ("DrudeLangevinIntegrator", "getDrudeTemperature") : ("unit.kelvin", ()),
 ("DrudeLangevinIntegrator", "getMaxDrudeDistance") : ("unit.nanometer", ()),
+("MonteCarloMembraneBarostat", "MonteCarloMembraneBarostat") : (None, ("unit.bar", "unit.bar*unit.nanometer", "unit.kelvin", None, None, None)),
 ("MonteCarloMembraneBarostat", "getXYMode") : (None, ()),
 ("MonteCarloMembraneBarostat", "getZMode") : (None, ()),
 ("DrudeLangevinIntegrator", "getDrudeFriction") : ("1/unit.picosecond", ()),

wrappers/python/tests/TestAPIUnits.py

@@ -1176,6 +1176,28 @@ class TestAPIUnits(unittest.TestCase):
         self.assertEqual(force.getDefaultTemperature(), 298.15*kelvin)
         self.assertAlmostEqualUnit(force.getDefaultCollisionFrequency(), 1/picosecond)
 
+    def testMonteCarloMembraneBarostat(self):
+        """ Tests the MonteCarloMembraneBarostat API features """
+        force = MonteCarloMembraneBarostat(1.0, 1.5, 300, MonteCarloMembraneBarostat.XYAnisotropic, MonteCarloMembraneBarostat.ZFixed, 25)
+        self.assertEqual(force.getDefaultPressure(), 1.0*bar)
+        self.assertEqual(force.getDefaultSurfaceTension(), 1.5*bar*nanometer)
+        self.assertEqual(force.getDefaultTemperature(), 300*kelvin)
+        self.assertEqual(force.getXYMode(), MonteCarloMembraneBarostat.XYAnisotropic)
+        self.assertEqual(force.getZMode(), MonteCarloMembraneBarostat.ZFixed)
+        self.assertEqual(force.getFrequency(), 25)
+
+        force = MonteCarloMembraneBarostat(1.1*bar, 2.0*bar*nanometer, 350*kelvin, MonteCarloMembraneBarostat.XYAnisotropic, MonteCarloMembraneBarostat.ZFixed, 25)
+        self.assertEqual(force.getDefaultPressure(), 1.1*bar)
+        self.assertEqual(force.getDefaultSurfaceTension(), 2.0*bar*nanometer)
+        self.assertEqual(force.getDefaultTemperature(), 350*kelvin)
+
+        force.setDefaultPressure(1.2*bar)
+        force.setDefaultSurfaceTension(2.5*bar*nanometer)
+        force.setDefaultTemperature(298.15)
+        self.assertEqual(force.getDefaultPressure(), 1.2*bar)
+        self.assertEqual(force.getDefaultSurfaceTension(), 2.5*bar*nanometer)
+        self.assertEqual(force.getDefaultTemperature(), 298.15*kelvin)
+
     def testDrudeSCFIntegrator(self):
         """ Tests the DrudeSCFIntegrator API features """
         integrator = DrudeSCFIntegrator(0.002)