Renamed methods for dealing with TabulatedFunctions to avoid problems in...

Renamed methods for dealing with TabulatedFunctions to avoid problems in wrapper APIs.  Also fixed a few bugs.

platforms/reference/src/ReferenceKernels.cpp

@@ -970,7 +970,7 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
 
     map<string, Lepton::CustomFunction*> functions;
     for (int i = 0; i < force.getNumFunctions(); i++)
-        functions[force.getFunctionName(i)] = createReferenceTabulatedFunction(force.getFunction(i));
+        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
 
     // Parse the various expressions used to calculate the force.
 
@@ -1252,7 +1252,7 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
 
     map<string, Lepton::CustomFunction*> functions;
     for (int i = 0; i < force.getNumFunctions(); i++)
-        functions[force.getFunctionName(i)] = createReferenceTabulatedFunction(force.getFunction(i));
+        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
 
     // Parse the expressions for computed values.
 
@@ -1466,7 +1466,7 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
 
     map<string, Lepton::CustomFunction*> functions;
     for (int i = 0; i < force.getNumFunctions(); i++)
-        functions[force.getFunctionName(i)] = createReferenceTabulatedFunction(force.getFunction(i));
+        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
 
     // Parse the expression and create the object used to calculate the interaction.
 
@@ -1563,7 +1563,7 @@ void ReferenceCalcCustomCompoundBondForceKernel::initialize(const System& system
 
     map<string, Lepton::CustomFunction*> functions;
     for (int i = 0; i < force.getNumFunctions(); i++)
-        functions[force.getFunctionName(i)] = createReferenceTabulatedFunction(force.getFunction(i));
+        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
 
     // Parse the expression and create the object used to calculate the interaction.
 

platforms/reference/tests/TestReferenceCustomCompoundBondForce.cpp

@@ -189,7 +189,7 @@ void testContinuous2DFunction() {
             table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
         }
     }
-    forceField->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
+    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(1);
@@ -240,7 +240,7 @@ void testContinuous3DFunction() {
             }
         }
     }
-    forceField->addFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
+    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(1);

platforms/reference/tests/TestReferenceCustomGBForce.cpp

@@ -281,7 +281,7 @@ void testTabulatedFunction() {
     vector<double> table;
     for (int i = 0; i < 21; i++)
         table.push_back(std::sin(0.25*i));
-    force->addFunction("fn", table, 1.0, 6.0);
+    force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
     system.addForce(force);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);

platforms/reference/tests/TestReferenceCustomHbondForce.cpp

@@ -217,7 +217,7 @@ void testCustomFunctions() {
     vector<double> function(2);
     function[0] = 0;
     function[1] = 1;
-    custom->addFunction("foo", function, 0, 10);
+    custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
     system.addForce(custom);
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);

platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp

@@ -239,7 +239,7 @@ void testContinuous1DFunction() {
     vector<double> table;
     for (int i = 0; i < 21; i++)
         table.push_back(sin(0.25*i));
-    forceField->addFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
+    forceField->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -290,7 +290,7 @@ void testContinuous2DFunction() {
             table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
         }
     }
-    forceField->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
+    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -346,7 +346,7 @@ void testContinuous3DFunction() {
             }
         }
     }
-    forceField->addFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
+    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -386,7 +386,7 @@ void testDiscrete1DFunction() {
     vector<double> table;
     for (int i = 0; i < 21; i++)
         table.push_back(sin(0.25*i));
-    forceField->addFunction("fn", new Discrete1DFunction(table));
+    forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -418,7 +418,7 @@ void testDiscrete2DFunction() {
     for (int i = 0; i < xsize; i++)
         for (int j = 0; j < ysize; j++)
             table.push_back(sin(0.25*i)+cos(0.33*j));
-    forceField->addFunction("fn", new Discrete2DFunction(xsize, ysize, table));
+    forceField->addTabulatedFunction("fn", new Discrete2DFunction(xsize, ysize, table));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -454,7 +454,7 @@ void testDiscrete3DFunction() {
         for (int j = 0; j < ysize; j++)
             for (int k = 0; k < zsize; k++)
                 table.push_back(sin(0.25*i)+cos(0.33*j)+0.12345*k);
-    forceField->addFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
+    forceField->addTabulatedFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);

wrappers/generateWrappers.py

@@ -123,8 +123,6 @@ class WrapperGenerator:
                 methodName = shortMethodDefinition.split()[-1]
                 if className+'::'+methodName in self.skipMethods:
                     continue
-                if any(getNodeText(node) == "Deprecated" for node in findNodes(memberNode, "detaileddescription/para/xrefsect/xreftitle")):
-                    continue    # Skip deprecated methods
                 methodList.append(memberNode)
         return methodList
     

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -136,6 +136,10 @@ NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
 STEAL_OWNERSHIP = {("Platform", "registerPlatform") : [0],
                    ("System", "addForce") : [0],
                    ("System", "setVirtualSite") : [1],
+                   ("CustomNonbondedForce", "addTabulatedFunction") : [1],
+                   ("CustomGBForce", "addTabulatedFunction") : [1],
+                   ("CustomHbondForce", "addTabulatedFunction") : [1],
+                   ("CustomCompoundBondForce", "addTabulatedFunction") : [1],
 }
 
 # This is a list of units to attach to return values and method args.
@@ -155,7 +159,6 @@ UNITS = {
 ("*", "getErrorTolerance") : (None, ()),
 ("*", "getEwaldErrorTolerance") : (None, ()),
 ("*", "getFriction") : ("1/unit.picosecond", ()),
-("*", "getFunction") : (None, ()),
 ("*", "getGlobalVariable") : (None, ()),
 ("*", "getIntegrator") : (None, ()),
 ("*", "getMapParameters") : (None, ()),
@@ -180,6 +183,7 @@ UNITS = {
 ("*", "getSolventDielectric") : (None, ()),
 ("*", "getStepSize") : ("unit.picosecond", ()),
 ("*", "getSystem") : (None, ()),
+("*", "getTabulatedFunction") : (None, ()),
 ("*", "getUseDispersionCorrection") : (None, ()),
 ("*", "getTemperature") : ("unit.kelvin", ()),
 ("*", "getUseDispersionCorrection") : (None, ()),