API improvements (#4437)

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

wrappers/python/src/swig_doxygen/swig_lib/python/extend.i

@@ -9,27 +9,30 @@
     def getIntegrator(self):
         return self._integrator
 
-    def getState(self, getPositions=False, getVelocities=False,
+    def getState(self, positions=False, velocities=False,
+                 forces=False, energy=False, parameters=False,
+                 parameterDerivatives=False, integratorParameters=False,
+                 enforcePeriodicBox=False, groups=-1,
+                 getPositions=False, getVelocities=False,
                  getForces=False, getEnergy=False, getParameters=False,
-                 getParameterDerivatives=False, getIntegratorParameters=False,
-                 enforcePeriodicBox=False, groups=-1):
+                 getParameterDerivatives=False, getIntegratorParameters=False):
         """Get a State object recording the current state information stored in this context.
 
         Parameters
         ----------
-        getPositions : bool=False
+        positions : bool=False
             whether to store particle positions in the State
-        getVelocities : bool=False
+        velocities : bool=False
             whether to store particle velocities in the State
-        getForces : bool=False
+        forces : bool=False
             whether to store the forces acting on particles in the State
-        getEnergy : bool=False
+        energy : bool=False
             whether to store potential and kinetic energy in the State
-        getParameters : bool=False
+        parameters : bool=False
             whether to store context parameters in the State
-        getParameterDerivatives : bool=False
+        parameterDerivatives : bool=False
             whether to store parameter derivatives in the State
-        getIntegratorParameters : bool=False
+        integratorParameters : bool=False
             whether to store integrator parameters in the State
         enforcePeriodicBox : bool=False
             if false, the position of each particle will be whatever position
@@ -41,6 +44,20 @@
             forces and energies. The default value includes all groups. groups
             can also be passed as an unsigned integer interpreted as a bitmask,
             in which case group i will be included if (groups&(1<<i)) != 0.
+        getPositions : bool=False
+            Deprecated.  Use `positions` instead.
+        getVelocities : bool=False
+            Deprecated.  Use `velocities` instead.
+        getForces : bool=False
+            Deprecated.  Use `forces` instead.
+        getEnergy : bool=False
+            Deprecated.  Use `energy` instead.
+        getParameters : bool=False
+            Deprecated.  Use `parameters` instead.
+        getParameterDerivatives : bool=False
+            Deprecated.  Use `parameterDerivatives` instead.
+        getIntegratorParameters : bool=False
+            Deprecated.  Use `integratorParameters` instead.
         """
         try:
             # is the input integer-like?
@@ -55,19 +72,19 @@
         if groups_mask >= 0x80000000:
             groups_mask -= 0x100000000
         types = 0
-        if getPositions:
+        if positions or getPositions:
             types += State.Positions
-        if getVelocities:
+        if velocities or getVelocities:
             types += State.Velocities
-        if getForces:
+        if forces or getForces:
             types += State.Forces
-        if getEnergy:
+        if energy or getEnergy:
             types += State.Energy
-        if getParameters:
+        if parameters or getParameters:
             types += State.Parameters
-        if getParameterDerivatives:
+        if parameterDerivatives or getParameterDerivatives:
             types += State.ParameterDerivatives
-        if getIntegratorParameters:
+        if integratorParameters or getIntegratorParameters:
             types += State.IntegratorParameters
         state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
         return state

wrappers/python/tests/TestATMForce.py

@@ -27,7 +27,7 @@ class TestATMForce(unittest.TestCase):
         system.addForce(atmforce)
 
         integrator = VerletIntegrator(1.0)
-        platform = Platform.getPlatformByName('Reference')
+        platform = Platform.getPlatform('Reference')
         context = Context(system, integrator, platform)
 
         positions = []

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -177,7 +177,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
         integrator = VerletIntegrator(1.0*femtoseconds)
         # Use reference platform, since it should always be present and
         # 'working', and the system is plenty small so this won't be too slow
-        sim = Simulation(prmtop3.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        sim = Simulation(prmtop3.topology, system, integrator, Platform.getPlatform('Reference'))
         # Check that the energy is about what we expect it to be
         sim.context.setPositions(inpcrd3.positions)
         ene = sim.context.getState(getEnergy=True, enforcePeriodicBox=True).getPotentialEnergy()
@@ -207,7 +207,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
         integrator = VerletIntegrator(1.0*femtoseconds)
         # Use reference platform, since it should always be present and
         # 'working', and the system is plenty small so this won't be too slow
-        sim = Simulation(prmtop3.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        sim = Simulation(prmtop3.topology, system, integrator, Platform.getPlatform('Reference'))
         # Check that the energy is about what we expect it to be
         sim.context.setPositions(inpcrd3.getPositions())
         ene = sim.context.getState(getEnergy=True, enforcePeriodicBox=True).getPotentialEnergy()
@@ -265,7 +265,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
         integrator = VerletIntegrator(1.0*femtoseconds)
         # Use reference platform, since it should always be present and
         # 'working', and the system is plenty small so this won't be too slow
-        sim = Simulation(prmtop4.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        sim = Simulation(prmtop4.topology, system, integrator, Platform.getPlatform('Reference'))
         # Check that the energy is about what we expect it to be
         sim.context.setPositions(inpcrd4.positions)
         ene = sim.context.getState(getEnergy=True, enforcePeriodicBox=True).getPotentialEnergy()
@@ -310,7 +310,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
         for i in range(5):
             system = prmtop2.createSystem(implicitSolvent=solventType[i], nonbondedMethod=nonbondedMethod[i], implicitSolventSaltConc=salt[i])
             integrator = VerletIntegrator(0.001)
-            context = Context(system, integrator, Platform.getPlatformByName("Reference"))
+            context = Context(system, integrator, Platform.getPlatform("Reference"))
             context.setPositions(pdb.positions)
             state1 = context.getState(getForces=True)
             with open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml') as infile:
@@ -380,7 +380,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
         for i,f in enumerate(system.getForces()):
             f.setForceGroup(i)
         integrator = VerletIntegrator(0.001)
-        context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+        context = Context(system, integrator, Platform.getPlatform('Reference'))
         context.setPositions(crd.positions)
         
         # Compare to energies computed with pytraj.energy_decomposition()
@@ -422,7 +422,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
                 if isinstance(f, CustomGBForce) or isinstance(f, GBSAOBCForce):
                     f.setForceGroup(1)
             integrator = VerletIntegrator(0.001)
-            context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+            context = Context(system, integrator, Platform.getPlatform('Reference'))
             context.setPositions(inpcrd.positions)
             energy = context.getState(getEnergy=True, groups={1}).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
             self.assertAlmostEqual(energy, expectedEnergy, delta=5e-4*abs(energy))
@@ -460,7 +460,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
             system = prmtop.createSystem(constraints=constraints)
             integrator = VerletIntegrator(0.001*picoseconds)
             # If a constraint was added to a massless particle, this will throw an exception.
-            context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+            context = Context(system, integrator, Platform.getPlatform('Reference'))
 
     def testWaterBonds(self):
         """Test that water molecules have the right set of bonds"""

wrappers/python/tests/TestBytes.py

@@ -8,7 +8,7 @@ class TestBytes(unittest.TestCase):
         system.addParticle(1.0)
         refPositions = [(0,0,0)]
 
-        platform = mm.Platform.getPlatformByName('Reference')
+        platform = mm.Platform.getPlatform('Reference')
         context = mm.Context(system, mm.VerletIntegrator(0), platform)
         context.setPositions(refPositions)
         chk = context.createCheckpoint()

wrappers/python/tests/TestCharmmFiles.py

@@ -139,7 +139,7 @@ class TestCharmmFiles(unittest.TestCase):
             a.charge = 0.0
 
         # Now compute the full energy
-        plat = Platform.getPlatformByName('Reference')
+        plat = Platform.getPlatform('Reference')
         system = psf.createSystem(params, nonbondedMethod=PME,
                                   nonbondedCutoff=8*angstroms)
 
@@ -168,7 +168,7 @@ class TestCharmmFiles(unittest.TestCase):
                 f.setForceGroup(1)
             else:
                 f.setForceGroup(0)
-        context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatformByName('Reference'))
+        context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatform('Reference'))
         context.setPositions(crd.positions)
         state = context.getState(getEnergy=True, groups={1})
         energy = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
@@ -184,7 +184,7 @@ class TestCharmmFiles(unittest.TestCase):
         psf.setBox(30.0*angstroms, 30.0*angstroms, 30.0*angstroms)
 
         # Now compute the full energy
-        plat = Platform.getPlatformByName('Reference')
+        plat = Platform.getPlatform('Reference')
         system = psf.createSystem(params, nonbondedMethod=PME, ewaldErrorTolerance=0.00005)
         integrator = DrudeLangevinIntegrator(300*kelvin, 1.0/picosecond, 1*kelvin, 10/picosecond, 0.001*picoseconds)
         con = Context(system, integrator, plat)
@@ -234,7 +234,7 @@ class TestCharmmFiles(unittest.TestCase):
         psf.setBox(33.2*angstroms, 33.2*angstroms, 33.2*angstroms)
 
         # Now compute the full energy
-        plat = Platform.getPlatformByName('Reference')
+        plat = Platform.getPlatform('Reference')
         system = psf.createSystem(params, nonbondedMethod=PME, ewaldErrorTolerance=0.00005)
         integrator = DrudeLangevinIntegrator(300*kelvin, 1.0/picosecond, 1*kelvin, 10/picosecond, 0.001*picoseconds)
         con = Context(system, integrator, plat)
@@ -251,7 +251,7 @@ class TestCharmmFiles(unittest.TestCase):
         crd = CharmmCrdFile('systems/chlb_cgenff.crd')
         params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
                                     'systems/par_all36_cgenff.prm')
-        plat = Platform.getPlatformByName('Reference')
+        plat = Platform.getPlatform('Reference')
         system = psf.createSystem(params)
         con = Context(system, VerletIntegrator(2*femtoseconds), plat)
         con.setPositions(crd.positions)
@@ -310,7 +310,7 @@ class TestCharmmFiles(unittest.TestCase):
         for i in range(5):
             system = self.psf_c.createSystem(self.params, implicitSolvent=solventType[i], nonbondedMethod=nonbondedMethod[i], implicitSolventSaltConc=salt[i])
             integrator = VerletIntegrator(0.001)
-            context = Context(system, integrator, Platform.getPlatformByName("Reference"))
+            context = Context(system, integrator, Platform.getPlatform("Reference"))
             context.setPositions(self.pdb.positions)
             state1 = context.getState(getForces=True)
             #out = open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml', 'w')
@@ -338,7 +338,7 @@ class TestCharmmFiles(unittest.TestCase):
             a.charge = 0.0
 
         # Now compute the full energy
-        plat = Platform.getPlatformByName('Reference')
+        plat = Platform.getPlatform('Reference')
 
         system_strict     = psf.createSystem(params_strict    , nonbondedMethod=PME,
                                   nonbondedCutoff=8*angstroms)
@@ -365,7 +365,7 @@ class TestCharmmFiles(unittest.TestCase):
         force = [f for f in system.getForces() if isinstance(f, CustomTorsionForce)][0]
         group = force.getForceGroup()
         integrator = VerletIntegrator(0.001)
-        context = Context(system, integrator, Platform.getPlatformByName("Reference"))
+        context = Context(system, integrator, Platform.getPlatform("Reference"))
         angle = 0.1
         pos1 = [Vec3(0,0,0), Vec3(1,0,0), Vec3(1,1,0), Vec3(0,1,math.tan(angle))] # theta = angle
         pos2 = [Vec3(0,0,0), Vec3(1,0,0), Vec3(1,1,0), Vec3(2,1,math.tan(angle))] # theta = pi-angle
@@ -448,7 +448,7 @@ class TestCharmmFiles(unittest.TestCase):
                 params = CharmmParameterSet('systems/charmm22.rtf', parfile.name)
                 os.remove(parfile.name)
             system = self.psf_c.createSystem(params, nonbondedMethod=NoCutoff)
-            context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatformByName('Reference'))
+            context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatform('Reference'))
             context.setPositions(crd.positions)
             energy = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilocalories_per_mole)
             self.assertAlmostEqual(energy, modeEnergy[abs(nbxmod)], delta=1e-3*abs(energy))
@@ -459,7 +459,7 @@ class TestCharmmFiles(unittest.TestCase):
         pdb = PDBFile('systems/MoS2.pdb')
         params = CharmmParameterSet('systems/MoS2.prm')
         system = psf.createSystem(params, nonbondedMethod=NoCutoff)
-        context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatformByName('Reference'))
+        context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         energy = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilocalories_per_mole)
         # Compare with value computed with NAMD.
@@ -507,7 +507,7 @@ class TestCharmmFiles(unittest.TestCase):
         crd = CharmmCrdFile('systems/ala3_solv.crd')
         params = CharmmParameterSet('systems/par_all36_prot.prm',
                                     'systems/toppar_water_ions.str')
-        plat = Platform.getPlatformByName('Reference')
+        plat = Platform.getPlatform('Reference')
         system_charmm = psf.createSystem(params, nonbondedMethod=PME,
                                   nonbondedCutoff=8 * angstroms)
         topology = psf.topology

wrappers/python/tests/TestDcdFile.py

@@ -39,7 +39,7 @@ class TestDCDFile(unittest.TestCase):
         # Create a simulation and write some frames to a DCD file.
         
         integrator = mm.VerletIntegrator(0.001*unit.picoseconds)
-        simulation = app.Simulation(pdb.topology, system, integrator, mm.Platform.getPlatformByName('Reference'))
+        simulation = app.Simulation(pdb.topology, system, integrator, mm.Platform.getPlatform('Reference'))
         dcd = app.DCDReporter(fname, 2)
         simulation.reporters.append(dcd)
         simulation.context.setPositions(pdb.positions)
@@ -53,7 +53,7 @@ class TestDCDFile(unittest.TestCase):
         # Create a new simulation and have it append some more frames.
 
         integrator = mm.VerletIntegrator(0.001*unit.picoseconds)
-        simulation = app.Simulation(pdb.topology, system, integrator, mm.Platform.getPlatformByName('Reference'))
+        simulation = app.Simulation(pdb.topology, system, integrator, mm.Platform.getPlatform('Reference'))
         dcd = app.DCDReporter(fname, 2, append=True)
         simulation.reporters.append(dcd)
         simulation.context.setPositions(pdb.positions)

wrappers/python/tests/TestDesmondDMSFile.py

@@ -90,7 +90,7 @@ class TestDesmondDMSFile(unittest.TestCase):
         """Test OPLS potential energy of nabumetone """
         system = self.dms_opls1.createSystem(nonbondedMethod=NoCutoff, OPLS = True)
         integrator = LangevinIntegrator(300*kelvin, 1.0/picosecond, 0.0005*picoseconds)
-        context = Context(system, integrator,Platform.getPlatformByName('Reference'))
+        context = Context(system, integrator,Platform.getPlatform('Reference'))
         context.setPositions(self.dms_opls1.positions)
         ene = context.getState(getEnergy=True).getPotentialEnergy()
         self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 94.21, places=2)
@@ -99,7 +99,7 @@ class TestDesmondDMSFile(unittest.TestCase):
         """Test OPLS potential energy of beta-cyclodextrin/nabumetone complex """
         system = self.dms_opls2.createSystem(nonbondedMethod=NoCutoff, OPLS = True)
         integrator = LangevinIntegrator(300*kelvin, 1.0/picosecond, 0.0005*picoseconds)
-        context = Context(system, integrator,Platform.getPlatformByName('Reference'))
+        context = Context(system, integrator,Platform.getPlatform('Reference'))
         context.setPositions(self.dms_opls2.positions)
         ene = context.getState(getEnergy=True).getPotentialEnergy()
         self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 903.04, places=2)

wrappers/python/tests/TestForceField.py

@@ -323,7 +323,7 @@ class TestForceField(unittest.TestCase):
             forcefield = ForceField('amber96.xml', f'implicit/{solventType[i]}.xml')
             system = forcefield.createSystem(self.pdb2.topology, nonbondedMethod=nonbondedMethod[i], implicitSolventKappa=kappa[i])
             integrator = VerletIntegrator(0.001)
-            context = Context(system, integrator, Platform.getPlatformByName("Reference"))
+            context = Context(system, integrator, Platform.getPlatform("Reference"))
             context.setPositions(self.pdb2.positions)
             state1 = context.getState(getForces=True)
             if file[i] is not None:
@@ -872,7 +872,7 @@ class TestForceField(unittest.TestCase):
             a.charge = 0.0
 
         # Now compute the full energy
-        plat = Platform.getPlatformByName('Reference')
+        plat = Platform.getPlatform('Reference')
         system = psf.createSystem(params, nonbondedMethod=PME,
                                   nonbondedCutoff=5*angstroms)
 
@@ -1122,7 +1122,7 @@ END"""))
             if isinstance(f, NonbondedForce):
                 f.setPMEParameters(3.4, 64, 64, 64)
         integrator = DrudeLangevinIntegrator(300, 1.0, 1.0, 10.0, 0.001)
-        context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+        context = Context(system, integrator, Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
 
         # Compare the energy to values computed by CHARMM.  Here is what it outputs:
@@ -1200,7 +1200,7 @@ self.scriptExecuted = True
         for i, f in enumerate(system.getForces()):
             f.setForceGroup(i)
         integrator = VerletIntegrator(0.001)
-        context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+        context = Context(system, integrator, Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         energies = {}
         for i, f in enumerate(system.getForces()):
@@ -1244,7 +1244,7 @@ self.scriptExecuted = True
 </ForceField> """
         ff = ForceField(StringIO(xml))
         system = ff.createSystem(pdb.topology)
-        context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatformByName('Reference'))
+        context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         energy1 = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
 
@@ -1257,7 +1257,7 @@ self.scriptExecuted = True
         f.addParticle(0, 0.404468018036, 0.6276)
         f.addParticle(0, 0.251367073323, 0.1962296)
         system.addForce(f)
-        context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatformByName('Reference'))
+        context = Context(system, VerletIntegrator(2*femtoseconds), Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         energy2 = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
         self.assertAlmostEqual(energy1, energy2)
@@ -1417,7 +1417,7 @@ class AmoebaTestForceField(unittest.TestCase):
         forcefield = ForceField('amoeba2013.xml', 'amoeba2013_gk.xml')
         system = forcefield.createSystem(pdb.topology, polarization='direct')
         integrator = VerletIntegrator(0.001)
-        context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+        context = Context(system, integrator, Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         state1 = context.getState(getForces=True)
         with open('systems/alanine-dipeptide-amoeba-forces.xml') as input:
@@ -1433,7 +1433,7 @@ class AmoebaTestForceField(unittest.TestCase):
         for i, f in enumerate(system.getForces()):
             f.setForceGroup(i)
         integrator = VerletIntegrator(0.001)
-        context = Context(system, integrator, Platform.getPlatformByName('Reference'))
+        context = Context(system, integrator, Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         energies = {}
         for i, f in enumerate(system.getForces()):

wrappers/python/tests/TestForceGroups.py

@@ -14,7 +14,7 @@ class TestForceGroups(unittest.TestCase):
             force.setForceGroup(i)
             system.addForce(force)
 
-        platform = mm.Platform.getPlatformByName('Reference')
+        platform = mm.Platform.getPlatform('Reference')
         context = mm.Context(system, mm.VerletIntegrator(0), platform)
         context.setPositions([(0,0,0)])
         self.context = context

wrappers/python/tests/TestGromacsTopFile.py

@@ -45,7 +45,7 @@ class TestGromacsTopFile(unittest.TestCase):
             if isinstance(force, PeriodicTorsionForce):
                 force.setForceGroup(1)
         context = Context(system, VerletIntegrator(1*femtosecond),
-                          Platform.getPlatformByName('Reference'))
+                          Platform.getPlatform('Reference'))
         context.setPositions(gro.positions)
         ene = context.getState(getEnergy=True, groups=2**1).getPotentialEnergy()
         self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), 341.6905133582857)
@@ -57,7 +57,7 @@ class TestGromacsTopFile(unittest.TestCase):
         system = top.createSystem()
 
         context = Context(system, VerletIntegrator(1*femtosecond),
-                          Platform.getPlatformByName('Reference'))
+                          Platform.getPlatform('Reference'))
         context.setPositions(gro.positions)
         ene = context.getState(getEnergy=True).getPotentialEnergy()
         self.assertAlmostEqual(ene.value_in_unit(kilojoules_per_mole), -346.940915296)
@@ -72,7 +72,7 @@ class TestGromacsTopFile(unittest.TestCase):
                 f.setUseLongRangeCorrection(True)
 
         context = Context(system, VerletIntegrator(1*femtosecond),
-                          Platform.getPlatformByName('Reference'))
+                          Platform.getPlatform('Reference'))
         context.setPositions(gro.positions)
         energy = context.getState(getEnergy=True).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
         self.assertAlmostEqual(energy, 3135.33, delta=energy*0.005)
@@ -173,7 +173,7 @@ class TestGromacsTopFile(unittest.TestCase):
         self.assertEqual(1, len(top._moleculeTypes['BENX'].vsites2))
 
         context = Context(system, VerletIntegrator(1*femtosecond),
-                          Platform.getPlatformByName('Reference'))
+                          Platform.getPlatform('Reference'))
         context.setPositions(gro.positions)
         context.computeVirtualSites()
         ene = context.getState(getEnergy=True).getPotentialEnergy()
@@ -203,7 +203,7 @@ class TestGromacsTopFile(unittest.TestCase):
         system = top.createSystem()
         for i, f in enumerate(system.getForces()):
             f.setForceGroup(i)
-        context = Context(system, VerletIntegrator(1*femtosecond), Platform.getPlatformByName('Reference'))
+        context = Context(system, VerletIntegrator(1*femtosecond), Platform.getPlatform('Reference'))
         context.setPositions(gro.positions)
         energy = {}
         for i, f in enumerate(system.getForces()):

wrappers/python/tests/TestIntegrators.py

@@ -64,7 +64,7 @@ class TestIntegrators(unittest.TestCase):
         velocities = [ (random.random()-0.5, random.random()-0.5, random.random()-0.5) for i in range(numParticles) ]
 
         # Create Context
-        platform = Platform.getPlatformByName('Reference')
+        platform = Platform.getPlatform('Reference')
         context = Context(system, integrator, platform)
         context.setPositions(positions)
         context.setVelocities(velocities)
@@ -161,7 +161,7 @@ class TestIntegrators(unittest.TestCase):
         # Create a System with a single particle and no forces
         system = System()
         system.addParticle(12.0*amu)
-        platform = Platform.getPlatformByName('Reference')
+        platform = Platform.getPlatform('Reference')
         initial_positions = [Vec3(0,0,0)]
         initial_velocities = [Vec3(1,0,0)]
         nsteps = 125 # number of steps to take

wrappers/python/tests/TestMetadynamics.py

@@ -25,7 +25,7 @@ class TestMetadynamics(unittest.TestCase):
         residue = topology.addResidue('H2', chain)
         topology.addAtom('H1', element.hydrogen, residue)
         topology.addAtom('H2', element.hydrogen, residue)
-        simulation = Simulation(topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation = Simulation(topology, system, integrator, Platform.getPlatform('Reference'))
         simulation.context.setPositions([Vec3(0, 0, 0), Vec3(1, 0, 0)])
         meta.step(simulation, 200000)
         fe = meta.getFreeEnergy()

wrappers/python/tests/TestNumpyCompatibility.py

@@ -22,7 +22,7 @@ class TestNumpyCompatibility(unittest.TestCase):
         integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds,
                                            2.0*unit.femtoseconds)
         self.simulation = app.Simulation(prmtop.topology, system, integrator,
-                                    mm.Platform.getPlatformByName('Reference'))
+                                    mm.Platform.getPlatform('Reference'))
 
 
     def test_setPositions(self):

wrappers/python/tests/TestPdbxFile.py

@@ -69,7 +69,7 @@ class TestPdbxFile(unittest.TestCase):
         parm = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
         system = parm.createSystem()
         sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
-                         Platform.getPlatformByName('Reference'))
+                         Platform.getPlatform('Reference'))
         sim.context.setPositions(PDBFile('systems/alanine-dipeptide-implicit.pdb').getPositions())
         sim.reporters.append(PDBxReporter('test.cif', 1))
         sim.step(10)
@@ -101,7 +101,7 @@ class TestPdbxFile(unittest.TestCase):
         parm = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
         system = parm.createSystem(nonbondedCutoff=1.0, nonbondedMethod=PME)
         sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
-                         Platform.getPlatformByName('Reference'))
+                         Platform.getPlatform('Reference'))
         orig_pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         sim.context.setPositions(orig_pdb.getPositions())
         sim.context.setPeriodicBoxVectors(*parm.topology.getPeriodicBoxVectors())

wrappers/python/tests/TestSimulatedTempering.py

@@ -20,7 +20,7 @@ class TestSimulatedTempering(unittest.TestCase):
         residue = topology.addResidue('H2', chain)
         topology.addAtom('H1', element.hydrogen, residue)
         topology.addAtom('H2', element.hydrogen, residue)
-        simulation = Simulation(topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation = Simulation(topology, system, integrator, Platform.getPlatform('Reference'))
         st = SimulatedTempering(simulation, numTemperatures=10, minTemperature=200*kelvin, maxTemperature=400*kelvin, tempChangeInterval=5, reportInterval=10000)
         self.assertEqual(10, len(st.temperatures))
         self.assertEqual(200*kelvin, st.temperatures[0])
@@ -72,7 +72,7 @@ class TestSimulatedTempering(unittest.TestCase):
         residue = topology.addResidue('H2', chain)
         topology.addAtom('H1', element.hydrogen, residue)
         topology.addAtom('H2', element.hydrogen, residue)
-        simulation = Simulation(topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation = Simulation(topology, system, integrator, Platform.getPlatform('Reference'))
         simulation.context.setPositions([Vec3(0, 0, 0), Vec3(1, 0, 0)])
 
         # Check the temperature is correct before creating the simulated tempering simulation

wrappers/python/tests/TestSimulation.py

@@ -17,7 +17,7 @@ class TestSimulation(unittest.TestCase):
 
         # Create a Simulation.
 
-        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatform('Reference'))
         simulation.context.setPositions(pdb.positions)
         simulation.context.setVelocitiesToTemperature(300*kelvin)
         initialState = simulation.context.getState(getPositions=True, getVelocities=True)
@@ -74,7 +74,7 @@ class TestSimulation(unittest.TestCase):
 
         # Create a Simulation.
 
-        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatform('Reference'))
         simulation.context.setPositions(pdb.positions)
         simulation.context.setVelocitiesToTemperature(300*kelvin)
         initialState = simulation.context.getState(getPositions=True, getVelocities=True)
@@ -107,7 +107,7 @@ class TestSimulation(unittest.TestCase):
 
         # Create a Simulation.
 
-        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatform('Reference'))
         simulation.context.setPositions(pdb.positions)
         simulation.context.setVelocitiesToTemperature(300*kelvin)
         self.assertEqual(0, simulation.currentStep)
@@ -130,7 +130,7 @@ class TestSimulation(unittest.TestCase):
 
         # Create a Simulation.
 
-        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation = Simulation(pdb.topology, system, integrator, Platform.getPlatform('Reference'))
         simulation.context.setPositions(pdb.positions)
         simulation.context.setVelocitiesToTemperature(300*kelvin)
         self.assertEqual(0, simulation.currentStep)

wrappers/python/tests/TestXtcFile.py

@@ -163,7 +163,7 @@ class TestXtcFile(unittest.TestCase):
                 pdb.topology,
                 system,
                 integrator,
-                mm.Platform.getPlatformByName("Reference"),
+                mm.Platform.getPlatform("Reference"),
             )
             xtc = app.XTCReporter(fname, 2)
             simulation.reporters.append(xtc)
@@ -182,7 +182,7 @@ class TestXtcFile(unittest.TestCase):
                 pdb.topology,
                 system,
                 integrator,
-                mm.Platform.getPlatformByName("Reference"),
+                mm.Platform.getPlatform("Reference"),
             )
             xtc = app.XTCReporter(fname, 2, append=True)
             simulation.reporters.append(xtc)