SD: Rename integrator and thermostat

Disambiguate Stokesian Dynamics from Steepest Descent.

samples/dancing.py

@@ -63,7 +63,7 @@
 system.cell_system.skin = 0.4
 system.periodicity = [False, False, False]
 
-system.integrator.set_sd(
+system.integrator.set_stokesian_dynamics(
     viscosity=1.0, radii={0: 1.0}, device=sd_device,
     approximation_method=sd_method)
 

src/python/espressomd/integrate.pyx

@@ -101,7 +101,7 @@ cdef class IntegratorHandle:
         """
         self._integrator = BrownianDynamics()
 
-    def set_sd(self, *args, **kwargs):
+    def set_stokesian_dynamics(self, *args, **kwargs):
         """
         Set the integration method to Stokesian Dynamics (:class:`StokesianDynamics`).
 

src/python/espressomd/thermostat.pyx

@@ -125,8 +125,7 @@ cdef class Thermostat:
                                   act_on_virtual=thmst["act_on_virtual"],
                                   seed=thmst["seed"])
             if thmst["type"] == "SD":
-                self.set_sd(kT=thmst["kT"],
-                            seed=thmst["seed"])
+                self.set_stokesian(kT=thmst["kT"], seed=thmst["seed"])
 
     def get_ts(self):
         return thermo_switch
@@ -710,7 +709,7 @@ cdef class Thermostat:
             mpi_bcast_parameter(FIELD_TEMPERATURE)
 
     IF STOKESIAN_DYNAMICS:
-        def set_sd(self, kT=None, seed=None):
+        def set_stokesian(self, kT=None, seed=None):
             """
             Sets the SD thermostat with required parameters.
 

testsuite/python/save_checkpoint.py

@@ -155,7 +155,7 @@
         system.thermostat.set_dpd(kT=1.0, seed=42)
     elif 'THERM.SDM' in modes and (has_features('STOKESIAN_DYNAMICS') or has_features('STOKESIAN_DYNAMICS_GPU')):
         system.periodicity = [0, 0, 0]
-        system.thermostat.set_sd(kT=1.0, seed=42)
+        system.thermostat.set_stokesian(kT=1.0, seed=42)
     # set integrator
     if 'INT.NPT' in modes and has_features('NPT'):
         system.integrator.set_isotropic_npt(ext_pressure=2.0, piston=0.01,
@@ -169,14 +169,14 @@
         system.integrator.set_brownian_dynamics()
     elif 'INT.SDM.CPU' in modes and has_features('STOKESIAN_DYNAMICS'):
         system.periodicity = [0, 0, 0]
-        system.integrator.set_sd(approximation_method='ft', viscosity=0.5,
-                                 device='cpu', radii={0: 1.5},
-                                 pair_mobility=False, self_mobility=True)
+        system.integrator.set_stokesian_dynamics(
+            approximation_method='ft', device='cpu', viscosity=0.5,
+            radii={0: 1.5}, pair_mobility=False, self_mobility=True)
     elif 'INT.SDM.GPU' in modes and has_features('STOKESIAN_DYNAMICS_GPU') and espressomd.gpu_available():
         system.periodicity = [0, 0, 0]
-        system.integrator.set_sd(approximation_method='fts', viscosity=2.0,
-                                 device='gpu', radii={0: 1.0},
-                                 pair_mobility=True, self_mobility=False)
+        system.integrator.set_stokesian_dynamics(
+            approximation_method='fts', device='gpu', viscosity=2.0,
+            radii={0: 1.0}, pair_mobility=True, self_mobility=False)
     # set minimization
     if 'MINIMIZATION' in modes:
         steepest_descent(system, f_max=1, gamma=10, max_steps=0,

testsuite/python/stokesian_dynamics.py

@@ -37,22 +37,21 @@ def setUp(self):
         self.system.time_step = 1.0
         self.system.cell_system.skin = 0.4
 
-        # unset SD integrator so we can test whether set_sd() fails.
-        # set_nvt() is the only way to ensure that integ_switch is
+        # unset SD integrator so we can test whether set_stokesian_dynamics()
+        # fails. set_nvt() is the only way to ensure that integ_switch is
         # set to a different value than INTEG_METHOD_SD
         self.system.integrator.set_nvt()
 
     def pbc_checks(self):
         self.system.periodicity = [0, 0, 1]
         with self.assertRaises(Exception):
-            self.system.integrator.set_sd(viscosity=1.0,
-                                          device=self.device,
-                                          radii={0: 1.0})
+            self.system.integrator.set_stokesian_dynamics(
+                viscosity=1.0, device=self.device, radii={0: 1.0})
 
         self.system.periodicity = [0, 0, 0]
-        self.system.integrator.set_sd(viscosity=1.0,
-                                      device=self.device,
-                                      radii={0: 1.0})
+        self.system.integrator.set_stokesian_dynamics(
+            viscosity=1.0, device=self.device, radii={0: 1.0})
+
         with self.assertRaises(Exception):
             self.system.periodicity = [0, 1, 0]
 
@@ -78,7 +77,7 @@ def falling_spheres(self, time_step, l_factor, t_factor,
         self.system.part.add(pos=[0 * l_factor, 0, 0], rotation=[1, 1, 1])
         self.system.part.add(pos=[7 * l_factor, 0, 0], rotation=[1, 1, 1])
 
-        self.system.integrator.set_sd(
+        self.system.integrator.set_stokesian_dynamics(
             viscosity=1.0 / (t_factor * l_factor),
             device=self.device, radii={0: 1.0 * l_factor},
             approximation_method=sd_method)
@@ -146,10 +145,9 @@ def setUp(self):
         self.system.part.add(pos=[0, 0, 0], rotation=[1, 1, 1])
 
     def check(self):
-        self.system.integrator.set_sd(viscosity=self.eta,
-                                      device=self.device,
-                                      radii={0: self.R})
-        self.system.thermostat.set_sd(kT=self.kT, seed=42)
+        self.system.integrator.set_stokesian_dynamics(
+            viscosity=self.eta, device=self.device, radii={0: self.R})
+        self.system.thermostat.set_stokesian(kT=self.kT, seed=42)
 
         intsteps = int(100000 / self.system.time_step)
         pos = np.empty([intsteps + 1, 3])
@@ -202,4 +200,4 @@ def check(self):
     def tearDown(self):
         self.system.constraints.clear()
         self.system.part.clear()
-        self.system.thermostat.set_sd(kT=0)
+        self.system.thermostat.set_stokesian(kT=0)