Updating Examples in Documentation

hoomd/md/angle.py

@@ -83,11 +83,13 @@ class Harmonic(Angle):
 
         U(\theta) = \frac{1}{2} k \left( \theta - \theta_0 \right)^2
 
-    Examples::
+    .. rubric:: Example:
 
-        harmonic = angle.Harmonic()
-        harmonic.params["A-A-A"] = dict(k=3.0, t0=0.7851)
-        harmonic.params["A-B-A"] = dict(k=100.0, t0=1.0)
+    .. code-block:: python
+
+            harmonic = angle.Harmonic()
+            harmonic.params["A-A-A"] = dict(k=3.0, t0=0.7851)
+            harmonic.params["A-B-A"] = dict(k=100.0, t0=1.0)
 
     {inherited}
 
@@ -132,11 +134,13 @@ class CosineSquared(Angle):
 
     `CosineSquared` is used in the gromos96 and MARTINI force fields.
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        cosinesq = angle.CosineSquared()
-        cosinesq.params["A-A-A"] = dict(k=3.0, t0=0.7851)
-        cosinesq.params["A-B-A"] = dict(k=100.0, t0=1.0)
+            cosinesq = angle.CosineSquared()
+            cosinesq.params["A-A-A"] = dict(k=3.0, t0=0.7851)
+            cosinesq.params["A-B-A"] = dict(k=100.0, t0=1.0)
 
     {inherited}
 

hoomd/md/bond.py

@@ -80,11 +80,13 @@ class Harmonic(Bond):
 
         U(r) = \frac{1}{2} k \left( r - r_0 \right)^2
 
-    Examples::
+    .. rubric:: Example:
 
-        harmonic = bond.Harmonic()
-        harmonic.params["A-A"] = dict(k=3.0, r0=2.38)
-        harmonic.params["A-B"] = dict(k=10.0, r0=1.0)
+    .. code-block:: python
+
+            harmonic = bond.Harmonic()
+            harmonic.params["A-A"] = dict(k=3.0, r0=2.38)
+            harmonic.params["A-B"] = dict(k=10.0, r0=1.0)
 
     {inherited}
 
@@ -143,13 +145,15 @@ class FENEWCA(Bond):
     bond, :math:`\varepsilon` is the repulsive interaction energy, and
     :math:`\sigma` is the repulsive interaction width.
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        fenewca = bond.FENEWCA()
-        fenewca.params['A-A'] = dict(k=3.0, r0=2.38, epsilon=1.0, sigma=1.0,
-                                     delta=0.0)
-        fenewca.params['A-B'] = dict(k=10.0, r0=1.0, epsilon=0.8, sigma=1.2,
-                                     delta=0.0)
+            fenewca = bond.FENEWCA()
+            fenewca.params['A-A'] = dict(k=3.0, r0=2.38, epsilon=1.0, sigma=1.0,
+                                        delta=0.0)
+            fenewca.params['A-B'] = dict(k=10.0, r0=1.0, epsilon=0.8, sigma=1.2,
+                                        delta=0.0)
 
     {inherited}
 
@@ -342,11 +346,13 @@ class Tether(Bond):
     .. math::
         l_{min} < l_{c1} < l_{c0} < l_{max}
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        bond_potential = bond.Tether()
-        bond_potential.params['A-A'] = dict(k_b=10.0, l_min=0.9, l_c1=1.2,
-                                               l_c0=1.8, l_max=2.1)
+            bond_potential = bond.Tether()
+            bond_potential.params['A-A'] = dict(k_b=10.0, l_min=0.9, l_c1=1.2,
+                                                l_c0=1.8, l_max=2.1)
 
     {inherited}
 

hoomd/md/compute.py

@@ -33,10 +33,12 @@ class ThermodynamicQuantities(Compute):
         rigid body centers - ignoring constituent particles to avoid double
         counting.
 
-    Examples::
+    .. rubric:: Example:
 
-        f = filter.Type("A")
-        compute.ThermodynamicQuantities(filter=f)
+    .. code-block:: python
+
+            f = filter.Type("A")
+            compute.ThermodynamicQuantities(filter=f)
 
     {inherited}
 
@@ -342,11 +344,13 @@ class HarmonicAveragedThermodynamicQuantities(Compute):
         by molecular simulation". Phys. Rev. E 92, 043303
         doi:10.1103/PhysRevE.92.043303
 
-    Examples::
+    .. rubric:: Example:
 
-        hma = hoomd.compute.HarmonicAveragedThermodynamicQuantities(
-            filter=hoomd.filter.Type("A"), kT=1.0
-        )
+    .. code-block:: python
+
+            hma = hoomd.compute.HarmonicAveragedThermodynamicQuantities(
+                filter=hoomd.filter.Type("A"), kT=1.0
+            )
 
     {inherited}
 

hoomd/md/dihedral.py

@@ -93,11 +93,13 @@ class Periodic(Dihedral):
         U(\phi) = \frac{1}{2}k \left( 1 + d \cos\left(n \phi - \phi_0 \right)
                \right)
 
-    Examples::
+    .. rubric:: Example:
 
-        harmonic = dihedral.Periodic()
-        harmonic.params["A-A-A-A"] = dict(k=3.0, d=-1, n=3, phi0=0)
-        harmonic.params["A-B-C-D"] = dict(k=100.0, d=1, n=4, phi0=math.pi / 2)
+    .. code-block:: python
+
+            harmonic = dihedral.Periodic()
+            harmonic.params["A-A-A-A"] = dict(k=3.0, d=-1, n=3, phi0=0)
+            harmonic.params["A-B-C-D"] = dict(k=100.0, d=1, n=4, phi0=math.pi / 2)
 
     {inherited}
 
@@ -226,10 +228,12 @@ class OPLS(Dihedral):
 
     :math:`k_n` are the force coefficients in the Fourier series.
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        opls = dihedral.OPLS()
-        opls.params["A-A-A-A"] = dict(k1=1.0, k2=1.0, k3=1.0, k4=1.0)
+            opls = dihedral.OPLS()
+            opls.params["A-A-A-A"] = dict(k1=1.0, k2=1.0, k3=1.0, k4=1.0)
 
     {inherited}
 

hoomd/md/force.py

@@ -242,13 +242,14 @@ def cpu_local_force_arrays(self):
             The local arrays are read only for built-in forces. Use `Custom` to
             implement custom forces.
 
-        Examples::
+        .. rubric:: Example:
 
-            with self.cpu_local_force_arrays as arrays:
-                arrays.force[:] = ...
-                arrays.potential_energy[:] = ...
-                arrays.torque[:] = ...
-                arrays.virial[:] = ...
+        .. code-block:: python
+                with self.cpu_local_force_arrays as arrays:
+                    arrays.force[:] = ...
+                    arrays.potential_energy[:] = ...
+                    arrays.torque[:] = ...
+                    arrays.virial[:] = ...
         """
         if self._in_context_manager:
             raise RuntimeError(
@@ -275,13 +276,15 @@ def gpu_local_force_arrays(self):
             The local arrays are read only for built-in forces. Use `Custom` to
             implement custom forces.
 
-        Examples::
+        .. rubric:: Example:
+
+        .. code-block:: python
 
-            with self.gpu_local_force_arrays as arrays:
-                arrays.force[:] = ...
-                arrays.potential_energy[:] = ...
-                arrays.torque[:] = ...
-                arrays.virial[:] = ...
+                with self.gpu_local_force_arrays as arrays:
+                    arrays.force[:] = ...
+                    arrays.potential_energy[:] = ...
+                    arrays.torque[:] = ...
+                    arrays.virial[:] = ...
 
         Note:
             GPU local force data is not available if the chosen device for the
@@ -427,17 +430,19 @@ class Active(Force):
 
             `hoomd.md.update.ActiveRotationalDiffusion`
 
-    Examples::
+    .. rubric:: Example:
 
-        all = hoomd.filter.All()
-        active = hoomd.md.force.Active(
-            filter=hoomd.filter.All()
-            )
-        active.active_force['A','B'] = (1,0,0)
-        active.active_torque['A','B'] = (0,0,0)
-        rotational_diffusion_updater = active.create_diffusion_updater(
-            trigger=10)
-        sim.operations += rotational_diffusion_updater
+    .. code-block:: python
+
+            all = hoomd.filter.All()
+            active = hoomd.md.force.Active(
+                filter=hoomd.filter.All()
+                )
+            active.active_force['A','B'] = (1,0,0)
+            active.active_torque['A','B'] = (0,0,0)
+            rotational_diffusion_updater = active.create_diffusion_updater(
+                trigger=10)
+            sim.operations += rotational_diffusion_updater
 
     Note:
         The energy and virial associated with the active force are 0.
@@ -559,17 +564,19 @@ class ActiveOnManifold(Active):
 
             `hoomd.md.update.ActiveRotationalDiffusion`
 
-    Examples::
+    .. rubric:: Example:
 
-        all = filter.All()
-        sphere = hoomd.md.manifold.Sphere(r=10)
-        active = hoomd.md.force.ActiveOnManifold(
-            filter=hoomd.filter.All(),
-            rotation_diff=0.01,
-            manifold_constraint=sphere,
-        )
-        active.active_force["A", "B"] = (1, 0, 0)
-        active.active_torque["A", "B"] = (0, 0, 0)
+    .. code-block:: python
+
+            all = filter.All()
+            sphere = hoomd.md.manifold.Sphere(r=10)
+            active = hoomd.md.force.ActiveOnManifold(
+                filter=hoomd.filter.All(),
+                rotation_diff=0.01,
+                manifold_constraint=sphere,
+            )
+            active.active_force["A", "B"] = (1, 0, 0)
+            active.active_torque["A", "B"] = (0, 0, 0)
 
     {inherited}
 
@@ -648,11 +655,13 @@ class Constant(Force):
     particles selected by the filter. `Constant` sets the force and torque
     to  ``(0,0,0)`` for particles not selected by the filter.
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        constant = hoomd.md.force.Constant(filter=hoomd.filter.All())
-        constant.constant_force["A"] = (1, 0, 0)
-        constant.constant_torque["A"] = (0, 0, 0)
+            constant = hoomd.md.force.Constant(filter=hoomd.filter.All())
+            constant.constant_force["A"] = (1, 0, 0)
+            constant.constant_torque["A"] = (0, 0, 0)
 
     Note:
         The energy and virial associated with the constant force are 0.

hoomd/md/integrate.py

@@ -239,15 +239,23 @@ class Integrator(_DynamicIntegrator):
 
     - `hoomd.md.constrain`
 
-    Examples::
-
-        nlist = hoomd.md.nlist.Cell()
-        lj = hoomd.md.pair.LJ(nlist=nlist)
-        lj.params.default = dict(epsilon=1.0, sigma=1.0)
-        lj.r_cut[('A', 'A')] = 2**(1/6)
-        nve = hoomd.md.methods.NVE(filter=hoomd.filter.All())
-        integrator = hoomd.md.Integrator(dt=0.001, methods=[nve], forces=[lj])
-        sim.operations.integrator = integrator
+    .. rubric:: Example:
+
+    .. code-block:: python
+
+            cell = hoomd.md.nlist.Cell(buffer=0.4)
+            lj = hoomd.md.pair.LJ(nlist=cell)       
+            lj.params[('A', 'A')]  = dict(epsilon=1.0, sigma=1.0)
+            lj.r_cut[('A', 'A')] = 2.5
+            nve = hoomd.md.methods.ConstantVolume(
+                filter=hoomd.filter.All(), 
+                thermostat=None,
+                )
+            integrator = hoomd.md.Integrator(dt=0.005, 
+                                            methods=[nve], 
+                                            forces=[lj],
+                                            )
+
 
     {inherited}