add docstrings

cmelab · Jan 22, 2024 · 746b85f · 746b85f
1 parent d2cb45e
commit 746b85f
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Showing 2 changed files with 31 additions and 23 deletions.
diff --git a/flowermd/base/simulation.py b/flowermd/base/simulation.py
@@ -621,29 +621,32 @@ def run_update_volume(
         and a box matching a density of 1.1 g/cm^3 is passed into
         `final_box_lengths`.
 
-        import unyt
-        from flowermd.base import Pack, Simulation
-        from flowermd.library import PPS, OPLS_AA_PPS
-
-        pps_mols = PPS(num_mols=20, lengths=15)
-        pps_system = Pack(
-            molecules=[pps_mols],
-            force_field=OPLS_AA_PPS(),
-            r_cut=2.5,
-            density=0.5,
-            auto_scale=True,
-            scale_charges=True
-        )
-        sim = Simulation(
-            initial_state=pps_system.hoomd_snapshot,
-            forcefield=pps_system.hoomd_forcefield
-        )
-        target_box = flowermd.utils.get_target_box_mass_density(
-            density=1.1 * unyt.g/unyt.cm**3, mass=sim.mass.to("g")
-        )
-        sim.run_update_volume(
-            n_steps=1e4, kT=1.0, tau_kt=1.0, final_box_lengths=target_box
-        )
+        ::
+
+            import unyt
+            from flowermd.base import Pack, Simulation
+            from flowermd.library import PPS, OPLS_AA_PPS
+
+            pps_mols = PPS(num_mols=20, lengths=15)
+            pps_system = Pack(
+                molecules=[pps_mols],
+                force_field=OPLS_AA_PPS(),
+                r_cut=2.5,
+                density=0.5,
+                auto_scale=True,
+                scale_charges=True
+            )
+            sim = Simulation(
+                initial_state=pps_system.hoomd_snapshot,
+                forcefield=pps_system.hoomd_forcefield
+            )
+            target_box = flowermd.utils.get_target_box_mass_density(
+                density=1.1 * unyt.g/unyt.cm**3, mass=sim.mass.to("g")
+            )
+            sim.run_update_volume(
+                n_steps=1e4, kT=1.0, tau_kt=1.0, final_box_lengths=target_box
+            )
+
         """
         if self.reference_length and hasattr(final_box_lengths, "to"):
             ref_unit = self.reference_length.units

diff --git a/flowermd/utils/base_types.py b/flowermd/utils/base_types.py
@@ -2,6 +2,11 @@
 
 
 class HOOMDThermostats:
+    """Types of HOOMD thermostats used in NVT or NPT simulations."""
+
     BERENDSEN = hoomd.md.methods.thermostats.Berendsen
+    """The Berendsen thermostat."""
     BUSSI = hoomd.md.methods.thermostats.Bussi
+    """The Bussi-Donadio-Parrinello thermostat."""
     MTTK = hoomd.md.methods.thermostats.MTTK
+    """The Nosé-Hoover thermostat."""