Merge pull request #90 from chrisjonesBSU/surface-wetting

Add initial classes for surface wetting module

flowermd/modules/surface_wetting.py

@@ -0,0 +1,133 @@
+"""Module for simulating surface wetting."""
+import hoomd
+import unyt as u
+from jankflow.base.simulation import Simulation
+from jankflow.utils import HOOMDThermostats
+
+
+class Surface:
+    """For creating an interface between two slabs.
+
+    Parameters
+    ----------
+    gsd_file : str
+        Path to gsd file of the slab.
+    interface_axis : tuple
+        Axis along which the interface is to be created.
+        The slab file is duplicated and translated along this axis.
+    gap : float, required
+        Distance (in simulation units) between the two slabs at the interface.
+    wall_sigma : float
+        Sigma parameter used for the wall potential when creating the slabs.
+
+    """
+
+    def __init__(self, drop_gsd_file, surface_gsd_file, gap):
+        self.drop_gsd_file = drop_gsd_file
+        self.surface_gsd_file = surface_gsd_file
+        self.gap = gap
+
+    def _build(self):
+        """Duplicates the slab and builds the interface."""
+        pass
+
+
+class DropletSimulation(Simulation):
+    """Simulation which creates a droplet."""
+
+    def __init__(
+        self,
+        initial_state,
+        forcefield,
+        r_cut=2.5,
+        reference_values=dict(),
+        dt=0.0001,
+        device=hoomd.device.auto_select(),
+        seed=42,
+        gsd_write_freq=1e4,
+        gsd_file_name="trajectory.gsd",
+        log_write_freq=1e3,
+        log_file_name="log.txt",
+        thermostat=HOOMDThermostats.MTTK,
+    ):
+        super(DropletSimulation, self).__init__(
+            initial_state=initial_state,
+            forcefield=forcefield,
+            r_cut=r_cut,
+            reference_values=reference_values,
+            dt=dt,
+            device=device,
+            seed=seed,
+            gsd_write_freq=gsd_write_freq,
+            gsd_file_name=gsd_file_name,
+            log_write_freq=log_write_freq,
+            log_file_name=log_file_name,
+            thermostat=thermostat,
+        )
+
+    def run_droplet(
+        self,
+        kT,
+        tau_kt,
+        shrink_steps,
+        expand_steps,
+        hold_steps,
+        shrink_period,
+        expand_period,
+        final_density,
+    ):
+        """Run droplet simulation."""
+        # Shrink down to high density
+        self.run_update_volume(
+            n_steps=shrink_steps,
+            period=shrink_period,
+            kT=kT,
+            tau_kt=tau_kt,
+            final_density=1.4 * (u.g / (u.cm**3)),
+            write_at_start=True,
+        )
+        # Expand back up to low density
+        self.run_update_volume(
+            n_steps=expand_steps,
+            period=expand_period,
+            kT=kT,
+            tau_kt=tau_kt,
+            final_density=final_density * (u.g / (u.cm**3)),
+            resize_filter=hoomd.filter.Null(),
+        )
+        # Run at low density
+        self.run_NVT(n_steps=hold_steps, kT=kT, tau_kt=tau_kt)
+
+
+class WettingSimulation(Simulation):
+    """For simulating welding of an interface joint."""
+
+    def __init__(
+        self,
+        initial_state,
+        forcefield,
+        r_cut=2.5,
+        reference_values=dict(),
+        dt=0.0001,
+        device=hoomd.device.auto_select(),
+        seed=42,
+        gsd_write_freq=1e4,
+        gsd_file_name="weld.gsd",
+        log_write_freq=1e3,
+        log_file_name="sim_data.txt",
+        thermostat=HOOMDThermostats.MTTK,
+    ):
+        super(WettingSimulation, self).__init__(
+            initial_state=initial_state,
+            forcefield=forcefield,
+            r_cut=r_cut,
+            reference_values=reference_values,
+            dt=dt,
+            device=device,
+            seed=seed,
+            gsd_write_freq=gsd_write_freq,
+            gsd_file_name=gsd_file_name,
+            log_write_freq=log_write_freq,
+            log_file_name=log_file_name,
+            thermostat=thermostat,
+        )