Finish welding tutorial

environment-cpu.yml

@@ -4,6 +4,7 @@ channels:
 dependencies:
   - boltons
   - foyer
+  - fresnel
   - freud>=2.13.1
   - gsd>=3.0
   - hoomd=4.1=*cpu*

environment-gpu.yml

@@ -4,6 +4,7 @@ channels:
 dependencies:
   - boltons
   - foyer
+  - fresnel
   - freud>=2.13.1
   - gsd>=3.0
   - hoomd=4.1=*gpu*

hoomd_organics/library/simulations/tensile.py

@@ -79,7 +79,7 @@ def strain(self):
         )
         return delta_L / self.initial_length
 
-    def run_tensile(self, strain, n_steps, period):
+    def run_tensile(self, strain, n_steps, kT, tau_kt, period):
         """Run a tensile test simulation.
 
         Parameters
@@ -88,6 +88,8 @@ def run_tensile(self, strain, n_steps, period):
             The strain to apply to the simulation.
         n_steps : int, required
             The number of steps to run the simulation for.
+        tau_kt : float, required
+            Thermostat coupling period (in simulation time units).
         period : int, required
             The period of the strain application.
 
@@ -119,8 +121,4 @@ def run_tensile(self, strain, n_steps, period):
         )
         self.operations.updaters.append(box_resizer)
         self.operations.updaters.append(particle_updater)
-        self.set_integrator_method(
-            integrator_method=hoomd.md.methods.ConstantVolume,
-            method_kwargs={"filter": self.integrate_group},
-        )
-        self.run(n_steps + 1)
+        self.run_NVT(n_steps=n_steps + 1, kT=kT, tau_kt=tau_kt)

hoomd_organics/modules/welding.py

@@ -161,9 +161,9 @@ def __init__(
         wall_epsilon=1.0,
         wall_r_cut=2.5,
         wall_r_extrap=0,
-        r_cut=2.5,
         reference_values=dict(),
         dt=0.0001,
+        r_cut=2.5,
         device=hoomd.device.auto_select(),
         seed=42,
         gsd_write_freq=1e4,
@@ -175,8 +175,8 @@ def __init__(
         super(SlabSimulation, self).__init__(
             initial_state=initial_state,
             forcefield=forcefield,
-            r_cut=r_cut,
             reference_values=reference_values,
+            r_cut=r_cut,
             dt=dt,
             device=device,
             seed=seed,
@@ -186,8 +186,7 @@ def __init__(
             log_file_name=log_file_name,
             thermostat=thermostat,
         )
-        self.interface_axis = interface_axis
-        # self._axis_index = np.where(interface_axis != 0)[0]
+        self.interface_axis = np.asarray(interface_axis)
         self.add_walls(
             self.interface_axis,
             wall_sigma,
@@ -208,14 +207,14 @@ def __init__(
         self,
         initial_state,
         forcefield,
-        interface_axis="x",
+        interface_axis=(1, 0, 0),
         wall_sigma=1.0,
         wall_epsilon=1.0,
         wall_r_cut=2.5,
         wall_r_extrap=0,
-        r_cut=2.5,
         reference_values=dict(),
         dt=0.0001,
+        r_cut=2.5,
         device=hoomd.device.auto_select(),
         seed=42,
         gsd_write_freq=1e4,
@@ -227,9 +226,9 @@ def __init__(
         super(WeldSimulation, self).__init__(
             initial_state=initial_state,
             forcefield=forcefield,
-            r_cut=r_cut,
             reference_values=reference_values,
             dt=dt,
+            r_cut=r_cut,
             device=device,
             seed=seed,
             gsd_write_freq=gsd_write_freq,
@@ -238,9 +237,11 @@ def __init__(
             log_file_name=log_file_name,
             thermostat=thermostat,
         )
-        axis_dict = {"x": (1, 0, 0), "y": (0, 1, 0), "z": (0, 0, 1)}
-        self.interface_axis = interface_axis.lower()
-        self.wall_axis = axis_dict[self.interface_axis]
+        self.interface_axis = interface_axis
         self.add_walls(
-            self.wall_axis, wall_sigma, wall_epsilon, wall_r_cut, wall_r_extrap
+            self.interface_axis,
+            wall_sigma,
+            wall_epsilon,
+            wall_r_cut,
+            wall_r_extrap,
         )

hoomd_organics/tests/library/test_tensile.py

@@ -26,5 +26,7 @@ def test_tensile(self):
             log_write_freq=1e6,
             gsd_write_freq=1e6,
         )
-        tensile_sim.run_tensile(strain=0.05, n_steps=1e3, period=10)
+        tensile_sim.run_tensile(
+            strain=0.05, kT=2.0, n_steps=1e3, period=10, tau_kt=0.001
+        )
         assert np.allclose(tensile_sim.strain, 0.05, 1e-4)

hoomd_organics/tests/modules/test_weld.py

@@ -5,7 +5,11 @@
 
 from hoomd_organics import Simulation
 from hoomd_organics.modules.utils import add_void_particles
-from hoomd_organics.modules.welding import Interface, SlabSimulation
+from hoomd_organics.modules.welding import (
+    Interface,
+    SlabSimulation,
+    WeldSimulation,
+)
 from hoomd_organics.tests.base_test import BaseTest
 
 
@@ -92,7 +96,7 @@ def test_weld_sim(self, polyethylene_system):
         interface = Interface(
             gsd_file="restart.gsd", interface_axis="x", gap=0.1
         )
-        sim = SlabSimulation(
+        sim = WeldSimulation(
             initial_state=interface.hoomd_snapshot,
             forcefield=polyethylene_system.hoomd_forcefield,
         )