update tests

flowermd/base/system.py

@@ -654,8 +654,7 @@ def __init__(
         edge=0.2,
         overlap=0.2,
     ):
-        # TODO: Remove this
-        self.density = density * u.g / (u.cm ** (3))
+        self.density = density
         self.packing_expand_factor = packing_expand_factor
         self.edge = edge
         self.overlap = overlap
@@ -669,7 +668,7 @@ def _build_system(self):
         number_density = u.Unit("m**-3")
         if self.density.units.dimensions == mass_density.dimensions:
             target_box = get_target_box_mass_density(
-                density=self.density, mass=self.mass
+                density=self.density, mass=(self.mass * u.Unit("amu")).to("g")
             )
         elif self.density.units.dimensions == number_density.dimensions:
             target_box = get_target_box_number_density(

flowermd/tests/base/test_simulation.py

@@ -10,6 +10,9 @@
 
 from flowermd import Simulation
 from flowermd.tests import BaseTest
+from flowermd.utils import (  # get_target_box_number_density,
+    get_target_box_mass_density,
+)
 
 
 class TestSimulate(BaseTest):
@@ -150,8 +153,15 @@ def test_update_volume_walls(self, benzene_system):
 
     def test_update_volume_density(self, benzene_system):
         sim = Simulation.from_system(benzene_system)
+        target_box = get_target_box_mass_density(
+            density=0.05 * u.Unit("g") / u.Unit("cm**3"), mass=sim.mass.to(u.g)
+        )
         sim.run_update_volume(
-            kT=1.0, tau_kt=0.01, n_steps=500, period=1, final_density=0.05
+            kT=1.0,
+            tau_kt=0.01,
+            n_steps=500,
+            period=1,
+            final_box_lengths=target_box,
         )
         assert np.isclose(
             sim.density.to(u.g / u.cm**3).value,

flowermd/tests/base_test.py

@@ -3,6 +3,7 @@
 import hoomd
 import mbuild as mb
 import pytest
+import unyt as u
 from gmso.external.convert_mbuild import from_mbuild
 
 from flowermd import Molecule, Pack, Polymer, Simulation
@@ -218,7 +219,7 @@ def benzene_system(self, benzene_mb):
         benzene = Molecule(num_mols=20, compound=benzene_mb)
         system = Pack(
             molecules=[benzene],
-            density=0.2,
+            density=0.2 * u.g / u.cm**3,
         )
         system.apply_forcefield(
             r_cut=2.5, force_field=OPLS_AA(), auto_scale=True