Fix terminology issues related to pressure

Author: tovrstra

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fix bug in `PairwiseForceField` class: use `rmax` only, never `rcut`.
 - Fix version import.
+- Fix pressure-related terminology.
 
 
 ## [0.2.0] - 2024-10-07

README.md

@@ -73,8 +73,9 @@ cell_length = 20.0
 # Compute stuff:
 # - The potential energy.
 # - An array with Cartesian forces, same shape as `atpos`.
-# - The (virial contribution to) the pressure, only the mechanical part.
-potential_energy, forces, mech_pressure = pwff(atpos, cell_length)
+# - The force contribution the pressure
+#   (often the written as the second term in the virial pressure).
+potential_energy, forces, frc_pressure = pwff(atpos, cell_length)
 ```
 
 This basic recipe can be extended by passing additional options

src/tinyff/forcefield.py

@@ -126,8 +126,9 @@ def __call__(self, atpos: NDArray, cell_length: float):
             The potential energy.
         forces
             The forces acting on the atoms, same shape as atpos.
-        mech_pressure
-            The force-contribution to the pressure.
+        frc_pressure
+            The force-contribution to the pressure,
+            i.e. usually the second term of the virial stress in most text books.
         """
         # Sanity check
         if cell_length < 2 * self.rmax:
@@ -152,7 +153,7 @@ def __call__(self, atpos: NDArray, cell_length: float):
         forces = np.zeros(atpos.shape, dtype=float)
         np.add.at(forces, nlist["iatom0"], nlist["gdelta"])
         np.add.at(forces, nlist["iatom1"], -nlist["gdelta"])
-        mech_pressure = -np.dot(nlist["gdist"], nlist["dist"]) / (3 * cell_length**3)
+        frc_pressure = -np.dot(nlist["gdist"], nlist["dist"]) / (3 * cell_length**3)
         # Keep the neigborlist for the following function call
         self.nlist = nlist
-        return energy, forces, mech_pressure
+        return energy, forces, frc_pressure

tests/test_forcefield.py

@@ -68,12 +68,12 @@ def test_pairwise_force_field_two(build_nlist):
     pwff = PairwiseForceField(lj, rcut, build_nlist=build_nlist)
 
     # Compute and check against manual result
-    energy, forces, mech_press = pwff(atpos, cell_length)
+    energy, forces, frc_press = pwff(atpos, cell_length)
     d = np.linalg.norm(atpos[0] - atpos[1])
     e, g = lj(d)
     assert energy == pytest.approx(e)
     assert forces == pytest.approx(np.array([[g, 0.0, 0.0], [-g, 0.0, 0.0]]))
-    assert mech_press == pytest.approx(-g * d / (3 * cell_length**3))
+    assert frc_press == pytest.approx(-g * d / (3 * cell_length**3))
 
 
 @pytest.mark.parametrize("build_nlist", [build_nlist_linked_cell, build_nlist_simple])
@@ -87,8 +87,8 @@ def test_pairwise_force_field_three(build_nlist):
     lj = CutOffWrapper(LennardJones(2.5, 1.3), rcut)
     pwff = PairwiseForceField(lj, rcut, build_nlist=build_nlist)
 
-    # Compute the energy, the forces and the mechanical pressure.
-    energy1, forces1, mech_press1 = pwff(atpos, cell_length)
+    # Compute the energy, the forces and the force contribution pressure.
+    energy1, forces1, frc_press1 = pwff(atpos, cell_length)
 
     # Compute the energy manually and compare.
     dists = [
@@ -110,8 +110,8 @@ def energy_volume(volume):
         scale = my_cell_length / cell_length
         return pwff(atpos * scale, my_cell_length)[0]
 
-    mech_press2 = -nd.Derivative(energy_volume)(cell_length**3)
-    assert mech_press1 == pytest.approx(mech_press2)
+    frc_press2 = -nd.Derivative(energy_volume)(cell_length**3)
+    assert frc_press1 == pytest.approx(frc_press2)
 
 
 @pytest.mark.parametrize("build_nlist", [build_nlist_linked_cell, build_nlist_simple])
@@ -143,8 +143,8 @@ def test_pairwise_force_field_fifteen(build_nlist):
     lj = CutOffWrapper(LennardJones(2.5, 1.3), rcut)
     pwff = PairwiseForceField(lj, rcut, build_nlist=build_nlist)
 
-    # Compute the energy, the forces and the mechanical pressure.
-    energy, forces1, mech_press1 = pwff(atpos, cell_length)
+    # Compute the energy, the forces and the force contribution to the pressure.
+    energy, forces1, frc_press1 = pwff(atpos, cell_length)
     assert energy < 0
 
     # Test forces with numdifftool
@@ -158,8 +158,8 @@ def energy_volume(volume):
         scale = my_cell_length / cell_length
         return pwff(atpos * scale, my_cell_length)[0]
 
-    mech_press2 = -nd.Derivative(energy_volume)(cell_length**3)
-    assert mech_press1 == pytest.approx(mech_press2)
+    frc_press2 = -nd.Derivative(energy_volume)(cell_length**3)
+    assert frc_press1 == pytest.approx(frc_press2)
 
 
 @pytest.mark.parametrize("build_nlist", [build_nlist_linked_cell, build_nlist_simple])