Fix Boltzmann KeyError

* use try except and update with mda 2.6.0 release
MDAnalysis · Aug 9, 2023 · 760bf9d · 760bf9d
1 parent 06539e7
commit 760bf9d
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Showing 2 changed files with 15 additions and 9 deletions.
diff --git a/transport_analysis/tests/test_viscosity.py b/transport_analysis/tests/test_viscosity.py
@@ -88,6 +88,12 @@ def characteristic_poly_helfand(
 ):
     result = np.zeros(total_frames)
 
+    # update when mda 2.6.0 releases with typo fix
+    try:
+        boltzmann = constants["Boltzmann_constant"]
+    except KeyError:
+        boltzmann = constants["Boltzman_constant"]
+
     for lag in range(total_frames):
         sum = 0
         sum = np.float64(sum)
@@ -102,13 +108,7 @@ def characteristic_poly_helfand(
         vis_helf = (
             sum
             * n_dim
-            / (
-                (total_frames - lag)
-                * 2
-                * constants["Boltzman_constant"]
-                * vol_avg
-                * temp_avg
-            )
+            / ((total_frames - lag) * 2 * boltzmann * vol_avg * temp_avg)
         )
 
         result[lag] = vis_helf

diff --git a/transport_analysis/viscosity.py b/transport_analysis/viscosity.py
@@ -112,6 +112,12 @@ def _prepare(self):
         )
         # self.results.timeseries not set here
 
+        # update when mda 2.6.0 releases with typo fix
+        try:
+            self.boltzmann = constants["Boltzmann_constant"]
+        except KeyError:
+            self.boltzmann = constants["Boltzman_constant"]
+
     @staticmethod
     def _parse_dim_type(dim_str):
         r"""Sets up the desired dimensionality of the calculation."""
@@ -194,9 +200,9 @@ def _conclude(self):
             # update viscosity by particle array
             self.results.visc_by_particle[lag, :] = np.mean(sq_diff, axis=0)
 
-        # divide by 2, boltzman constant, vol_avg, and temp_avg
+        # divide by 2, boltzmann constant, vol_avg, and temp_avg
         self.results.visc_by_particle = self.results.visc_by_particle / (
-            2 * constants["Boltzman_constant"] * self._vol_avg * self.temp_avg
+            2 * self.boltzmann * self._vol_avg * self.temp_avg
         )
         # average over # particles and update results array
         self.results.timeseries = self.results.visc_by_particle.mean(axis=1)