test vibrational entropy

Author: skfegan

CodeEntropy/tests/test_EntropyFunctions/test_frequency_calculation.py

@@ -15,6 +15,7 @@ def test_frequency_calculation_0():
     assert frequencies == 0
 
 # test when lambdas are positive 
+# the data for this test came from running CodeEntropy0.3 at the whole molecule level with 1AKI_ws.tpr and 1AKI_ws.trr from the CodeEntropy0.3/Examples
 def test_frequency_calculation_pos():
     lambdas = numpy.array([585495.0917897299, 658074.5130064893, 782425.305888707])
     temp = 298

CodeEntropy/tests/test_EntropyFunctions/test_vibrational_entropy.py

@@ -6,6 +6,7 @@
 # Given a matrix does the code calculate the correct entropy value
 
 # test for matrix_type force, highest level=yes
+# the data for this test came from running CodeEntropy0.3 at the whole molecule level with 1AKI_ws.tpr and 1AKI_ws.trr from the CodeEntropy0.3/Examples
 def test_vibrational_entropy_polymer_force():
     matrix = numpy.array([[4.67476, -0.04069, -0.19714],[-0.04069, 3.86300, -0.17922],[-0.19714, -0.17922, 3.66307]])
     matrix_type = "force"
@@ -19,6 +20,7 @@ def test_vibrational_entropy_polymer_force():
 # test for matrix_type force, highest level=no
 
 # test for matrix_type torque
+# the data for this test came from running CodeEntropy0.3 at the whole molecule level with 1AKI_ws.tpr and 1AKI_ws.trr from the CodeEntropy0.3/Examples
 def test_vibrational_entropy_polymer_torque():
     matrix = numpy.array([[6.69611, 0.39754, 0.57763],[0.39754, 4.63265, 0.38648],[0.57763, 0.38648, 6.34589]])
     matrix_type = "torque"

CodeEntropy/tests/test_GeometricFunctions/test_get_sphCoord_axes.py

@@ -0,0 +1,22 @@
+import pytest
+import numpy
+from CodeEntropy import GeometricFunctions as GF
+
+## Test get_sphCoord_axes
+# Given a vector does the code calculate the correct spherical basis to use as rotational axes
+
+# The data for this test comes from running CodeEntropy0.3 at the united atom level with 1AKI_ws.tpr and 1AKI_ws.trr from the CodeEntropy0.3/Examples
+# Using the value from the first bead in the first frame
+def test_get_sphCoord_axes():
+    arg_r = [-0.1240921, 0.2787145, -0.0764211] # input vector
+
+    spherical_basis = GF.get_sphCoord_axes(arg_r)
+
+    ref = [[-0.39454843, 0.88616733, -0.24297941],[0.0988289, -0.22197261, -0.97003145],[-0.91354496, -0.40673777, 0.0]]
+  
+    assert spherical_basis[0] == pytest.approx(ref[0])
+    assert spherical_basis[1] == pytest.approx(ref[1])
+    assert spherical_basis[2] == pytest.approx(ref[2])
+
+# TODO test for error handling on invalid inputs
+

CodeEntropy/tests/test_main.py

@@ -4,9 +4,7 @@
 
 # Import package, test suite, and other packages as needed
 import sys
-
 import pytest
-
 import CodeEntropy