Add more equipartition regressions (#124)

Add regressions for the random divisions and the predefined molecule
groups in the equipartition checks.

Refs #59

physical_validation/tests/test_kinetic_energy_regression.py

@@ -111,7 +111,9 @@ def run_kinetic_energy_equipartition_check(
 
     result = {}
     print("\n## Validating kinetic energy equipartition (strict)")
-    result["strict"] = pv.kinetic_energy.equipartition(
+    # Run once calculating only the rotational, translational and internal
+    # degrees of freedom for the entire system, and plotting the results
+    pv.kinetic_energy.equipartition(
         simulation_data,
         strict=True,
         molec_groups=None,
@@ -122,8 +124,23 @@ def run_kinetic_energy_equipartition_check(
         bootstrap_seed=7,
         data_is_uncorrelated=True,
     )
+    # Run again including molec_groups and random divisions, but no plots
+    # to speed up execution
+    result["strict"] = pv.kinetic_energy.equipartition(
+        simulation_data,
+        strict=True,
+        molec_groups=[[0], []],
+        random_divisions=1,
+        random_groups=2,
+        random_division_seed=14,
+        verbosity=2,
+        bootstrap_seed=7,
+        data_is_uncorrelated=True,
+    )
     print("\n## Validating kinetic energy equipartition (non-strict)")
-    result["non-strict"] = pv.kinetic_energy.equipartition(
+    # Run once calculating only the rotational, translational and internal
+    # degrees of freedom for the entire system, and plotting the results
+    pv.kinetic_energy.equipartition(
         simulation_data,
         strict=False,
         molec_groups=None,
@@ -134,6 +151,19 @@ def run_kinetic_energy_equipartition_check(
         bootstrap_seed=7,
         data_is_uncorrelated=True,
     )
+    # Run again including molec_groups and random divisions, but no plots
+    # to speed up execution
+    result["non-strict"] = pv.kinetic_energy.equipartition(
+        simulation_data,
+        strict=False,
+        molec_groups=[[0], []],
+        random_divisions=1,
+        random_groups=2,
+        random_division_seed=19,
+        verbosity=2,
+        bootstrap_seed=7,
+        data_is_uncorrelated=True,
+    )
 
     # Regression fixture can only check dicts of strings
     # Use 6 digits to keep reproducibility reasonable

physical_validation/tests/test_kinetic_energy_regression/test_kinetic_energy_regression_equipartition.txt

@@ -19,6 +19,90 @@ p = 0.865841
 * int:
 Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
 p = 0.824824
+Equipartition: Testing group-wise kinetic energies (strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.746394
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.688716
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.644841
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.865841
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.824824
+Testing randomly divided group 0
+Equipartition: Testing group-wise kinetic energies (strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.96101
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.082419
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.387798
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.785126
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.772364
+Testing randomly divided group 1
+Equipartition: Testing group-wise kinetic energies (strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.810328
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.159323
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.913282
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.655927
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.703896
+Testing predifined divided group 0
+Equipartition: Testing group-wise kinetic energies (strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.810328
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.159323
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.913282
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.655927
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.703896
+Testing predifined divided group 1
+Equipartition: Testing group-wise kinetic energies (strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.96101
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.082419
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.387798
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.785126
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+p = 0.772364
 
 ## Validating kinetic energy equipartition (non-strict)
 Equipartition: Testing group-wise kinetic energies (non-strict)
@@ -42,3 +126,112 @@ T(sigma) = 303.22 +- 16.23 K
 Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
 T(mu) = 297.35 +- 4.72 K
 T(sigma) = 293.71 +- 12.57 K
+Equipartition: Testing group-wise kinetic energies (non-strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 298.20 +- 4.15 K
+T(sigma) = 308.64 +- 13.18 K
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 302.58 +- 10.89 K
+T(sigma) = 306.93 +- 14.92 K
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 297.48 +- 4.36 K
+T(sigma) = 299.80 +- 12.87 K
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 298.10 +- 10.32 K
+T(sigma) = 303.22 +- 16.23 K
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 297.35 +- 4.72 K
+T(sigma) = 293.71 +- 12.57 K
+Testing randomly divided group 0
+Equipartition: Testing group-wise kinetic energies (non-strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 297.17 +- 5.94 K
+T(sigma) = 296.33 +- 15.00 K
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 307.15 +- 15.39 K
+T(sigma) = 293.07 +- 20.47 K
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 295.51 +- 6.51 K
+T(sigma) = 300.44 +- 11.96 K
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 302.47 +- 14.23 K
+T(sigma) = 297.86 +- 16.74 K
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 294.11 +- 7.06 K
+T(sigma) = 288.10 +- 11.78 K
+Testing randomly divided group 1
+Equipartition: Testing group-wise kinetic energies (non-strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 299.24 +- 5.56 K
+T(sigma) = 306.73 +- 14.17 K
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 298.01 +- 15.93 K
+T(sigma) = 320.28 +- 20.67 K
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 299.45 +- 6.11 K
+T(sigma) = 302.41 +- 12.31 K
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 293.73 +- 14.18 K
+T(sigma) = 286.74 +- 17.58 K
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 300.59 +- 6.64 K
+T(sigma) = 307.24 +- 12.32 K
+Testing predifined divided group 0
+Equipartition: Testing group-wise kinetic energies (non-strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 299.24 +- 5.56 K
+T(sigma) = 306.73 +- 14.17 K
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 298.01 +- 15.93 K
+T(sigma) = 320.28 +- 20.67 K
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 299.45 +- 6.11 K
+T(sigma) = 302.41 +- 12.31 K
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 293.73 +- 14.18 K
+T(sigma) = 286.74 +- 17.58 K
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 300.59 +- 6.64 K
+T(sigma) = 307.24 +- 12.32 K
+Testing predifined divided group 1
+Equipartition: Testing group-wise kinetic energies (non-strict)
+* tot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 297.17 +- 5.94 K
+T(sigma) = 296.33 +- 15.00 K
+* tra:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 307.15 +- 15.39 K
+T(sigma) = 293.07 +- 20.47 K
+* rni:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 295.51 +- 6.51 K
+T(sigma) = 300.44 +- 11.96 K
+* rot:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 302.47 +- 14.23 K
+T(sigma) = 297.86 +- 16.74 K
+* int:
+Equilibration, decorrelation and tail pruning was skipped on user request. Note that if the provided trajectory is statistically correlated, the results of the physical validation checks might be invalid.
+T(mu) = 294.11 +- 7.06 K
+T(sigma) = 288.10 +- 11.78 K

physical_validation/tests/test_kinetic_energy_regression/test_kinetic_energy_regression_equipartition.yml

@@ -1,2 +1,2 @@
-non-strict: '[(0.013067,0.796377),(0.406843,0.588891),(0.154599,0.128358),(0.004732,0.312300),(0.169101,0.353289)]'
-strict: '[0.746394,0.688716,0.644841,0.865841,0.824824]'
+non-strict: '[(0.013067,0.796377),(0.406843,0.588891),(0.154599,0.128358),(0.004732,0.312300),(0.169101,0.353289),(0.165436,0.121112),(0.584908,0.247993),(0.405995,0.191838),(0.303447,0.017071),(0.571374,0.852889),(0.196023,0.605645),(0.008894,1.070967),(0.212210,0.346322),(0.311499,0.649264),(0.366991,0.737305),(0.196023,0.605645),(0.008894,1.070967),(0.212210,0.346322),(0.311499,0.649264),(0.366991,0.737305),(0.165436,0.121112),(0.584908,0.247993),(0.405995,0.191838),(0.303447,0.017071),(0.571374,0.852889)]'
+strict: '[0.746394,0.688716,0.644841,0.865841,0.824824,0.961010,0.082419,0.387798,0.785126,0.772364,0.810328,0.159323,0.913282,0.655927,0.703896,0.810328,0.159323,0.913282,0.655927,0.703896,0.961010,0.082419,0.387798,0.785126,0.772364]'