Add test for CalcOutput.from_directory.

emmet-core/tests/classical_md/openmm_md/test_tasks.py

@@ -0,0 +1,37 @@
+from pathlib import Path
+
+import numpy as np
+from emmet.core.classical_md.openmm import CalculationOutput
+
+
+def test_calc_output_from_directory(test_dir):
+    output_dir = test_dir / "classical_md" / "calc_output"
+    # Call the from_directory function
+    calc_out = CalculationOutput.from_directory(
+        output_dir,
+        "state.csv",
+        "trajectory.dcd",
+        elapsed_time=10.0,
+        n_steps=1500,
+        state_interval=100,
+    )
+
+    # Assert the expected attributes of the CalculationOutput object
+    assert isinstance(calc_out, CalculationOutput)
+    assert calc_out.dir_name == str(output_dir)
+    assert calc_out.elapsed_time == 10.0
+    assert calc_out.traj_file == "trajectory.dcd"
+    assert calc_out.state_file == "state.csv"
+
+    # Assert the contents of the state data
+    assert np.array_equal(calc_out.steps_reported[:3], [100, 200, 300])
+    assert np.allclose(calc_out.potential_energy[:3], [-26192.4, -25648.6, -25149.6])
+    assert np.allclose(calc_out.kinetic_energy[:3], [609.4, 1110.4, 1576.4], atol=0.1)
+    assert np.allclose(calc_out.total_energy[:3], [-25583.1, -24538.1, -23573.2])
+    assert np.allclose(calc_out.temperature[:3], [29.6, 54.0, 76.6], atol=0.1)
+    assert np.allclose(calc_out.volume[:3], [21.9, 21.9, 21.9], atol=0.1)
+    assert np.allclose(calc_out.density[:3], [1.0, 0.99, 0.99], atol=0.1)
+
+    # Assert the existence of the DCD and state files
+    assert Path(calc_out.dir_name, calc_out.traj_file).exists()
+    assert Path(calc_out.dir_name, calc_out.state_file).exists()

test_files/classical_md/calc_output/state.csv

@@ -0,0 +1,18 @@
+#"Step","Potential Energy (kJ/mole)","Kinetic Energy (kJ/mole)","Total Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)","Density (g/mL)"
+1000,-26192.479795343505,609.4196914344211,-25583.060103909083,29.614683433627977,21.873459457163882,0.9954543820541577
+2000,-25648.552310042112,1110.4255423058567,-24538.126767736256,53.96100811019054,21.896418997832697,0.9944105960647234
+100,-26192.479795343505,609.4196914344211,-25583.060103909083,29.614683433627977,21.873459457163882,0.9954543820541577
+200,-25648.552310042112,1110.4255423058567,-24538.126767736256,53.96100811019054,21.896418997832697,0.9944105960647234
+300,-25149.615762218746,1576.3685252566356,-23573.24723696211,76.60345654458364,21.902472359270778,0.9941357628560747
+400,-24737.794927124953,2048.908203465864,-22688.88672365909,99.5664706655355,22.025973627010902,0.988561569901083
+500,-24236.83499597991,2362.5727053481387,-21874.26229063177,114.80896292197377,22.427603013306435,0.9708585912814258
+600,-23952.5612414965,2744.7859341483563,-21207.775307348144,133.38257308612992,22.451255694017004,0.9698357795248072
+700,-23561.24490686599,2981.7360809766687,-20579.508825889323,144.89713962623532,22.617654864431856,0.9627006512314953
+800,-23257.599271389336,3263.6894834260456,-19993.90978796329,158.59863446457717,22.561532702010723,0.9650953840284621
+900,-22989.069612634717,3515.5816009845585,-19473.48801165016,170.83930444254142,22.982310428217957,0.9474256792121007
+1000,-22721.45251535368,3712.6360813537613,-19008.81643399992,180.4151454226322,23.05915218995153,0.9442685007650109
+1100,-22390.948659398535,3880.3415879751556,-18510.60707142338,188.5647762246478,23.158223282091488,0.9402289114362175
+1200,-22183.04180200165,4033.800234109862,-18149.24156789179,196.02208239526976,23.20718359651434,0.9382453056728586
+1300,-22048.592668279394,4216.629234793596,-17831.9634334858,204.90663774167015,22.84203464974821,0.9532439382565145
+1400,-21737.752101440245,4308.225194310769,-17429.526907129475,209.35773340370193,23.121043846718113,0.94174083193084
+1500,-21603.87279039141,4662.04510079883,-16941.82768959258,226.55157316706197,23.185483890016233,0.9391234261318885