add mds.units.<unit_system> (#543)

* add `mds.units.<unit_system>`

* Update project.py

[skip ci]

* fix frozen dataclass issue

* lint

[skip ci]

* fix test

[skip ci]

Co-authored-by: Samuel Tovey <tovey.samuel@gmail.com>

Author: PythonFZ

CI/functional_tests/test_molten_salts.py

@@ -85,7 +85,7 @@ def mdsuite_project(traj_files, tmp_path) -> mds.Project:
         name="NaCl",
         timestep=0.002,
         temperature=1200.0,
-        units="metal",
+        units=mds.units.METAL,
         simulation_data=na_cl_file,
     )
     project.add_experiment(

CI/integration_tests/calculators/test_einstein_diffusion_coefficients.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+import dataclasses
 import os
 
 import numpy as np
@@ -60,9 +61,7 @@ def test_calculator(tmp_path):
     os.chdir(tmp_path)
     project = mds.Project()
     # introduce nontrivial units to make sure all conversions are correct
-    units = mdsuite.utils.units.si
-    units.length = 0.5
-    units.time = 1.3
+    units = dataclasses.replace(mdsuite.units.SI, length=0.5, time=1.3)
     exp = project.add_experiment(
         "test_diff_coeff", timestep=time_step, temperature=4.321, units=units
     )

CI/integration_tests/calculators/test_green_kubo_self_diffusion_coefficients.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+import dataclasses
 import os
 
 import numpy as np
@@ -71,9 +72,9 @@ def test_calculator(tmp_path):
     os.chdir(tmp_path)
     project = mds.Project()
     # introduce nontrivial units to make sure all conversions are correct
-    units = mdsuite.utils.units.si
-    units.length = 0.000007654
-    units.time = 0.0056789
+
+    units = dataclasses.replace(mdsuite.units.SI, length=0.000007654, time=0.0056789)
+
     exp = project.add_experiment(
         "test_diff_coeff", timestep=time_step, temperature=kT, units=units
     )

CI/unit_tests/database/test_experiment_database.py

@@ -206,7 +206,7 @@ def test_experiment_simulation_data_nested(tmp_path):
 
 def test_experiment_units(tmp_path):
     """Test that the experiment simulation data is stored correctly in the database"""
-    from mdsuite.utils.units import Units, si
+    from mdsuite.utils.units import Units
 
     os.chdir(tmp_path)
     custom_units = Units(
@@ -220,10 +220,10 @@ def test_experiment_units(tmp_path):
     )
 
     project_1 = mds.Project()
-    project_1.add_experiment(name="Exp01", units="si")
+    project_1.add_experiment(name="Exp01", units=mds.units.SI)
     project_1.add_experiment(name="Exp02", units=custom_units)
 
     project_2 = mds.Project()
 
-    assert project_2.experiments["Exp01"].units == si
+    assert project_2.experiments["Exp01"].units == mds.units.SI
     assert project_2.experiments["Exp02"].units == custom_units

CI/unit_tests/utils/test_units.py

@@ -0,0 +1,8 @@
+import mdsuite as mds
+
+
+def test_units_loading():
+    """Test that the import works"""
+    assert mds.units.SI.pressure == 1
+    assert mds.units.METAL.pressure == 100000
+    assert mds.units.REAL.pressure == 101325.0

mdsuite/__init__.py

@@ -28,12 +28,13 @@
     from importlib import metadata
 except ImportError:  # for Python<3.8
     import importlib_metadata as metadata
+
 import logging
 import sys
 
 from mdsuite.experiment import Experiment
 from mdsuite.project import Project
-from mdsuite.utils import config
+from mdsuite.utils import config, units
 from mdsuite.utils.molecule import Molecule
 from mdsuite.utils.report_computer_characteristics import Report
 
@@ -43,6 +44,7 @@
     Report.__name__,
     "config",
     Molecule.__name__,
+    "units",
 ]
 __version__ = metadata.version("mdsuite")
 

mdsuite/experiment/experiment.py

@@ -190,7 +190,7 @@ def __init__(
 
         if self.units is None:
             if units is None:
-                units = "real"
+                units = mdsuite.units.REAL
             self.units = self.units_to_si(units)  # Units used during the simulation.
 
         self.box_array = None  # Box vectors.

mdsuite/utils/units.py

@@ -42,7 +42,7 @@
 golden_ratio = 1.618033988749895  # The golden ratio as taken from scipy
 
 
-@dataclass()
+@dataclass(frozen=True)
 class Units:
     """
     Dataclass for the units.
@@ -64,7 +64,7 @@ def volume(self) -> float:
         return self.length**3
 
 
-real = Units(
+REAL = Units(
     time=1e-15,
     length=1e-10,
     energy=4184 / 6.02214076e23,
@@ -75,7 +75,7 @@ def volume(self) -> float:
 )
 
 
-metal = Units(
+METAL = Units(
     time=1e-12,
     length=1e-10,
     energy=1.6022e-19,
@@ -86,7 +86,7 @@ def volume(self) -> float:
 )
 
 
-si = Units(
+SI = Units(
     time=1,
     length=1,
     energy=1,
@@ -97,4 +97,4 @@ def volume(self) -> float:
 )
 
 
-units_dict = {"real": real, "metal": metal, "si": si}
+units_dict = {"real": REAL, "metal": METAL, "si": SI}