Include units in test driver arguments

Author: PhilippHoellmer

test_driver/helper_functions.py

@@ -8,8 +8,9 @@
 import numpy.typing as npt
 
 
-def run_lammps(modelname: str, temperature: float, pressure: float, timestep: float, number_sampling_timesteps: int,
-               species: List[str], msd_threshold: float, lammps_command: str,
+def run_lammps(modelname: str, temperature_K: float, pressure_bar: float, timestep_ps: float,
+               number_sampling_timesteps: int, species: List[str],
+               msd_threshold_angstrom_squared_per_hundred_timesteps: float, lammps_command: str,
                random_seed: int) -> Tuple[str, str, str, str]:
     """
     Run LAMMPS NPT simulation with the given parameters.
@@ -23,24 +24,24 @@ def run_lammps(modelname: str, temperature: float, pressure: float, timestep: fl
     :param modelname:
         Name of the OpenKIM interatomic model.
     :type modelname: str
-    :param temperature:
+    :param temperature_K:
         Target temperature in Kelvin.
-    :type temperature: float
-    :param pressure:
+    :type temperature_K: float
+    :param pressure_bar:
         Target pressure in bars.
-    :type pressure: float
-    :param timestep:
+    :type pressure_bar: float
+    :param timestep_ps:
         Timestep in picoseconds.
-    :type timestep: float
+    :type timestep_ps: float
     :param number_sampling_timesteps:
         Number of timesteps for sampling thermodynamic quantities.
     :type number_sampling_timesteps: int
     :param species:
         List of chemical species in the system.
     :type species: List[str]
-    :param msd_threshold:
+    :param msd_threshold_angstrom_squared_per_hundred_timesteps:
         Mean squared displacement threshold for vaporization in Angstroms^2 per 100*timestep.
-    :type msd_threshold: float
+    :type msd_threshold_angstrom_squared_per_hundred_timesteps: float
     :param lammps_command:
         Command to run LAMMPS (e.g., "mpirun -np 4 lmp_mpi" or "lmp").
     :type lammps_command: str
@@ -53,26 +54,26 @@ def run_lammps(modelname: str, temperature: float, pressure: float, timestep: fl
         file.
     :rtype: Tuple[str, str, str, str]
     """
-    pdamp = timestep * 100.0
-    tdamp = timestep * 1000.0
+    pdamp = timestep_ps * 100.0
+    tdamp = timestep_ps * 1000.0
 
     log_filename = "output/lammps.log"
     restart_filename = "output/final_configuration.restart"
     variables = {
         "modelname": modelname,
-        "temperature": temperature,
+        "temperature": temperature_K,
         "temperature_seed": random_seed,
         "temperature_damping": tdamp,
-        "pressure": pressure,
+        "pressure": pressure_bar,
         "pressure_damping": pdamp,
-        "timestep": timestep,
+        "timestep": timestep_ps,
         "number_sampling_timesteps": number_sampling_timesteps,
         "species": " ".join(species),
         "average_position_filename": "output/average_position.dump.*",
         "average_cell_filename": "output/average_cell.dump",
         "write_restart_filename": restart_filename,
         "trajectory_filename": "output/trajectory.lammpstrj",
-        "msd_threshold": msd_threshold
+        "msd_threshold": msd_threshold_angstrom_squared_per_hundred_timesteps
     }
 
     command = (

test_driver/test_driver.py

@@ -10,8 +10,9 @@
 
 
 class TestDriver(SingleCrystalTestDriver):
-    def _calculate(self, timestep: float, number_sampling_timesteps: int = 100, repeat: Sequence[int] = (0, 0, 0),
-                   lammps_command = "lmp", msd_threshold: float = 0.1, random_seed: int = 1, **kwargs) -> None:
+    def _calculate(self, timestep_ps: float, number_sampling_timesteps: int = 100, repeat: Sequence[int] = (0, 0, 0),
+                   lammps_command = "lmp", msd_threshold_angstrom_squared_per_hundred_timesteps: float = 0.1,
+                   random_seed: int = 1, **kwargs) -> None:
         """
         Compute crystal structure at constant pressure and temperature (NPT) with a Lammps molecular-dynamics simulation.
 
@@ -32,10 +33,10 @@ def _calculate(self, timestep: float, number_sampling_timesteps: int = 100, repe
 
         All output files are written to the "output" directory.
 
-        :param timestep:
+        :param timestep_ps:
             Time step in picoseconds.
             Should be bigger than zero.
-        :type timestep: float
+        :type timestep_ps: float
         :param number_sampling_timesteps:
             Sample thermodynamic variables every number_sampling_timesteps timesteps in Lammps.
             Should be bigger than zero.
@@ -51,11 +52,11 @@ def _calculate(self, timestep: float, number_sampling_timesteps: int = 100, repe
             Command to run Lammps.
             Default is "lmp".
         :type lammps_command: str
-        :param msd_threshold:
+        :param msd_threshold_angstrom_squared_per_hundred_timesteps:
             Mean-squared displacement threshold in Angstroms^2 per 100*timestep to detect melting or vaporization.
             Default is 0.1.
             Should be bigger than zero.
-        :type msd_threshold: float
+        :type msd_threshold_angstrom_squared_per_hundred_timesteps: float
         :param random_seed:
             Random seed for Lammps simulation.
             Default is 1.
@@ -93,7 +94,7 @@ def _calculate(self, timestep: float, number_sampling_timesteps: int = 100, repe
             raise ValueError("The off-diagonal entries of the stress tensor have to be zero so that a hydrostatic "
                              "pressure is used.")
 
-        if not timestep > 0.0:
+        if not timestep_ps > 0.0:
             raise ValueError("Timestep has to be larger than zero.")
 
         if not number_sampling_timesteps > 0:
@@ -105,7 +106,7 @@ def _calculate(self, timestep: float, number_sampling_timesteps: int = 100, repe
         if not all(r >= 0 for r in repeat):
             raise RuntimeError("All number of repeats must be bigger than zero.")
 
-        if not msd_threshold > 0.0:
+        if not msd_threshold_angstrom_squared_per_hundred_timesteps > 0.0:
             raise RuntimeError("The mean-squared displacement threshold has to be bigger than zero.")
 
         if not random_seed > 0:
@@ -172,8 +173,9 @@ def _calculate(self, timestep: float, number_sampling_timesteps: int = 100, repe
 
         # Run single Lammps simulation.
         log_filename, restart_filename, average_position_filename, average_cell_filename = run_lammps(
-            self.kim_model_name, temperature_K, pressure_bar, timestep, number_sampling_timesteps, species,
-            msd_threshold, lammps_command=lammps_command, random_seed=random_seed)
+            self.kim_model_name, temperature_K, pressure_bar, timestep_ps, number_sampling_timesteps, species,
+            msd_threshold_angstrom_squared_per_hundred_timesteps, lammps_command=lammps_command,
+            random_seed=random_seed)
 
         # Check that crystal did not melt or vaporize.
         with open(log_filename, "r") as f: