partial revert of 93056ff and further changes to make both lammps and post-processing to work

Author: ilia-nikiforov-umn

test_driver/helper_functions.py

@@ -76,11 +76,11 @@ def run_lammps(modelname: str, temperature_K: float, pressure_bar: float, timest
     pdamp = timestep_ps * 1000.0
     tdamp = timestep_ps * 100.0
 
-    log_filename = os.path.join(output_dir, "lammps.log")
-    restart_filename = os.path.join(output_dir, "final_configuration.restart")
-    melted_crystal_filename = os.path.join(output_dir, "melted_crystal.dump")
-    average_position_filename = os.path.join(output_dir, "average_position.dump")
-    average_cell_filename = os.path.join(output_dir, "average_cell.dump")
+    log_filename = "lammps.log"
+    restart_filename = "final_configuration.restart"
+    melted_crystal_filename = "melted_crystal.dump"
+    average_position_filename = "average_position.dump"
+    average_cell_filename = "average_cell.dump"
     variables = {
         "modelname": modelname,
         "temperature": temperature_K,
@@ -92,22 +92,22 @@ def run_lammps(modelname: str, temperature_K: float, pressure_bar: float, timest
         "thermo_sampling_period": thermo_sampling_period,
         "species": " ".join(species),
         "zero_temperature_crystal_filename": os.path.join(output_dir, "zero_temperature_crystal.lmp"),
-        "average_position_filename": f"{average_position_filename}.*",
-        "average_cell_filename": average_cell_filename,
-        "write_restart_filename": restart_filename,
+        "average_position_filename": f"{os.path.join(output_dir, average_position_filename)}.*",
+        "average_cell_filename": os.path.join(output_dir, average_cell_filename),
+        "write_restart_filename": os.path.join(output_dir, restart_filename),
         "trajectory_filename": os.path.join(output_dir, "trajectory.lammpstrj"),
         "msd_trajectory_filename": os.path.join(output_dir, "msd_trajectory.lammpstrj"),
         "msd_threshold": msd_threshold_angstrom_squared_per_sampling_timesteps,
         "msd_timesteps": number_msd_timesteps,
         "rlc_run_length": rlc_run_length,
         "rlc_n_every": rlc_n_every,
-        "melted_crystal_output": melted_crystal_filename
+        "melted_crystal_output": os.path.join(output_dir, melted_crystal_filename)
     }
 
     command = (
             f"{lammps_command} "
             + " ".join(f"-var {key} '{item}'" for key, item in variables.items())
-            + f" -log {log_filename}"
+            + f" -log {os.path.join(output_dir, log_filename)}"
             + f" -in {os.path.join(output_dir, 'npt.lammps')}")
 
     patched_env = os.environ.copy()