Log now only cleaned AFTER LAMMPS instance is closed

mala-project · May 31, 2024 · fe911a2 · fe911a2
1 parent 92831ff
commit fe911a2
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Showing 4 changed files with 11 additions and 12 deletions.
diff --git a/mala/descriptors/atomic_density.py b/mala/descriptors/atomic_density.py
@@ -185,7 +185,6 @@ def __calculate_lammps(self, outdir, **kwargs):
 
         # Do the LAMMPS calculation and clean up.
         lmp.file(self.parameters.lammps_compute_file)
-        self._clean_calculation(keep_logs)
 
         # Extract the data.
         nrows_ggrid = extract_compute_np(
@@ -209,7 +208,7 @@ def __calculate_lammps(self, outdir, **kwargs):
             array_shape=(nrows_ggrid, ncols_ggrid),
             use_fp64=use_fp64,
         )
-        lmp.close()
+        self._clean_calculation(lmp, keep_logs)
 
         # In comparison to SNAP, the atomic density always returns
         # in the "local mode". Thus we have to make some slight adjustments

diff --git a/mala/descriptors/bispectrum.py b/mala/descriptors/bispectrum.py
@@ -184,7 +184,6 @@ def __calculate_lammps(self, outdir, **kwargs):
 
         # Do the LAMMPS calculation and clean up.
         lmp.file(self.parameters.lammps_compute_file)
-        self._clean_calculation(keep_logs)
 
         # Set things not accessible from LAMMPS
         # First 3 cols are x, y, z, coords
@@ -228,7 +227,7 @@ def __calculate_lammps(self, outdir, **kwargs):
                 array_shape=(nrows_local, ncols_local),
                 use_fp64=use_fp64,
             )
-            lmp.close()
+            self._clean_calculation(lmp, keep_logs)
 
             # Copy the grid dimensions only at the end.
             self.grid_dimensions = [nx, ny, nz]
@@ -244,7 +243,7 @@ def __calculate_lammps(self, outdir, **kwargs):
                 (nz, ny, nx, self.fingerprint_length),
                 use_fp64=use_fp64,
             )
-            lmp.close()
+            self._clean_calculation(lmp, keep_logs)
 
             # switch from x-fastest to z-fastest order (swaps 0th and 2nd
             # dimension)

diff --git a/mala/descriptors/descriptor.py b/mala/descriptors/descriptor.py
@@ -820,7 +820,8 @@ def _setup_lammps(self, nx, ny, nz, lammps_dict):
 
         return lmp
 
-    def _clean_calculation(self, keep_logs):
+    def _clean_calculation(self, lmp, keep_logs):
+        lmp.close()
         if not keep_logs:
             if get_rank() == 0:
                 os.remove(self.lammps_temporary_log)

diff --git a/mala/descriptors/minterpy_descriptors.py b/mala/descriptors/minterpy_descriptors.py
@@ -171,14 +171,15 @@ def _calculate(self, atoms, outdir, grid_dimensions, **kwargs):
             )
 
             # Create LAMMPS instance.
-            lammps_dict = {}
-            lammps_dict["sigma"] = self.parameters.atomic_density_sigma
-            lammps_dict["rcutfac"] = self.parameters.atomic_density_cutoff
+            lammps_dict = {
+                "sigma": self.parameters.atomic_density_sigma,
+                "rcutfac": self.parameters.atomic_density_cutoff,
+            }
             self.lammps_temporary_log = os.path.join(
                 outdir,
                 "lammps_bgrid_log_" + self.calculation_timestamp + ".tmp",
             )
-            lmp = self._setup_lammps(nx, ny, nz, lammps_dict, log_path)
+            lmp = self._setup_lammps(nx, ny, nz, lammps_dict)
 
             # For now the file is chosen automatically, because this is used
             # mostly under the hood anyway.
@@ -199,7 +200,6 @@ def _calculate(self, atoms, outdir, grid_dimensions, **kwargs):
 
             # Do the LAMMPS calculation and clean up.
             lmp.file(self.parameters.lammps_compute_file)
-            self._clean_calculation(keep_logs)
 
             # Extract the data.
             nrows_ggrid = extract_compute_np(
@@ -223,7 +223,7 @@ def _calculate(self, atoms, outdir, grid_dimensions, **kwargs):
                 array_shape=(nrows_ggrid, ncols_ggrid),
             )
 
-            lmp.close()
+            self._clean_calculation(lmp, keep_logs)
 
             gaussian_descriptors_np = gaussian_descriptors_np.reshape(
                 (