fixed a bug in the configuration class where sample.h5 would not be s…

…aved in the correct directory
ccpem · Jul 5, 2024 · 3f77a5d · 3f77a5d
1 parent 34da066
commit 3f77a5d
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/scripts/run_parakeet_example.sh b/scripts/run_parakeet_example.sh
@@ -22,8 +22,8 @@ C_C=2.7
 BOX_X=4000.0
 BOX_Y=4000.0
 BOX_Z=500.0
-CENTRE_X=500.0
-CENTRE_Y=500.0
+CENTRE_X=2000.0
+CENTRE_Y=2000.0
 CENTRE_Z=250.
 TYPE=$"cuboid"
 CUBOID_LENGTH_X=4000.0
@@ -33,7 +33,7 @@ SIMULATION_MARGIN=0
 SIMULATION_PADDING=1
 SENSITIVITY_COEFFICIENT=0.022
 
-LOGFILE=$MRC_DIR$"run_parakeet.log"
+LOGFILE=$MRC_DIR$"/run_parakeet.log"
 
 nohup $EXECUTABLE $SUBROUTINE \
     --pdb_dir $PDB_DIR \
@@ -66,4 +66,4 @@ nohup $EXECUTABLE $SUBROUTINE \
     --dqe \
     --radiation_damage_model \
     --sensitivity_coefficient $SENSITIVITY_COEFFICIENT > $LOGFILE 2>&1 &
-
+
diff --git a/src/roodmus/simulation/configuration.py b/src/roodmus/simulation/configuration.py
@@ -52,7 +52,7 @@ def __init__(self, config_filename, args=None):
 
         self.config = config.new(filename=self.config_filename, full=True)
         if args:
-            self.sample_filename = "sample.h5"
+            self.sample_filename = os.path.join(args.mrc_dir, "sample.h5")
             self.exit_wave_filename = os.path.join(
                 args.mrc_dir, "exit_wave.h5"
             )