updating the example script to default to using radiation damage model

ccpem · Jul 2, 2024 · 8fded02 · 8fded02
1 parent 7fa707d
commit 8fded02
Showing 1 changed file with 15 additions and 12 deletions.
diff --git a/scripts/run_parakeet_example.sh b/scripts/run_parakeet_example.sh
@@ -12,38 +12,37 @@ N_MOLECULES=10
 DEVICE=$"cpu"
 ELECTRONS_PER_ANGSTROM=45.0
 ENERGY=300.0
-NX=1000
-NY=1000
+NX=4000
+NY=4000
 PIXEL_SIZE=1.0
 C_10=-20000.0
 C_10_STDDEV=5000.0
 C_C=2.7
-BOX_X=1000.0
-BOX_Y=1000.0
+BOX_X=4000.0
+BOX_Y=4000.0
 BOX_Z=500.0
 CENTRE_X=500.0
 CENTRE_Y=500.0
 CENTRE_Z=250.
 TYPE=$"cuboid"
-CUBOID_LENGTH_X=1000.0
-CUBOID_LENGTH_Y=1000.0
+CUBOID_LENGTH_X=4000.0
+CUBOID_LENGTH_Y=4000.0
 CUBOID_LENGTH_Z=500.0
 SIMULATION_MARGIN=0
 SIMULATION_PADDING=1
+SENSITIVITY_COEFFICIENT=0.022
 
-LOGFILE=$MRC_DIR$".log"
+LOGFILE=$MRC_DIR$"run_parakeet.log"
 
 nohup $EXECUTABLE $SUBROUTINE \
-    --dqe \
-    --fast_ice \
     --pdb_dir $PDB_DIR \
     --mrc_dir $MRC_DIR \
     --n_images $N_IMAGES \
     --n_molecules $N_MOLECULES \
     --device $DEVICE \
     --electrons_per_angstrom $ELECTRONS_PER_ANGSTROM \
-    --energy $ENERGY -\
-    -nx $NX \
+    --energy $ENERGY \
+    --nx $NX \
     --ny $NY \
     --pixel_size $PIXEL_SIZE \
     --c_10 $C_10 \
@@ -60,5 +59,9 @@ nohup $EXECUTABLE $SUBROUTINE \
     --cuboid_length_y $CUBOID_LENGTH_Y \
     --cuboid_length_z $CUBOID_LENGTH_Z \
     --simulation_margin $SIMULATION_MARGIN \
-    --simulation_padding $SIMULATION_PADDING > $LOGFILE 2>&1 &
+    --simulation_padding $SIMULATION_PADDING \
+    --fast_ice \
+    --dqe \
+    --radiation_damage_model \
+    --sensitivity_coefficient $SENSITIVITY_COEFFICIENT > $LOGFILE 2>&1 &