Refactor Cleanup of MDTools Analyses

analysis/lintf2_ether/gmx/.cleanup_gmx_analyses.sh

@@ -6,7 +6,7 @@
 # * Move similar analyses into one directory.
 
 gather() {
-    # Gather output of similar analyses scripts.
+    # Gather output of similar analysis scripts.
     local root="${1}"
     if [[ -d ${root} ]]; then
         echo "WARNING: Directory already exists: '${root}'"
@@ -25,7 +25,7 @@ gather() {
 }
 
 gather_cmps() {
-    # Gather output of similar analyses scripts ordered by compounds
+    # Gather output of similar analysis scripts ordered by compounds
     # into sub-directories.
     local root="${1}"
     local cmps="${2}"

analysis/lintf2_ether/mdt/.cleanup_mdt_analyses.sh

@@ -6,7 +6,7 @@
 # * Move similar analyses into one directory.
 
 gather() {
-    # Gather output of similar analyses scripts.
+    # Gather output of similar analysis scripts.
     local root="${1}"
     if [[ -d ${root} ]]; then
         echo "WARNING: Directory already exists: '${root}'"
@@ -24,8 +24,23 @@ gather() {
     fi
 }
 
+gather_dirs() {
+    # Gather directories that have the same prefix.
+    local root="${1}"
+    if [[ -d ${root} ]]; then
+        echo "WARNING: Directory already exists: '${root}'"
+        return 0
+    fi
+    if [[ -n $(find . -maxdepth 1 -type d -name "${root}?*" -print -quit) ]]; then
+        mkdir "${root}/" || exit
+        mv "${root}"?*/ "${root}/" || exit
+    else
+        echo "WARNING: No directory matching pattern '${root}?*'"
+    fi
+}
+
 gather_cmps() {
-    # Gather output of similar analyses scripts ordered by compounds
+    # Gather output of similar analysis scripts ordered by compounds
     # into sub-directories.
     local root="${1}"
     local cmps="${2}"
@@ -60,27 +75,79 @@ gather_cmps() {
     cd ../ || exit
 }
 
+gather_cmps_keep_dir() {
+    # Gather output of similar analysis scripts ordered by compounds
+    # into sub-directories but opposed to `gather_cmps` do not move the
+    # files out of their respective *_slurm-[0-9] directories.
+    local root="${1}"
+    local cmps="${2}"
+
+    # Create "root" directory.
+    if [[ -d ${root} ]]; then
+        echo "WARNING: Directory already exists: '${root}'"
+        return 0
+    else
+        mkdir "${root}/" || exit
+    fi
+
+    for cmp in ${cmps}; do
+        if [[ -n $(find . -maxdepth 1 -type d -name "${root}_${cmp}*_slurm-[0-9]*" -print -quit) ]]; then
+            if [[ -d ${root}/${root}_${cmp} ]]; then
+                echo "WARNING: Directory already exists: '${root}/${root}_${cmp}'"
+                continue
+            else
+                # Create compound directory.
+                mkdir "${root}/${root}_${cmp}/" || exit
+                # Move analysis directories to the compound directory.
+                mv "${root}_${cmp}"*_slurm-[0-9]*/ "${root}/${root}_${cmp}/" || exit
+                cd "${root}/${root}_${cmp}/" || exit
+                for dir in "${root}_${cmp}"*_slurm-[0-9]*; do
+                    if [[ -d ${dir%_slurm-[0-9]*} ]]; then
+                        echo "WARNING: Directory already exists: '${dir%_slurm-[0-9]*}'"
+                        continue
+                    else
+                        # Remove the "_slurm-[0-9]*" suffix of the
+                        # directory names.
+                        mv "${dir}" "${dir%_slurm-[0-9]*}" || exit
+                    fi
+                done
+                cd ../../ || exit
+            fi
+        fi
+    done
+
+    # Check if the root directory is empty.
+    if [[ -n $(find "${root}/" -prune -empty) ]]; then
+        echo "WARNING: No directory matching pattern '${root}_<compound>*_slurm-[0-9]*'"
+        rm -r "${root:?}/" || exit
+        return 0
+    fi
+}
+
 gather "create_mda_universe"
 gather "energy_dist"
 gather "lifetime_autocorr"
-gather "lig_change_at_pos_change_blocks_hist"
-gather "lig_change_at_pos_change_blocks"
-gather "lig_change_at_pos_change"
 gather "subvolume_charge"
 
 gather_cmps "attribute_hist" "Li NBT OBT OE NTf2 ether"
-gather_cmps "axial_hex_dist" "1nn 2nn"
 gather_cmps "densmap-z" "Li NBT OBT OE NTf2 ether"
+gather_cmps "lig_change_at_pos_change_blocks_hist" "Li-OBT Li-OE"
+gather_cmps "lig_change_at_pos_change_blocks" "Li-OBT Li-OE"
+gather_cmps "lig_change_at_pos_change" "Li-OBT Li-OE"
 gather_cmps "renewal_events" "Li-ether Li-NTf2"
 gather_cmps "topo_map" "Li-OBT Li-OE"
 
+gather_cmps "axial_hex_dist_1nn" "Li NBT OBT OE"
+gather_cmps "axial_hex_dist_2nn" "Li NBT OBT OE"
+gather_dirs "axial_hex_dist"
+
 gather_cmps "contact_hist_slab-z" "Li-OBT Li-OE"
-gather "contact_hist_at_pos_change"
+gather_cmps "contact_hist_at_pos_change" "Li-OBT Li-OE"
 gather "contact_hist"
 
-gather_cmps "discrete-hex" "Li NBT OBT OE"
-gather "discrete-z"
-
 gather_cmps "msd_layer" "Li NBT OBT OE NTf2 ether"
 gather "msd_at_coord_change"
 gather "msd"
+
+gather_cmps_keep_dir "discrete-hex" "Li NBT OBT OE"
+gather "discrete-z"