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Merged
andthum merged 9 commits into from
Nov 16, 2023
Merged

Refactor Scripts That Analyze a Slab in xy Plane #137

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949b82a
[discrete-hex_*.sh]: Refactor Cleanup
andthum Nov 16, 2023
61ecebf
[axial_hex_dist_*nn_*.sh]: Refactor Cleanup
andthum Nov 16, 2023
2c9b42d
[contact_hist_slab-z_Li-*.sh]: Refactor Cleanup
andthum Nov 16, 2023
9011634
[densmap-z_*.sh]: Refactor Cleanup
andthum Nov 16, 2023
381fda1
[*rdf_slab-z_*.sh]: Refactor Cleanup
andthum Nov 16, 2023
7c6904f
[axial_hex_dist_1nn_OBT.sh]: Fix Typo in Analysis Name
andthum Nov 16, 2023
95b50f5
[axial_hex_dist_*nn_*.sh]: Decrease Time and Memory Limit
andthum Nov 16, 2023
e0d544d
[discrete-hex_*.sh]: Decrease Time Limit
andthum Nov 16, 2023
9bdc202
[contact_hist_slab-z_Li-*.sh]: Decrease Memory Limit
andthum Nov 16, 2023
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7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/.rdf_slab-z_Li-com.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -120,14 +120,19 @@ gzip --best --verbose "${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/.rdf_slab-z_NTf2-com.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -119,14 +119,19 @@ gzip --best --verbose "${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/.rdf_slab-z_ether-com.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,14 +116,19 @@ gzip --best --verbose "${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/densmap-z_Li.sh
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -102,13 +102,18 @@ gzip --best --verbose "${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat"
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/densmap-z_NBT.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -108,13 +108,18 @@ gzip --best --verbose "${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat"
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/densmap-z_OBT.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -108,13 +108,18 @@ gzip --best --verbose "${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat"
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/densmap-z_OE.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -108,13 +108,18 @@ gzip --best --verbose "${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat"
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/densmap-z_gra.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -109,13 +109,18 @@ gzip --best --verbose "${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat"
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.dat.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/rdf_slab-z_Li.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,14 +105,19 @@ gzip --best --verbose "${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/rdf_slab-z_NBT.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -103,14 +103,19 @@ gzip --best --verbose "${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
7 changes: 6 additions & 1 deletion analysis/lintf2_ether/gmx/rdf_slab-z_OE.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -102,14 +102,19 @@ gzip --best --verbose "${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_cn${analysis}_${zmin}-${zmax}nm.xvg.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}nm_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
11 changes: 8 additions & 3 deletions analysis/lintf2_ether/mdt/axial_hex_dist_1nn_Li.sh
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#!/bin/bash

#SBATCH --time=1-00:00:00
#SBATCH --time=0-06:00:00
#SBATCH --job-name="mdt_axial_hex_dist_1nn_Li"
#SBATCH --output="mdt_axial_hex_dist_1nn_Li_slurm-%j.out"
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=1G
#SBATCH --mem=256M
# The above options are only default values that can be overwritten by
# command-line arguments

Expand Down Expand Up @@ -105,13 +105,18 @@ echo "=================================================================="
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A.txt.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
11 changes: 8 additions & 3 deletions analysis/lintf2_ether/mdt/axial_hex_dist_1nn_NBT.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#!/bin/bash

#SBATCH --time=1-00:00:00
#SBATCH --time=0-06:00:00
#SBATCH --job-name="mdt_axial_hex_dist_1nn_NBT"
#SBATCH --output="mdt_axial_hex_dist_1nn_NBT_slurm-%j.out"
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=1G
#SBATCH --mem=256M
# The above options are only default values that can be overwritten by
# command-line arguments

Expand Down Expand Up @@ -105,13 +105,18 @@ echo "=================================================================="
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A.txt.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
11 changes: 8 additions & 3 deletions analysis/lintf2_ether/mdt/axial_hex_dist_1nn_OBT.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/bin/bash

#SBATCH --time=1-00:00:00
#SBATCH --time=0-06:00:00
#SBATCH --job-name="mdt_axial_hex_dist_1nn_OBT"
#SBATCH --output="mdt_axial_hex_dist_1nn_OBT_slurm-%j.out"
#SBATCH --nodes=1
Expand All @@ -15,7 +15,7 @@
# This script is meant to be submitted by
# submit_mdt_analyses_lintf2_ether.py

analysis="_axial_hex_dist_1nn_OBT"
analysis="axial_hex_dist_1nn_OBT"
thisfile=$(basename "${BASH_SOURCE[0]}")
echo "${thisfile}"
start_time=$(date --rfc-3339=seconds || exit)
Expand Down Expand Up @@ -105,13 +105,18 @@ echo "=================================================================="
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A.txt.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
11 changes: 8 additions & 3 deletions analysis/lintf2_ether/mdt/axial_hex_dist_1nn_OE.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#!/bin/bash

#SBATCH --time=1-00:00:00
#SBATCH --time=0-06:00:00
#SBATCH --job-name="mdt_axial_hex_dist_1nn_OE"
#SBATCH --output="mdt_axial_hex_dist_1nn_OE_slurm-%j.out"
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=1G
#SBATCH --mem=512M
# The above options are only default values that can be overwritten by
# command-line arguments

Expand Down Expand Up @@ -105,13 +105,18 @@ echo "=================================================================="
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A.txt.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
11 changes: 8 additions & 3 deletions analysis/lintf2_ether/mdt/axial_hex_dist_2nn_Li.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#!/bin/bash

#SBATCH --time=1-00:00:00
#SBATCH --time=0-06:00:00
#SBATCH --job-name="mdt_axial_hex_dist_2nn_Li"
#SBATCH --output="mdt_axial_hex_dist_2nn_Li_slurm-%j.out"
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=1G
#SBATCH --mem=256M
# The above options are only default values that can be overwritten by
# command-line arguments

Expand Down Expand Up @@ -105,13 +105,18 @@ echo "=================================================================="
# Cleanup #
########################################################################

echo -e "\n"
mv -v \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out"

save_dir="${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}"
if [[ ! -d ${save_dir} ]]; then
echo -e "\n"
mkdir -v "${save_dir}" || exit
mv -v \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A.txt.gz" \
"${settings}_${system}_${analysis}_slurm-${SLURM_JOB_ID}.out" \
"${settings}_${system}_${analysis}_${zmin}-${zmax}A_slurm-${SLURM_JOB_ID}.out" \
"${save_dir}"
bash "${bash_dir}/cleanup_analysis.sh" \
"${system}" \
Expand Down
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