# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1689686835 0
# Node ID ec5f6b22417cbfa91ca9def0545832c5568b211d
# Parent 523d44fcd03fb05e61b2555c37535697dc0de582
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_uep_opt commit 70a4d37ecdf5d586703cfc509922311e95d3205c
diff -r 523d44fcd03f -r ec5f6b22417c muon_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/muon_macros.xml Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,29 @@
+
+
+
+
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+
+
+
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+
+
+ ^[\s\d,\[\]]+$
+
+
+
+
+
+ 2.2.1
+ 10.5281/zenodo.7733979
+ 10.5281/zenodo.6517626
+ 0.3.0
+ 10.5281/zenodo.8026711
+ 10.5281/zenodo.7025643
+
\ No newline at end of file
diff -r 523d44fcd03f -r ec5f6b22417c pm_uep_opt.xml
--- a/pm_uep_opt.xml Fri Feb 03 15:40:08 2023 +0000
+++ b/pm_uep_opt.xml Tue Jul 18 13:27:15 2023 +0000
@@ -1,32 +1,18 @@
-
+
run UEP optimisation
-
- 0.2.3
0
-
-
-
- @software{Sturniolo_pymuon-suite_2022,
- author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
- license = {GPL-3.0},
- month = {8},
- title = {{pymuon-suite}},
- url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
- version = {v0.2.3},
- doi = {10.5281/zenodo.7025644},
- year = {2022}
- }
-
+ muon_macros.xml
+
- pymuonsuite
+ pymuonsuite
zip
@@ -34,101 +20,230 @@
.den_fmt' and
- ## '.castep', but $charge_density.name may or may not end
- ## with '.den_fmt' so strip any extension and manually include 'den_fmt'
- ## and '.castep' in the linked file names
- charge_density_name=\$(sed 's/ //g' <<< '$charge_density.name') &&
- charge_density_seed=\${charge_density_name%%.*} &&
- echo "Calculated seed name \$charge_density_seed" &&
- ln -s '$charge_density' \$charge_density_seed.den_fmt &&
- ln -s '$castep_log' \$charge_density_seed.castep &&
+ cat $params_yaml > params.yaml &&
+ structure_name_internal='input_structure.$structure.ext' &&
+ ln -s '$structure' \$structure_name_internal &&
+ pm-muairss -t w \$structure_name_internal params.yaml &&
+ #if $generation_params.allpos_ext != "none":
+ mv allpos.$generation_params.allpos_ext $allpos_file &&
+ #end if
+ ln -s '$charge_density' input_structure.den_fmt &&
+ ln -s '$castep_log' input_structure.castep &&
out_folder="`python '${__tool_directory__}/get_out_folder.py'`" &&
find \$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_path: .*#chden_path: .\/#g" &&
- find \$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_seed: .*#chden_seed: \$charge_density_seed#g" &&
+ find \$out_folder -type f -name "*.yaml" | xargs sed -i "s#^chden_seed: .*#chden_seed: input_structure#g" &&
bash '${__tool_directory__}/run.sh' \$out_folder &&
- zip -r out_zip.zip \$out_folder params.yaml input_structure.* &&
+ zip -r out_zip.zip \$out_folder params.yaml \$structure_name_internal &&
find \$out_folder > tree.txt
]]>
+
+ poisson_r: $generation_params.poisson_r
+vdw_scale: $generation_params.vdw_scale
+#if $generation_params.random_seed:
+random_seed: $generation_params.random_seed
+#end if
+#if $generation_params.allpos_ext!="none":
+allpos_filename: allpos.$generation_params.allpos_ext
+#end if
+calculator: uep
+charged: true
+geom_steps: $optimisation_params.geom_steps
+geom_force_tol: $optimisation_params.geom_force_tol
+uep_gw_factor: $optimisation_params.uep_gw_factor
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+ (generation_params["allpos_ext"] != "none")
+
(testing == "true")
-
+
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+
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-
+
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-
+
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+
-
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+
-
+
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+
-
+
+
+
-
- @TOOL_CITATION@
-
+ @PYMUONSUITE_CITATION@
10.1063/1.5024450
10.1063/1.5085197
10.1063/5.0012381
diff -r 523d44fcd03f -r ec5f6b22417c run.sh
--- a/run.sh Fri Feb 03 15:40:08 2023 +0000
+++ b/run.sh Tue Jul 18 13:27:15 2023 +0000
@@ -2,14 +2,33 @@
set -o errexit
-for x in $1/*/*/*.yaml
-do
-
- if ! out=$(pm-uep-opt $x)
- then
- echo 1>&2 "$out"; exit 1
+run(){
+ if ! out=$(pm-uep-opt $1); then
+ echo 1>&2 "$out"; exit 1
else
- echo "$out"
+ echo "$out"
fi
-done || exit
-#pm-uep-opt
\ No newline at end of file
+}
+
+pids=()
+for x in $1/*/*/*.yaml; do
+ run $x & pids+=($!)
+done
+
+declare -i failed=0
+for pid in ${pids[@]}; do
+ if ! wait $pid; then
+ failed+=1
+ fi
+done
+
+if [ $failed -eq ${#pids[@]} ]; then
+ >&2 echo "ERROR: All optimisations failed"
+ exit 1
+elif [ $failed -eq 0 ]; then
+ echo "All optimisations succeeded"
+ exit 0
+else
+ echo "WARNING: $failed optimisation(s) failed"
+ exit 0
+fi
diff -r 523d44fcd03f -r ec5f6b22417c test-data/Si.cell
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.cell Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,43 @@
+# CELL file written 11:14:42 (GMT-0.0) 17th February 2021 from run Si
+
+%BLOCK lattice_cart
+ ANG
+ 5.47538171155659 0.530767321973160E-35 -0.131324260787022E-34
+ 0.530767321973160E-35 5.47538171155659 0.313104997179767E-35
+ -0.131324260787022E-34 0.313104997179767E-35 5.47538171155659
+%ENDBLOCK lattice_cart
+
+%BLOCK cell_constraints
+ 1 1 1
+ 0 0 0
+%ENDBLOCK cell_constraints
+
+%BLOCK positions_frac
+ Si 0.000000000000000 0.000000000000000 0.000000000000000
+ Si 0.000000000000000 0.500000000000000 0.500000000000000
+ Si 0.250000000000000 0.250000000000000 0.250000000000000
+ Si 0.500000000000000 0.000000000000000 0.500000000000000
+ Si 0.250000000000000 0.750000000000000 0.750000000000000
+ Si 0.750000000000000 0.250000000000000 0.750000000000000
+ Si 0.750000000000000 0.750000000000000 0.250000000000000
+ Si 0.500000000000000 0.500000000000000 0.000000000000000
+%ENDBLOCK positions_frac
+
+FIX_COM : true
+
+%BLOCK species_pot
+ Si 3|1.8|5|6|7|30:31:32
+%ENDBLOCK species_pot
+
+SYMMETRY_TOL : 0.001000
+
+%BLOCK symmetry_ops
+# Symm. op. 1 E
+ 1.000000000000000 0.000000000000000 0.000000000000000
+ 0.000000000000000 1.000000000000000 0.000000000000000
+ 0.000000000000000 0.000000000000000 1.000000000000000
+ 0.000000000000000 0.000000000000000 0.000000000000000
+%ENDBLOCK symmetry_ops
+
+kpoint_mp_grid : 2 2 2
+
diff -r 523d44fcd03f -r ec5f6b22417c test-data/Si.cif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.cif Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,33 @@
+data_image0
+_chemical_formula_structural Si8
+_chemical_formula_sum "Si8"
+_cell_length_a 5.47545
+_cell_length_b 5.47545
+_cell_length_c 5.47545
+_cell_angle_alpha 90
+_cell_angle_beta 90
+_cell_angle_gamma 90
+
+_space_group_name_H-M_alt "P 1"
+_space_group_IT_number 1
+
+loop_
+ _space_group_symop_operation_xyz
+ 'x, y, z'
+
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+ Si Si1 1.0 0.00000 0.00000 0.00000 1.0000
+ Si Si2 1.0 0.75000 0.75000 0.25000 1.0000
+ Si Si3 1.0 0.50000 0.00000 0.50000 1.0000
+ Si Si4 1.0 0.75000 0.25000 0.75000 1.0000
+ Si Si5 1.0 0.00000 0.50000 0.50000 1.0000
+ Si Si6 1.0 0.25000 0.25000 0.25000 1.0000
+ Si Si7 1.0 0.25000 0.75000 0.75000 1.0000
+ Si Si8 1.0 0.50000 0.50000 0.00000 1.0000
diff -r 523d44fcd03f -r ec5f6b22417c test-data/Si.extxyz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.extxyz Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,10 @@
+8
+Lattice="5.47545112629462 4.96819156878786e-36 1.10608096941637e-36 4.96819156878786e-36 5.47545112629462 -3.12695835139248e-36 1.10608096941637e-36 -3.12695835139248e-36 5.47545112629462" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:castep_labels:S:1 pbc="T T T"
+Si 0.00000000 0.00000000 0.00000000 0.00000000 NULL
+Si 4.10658834 4.10658834 1.36886278 0.00000000 NULL
+Si 2.73772556 0.00000000 2.73772556 0.00000000 NULL
+Si 4.10658834 1.36886278 4.10658834 0.00000000 NULL
+Si 0.00000000 2.73772556 2.73772556 0.00000000 NULL
+Si 1.36886278 1.36886278 1.36886278 0.00000000 NULL
+Si 1.36886278 4.10658834 4.10658834 0.00000000 NULL
+Si 2.73772556 2.73772556 -0.00000000 0.00000000 NULL
diff -r 523d44fcd03f -r ec5f6b22417c test-data/Si.xyz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.xyz Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,10 @@
+8
+Generated by cif2cell 2.0.0. : Kitano, A. et al., Physical Review, Serie 3. B - Condensed Matter (18,1978-) 64, 0452061-0452069 (2001).
+Si 0.000000000000000 0.000000000000000 0.000000000000000
+Si 4.035750000000000 4.035750000000000 1.345250000000000
+Si 2.690500000000000 0.000000000000000 2.690500000000000
+Si 4.035750000000000 1.345250000000000 4.035750000000000
+Si 0.000000000000000 2.690500000000000 2.690500000000000
+Si 1.345250000000000 1.345250000000000 1.345250000000000
+Si 1.345250000000000 4.035750000000000 4.035750000000000
+Si 2.690500000000000 2.690500000000000 0.000000000000000
diff -r 523d44fcd03f -r ec5f6b22417c test-data/allpos.cell
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/allpos.cell Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,38 @@
+#######################################################
+#CASTEP cell file: allpos.cell
+#Created using the Atomic Simulation Environment (ASE)#
+#######################################################
+
+%BLOCK LATTICE_CART
+ 5.475382 0.000000 -0.000000
+ 0.000000 5.475382 0.000000
+-0.000000 0.000000 5.475382
+%ENDBLOCK LATTICE_CART
+
+%BLOCK POSITIONS_ABS
+Si 0.000000 0.000000 0.000000
+Si -0.000000 2.737691 2.737691
+Si 1.368845 1.368845 1.368845
+Si 2.737691 0.000000 2.737691
+Si 1.368845 4.106536 4.106536
+Si 4.106536 1.368845 4.106536
+Si 4.106536 4.106536 1.368845
+Si 2.737691 2.737691 -0.000000
+H:mu 3.125152 3.041799 2.994236
+H:mu 4.170048 2.685234 3.919204
+H:mu 2.896190 3.055878 1.069474
+H:mu 2.499357 2.738732 5.011782
+H:mu 1.856384 1.305645 0.684300
+H:mu 0.710100 1.663543 1.366143
+H:mu 2.926805 4.554958 3.173796
+H:mu 4.041556 2.285971 2.357787
+H:mu 2.153772 1.685845 2.712357
+H:mu 3.369247 0.881320 2.641127
+H:mu 4.631185 3.830276 4.640470
+H:mu 2.828731 1.963913 1.697286
+H:mu 2.176625 2.144297 3.912156
+H:mu 1.805850 2.882961 2.746759
+H:mu 1.403305 0.559980 1.522521
+H:mu 3.251047 3.565876 4.157223
+%ENDBLOCK POSITIONS_ABS
+
diff -r 523d44fcd03f -r ec5f6b22417c test-data/allpos.cif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/allpos.cif Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,49 @@
+data_image0
+_chemical_formula_structural Si8H16
+_chemical_formula_sum "Si8 H16"
+_cell_length_a 5.47545
+_cell_length_b 5.47545
+_cell_length_c 5.47545
+_cell_angle_alpha 90
+_cell_angle_beta 90
+_cell_angle_gamma 90
+
+_space_group_name_H-M_alt "P 1"
+_space_group_IT_number 1
+
+loop_
+ _space_group_symop_operation_xyz
+ 'x, y, z'
+
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+ Si Si1 1.0 0.00000 0.00000 0.00000 1.0000
+ Si Si2 1.0 0.75000 0.75000 0.25000 1.0000
+ Si Si3 1.0 0.50000 0.00000 0.50000 1.0000
+ Si Si4 1.0 0.75000 0.25000 0.75000 1.0000
+ Si Si5 1.0 0.00000 0.50000 0.50000 1.0000
+ Si Si6 1.0 0.25000 0.25000 0.25000 1.0000
+ Si Si7 1.0 0.25000 0.75000 0.75000 1.0000
+ Si Si8 1.0 0.50000 0.50000 0.00000 1.0000
+ H H1 1.0 0.57076 0.55554 0.54685 1.0000
+ H H2 1.0 0.76160 0.49042 0.71579 1.0000
+ H H3 1.0 0.52895 0.55811 0.19532 1.0000
+ H H4 1.0 0.45647 0.50019 0.91533 1.0000
+ H H5 1.0 0.33904 0.23846 0.12498 1.0000
+ H H6 1.0 0.12969 0.30382 0.24951 1.0000
+ H H7 1.0 0.53454 0.83190 0.57965 1.0000
+ H H8 1.0 0.73813 0.41750 0.43062 1.0000
+ H H9 1.0 0.39336 0.30790 0.49537 1.0000
+ H H10 1.0 0.61534 0.16096 0.48236 1.0000
+ H H11 1.0 0.84582 0.69955 0.84752 1.0000
+ H H12 1.0 0.51663 0.35868 0.30999 1.0000
+ H H13 1.0 0.39753 0.39163 0.71450 1.0000
+ H H14 1.0 0.32981 0.52653 0.50166 1.0000
+ H H15 1.0 0.25629 0.10227 0.27807 1.0000
+ H H16 1.0 0.59376 0.65126 0.75926 1.0000
diff -r 523d44fcd03f -r ec5f6b22417c test-data/allpos.xyz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/allpos.xyz Tue Jul 18 13:27:15 2023 +0000
@@ -0,0 +1,26 @@
+24
+Lattice="5.47545112629462 4.96819156878786e-36 1.10608096941637e-36 4.96819156878786e-36 5.47545112629462 -3.12695835139248e-36 1.10608096941637e-36 -3.12695835139248e-36 5.47545112629462" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:castep_labels:S:1:masses:R:1:castep_custom_species:S:1 pbc="T T T"
+Si 0.00000000 0.00000000 0.00000000 0.00000000 NULL 28.08500000 Si
+Si 4.10658834 4.10658834 1.36886278 0.00000000 NULL 28.08500000 Si
+Si 2.73772556 0.00000000 2.73772556 0.00000000 NULL 28.08500000 Si
+Si 4.10658834 1.36886278 4.10658834 0.00000000 NULL 28.08500000 Si
+Si 0.00000000 2.73772556 2.73772556 0.00000000 NULL 28.08500000 Si
+Si 1.36886278 1.36886278 1.36886278 0.00000000 NULL 28.08500000 Si
+Si 1.36886278 4.10658834 4.10658834 0.00000000 NULL 28.08500000 Si
+Si 2.73772556 2.73772556 -0.00000000 0.00000000 NULL 28.08500000 Si
+H 3.12519205 3.04183727 2.99427396 0.00000000 0 0.11342893 H:mu
+H 4.17010122 2.68526782 3.91925381 0.00000000 0 0.11342893 H:mu
+H 2.89622675 3.05591660 1.06948758 0.00000000 0 0.11342893 H:mu
+H 2.49938846 2.73876636 5.01184564 0.00000000 0 0.11342893 H:mu
+H 1.85640768 1.30566198 0.68430879 0.00000000 0 0.11342893 H:mu
+H 0.71010928 1.66356372 1.36616075 0.00000000 0 0.11342893 H:mu
+H 2.92684216 4.55501571 3.17383586 0.00000000 0 0.11342893 H:mu
+H 4.04160737 2.28599955 2.35781702 0.00000000 0 0.11342893 H:mu
+H 2.15379948 1.68586666 2.71239184 0.00000000 0 0.11342893 H:mu
+H 3.36928999 0.88133137 2.64116057 0.00000000 0 0.11342893 H:mu
+H 4.63124403 3.83032454 4.64052920 0.00000000 0 0.11342893 H:mu
+H 2.82876687 1.96393752 1.69730779 0.00000000 0 0.11342893 H:mu
+H 2.17665215 2.14432399 3.91220567 0.00000000 0 0.11342893 H:mu
+H 1.80587242 2.88299761 2.74679403 0.00000000 0 0.11342893 H:mu
+H 1.40332274 0.55998727 1.52254060 0.00000000 0 0.11342893 H:mu
+H 3.25108839 3.56592083 4.15727584 0.00000000 0 0.11342893 H:mu
diff -r 523d44fcd03f -r ec5f6b22417c test-data/muonated-default-folder.zip
Binary file test-data/muonated-default-folder.zip has changed
diff -r 523d44fcd03f -r ec5f6b22417c test-data/muonated.zip
Binary file test-data/muonated.zip has changed
diff -r 523d44fcd03f -r ec5f6b22417c test-data/tree.txt
--- a/test-data/tree.txt Fri Feb 03 15:40:08 2023 +0000
+++ b/test-data/tree.txt Tue Jul 18 13:27:15 2023 +0000
@@ -1,73 +1,83 @@
-Si-out
-Si-out/uep
-Si-out/uep/Si_1
-Si-out/uep/Si_1/Si_1.yaml
-Si-out/uep/Si_1/Si_1.uep
-Si-out/uep/Si_1/Si_1.uep.pkl
-Si-out/uep/Si_1/Si_1.xyz
-Si-out/uep/Si_2
-Si-out/uep/Si_2/Si_2.yaml
-Si-out/uep/Si_2/Si_2.uep
-Si-out/uep/Si_2/Si_2.uep.pkl
-Si-out/uep/Si_2/Si_2.xyz
-Si-out/uep/Si_3
-Si-out/uep/Si_3/Si_3.yaml
-Si-out/uep/Si_3/Si_3.uep
-Si-out/uep/Si_3/Si_3.uep.pkl
-Si-out/uep/Si_3/Si_3.xyz
-Si-out/uep/Si_4
-Si-out/uep/Si_4/Si_4.yaml
-Si-out/uep/Si_4/Si_4.uep
-Si-out/uep/Si_4/Si_4.uep.pkl
-Si-out/uep/Si_4/Si_4.xyz
-Si-out/uep/Si_5
-Si-out/uep/Si_5/Si_5.yaml
-Si-out/uep/Si_5/Si_5.uep
-Si-out/uep/Si_5/Si_5.uep.pkl
-Si-out/uep/Si_5/Si_5.xyz
-Si-out/uep/Si_6
-Si-out/uep/Si_6/Si_6.yaml
-Si-out/uep/Si_6/Si_6.uep
-Si-out/uep/Si_6/Si_6.uep.pkl
-Si-out/uep/Si_6/Si_6.xyz
-Si-out/uep/Si_7
-Si-out/uep/Si_7/Si_7.yaml
-Si-out/uep/Si_7/Si_7.uep
-Si-out/uep/Si_7/Si_7.uep.pkl
-Si-out/uep/Si_7/Si_7.xyz
-Si-out/uep/Si_8
-Si-out/uep/Si_8/Si_8.yaml
-Si-out/uep/Si_8/Si_8.uep
-Si-out/uep/Si_8/Si_8.uep.pkl
-Si-out/uep/Si_8/Si_8.xyz
-Si-out/uep/Si_9
-Si-out/uep/Si_9/Si_9.yaml
-Si-out/uep/Si_9/Si_9.uep
-Si-out/uep/Si_9/Si_9.uep.pkl
-Si-out/uep/Si_9/Si_9.xyz
-Si-out/uep/Si_10
-Si-out/uep/Si_10/Si_10.yaml
-Si-out/uep/Si_10/Si_10.uep
-Si-out/uep/Si_10/Si_10.uep.pkl
-Si-out/uep/Si_10/Si_10.xyz
-Si-out/uep/Si_11
-Si-out/uep/Si_11/Si_11.yaml
-Si-out/uep/Si_11/Si_11.uep
-Si-out/uep/Si_11/Si_11.uep.pkl
-Si-out/uep/Si_11/Si_11.xyz
-Si-out/uep/Si_12
-Si-out/uep/Si_12/Si_12.yaml
-Si-out/uep/Si_12/Si_12.uep
-Si-out/uep/Si_12/Si_12.uep.pkl
-Si-out/uep/Si_12/Si_12.xyz
-Si-out/uep/Si_13
-Si-out/uep/Si_13/Si_13.yaml
-Si-out/uep/Si_13/Si_13.uep
-Si-out/uep/Si_13/Si_13.uep.pkl
-Si-out/uep/Si_13/Si_13.xyz
-Si-out/uep/Si_14
-Si-out/uep/Si_14/Si_14.yaml
-Si-out/uep/Si_14/Si_14.uep
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