| Previous changeset 1:150301c057b0 (2022-09-15) |
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Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_write commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507 |
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modified:
pm_muairss_write.xml |
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added:
test-data/S i.param test-data/allpos.cell test-data/allpos.cif test-data/allpos.xyz test-data/configcastep_t_with_script_file.yaml test-data/s u b m i t.sh test-data/submit.sh test-data/tree_castep_t_with_script_file.txt |
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| diff -r 150301c057b0 -r 8e5dbded3070 pm_muairss_write.xml --- a/pm_muairss_write.xml Thu Sep 15 10:20:27 2022 +0000 +++ b/pm_muairss_write.xml Fri Feb 03 15:39:39 2023 +0000 |
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| b'@@ -1,22 +1,22 @@\n-<tool id="pm_muairss_write" name="PyMuonSuite AIRSS Generate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">\n+<tool id="pm_muairss_write" name="PyMuonSuite AIRSS Generate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">\n <description>generate muonated structures</description>\n <macros>\n <!-- version of underlying tool (PEP 440) -->\n- <token name="@TOOL_VERSION@">0.2.1</token>\n+ <token name="@TOOL_VERSION@">0.2.3</token>\n <!-- version of this tool wrapper (integer) -->\n- <token name="@WRAPPER_VERSION@">1</token>\n+ <token name="@WRAPPER_VERSION@">0</token>\n <!-- citation should be updated with every underlying tool version -->\n <!-- typical fields to update are version, month, year, and doi -->\n <token name="@TOOL_CITATION@">\n- @software{pymuon-suite,\n- author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},\n+ @software{Sturniolo_pymuon-suite_2022,\n+ author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},\n license = {GPL-3.0},\n+ month = {8},\n title = {{pymuon-suite}},\n url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},\n- version = {v0.2.1},\n- month = {2},\n- year = {2022},\n- doi = {}\n+ version = {v0.2.3},\n+ doi = {10.5281/zenodo.7025644},\n+ year = {2022}\n }\n </token>\n </macros>\n@@ -33,22 +33,34 @@\n <include type="literal" path="get_out_folder.py"/>\n </required_files>\n <command detect_errors="exit_code"><![CDATA[\n- structure_name_internal="input_structure.$structure.ext" &&\n- ln -s $structure \\$structure_name_internal &&\n- ln -s $params params.yaml &&\n- #if str($iscastep.iscastep_sel)=="true":\n- castep_param_name=\\$(sed \'s/ //g\' <<< "$castep_param.name") &&\n- ln -s $castep_param \\$castep_param_name &&\n- sed -i \'/^castep_param: /{h;s/:.*/: $castep_param.name/};\\${x;/^$/{s//castep_param: $castep_param.name/;H};x}\' params.yaml &&\n+ structure_name_internal=\'input_structure.$structure.ext\' &&\n+ ln -s \'$structure\' \\$structure_name_internal &&\n+ ln -s \'$params\' params.yaml &&\n+ echo \'$castep_param\' &&\n+ #if $castep_param:\n+ castep_param_name=\\$(sed \'s/ //g\' <<< \'$castep_param.name\') &&\n+ ln -s \'$castep_param\' \\$castep_param_name &&\n+ sed -i \'/^castep_param: /{h;s/:.*/: \'"\\$castep_param_name"\'/};\\${x;/^$/{s//castep_param: \'"\\$castep_param_name"\'/;H};x}\' params.yaml &&\n+ #if $script_file:\n+ script_file_name=\\$(sed \'s/ //g\' <<< \'$script_file.name\') &&\n+ ln -s \'$script_file\' \\$script_file_name &&\n+ sed -i \'/^script_file: /{h;s/:.*/: \'"\\$script_file_name"\'/};\\${x;/^$/{s//script_file: \'"\\$script_file_name"\'/;H};x}\' params.yaml &&\n+ #end if\n+ #end if\n+ #if $allpos_ext!="none":\n+ sed -i \'/^allpos_filename: /{h;s/:.*/: allpos.$allpos_ext/};\\${x;/^$/{s//allpos_filename: allpos.$allpos_ext/;H};x}\' params.yaml &&\n #end if\n pm-muairss -t w \\$structure_name_internal params.yaml &&\n- out_folder="`python ${__tool_directory__}/get_out_folder.py`" &&\n- #if str($iscastep.iscastep_sel)=="true":\n+ out_folder="`python \'${__tool_directory__}/get_out_folder.py\'`" &&\n+ #if $castep_param:\n zip -r out_zip.zip \\$out_folder params.yaml \\$structure_name_internal \\$castep_param_name &&\n- '..b'olume = {148},\n- pages = {134114},\n- year = {2018},\n- doi={10.1063/1.5024450},\n- URL={\n- https://doi.org/10.1063/1.5024450\n- },\n- eprint={\n- https://doi.org/10.1063/1.5024450\n- }\n- }\n- </citation>\n- <citation type="bibtex">\n- @article{doi:10.1063/1.5085197,\n- author = {Sturniolo,Simone and Liborio,Leandro and Jackson,Samuel },\n- title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},\n- journal = {The Journal of Chemical Physics},\n- volume = {150},\n- number = {15},\n- pages = {154301},\n- year = {2019},\n- doi = {10.1063/1.5085197},\n- URL = {\n- https://doi.org/10.1063/1.5085197\n- },\n- eprint = {\n- https://doi.org/10.1063/1.5085197\n- }\n- }\n- </citation>\n- <citation type="bibtex">\n- @article{doi:10.1063/5.0012381,\n- author = {Sturniolo,Simone and Liborio,Leandro },\n- title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method},\n- journal = {The Journal of Chemical Physics},\n- volume = {153},\n- number = {4},\n- pages = {044111},\n- year = {2020},\n- doi = {10.1063/5.0012381},\n- URL = {\n- https://doi.org/10.1063/5.0012381\n- },\n- eprint = {\n- https://doi.org/10.1063/5.0012381\n- },\n- abstract = { Finding the stopping site of the muon in a muon-spin relaxation experiment is one of the main problems of muon spectroscopy, and computational techniques that make use of quantum chemistry simulations can be of great help when looking for this stopping site. The most thorough approach would require the use of simulations, such as Density Functional Theory (DFT), to test and optimize multiple possible sites, accounting for the effect that the added muon has on its surroundings. However, this can be computationally expensive and sometimes unnecessary. Hence, in this work, we present a software implementation of the Unperturbed Electrostatic Potential (UEP) Method: an approach used for finding the muon stopping site in crystalline materials. The UEP method requires only one DFT calculation, necessary to compute the electronic density. This, in turn, is used to calculate the minima of the crystalline material\xe2\x80\x99s electrostatic potential and the estimates of the muon stopping site, relying on the approximation that the muon\xe2\x80\x99s presence does not significantly affect its surroundings. One of the main UEP\xe2\x80\x99s assumptions is that the muon stopping site will be one of the crystalline material\xe2\x80\x99s electrostatic potential minima. In this regard, we also propose some symmetry-based considerations about the properties of this crystalline material\xe2\x80\x99s electrostatic potential, in particular, which sites are more likely to be its minima and why the unperturbed approximation may be sufficiently robust for them. We introduce the Python software package pymuon-suite and the various utilities it provides to facilitate these calculations, and finally, we demonstrate the effectiveness of the method with some chosen example systems. }\n- }\n- </citation>\n+ <citation type="doi">10.1063/1.5024450</citation>\n+ <citation type="doi">10.1063/1.5085197</citation>\n+ <citation type="doi">10.1063/5.0012381</citation>\n <citation type="bibtex">\n @TOOL_CITATION@\n </citation>\n' |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/S i.param --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/S i.param Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -0,0 +1,13 @@ +task : geometryoptimisation +opt_strategy : speed +num_dump_cycles : 0 +cutoff_energy : 450 eV +elec_energy_tol : 1.0e-9 eV +write_cell_structure : true +max_scf_cycles : 100 +xc_functional : pbe +geom_max_iter : 100 +geom_force_tol : 0.05 +backup_interval : 3600 +continuation : default +write_formatted_density : true |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/allpos.cell --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/allpos.cell Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -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 + |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/allpos.cif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/allpos.cif Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -0,0 +1,49 @@ +data_image0 +_chemical_formula_structural Si8H16 +_chemical_formula_sum "Si8 H16" +_cell_length_a 5.47538 +_cell_length_b 5.47538 +_cell_length_c 5.47538 +_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 0.00000 0.50000 0.50000 1.0000 + Si Si3 1.0 0.25000 0.25000 0.25000 1.0000 + Si Si4 1.0 0.50000 0.00000 0.50000 1.0000 + Si Si5 1.0 0.25000 0.75000 0.75000 1.0000 + Si Si6 1.0 0.75000 0.25000 0.75000 1.0000 + Si Si7 1.0 0.75000 0.75000 0.25000 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 |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/allpos.xyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/allpos.xyz Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -0,0 +1,26 @@ +24 +Lattice="5.47538171155659 5.3076732197316e-36 -1.31324260787022e-35 5.3076732197316e-36 5.47538171155659 3.13104997179767e-36 -1.31324260787022e-35 3.13104997179767e-36 5.47538171155659" 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 -0.00000000 2.73769086 2.73769086 0.00000000 NULL 28.08500000 Si +Si 1.36884543 1.36884543 1.36884543 0.00000000 NULL 28.08500000 Si +Si 2.73769086 0.00000000 2.73769086 0.00000000 NULL 28.08500000 Si +Si 1.36884543 4.10653628 4.10653628 0.00000000 NULL 28.08500000 Si +Si 4.10653628 1.36884543 4.10653628 0.00000000 NULL 28.08500000 Si +Si 4.10653628 4.10653628 1.36884543 0.00000000 NULL 28.08500000 Si +Si 2.73769086 2.73769086 -0.00000000 0.00000000 NULL 28.08500000 Si +H 3.12515243 3.04179871 2.99423600 0.00000000 0.11342893 H:mu +H 4.17004836 2.68523378 3.91920412 0.00000000 0.11342893 H:mu +H 2.89619003 3.05587786 1.06947402 0.00000000 0.11342893 H:mu +H 2.49935677 2.73873164 5.01178210 0.00000000 0.11342893 H:mu +H 1.85638414 1.30564543 0.68430012 0.00000000 0.11342893 H:mu +H 0.71010028 1.66354263 1.36614343 0.00000000 0.11342893 H:mu +H 2.92680506 4.55495797 3.17379562 0.00000000 0.11342893 H:mu +H 4.04155613 2.28597057 2.35778713 0.00000000 0.11342893 H:mu +H 2.15377218 1.68584529 2.71235746 0.00000000 0.11342893 H:mu +H 3.36924728 0.88132020 2.64112709 0.00000000 0.11342893 H:mu +H 4.63118531 3.83027598 4.64047037 0.00000000 0.11342893 H:mu +H 2.82873101 1.96391263 1.69728627 0.00000000 0.11342893 H:mu +H 2.17662455 2.14429680 3.91215608 0.00000000 0.11342893 H:mu +H 1.80584952 2.88296106 2.74675920 0.00000000 0.11342893 H:mu +H 1.40330495 0.55998017 1.52252130 0.00000000 0.11342893 H:mu +H 3.25104718 3.56587562 4.15722314 0.00000000 0.11342893 H:mu |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/configcastep_t_with_script_file.yaml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/configcastep_t_with_script_file.yaml Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -0,0 +1,15 @@ +poisson_r: 1.18 +name: Si +charged: true +geom_steps: 300 +vdw_scale: 0.25 +calculator: castep +geom_force_tol: 0.05 +clustering_method: hier +clustering_hier_t: 0.2 +out_folder: Si-out +castep_command: castep.serial +castep_param: test.param +mu_symbol: H:mu +random_seed: 7357 +script_file: s u b m i t.sh \ No newline at end of file |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/s u b m i t.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s u b m i t.sh Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -0,0 +1,9 @@ +#!/bin/sh +#SBATCH -o %J.o +#SBATCH -e %J.e +#SBATCH -t 24:00:00 +#SBATCH -n 16 +#SBATCH --job-name= {seedname} +#SBATCH --exclusive +module load castep/19 +mpirun castep.mpi {seedname} |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/submit.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/submit.sh Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -0,0 +1,9 @@ +#!/bin/sh +#SBATCH -o %J.o +#SBATCH -e %J.e +#SBATCH -t 24:00:00 +#SBATCH -n 16 +#SBATCH --job-name= {seedname} +#SBATCH --exclusive +module load castep/19 +mpirun castep.mpi {seedname} |
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| diff -r 150301c057b0 -r 8e5dbded3070 test-data/tree_castep_t_with_script_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_castep_t_with_script_file.txt Fri Feb 03 15:39:39 2023 +0000 |
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| @@ -0,0 +1,68 @@ +castep_param: Si.param +Si-out +Si-out/castep +Si-out/castep/Si_1 +Si-out/castep/Si_1/Si_1.cell +Si-out/castep/Si_1/Si_1.param +Si-out/castep/Si_1/script.sh +Si-out/castep/Si_2 +Si-out/castep/Si_2/Si_2.cell +Si-out/castep/Si_2/Si_2.param +Si-out/castep/Si_2/script.sh +Si-out/castep/Si_3 +Si-out/castep/Si_3/Si_3.cell +Si-out/castep/Si_3/Si_3.param +Si-out/castep/Si_3/script.sh +Si-out/castep/Si_4 +Si-out/castep/Si_4/Si_4.cell +Si-out/castep/Si_4/Si_4.param +Si-out/castep/Si_4/script.sh +Si-out/castep/Si_5 +Si-out/castep/Si_5/Si_5.cell +Si-out/castep/Si_5/Si_5.param +Si-out/castep/Si_5/script.sh +Si-out/castep/Si_6 +Si-out/castep/Si_6/Si_6.cell +Si-out/castep/Si_6/Si_6.param +Si-out/castep/Si_6/script.sh +Si-out/castep/Si_7 +Si-out/castep/Si_7/Si_7.cell +Si-out/castep/Si_7/Si_7.param +Si-out/castep/Si_7/script.sh +Si-out/castep/Si_8 +Si-out/castep/Si_8/Si_8.cell +Si-out/castep/Si_8/Si_8.param +Si-out/castep/Si_8/script.sh +Si-out/castep/Si_9 +Si-out/castep/Si_9/Si_9.cell +Si-out/castep/Si_9/Si_9.param +Si-out/castep/Si_9/script.sh +Si-out/castep/Si_10 +Si-out/castep/Si_10/Si_10.cell +Si-out/castep/Si_10/Si_10.param +Si-out/castep/Si_10/script.sh +Si-out/castep/Si_11 +Si-out/castep/Si_11/Si_11.cell +Si-out/castep/Si_11/Si_11.param +Si-out/castep/Si_11/script.sh +Si-out/castep/Si_12 +Si-out/castep/Si_12/Si_12.cell +Si-out/castep/Si_12/Si_12.param +Si-out/castep/Si_12/script.sh +Si-out/castep/Si_13 +Si-out/castep/Si_13/Si_13.cell +Si-out/castep/Si_13/Si_13.param +Si-out/castep/Si_13/script.sh +Si-out/castep/Si_14 +Si-out/castep/Si_14/Si_14.cell +Si-out/castep/Si_14/Si_14.param +Si-out/castep/Si_14/script.sh +Si-out/castep/Si_15 +Si-out/castep/Si_15/Si_15.cell +Si-out/castep/Si_15/Si_15.param +Si-out/castep/Si_15/script.sh +Si-out/castep/Si_16 +Si-out/castep/Si_16/Si_16.cell +Si-out/castep/Si_16/Si_16.param +Si-out/castep/Si_16/script.sh +Si-out/castep/.collection |