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author muon-spectroscopy-computational-project
date Fri, 03 Feb 2023 15:39:07 +0000
parents 52d3a28902e8
children e1e338f56656
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331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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1 <tool id="muspinsim_config" name="MuSpinSim Configure" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>define simulation parameters</description>
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3 <macros>
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4 <!-- version of underlying tool (PEP 440) -->
3
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5 <token name="@TOOL_VERSION@">2.0.2</token>
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6 <!-- version of this tool wrapper (integer) -->
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7 <token name="@WRAPPER_VERSION@">0</token>
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8 <!-- citation should be updated with every underlying tool version -->
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9 <!-- typical fields to update are version, month, year, and doi -->
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10 <token name="@TOOL_CITATION@">
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11 @software{muspinsim,
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12 author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and Davies, Joel and Wilkinson, John and {Muon Spectroscopy Computational Project}},
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13 license = {MIT},
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14 title = {{muspinsim}},
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15 url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
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16 version = {v2.0.2},
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17 month = {1},
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18 year = {2023}
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19 doi = {10.5281/zenodo.7568830}
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20 }
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21 </token>
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22 <import>config_macros.xml</import>
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23 </macros>
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24 <creator>
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25 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
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26 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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27 <person givenName="Joel" familyName="Davies" url="https://github.com/joelvdavies" identifier="https://orcid.org/0000-0002-4153-6819"/>
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28 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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29 </creator>
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30 <requirements>
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31 <requirement type="package" version="@TOOL_VERSION@">muspinsim</requirement>
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32 </requirements>
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33 <required_files>
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34 <include type="literal" path="sample_fitting_data.dat"/>
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35 <include type="literal" path="build_file.py"/>
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36 </required_files>
0
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37 <command detect_errors="exit_code"><![CDATA[
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38 cp '${__tool_directory__}/sample_fitting_data.dat' ./fitting_data.dat &&
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39 python '${__tool_directory__}/build_file.py' inputs.json
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40 ]]></command>
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41 <configfiles>
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42 <inputs name="inputs" filename="inputs.json"/>
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43 </configfiles>
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44 <inputs>
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45 <param type="text" name="out_file_prefix" label="Name" help="A name with which to label this configuration" optional="true" value="muspinsim"/>
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46 <section name="spins" expanded="true" title="Spins">
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47 <repeat name="spins" title="Spins to simulate" min="1" help="Specify the spins to be used in the system. This should include a muon (mu) and one or more electrons (e)">
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48 <conditional name="spin_options">
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49 <param name="spin_preset" type="select" value="mu" label="Species" help="Select 'custom' to define own">
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50 <option selected="true" value="mu">mu</option>
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51 <option value="e">e</option>
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52 <option value="custom">custom</option>
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53 </param>
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54 <when value="custom">
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55 <param name="spin" optional="false" type="text" label="Species name"/>
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56 <param name="atomic_mass" optional="true" type="integer" min="0" value="" label="Atomic mass" help="Leave blank to use default mass - whole numbers only"/>
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57 </when>
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58 <when value="mu"/>
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59 <when value="e"/>
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60 </conditional>
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61 </repeat>
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62 </section>
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63 <section name="interaction_params" expanded="true" title="Spin Interactions" help="">
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64 <repeat name="interactions" title="Interactions to simulate" help="Add couplings between spins, and/or dissipation terms. Interaction terms available: Zeeman, hyperfine, dipolar, quadrupolar or dissipation. See MuSpinSim docs for more info">
0
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65 <conditional name="interaction_options">
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66 <param name="interaction" type="select" label="Choose interaction type">
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67 <option value="zeeman">Zeeman</option>
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68 <option value="hyperfine">hyperfine</option>
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69 <option value="dipolar">dipolar</option>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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70 <option value="quadrupolar">quadrupolar</option>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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71 <option value="dissipation">dissipation</option>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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72 </param>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
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73 <when value="zeeman">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
parents: 2
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74 <param name="zeeman_index" type="integer" value="" label="Index of coupled spin" min="1" help="Index refers to the order of the spins listed in 'spins' section. The first spin in the list has index 1, the second has index 2, and so on."/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
parents: 2
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75 <param name="zeeman_vector" type="text" value="" label="Zeeman coupling vector" help="Define 1X3 vector for local magnetic field coupling (T). Allows default expressions, constants and functions (see help)"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
76 </when>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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77 <when value="hyperfine">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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78 <param name="hfine_index" type="integer" value="" label="Index of nuclear coupled spin" min="1" help="Non-electronic spin - muon or otherwise. Index refers to the order of the spins listed in 'spins' section. The first spin in the list has index 1, the second has index 2, and so on."/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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79 <param name="hfine_e_index" type="integer" value="" optional="true" min="1" label="Index of electronic coupled spin" help="Optional, will use first defined electronic spin if unspecified"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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80 <param name="hfine_matrix" area="true" type="text" value="" label="Hyperfine coupling tensor" help="Define 3X3 tensor for coupling between electron and non-electron spins (in MHz). Allows default expressions, constants and functions (see help)">
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
81 <sanitizer>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
82 <valid initial="string.printable">
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
83 </valid>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
84 </sanitizer>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
85 </param>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
86 </when>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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diff changeset
87 <when value="dipolar">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
parents: 2
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88 <param name="di_index" type="integer" value="" min="1" label="Index of 1st coupled spin" help="Index refers to the order of the spins listed in 'spins' section. The first spin in the list has index 1, the second has index 2, and so on."/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
parents: 2
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89 <param name="di_index_2" type="integer" value="" label="Index of 2nd coupled spin" help="Index refers to the order of the spins listed in 'spins' section. The first spin in the list has index 1, the second has index 2, and so on."/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
parents: 2
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90 <param name="di_vector" type="text" value="" label="Dipole coupling vector" help="Define 1X3 vector for coupling between two spins (Angstrom). Allows default expressions, constants and functions (see help)"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
91 </when>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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92 <when value="quadrupolar">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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93 <param name="quad_index" type="integer" value="" label="Index of coupled spin" help="Index refers to the order of the spins listed in 'spins' section. The first spin in the list has index 1, the second has index 2, and so on."/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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94 <param name="quad_matrix" area="true" type="text" value="" label="Electric Field Gradient tensor" help="Define 3X3 tensor (in atomic units) for quadrupolar coupling. Allows default expressions, constants and functions (see help). Warning: spins with zero quadrupole moment will have zero coupling regardless of the input">
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
95 <sanitizer>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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diff changeset
96 <valid initial="string.printable">
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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diff changeset
97 </valid>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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diff changeset
98 </sanitizer>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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diff changeset
99 </param>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
parents:
diff changeset
100 </when>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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101 <when value="dissipation">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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102 <param name="dis_index" type="integer" value="" label="Index of spin with dissipation" help="Index refers to the order of the spins listed in 'spins' section. The first spin in the list has index 1, the second has index 2, and so on."/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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diff changeset
103 <param name="dis_val" type="text" value="" label="Dissipation" help="Define dissipation term (MHz). Allows default expressions, constants and functions (see help)"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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104 </when>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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105 </conditional>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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106 </repeat>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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107 </section>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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108 <section name="experiment_params" expanded="true" title="Experiment Parameters">
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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109 <conditional name="experiment">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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110 <param name="experiment_preset" type="select" value="custom" display="radio" label="Experiment type" help="Experiment preset to use. Avoided Level Crossing (ALC): sets polarization to longitudinal, x-axis to field and y-axis to integral. Zero field: sets polarization to transverse, field to 0, x-axis to time and y-axis to asymmetry. Choose custom for no preset">
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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111 <option value="alc">Avoided Level Crossing (ALC)</option>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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112 <option value="zero_field">Zero Field</option>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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113 <option selected="true" value="custom">Custom</option>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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114 </param>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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115 <when value="alc">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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116 <expand macro="restricted_axes_options"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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117 <expand macro="fields"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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118 <expand macro="temperatures"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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119 <expand macro="orientations"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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120 <expand macro="euler_convention"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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121 </when>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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122 <when value="zero_field">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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123 <expand macro="restricted_axes_options"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
124 <expand macro="times"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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125 <expand macro="temperatures"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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126 <expand macro="orientations"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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127 <expand macro="euler_convention"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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128 <expand macro="celio_options"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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129 </when>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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130 <when value="custom">
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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131 <expand macro="axes_options"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
132 <expand macro="times"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
133 <expand macro="fields"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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134 <expand macro="intrinsic_fields"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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135 <expand macro="temperatures"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
136 <expand macro="polarizations"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
137 <expand macro="orientations"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
138 <expand macro="euler_convention"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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139 <expand macro="celio_options"/>
0
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140 </when>
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141 </conditional>
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142 </section>
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143 <section name="fitting_params" expanded="true" title="Fitting Parameters">
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144 <conditional name="fitting_options">
3
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145 <param name="fitting" type="select" display="radio" optional="false" value="" label="Fit experimental data with simulations" help="Fitting requires a file with data to fit. File must be given in MuSpinSim tool, or by manually setting filepath for keyword 'fitting_data' if running MuSpinSim externally">
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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146 <option value="true">Yes</option>
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147 <option selected="true" value="">No</option>
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148 </param>
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149 <when value="true">
3
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150 <param name="fitting_method" type="select" display="radio" optional="false" value="nelder-mead" label="Method to use to fit the data" help="See the help section for a description of each method">
0
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151 <option selected="true" value="nelder-mead">Nelder-Mead</option>
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152 <option value="lbfgs">L-BFGS</option>
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153 </param>
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154 <repeat name="fitting_variables" title="Variable to fit to the experimental data">
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155 <param name="var_name" type="text" optional="false" label="Name of the variable"/>
3
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156 <param name="start_val" type="text" value="0" label="Starting value" help="Allows default expressions, constants and functions, plus MHz, muon_gyr constants. Cannot contain names of other variables"/>
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157 <param name="min_bound" type="text" value="-inf" label="minimum bound" help="Allows default expressions, constants and functions, plus MHz, muon_gyr constants"/>
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158 <param name="max_bound" type="text" value="inf" label="maximum bound" help="Allows default expressions, constants and functions, plus MHz, muon_gyr constants"/>
0
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159 </repeat>
3
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160 <param name="fitting_tolerance" type="float" optional="true" value="" label="Fitting Tolerance" help="Used as the tol parameter in Scipy's scipy.optimize.minimize method. Will use scipy defaults if left blank. Does not accept expressions/functions/constants"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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161 </when>
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162 <when value=""/>
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163 </conditional>
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164 </section>
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165 </inputs>
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166 <outputs>
3
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167 <data format="txt" label="muspinsim input file $out_file_prefix" name="out_file" from_work_dir="outfile.in"/>
0
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168 </outputs>
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169 <tests>
2
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170 <test expect_num_outputs="1">
0
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171 <param name="out_file_prefix" value="test_1"/>
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172 <param name="spin_preset" value="custom"/>
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173 <param name="spin" value="H"/>
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174 <param name="spin_preset" value="mu"/>
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175 <param name="interaction" value="zeeman"/>
3
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176 <param name="zeeman_index" value="1"/>
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177 <param name="zeeman_vector" value="1 0 0"/>
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178 <param name="zeeman_index" value="2"/>
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179 <param name="zeeman_vector" value="2 0 0"/>
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180 <param name="y_axis" value="asymmetry"/>
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181 <param name="x_axis" value="time"/>
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182 <param name="average_axes" value="orientation"/>
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183 <output name="out_file" file="test_1.in" ftype="txt" compare="diff"/>
0
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184 </test>
2
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185 <test expect_num_outputs="1">
0
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186 <param name="out_file_prefix" value="test_2"/>
3
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187 <param name="experiment_preset" value="custom"/>
0
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188 <param name="spin_preset" value="e"/>
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189 <param name="spin_preset" value="mu"/>
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190 <param name="interaction" value="hyperfine"/>
3
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191 <param name="hfine_index" value="1"/>
0
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192 <param name="hfine_matrix" value="[1 0 0 sin(10) (5*2) 0 10*pi 5 cos(20)]"/>
3
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193 <param name="time" value="range(0, 0.1)"/>
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194 <param name="y_axis" value="asymmetry"/>
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195 <param name="x_axis" value="time"/>
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196 <param name="field" value="1.0"/>
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197 <param name="temperature" value="1.0"/>
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198 <output name="out_file" file="test_2.in" ftype="txt" compare="diff"/>
0
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199 </test>
2
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200 <test expect_num_outputs="1">
0
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201 <param name="out_file_prefix" value="test_3"/>
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202 <param name="spin_preset" value="custom"/>
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203 <param name="spin" value="H"/>
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204 <param name="spin_preset" value="mu"/>
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205 <param name="spin_preset" value="e"/>
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206 <param name="interaction" value="hyperfine"/>
3
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207 <param name="hfine_index" value="2"/>
0
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208 <param name="hfine_matrix" value="[580 5 10 5 580 9 10 9 580]"/>
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209 <param name="interaction" value="hyperfine"/>
3
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210 <param name="hfine_index" value="3"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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211 <param name="hfine_matrix" value="[(300/2) 3 4*10 ], [3 15*10 6-3+2] ,[4 5 15 ]"/>
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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212 <param name="average_axes" value="orientation,temperature"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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213 <param name="experiment_preset" value="alc"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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214 <param name="field" value="range(1.8, 2.6, 100)"/>
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muon-spectroscopy-computational-project
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215 <param name="orientation_preset" value="zcw"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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216 <param name="zcw_n" value="20"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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217 <output name="out_file" file="test_3.in" ftype="txt" compare="diff"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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218 </test>
2
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219 <test expect_num_outputs="1">
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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220 <param name="out_file_prefix" value="test_4"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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221 <param name="spin_preset" value="custom"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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222 <param name="spin" value="F"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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223 <param name="spin_preset" value="custom"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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224 <param name="spin" value="F"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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225 <param name="spin_preset" value="mu"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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226 <param name="interaction" value="dipolar"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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227 <param name="di_index" value="1"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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228 <param name="di_index_2" value="2"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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229 <param name="di_vector" value="0.9 0.9 0"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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230 <param name="interaction" value="dipolar"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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231 <param name="di_index" value="1"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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232 <param name="di_index_2" value="3"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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233 <param name="di_vector" value="-0.9 -0.9 0"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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234 <param name="interaction" value="dissipation"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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235 <param name="dis_index" value="1"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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236 <param name="dis_val" value="0.5"/>
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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237 <param name="average_axes" value=""/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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238 <param name="experiment_preset" value="custom"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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239 <param name="field" value="1.5e-2 1.0e-2 1.0e-2"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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240 <param name="field" value="0.01"/>
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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241 <param name="intrinsic_field" value="1.6e-2 1.1e-2 1.1e-2"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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242 <param name="intrinsic_field" value="0.02"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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243 <param name="polarization_preset" value="custom"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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244 <param name="polarization" value="1 0 0"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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245 <param name="time" value="range(0,8.0,1000)"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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246 <param name="time" value="range(0,1.0)"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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247 <param name="orientation_preset" value="eulrange"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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248 <param name="eul_n" value="10"/>
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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249 <param name="celio_enabled" value="true"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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250 <param name="celio_k" value="10"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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251 <output name="out_file" file="test_4.in" ftype="txt" compare="diff"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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252 </test>
2
52d3a28902e8 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb
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253 <test expect_num_outputs="1">
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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254 <param name="out_file_prefix" value="test_5"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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255 <param name="spin_preset" value="mu"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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256 <param name="interaction" value="dissipation"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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257 <param name="dis_index" value="1"/>
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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258 <param name="dis_val" value="g"/>
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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diff changeset
259 <param name="experiment_preset" value="custom"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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260 <param name="field" value="1.0/muon_gyr"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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261 <param name="intrinsic_field" value="2.0/muon_gyr"/>
0
c70012022f0f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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262 <param name="fitting" value="true"/>
3
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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263 <param name="var_name" value="g"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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264 <param name="min_bound" value="0.0"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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265 <param name="fitting_tolerance" value="1.0"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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266 <param name="celio_enabled" value="true"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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267 <param name="celio_k" value="10"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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268 <param name="celio_averages" value="4"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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269 <output name="out_file" file="test_5.in" ftype="txt" compare="diff"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
270 </test>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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diff changeset
271 <test expect_num_outputs="1">
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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272 <param name="out_file_prefix" value="test_6"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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273 <param name="experiment_preset" value="zero_field"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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274 <param name="spin_preset" value="custom"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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275 <param name="spin" value="H"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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276 <param name="spin_preset" value="mu"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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277 <param name="interaction" value="zeeman"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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278 <param name="zeeman_index" value="1"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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279 <param name="zeeman_vector" value="1 0 0"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
280 <param name="zeeman_index" value="2"/>
331d0776abb4 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_config commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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diff changeset
281 <param name="zeeman_vector" value="2 0 0"/>
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282 <param name="average_axes" value="orientation,temperature"/>
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283 <output name="out_file" file="test_6.in" ftype="txt" compare="diff"/>
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284 </test>
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285 <test expect_num_outputs="1">
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286 <param name="out_file_prefix" value="test_7"/>
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287 <param name="experiment_preset" value="custom"/>
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288 <param name="spin_preset" value="custom"/>
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289 <param name="spin" value="H"/>
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290 <param name="spin_preset" value="mu"/>
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291 <param name="interaction" value="zeeman"/>
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292 <param name="zeeman_index" value="1"/>
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293 <param name="zeeman_vector" value="1 0 0"/>
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294 <param name="zeeman_index" value="2"/>
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295 <param name="zeeman_vector" value="2 0 0"/>
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296 <param name="y_axis" value="integral"/>
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297 <param name="x_axis" value="field"/>
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298 <param name="average_axes" value="orientation,temperature"/>
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299 <output name="out_file" file="test_7.in" ftype="txt" compare="diff"/>
0
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300 </test>
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301 </tests>
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302 <help><![CDATA[
3
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303 Tool to create input parameter file for MuSpinSim.
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304
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305
3
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306 This tool creates a structured text file with keywords and values which describe the system to model for MuSpinSim.
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307 See MuSpinSim docs for more information https://muon-spectroscopy-computational-project.github.io/muspinsim/input/.
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308
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309
3
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310 MuSpinSim allows expressions and special functions to be used when defining certain keywords. This tool also allows this.
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311 Check the hint at the bottom of each input to see what, if any, special function or expressions can be used.
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312
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313
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314 Default expressions include the use of the operators :code:`+ - * /` and :code:`^` for exponentiation. Expressions
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315 should not contain whitespace. For example, use :code:`1+2` not :code:`1 + 2`.
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316
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317
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318 Default constants include:
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319 - :code:`pi`: ratio of a circle and its diameter
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320 - :code:`e`: base of the natural logarithm
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321 - :code:`deg`: conversion factor between radians and degrees, equivalent to 180/pi
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322 - :code:`inf`: infinity
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323
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324 Special constants include:
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325 - :code:`muon_gyr`: gyromagnetic ratio of muon (135.5388 MHz/T)
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326 - :code:`MHz`: :code:`1/(2*muon_gyr)`
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327
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328
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329 Default functions include:
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330 - :code:`sin(x)`: sine
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331 - :code:`cos(x)`: cosine
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332 - :code:`tan(x)`: tangent
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333 - :code:`arcsin(x)`: inverse of the sine
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334 - :code:`arccos(x)`: inverse of the cosine
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335 - :code:`arctan(x)`: inverse of the tangent
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336 - :code:`arctan2(y, x)`: inverse of the tangent taking two arguments as (sine, cosine) to resolve the quadrant
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337 - :code:`exp(x)`: exponential with base e
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338 - :code:`log(x)`: natural logarithm
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339 - :code:`sqrt(x)`: square root
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340
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341 Special functions include:
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342 - :code:`range(x, y, z)`: get z equally spaced values between x and y
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343 - :code:`zcw(n)`: Zaremba-Conroy-Wolfsberg helper function
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344 - :code:`eulrange(n)`: helper function to create regular grid of n × n × n Euler angles with appropriate weights.
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345
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346
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347 To enter vectors or matrices the following formats are accepted:
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348 - :code:`[[1, 2, 3], [4, 5, 6], [7, 8, 9]]`
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349 - :code:`1 2 3 4 5 6 7 8 9`
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350 - :code:`[1 2 3] [4 5 6] [7 8 9]`
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351
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352
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353 The fitting (function minimization) algorithms available are:
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354
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355
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356 Nelder-Mead
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357 - A direct search method.
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358 - Starting with a 'simplex' of candidates, the algorithm will iteratively move the position of the worst candidate towards the optimum until all candidates converge (have values within a predefined tolerance level).
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359 - Scipy default tolerance is :code:`1e-4`
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360
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361
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362 L-BFGS
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363 - Limited Memory Broyden–Fletcher–Goldfarb–Shanno algorithm.
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364 - A second-order Quasi-Newton optimization algorithm
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365 - Makes use of second-order derivative (Hessian Matrix) to converge on optimum.
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366 - Scipy default tolerance is :code:`1e-5`
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367 ]]></help>
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368 <citations>
3
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369 <citation type="doi">10.1093/comjnl/7.4.308</citation>
0
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370 <citation type="bibtex">
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371 @book{nocedal_wright_2006,
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372 place={New York (NY)},
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373 title={Numerical Optimization},
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374 publisher={Springer},
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375 author={Nocedal, Jorge and Wright, Stephen J},
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376 year={2006}
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377 }
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378 </citation>
3
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379 <citation type="doi">10.1103/PhysRevLett.56.2720</citation>
0
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380 <citation type="bibtex">
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381 @TOOL_CITATION@
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382 </citation>
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383 </citations>
3
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384 </tool>