Mercurial > repos > muon-spectroscopy-computational-project > larch_artemis
changeset 2:f802cd616862 draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Mon, 04 Mar 2024 11:43:09 +0000 |
| parents | 84c8e04bc1a1 |
| children | 2ceaa943a2ad |
| files | common.py larch_artemis.xml test-data/fit_report.txt |
| diffstat | 3 files changed, 46 insertions(+), 46 deletions(-) [+] |
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--- a/common.py Wed Dec 06 13:03:46 2023 +0000 +++ b/common.py Mon Mar 04 11:43:09 2024 +0000 @@ -29,6 +29,7 @@ ) all_groups = {} for key in athena_group._athena_groups.keys(): + print(f"\nExtracting group {key}") group = get_group(athena_group, key) pre_edge_with_defaults(group=group) xftf_with_defaults(group=group) @@ -68,8 +69,7 @@ ("nnorm", "nnorm", None), ("make_flat", "flatten", None), ("step", "step", None), - # This cannot be read from file as it is not stored by Larch (0.9.71) - # ("nvict", "nvict", None), + ("nvict", "nvict", None), ) for key, parameters_key, default in keys: extract_attribute(
--- a/larch_artemis.xml Wed Dec 06 13:03:46 2023 +0000 +++ b/larch_artemis.xml Mon Mar 04 11:43:09 2024 +0000 @@ -2,9 +2,9 @@ <description>generate Artemis projects from XAFS data</description> <macros> <!-- version of underlying tool (PEP 440) --> - <token name="@TOOL_VERSION@">0.9.71</token> + <token name="@TOOL_VERSION@">0.9.74</token> <!-- version of this tool wrapper (integer) --> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">0</token> <!-- citation should be updated with every underlying tool version --> <!-- typical fields to update are version, month, year, and doi --> <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
--- a/test-data/fit_report.txt Wed Dec 06 13:03:46 2023 +0000 +++ b/test-data/fit_report.txt Mon Mar 04 11:43:09 2024 +0000 @@ -2,11 +2,11 @@ \[\[Statistics\]\] nvarys, npts = 6, 104 n_independent = 12\.205 - chi_square = [\d\.]{10} - reduced chi_square = [\d\.]{10} - r-factor = [\d\.]{10} - Akaike info crit = [\d\.]{10} - Bayesian info crit = [\d\.]{10} + chi_square = [\d\.]{9} + reduced chi_square = [\d\.]{9} + r-factor = [\d\.]{9} + Akaike info crit = [\d\.]{9} + Bayesian info crit = [\d\.]{9} \[\[Data\]\] fit space = 'r' @@ -15,18 +15,18 @@ k window, dk = 'hanning', 1\.000 paths used in fit = \['feff/feff0001\.dat', 'feff/feff0002\.dat', 'feff/feff0003\.dat', 'feff/feff0004\.dat'\] k-weight = 2 - epsilon_k = Array\(mean=5\.19133e-4, std=4\.56760e-4\) - epsilon_r = [\d\.]{10} + epsilon_k = Array\(mean=5\.1913e-4, std=4\.5676e-4\) + epsilon_r = [\d\.]{9} n_independent = 12\.205 \[\[Variables\]\] - alpha = [-\s][\d\.]{10} \+/- [\d\.]{10} \(init= 1\.00000e-7\) - amp = [-\s][\d\.]{10} \+/- [\d\.]{10} \(init= 1\.00000000\) - enot = [-\s][\d\.]{10} \+/- [\d\.]{10} \(init= 1\.00000e-7\) - ss = [-\s][\d\.]{10} \+/- [\d\.]{10} \(init= 0\.00300000\) - ss2 = [-\s][\d\.]{10} \+/- [\d\.]{10} \(init= 0\.00300000\) - ss3 = [-\s][\d\.]{10} \+/- [\d\.]{10} = 'ss2' - ssfe = [-\s][\d\.]{10} \+/- [\d\.]{10} \(init= 0\.00300000\) + alpha = [-\s][\d\.]{9} \+/- [\d\.]{9} \(init= 1\.0000e-7\) + amp = [-\s][\d\.]{9} \+/- [\d\.]{9} \(init= 1\.0000000\) + enot = [-\s][\d\.]{9} \+/- [\d\.]{9} \(init= 1\.0000e-7\) + ss = [-\s][\d\.]{9} \+/- [\d\.]{9} \(init= 0\.0030000\) + ss2 = [-\s][\d\.]{9} \+/- [\d\.]{9} \(init= 0\.0030000\) + ss3 = [-\s][\d\.]{9} \+/- [\d\.]{9} = 'ss2' + ssfe = [-\s][\d\.]{9} \+/- [\d\.]{9} \(init= 0\.0030000\) \[\[Correlations\]\] \(unreported correlations are < 0\.100\) \w+, \w+\s+= [\s\-]0\.\d{3} @@ -51,51 +51,51 @@ geometry atom x y z ipot Rh 0\.0000, 0\.0000, 0\.0000 0 \(absorber\) C -0\.7410, 0\.2885, -1\.7419 3 - reff = [\d\.]{10} - degen = 1\.00000000 - n\*s02 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'amp' - e0 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'enot' - r = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'reff \+ alpha\*reff' - deltar = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'alpha\*reff' - sigma2 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'ss' + reff = [\d\.]{9} + degen = 1\.0000000 + n\*s02 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'amp' + e0 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'enot' + r = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'reff \+ alpha\*reff' + deltar = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'alpha\*reff' + sigma2 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'ss' = Path 'S2' = Rh K Edge feffdat file = feff/feff0002\.dat, from feff run 'feff' geometry atom x y z ipot Rh 0\.0000, 0\.0000, 0\.0000 0 \(absorber\) C 1\.4414, 0\.4279, 1\.2965 3 - reff = [\d\.]{10} - degen = 1\.00000000 - n\*s02 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'amp' - e0 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'enot' - r = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'reff \+ alpha\*reff' - deltar = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'alpha\*reff' - sigma2 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'ss2' + reff = [\d\.]{9} + degen = 1\.0000000 + n\*s02 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'amp' + e0 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'enot' + r = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'reff \+ alpha\*reff' + deltar = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'alpha\*reff' + sigma2 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'ss2' = Path 'S3' = Rh K Edge feffdat file = feff/feff0003\.dat, from feff run 'feff' geometry atom x y z ipot Rh 0\.0000, 0\.0000, 0\.0000 0 \(absorber\) C -1\.6586, -0\.1094, 1\.2084 3 - reff = [\d\.]{10} - degen = 1\.00000000 - n\*s02 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'amp' - e0 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'enot' - r = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'reff \+ alpha\*reff' - deltar = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'alpha\*reff' - sigma2 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'ss3' + reff = [\d\.]{9} + degen = 1\.0000000 + n\*s02 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'amp' + e0 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'enot' + r = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'reff \+ alpha\*reff' + deltar = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'alpha\*reff' + sigma2 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'ss3' = Path 'Fe' = Rh K Edge feffdat file = feff/feff0004\.dat, from feff run 'feff' geometry atom x y z ipot Rh 0\.0000, 0\.0000, 0\.0000 0 \(absorber\) C 0\.6043, -2\.0001, 0\.0975 3 - reff = [\d\.]{10} - degen = 1\.00000000 - n\*s02 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'amp' - e0 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'enot' - r = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'reff \+ alpha\*reff' - deltar = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'alpha\*reff' - sigma2 = [-\s][\d\.]{10} \+/- [\d\.]{10} := 'ssfe' + reff = [\d\.]{9} + degen = 1\.0000000 + n\*s02 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'amp' + e0 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'enot' + r = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'reff \+ alpha\*reff' + deltar = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'alpha\*reff' + sigma2 = [-\s][\d\.]{9} \+/- [\d\.]{9} := 'ssfe' ======================================================= \ No newline at end of file