# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1709552589 0
# Node ID f802cd616862e37264595b9f11c2f3e773a67193
# Parent 84c8e04bc1a12e31d709a12cf8fb1842b6701b7f
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
diff -r 84c8e04bc1a1 -r f802cd616862 common.py
--- 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(
diff -r 84c8e04bc1a1 -r f802cd616862 larch_artemis.xml
--- 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 @@
generate Artemis projects from XAFS data
- 0.9.71
+ 0.9.74
- 1
+ 0
10.1088/1742-6596/430/1/012007
diff -r 84c8e04bc1a1 -r f802cd616862 test-data/fit_report.txt
--- 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