Mercurial > repos > muon-spectroscopy-computational-project > larch_artemis

changeset 6:d17c5d62802f draft

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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit be7fc75b35a77b50a588575ca0749c43f8fd7cf5
author muon-spectroscopy-computational-project
date Fri, 23 Aug 2024 16:44:13 +0000
parents 7acb53ffb96f
children e0407f36fcea
files larch_artemis.xml test-data/fit_report_simultaneous.txt
diffstat 2 files changed, 184 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/larch_artemis.xml	Fri Aug 23 13:46:13 2024 +0000
+++ b/larch_artemis.xml	Fri Aug 23 16:44:13 2024 +0000
@@ -4,11 +4,10 @@
         <!-- version of underlying tool (PEP 440) -->
         <token name="@TOOL_VERSION@">0.9.80</token>
         <!-- version of this tool wrapper (integer) -->
-        <token name="@WRAPPER_VERSION@">0</token>
+        <token name="@WRAPPER_VERSION@">1</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>
-        <import>macros.xml</import>
     </macros>
     <creator>
         <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
@@ -58,7 +57,7 @@
                 <repeat name="simultaneous" title="Simultaneous datasets" min="1" default="1">
                     <param name="prj_file" type="data" format="prj" label="Athena project files" help="Normalised X-ray Absorption Fine Structure (XAFS) data, in Athena project format. These will be submitted as a single job performing a simultaneous fit."/>
                     <repeat name="paths" title="Path IDs to select" min="1" default="1">
-                        <param name="path_id" type="integer" min="1" label="Path ID"/>
+                        <param name="path_id" type="integer" value="1" min="1" label="Path ID"/>
                     </repeat>
                 </repeat>
             </when>
@@ -362,8 +361,14 @@
                 <param name="prj_file" value="test.prj"/>
                 <repeat name="paths">
                     <param name="path_id" value="1"/>
+                </repeat>
+                <repeat name="paths">
                     <param name="path_id" value="2"/>
+                </repeat>
+                <repeat name="paths">
                     <param name="path_id" value="3"/>
+                </repeat>
+                <repeat name="paths">
                     <param name="path_id" value="4"/>
                 </repeat>
             </repeat>
@@ -371,8 +376,14 @@
                 <param name="prj_file" value="test.prj"/>
                 <repeat name="paths">
                     <param name="path_id" value="1"/>
+                </repeat>
+                <repeat name="paths">
                     <param name="path_id" value="2"/>
+                </repeat>
+                <repeat name="paths">
                     <param name="path_id" value="3"/>
+                </repeat>
+                <repeat name="paths">
                     <param name="path_id" value="4"/>
                 </repeat>
             </repeat>
@@ -387,7 +398,7 @@
             <param name="window" value="hanning"/>
             <param name="rmin" value="1.4"/>
             <param name="rmax" value="3.0"/>
-            <output name="fit_report" file="fit_report.txt" compare="re_match"/>
+            <output name="fit_report" file="fit_report_simultaneous.txt" compare="re_match"/>
         </test>
     </tests>
     <help><![CDATA[
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fit_report_simultaneous.txt	Fri Aug 23 16:44:13 2024 +0000
@@ -0,0 +1,169 @@
+=================== FEFFIT RESULTS ====================
+\[\[Statistics\]\]
+  n_function_calls     = 4\d\d
+  n_variables          = 6
+  n_data_points        = 208
+  n_independent        = 24\.4090160
+  chi_square           = [\d\.]{10}
+  reduced chi_square   = [\d\.]{10}
+  r-factor             = [\d\.]{10}
+  Akaike info crit     = [\d\.]{10}
+  Bayesian info crit   = [\d\.]{10}
+
+\[\[Variables\]\]
+  alpha                = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 1\.0000e-7\)
+  e0                   = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 1\.0000e-7\)
+  s02                  = [-\s][\d\.]{9} \+/- [\d\.]{9}  \(init= 1\.0000000\)
+  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}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+  \w+, \w+\s+= [\s\-]0\.\d{3}
+
+
+\[\[Dataset 1 of 2\]\]
+  unique_id            = 'dm7xe57x'
+  fit space            = 'r'
+  r-range              = 1\.400, 3\.000
+  k-range              = 3\.000, 14\.000
+  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\(mean=5\.1913e-4, std=4\.5676e-4\)
+  epsilon_r            = [\d\.]{9}
+  n_independent        = 12\.205
+
+\[\[Paths\]\]
+ = Path 'S1' = Rh K Edge
+    feffdat file = feff/feff0001\.dat, from feff run 'feff'
+    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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     r      = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'reff \+ alpha\*reff'
+     deltar = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'alpha\*reff'
+     sigma2 = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'ssfe'
+
+\[\[Dataset 2 of 2\]\]
+  unique_id            = '\w{8}'
+  fit space            = 'r'
+  r-range              = 1\.400, 3\.000
+  k-range              = 3\.000, 14\.000
+  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\(mean=5\.1913e-4, std=4\.5676e-4\)
+  epsilon_r            = [\d\.]{9}
+  n_independent        = 12\.205
+
+\[\[Paths\]\]
+ = Path 'S1' = Rh K Edge
+    feffdat file = feff/feff0001\.dat, from feff run 'feff'
+    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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     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\.]{9}
+     degen  =  1\.0000000
+     n\*s02  = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 's02'
+     e0     = [-\s][\d\.]{9} \+/- [\d\.]{9}  := 'e0'
+     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