# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1661444179 0
# Node ID 64e6816a672707334ce3fafa8b546fcee23ed7ea

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4

diff -r 000000000000 -r 64e6816a6727 muspinsim.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muspinsim.xml	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,151 @@
+<tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">
+    <description>perform spin dynamics calculations for muon science experiments</description>
+    <macros>
+        <!-- version of underlying tool (PEP 440) -->
+        <token name="@TOOL_VERSION@">1.1.0</token>
+        <!-- version of this tool wrapper (integer) -->
+        <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@">
+            @software{muspinsim,
+                author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
+                license = {MIT},
+                title = {{muspinsim}},
+                url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
+                version = {v1.1.0},
+                month = {5},
+                year = {2022},
+                doi = {10.5281/zenodo.6563074}
+            }
+        </token>
+    </macros>
+    <creator>
+        <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
+        <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
+        <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
+    </creator>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">muspinsim</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ## remove spaces in names
+        mu_sim_name=\$(sed 's/ //g' <<< "$mu_sim.name") &&
+        ## create links
+        ln -s $mu_sim \$mu_sim_name &&
+        ## grab 'name' field from input file, if it doesn't exist, set name as 'muspinsim'
+        mu_out=\$(grep -A1 '^name' \$mu_sim_name | grep -v 'name' | sed -e 's/^[ \t]*//') &&
+        fitreport_out=\${mu_out:-"fitting_data"}_fitreport.txt &&
+        mu_out=\${mu_out:-"muspinsim"} &&
+        log_out=\$(echo \$mu_sim_name | cut -d '.' -f1).log &&
+        ## if fitting data required, check if fitting data exists
+        ## create symlink and change filepath in input file to point to symlink
+        if grep '^fitting_data' $mu_sim; then
+            if [[ '$mu_exp_in.name' != 'None' ]]; then
+                mu_exp_in_name=\$(sed 's/ //g' <<< "$mu_exp_in.name") &&
+                ln -s $mu_exp_in \$mu_exp_in_name &&
+                sed -iE "/^fitting_data/{n;s/([^)]*)/(\"\$mu_exp_in_name\")/g}" \$mu_sim_name;
+            else
+                echo "fitting data required, but no experiment data given" && exit 64;
+            fi;
+        fi &&
+        muspinsim \$mu_sim_name &&
+        mkdir data &&
+        mv \$mu_out*.dat data &&
+        if test -f \$fitreport_out; then mv -f \$fitreport_out fit_report.txt; fi &&
+        mv \$log_out log_out.log
+    ]]></command>
+    <inputs>
+        <param type="data" name="mu_sim" format="txt" label="Configuration file containing simulation parameters"/>
+        <param type="data" name="mu_exp_in" format="txt" optional="true" label="Experiment data to fit (.dat) (Optional)" help="Only required if the 'fitting_data' parameter is set in the configuration file above."/>
+    </inputs>
+    <outputs>
+        <collection name="muspinsim_results" type="list" label="Muspinsim output collection">
+            <discover_datasets pattern="__name__" directory="data" format="txt"/>
+        </collection>
+        <data label="muspinsim log for $mu_sim.name" name="log_out" format="txt" from_work_dir="log_out.log"/>
+        <data label="fit report for $mu_sim.name" name="fit_report" format="txt" from_work_dir="fit_report.txt">
+            <filter>mu_exp_in</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- log files have a timestamp on each line, and .dat files vary by machine
+                so use compare="re_match" or "contains" with some generalised test files -->
+        <test>
+            <param name="mu_sim" value="hfine.in" ftype="txt"/>
+            <output_collection name="muspinsim_results" type="list">
+                <element name="hfine.dat" file="hfine.dat" ftype="txt" lines_diff="4"/>
+            </output_collection>
+            <output name="log_out" file="hfine.log" ftype="txt" compare="re_match"/>
+        </test>
+        <test>
+            <param name="mu_sim" value="hfine_powder.in" ftype="txt"/>
+            <output_collection name="muspinsim_results" type="list">
+                <element name="muspinsim.dat" file="generic_out.dat" ftype="txt" compare="re_match_multiline">
+                    <assert_contents>
+                        <has_size value="5100" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="log_out" file="hfine_powder.log" ftype="txt" compare="re_match">
+                <assert_contents>
+                    <has_size value="802"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="mu_sim" value="fitting.in" ftype="txt"/>
+            <param name="mu_exp_in" value="fitting_input.dat" ftype="txt"/>
+            <output_collection name="muspinsim_results" type="list">
+                <element name="fitting_data.dat" file="fitting_data.dat" ftype="txt" lines_diff="4"/>
+            </output_collection>
+            <output name="log_out" file="fitting.log" ftype="txt" compare="contains">
+                <assert_contents>
+                    <has_size value="17145"/>
+                </assert_contents>
+            </output>
+            <output name="fit_report" file="fitting_fitreport.txt" ftype="txt" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="mu_sim" value="multi_out.in" ftype="txt"/>
+            <output_collection name="muspinsim_results" type="list">
+                <element name="multi_out_0_0.dat" file="multi_out_0_0.dat" ftype="txt" compare="re_match_multiline">
+                    <assert_contents>
+                        <has_size value="1164" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="multi_out_0_1.dat" file="multi_out_0_1.dat" ftype="txt" compare="re_match_multiline">
+                    <assert_contents>
+                        <has_size value="1164" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="multi_out_1_0.dat" file="multi_out_1_0.dat" ftype="txt" compare="re_match_multiline">
+                    <assert_contents>
+                        <has_size value="1164" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="multi_out_1_1.dat" file="multi_out_1_1.dat" ftype="txt" compare="re_match_multiline">
+                    <assert_contents>
+                        <has_size value="1164" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="log_out" file="multi_out.log" ftype="txt" compare="re_match"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        MuSpinSim is a program designed to carry out spin dynamics calculations.
+
+        Tool requires an input (.in) file which describes system and experiment details.
+        This is a text file containing keywords and values in indented blocks.
+
+        Full documentation: https://muon-spectroscopy-computational-project.github.io/muspinsim/
+
+        Command-line usage: muspinsim muspinsim.in
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @TOOL_CITATION@
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 64e6816a6727 test-data/fitting.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitting.in	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,27 @@
+# A basic test of fitting. We define a single muon with no interactions except
+# for a dissipation term, causing an exponential decay. We then fit the rate
+# of decay using a single variable g, starting at g=0.1, bounded from 0 to
+# positive infinity.
+#
+# Some target data with added artificial noise is used as the "experiment"
+# that we are trying to fit. We expect the decay to go like
+#
+#    0.5*cos(2*pi*t)*exp(-g*t)
+#
+# with g our variable, t the time, and pi = 3.1415...
+#
+# The 0.5 factor appears in front as that's the moment of the muon.
+# With the data provided, we expect the fitting to find that g = 3.0
+
+name
+    fitting_data
+spins
+    mu
+field
+    1.0/muon_gyr
+fitting_data
+    load("fitting_input.dat")
+fitting_variables
+    g 0.1 0.0 inf
+dissipation 1
+    g
diff -r 000000000000 -r 64e6816a6727 test-data/fitting.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitting.log	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,9 @@
+Launching MuSpinSim calculation from file: fitting.in
+Performing fitting in variables: g
+Using X axis:
+		t => 100 points
+Created spin system with spins:
+		mu
+Total number of configurations to simulate: 1
+Total number of configurations to average: 1
+Simulation completed in
diff -r 000000000000 -r 64e6816a6727 test-data/fitting_data.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitting_data.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,104 @@
+# MUSPINSIM v.1.0.3
+# Output file written on Thu Mar 31 18:26:46 2022
+# Parameters used:
+# 
+0.000000000000000000e+00 5.000000000000000000e-01
+1.010101010101010187e-02 4.839188562974035546e-01
+2.020202020202020374e-02 4.664633082870883185e-01
+3.030303030303030387e-02 4.477992370076759321e-01
+4.040404040404040747e-02 4.280884746475391855e-01
+5.050505050505051108e-02 4.074882658312278805e-01
+6.060606060606060774e-02 3.861507830642957884e-01
+7.070707070707071829e-02 3.642226954481366796e-01
+8.080808080808081495e-02 3.418447895726685060e-01
+9.090909090909091161e-02 3.191516413083217985e-01
+1.010101010101010222e-01 2.962713370496566911e-01
+1.111111111111111188e-01 2.733252428108397525e-01
+1.212121212121212155e-01 2.504278194378757871e-01
+1.313131313131313260e-01 2.276864820835683423e-01
+1.414141414141414366e-01 2.052015019882667823e-01
+1.515151515151515194e-01 1.830659485220967053e-01
+1.616161616161616299e-01 1.613656693720554314e-01
+1.717171717171717404e-01 1.401793066995395964e-01
+1.818181818181818232e-01 1.195783470499733880e-01
+1.919191919191919338e-01 9.962720276560653454e-02
+2.020202020202020443e-01 8.038332263460844229e-02
+2.121212121212121271e-01 6.189732950362884095e-02
+2.222222222222222376e-01 4.421318258634338721e-02
+2.323232323232323482e-01 2.736836221646109929e-02
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+9.797979797979798899e-01 2.530511082451557259e-02
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+1.000000000000000000e+00 2.399230366807731177e-02
diff -r 000000000000 -r 64e6816a6727 test-data/fitting_fitreport.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitting_fitreport.txt	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,11 @@
+Fitting process for fitting_data completed
+Success achieved: True
+Final absolute error <|f-f_targ|>: 0.0
+Number of simulations: 40
+Number of iterations: 20
+
+====================
+
+Values found for fitting variables:
+
+	g = 3.0368750000000104
\ No newline at end of file
diff -r 000000000000 -r 64e6816a6727 test-data/fitting_input.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fitting_input.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,100 @@
+0.000000000000000000e+00 5.005778399056657335e-01
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+5.252525252525253041e-01 -1.034044696616238934e-01
+5.353535353535353591e-01 -1.038026012968156359e-01
+5.454545454545455252e-01 -9.333574543107070465e-02
+5.555555555555555802e-01 -8.119043575888182374e-02
+5.656565656565657463e-01 -8.780715526363727652e-02
+5.757575757575758013e-01 -8.678757402752533545e-02
+5.858585858585858563e-01 -6.561193781199284314e-02
+5.959595959595960224e-01 -7.819537284931875332e-02
+6.060606060606060774e-01 -5.943809785495194481e-02
+6.161616161616162435e-01 -5.661945047010875920e-02
+6.262626262626262985e-01 -5.050281252925081094e-02
+6.363636363636364646e-01 -5.175403740852566048e-02
+6.464646464646465196e-01 -4.872824696376772818e-02
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+6.666666666666667407e-01 -3.687545675512928639e-02
+6.767676767676767957e-01 -3.686197477560970714e-02
+6.868686868686869618e-01 -3.003067438142277903e-02
+6.969696969696970168e-01 -1.658939118843251806e-02
+7.070707070707071829e-01 -2.419886325838571661e-02
+7.171717171717172379e-01 -1.749710923657482944e-02
+7.272727272727272929e-01 -4.515936967325259732e-03
+7.373737373737374590e-01 -7.209833178823250172e-03
+7.474747474747475140e-01 -5.996664146736436010e-03
+7.575757575757576801e-01 4.146914696571531167e-03
+7.676767676767677351e-01 1.085995026796996235e-02
+7.777777777777777901e-01 1.122574572656667886e-02
+7.878787878787879562e-01 4.797691564737849995e-03
+7.979797979797980112e-01 1.160846007642780779e-02
+8.080808080808081773e-01 2.492767767864879913e-02
+8.181818181818182323e-01 1.437525093680377952e-02
+8.282828282828283983e-01 1.743612669587774056e-02
+8.383838383838384534e-01 1.966626934151189873e-02
+8.484848484848485084e-01 1.296194227363287738e-02
+8.585858585858586745e-01 3.349420140461304568e-02
+8.686868686868687295e-01 2.032633571368781811e-02
+8.787878787878788955e-01 3.197523032500756285e-02
+8.888888888888889506e-01 2.197314183479991481e-02
+8.989898989898991166e-01 3.365403812295356123e-02
+9.090909090909091717e-01 2.979919581225816752e-02
+9.191919191919192267e-01 2.304239947081147127e-02
+9.292929292929293927e-01 2.497743178699073086e-02
+9.393939393939394478e-01 2.961947122261034820e-02
+9.494949494949496138e-01 1.826282252184947136e-02
+9.595959595959596689e-01 2.396972947884037919e-02
+9.696969696969697239e-01 2.651899324456775606e-02
+9.797979797979798899e-01 2.162884710493336027e-02
+9.898989898989899450e-01 3.167384830249942579e-02
+1.000000000000000000e+00 2.097011271926497306e-02
diff -r 000000000000 -r 64e6816a6727 test-data/generic_out.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generic_out.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,5 @@
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
+# Parameters used:
+# 
+(-?\d\.\d{18}e[+-]\d{2} -?\d\.\d{18}e[+-]\d{2}\n){100}
\ No newline at end of file
diff -r 000000000000 -r 64e6816a6727 test-data/hfine.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hfine.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,104 @@
+# MUSPINSIM v.1.0.3
+# Output file written on Thu Mar 31 15:40:40 2022
+# Parameters used:
+# 
+0.000000000000000000e+00 4.999999999999998890e-01
+1.010101010101010100e-03 4.994966691179709706e-01
+2.020202020202020200e-03 4.979887032076987241e-01
+3.030303030303030300e-03 4.954821743156765934e-01
+4.040404040404040401e-03 4.919871753490889787e-01
+5.050505050505050067e-03 4.875177794352362204e-01
+6.060606060606060601e-03 4.820919832540180305e-01
+7.070707070707071135e-03 4.757316345716551820e-01
+8.080808080808080801e-03 4.684623442674461513e-01
+9.090909090909090468e-03 4.603133832077952459e-01
+1.010101010101010013e-02 4.513175643827646022e-01
+1.111111111111111154e-02 4.415111107797444201e-01
+1.212121212121212120e-02 4.309335095262674664e-01
+1.313131313131313087e-02 4.196273528892829896e-01
+1.414141414141414227e-02 4.076381667711305168e-01
+1.515151515151515194e-02 3.950142273927994552e-01
+1.616161616161616160e-02 3.818063669026254825e-01
+1.717171717171717127e-02 3.680677686931705939e-01
+1.818181818181818094e-02 3.538537532504715255e-01
+1.919191919191919060e-02 3.392215553979679443e-01
+2.020202020202020027e-02 3.242300938320686887e-01
+2.121212121212121340e-02 3.089397338773567370e-01
+2.222222222222222307e-02 2.934120444167325203e-01
+2.323232323232323274e-02 2.777095499752527119e-01
+2.424242424242424240e-02 2.618954789559355678e-01
+2.525252525252525207e-02 2.460335090412980041e-01
+2.626262626262626174e-02 2.301875107858028791e-01
+2.727272727272727140e-02 2.144212904316786794e-01
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+3.030303030303030387e-02 1.682330091706445430e-01
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+3.232323232323232320e-02 1.389833468485564272e-01
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+3.535353535353535220e-02 9.859757821558334800e-02
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+4.343434343434343647e-02 2.097288564198256100e-02
+4.444444444444444614e-02 1.507684480352292078e-02
+4.545454545454545581e-02 1.012675659637563008e-02
+4.646464646464646547e-02 6.142553278648238413e-03
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+4.949494949494949447e-02 1.258644042037293520e-04
+5.050505050505050414e-02 1.258644042036738409e-04
+5.151515151515151381e-02 1.132019356728866666e-03
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+5.757575757575757874e-02 2.779113783626911693e-02
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+6.060606060606060774e-02 5.348672631430315128e-02
+6.161616161616161741e-02 6.368388758106127701e-02
+6.262626262626262708e-02 7.463127807341965458e-02
+6.363636363636362980e-02 8.628481651367858607e-02
+6.464646464646464641e-02 9.859757821558332025e-02
+6.565656565656566301e-02 1.115199840334725467e-01
+6.666666666666666574e-02 1.249999999999998612e-01
+6.767676767676768235e-02 1.389833468485564827e-01
+6.868686868686868507e-02 1.534137185767177891e-01
+6.969696969696970168e-02 1.682330091706444875e-01
+7.070707070707070441e-02 1.833815465774910891e-01
+7.171717171717172101e-02 1.987983329837023083e-01
+7.272727272727272374e-02 2.144212904316786517e-01
+7.373737373737374035e-02 2.301875107858027680e-01
+7.474747474747474307e-02 2.460335090412978376e-01
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+7.979797979797979834e-02 3.242300938320686887e-01
+8.080808080808080107e-02 3.392215553979678333e-01
+8.181818181818181768e-02 3.538537532504714145e-01
+8.282828282828283428e-02 3.680677686931706494e-01
+8.383838383838383701e-02 3.818063669026254825e-01
+8.484848484848485362e-02 3.950142273927993997e-01
+8.585858585858585634e-02 4.076381667711304058e-01
+8.686868686868687295e-02 4.196273528892829896e-01
+8.787878787878787568e-02 4.309335095262674109e-01
+8.888888888888889228e-02 4.415111107797443646e-01
+8.989898989898989501e-02 4.513175643827644912e-01
+9.090909090909091161e-02 4.603133832077952459e-01
+9.191919191919191434e-02 4.684623442674461513e-01
+9.292929292929293095e-02 4.757316345716551265e-01
+9.393939393939393367e-02 4.820919832540179750e-01
+9.494949494949495028e-02 4.875177794352362204e-01
+9.595959595959595301e-02 4.919871753490888677e-01
+9.696969696969696961e-02 4.954821743156765379e-01
+9.797979797979798622e-02 4.979887032076987241e-01
+9.898989898989898895e-02 4.994966691179709706e-01
+1.000000000000000056e-01 4.999999999999998890e-01
diff -r 000000000000 -r 64e6816a6727 test-data/hfine.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hfine.in	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,12 @@
+name
+    hfine
+spins
+    mu e
+hyperfine 1
+    10   0    0
+    0    10   0
+    0    0    10
+time
+    range(0, 0.1)
+y_axis
+    asymmetry
\ No newline at end of file
diff -r 000000000000 -r 64e6816a6727 test-data/hfine.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hfine.log	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,9 @@
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Launching MuSpinSim calculation from file: hfine.in
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Using X axis:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		t => 100 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Created spin system with spins:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		mu e
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding hyperfine term to spins 1-2
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to simulate: 1
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to average: 1
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Simulation completed in [\d\.]+ seconds
\ No newline at end of file
diff -r 000000000000 -r 64e6816a6727 test-data/hfine_powder.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hfine_powder.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,104 @@
+# MUSPINSIM v.1.0.3
+# Output file written on Thu Mar 31 15:53:05 2022
+# Parameters used:
+# 
+0.000000000000000000e+00 4.999999999999978906e-01
+1.010101010101010187e-02 4.898216198091702722e-01
+2.020202020202020374e-02 4.601457670929889887e-01
+3.030303030303030387e-02 4.134280246157800986e-01
+4.040404040404040747e-02 3.534061443706255079e-01
+5.050505050505051108e-02 2.847009690826324269e-01
+6.060606060606060774e-02 2.123996346828892212e-01
+7.070707070707071829e-02 1.416188793458658113e-01
+8.080808080808081495e-02 7.703667452850616881e-02
+9.090909090909091161e-02 2.243923686011758262e-02
+1.010101010101010222e-01 -1.961818153149216121e-02
+1.111111111111111188e-01 -4.795996320947538277e-02
+1.212121212121212155e-01 -6.274744672148406532e-02
+1.313131313131313260e-01 -6.530158863075111175e-02
+1.414141414141414366e-01 -5.784563669914950801e-02
+1.515151515151515194e-01 -4.318881024320503359e-02
+1.616161616161616299e-01 -2.435953288228472069e-02
+1.717171717171717404e-01 -4.221383713715486444e-03
+1.818181818181818232e-01 1.486478152761657422e-02
+1.919191919191919338e-01 3.127029875868032882e-02
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+9.191919191919192267e-01 6.249450370225932000e-02
+9.292929292929293927e-01 6.100450723160437405e-02
+9.393939393939394478e-01 6.011377189968813289e-02
+9.494949494949496138e-01 5.988117728733665518e-02
+9.595959595959596689e-01 6.027790852948173433e-02
+9.696969696969697239e-01 6.123922365651523342e-02
+9.797979797979798899e-01 6.269414643787388219e-02
+9.898989898989899450e-01 6.456212771807727513e-02
+1.000000000000000000e+00 6.674271208912255227e-02
diff -r 000000000000 -r 64e6816a6727 test-data/hfine_powder.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hfine_powder.in	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,12 @@
+spins
+    mu e
+hyperfine 1
+    5    2    3
+    2    5    2
+    3    2    5
+field
+    0.01
+time
+    range(0, 1.0)
+orientation
+    eulrange(10)
diff -r 000000000000 -r 64e6816a6727 test-data/hfine_powder.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hfine_powder.log	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,11 @@
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Launching MuSpinSim calculation from file: hfine_powder.in
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Using X axis:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		t => 100 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Averaging over:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		orient => 1000 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Created spin system with spins:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		mu e
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding hyperfine term to spins 1-2
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to simulate: 1000
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to average: 1000
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Simulation completed in [\d\.]+ seconds
diff -r 000000000000 -r 64e6816a6727 test-data/multi_out.in
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multi_out.in	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,31 @@
+name
+    multi_out
+spins
+    mu 2H e
+field
+    0
+    10
+temperature
+    inf
+    0
+time
+    range(0, 10, 20)
+orientation
+    0 0
+    0 180
+polarization
+    0 1 1
+zeeman 1
+    1 0 0
+dipolar 1 2
+    0 1 0
+hyperfine 1 3
+    10 2 2
+    2 10 2
+    2 2 10
+quadrupolar 2
+    -2 0 0
+    0  1 0
+    0  0 1
+dissipation 2
+    0.1
diff -r 000000000000 -r 64e6816a6727 test-data/multi_out.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multi_out.log	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,19 @@
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Launching MuSpinSim calculation from file: multi_out.in
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Using X axis:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		t => 20 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Averaging over:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		orient => 2 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Scanning over:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		B => 2 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		T => 2 points
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Created spin system with spins:
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] 		mu 2H e
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding dipolar term to spins 1-2
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding hyperfine term to spins 1-3
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding quadrupolar term to spin 2
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Adding Zeeman term to spin 1
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to simulate: 8
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Total number of configurations to average: 2
+\[WARNING\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] WARNING: initial density matrix is computed with an approximation that can fail at low fields and finite temperature
+\[WARNING\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] WARNING: initial density matrix is computed with an approximation that can fail at low fields and finite temperature
+\[INFO\] \[MainThread\] \[\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}\] Simulation completed in [\d\.]+ seconds
diff -r 000000000000 -r 64e6816a6727 test-data/multi_out_0_0.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multi_out_0_0.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,7 @@
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
+# Parameters used:
+# 	B                    = \[0. 0. 0.\] T
+# 	T                    = inf
+# 
+(-?\d\.\d{18}e[+-]\d{2} -?\d\.\d{18}e[+-]\d{2}\n){20}
\ No newline at end of file
diff -r 000000000000 -r 64e6816a6727 test-data/multi_out_0_1.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multi_out_0_1.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,7 @@
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
+# Parameters used:
+# 	B                    = \[0. 0. 0.\] T
+# 	T                    = 0.0
+# 
+(-?\d\.\d{18}e[+-]\d{2} -?\d\.\d{18}e[+-]\d{2}\n){20}
\ No newline at end of file
diff -r 000000000000 -r 64e6816a6727 test-data/multi_out_1_0.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multi_out_1_0.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,7 @@
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
+# Parameters used:
+# 	B                    = \[ 0.  0. 10.\] T
+# 	T                    = inf
+# 
+(-?\d\.\d{18}e[+-]\d{2} -?\d\.\d{18}e[+-]\d{2}\n){20}
\ No newline at end of file
diff -r 000000000000 -r 64e6816a6727 test-data/multi_out_1_1.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multi_out_1_1.dat	Thu Aug 25 16:16:19 2022 +0000
@@ -0,0 +1,7 @@
+# MUSPINSIM v.\d+.\d+.\d+
+# Output file written on [A-Za-z]{3} [A-Za-z]{3} [ 1-3][0-9] \d{2}:\d{2}:\d{2} \d{4}
+# Parameters used:
+# 	B                    = \[ 0.  0. 10.\] T
+# 	T                    = 0.0
+# 
+(-?\d\.\d{18}e[+-]\d{2} -?\d\.\d{18}e[+-]\d{2}\n){20}
\ No newline at end of file