<tool id="muspinsim_config" name="MuSpinSim Configure" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
    <description>define simulation parameters</description>
    <macros>
        <!-- version of underlying tool (PEP 440) -->
        <token name="@TOOL_VERSION@">2.0.2</token>
        <!-- version of this tool wrapper (integer) -->
        <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@">
            @software{muspinsim,
                author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and Davies, Joel and Wilkinson, John and {Muon Spectroscopy Computational Project}},
                license = {MIT},
                title = {{muspinsim}},
                url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
                version = {v2.0.2},
                month = {1},
                year = {2023}
                doi = {10.5281/zenodo.7568830}
            }
        </token>
        <import>config_macros.xml</import>
    </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"/>
        <person givenName="Joel" familyName="Davies" url="https://github.com/joelvdavies" identifier="https://orcid.org/0000-0002-4153-6819"/>
        <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>
    <required_files>
        <include type="literal" path="sample_fitting_data.dat"/>
        <include type="literal" path="build_file.py"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        cp '${__tool_directory__}/sample_fitting_data.dat' ./fitting_data.dat &&
        python '${__tool_directory__}/build_file.py' inputs.json
    ]]></command>
    <configfiles>
        <inputs name="inputs" filename="inputs.json"/>
    </configfiles>
    <inputs>
        <param type="text" name="out_file_prefix" label="Name" help="A name with which to label this configuration" optional="true" value="muspinsim"/>
        <section name="spins" expanded="true" title="Spins">
            <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)">
                <conditional name="spin_options">
                    <param name="spin_preset" type="select" value="mu" label="Species" help="Select 'custom' to define own">
                        <option selected="true" value="mu">mu</option>
                        <option value="e">e</option>
                        <option value="custom">custom</option>
                    </param>
                    <when value="custom">
                        <param name="spin" optional="false" type="text" label="Species name"/>
                        <param name="atomic_mass" optional="true" type="integer" min="0" value="" label="Atomic mass" help="Leave blank to use default mass - whole numbers only"/>
                    </when>
                    <when value="mu"/>
                    <when value="e"/>
                </conditional>
            </repeat>
        </section>
        <section name="interaction_params" expanded="true" title="Spin Interactions" help="">
            <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">
                <conditional name="interaction_options">
                    <param name="interaction" type="select" label="Choose interaction type">
                        <option value="zeeman">Zeeman</option>
                        <option value="hyperfine">hyperfine</option>
                        <option value="dipolar">dipolar</option>
                        <option value="quadrupolar">quadrupolar</option>
                        <option value="dissipation">dissipation</option>
                    </param>
                    <when value="zeeman">
                        <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."/>
                        <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)"/>
                    </when>
                    <when value="hyperfine">
                        <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."/>
                        <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"/>
                        <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)">
                            <sanitizer>
                                <valid initial="string.printable">
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="dipolar">
                        <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."/>
                        <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."/>
                        <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)"/>
                    </when>
                    <when value="quadrupolar">
                        <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."/>
                        <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">
                            <sanitizer>
                                <valid initial="string.printable">
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                    <when value="dissipation">
                        <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."/>
                        <param name="dis_val" type="text" value="" label="Dissipation" help="Define dissipation term (MHz). Allows default expressions, constants and functions (see help)"/>
                    </when>
                </conditional>
            </repeat>
        </section>
        <section name="experiment_params" expanded="true" title="Experiment Parameters">
            <conditional name="experiment">
                <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">
                    <option value="alc">Avoided Level Crossing (ALC)</option>
                    <option value="zero_field">Zero Field</option>
                    <option selected="true" value="custom">Custom</option>
                </param>
                <when value="alc">
                    <expand macro="restricted_axes_options"/>
                    <expand macro="fields"/>
                    <expand macro="temperatures"/>
                    <expand macro="orientations"/>
                    <expand macro="euler_convention"/>
                </when>
                <when value="zero_field">
                    <expand macro="restricted_axes_options"/>
                    <expand macro="times"/>
                    <expand macro="temperatures"/>
                    <expand macro="orientations"/>
                    <expand macro="euler_convention"/>
                    <expand macro="celio_options"/>
                </when>
                <when value="custom">
                    <expand macro="axes_options"/>
                    <expand macro="times"/>
                    <expand macro="fields"/>
                    <expand macro="intrinsic_fields"/>
                    <expand macro="temperatures"/>
                    <expand macro="polarizations"/>
                    <expand macro="orientations"/>
                    <expand macro="euler_convention"/>
                    <expand macro="celio_options"/>
                </when>
            </conditional>
        </section>
        <section name="fitting_params" expanded="true" title="Fitting Parameters">
            <conditional name="fitting_options">
                <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">
                    <option value="true">Yes</option>
                    <option selected="true" value="">No</option>
                </param>
                <when value="true">
                    <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">
                        <option selected="true" value="nelder-mead">Nelder-Mead</option>
                        <option value="lbfgs">L-BFGS</option>
                    </param>
                    <repeat name="fitting_variables" title="Variable to fit to the experimental data">
                        <param name="var_name" type="text" optional="false" label="Name of the variable"/>
                        <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"/>
                        <param name="min_bound" type="text" value="-inf" label="minimum bound" help="Allows default expressions, constants and functions, plus MHz, muon_gyr constants"/>
                        <param name="max_bound" type="text" value="inf" label="maximum bound" help="Allows default expressions, constants and functions, plus MHz, muon_gyr constants"/>
                    </repeat>
                    <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"/>
                </when>
                <when value=""/>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data format="txt" label="muspinsim input file $out_file_prefix" name="out_file" from_work_dir="outfile.in"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="out_file_prefix" value="test_1"/>
            <param name="spin_preset" value="custom"/>
            <param name="spin" value="H"/>
            <param name="spin_preset" value="mu"/>
            <param name="interaction" value="zeeman"/>
            <param name="zeeman_index" value="1"/>
            <param name="zeeman_vector" value="1 0 0"/>
            <param name="zeeman_index" value="2"/>
            <param name="zeeman_vector" value="2 0 0"/>
            <param name="y_axis" value="asymmetry"/>
            <param name="x_axis" value="time"/>
            <param name="average_axes" value="orientation"/>
            <output name="out_file" file="test_1.in" ftype="txt" compare="diff"/>
        </test>
        <test expect_num_outputs="1">
            <param name="out_file_prefix" value="test_2"/>
            <param name="experiment_preset" value="custom"/>
            <param name="spin_preset" value="e"/>
            <param name="spin_preset" value="mu"/>
            <param name="interaction" value="hyperfine"/>
            <param name="hfine_index" value="1"/>
            <param name="hfine_matrix" value="[1 0 0 sin(10) (5*2) 0 10*pi 5 cos(20)]"/>
            <param name="time" value="range(0, 0.1)"/>
            <param name="y_axis" value="asymmetry"/>
            <param name="x_axis" value="time"/>
            <param name="field" value="1.0"/>
            <param name="temperature" value="1.0"/>
            <output name="out_file" file="test_2.in" ftype="txt" compare="diff"/>
        </test>
        <test expect_num_outputs="1">
            <param name="out_file_prefix" value="test_3"/>
            <param name="spin_preset" value="custom"/>
            <param name="spin" value="H"/>
            <param name="spin_preset" value="mu"/>
            <param name="spin_preset" value="e"/>
            <param name="interaction" value="hyperfine"/>
            <param name="hfine_index" value="2"/>
            <param name="hfine_matrix" value="[580 5  10 5   580 9 10  9   580]"/>
            <param name="interaction" value="hyperfine"/>
            <param name="hfine_index" value="3"/>
            <param name="hfine_matrix" value="[(300/2)  3   4*10 ], [3  15*10 6-3+2]  ,[4  5   15 ]"/>
            <param name="average_axes" value="orientation,temperature"/>
            <param name="experiment_preset" value="alc"/>
            <param name="field" value="range(1.8, 2.6, 100)"/>
            <param name="orientation_preset" value="zcw"/>
            <param name="zcw_n" value="20"/>
            <output name="out_file" file="test_3.in" ftype="txt" compare="diff"/>
        </test>
        <test expect_num_outputs="1">
            <param name="out_file_prefix" value="test_4"/>
            <param name="spin_preset" value="custom"/>
            <param name="spin" value="F"/>
            <param name="spin_preset" value="custom"/>
            <param name="spin" value="F"/>
            <param name="spin_preset" value="mu"/>
            <param name="interaction" value="dipolar"/>
            <param name="di_index" value="1"/>
            <param name="di_index_2" value="2"/>
            <param name="di_vector" value="0.9 0.9 0"/>
            <param name="interaction" value="dipolar"/>
            <param name="di_index" value="1"/>
            <param name="di_index_2" value="3"/>
            <param name="di_vector" value="-0.9 -0.9 0"/>
            <param name="interaction" value="dissipation"/>
            <param name="dis_index" value="1"/>
            <param name="dis_val" value="0.5"/>
            <param name="average_axes" value=""/>
            <param name="experiment_preset" value="custom"/>
            <param name="field" value="1.5e-2 1.0e-2 1.0e-2"/>
            <param name="field" value="0.01"/>
            <param name="intrinsic_field" value="1.6e-2 1.1e-2 1.1e-2"/>
            <param name="intrinsic_field" value="0.02"/>
            <param name="polarization_preset" value="custom"/>
            <param name="polarization" value="1 0 0"/>
            <param name="time" value="range(0,8.0,1000)"/>
            <param name="time" value="range(0,1.0)"/>
            <param name="orientation_preset" value="eulrange"/>
            <param name="eul_n" value="10"/>
            <param name="celio_enabled" value="true"/>
            <param name="celio_k" value="10"/>
            <output name="out_file" file="test_4.in" ftype="txt" compare="diff"/>
        </test>
        <test expect_num_outputs="1">
            <param name="out_file_prefix" value="test_5"/>
            <param name="spin_preset" value="mu"/>
            <param name="interaction" value="dissipation"/>
            <param name="dis_index" value="1"/>
            <param name="dis_val" value="g"/>
            <param name="experiment_preset" value="custom"/>
            <param name="field" value="1.0/muon_gyr"/>
            <param name="intrinsic_field" value="2.0/muon_gyr"/>
            <param name="fitting" value="true"/>
            <param name="var_name" value="g"/>
            <param name="min_bound" value="0.0"/>
            <param name="fitting_tolerance" value="1.0"/>
            <param name="celio_enabled" value="true"/>
            <param name="celio_k" value="10"/>
            <param name="celio_averages" value="4"/>
            <output name="out_file" file="test_5.in" ftype="txt" compare="diff"/>
        </test>
        <test expect_num_outputs="1">
            <param name="out_file_prefix" value="test_6"/>
            <param name="experiment_preset" value="zero_field"/>
            <param name="spin_preset" value="custom"/>
            <param name="spin" value="H"/>
            <param name="spin_preset" value="mu"/>
            <param name="interaction" value="zeeman"/>
            <param name="zeeman_index" value="1"/>
            <param name="zeeman_vector" value="1 0 0"/>
            <param name="zeeman_index" value="2"/>
            <param name="zeeman_vector" value="2 0 0"/>
            <param name="average_axes" value="orientation,temperature"/>
            <output name="out_file" file="test_6.in" ftype="txt" compare="diff"/>
        </test>
        <test expect_num_outputs="1">
            <param name="out_file_prefix" value="test_7"/>
            <param name="experiment_preset" value="custom"/>
            <param name="spin_preset" value="custom"/>
            <param name="spin" value="H"/>
            <param name="spin_preset" value="mu"/>
            <param name="interaction" value="zeeman"/>
            <param name="zeeman_index" value="1"/>
            <param name="zeeman_vector" value="1 0 0"/>
            <param name="zeeman_index" value="2"/>
            <param name="zeeman_vector" value="2 0 0"/>
            <param name="y_axis" value="integral"/>
            <param name="x_axis" value="field"/>
            <param name="average_axes" value="orientation,temperature"/>
            <output name="out_file" file="test_7.in" ftype="txt" compare="diff"/>
        </test>
    </tests>
    <help><![CDATA[
    Tool to create input parameter file for MuSpinSim.


    This tool creates a structured text file with keywords and values which describe the system to model for MuSpinSim.
    See MuSpinSim docs for more information https://muon-spectroscopy-computational-project.github.io/muspinsim/input/.


    MuSpinSim allows expressions and special functions to be used when defining certain keywords. This tool also allows this.
    Check the hint at the bottom of each input to see what, if any, special function or expressions can be used.


    Default expressions include the use of the operators :code:`+ - * /` and :code:`^` for exponentiation. Expressions
    should not contain whitespace. For example, use :code:`1+2` not :code:`1 + 2`.


    Default constants include:
        - :code:`pi`: ratio of a circle and its diameter
        - :code:`e`: base of the natural logarithm
        - :code:`deg`: conversion factor between radians and degrees, equivalent to 180/pi
        - :code:`inf`: infinity

    Special constants include:
        - :code:`muon_gyr`: gyromagnetic ratio of muon (135.5388 MHz/T)
        - :code:`MHz`: :code:`1/(2*muon_gyr)`


    Default functions include:
        - :code:`sin(x)`: sine
        - :code:`cos(x)`: cosine
        - :code:`tan(x)`: tangent
        - :code:`arcsin(x)`: inverse of the sine
        - :code:`arccos(x)`: inverse of the cosine
        - :code:`arctan(x)`: inverse of the tangent
        - :code:`arctan2(y, x)`: inverse of the tangent taking two arguments as (sine, cosine) to resolve the quadrant
        - :code:`exp(x)`: exponential with base e
        - :code:`log(x)`: natural logarithm
        - :code:`sqrt(x)`: square root

    Special functions include:
        - :code:`range(x, y, z)`: get z equally spaced values between x and y
        - :code:`zcw(n)`: Zaremba-Conroy-Wolfsberg helper function
        - :code:`eulrange(n)`: helper function to create regular grid of n × n × n Euler angles with appropriate weights.


    To enter vectors or matrices the following formats are accepted:
        - :code:`[[1, 2, 3], [4, 5, 6], [7, 8, 9]]`
        - :code:`1 2 3 4 5 6 7 8 9`
        - :code:`[1 2 3] [4 5 6] [7 8 9]`


    The fitting (function minimization) algorithms available are:


    Nelder-Mead
        - A direct search method.
        - 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).
        - Scipy default tolerance is :code:`1e-4`


    L-BFGS
        - Limited Memory Broyden–Fletcher–Goldfarb–Shanno algorithm.
        - A second-order Quasi-Newton optimization algorithm
        - Makes use of second-order derivative (Hessian Matrix) to converge on optimum.
        - Scipy default tolerance is :code:`1e-5`
    ]]></help>
    <citations>
        <citation type="doi">10.1093/comjnl/7.4.308</citation>
        <citation type="bibtex">
            @book{nocedal_wright_2006,
                place={New York (NY)},
                title={Numerical Optimization},
                publisher={Springer},
                author={Nocedal, Jorge and Wright, Stephen J},
                year={2006}
            }
        </citation>
        <citation type="doi">10.1103/PhysRevLett.56.2720</citation>
        <citation type="bibtex">
            @TOOL_CITATION@
        </citation>
    </citations>
</tool>