<macros>
    <xml name="celio_options">
        <section name="celio_params" expanded="true" title="Celio's Method" help="Celio's method is an approximate method for computing asymmetry values over a range of times. It is particularly useful for larger systems of higher spins.">
            <conditional name="celio_options">
                <param name="celio_enabled" type="select" label="Use Celio's method?" display="radio">
                    <option value="true">Yes</option>
                    <option selected="true" value="">No</option>
                </param>
                <when value="true">
                    <param name="celio_k" type="integer" value="10" label="Trotter number, k" help="Value used in the Trotter expansion."/>
                    <param name="celio_averages" type="integer" optional="true" label="Number of averages" help="When given a value MuSpinSim will randomise initial polarisation states and perform an average. This method is more approximate but much faster and reduces memory usage. It will also assume T-&gt;inf and zero magnetic fields. See the MuSpinSim docs for more info."/>
                </when>
                <when value=""/>
            </conditional>
        </section>
    </xml>
    <xml name="times">
        <repeat name="times" title="Time" help="A time or range of times (μs)">
            <param name="time" type="text" label="Time" help="Either a single time value or `range` function - allows default expressions, default constants, and special 'range()' function (see help section)" optional="true" value="range(0, 10, 101)"/>
        </repeat>
    </xml>
    <xml name="fields">
        <repeat name="fields" title="Fields" help="Magnetic fields">
            <param name="field" type="text" value="0" label="Field" optional="true" help="Optional, (default is 0). Accepts 1X3 vector, or scalar value. Scalar value means field is assumed to be aligned with z axis. Allows default expressions, constants and functions, plus MHz, muon_gyr constants and special 'range()' function (see help section)"/>
        </repeat>
    </xml>
    <xml name="intrinsic_fields">
        <repeat name="intrinsic_fields" title="Intrinsic Fields" help="Intrinsic magnetic fields (these are unaffected by rotations when using angular averaging via the orientations parameter).">
            <param name="intrinsic_field" type="text" value="0" label="Intrinsic Field (T)" optional="true" help="Optional, (default is 0). Accepts 1X3 vector, or scalar value. Scalar value means field is assumed to be aligned with z axis. Allows default expressions, constants and functions, plus MHz, muon_gyr constants and special 'range()' function (see help section)"/>
        </repeat>
    </xml>
    <xml name="polarizations">
        <repeat name="polarizations" title="Polarizations" help="The direction along which the muon should be polarized when starting, as well as the one in which it will be measured. Each entry will generate a separate calculation when MuSpinSim is run">
            <conditional name="polarization_options">
                <param name="polarization_preset" value="custom" type="select" display="radio" label="Polarization" help="transverse: along x-axis, longitudinal: along z-axis, custom: define vector">
                    <option value="longitudinal">longitudinal</option>
                    <option value="transverse">transverse</option>
                    <option selected="true" value="custom">custom</option>
                </param>
                <when value="custom">
                    <param name="polarization" type="text" value="" label="Enter custom vector for polarization" help="Accepts 1X3 vector. Allows default expressions, constants and functions (see help section)"/>
                </when>
                <when value="longitudinal"/>
                <when value="transverse"/>
            </conditional>
        </repeat>
    </xml>
    <xml name="orientations">
        <repeat name="orientations" title="Orientations" help="Orientations to use for crystallites - (define powder averages)">
            <conditional name="orientation_options">
                <param name="orientation_preset" type="select" display="radio" label="Orientation" optional="false" help="Polar angles: Define two polar angles θ and ϕ, defining only the direction of the z-axis (recommended for powder averages). Euler angles: Define 3 Euler angles defining a new frame, convention used is ZYZ by default. Euler angles with weight: define 3 Euler angles and a weight (will be normalized automatically). Euler angles helper function: eulrange(n). Zaremba-Conroy-Wolfsberg helper function: zcw(n)">
                    <option value="2_polar">Polar angles</option>
                    <option value="3_euler">Euler angles</option>
                    <option value="4_euler">Euler angles with weight</option>
                    <option value="eulrange">Euler angles helper function (eulrange(n))</option>
                    <option selected="true" value="zcw">Zaremba-Conroy-Wolfsberg helper function (zcw(n))</option>
                </param>
                <when value="eulrange">
                    <param name="eul_n" type="text" value="0" label="n" help="Value for n for eulrange(n) - allows default expressions, constants and functions. WARNING: large values are more computationally expensive."/>
                </when>
                <when value="zcw">
                    <param name="zcw_n" type="text" value="0" label="n" help="Value for n for zcw(n) - Allows default expressions, constants and functions. WARNING: large values are more computationally expensive."/>
                </when>
                <when value="2_polar">
                    <param name="theta" type="text" value="" label="θ (theta/inclination) angle" help="All polar angle entries allow default expressions, constants and functions"/>
                    <param name="phi" type="text" value="" label="ϕ (phi/azimuth) angle" help="All polar angle entries allow default expressions, constants and functions"/>
                </when>
                <when value="3_euler">
                    <param name="eul_1" type="text" value="" label="Euler angle 1" help="All Euler angle entries allow default expressions, constants and functions"/>
                    <param name="eul_2" type="text" value="" label="Euler angle 2" help="All Euler angle entries allow default expressions, constants and functions"/>
                    <param name="eul_3" type="text" value="" label="Euler angle 3" help="All Euler angle entries allow default expressions, constants and functions"/>
                </when>
                <when value="4_euler">
                    <param name="eul_1" type="text" value="" label="Euler angle 1" help="All Euler angle entries allow default expressions and constants"/>
                    <param name="eul_2" type="text" value="" label="Euler angle 2" help="All Euler angle entries allow default expressions and constants"/>
                    <param name="eul_3" type="text" value="" label="Euler angle 3" help="All Euler angle entries allow default expressions and constants"/>
                    <param name="weight" type="float" value="0" label="Weight" help="Allows only floating point value, weights will automatically be normalised"/>
                </when>
            </conditional>
        </repeat>
    </xml>
    <xml name="euler_convention">
        <param name="euler_convention" type="select" display="radio" label="Euler Convention" help="Euler angle convention to use for orientation definitions (ignored if Euler angles not defined)">
            <option selected="true" value="zyz">ZYZ</option>
            <option value="zxz">ZXZ</option>
        </param>
    </xml>
    <xml name="temperatures">
        <repeat name="temperatures" title="Temperature" help="Temperature or range of temperatures (K)">
            <param name="temperature" type="text" help="Either single value or 'range()' function - allows default expressions, default constants, and special 'range()' function (see help section). Warning: both density matrices and dissipative couplings for finite temperatures are only calculated approximatively, see MuSpinSim docs." optional="true" value="inf"/>
        </repeat>
    </xml>
    <xml name="average_axis_options_no_time">
        <param name="average_axes" type="select" display="checkboxes" multiple="true" optional="true" value="orientation" label="Average axes" help="Keywords that should have an average carried out over them. Each keyword ticked should have a range specified. Keywords not ticked or set as X axis, but which have a range set, will generate separate calculations for each value in the range when muspinsim is run.">
            <option value="field">field</option>
            <option value="intrinsic_field">intrinsic_field</option>
            <option value="temperature">temperature</option>
            <option value="polarization">polarization</option>
            <option selected="true" value="orientation">orientation</option>
        </param>
    </xml>
    <xml name="average_axis_options_no_field">
        <param name="average_axes" type="select" display="checkboxes" multiple="true" optional="true" value="orientation" label="Average axes" help="Keywords that should have an average carried out over them. Each keyword ticked should have a range specified. Keywords not ticked or set as X axis, but which have a range set, will generate separate calculations for each value in the range when muspinsim is run.">
            <option value="time">time</option>
            <option value="intrinsic_field">intrinsic_field</option>
            <option value="temperature">temperature</option>
            <option value="polarization">polarization</option>
            <option selected="true" value="orientation">orientation</option>
        </param>
    </xml>
    <xml name="restricted_axes_options">
        <param name="average_axes" type="select" display="checkboxes" multiple="true" optional="true" value="orientation" label="Average axes" help="Keywords that should have an average carried out over them. Each keyword ticked should have a range specified. Keywords not ticked or set as X axis, but which have a range set, will generate separate calculations for each value in the range when MuSpinSim is run.">
            <option selected="true" value="orientation">orientation</option>
            <option value="temperature">temperature</option>
        </param>
    </xml>
    <xml name="axes_options">
        <conditional name="axes_options">
            <param name="y_axis" type="select" value="asymmetry" display="radio" label="Y axis" help="Range to use as y axis for output file(s). Asymmetry: use muon's polarization. Integral: use muon's polarization integral over time.">
                <option selected="true" value="asymmetry">asymmetry</option>
                <option value="integral">integral</option>
            </param>
            <when value="asymmetry">
                <conditional name="x_axis_options">
                    <param name="x_axis" type="select" value="time" display="radio" label="X axis" help="Range to use as X axis for output file(s)">
                        <option selected="true" value="time">time</option>
                        <option value="field">field</option>
                    </param>
                    <when value="time">
                        <expand macro="average_axis_options_no_time"/>
                    </when>
                    <when value="field">
                        <expand macro="average_axis_options_no_field"/>
                    </when>
                </conditional>
            </when>
            <when value="integral">
                <param name="x_axis" type="select" value="time" display="radio" label="X axis" help="Range to use as X axis for output file(s)">
                    <option selected="true" value="field">field</option>
                </param>
                <expand macro="average_axis_options_no_field"/>
            </when>
        </conditional>
    </xml>
    <xml name="spin_options">
        <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>
    </xml>
    <xml name="additional_spin_options">
        <repeat name="spins" title="Additional spins to simulate" min="0" help="Specify any additional spins to be used in the system other than those generated from the structure file.">
            <conditional name="spin_options">
                <param name="spin_preset" type="select" value="e" label="Species" help="Select 'custom' to define own">
                    <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="e"/>
            </conditional>
        </repeat>
    </xml>
    <xml name="interaction_options">
        <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>
    </xml>
    <xml name="generator_options">
        <param name="structure_file" type="data" format="cif,cell,magres,extxyz" label="File containing the structure (.cif, .cell, .magres or .extxyz)"/>
        <param name="number_closest" type="integer" value="4" label="Number of closest nuclei" help="Number of closest nuclei to the muon which should included in the generated file"/>
        <param name="dipolar" type="boolean" checked="true" truevalue="--dipolar" falsevalue="" label="Include dipole interactions?"/>
        <param name="quadrupolar" type="boolean" checked="false" truevalue="--quadrupolar" falsevalue="" label="Include quadrupole interactions?" help="Requires a Magres input file with EFG tensors calculated via CASTEP."/>
        <param name="include_interatomic" type="boolean" checked="false" truevalue="--include_interatomic" falsevalue="" label="Include interatomic interactions?" help="Whether to include interactions between selected nuclei which don't involve the muon."/>
        <repeat name="ignored_symbols" title="Ignored symbols" min="0" help="Specify symbols that should be ignored e.g. if they have zero spin">
            <param type="text" name="ignored_symbol" label="Ignored symbol">
                <validator type="regex" message="Input should only contain letters">^[a-zA-Z]+$</validator>
            </param>
        </repeat>
        <param name="muon_symbol" type="text" value="H" label="Muon Symbol" help="Symbol representing the muon in the given structure file."/>
    </xml>
</macros>