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Webdoc issues

  • Code in multiple blocks is deprecated, e.g. kvector_t -> !1462 (merged)

Observations by pages (some problems may have already been fixed):

sudo make install <-- DO NOT DO THIS

installation paths <-- no installation anymore

$ cmake -DCMAKE_INSTALL_PREFIX=<install_dir> ..
$ cmake -DCMAKE_PREFIX_PATH=/opt/local -DCMAKE_INSTALL_PREFIX=<install_dir> ..

Installing the framework <-- no installation anymore

Drag-and-drop interface description:

A graphical sample editor allows users to assemble multilayer models by drag-and-drop. Model components like embedded particles or inter-particle correlation functions are represented by boxes that are connected by flexible lines to their parent components.

Installing the Python package <-- mv to Installation page?

Then read on to understand some example scripts line by line, and to discover further functionality <-- The link should refer to https://bornagainproject.org/git-main/py/start/syntax/

No such blocks in code:

def get_sample():
    from bornagain import std_samples
    return std_samples.alternating_layers()
def get_simulation(sample, scan_size=500):
    from bornagain import std_simulations
    return std_simulations.specular(sample, scan_size)

ba_plot.run_and_plot(simulation)

The function run_and_plot is implemented in the module ba_plot. <-- Wrong function name, broken link

AlternatingLayers1.py from the preceding pages <--- broken link

Instead of the shorthand calls to modules std_samples and std_simulations <---- ???

The function MaterialBySLD instantiates an object of type Material the function Layer an object of type Layer. <--- of type material, not layer

get_simulation(sample, scan_size=500) is a function with one required argument (sample) and one optional keyword argument (scan_size). If the function is called with only one argument, then scan_size is assigned the default value 500. <-- scan size is passed separately

angstrom and deg are numeric constants. They are used to convert physical quantities to internal units nanometer and radian. <-- angstrom, not radian

I suggest to merge Understand the syntax and Modify the script pages.

Deprecated code

    qzs = np.linspace(0.01, 1.0, scan_size)  # qz-values
    scan = ba.QSpecScan(qzs)
    simulation = ba.SpecularSimulation()
    simulation.setScan(scan)

Deprecated block

    qzs = np.linspace(0.01, 1.0, scan_size)  # qz-values
    dq = 0.03 * qzs
    n_sig = 2.0
    n_samples = 25

    distr = ba.RangedDistributionGaussian(n_samples, n_sig)

    scan = ba.QSpecScan(qzs)
    scan.setAbsoluteQResolution(distr, dq)

    simulation = ba.SpecularSimulation()
    simulation.setScan(scan)

Deprecated distribution names

Gate: RangedDistributionGate(n_samples, sigma_factor, min, max)
Lorentz: RangedDistributionLorentz(n_samples, hwhm_factor, min, max)
Gaussian: RangedDistributionGaussian(n_samples, sigma_factor, min, max)
LogNormal: RangedDistributionLogNormal(n_samples, sigma_factor, min, max)
Cosine: RangedDistributionCosine(n_samples, sigma_factor, min, max)

Suggestion: rename page to "GISAS in Born Approximation". "No reflection" can be misunderstood.

deprecated syntax

simulation.getOptions().setIncludeSpecular(True)

deprecated variable name

multiLayer = ba.MultiLayer()
multiLayer.addLayer(solvent_layer)

https://bornagainproject.org/git-main/py/sample/avge/half-spheres-in-average-top-layer/

deprecated syntax simulation.getOptions().setUseAvgMaterials(True)

Faked experimenta data <-- typo

Faked experimental data have been generated by the script devtools/fakeData/fake-gisas1.py. <-- broken link

Lines 55, 56, 57 <-- rm references to exact lines of code

at line 42 <-- rm references to exact lines of code

At lines 171-145 <-- rm references to exact lines of code

deprecated syntax?

data = ba.IntensityDataIOFactory.readIntensityData("experimental_data.int.gz").array()

Edited by Wuttke, Joachim