SampleToPython.cpp

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//  ************************************************************************************************
//
//  BornAgain: simulate and fit reflection and scattering
//
//! @file      Sim/Export/SampleToPython.cpp
//! @brief     Implements class SampleToPython.
//!
//! @homepage  http://www.bornagainproject.org
//! @license   GNU General Public License v3 or higher (see COPYING)
//! @copyright Forschungszentrum Jülich GmbH 2018
//! @authors   Scientific Computing Group at MLZ (see CITATION, AUTHORS)
//
//  ************************************************************************************************
 
#include "Sim/Export/SampleToPython.h"
#include "Base/Py/PyFmt.h"
#include "Base/Util/Assert.h"
#include "Base/Vector/RotMatrix.h"
#include "Param/Node/NodeUtils.h"
#include "Sample/Aggregate/Interferences.h"
#include "Sample/Aggregate/ParticleLayout.h"
#include "Sample/Interface/LayerInterface.h"
#include "Sample/Interface/LayerRoughness.h"
#include "Sample/Multilayer/Layer.h"
#include "Sample/Multilayer/MultiLayer.h"
#include "Sample/Particle/Crystal.h"
#include "Sample/Particle/MesoCrystal.h"
#include "Sample/Particle/Particle.h"
#include "Sample/Particle/ParticleComposition.h"
#include "Sample/Particle/ParticleCoreShell.h"
#include "Sample/Scattering/Rotations.h"
#include "Sim/Export/ComponentKeyHandler.h"
#include "Sim/Export/MaterialKeyHandler.h"
#include "Sim/Export/PyFmt2.h"
#include <iomanip>
#include <map>
#include <memory>
#include <set>
 
using Py::Fmt::indent;
 
static const std::map<int, char> axisChar{{0, 'X'}, {1, 'Y'}, {2, 'Z'}};
 
namespace {
 
void setRotationInformation(const IParticle* particle, std::string name, std::ostringstream& result)
{
    if (!particle->rotation())
        return;
    const RotMatrix matrix = particle->rotation()->rotMatrix();
    // Identity matrix?
    if (matrix.isIdentity())
        return;
    // Rotation around coordinate axis?
    for (int iAxis = 0; iAxis < 3; ++iAxis) {
        std::optional<double> angle = matrix.angleAroundCoordAxis(iAxis);
        if (angle) {
            result << indent() << name << "_rotation = ba.Rotation" << axisChar.at(iAxis) << "("
                   << Py::Fmt::printDegrees(angle.value()) << ")\n";
            result << indent() << name << ".setRotation(" << name << "_rotation)\n";
            return;
        }
    }
    // Generic rotation.
    auto angles = matrix.zxzEulerAngles();
    result << indent() << name << "_rotation = ba.RotationEuler("
           << Py::Fmt::printDegrees(angles[0]) << ", " << Py::Fmt::printDegrees(angles[1]) << ", "
           << Py::Fmt::printDegrees(angles[2]) << ")\n";
    result << indent() << name << ".setRotation(" << name << "_rotation)\n";
}
 
void setPositionInformation(const IParticle* particle, std::string name, std::ostringstream& result)
{
    R3 pos = particle->particlePosition();
    if (pos == R3())
        return;
 
    result << indent() << name << "_position = R3(" << Py::Fmt::printNm(pos.x()) << ", "
           << Py::Fmt::printNm(pos.y()) << ", " << Py::Fmt::printNm(pos.z()) << ")\n";
    result << indent() << name << ".setParticlePosition(" << name << "_position)\n";
}
 
} // namespace
 
//  ************************************************************************************************
//  class SampleToPython
//  ************************************************************************************************
 
std::string SampleToPython::sampleCode(const MultiLayer& sample)
{
    initLabels(sample);
    return defineGetSample();
}
 
void SampleToPython::initLabels(const MultiLayer& sample)
{
    m_objs = std::make_unique<ComponentKeyHandler>();
    m_materials = std::make_unique<MaterialKeyHandler>();
 
    for (const auto* x : sample.containedMaterials())
        m_materials->insertMaterial(x);
 
    m_objs->insertModel("sample", &sample);
    for (const auto* x : NodeUtils::AllDescendantsOfType<Layer>(sample))
        m_objs->insertModel("layer", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<LayerRoughness>(sample))
        m_objs->insertModel("roughness", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<ParticleLayout>(sample))
        m_objs->insertModel("layout", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<IFormFactor>(sample))
        m_objs->insertModel("ff", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<IInterference>(sample))
        m_objs->insertModel("iff", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<Particle>(sample))
        m_objs->insertModel("particle", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<ParticleComposition>(sample))
        m_objs->insertModel("particle", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<ParticleCoreShell>(sample))
        m_objs->insertModel("particle", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<MesoCrystal>(sample))
        m_objs->insertModel("particle", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<Lattice2D>(sample))
        m_objs->insertModel("lattice", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<Lattice3D>(sample))
        m_objs->insertModel("lattice", x);
    for (const auto* x : NodeUtils::AllDescendantsOfType<Crystal>(sample))
        m_objs->insertModel("crystal", x);
}
 
SampleToPython::SampleToPython() = default;
 
SampleToPython::~SampleToPython() = default;
 
std::string SampleToPython::defineGetSample() const
{
    return "def get_sample():\n" + defineMaterials() + defineFormFactors() + defineParticles()
           + defineCoreShellParticles() + defineParticleCompositions() + defineLattices2D()
           + defineLattices3D() + defineCrystals() + defineMesoCrystals() + defineInterferences()
           + defineParticleLayouts() + defineRoughnesses() + defineLayers() + defineMultiLayers()
           + "\n\n";
}
 
const std::map<MATERIAL_TYPES, std::string> factory_names{
    {MATERIAL_TYPES::RefractiveMaterial, "RefractiveMaterial"},
    {MATERIAL_TYPES::MaterialBySLD, "MaterialBySLD"}};
 
std::string SampleToPython::defineMaterials() const
{
    const auto themap = m_materials->materialMap();
    if (themap.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << indent() << "# Define materials\n";
    std::set<std::string> visitedMaterials;
    for (const auto& it : themap) {
        const std::string& key = it.first;
        if (visitedMaterials.find(key) != visitedMaterials.end())
            continue;
        visitedMaterials.insert(key);
        const Material* p_material = it.second;
        const auto factory_name = factory_names.find(p_material->typeID());
        if (factory_name == factory_names.cend())
            throw std::runtime_error(
                "Error in Py::Export::defineMaterials(): unknown material type");
        const complex_t& material_data = p_material->materialData();
        if (p_material->isScalarMaterial()) {
            result << indent() << m_materials->mat2key(p_material) << " = ba."
                   << factory_name->second << "(\"" << p_material->materialName() << "\", "
                   << Py::Fmt::printDouble(material_data.real()) << ", "
                   << Py::Fmt::printDouble(material_data.imag()) << ")\n";
        } else {
            R3 magnetic_field = p_material->magnetization();
            result << indent() << "magnetic_field = R3(" << magnetic_field.x() << ", "
                   << magnetic_field.y() << ", " << magnetic_field.z() << ")\n";
            result << indent() << m_materials->mat2key(p_material) << " = ba."
                   << factory_name->second << "(\"" << p_material->materialName();
            result << "\", " << Py::Fmt::printDouble(material_data.real()) << ", "
                   << Py::Fmt::printDouble(material_data.imag()) << ", "
                   << "magnetic_field)\n";
        }
    }
    return result.str();
}
 
std::string SampleToPython::defineLayers() const
{
    std::vector<const Layer*> v = m_objs->objectsOfType<Layer>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << "\n" << indent() << "# Define layers\n";
    result << std::setprecision(12);
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba.Layer(" << m_materials->mat2key(s->material());
        if (s->thickness() != 0)
            result << ", " << Py::Fmt::printNm(s->thickness());
        result << ")\n";
        if (s->numberOfSlices() != 1)
            result << indent() << key << ".setNumberOfSlices(" << s->numberOfSlices() << ")\n";
        for (const auto* layout : s->layouts())
            result << indent() << key << ".addLayout(" << m_objs->obj2key(layout) << ")\n";
    }
    return result.str();
}
 
std::string SampleToPython::defineRoughnesses() const
{
    std::vector<const LayerRoughness*> v = m_objs->objectsOfType<LayerRoughness>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define roughness\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba." << s->pythonConstructor() << "\n";
    }
    return result.str();
}
 
std::string SampleToPython::defineFormFactors() const
{
    std::vector<const IFormFactor*> formfactors = m_objs->objectsOfType<IFormFactor>();
    if (formfactors.empty())
        return "";
    std::ostringstream result;
    result << "\n" << indent() << "# Define form factors\n";
    result << std::setprecision(12);
    for (const auto* s : formfactors) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba." << s->pythonConstructor() << "\n";
    }
 
    return result.str();
}
 
std::string SampleToPython::defineInterferences() const
{
    std::vector<const IInterference*> v = m_objs->objectsOfType<IInterference>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define interference functions\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
 
        if (dynamic_cast<const InterferenceNone*>(s))
            result << indent() << key << " = ba.InterferenceNone()\n";
 
        else if (const auto* iff = dynamic_cast<const Interference1DLattice*>(s)) {
            result << indent() << key << " = ba.Interference1DLattice("
                   << Py::Fmt::printNm(iff->length()) << ", " << Py::Fmt::printDegrees(iff->xi())
                   << ")\n";
 
            const auto* pdf = NodeUtils::OnlyChildOfType<IProfile1D>(*iff);
 
            if (pdf->decayLength() != 0.0)
                result << indent() << key << "_pdf  = ba." << pdf->pythonConstructor() << "\n"
                       << indent() << key << ".setDecayFunction(" << key << "_pdf)\n";
        } else if (const auto* iff = dynamic_cast<const InterferenceRadialParaCrystal*>(s)) {
            result << indent() << key << " = ba.InterferenceRadialParaCrystal("
                   << Py::Fmt::printNm(iff->peakDistance()) << ", "
                   << Py::Fmt::printNm(iff->dampingLength()) << ")\n";
 
            if (iff->kappa() != 0.0)
                result << indent() << key << ".setKappa(" << Py::Fmt::printDouble(iff->kappa())
                       << ")\n";
 
            if (iff->domainSize() != 0.0)
                result << indent() << key << ".setDomainSize("
                       << Py::Fmt::printDouble(iff->domainSize()) << ")\n";
 
            const auto* pdf = NodeUtils::OnlyChildOfType<IProfile1D>(*iff);
 
            if (pdf->omega() != 0.0)
                result << indent() << key << "_pdf  = ba." << pdf->pythonConstructor() << "\n"
                       << indent() << key << ".setProbabilityDistribution(" << key << "_pdf)\n";
        } else if (const auto* iff = dynamic_cast<const Interference2DLattice*>(s)) {
            const auto* lattice = NodeUtils::OnlyChildOfType<Lattice2D>(*iff);
 
            result << indent() << key << " = ba.Interference2DLattice(" << m_objs->obj2key(lattice)
                   << ")\n";
 
            const auto* pdf = NodeUtils::OnlyChildOfType<IProfile2D>(*iff);
 
            result << indent() << key << "_pdf  = ba." << pdf->pythonConstructor() << "\n"
                   << indent() << key << ".setDecayFunction(" << key << "_pdf)\n";
 
            if (iff->integrationOverXi())
                result << indent() << key << ".setIntegrationOverXi(True)\n";
        } else if (const auto* iff = dynamic_cast<const InterferenceFinite2DLattice*>(s)) {
            const auto* lattice = NodeUtils::OnlyChildOfType<Lattice2D>(*iff);
 
            result << indent() << key << " = ba.InterferenceFinite2DLattice("
                   << m_objs->obj2key(lattice) << ", " << iff->numberUnitCells1() << ", "
                   << iff->numberUnitCells2() << ")\n";
 
            if (iff->integrationOverXi())
                result << indent() << key << ".setIntegrationOverXi(True)\n";
        } else if (const auto* iff = dynamic_cast<const Interference2DParaCrystal*>(s)) {
            const auto* lattice = NodeUtils::OnlyChildOfType<Lattice2D>(*iff);
            std::vector<double> domainSize = iff->domainSizes();
 
            result << indent() << key << " = ba.Interference2DParaCrystal("
                   << m_objs->obj2key(lattice) << ", " << Py::Fmt::printNm(iff->dampingLength())
                   << ", " << Py::Fmt::printNm(domainSize[0]) << ", "
                   << Py::Fmt::printNm(domainSize[1]) << ")\n";
 
            if (iff->integrationOverXi())
                result << indent() << key << ".setIntegrationOverXi(True)\n";
 
            const auto pdf_vector = NodeUtils::ChildNodesOfType<IProfile2D>(*iff);
            if (pdf_vector.size() != 2)
                continue;
            const IProfile2D* pdf = pdf_vector[0];
 
            result << indent() << key << "_pdf_1  = ba." << pdf->pythonConstructor() << "\n";
 
            pdf = pdf_vector[1];
 
            result << indent() << key << "_pdf_2  = ba." << pdf->pythonConstructor() << "\n";
            result << indent() << key << ".setProbabilityDistributions(" << key << "_pdf_1, " << key
                   << "_pdf_2)\n";
        } else if (const auto* lattice_hd = dynamic_cast<const InterferenceHardDisk*>(s)) {
            result << indent() << key << " = ba.InterferenceHardDisk("
                   << Py::Fmt::printNm(lattice_hd->radius()) << ", "
                   << Py::Fmt::printDouble(lattice_hd->density()) << ")\n";
        } else
            ASSERT(0);
 
        if (s->positionVariance() > 0.0) {
            result << indent() << key << ".setPositionVariance("
                   << Py::Fmt::printNm2(s->positionVariance()) << ")\n";
        }
    }
    return result.str();
}
 
std::string SampleToPython::defineParticleLayouts() const
{
    std::vector<const ParticleLayout*> v = m_objs->objectsOfType<ParticleLayout>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define particle layouts\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba.ParticleLayout()\n";
        const auto particles = NodeUtils::ChildNodesOfType<IParticle>(*s);
        for (const auto* particle : particles) {
            double abundance = particle->abundance();
            result << indent() << key << ".addParticle(" << m_objs->obj2key(particle) << ", "
                   << Py::Fmt::printDouble(abundance) << ")\n";
        }
        if (const auto* iff = NodeUtils::OnlyChildOfType<IInterference>(*s))
            result << indent() << key << ".setInterference(" << m_objs->obj2key(iff) << ")\n";
        result << indent() << key << ".setWeight(" << s->weight() << ")\n";
        result << indent() << key << ".setTotalParticleSurfaceDensity("
               << s->totalParticleSurfaceDensity() << ")\n";
    }
    return result.str();
}
 
std::string SampleToPython::defineParticles() const
{
    std::vector<const Particle*> v = m_objs->objectsOfType<Particle>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define particles\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        const auto* ff = NodeUtils::OnlyChildOfType<IFormFactor>(*s);
        ASSERT(ff);
        result << indent() << key << " = ba.Particle(" << m_materials->mat2key(s->material())
               << ", " << m_objs->obj2key(ff) << ")\n";
        setRotationInformation(s, key, result);
        setPositionInformation(s, key, result);
    }
    return result.str();
}
 
std::string SampleToPython::defineCoreShellParticles() const
{
    std::vector<const ParticleCoreShell*> v = m_objs->objectsOfType<ParticleCoreShell>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define core shell particles\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba.ParticleCoreShell("
               << m_objs->obj2key(s->shellParticle()) << ", " << m_objs->obj2key(s->coreParticle())
               << ")\n";
        setRotationInformation(s, key, result);
        setPositionInformation(s, key, result);
    }
    return result.str();
}
 
std::string SampleToPython::defineParticleCompositions() const
{
    std::vector<const ParticleComposition*> v = m_objs->objectsOfType<ParticleComposition>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define composition of particles at specific positions\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba.ParticleComposition()\n";
        const auto particle_list = NodeUtils::ChildNodesOfType<IParticle>(*s);
        for (const auto* particle : particle_list)
            result << indent() << key << ".addParticle(" << m_objs->obj2key(particle) << ")\n";
        setRotationInformation(s, key, result);
        setPositionInformation(s, key, result);
    }
    return result.str();
}
 
std::string SampleToPython::defineMesoCrystals() const
{
    std::vector<const MesoCrystal*> v = m_objs->objectsOfType<MesoCrystal>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define mesocrystals\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        const auto* crystal = NodeUtils::OnlyChildOfType<Crystal>(*s);
        const auto* outer_shape = NodeUtils::OnlyChildOfType<IFormFactor>(*s);
        if (!crystal || !outer_shape)
            continue;
        result << indent() << key << " = ba.MesoCrystal(";
        result << m_objs->obj2key(crystal) << ", ";
        result << m_objs->obj2key(outer_shape) << ")\n";
        setRotationInformation(s, key, result);
        setPositionInformation(s, key, result);
    }
    return result.str();
}
 
std::string SampleToPython::defineLattices2D() const
{
    std::vector<const Lattice2D*> v = m_objs->objectsOfType<Lattice2D>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define 2D lattices\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba.BasicLattice2D(\n";
        result << indent() << indent() << Py::Fmt::printNm(s->length1()) << ", "
               << Py::Fmt::printNm(s->length2()) << ", " << Py::Fmt::printDegrees(s->latticeAngle())
               << ", " << Py::Fmt::printDegrees(s->rotationAngle()) << ")\n";
    }
    return result.str();
}
 
std::string SampleToPython::defineLattices3D() const
{
    std::vector<const Lattice3D*> v = m_objs->objectsOfType<Lattice3D>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define 3D lattices\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        R3 bas_a = s->basisVectorA();
        R3 bas_b = s->basisVectorB();
        R3 bas_c = s->basisVectorC();
        result << indent() << key << " = ba.Lattice3D(\n";
        result << indent() << indent() << "ba.R3(" << Py::Fmt::printNm(bas_a.x()) << ", "
               << Py::Fmt::printNm(bas_a.y()) << ", " << Py::Fmt::printNm(bas_a.z()) << "),\n";
        result << indent() << indent() << "ba.R3(" << Py::Fmt::printNm(bas_b.x()) << ", "
               << Py::Fmt::printNm(bas_b.y()) << ", " << Py::Fmt::printNm(bas_b.z()) << "),\n";
        result << indent() << indent() << "ba.R3(" << Py::Fmt::printNm(bas_c.x()) << ", "
               << Py::Fmt::printNm(bas_c.y()) << ", " << Py::Fmt::printNm(bas_c.z()) << "))\n";
    }
    return result.str();
}
 
std::string SampleToPython::defineCrystals() const
{
    std::vector<const Crystal*> v = m_objs->objectsOfType<Crystal>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    result << "\n" << indent() << "# Define crystals\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        const auto* lattice = NodeUtils::OnlyChildOfType<Lattice3D>(*s);
        const auto* basis = NodeUtils::OnlyChildOfType<IParticle>(*s);
        if (!lattice || !basis)
            continue;
        result << indent() << key << " = ba.Crystal(";
        result << m_objs->obj2key(basis) << ", ";
        result << m_objs->obj2key(lattice) << ")\n";
    }
    return result.str();
}
 
std::string SampleToPython::defineMultiLayers() const
{
    std::vector<const MultiLayer*> v = m_objs->objectsOfType<MultiLayer>();
    if (v.empty())
        return "";
    std::ostringstream result;
    result << std::setprecision(12);
    ASSERT(v.size() == 1); // as long as there is exactly one sample, we shall use the singular
    result << "\n" << indent() << "# Define sample\n";
    for (const auto* s : v) {
        const std::string& key = m_objs->obj2key(s);
        result << indent() << key << " = ba.MultiLayer()\n";
        double ccl = s->crossCorrLength();
        if (ccl > 0.0)
            result << indent() << key << ".setCrossCorrLength(" << ccl << ")\n";
        auto external_field = s->externalField();
        if (external_field.mag() > 0.0) {
            std::string field_name = key + "_external_field";
            result << indent() << field_name << " = R3("
                   << Py::Fmt::printScientificDouble(external_field.x()) << ", "
                   << Py::Fmt::printScientificDouble(external_field.y()) << ", "
                   << Py::Fmt::printScientificDouble(external_field.z()) << ")\n";
            result << indent() << key << ".setExternalField(" << field_name << ")\n";
        }
        size_t numberOfLayers = s->numberOfLayers();
        if (numberOfLayers) {
            result << indent() << key << ".addLayer(" << m_objs->obj2key(s->layer(0)) << ")\n";
 
            size_t i_layer = 1;
            while (i_layer != numberOfLayers) {
                const LayerInterface* layerInterface = s->layerInterface(i_layer - 1);
                if (const LayerRoughness* rough = layerInterface->roughness())
                    result << indent() << key << ".addLayerWithTopRoughness("
                           << m_objs->obj2key(s->layer(i_layer)) << ", " << m_objs->obj2key(rough)
                           << ")\n";
                else
                    result << indent() << key << ".addLayer(" << m_objs->obj2key(s->layer(i_layer))
                           << ")\n";
                i_layer++;
            }
        }
        result << "\n" << indent() << "return " << key << "\n";
    }
    return result.str();
}