xcoll 0.5.12__py3-none-any.whl → 0.6.1__py3-none-any.whl

xcoll/scattering_routines/geant4/collimasim/src/collimasim/BDSXtrackInterface.hh

@@ -1,118 +0,0 @@
-#include "BDSBunchSixTrackLink.hh"
-#include "BDSException.hh"
-#include "BDSIMLink.hh"
-#include "BDSIonDefinition.hh"
-#include "BDSParticleCoordsFull.hh"
-#include "BDSParticleDefinition.hh"
-#include "BDSPhysicsUtilities.hh"
-
-#include "G4Electron.hh"
-#include "G4GenericIon.hh"
-#include "G4IonTable.hh"
-#include "G4ParticleDefinition.hh"
-#include "G4ParticleTable.hh"
-#include "G4Types.hh"
-
-#include "CLHEP/Units/PhysicalConstants.h"
-#include "CLHEP/Units/SystemOfUnits.h"
-
-#include <algorithm>
-#include <cmath>
-#include <iostream>
-#include <set>
-#include <string>
-#include <vector>
-
-#include <pybind11/pybind11.h>
-#include <pybind11/numpy.h>
-
-namespace py = pybind11;
-
-// The struct is only used for inactive particle coodrinates for now
-struct XtrackCoordinates{
-    double x;
-    double y;
-    double px;
-    double py;
-    double zeta;
-    double delta;
-    double chi;
-    double charge_ratio;
-    double s;
-    int64_t pdgid;
-    int64_t trackid;
-    int64_t state;
-    int64_t at_element;
-    int64_t at_turn;
-};
-
-BDSParticleDefinition* PrepareBDSParticleDefition(long long int pdgIDIn, double momentumIn, 
-                                                  double kineticEnergyIn, double ionChargeIn);
-
-/// TODO: make a base class for the interface classes as there is a lot of shared functionality
-class XtrackInterface
-{
-public:
-    XtrackInterface() = delete;  // No default constructor
-
-    XtrackInterface(const std::string&  bdsimConfigFile,
-                    long long int       referencePdgIdIn,
-                    double              referenceEkIn,
-                    double              relativeEnergyCutIn,
-                    int                 seedIn,
-                    int                 referenceIonChargeIn=0,
-                    bool                batchMode=true);
-
-    virtual ~XtrackInterface();
-
-    void addCollimator(const  std::string&   name,
-                       const  std::string&   material,
-                       double lengthIn,
-                       double apertureLeftIn,
-                       double apertureRightIn,
-                       double rotationIn,
-                       double xOffsetIn,
-                       double yOffsetIn,
-                       double jawTiltLeft,
-                       double jawTiltRight,
-                       int    side);
-
-    void addParticles(const py::list& coordinates);
-
-    // This is not exposed to python
-    void addParticle(double xIn,
-                     double yIn,
-                     double pxIn,
-                     double pyIn,
-                     double ctIn,
-                     double deltapIn,
-                     double chiIn,
-                     double chargeRatioIn,
-                     double sIn,
-                     int64_t pdgIDIn,
-                     int64_t trackidIn);
-
-    void collimate();
-    void clearData();
-    void selectCollimator(const std::string& name);
-
-    double getReferenceMass() { return refParticleDefinition->Mass() / CLHEP::GeV; }
-
-    py::dict collimateReturn(const py::list& coordinates);
-
-private:
-    BDSIMLink* bds = nullptr;
-    BDSBunchSixTrackLink* stp = nullptr;
-    std::vector<char *> argv;
-
-    std::vector<bool> particleActiveState;
-    std::vector<XtrackCoordinates*> xtrackParticles;
-
-    BDSParticleDefinition* refParticleDefinition = nullptr;
-
-    std::string currentCollimatorName;
-
-    int64_t maxParticleID=0;
-    double relativeEnergyCut=0.0;
-    int seed=0;
-};

xcoll/scattering_routines/geant4/collimasim/src/collimasim/__init__.py

@@ -1,8 +0,0 @@
-from .g4interface import PyATInterface, XtrackInterface
-
-try:
-    import xtrack
-except ModuleNotFoundError:
-    print("Xtrack not installed, will not import related features")
-else:
-    from .xtrack_collimator import Geant4CollimationManager, Geant4Collimator

xcoll/scattering_routines/geant4/collimasim/src/collimasim/bindings.cpp

@@ -1,63 +0,0 @@
-#include <pybind11/pybind11.h>
-#include <pybind11/iostream.h>
-
-#include "BDSPyATInterface.hh"
-#include "BDSXtrackInterface.hh"
-
-#define STRINGIFY(x) #x
-#define MACRO_STRINGIFY(x) STRINGIFY(x)
-
-namespace py = pybind11;
-using namespace pybind11::literals;
-
-PYBIND11_MODULE(g4interface, m) {
-  m.doc() = R"pbdoc(Python interface to BDSIM (Geant4). The main purpose of the interface is to enable collimation studies, including particle-matter interaction in collimators, for pure particle tracking codes.)pbdoc";
-
-  py::class_<PyATInterface>(m, "PyATInterface")
-            .def(py::init<const std::string&, int, double, double, int, bool>(),
-                    "bdsimConfigFile"_a, "referencePdgId"_a, "referenceEk"_a,
-                    "relativeEnergyCut"_a, "seed"_a, "batchMode"_a=true)
-            .def("addCollimator", &PyATInterface::addCollimator,
-                 "name"_a, "material"_a, "length"_a, "aperture"_a, "rotation"_a,
-                 "xOffset"_a, "yOffset"_a,  "jawTiltLeft"_a, "jawTiltRight"_a, "side"_a,
-                 py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
-            .def("addParticle",
-                 static_cast<void (PyATInterface::*)(const py::array_t<double>&)>(&PyATInterface::addParticle),
-                 "coordinate_array"_a)
-            .def("collimate", &PyATInterface::collimate,
-                 py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
-            .def("selectCollimator", &PyATInterface::selectCollimator, "collimatorName"_a)
-            .def("collimateReturn", &PyATInterface::collimateReturn,
-                 py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
-            .def("GetEnergyDifferential", &PyATInterface::GetEnergyDifferential)
-            .def("clearData", &PyATInterface::clearData);
-
-  py::class_<XtrackInterface>(m, "XtrackInterface")
-            .def(py::init<const std::string&, int, double, double, int, int, bool>(),
-                 "bdsimConfigFile"_a, "referencePdgId"_a, "referenceEk"_a,
-                 "relativeEnergyCut"_a, "seed"_a, "referenceIonCharge"_a=0,"batchMode"_a=true,
-                 py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
-            .def("addCollimator", &XtrackInterface::addCollimator,
-                 "name"_a, "material"_a, "length"_a, "apertureLeft"_a, "apertureRight"_a, "rotation"_a,
-                 "xOffset"_a, "yOffset"_a, "jawTiltLeft"_a, "jawTiltRight"_a, "side"_a,
-                 py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
-            /// The cast here to disambiguate overloaded methods. The other versions of
-            /// addParticles were removed, but keep the cast for reference for now.
-            .def("addParticles", static_cast<void (XtrackInterface::*)
-            (const py::list& coordinates)>(&XtrackInterface::addParticles), "coordinates"_a)
-            /// The C++ ostream and estream are redirected to the Python streams
-            /// so all io can be handled on the Python side
-            .def("collimate", &XtrackInterface::collimate,
-                 py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
-            .def("selectCollimator", &XtrackInterface::selectCollimator, "collimatorName"_a)
-            .def("collimateReturn", &XtrackInterface::collimateReturn,
-                 py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
-            .def("clearData", &XtrackInterface::clearData)
-            .def("getReferenceMass", &XtrackInterface::getReferenceMass);
-
-#ifdef VERSION_INFO
-  m.attr("__version__") = MACRO_STRINGIFY(VERSION_INFO);
-#else
-  m.attr("__version__") = "dev";
-#endif
-}

xcoll/scattering_routines/geant4/collimasim/src/collimasim/pyCollimatorPass.py

@@ -1,142 +0,0 @@
-import numpy
-
-import collimasim
-
-'''
-This is a specialised pass method that performs a full simulation of physical
-interactions in collimators using Geant4. The interface to BDSIM (Geant4) is
-provided by the collimasim package.
-
-The interface must be initialised first, with a list of parameters and a file
-containing the collimator specification. All collimators that will be used
-must be provided in the collimator file and are accessed by name. Currently,
-collimators are limited to block jaw collimators, and the geometry model is
-built automatically.
-
-The passmethods contains a function trackFunction(), used for tracking by pyat,
-and has to be in the python path or in at.integrators
-
-The element creation is as follows:
-
-collimator = elements.Element('MyColl', 1.0, PassMethod='pyCollimatorPass')
-
-To be noted:
-The name of a collimator using the pyCollimatorPass method must match a
-collimator defined during initialisation. For collimators where a physical
-interaction simulation is not required, please specify a different pass method,
-e.g. drift.
-'''
-
-bdsimlink = None # Keep this as a global variable for now
-
-def load_collgaps(collgaps_file):
-    coll_dict = {}
-
-    coll_data = numpy.genfromtxt(collgaps_file, dtype=None, encoding=None, comments='#')
-
-    for coll in coll_data:
-        name = coll[1].lower()
-        one_coll = {}
-
-        one_coll["material"] = coll[6]
-        one_coll["length"] = float(coll[7])
-        one_coll["angle"] = float(coll[2])
-        one_coll["halfgap"] = float(coll[5])
-        # The collgaps do not specify the offsets
-        # or if a collimator is one-sided
-        # TODO: add the closed orbit at the collimator
-        one_coll["xoffs"] = 0
-        one_coll["yoffs"] = 0
-        one_coll["side"] = 0 # 0 is two sided
-
-        coll_dict[name] = one_coll
-
-    return coll_dict
-
-
-def initialise(bdsim_config_file, collimator_info, reference_pdg_id,
-               reference_Ek, relative_energy_cut, seed):
-
-    global bdsimlink
-
-    # Initialise a code interface
-    if bdsimlink is not None:
-        return
-
-    bdsimlink = collimasim.PyATInterface(bdsimConfigFile=bdsim_config_file,
-                                         referencePdgId=reference_pdg_id,
-                                         referenceEk=reference_Ek,
-                                         relativeEnergyCut=relative_energy_cut,
-                                         seed=seed, batchMode=True)
-
-    if isinstance(collimator_info, dict):
-        collimators = collimator_info
-    else:
-        collimators = load_collgaps(collimator_info)
-
-    for name in collimators:
-        cdict = collimators[name]
-        material = cdict["material"]
-        length = cdict["length"]
-        angle = cdict["angle"]
-        halfgap = cdict["halfgap"]
-        xoffs = cdict["xoffs"]
-        yoffs = cdict["yoffs"]
-        side = cdict["side"]
-
-        bdsimlink.addCollimator(name, material, length, aperture=halfgap*2,
-                                rotation=angle, xOffset=xoffs, yOffset=yoffs,
-                                jawTiltLeft=0.0, jawTiltRight=0.0,
-                                side=side)
-
-
-def process_particles(collimator_name):
-    # MAD-X convention uses . in the names, while pyAT convention uses _
-    # Provide handling for MAD-X name to avoid trivial issues
-    try:
-        bdsimlink.selectCollimator(collimator_name)
-    except RuntimeError:
-        try:
-            collimator_name_madx = collimator_name.replace("_", ".").lower()
-            bdsimlink.selectCollimator(collimator_name_madx)
-        except RuntimeError:
-            raise ValueError(f"No collimator {collimator_name} (or "
-                             f"{collimator_name_madx} defined)")
-
-    print(f"Processing collimator: {collimator_name}")
-    # Perform the Geant4 simulation
-    bdsimlink.collimate()
-
-    # Collect the surviving particles - a 1D array with n * 6 elements
-    arr_out = bdsimlink.collimateReturn()
-
-    return arr_out
-
-
-def trackFunction(rin,elem=None):
-    if bdsimlink is None:
-        raise ValueError("The Geant4 interface is not initialised. Call"
-                         " pyCollimatorPass.initialise(...) before tracking")
-
-    bdsimlink.clearData() # Clear the old data
-
-    name = elem.FamName
-    # rin is a (6,n) array
-    for rtmp in numpy.atleast_2d(rin.T):
-        if hasattr(elem,'T1'): rtmp += elem.T1
-        if hasattr(elem,'R1'): rtmp[:] = numpy.dot(elem.R1,rtmp)
-        bdsimlink.addParticle(rtmp)
-
-    rout = process_particles(name)
-
-    # The returned array may be longer than the original
-    # due to secondary particles. Access by index and only
-    # change only the primary coordinates
-    for i in range(len(rin.T)):
-        part = rout.T[i, :]
-        if hasattr(elem,'R2'): part[:] = numpy.dot(elem.R2, part)
-        if hasattr(elem,'T2'): part += elem.T2
-
-        rin.T[i, :] = part
-
-    #return rin # This return value doesn't seem to be used by pyAT