Merge branch 'master' into add-ID_sympletic

Author: Gabrielrezende-asc

include/trackcpp/accelerator.h

@@ -34,12 +34,15 @@ class Accelerator {
   int                     harmonic_number = 0;
   std::vector<Element>    lattice;
   std::string             lattice_version = "";
+  mutable std::vector<unsigned int> time_aware_indices;
+  mutable std::vector<double> time_aware_dl_kicks;
 
   bool operator==(const Accelerator& o) const;
   bool operator!=(const Accelerator& o) const { return !(*this == o); };
   bool isequal(const Accelerator& a) const { return *this == a; } // necessary for python_package
   double get_length() const;
   friend std::ostream& operator<< (std::ostream &out, const Accelerator& a);
+  void update_time_aware_info(void) const;
 };
 
 #endif

include/trackcpp/auxiliary.h

@@ -23,6 +23,7 @@
 #include <iostream>
 #include <cmath>
 #include <random>
+#include <algorithm>
 
 class PassMethodsClass {
 public:
@@ -39,6 +40,7 @@ class PassMethodsClass {
     static const int pm_drift_g2l_pass                 = 10;
     static const int pm_field3d_pass                   = 11;
     static const int pm_nr_pms                         = 12;  // counter for number of passmethods
+    static const std::vector<int> time_aware_passmethods;
     PassMethodsClass() {
         passmethods.push_back("identity_pass");
         passmethods.push_back("drift_pass");
@@ -55,6 +57,9 @@ class PassMethodsClass {
     }
     int size() const { return passmethods.size(); }
     std::string operator[](const int i) const { return passmethods[i]; }
+    bool is_time_aware_pm(const int i) const {
+        return std::find(time_aware_passmethods.begin(), time_aware_passmethods.end(), i) != time_aware_passmethods.end();
+    };
 private:
     std::vector<std::string> passmethods;
 };

include/trackcpp/passmethods.hpp

@@ -33,6 +33,7 @@
 #include "linalg.h"
 #include "field3d.hpp"
 #include <cmath>
+#include <algorithm>
 
 template <typename T> inline T SQR(const T& X) { return X*X; }
 template <typename T> inline T POW3(const T& X) { return X*X*X; }
@@ -518,4 +519,17 @@ Status::type pm_matrix_pass(Pos<T> &pos, const Element &elem,
   return Status::success;
 }
 
+template <typename T>
+inline void adjust_path_length(
+  const Accelerator& accelerator,
+  unsigned int& element_index,
+  Pos<T>& pos
+) {
+  auto it = std::find(accelerator.time_aware_indices.begin(), accelerator.time_aware_indices.end(), element_index);
+  if (it != accelerator.time_aware_indices.end()) {
+    auto idx = std::distance(accelerator.time_aware_indices.begin(), it);
+    pos.dl -= accelerator.time_aware_dl_kicks[idx];
+  }
+}
+
 #endif

include/trackcpp/tracking.h

@@ -167,6 +167,11 @@ Status::type track_linepass (
         // syntactic-sugar for read-only access to element object parameters
         const Element& element = line[element_offset];
 
+        // adjust dl to keep the arrival-time in sync with wall clock
+        // note: for performance reasons, the adjustment of the path length
+        // is done only at the beginning of "time aware" elements (e.g. RF cavities)
+        adjust_path_length(accelerator, element_offset, orig_pos);
+        
         // stores trajectory at entrance of each element
         if (indcs[i]) pos.push_back(orig_pos);
 
@@ -292,7 +297,12 @@ Status::type track_linepass (
         unsigned int le = element_offset;
 
         status2 = track_linepass(
-            accelerator, orig_pos[i], indices, le, final_pos, lp
+            accelerator,
+            orig_pos[i],
+            indices,
+            le,
+            final_pos,
+            lp
         );
 
         if (status2 != Status::success){
@@ -372,6 +382,9 @@ Status::type track_ringpass (
     Status::type status  = Status::success;
     std::vector<Pos<T> > final_pos;
 
+    // adjust dl to keep the arrival-time in sync with wall clock
+    accelerator.update_time_aware_info();
+
     if (turn_by_turn) pos.reserve(nr_turns+1);
 
     for(lost_turn=0; lost_turn<nr_turns; ++lost_turn) {

python_package/LICENSE

@@ -0,0 +1 @@
+../LICENSE

python_package/README.md

@@ -0,0 +1 @@
+../README.md

python_package/interface.cpp

@@ -61,6 +61,10 @@ Status::type track_linepass_wrapper(
             orig_pos[4*ni2 + i], orig_pos[5*ni2 + i]
         );
     }
+
+    // adjust dl to keep the arrival-time in sync with wall clock
+    accelerator.update_time_aware_info();
+
     Status::type status = track_linepass(
         accelerator,
         orig_post,

python_package/pyproject.toml

@@ -0,0 +1,73 @@
+[build-system]
+requires = ["setuptools>=44"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "trackcpp"
+authors = [ { name = "lnls-fac" }, ]
+maintainers = [
+  {name = "Ana Oliveira", email = "ana.clara@lnls.br"},
+  {name = "Ximenes Resende", email = "xresende@gmail.com"},
+  {name = "Fernando H. de Sá", email = "fernandohds564@gmail.com"},
+  {name = "Murilo Barbosa Alves", email= "alvesb.murilo@gmail.com"}
+]
+description = "trackcpp python package"
+readme = "README.md"
+dynamic = ["version", "dependencies"]
+requires-python = ">=3.6"
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering",
+]
+license = "MIT"
+license-files= [ "LICENSE", ]
+
+[project.urls]
+Homepage = "https://github.com/lnls-fac/trackcpp"
+Download = "https://github.com/lnls-fac/trackcpp"
+Repository = "https://github.com/lnls-fac/trackcpp.git"
+Issues = "https://github.com/lnls-fac/trackcpp/issues"
+
+# --- Configurações específicas do Setuptools ---
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.dynamic]
+version = { file = "VERSION" }
+dependencies = { file = "requirements.txt" }
+
+[tool.setuptools.package-data]
+trackcpp = ["VERSION", "_trackcpp.so"]
+
+# --- linter and formatter configurations ---
+[tool.ruff]
+select = [
+    "W", "E", "A", "B", "C90", "D", "I002", "N", "F", "G", "ARG", "S", "NPY"]
+ignore = [
+    "D203", "D204", "D213", "D215", "D400", "D401", "D404", "D406", "D407",
+    "D408", "D409", "D413", "E203", "E226"]
+ignore-init-module-imports = true
+preview = true
+line-length = 79
+fix = true
+
+[tool.ruff.extend-per-file-ignores]
+"__init__.py" = ["F401", "F821"]
+
+[tool.ruff.format]
+skip-magic-trailing-comma = true
+
+[tool.ruff.lint.isort]
+split-on-trailing-comma = false
+combine-as-imports = true
+
+[tool.isort]
+split_on_trailing_comma = false
+combine_as_imports = true
+combine_star = true
+multi_line_output = "HANGING_INDENT"
+order_by_type = false
+
+[tool.black]
+line-length = 79

python_package/requirements.txt

@@ -0,0 +1 @@
+numpy>=1.8

python_package/setup.py

@@ -1,22 +1,36 @@
 #!/usr/bin/env python-sirius
 
 from setuptools import setup
+import pathlib
 
-with open('VERSION','r') as _f:
+
+def get_abs_path(relative):
+    return str(pathlib.Path(__file__).parent / relative)
+
+
+with open(get_abs_path("README.md"), "r") as _f:
+    _long_description = _f.read().strip()
+
+with open(get_abs_path("VERSION"), "r") as _f:
     __version__ = _f.read().strip()
 
+with open(get_abs_path("requirements.txt"), "r") as _f:
+    _requirements = _f.read().strip().split("\n")
+
 setup(
     name='trackcpp',
     version=__version__,
     author='lnls-fac',
     description='trackcpp python package',
+    long_description=_long_description,
     url='https://github.com/lnls-fac/trackcpp',
     download_url='https://github.com/lnls-fac/trackcpp',
     classifiers=[
         'Intended Audience :: Science/Research',
         'Programming Language :: Python',
         'Topic :: Scientific/Engineering'
     ],
+    install_requires=_requirements,
     packages=['trackcpp'],
     package_data={'trackcpp': ['_trackcpp.so', 'VERSION']},
     zip_safe=False