Fix undefined variables

doc/conf.py

@@ -10,10 +10,14 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
+
 with open("../src/struphy/console/main.py") as f:
     exec(f.read())
 
 # -- Project information -----------------------------------------------------
+import importlib.metadata
+
+__version__ = importlib.metadata.version("struphy")
 
 project = "struphy"
 copyright = "2019-2025 (c) Struphy dev team | Max Planck Institute for Plasma Physics"
@@ -78,7 +82,10 @@
     "primary_sidebar_end": ["sidebar-ethical-ads"],
     "external_links": [
         {"name": "Struphy repo", "url": "https://github.com/struphy-hub/struphy"},
-        {"name": "Struphy LinkedIn", "url": "https://www.linkedin.com/company/struphy/"},
+        {
+            "name": "Struphy LinkedIn",
+            "url": "https://www.linkedin.com/company/struphy/",
+        },
         {
             "name": "Struphy MatrixChat",
             "url": "https://matrix.to/#/!wqjcJpsUvAbTPOUXen:mpg.de?via=mpg.de&via=academiccloud.de",
@@ -121,9 +128,21 @@
 # }
 
 # inheritance diagrams
-inheritance_graph_attrs = dict(rankdir="LR", ratio="auto", size='"4.0, 20.0"', fontsize="8", resolution=300.0)
-
-inheritance_node_attrs = dict(shape="ellipse", fontsize="8", height=0.25, color="maroon4", style="filled")
+inheritance_graph_attrs = dict(
+    rankdir="LR",
+    ratio="auto",
+    size='"4.0, 20.0"',
+    fontsize="8",
+    resolution=300.0,
+)
+
+inheritance_node_attrs = dict(
+    shape="ellipse",
+    fontsize="8",
+    height=0.25,
+    color="maroon4",
+    style="filled",
+)
 
 # markdown parsing
 myst_enable_extensions = [

src/struphy/feec/mass.py

@@ -2997,8 +2997,7 @@ def __isub__(self, M):
         else:
             return LinOpWithTransp.__sub__(self, M)
 
-    @staticmethod
-    def eval_quad(W, coeffs, out=None):
+    def eval_quad(self, W, coeffs, out=None):
         """
         Evaluates a given FEM field defined by its coefficients at the L2 quadrature points.
 

src/struphy/feec/utilities.py

@@ -467,23 +467,19 @@ def create_weight_weightedmatrix_hybrid(b, weight_pre, derham, accum_density, do
 
     for aa, wspace in enumerate(derham.Vh_fem["2"].spaces):
         # knot span indices of elements of local domain
-        spans_out = [
-            quad_grid[nquad].spans for quad_grid, nquad in zip(self.derham.get_quad_grids(wspace), derham.nquads)
-        ]
+        spans_out = [quad_grid[nquad].spans for quad_grid, nquad in zip(derham.get_quad_grids(wspace), derham.nquads)]
         # global start spline index on process
         starts_out = [int(start) for start in wspace.coeff_space.starts]
 
         # Iniitialize hybrid linear operators
         # global quadrature points (flattened) and weights in format (local element, local weight)
-        pts = [quad_grid[nquad].points for quad_grid, nquad in zip(self.derham.get_quad_grids(wspace), derham.nquads)]
-        wts = [quad_grid[nquad].weights for quad_grid, nquad in zip(self.derham.get_quad_grids(wspace), derham.nquads)]
+        pts = [quad_grid[nquad].points for quad_grid, nquad in zip(derham.get_quad_grids(wspace), derham.nquads)]
+        wts = [quad_grid[nquad].weights for quad_grid, nquad in zip(derham.get_quad_grids(wspace), derham.nquads)]
 
         p = wspace.degree
 
         # evaluated basis functions at quadrature points of the space
-        basis_o = [
-            quad_grid[nquad].basis for quad_grid, nquad in zip(self.derham.get_quad_grids(wspace), derham.nquads)
-        ]
+        basis_o = [quad_grid[nquad].basis for quad_grid, nquad in zip(derham.get_quad_grids(wspace), derham.nquads)]
 
         pads_out = wspace.coeff_space.pads
 

src/struphy/fields_background/coil_fields/base.py

@@ -1,6 +1,7 @@
 from abc import ABCMeta, abstractmethod
 
 import cunumpy as xp
+import pandas as pd
 from matplotlib import pyplot as plt
 from pyevtk.hl import gridToVTK
 

src/struphy/geometry/utilities.py

@@ -173,6 +173,8 @@ def field_line_tracing(
     R = xp.zeros((s_gr.size, x_gr.size), dtype=float)
     Z = xp.zeros((s_gr.size, x_gr.size), dtype=float)
 
+    r_flux_surface = None
+
     # function whose root must be found
     for j, x in enumerate(x_gr):
         for i, s in enumerate(s_gr):

src/struphy/models/variables.py

@@ -261,7 +261,7 @@ def allocate(
             self._n_to_save = n_markers
 
         assert self._n_to_save <= self.particles.Np, (
-            f"The number of markers for which data should be stored (={self._n_to_save}) murst be <= than the total number of markers (={obj.Np})"
+            f"The number of markers for which data should be stored (={self._n_to_save}) murst be <= than the total number of markers (={self.particles.Np})"
         )
         if self._n_to_save > 0:
             self._saved_markers = xp.zeros(
@@ -405,7 +405,7 @@ def allocate(
             self._n_to_save = n_markers
 
         assert self._n_to_save <= self.particles.Np, (
-            f"The number of markers for which data should be stored (={self._n_to_save}) murst be <= than the total number of markers (={obj.Np})"
+            f"The number of markers for which data should be stored (={self._n_to_save}) murst be <= than the total number of markers (={self.particles.Np})"
         )
         if self._n_to_save > 0:
             self._saved_markers = xp.zeros(

src/struphy/pic/accumulation/filter.py

@@ -1,5 +1,6 @@
 from dataclasses import dataclass
 
+import cunumpy as xp
 import numpy as np
 from scipy.fft import irfft, rfft
 

src/struphy/post_processing/cprofile_analyser.py

@@ -27,7 +27,7 @@ def get_cprofile_data(path, print_callers=None):
     p = pstats.Stats(os.path.join(path, "profile_tmp"), stream=stdout)
     p.strip_dirs().sort_stats(SortKey.CUMULATIVE).print_stats()
     stdout.close()
-
+    name_li = None
     data_cprofile = dict()
     with open(os.path.join(path, "profile_out.txt")) as f:
         lines = f.readlines()

src/struphy/post_processing/orbits/orbits_tools.py

@@ -47,7 +47,7 @@ def post_process_orbit_guiding_center(path_in, path_kinetics_species, species):
         params = yaml.load(f, Loader=yaml.FullLoader)
 
     # create domain for calculating markers' physical coordinates
-    domain, equil = setup_domain_and_equil(params)
+    domain, equil = model.setup_domain_and_equil(params)
 
     # path for orbit data
     path_orbits = os.path.join(path_kinetics_species, "orbits")

src/struphy/propagators/propagators_fields.py

@@ -1639,22 +1639,23 @@ def __call__(self, dt):
             _RHS2 = HybridM1.dot(self._RHS) + self._rhs
 
             # TODO: unknown function 'pcg', use new solver API
-            a_new, info = pcg(
-                _LHS,
-                _RHS2,
-                self._pc,
-                x0=self._a,
-                tol=self._solver_params["tol"],
-                maxiter=self._solver_params["maxiter"],
-                verbose=self._solver_params["verbose"],
-            )
+            raise NotImplementedError("pcg solver not available, use new solver API!")
+            # a_new, info = pcg(
+            #     _LHS,
+            #     _RHS2,
+            #     self._pc,
+            #     x0=self._a,
+            #     tol=self._solver_params["tol"],
+            #     maxiter=self._solver_params["maxiter"],
+            #     verbose=self._solver_params["verbose"],
+            # )
 
             # write new coeffs into Propagator.variables
-            max_da = self.feec_vars_update(a_new)
-            print("++++====check_iteration_error=====+++++", max_da)
+            # max_da = self.feec_vars_update(a_new)
+            # print("++++====check_iteration_error=====+++++", max_da)
             # we can modify the diff function in in_place_update to get another type errors
-            if max_da[0] < 10 ** (-6):
-                break
+            # if max_da[0] < 10 ** (-6):
+            #     break
 
     @classmethod
     def options(cls):
@@ -7859,6 +7860,8 @@ def allocate(self):
 
         solver_params = self.options.solver_params
 
+        u = self.variables.u.spline.vector
+
         # Lifting for nontrivial boundary conditions
         # derham had boundary conditions in eta1 direction, the following is in space Hdiv_0
         if self._lifting: