From 39edc7f96e0c514488fd3ce78ef8bf65cfc0f113 Mon Sep 17 00:00:00 2001
From: "V. Ferreira" <vascocbf@gmail.com>
Date: Tue, 24 Feb 2026 03:47:06 +0100
Subject: [PATCH] corrected periodic boundaries, more to be done on this

---
 density.vtk        |  2 +-
 electric_field.vtk |  2 +-
 nufi_poisson.cc    | 25 ++++++++++++++++++++-----
 plotting.ipynb     |  6 +++---
 4 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/density.vtk b/density.vtk
index e91f56c..80de449 100644
--- a/density.vtk
+++ b/density.vtk
@@ -1,5 +1,5 @@
 # vtk DataFile Version 3.0
-#This file was generated by the deal.II library on 2026/2/23 at 20:47:29
+#This file was generated by the deal.II library on 2026/2/24 at 3:42:25
 ASCII
 DATASET UNSTRUCTURED_GRID
 
diff --git a/electric_field.vtk b/electric_field.vtk
index 5ac1196..cc32d28 100644
--- a/electric_field.vtk
+++ b/electric_field.vtk
@@ -1,5 +1,5 @@
 # vtk DataFile Version 3.0
-#This file was generated by the deal.II library on 2026/2/23 at 20:47:29
+#This file was generated by the deal.II library on 2026/2/24 at 3:42:25
 ASCII
 DATASET UNSTRUCTURED_GRID
 
diff --git a/nufi_poisson.cc b/nufi_poisson.cc
index b7fbc6a..8d8c5fe 100644
--- a/nufi_poisson.cc
+++ b/nufi_poisson.cc
@@ -3,6 +3,7 @@
 #include <deal.II/base/function.h>
 #include <deal.II/base/quadrature_lib.h>
 #include <deal.II/base/logstream.h>
+#include <deal.II/base/tensor.h>
 #include <deal.II/base/utilities.h>
 #include <deal.II/base/tensor_function.h>
 #include <deal.II/base/index_set.h>
@@ -21,6 +22,7 @@
 
 #include <deal.II/dofs/dof_handler.h>
 #include <deal.II/dofs/dof_tools.h>
+#include <deal.II/dofs/dof_renumbering.h>
 
 #include <deal.II/fe/fe_q.h>
 #include <deal.II/fe/fe_values.h>
@@ -28,6 +30,7 @@
 #include <deal.II/numerics/data_out.h>
 #include <deal.II/numerics/vector_tools.h>
 
+#include <deal.II/numerics/vector_tools_boundary.h>
 #include <fstream>
 #include <iostream>
 
@@ -116,6 +119,16 @@ private:
   const unsigned int Nv;
 };
 
+template <int dim>
+class BoundaryValues : public Function<dim>
+{
+public:
+  virtual double value(const Point<dim> &p,
+                       const unsigned int component = 0) const override
+  {
+    return 0.; // boundary value at periodic boundary
+  }
+};
 
 // =-=-=-=-= Poisson Solver =-=-=-=-=
 
@@ -147,6 +160,8 @@ private:
   Vector<double> solution;      // phi
   Vector<double> system_rhs;
 
+  MappingQ<dim> mapping;
+
   unsigned int Nv;
 };
 
@@ -161,6 +176,7 @@ template <int dim>
 PoissonProblem<dim>::PoissonProblem(unsigned int degree, unsigned int Nv)
   : fe(degree)
   , dof_handler(triangulation)
+  , mapping(degree)
   , Nv(Nv)
 {}
 
@@ -175,14 +191,16 @@ void PoissonProblem<dim>::create_mesh()
                             X_DOMAIN_RIGHT);
 
   // Make x-dim boundaries periodic
+  Tensor<1, dim> offset;
   std::vector<GridTools::PeriodicFacePair<
               typename Triangulation<dim>::cell_iterator>> periodicity_vector;
-  
+
   GridTools::collect_periodic_faces(triangulation,
                                     0,
                                     1,
                                     0,
-                                    periodicity_vector);
+                                    periodicity_vector,
+                                    offset);
   
   triangulation.add_periodicity(periodicity_vector);
 
@@ -215,7 +233,6 @@ void PoissonProblem<dim>::setup_system()
   system_rhs.reinit(dof_handler.n_dofs());
 }
 
-
 // =-=-=-=-= E_field = -dPhi/dx =-=-=-=-=
 
 template <int dim>
@@ -320,7 +337,6 @@ void PoissonProblem<dim>::output_results() const
   // --- extract DoF coordinates ---
   std::vector<Point<dim>> support_points(dof_handler.n_dofs());
 
-  MappingQ1<dim> mapping;
   DoFTools::map_dofs_to_support_points(mapping,
                                        dof_handler,
                                        support_points);
@@ -370,7 +386,6 @@ template <int dim>
 void PoissonProblem<dim>::run()
 {
   create_mesh();
-
   setup_system();
   assemble_system();
   solve();
diff --git a/plotting.ipynb b/plotting.ipynb
index c9b47df..8fb68f7 100644
--- a/plotting.ipynb
+++ b/plotting.ipynb
@@ -35,12 +35,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "aa222ee6ba03446d87ead5ffb3d25af2",
+       "model_id": "aa88a047e54c4ea7befbb1b0f6e71ec6",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Widget(value='<iframe src=\"http://localhost:37595/index.html?ui=P_0x7af6f37f0590_0&reconnect=auto\" class=\"pyvi…"
+       "Widget(value='<iframe src=\"http://localhost:37563/index.html?ui=P_0x7901e7af86e0_0&reconnect=auto\" class=\"pyvi…"
       ]
      },
      "metadata": {},
@@ -71,7 +71,7 @@
        "</td></tr> </table>"
       ],
       "text/plain": [
-       "UnstructuredGrid (0x7af6f37b7e20)\n",
+       "UnstructuredGrid (0x7901e7e77ee0)\n",
        "  N Cells:    128\n",
        "  N Points:   256\n",
        "  X Bounds:   0.000e+00, 1.200e+01\n",