feature: added an automatic logger that saves the simulation parameters in a logfile (#31)

* WIP: logfile

* Created Logfile and amended the test

* Delete build/lib/wakis/__init__.py

* Delete build/lib/wakis/_version.py

* Delete build/lib/wakis/conductors.py

* Delete build/lib/wakis/conductors3d.py

* Delete build/lib/wakis/field.py

* Delete build/lib/wakis/pmlBlock2D.py

* Delete build/lib/wakis/pmlBlock3D.py

* Delete build/lib/wakis/routines.py

* Delete build/lib/wakis/plotting.py

* Delete build/lib/wakis/geometry.py

* Delete build/lib/wakis/grid2D.py

* Delete build/lib/wakis/grid3D.py

* Delete build/lib/wakis/gridFIT3D.py

* Delete build/lib/wakis/materials.py

* Delete build/lib/wakis/solver2D.py

* Delete build/lib/wakis/solver3D.py

* Delete build/lib/wakis/solverFIT3D.py

* Delete build/lib/wakis/sources.py

* Delete build/lib/wakis/wakeSolver.py

* Refactor log variable names in test file

* Refactor logger to use 'grid' instead of 'grid_logs'

* Refactor Logger class to stick to camelCase

* Fix logger attribute assignment for wakeSolver

* Refactor logger attribute assignments in solverFIT3D

* Change logger dictionary from wakeSolver_logs to wakeSolver

* Fix logger reference for wakeSolver

* Fix logger grid assignment in solverFIT3D.py

* Rename bg_log to bgLog in solverFIT3D.py

* Update logger attribute access in test case

* Fix logfile path in MPI lossy cavity test

* Exchanged function assign_logger by update_logger

* Fixed bugs

* Fixed bug

* Exchange list by dictionary in comparison

* Fix indentation in gridLogs dictionary

* Fix indentation in solverLogs dictionary

* Separate changes from another pull request

Author: Antoniahuber

tests/test_001_pec_cubic_cavity.py

@@ -99,7 +99,7 @@ def test_simulation(self):
         skip_cells = 12  # no. cells to skip in WP integration
         wake = WakeSolver(q=q, sigmaz=sigmaz, beta=beta, 
                     xsource=xs, ysource=ys, xtest=xt, ytest=yt,
-                    save=False, logfile=False, Ez_file='tests/001_Ez.h5',
+                    save=False, Ez_file='tests/001_Ez.h5',
                     skip_cells=skip_cells,
                     )
 

tests/test_007_mpi_lossy_cavity.py

@@ -82,6 +82,18 @@ class TestMPILossyCavity:
                     -6.04105997e+01 ,-3.06532160e+01 ,-1.17749936e+01 ,-3.12574866e+00,
                     -7.35339521e-01 ,-1.13085658e-01 , 7.18247535e-01 , 8.73829036e-02])
 
+    gridLogs = {'use_mesh_refinement': False, 'Nx': 60, 'Ny': 60, 'Nz': 140, 'dx': 0.008666666348775227, 'dy': 0.008666666348775227,
+                 'dz': 0.005714285799435207, 'stl_solids': {'cavity': 'tests/stl/007_vacuum_cavity.stl', 'shell': 'tests/stl/007_lossymetal_shell.stl'},
+                 'stl_materials': {'cavity': 'vacuum', 'shell': [30, 1.0, 30]}, 'gridInitializationTime': 0}
+    
+    solverLogs = {'use_gpu': False, 'use_mpi': False, 'background': 'pec','bc_low': ['pec', 'pec', 'pec'],
+                   'bc_high': ['pec', 'pec', 'pec'], 
+                   'dt': 6.970326728398968e-12, 'solverInitializationTime': 0}
+    
+    wakeSolverLogs = {'ti': 2.8516132094735135e-09, 'q': 1e-09, 'sigmaz': 0.1, 'beta': 1.0,
+                       'xsource': 0.0, 'ysource': 0.0, 'xtest': 0.0, 'ytest': 0.0, 'chargedist': None,
+                       'skip_cells': 10, 'results_folder': 'tests/007_results/', 'wakelength': 10.0, 'simulationTime': 0}
+
     img_folder = 'tests/007_img/'
 
     def test_mpi_import(self):
@@ -314,4 +326,14 @@ def test_long_impedance(self):
             assert np.allclose(np.real(wake.Z)[::20], np.real(self.Z), rtol=0.1), "Real Impedance samples failed"
             assert np.allclose(np.imag(wake.Z)[::20], np.imag(self.Z), rtol=0.1), "Imag Impedance samples failed"
             assert np.cumsum(np.abs(wake.Z))[-1] == pytest.approx(250910.51090497518, 0.1), "Abs Impedance cumsum failed"
-    
+    
+    def test_log_file(self):
+        global solver
+        solver.logger.grid["gridInitializationTime"] = 0 #times can vary
+        solver.logger.solver["solverInitializationTime"] = 0
+        solver.logger.wakeSolver["simulationTime"] = 0
+        logfile = os.path.join(solver.logger.wakeSolver["results_folder"], "wakis.log")
+        assert os.path.exists(logfile), "Log file not created"
+        assert solver.logger.grid == self.gridLogs, "Grid logs do not match expected values"
+        assert solver.logger.solver == self.solverLogs, "Solver logs do not match expected values"
+        assert solver.logger.wakeSolver == self.wakeSolverLogs, "WakeSolver logs do not match expected values"

wakis/__init__.py

@@ -10,12 +10,14 @@
 from . import materials
 from . import wakeSolver
 from . import geometry
+from . import logger
 from . import field_monitors
 
 from .field_monitors import FieldMonitor
 from .field import Field
 from .gridFIT3D import GridFIT3D
 from .solverFIT3D import SolverFIT3D
 from .wakeSolver import WakeSolver
+from .logger import Logger
 
 from ._version import __version__

wakis/gridFIT3D.py

@@ -7,8 +7,10 @@
 import pyvista as pv
 from functools import partial
 from scipy.optimize import least_squares
+import time
 
 from .field import Field
+from .logger import Logger
 
 try:
     from mpi4py import MPI
@@ -63,10 +65,13 @@ def __init__(self, xmin, xmax, ymin, ymax, zmin, zmax,
                 stl_rotate=[0., 0., 0.], stl_translate=[0., 0., 0.], stl_scale=1.0,
                 stl_colors=None, verbose=1, stl_tol=1e-3):
 
+        t0 = time.time()
+        self.logger = Logger()
         if verbose: print('Generating grid...')
         self.verbose = verbose
         self.use_mpi = use_mpi
         self.use_mesh_refinement = use_mesh_refinement
+        self.update_logger(['use_mesh_refinement'])
 
         # domain limits
         self.xmin = xmin
@@ -81,6 +86,7 @@ def __init__(self, xmin, xmax, ymin, ymax, zmin, zmax,
         self.dx = (xmax - xmin) / Nx
         self.dy = (ymax - ymin) / Ny
         self.dz = (zmax - zmin) / Nz
+        self.update_logger(['Nx', 'Ny', 'Nz', 'dx', 'dy', 'dz'])
 
         # stl info
         self.stl_solids = stl_solids
@@ -89,6 +95,14 @@ def __init__(self, xmin, xmax, ymin, ymax, zmin, zmax,
         self.stl_translate = stl_translate
         self.stl_scale = stl_scale
         self.stl_colors = stl_colors
+        self.update_logger(['stl_solids', 'stl_materials'])
+        if stl_rotate != [0., 0., 0.]:
+            self.update_logger(['stl_rotate'])
+        if stl_translate != [0., 0., 0.]:
+            self.update_logger(['stl_translate'])
+        if stl_scale != 1.0:
+            self.update_logger(['stl_scale'])
+
         if stl_solids is not None:
             self._prepare_stl_dicts()
 
@@ -143,6 +157,9 @@ def __init__(self, xmin, xmax, ymin, ymax, zmin, zmax,
             if stl_colors is None:
                 self.assign_colors()
 
+        self.gridInitializationTime = time.time()-t0
+        self.update_logger(['gridInitializationTime'])
+
     def compute_grid(self):
         X, Y, Z = np.meshgrid(self.x, self.y, self.z, indexing='ij')
         self.grid = pv.StructuredGrid(X.transpose(), Y.transpose(), Z.transpose())
@@ -838,4 +855,11 @@ def clip(widget):
         if offscreen:
             pl.export_html('grid_inspect.html')
         else:
-            pl.show()
+            pl.show()
+
+    def update_logger(self, attrs):
+        """
+        Assigns the parameters handed via attrs to the logger
+        """
+        for atr in attrs:
+            self.logger.grid[atr] = getattr(self, atr)

wakis/logger.py

@@ -0,0 +1,67 @@
+# copyright ################################# #
+# This file is part of the wakis Package.     #
+# Copyright (c) CERN, 2025.                   #
+# ########################################### #
+
+from tqdm import tqdm
+
+import numpy as np
+import time
+import h5py
+import os
+import json
+
+from scipy.constants import c as c_light, epsilon_0 as eps_0, mu_0 as mu_0
+from scipy.sparse import csc_matrix as sparse_mat
+from scipy.sparse import diags, hstack, vstack
+
+
+
+class Logger():
+
+    def __init__(self):
+        self.grid = {}
+        self.solver = {}
+        self.wakeSolver = {}
+
+    def save_logs(self):
+        """
+        Save all logs (grid, solver, wakeSolver) into log-file inside the results folder.
+        """
+        logfile = os.path.join(self.wakeSolver["results_folder"], "wakis.log")
+
+        # Write sections
+        if not os.path.exists(self.wakeSolver["results_folder"]): 
+            os.mkdir(self.wakeSolver["results_folder"])
+        
+        with open(logfile, "w", encoding="utf-8") as fh:
+            fh.write("Simulation Parameters\n")
+            fh.write("""=====================\n\n""")
+
+            sections = [
+                ("WakeSolver Logs", self.wakeSolver),
+                ("Solver Logs", self.solver),
+                ("Grid Logs", self.grid),
+            ]
+
+            for title, data in sections:
+                fh.write(f"\n## {title} ##\n")
+                if not data:
+                    fh.write("(empty)\n")
+                    continue
+
+                # convert non-serializable values to strings recursively
+                def _convert(obj):
+                    if isinstance(obj, dict):
+                        return {k: _convert(v) for k, v in obj.items()}
+                    if isinstance(obj, (list, tuple)):
+                        return [_convert(v) for v in obj]
+                    try:
+                        json.dumps(obj)
+                        return obj
+                    except Exception:
+                        return str(obj)
+
+                clean = _convert(data)
+                fh.write(json.dumps(clean, indent=2, ensure_ascii=False))
+                fh.write("\n")

wakis/routines.py

@@ -5,6 +5,7 @@
 
 import numpy as np
 import h5py
+import time
 from tqdm import tqdm
 from scipy.constants import c as c_light
 from wakis.sources import Beam
@@ -297,6 +298,7 @@ def save_to_h5(self, hf, field, x, y, z, comp, n):
         if plot_from is None: plot_from = int(self.ti/self.dt)
 
         print('Running electromagnetic time-domain simulation...')
+        t0 = time.time()
         for n in tqdm(range(Nt)):
 
             # Initial condition
@@ -340,4 +342,9 @@ def save_to_h5(self, hf, field, x, y, z, comp, n):
 
             # Compute wakefield magnitudes is done inside WakeSolver
             self.wake.solve(compute_plane=compute_plane)
-            
+        
+        # Forward parameters to logger
+        self.logger.wakeSolver=self.wake.logger.wakeSolver
+        self.logger.wakeSolver["wakelength"]=wakelength            
+        self.logger.wakeSolver["simulationTime"]=time.time()-t0
+        self.logger.save_logs()

wakis/solverFIT3D.py

@@ -17,6 +17,7 @@
 from .materials import material_lib
 from .plotting import PlotMixin
 from .routines import RoutinesMixin
+from .logger import Logger
 
 try:
     from cupyx.scipy.sparse import csc_matrix as gpu_sparse_mat
@@ -93,7 +94,8 @@ def __init__(self, grid, wake=None, cfln=0.5, dt=None,
         '''
 
         self.verbose = verbose
-        if verbose:  t0 = time.time()
+        t0 = time.time()
+        self.logger = Logger()
 
         # Flags
         self.step_0 = True
@@ -110,10 +112,11 @@ def __init__(self, grid, wake=None, cfln=0.5, dt=None,
         self.one_step = self._one_step
         if use_stl:
             self.use_conductors = False
+        self.update_logger(['use_gpu', 'use_mpi'])
 
         # Grid 
         self.grid = grid
-
+        self.background = bg
         self.Nx = self.grid.Nx
         self.Ny = self.grid.Ny
         self.Nz = self.grid.Nz
@@ -131,6 +134,7 @@ def __init__(self, grid, wake=None, cfln=0.5, dt=None,
         self.iA = self.grid.iA
         self.tL = self.grid.tL
         self.itA = self.grid.itA
+        self.update_logger(['grid','background'])
 
         # Wake computation
         self.wake = wake
@@ -175,6 +179,7 @@ def __init__(self, grid, wake=None, cfln=0.5, dt=None,
         if verbose: print('Applying boundary conditions...')
         self.bc_low = bc_low
         self.bc_high = bc_high
+        self.update_logger(['bc_low', 'bc_high'])
         self.apply_bc_to_C() 
 
         # Materials 
@@ -203,6 +208,7 @@ def __init__(self, grid, wake=None, cfln=0.5, dt=None,
             self.pml_hi = 1.e-1
             self.pml_func = np.geomspace
             self.fill_pml_sigmas()
+            self.update_logger(['n_pml'])
 
         # Timestep calculation 
         if verbose: print('Calculating maximal stable timestep...') 
@@ -212,6 +218,7 @@ def __init__(self, grid, wake=None, cfln=0.5, dt=None,
         else:
             self.dt = dt
         self.dt = dtype(self.dt)
+        self.update_logger(['dt'])
 
         if self.use_conductivity: # relaxation time criterion tau
 
@@ -252,6 +259,9 @@ def __init__(self, grid, wake=None, cfln=0.5, dt=None,
 
         if verbose:  print(f'Total initialization time: {time.time() - t0} s')
 
+        self.solverInitializationTime = time.time() - t0
+        self.update_logger(['solverInitializationTime'])
+
     def update_tensors(self, tensor='all'):
         '''Update tensor matrices after 
         Field ieps, imu or sigma have been modified 
@@ -1107,4 +1117,14 @@ def reset_fields(self):
         for d in ['x', 'y', 'z']:
             self.E[:, :, :, d] = 0.0
             self.H[:, :, :, d] = 0.0
-            self.J[:, :, :, d] = 0.0
+            self.J[:, :, :, d] = 0.0
+
+    def update_logger(self, attrs):
+        """
+        Assigns the parameters handed via attrs to the logger
+        """
+        for atr in attrs:
+            if atr == 'grid':
+                self.logger.grid = self.grid.logger.grid
+            else:
+                self.logger.solver[atr] = getattr(self, atr)