From 03b29f29f4a804cc129cf73fb6a7d703d2efeadc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Beno=C3=AEt=20Sierro?= <benoitsierro@bluewin.ch>
Date: Thu, 10 Jun 2021 16:20:39 +0200
Subject: [PATCH] updated testing

---
 developement_help.md                          |   4 +-
 lol.txt                                       |  26 +++
 src/scgenerator/initialize.py                 | 104 ++++++-----
 src/scgenerator/io.py                         |   4 -
 src/scgenerator/physics/pulse.py              |  10 ++
 src/scgenerator/spectra.py                    |  14 +-
 src/scgenerator/utils/__init__.py             |   2 +-
 src/scgenerator/utils/parameter.py            |  10 +-
 .../configs/compute_init_parameters/good.toml |   6 +-
 .../count_variations/120sim_3vary.toml        |  19 +-
 .../configs/count_variations/1sim_0vary.toml  |   8 +-
 .../configs/count_variations/1sim_1vary.toml  |  13 +-
 .../configs/count_variations/2sim_0vary.toml  |   8 +-
 .../configs/count_variations/2sim_1vary.toml  |  14 +-
 testing/configs/custom_field/peak_power.toml  |   2 +-
 .../custom_field/wavelength_shift1.toml       |   6 +-
 .../custom_field/wavelength_shift2.toml       |  12 +-
 testing/configs/ensure_consistency/bad1.toml  |  13 +-
 testing/configs/ensure_consistency/bad2.toml  |  15 +-
 testing/configs/ensure_consistency/bad3.toml  |  15 +-
 testing/configs/ensure_consistency/bad4.toml  |  15 +-
 testing/configs/ensure_consistency/bad5.toml  |  15 +-
 testing/configs/ensure_consistency/bad6.toml  |  15 +-
 testing/configs/ensure_consistency/good1.toml |  15 +-
 testing/configs/ensure_consistency/good2.toml |  15 +-
 testing/configs/ensure_consistency/good3.toml |  15 +-
 testing/configs/ensure_consistency/good4.toml |  22 +--
 testing/configs/ensure_consistency/good5.toml |  15 +-
 testing/configs/ensure_consistency/good6.toml |  15 +-
 testing/configs/override/fiber2.toml          |  10 +-
 testing/configs/override/initial_config.toml  |   9 +-
 .../configs/param_sequence/almost_equal.toml  |  13 +-
 testing/configs/param_sequence/equal.toml     |  13 +-
 .../configs/param_sequence/no_variations.toml |   6 +-
 .../run_simulations/full_anomalous.toml       |  13 +-
 testing/configs/validate_types/bad1.toml      |  15 +-
 testing/configs/validate_types/bad2.toml      |  15 +-
 testing/configs/validate_types/bad3.toml      |  15 +-
 testing/configs/validate_types/bad4.toml      |  16 +-
 testing/configs/validate_types/bad5.toml      |  15 +-
 testing/configs/validate_types/bad6.toml      |  13 +-
 testing/configs/validate_types/bad7.toml      |  15 +-
 testing/configs/validate_types/good.toml      |  15 +-
 testing/test_initialize.py                    | 162 +++++++++---------
 testing/test_new_params.py                    |  37 ----
 testing/test_utils.py                         |  10 +-
 46 files changed, 428 insertions(+), 411 deletions(-)
 create mode 100644 lol.txt
 delete mode 100644 testing/test_new_params.py

diff --git a/developement_help.md b/developement_help.md
index 02658e1..cf259ca 100644
--- a/developement_help.md
+++ b/developement_help.md
@@ -1,6 +1,6 @@
 ## add parameter
-- add it to ```const.valid_param_types```
+- add it to ```utils.parameters```
 - add it to README.md
-- add the necessary logic in the appropriate ```initialize._ensure_consistency``` subfunction
+- add the necessary logic in the appropriate ```initialize:Config``` class
 - optional : add a default value
 - optional : add to valid_variable
diff --git a/lol.txt b/lol.txt
new file mode 100644
index 0000000..87ffddf
--- /dev/null
+++ b/lol.txt
@@ -0,0 +1,26 @@
+name = "test config"
+
+# fiber
+# gamma = 0.018
+length = 1
+model = "pcf"
+pitch = 1.5e-6
+pitch_ratio = 0.37
+
+# pulse
+intensity_noise = 0.05e-2
+peak_power = 100e3
+quantum_noise = true
+shape = "gaussian"
+wavelength = 1050e-9
+width = 50e-15
+
+# simulation
+behaviors = ["spm", "raman", "ss"]
+parallel = false
+raman_type = "agrawal"
+repeat = 4
+t_num = 16384
+time_window = 37e-12
+tolerated_error = 1e-11
+z_num = 128
diff --git a/src/scgenerator/initialize.py b/src/scgenerator/initialize.py
index 752e85d..0aab720 100644
--- a/src/scgenerator/initialize.py
+++ b/src/scgenerator/initialize.py
@@ -29,19 +29,7 @@ class Params(BareParams):
     def compute(self):
         logger = get_logger(__name__)
 
-        (
-            self.z_targets,
-            self.t,
-            self.time_window,
-            self.t_num,
-            self.dt,
-            self.w_c,
-            self.w0,
-            self.w,
-            self.w_power_fact,
-        ) = build_sim_grid(
-            self.length, self.z_num, self.wavelength, self.time_window, self.t_num, self.dt
-        )
+        build_sim_grid_in_place(self)
 
         # Initial field may influence the grid
         if self.mean_power is not None:
@@ -54,9 +42,9 @@ class Params(BareParams):
             self.field_0,
         ) = pulse.setup_custom_field(self)
         if self.readjust_wavelength:
-            delta_w = self.w_c[np.argmax(abs2(np.fft.fft(self.field_0)))]
-            logger.debug(f"adjusted w by {delta_w}")
-            self.wavelength = units.m.inv(units.m(self.wavelength) - delta_w)
+            old_wl = self.wavelength
+            self.wavelength = pulse.correct_wavelength(self.wavelength, self.w_c, self.field_0)
+            logger.info(f"moved wavelength from {1e9*old_wl:.2f} to {1e9*self.wavelength:.2f}")
             self.w_c, self.w0, self.w, self.w_power_fact = update_frequency_domain(
                 self.t, self.wavelength
             )
@@ -138,21 +126,6 @@ class Params(BareParams):
 
         self.spec_0 = np.fft.fft(self.field_0)
 
-    def build_sim_grid(self):
-        (
-            self.z_targets,
-            self.t,
-            self.time_window,
-            self.t_num,
-            self.dt,
-            self.w_c,
-            self.w0,
-            self.w,
-            self.w_power_fact,
-        ) = build_sim_grid(
-            self.length, self.z_num, self.wavelength, self.time_window, self.t_num, self.dt
-        )
-
 
 @dataclass
 class Config(BareConfig):
@@ -174,24 +147,24 @@ class Config(BareConfig):
     def fiber_consistency(self):
         if self.contains("beta"):
             if not (self.contains("A_eff") or self.contains("effective_mode_diameter")):
-                self.gamma = self.get("gamma", specified_parameters=["beta"])
+                self.get("gamma", specified_parameters=["beta"])
             self.setdefault("model", "custom")
 
         elif self.contains("dispersion_file"):
             if not (self.contains("A_eff") or self.contains("effective_mode_diameter")):
-                fiber = self.get("gamma", specified_parameters=["dispersion_file"])
+                self.get("gamma", specified_parameters=["dispersion_file"])
             self.setdefault("model", "custom")
 
         else:
-            fiber = self.get("model")
+            self.get("model")
 
             if self.model == "pcf":
-                fiber = self.get_fiber("pitch")
-                fiber = self.get_fiber("pitch_ratio")
+                self.get_fiber("pitch")
+                self.get_fiber("pitch_ratio")
 
             elif self.model == "hasan":
-                fiber = self.get_multiple(
-                    fiber, ["capillary_spacing", "capillary_outer_d"], 1, fiber_model="hasan"
+                self.get_multiple(
+                    ["capillary_spacing", "capillary_outer_d"], 1, fiber_model="hasan"
                 )
                 for param in [
                     "core_radius",
@@ -200,12 +173,12 @@ class Config(BareConfig):
                     "capillary_resonance_strengths",
                     "capillary_nested",
                 ]:
-                    fiber = self.get_fiber(param)
+                    self.get_fiber(param)
             else:
                 for param in hc_model_specific_parameters[self.model]:
-                    fiber = self.get_fiber(param)
+                    self.get_fiber(param)
         for param in ["length", "input_transmission"]:
-            fiber = self.get(param)
+            self.get(param)
 
     def gas_consistency(self):
         for param in ["gas_name", "temperature", "pressure", "plasma_density"]:
@@ -578,19 +551,7 @@ def recover_params(params: BareParams, data_folder: Path) -> Params:
     params = Params.from_bare(params)
     try:
         prev = io.load_params(data_folder / "params.toml")
-        (
-            prev.z_targets,
-            prev.t,
-            prev.time_window,
-            prev.t_num,
-            prev.dt,
-            prev.w_c,
-            prev.w0,
-            prev.w,
-            prev.w_power_fact,
-        ) = build_sim_grid(
-            prev.length, prev.z_num, prev.wavelength, prev.time_window, prev.t_num, prev.dt
-        )
+        build_sim_grid_in_place(prev)
     except FileNotFoundError:
         prev = BareParams()
     for k, v in filter(lambda el: el[1] is not None, vars(prev).items()):
@@ -634,7 +595,40 @@ def build_sim_grid(
     return z_targets, t, time_window, t_num, dt, w_c, w0, w, w_power_fact
 
 
-def update_frequency_domain(t, wavelength):
+def build_sim_grid_in_place(params: BareParams):
+    """similar to calling build_sim_grid, but sets the attributes in place"""
+    (
+        params.z_targets,
+        params.t,
+        params.time_window,
+        params.t_num,
+        params.dt,
+        params.w_c,
+        params.w0,
+        params.w,
+        params.w_power_fact,
+    ) = build_sim_grid(
+        params.length, params.z_num, params.wavelength, params.time_window, params.t_num, params.dt
+    )
+
+
+def update_frequency_domain(
+    t: np.ndarray, wavelength: float
+) -> Tuple[np.ndarray, float, np.ndarray, np.ndarray]:
+    """updates the frequency grid
+
+    Parameters
+    ----------
+    t : np.ndarray
+        time array
+    wavelength : float
+        wavelength
+
+    Returns
+    -------
+    Tuple[np.ndarray, float, np.ndarray, np.ndarray]
+        w_c, w0, w, w_power_fact
+    """
     w_c = wspace(t)
     w0 = units.m(wavelength)
     w = w_c + w0
diff --git a/src/scgenerator/io.py b/src/scgenerator/io.py
index f1d0f9f..731227f 100644
--- a/src/scgenerator/io.py
+++ b/src/scgenerator/io.py
@@ -88,10 +88,6 @@ def load_toml(path: os.PathLike):
     path = conform_toml_path(path)
     with open(path, mode="r") as file:
         dico = toml.load(file)
-
-    for section in ["simulation", "fiber", "pulse", "gas"]:
-        dico.update(dico.pop(section, {}))
-
     return dico
 
 
diff --git a/src/scgenerator/physics/pulse.py b/src/scgenerator/physics/pulse.py
index 060296b..881e3d9 100644
--- a/src/scgenerator/physics/pulse.py
+++ b/src/scgenerator/physics/pulse.py
@@ -26,6 +26,7 @@ from ..logger import get_logger
 from ..math import *
 from ..plotting import plot_setup
 from ..utils.parameter import BareParams
+from . import units
 
 c = 299792458.0
 hbar = 1.05457148e-34
@@ -248,6 +249,15 @@ def setup_custom_field(params: BareParams) -> bool:
     return did_set, width, peak_power, energy, field_0
 
 
+def correct_wavelength(init_wavelength: float, w_c: np.ndarray, field_0: np.ndarray) -> float:
+    """
+    finds a new wavelength parameter such that the maximum of the spectrum corresponding
+    to field_0 is located at init_wavelength
+    """
+    delta_w = w_c[np.argmax(abs2(np.fft.fft(field_0)))]
+    return units.m.inv(units.m(init_wavelength) - delta_w)
+
+
 def E0_to_P0(E0, t0, shape="gaussian"):
     """convert an initial total pulse energy to a pulse peak peak_power"""
     return E0 / (t0 * P0T0_to_E0_fac[shape])
diff --git a/src/scgenerator/spectra.py b/src/scgenerator/spectra.py
index 843373d..159c590 100644
--- a/src/scgenerator/spectra.py
+++ b/src/scgenerator/spectra.py
@@ -45,13 +45,13 @@ class Pulse(Sequence):
         except FileNotFoundError:
             self.logger.info(f"parameters corresponding to {self.path} not found")
 
-        self.params = initialize.build_sim_grid(self.params)
+        initialize.build_sim_grid_in_place(self.params)
 
         try:
             self.z = np.load(os.path.join(path, "z.npy"))
         except FileNotFoundError:
             if self.params is not None:
-                self.z = self.params["z_targets"]
+                self.z = self.params.z_targets
             else:
                 raise
         self.cache: Dict[int, Spectrum] = {}
@@ -59,13 +59,13 @@ class Pulse(Sequence):
         if self.nmax <= 0:
             raise FileNotFoundError(f"No appropriate file in specified folder {self.path}")
 
-        self.t = self.params["t"]
-        w = initialize.wspace(self.t) + units.m(self.params["wavelength"])
+        self.t = self.params.t
+        w = initialize.wspace(self.t) + units.m(self.params.wavelength)
         self.w_order = np.argsort(w)
         self.w = w
         self.wl = units.m.inv(self.w)
-        self.params["w"] = self.w
-        self.params["z_targets"] = self.z
+        self.params.w = self.w
+        self.params.z_targets = self.z
 
     def __iter__(self):
         """
@@ -197,6 +197,6 @@ class Pulse(Sequence):
         spec = np.load(self.path / SPECN_FN.format(i))
         if self.__ensure_2d:
             spec = np.atleast_2d(spec)
-        spec = Spectrum(spec, self.wl, self.params["frep"])
+        spec = Spectrum(spec, self.wl, self.params.frep)
         self.cache[i] = spec
         return spec
diff --git a/src/scgenerator/utils/__init__.py b/src/scgenerator/utils/__init__.py
index 50ba13d..4b3e839 100644
--- a/src/scgenerator/utils/__init__.py
+++ b/src/scgenerator/utils/__init__.py
@@ -275,5 +275,5 @@ def override_config(new: Dict[str, Any], old: BareConfig = None) -> BareConfig:
     variable = deepcopy(old.variable)
     variable.update(new.pop("variable", {}))  # add new variable
     for k in new:
-        variable.pop(k)  # remove old ones
+        variable.pop(k, None)  # remove old ones
     return replace(old, variable=variable, **{k: None for k in variable}, **new)
diff --git a/src/scgenerator/utils/parameter.py b/src/scgenerator/utils/parameter.py
index 0f317b1..a0b1c69 100644
--- a/src/scgenerator/utils/parameter.py
+++ b/src/scgenerator/utils/parameter.py
@@ -1,4 +1,4 @@
-import datetime
+import datetime as datetime_module
 from copy import copy
 from dataclasses import asdict, dataclass
 from functools import lru_cache
@@ -205,6 +205,7 @@ class Parameter:
 class VariableParameter:
     def __init__(self, parameterBase):
         self.pbase = parameterBase
+        self.list_checker = type_checker(list, tuple, np.ndarray)
 
     def __set_name__(self, owner, name):
         self.name = name
@@ -222,8 +223,9 @@ class VariableParameter:
             value = {}
         else:
             for k, v in value.items():
+                self.list_checker("variable " + k, v)
                 if k not in valid_variable:
-                    raise TypeError(f"{k!r} is not a valide variable parameter")
+                    raise TypeError(f"{k!r} is not a valid variable parameter")
                 if len(v) == 0:
                     raise ValueError(f"variable parameter {k!r} must not be empty")
 
@@ -381,11 +383,13 @@ class BareParams:
     beta_func: Callable[[float], List[float]] = Parameter(func_validator)
     gamma_func: Callable[[float], float] = Parameter(func_validator)
     interp_range: Tuple[float, float] = Parameter(float_pair)
+    datetime: datetime_module.datetime = Parameter(type_checker(datetime_module.datetime))
+    version: str = Parameter(string)
 
     def prepare_for_dump(self) -> Dict[str, Any]:
         param = asdict(self)
         param = BareParams.strip_params_dict(param)
-        param["datetime"] = datetime.datetime.now()
+        param["datetime"] = datetime_module.datetime.now()
         param["version"] = __version__
         return param
 
diff --git a/testing/configs/compute_init_parameters/good.toml b/testing/configs/compute_init_parameters/good.toml
index 6f6527d..87ffddf 100644
--- a/testing/configs/compute_init_parameters/good.toml
+++ b/testing/configs/compute_init_parameters/good.toml
@@ -1,13 +1,13 @@
 name = "test config"
 
-[fiber]
+# fiber
 # gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 intensity_noise = 0.05e-2
 peak_power = 100e3
 quantum_noise = true
@@ -15,7 +15,7 @@ shape = "gaussian"
 wavelength = 1050e-9
 width = 50e-15
 
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = false
 raman_type = "agrawal"
diff --git a/testing/configs/count_variations/120sim_3vary.toml b/testing/configs/count_variations/120sim_3vary.toml
index b05a694..0d34ff5 100644
--- a/testing/configs/count_variations/120sim_3vary.toml
+++ b/testing/configs/count_variations/120sim_3vary.toml
@@ -1,19 +1,13 @@
-[fiber]
+# fiber
 core_radius = 50e-6
 length = 50e-2
 model = "marcatili"
 
-[gas.variable]
-gas_name = ["air", "helium"]
-
-[pulse]
+# pulse
 peak_power = 100e3
 wavelength = 800e-9
 
-[pulse.variable]
-width = [250e-15, 240e-15, 230e-15, 220e-15, 210e-15]
-
-[simulation]
+# simulation
 parallel = true
 repeat = 4
 t_num = 16384
@@ -21,5 +15,10 @@ time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
 
-[simulation.variable]
+[variable]
+# gas.variable
+gas_name = ["air", "helium"]
+# pulse.variable
+width = [250e-15, 240e-15, 230e-15, 220e-15, 210e-15]
+# simulation.variable
 behaviors = [["spm", "raman", "ss"], ["spm", "raman"], ["spm"]]
diff --git a/testing/configs/count_variations/1sim_0vary.toml b/testing/configs/count_variations/1sim_0vary.toml
index 20339d3..c5252bf 100644
--- a/testing/configs/count_variations/1sim_0vary.toml
+++ b/testing/configs/count_variations/1sim_0vary.toml
@@ -1,17 +1,17 @@
-[fiber]
+# fiber
 core_radius = 50e-6
 length = 50e-2
 model = "marcatili"
 
-[gas]
+# gas
 gas_name = "air"
 
-[pulse]
+# pulse
 peak_power = 100e3
 wavelength = 800e-9
 width = 250e-15
 
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 1
diff --git a/testing/configs/count_variations/1sim_1vary.toml b/testing/configs/count_variations/1sim_1vary.toml
index 1df17c1..8d76982 100644
--- a/testing/configs/count_variations/1sim_1vary.toml
+++ b/testing/configs/count_variations/1sim_1vary.toml
@@ -1,19 +1,16 @@
-[fiber]
+# fiber
 core_radius = 50e-6
 length = 50e-2
 model = "marcatili"
 
-[gas]
+# gas
 gas_name = "air"
 
-[pulse]
+# pulse
 peak_power = 100e3
 wavelength = 800e-9
 
-[pulse.variable]
-width = [250e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 1
@@ -21,3 +18,5 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+[variable]
+width = [250e-15]
diff --git a/testing/configs/count_variations/2sim_0vary.toml b/testing/configs/count_variations/2sim_0vary.toml
index e22cf46..5c8b83c 100644
--- a/testing/configs/count_variations/2sim_0vary.toml
+++ b/testing/configs/count_variations/2sim_0vary.toml
@@ -1,17 +1,17 @@
-[fiber]
+# fiber
 core_radius = 50e-6
 length = 50e-2
 model = "marcatili"
 
-[gas]
+# gas
 gas_name = "air"
 
-[pulse]
+# pulse
 peak_power = 100e3
 wavelength = 800e-9
 width = 250e-15
 
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 2
diff --git a/testing/configs/count_variations/2sim_1vary.toml b/testing/configs/count_variations/2sim_1vary.toml
index 71dd68c..fed14b1 100644
--- a/testing/configs/count_variations/2sim_1vary.toml
+++ b/testing/configs/count_variations/2sim_1vary.toml
@@ -1,20 +1,17 @@
-[fiber]
+# fiber
 core_radius = 50e-6
 length = 50e-2
 model = "marcatili"
 
-[gas]
+# gas
 gas_name = "air"
 
-[pulse]
+# pulse
 soliton_num = 5
 wavelength = 800e-9
 width = 250e-15
 
-[pulse.variable]
-shape = ["gaussian", "sech"]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 1
@@ -22,3 +19,6 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+shape = ["gaussian", "sech"]
diff --git a/testing/configs/custom_field/peak_power.toml b/testing/configs/custom_field/peak_power.toml
index 5a0509a..064e04d 100644
--- a/testing/configs/custom_field/peak_power.toml
+++ b/testing/configs/custom_field/peak_power.toml
@@ -2,7 +2,7 @@ dt = 1e-15
 field_file = "testing/configs/custom_field/init_field.npz"
 length = 1
 peak_power = 20000
-readjust_wavelength = true
+readjust_wavelength = false
 t_num = 2048
 wavelength = 1593e-9
 z_num = 32
diff --git a/testing/configs/custom_field/wavelength_shift1.toml b/testing/configs/custom_field/wavelength_shift1.toml
index 554c4cb..18e6537 100644
--- a/testing/configs/custom_field/wavelength_shift1.toml
+++ b/testing/configs/custom_field/wavelength_shift1.toml
@@ -1,17 +1,17 @@
 name = "test config"
 
-[fiber]
+# fiber
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 field_file = "testing/configs/custom_field/init_field.npz"
 quantum_noise = false
 wavelength = 1050e-9
 
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 lower_wavelength_interp_limit = 300e-9
 raman_type = "agrawal"
diff --git a/testing/configs/custom_field/wavelength_shift2.toml b/testing/configs/custom_field/wavelength_shift2.toml
index aebd67f..54b457d 100644
--- a/testing/configs/custom_field/wavelength_shift2.toml
+++ b/testing/configs/custom_field/wavelength_shift2.toml
@@ -1,18 +1,16 @@
 name = "test config"
 
-[fiber]
+# fiber
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 field_file = "testing/configs/custom_field/init_field.npz"
 quantum_noise = false
-[pulse.variable]
-wavelength = [1050e-9, 1321e-9, 1593e-9]
 
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 lower_wavelength_interp_limit = 300e-9
 raman_type = "agrawal"
@@ -22,3 +20,7 @@ time_window = 37e-12
 tolerated_error = 1e-11
 upper_wavelength_interp_limit = 1900e-9
 z_num = 128
+
+[variable]
+# pulse.variable
+wavelength = [1050e-9, 1321e-9, 1593e-9]
diff --git a/testing/configs/ensure_consistency/bad1.toml b/testing/configs/ensure_consistency/bad1.toml
index 1fb03f5..00018c7 100644
--- a/testing/configs/ensure_consistency/bad1.toml
+++ b/testing/configs/ensure_consistency/bad1.toml
@@ -2,23 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -27,3 +24,7 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
diff --git a/testing/configs/ensure_consistency/bad2.toml b/testing/configs/ensure_consistency/bad2.toml
index c35d65f..629d4a1 100644
--- a/testing/configs/ensure_consistency/bad2.toml
+++ b/testing/configs/ensure_consistency/bad2.toml
@@ -2,23 +2,19 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-soliton_num = [1, 2, 3, 4]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -27,3 +23,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+soliton_num = [1, 2, 3, 4]
diff --git a/testing/configs/ensure_consistency/bad3.toml b/testing/configs/ensure_consistency/bad3.toml
index 8e271a5..d18888e 100644
--- a/testing/configs/ensure_consistency/bad3.toml
+++ b/testing/configs/ensure_consistency/bad3.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -27,3 +23,8 @@ repeat = 4
 t_num = 16384
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/bad4.toml b/testing/configs/ensure_consistency/bad4.toml
index 898c310..c75ac97 100644
--- a/testing/configs/ensure_consistency/bad4.toml
+++ b/testing/configs/ensure_consistency/bad4.toml
@@ -2,25 +2,21 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 width = 120e-15
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -29,3 +25,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/bad5.toml b/testing/configs/ensure_consistency/bad5.toml
index 6b13fb9..dc3e33d 100644
--- a/testing/configs/ensure_consistency/bad5.toml
+++ b/testing/configs/ensure_consistency/bad5.toml
@@ -2,7 +2,7 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 capillary_num = 6
 capillary_outer_d = 2e-6
 capillary_spacing = 4e-6
@@ -11,17 +11,13 @@ gamma = 0.018
 length = 1
 model = "hasan"
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -30,3 +26,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/bad6.toml b/testing/configs/ensure_consistency/bad6.toml
index b7deceb..e38caf3 100644
--- a/testing/configs/ensure_consistency/bad6.toml
+++ b/testing/configs/ensure_consistency/bad6.toml
@@ -2,7 +2,7 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 capillary_num = 6
 capillary_thickness = 4e-6
 core_radius = 50e-6
@@ -10,17 +10,13 @@ gamma = 0.018
 length = 1
 model = "hasan"
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -29,3 +25,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/good1.toml b/testing/configs/ensure_consistency/good1.toml
index c1b778d..03c0082 100644
--- a/testing/configs/ensure_consistency/good1.toml
+++ b/testing/configs/ensure_consistency/good1.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -28,3 +24,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/good2.toml b/testing/configs/ensure_consistency/good2.toml
index f44baf2..ad38cda 100644
--- a/testing/configs/ensure_consistency/good2.toml
+++ b/testing/configs/ensure_consistency/good2.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 4
@@ -27,3 +23,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/good3.toml b/testing/configs/ensure_consistency/good3.toml
index b871685..1e5c77c 100644
--- a/testing/configs/ensure_consistency/good3.toml
+++ b/testing/configs/ensure_consistency/good3.toml
@@ -1,23 +1,19 @@
 # name should be added
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -26,3 +22,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/good4.toml b/testing/configs/ensure_consistency/good4.toml
index 7d68bc5..4c842f0 100644
--- a/testing/configs/ensure_consistency/good4.toml
+++ b/testing/configs/ensure_consistency/good4.toml
@@ -2,7 +2,7 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 capillary_num = 6
 capillary_outer_d = 2e-6
 capillary_spacing = 4e-6
@@ -11,23 +11,16 @@ core_radius = 50e-6
 length = 1
 model = "hasan"
 
-[gas]
+# gas
 gas_name = "helium"
 
-[gas.variable]
-temperature = [300, 350, 400]
-
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -36,3 +29,10 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# gas.variable
+temperature = [300, 350, 400]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/good5.toml b/testing/configs/ensure_consistency/good5.toml
index 27c607d..29cf7dc 100644
--- a/testing/configs/ensure_consistency/good5.toml
+++ b/testing/configs/ensure_consistency/good5.toml
@@ -2,23 +2,19 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 core_radius = 50e-6
 gamma = 0.018
 length = 1
 model = "marcatili"
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -27,3 +23,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/ensure_consistency/good6.toml b/testing/configs/ensure_consistency/good6.toml
index 0c12c7b..b297d15 100644
--- a/testing/configs/ensure_consistency/good6.toml
+++ b/testing/configs/ensure_consistency/good6.toml
@@ -3,24 +3,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -29,3 +25,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/override/fiber2.toml b/testing/configs/override/fiber2.toml
index 6eff163..e99ee15 100644
--- a/testing/configs/override/fiber2.toml
+++ b/testing/configs/override/fiber2.toml
@@ -1,13 +1,13 @@
 name = "fiber 2"
 
-[fiber]
+# fiber
 beta = [-1.183e-26, 8.1038e-41, -9.5205e-56, 2.0737e-70, -5.3943e-85, 1.3486e-99, -2.5495e-114, 3.0524e-129, -1.714e-144]
 gamma = 0.13
 length = 0.05
 model = "custom"
 
-[fiber.variable]
-input_transmission = [0.9, 0.95]
-
-[simulation]
+# simulation
 z_num = 16
+[variable]
+# fiber.variable
+input_transmission = [0.9, 0.95]
diff --git a/testing/configs/override/initial_config.toml b/testing/configs/override/initial_config.toml
index 707022e..37c6558 100644
--- a/testing/configs/override/initial_config.toml
+++ b/testing/configs/override/initial_config.toml
@@ -1,20 +1,20 @@
 name = "full anomalous"
 
-[fiber]
+# fiber
 beta = [-1.183e-26, 8.1038e-41, -9.5205e-56, 2.0737e-70, -5.3943e-85, 1.3486e-99, -2.5495e-114, 3.0524e-129, -1.714e-144]
 gamma = 0.11
 input_transmission = 1.0
 length = 0.02
 model = "custom"
 
-[pulse]
+# pulse
 intensity_noise = 0
 peak_power = 10000
 quantum_noise = false
 shape = "gaussian"
 t0 = 2.84e-14
 
-[simulation]
+# simulation
 behaviors = ["spm", "ss"]
 dt = 1e-15
 frep = 80000000.0
@@ -28,5 +28,6 @@ tolerated_error = 1e-9
 upper_wavelength_interp_limit = 1.9e-6
 z_num = 64
 
-[pulse.variable]
+[variable]
+# pulse.variable
 wavelength = [8.35e-7, 8.3375e-7]
diff --git a/testing/configs/param_sequence/almost_equal.toml b/testing/configs/param_sequence/almost_equal.toml
index 696cba4..ee11027 100644
--- a/testing/configs/param_sequence/almost_equal.toml
+++ b/testing/configs/param_sequence/almost_equal.toml
@@ -2,24 +2,21 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 width = 50e-15
 
-[pulse.variable]
-intensity_noise = [0.10000000005e-2, 0.1e-2]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 4
@@ -27,3 +24,7 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.10000000005e-2, 0.1e-2]
diff --git a/testing/configs/param_sequence/equal.toml b/testing/configs/param_sequence/equal.toml
index 5892468..f054c62 100644
--- a/testing/configs/param_sequence/equal.toml
+++ b/testing/configs/param_sequence/equal.toml
@@ -2,24 +2,21 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 width = 50e-15
 
-[pulse.variable]
-intensity_noise = [0.1e-2, 0.001]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 4
@@ -27,3 +24,7 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.1e-2, 0.001]
diff --git a/testing/configs/param_sequence/no_variations.toml b/testing/configs/param_sequence/no_variations.toml
index 2acdf2a..5abb35d 100644
--- a/testing/configs/param_sequence/no_variations.toml
+++ b/testing/configs/param_sequence/no_variations.toml
@@ -2,14 +2,14 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 intensity_noise = 0.1e-2
 peak_power = 100e3
 quantum_noise = true
@@ -17,7 +17,7 @@ shape = "gaussian"
 wavelength = 1050e-9
 width = 50e-15
 
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 repeat = 4
diff --git a/testing/configs/run_simulations/full_anomalous.toml b/testing/configs/run_simulations/full_anomalous.toml
index 6ea65d8..6aa0702 100644
--- a/testing/configs/run_simulations/full_anomalous.toml
+++ b/testing/configs/run_simulations/full_anomalous.toml
@@ -1,6 +1,6 @@
 name = "full anomalous"
 
-[fiber]
+# fiber
 beta = [
   -1.183e-26,
   8.1038e-41,
@@ -15,14 +15,11 @@ beta = [
 gamma = 0.11
 length = 0.02
 
-[pulse]
+# pulse
 peak_power = 10000
 t0 = 2.84e-14
 
-[pulse.variable]
-wavelength = [835e-9, 830e-9]
-
-[simulation]
+# simulation
 dt = 1e-15
 parallel = true
 raman_type = "measured"
@@ -30,3 +27,7 @@ repeat = 4
 t_num = 16384
 tolerated_error = 1e-10
 z_num = 64
+
+[variable]
+# pulse.variable
+wavelength = [835e-9, 830e-9]
diff --git a/testing/configs/validate_types/bad1.toml b/testing/configs/validate_types/bad1.toml
index ce628c5..334f706 100644
--- a/testing/configs/validate_types/bad1.toml
+++ b/testing/configs/validate_types/bad1.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 pitch = 1.5e-6
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -28,3 +24,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/validate_types/bad2.toml b/testing/configs/validate_types/bad2.toml
index 7016eec..bf7f2ab 100644
--- a/testing/configs/validate_types/bad2.toml
+++ b/testing/configs/validate_types/bad2.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss", "q_noise"]
 parallel = true
 raman_type = "agrawal"
@@ -28,3 +24,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/validate_types/bad3.toml b/testing/configs/validate_types/bad3.toml
index 02875f1..c37ebcf 100644
--- a/testing/configs/validate_types/bad3.toml
+++ b/testing/configs/validate_types/bad3.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = ["gaussian", "sech"]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -28,3 +24,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = ["gaussian", "sech"]
diff --git a/testing/configs/validate_types/bad4.toml b/testing/configs/validate_types/bad4.toml
index 935dc1d..c244854 100644
--- a/testing/configs/validate_types/bad4.toml
+++ b/testing/configs/validate_types/bad4.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 raman_type = "agrawal"
 repeat = 4
@@ -28,5 +24,9 @@ time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 1
 
-[simulation.variable]
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
+# simulation.variable
 parallel = [true, false]
diff --git a/testing/configs/validate_types/bad5.toml b/testing/configs/validate_types/bad5.toml
index 6cbcb19..b5bd4c2 100644
--- a/testing/configs/validate_types/bad5.toml
+++ b/testing/configs/validate_types/bad5.toml
@@ -2,24 +2,20 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = 0.05e-2
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -28,3 +24,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = 0.05e-2
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/validate_types/bad6.toml b/testing/configs/validate_types/bad6.toml
index e45989c..073b014 100644
--- a/testing/configs/validate_types/bad6.toml
+++ b/testing/configs/validate_types/bad6.toml
@@ -2,24 +2,21 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 intensity_noise = 0.05e-2
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -28,3 +25,7 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/validate_types/bad7.toml b/testing/configs/validate_types/bad7.toml
index 73fb985..c1863a4 100644
--- a/testing/configs/validate_types/bad7.toml
+++ b/testing/configs/validate_types/bad7.toml
@@ -2,22 +2,18 @@
 
 name = "test config"
 
-[fiber]
+# fiber
 beta = [1, 2, 3]
 gamma = 0.018
 length = 1
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = []
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -26,3 +22,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = []
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/configs/validate_types/good.toml b/testing/configs/validate_types/good.toml
index bd5196f..0452231 100644
--- a/testing/configs/validate_types/good.toml
+++ b/testing/configs/validate_types/good.toml
@@ -1,23 +1,19 @@
 name = "test config"
 
-[fiber]
+# fiber
 gamma = 0.018
 length = 1
 model = "pcf"
 pitch = 1.5e-6
 pitch_ratio = 0.37
 
-[pulse]
+# pulse
 peak_power = 100e3
 quantum_noise = true
 shape = "gaussian"
 wavelength = 1050e-9
 
-[pulse.variable]
-intensity_noise = [0.05e-2, 0.1e-2]
-width = [50e-15, 100e-15, 200e-15]
-
-[simulation]
+# simulation
 behaviors = ["spm", "raman", "ss"]
 parallel = true
 raman_type = "agrawal"
@@ -26,3 +22,8 @@ t_num = 16384
 time_window = 37e-12
 tolerated_error = 1e-11
 z_num = 128
+
+[variable]
+# pulse.variable
+intensity_noise = [0.05e-2, 0.1e-2]
+width = [50e-15, 100e-15, 200e-15]
diff --git a/testing/test_initialize.py b/testing/test_initialize.py
index 9106b6d..0be45be 100644
--- a/testing/test_initialize.py
+++ b/testing/test_initialize.py
@@ -6,7 +6,8 @@ import numpy as np
 import toml
 from scgenerator import defaults, utils, math
 from scgenerator.errors import *
-from scgenerator.physics import units
+from scgenerator.physics import pulse, units
+from scgenerator.utils.parameter import BareConfig, BareParams
 
 
 def load_conf(name):
@@ -38,12 +39,6 @@ class TestParamSequence(unittest.TestCase):
                 l.append(vary_list)
                 s.append(utils.format_variable_list(vary_list))
 
-    def test_init_config_not_affected_by_iteration(self):
-        for param_seq in self.iterconf(["almost_equal", "equal", "no_variations"]):
-            config = deepcopy(param_seq.config)
-            for _ in utils.required_simulations(param_seq.config):
-                self.assertEqual(config.items(), param_seq.config.items())
-
     def test_no_variations_yields_only_num_and_id(self):
         for param_seq in self.iterconf(["no_variations"]):
             for vary_list, _ in utils.required_simulations(param_seq.config):
@@ -55,34 +50,30 @@ class TestParamSequence(unittest.TestCase):
 class TestInitializeMethods(unittest.TestCase):
     def test_validate_types(self):
         conf = lambda s: load_conf("validate_types/" + s)
-        with self.assertRaisesRegex(TypeError, "belong"):
-            init._validate_types(conf("bad1"))
 
-        with self.assertRaisesRegex(TypeError, "valid list of behaviors"):
-            init._validate_types(conf("bad2"))
+        with self.assertRaisesRegex(ValueError, r"'behaviors\[3\]' must be a str in"):
+            init.Config(**conf("bad2"))
 
-        with self.assertRaisesRegex(TypeError, "single, real, non-negative number"):
-            init._validate_types(conf("bad3"))
+        with self.assertRaisesRegex(TypeError, "value must be of type <class 'float'>"):
+            init.Config(**conf("bad3"))
 
         with self.assertRaisesRegex(TypeError, "'parallel' is not a valid variable parameter"):
-            init._validate_types(conf("bad4"))
-
-        with self.assertRaisesRegex(TypeError, "Variable parameters should be specified in a list"):
-            init._validate_types(conf("bad5"))
+            init.Config(**conf("bad4"))
 
         with self.assertRaisesRegex(
-            TypeError,
-            "value '0' of type .*int.* for key 'repeat' is not valid, must be a strictly positive integer",
+            TypeError, "'variable intensity_noise' value must be of type <class 'list'>"
         ):
-            init._validate_types(conf("bad6"))
+            init.Config(**conf("bad5"))
+
+        with self.assertRaisesRegex(ValueError, "'repeat' must be positive"):
+            init.Config(**conf("bad6"))
 
         with self.assertRaisesRegex(
-            ValueError,
-            r"Variable parameters lists should contain at least 1 element",
+            ValueError, "variable parameter 'intensity_noise' must not be empty"
         ):
-            init._ensure_consistency(conf("bad7"))
+            init.Config(**conf("bad7"))
 
-        self.assertIsNone(init._validate_types(conf("good")))
+        self.assertIsNone(init.Config(**conf("good")).hr_w)
 
     def test_ensure_consistency(self):
         conf = lambda s: load_conf("ensure_consistency/" + s)
@@ -90,68 +81,66 @@ class TestInitializeMethods(unittest.TestCase):
             MissingParameterError,
             r"1 of '\['t0', 'width'\]' is required and no defaults have been set",
         ):
-            init._ensure_consistency(conf("bad1"))
+            init.Config(**conf("bad1"))
 
         with self.assertRaisesRegex(
             MissingParameterError,
             r"1 of '\['peak_power', 'mean_power', 'energy', 'width', 't0'\]' is required when 'soliton_num' is specified and no defaults have been set",
         ):
-            init._ensure_consistency(conf("bad2"))
+            init.Config(**conf("bad2"))
 
         with self.assertRaisesRegex(
             MissingParameterError,
             r"2 of '\['dt', 't_num', 'time_window'\]' are required and no defaults have been set",
         ):
-            init._ensure_consistency(conf("bad3"))
+            init.Config(**conf("bad3"))
 
         with self.assertRaisesRegex(
             DuplicateParameterError,
             r"got multiple values for parameter 'width'",
         ):
-            init._ensure_consistency(conf("bad4"))
+            init.Config(**conf("bad4"))
 
         with self.assertRaisesRegex(
             MissingParameterError,
             r"'capillary_thickness' is a required parameter for fiber model 'hasan' and no defaults have been set",
         ):
-            init._ensure_consistency(conf("bad5"))
+            init.Config(**conf("bad5"))
 
         with self.assertRaisesRegex(
             MissingParameterError,
             r"1 of '\['capillary_spacing', 'capillary_outer_d'\]' is required for fiber model 'hasan' and no defaults have been set",
         ):
-            init._ensure_consistency(conf("bad6"))
+            init.Config(**conf("bad6"))
 
         self.assertLessEqual(
-            {"model": "pcf"}.items(), init._ensure_consistency(conf("good1"))["fiber"].items()
+            {"model": "pcf"}.items(), init.Config(**conf("good1")).__dict__.items()
         )
 
-        self.assertNotIn("gas", init._ensure_consistency(conf("good1")))
-
-        self.assertNotIn("gamma", init._ensure_consistency(conf("good4"))["fiber"])
+        self.assertIsNone(init.Config(**conf("good4")).gamma)
 
         self.assertLessEqual(
             {"raman_type": "agrawal"}.items(),
-            init._ensure_consistency(conf("good2"))["simulation"].items(),
+            init.Config(**conf("good2")).__dict__.items(),
         )
 
         self.assertLessEqual(
-            {"name": "no name"}.items(), init._ensure_consistency(conf("good3")).items()
+            {"name": "no name"}.items(), init.Config(**conf("good3")).__dict__.items()
         )
 
         self.assertLessEqual(
             {"capillary_nested": 0, "capillary_resonance_strengths": []}.items(),
-            init._ensure_consistency(conf("good4"))["fiber"].items(),
+            init.Config(**conf("good4")).__dict__.items(),
         )
 
         self.assertLessEqual(
             dict(he_mode=(1, 1)).items(),
-            init._ensure_consistency(conf("good5"))["fiber"].items(),
+            init.Config(**conf("good5")).__dict__.items(),
         )
 
         self.assertLessEqual(
             dict(temperature=300, pressure=1e5, gas_name="vacuum", plasma_density=0).items(),
-            init._ensure_consistency(conf("good5"))["gas"].items(),
+            init.Config(**conf("good5")).__dict__.items(),
         )
 
         self.assertLessEqual(
@@ -165,62 +154,75 @@ class TestInitializeMethods(unittest.TestCase):
                     "upper_wavelength_interp_limit"
                 ],
             ).items(),
-            init._ensure_consistency(conf("good6"))["simulation"].items(),
+            init.Config(**conf("good6")).__dict__.items(),
         )
 
+    def setup_conf_custom_field(self, path) -> BareParams:
+
+        conf = load_conf(path)
+        conf = BareParams(**conf)
+        init.build_sim_grid_in_place(conf)
+        return conf
+
     def test_setup_custom_field(self):
         d = np.load("testing/configs/custom_field/init_field.npz")
         t = d["time"]
         field = d["field"]
-        conf = load_conf("custom_field/no_change")
-        conf = init.build_sim_grid(conf)
-        result = init.setup_custom_field(conf)
-        self.assertAlmostEqual(conf["field_0"].real.max(), field.real.max(), 4)
-        self.assertTrue(result)
-
-        conf = load_conf("custom_field/peak_power")
-        conf = init.build_sim_grid(conf)
-        result = init.setup_custom_field(conf)
-        self.assertAlmostEqual(math.abs2(conf["field_0"]).max(), 20000, 4)
-        self.assertTrue(result)
-        self.assertNotAlmostEqual(conf["wavelength"], 1593e-9)
-
-        conf = load_conf("custom_field/mean_power")
-        conf = init.build_sim_grid(conf)
-        result = init.setup_custom_field(conf)
-        self.assertAlmostEqual(np.trapz(math.abs2(conf["field_0"]), conf["t"]), 0.22 / 40e6, 4)
-        self.assertTrue(result)
-
-        conf = load_conf("custom_field/recover1")
-        conf = init.build_sim_grid(conf)
-        result = init.setup_custom_field(conf)
-        self.assertAlmostEqual(math.abs2(conf["field_0"] - field).sum(), 0)
-        self.assertTrue(result)
-
-        conf = load_conf("custom_field/recover2")
-        conf = init.build_sim_grid(conf)
-        result = init.setup_custom_field(conf)
-        self.assertAlmostEqual((math.abs2(conf["field_0"]) / 0.9 - math.abs2(field)).sum(), 0)
-        self.assertTrue(result)
-
-        conf = load_conf("custom_field/wavelength_shift1")
-        result = init.compute_init_parameters(conf)
-        self.assertAlmostEqual(
-            units.m.inv(result["w"])[np.argmax(math.abs2(result["spec_0"]))], 1050e-9
+        conf = self.setup_conf_custom_field("custom_field/no_change")
+        result, conf.width, conf.peak_power, conf.energy, conf.field_0 = pulse.setup_custom_field(
+            conf
         )
+        self.assertAlmostEqual(conf.field_0.real.max(), field.real.max(), 4)
+        self.assertTrue(result)
 
-        conf = load_conf("custom_field/wavelength_shift1")
-        conf["pulse"]["wavelength"] = 1593e-9
-        result = init.compute_init_parameters(conf)
+        conf = self.setup_conf_custom_field("custom_field/peak_power")
+        result, conf.width, conf.peak_power, conf.energy, conf.field_0 = pulse.setup_custom_field(
+            conf
+        )
+        conf.wavelength = pulse.correct_wavelength(conf.wavelength, conf.w_c, conf.field_0)
+        self.assertAlmostEqual(math.abs2(conf.field_0).max(), 20000, 4)
+        self.assertTrue(result)
+        self.assertNotAlmostEqual(conf.wavelength, 1593e-9)
+
+        conf = self.setup_conf_custom_field("custom_field/mean_power")
+        result, conf.width, conf.peak_power, conf.energy, conf.field_0 = pulse.setup_custom_field(
+            conf
+        )
+        self.assertAlmostEqual(np.trapz(math.abs2(conf.field_0), conf.t), 0.22 / 40e6, 4)
+        self.assertTrue(result)
+
+        conf = self.setup_conf_custom_field("custom_field/recover1")
+        result, conf.width, conf.peak_power, conf.energy, conf.field_0 = pulse.setup_custom_field(
+            conf
+        )
+        self.assertAlmostEqual(math.abs2(conf.field_0 - field).sum(), 0)
+        self.assertTrue(result)
+
+        conf = self.setup_conf_custom_field("custom_field/recover2")
+        result, conf.width, conf.peak_power, conf.energy, conf.field_0 = pulse.setup_custom_field(
+            conf
+        )
+        self.assertAlmostEqual((math.abs2(conf.field_0) / 0.9 - math.abs2(field)).sum(), 0)
+        self.assertTrue(result)
+
+        conf = self.setup_conf_custom_field("custom_field/wavelength_shift1")
+        result = init.Params.from_bare(conf)
+        self.assertAlmostEqual(units.m.inv(result.w)[np.argmax(math.abs2(result.spec_0))], 1050e-9)
+
+        conf = self.setup_conf_custom_field("custom_field/wavelength_shift1")
+        conf.wavelength = 1593e-9
+        result = init.Params.from_bare(conf)
 
         conf = load_conf("custom_field/wavelength_shift2")
+        conf = init.Config(**conf)
         for target, (variable, config) in zip(
             [1050e-9, 1321e-9, 1593e-9], init.ParamSequence(conf)
         ):
+            init.build_sim_grid_in_place(conf)
             self.assertAlmostEqual(
-                units.m.inv(config["w"])[np.argmax(math.abs2(config["spec_0"]))], target
+                units.m.inv(config.w)[np.argmax(math.abs2(config.spec_0))], target
             )
-            print(config["wavelength"], target)
+            print(config.wavelength, target)
 
 
 if __name__ == "__main__":
diff --git a/testing/test_new_params.py b/testing/test_new_params.py
deleted file mode 100644
index 82e900d..0000000
--- a/testing/test_new_params.py
+++ /dev/null
@@ -1,37 +0,0 @@
-from numba.core import config
-from scgenerator.initialize import Config, Params, BareParams
-from scgenerator.utils import variable_iterator, override_config
-from scgenerator.io import load_toml
-from pprint import pprint
-from dataclasses import asdict
-
-dico = load_toml("testing/configs/ensure_consistency/good2.toml")
-out = dict(variable=dict())
-for k, v in dico.items():
-    if isinstance(v, dict):
-        for kk, vv in v.items():
-            if kk == "variable":
-                for kkk, vvv in vv.items():
-                    out["variable"][kkk] = vvv
-            else:
-                out[kk] = vv
-
-pprint(out)
-p = Config(**out)
-print(p)
-
-for l, c in variable_iterator(p):
-    print(l, c.width, c.intensity_noise)
-    print()
-
-config2 = override_config(dict(width=1.2e-13, variable=dict(peak_power=[1e5, 2e5])), p)
-print(
-    f"{config2.variable=}",
-    f"{config2.intensity_noise=}",
-    f"{config2.width=}",
-    f"{config2.peak_power=}",
-)
-
-par = BareParams()
-
-print(all(v is None for v in vars(par).values()))
diff --git a/testing/test_utils.py b/testing/test_utils.py
index 20429d7..3edd114 100644
--- a/testing/test_utils.py
+++ b/testing/test_utils.py
@@ -14,9 +14,9 @@ def load_conf(name):
 def conf_maker(folder, val=True):
     def conf(name):
         if val:
-            return initialize.validate(load_conf(folder + "/" + name))
+            return initialize.Config(**load_conf(folder + "/" + name))
         else:
-            return load_conf(folder + "/" + name)
+            return initialize.BareConfig(**load_conf(folder + "/" + name))
 
     return conf
 
@@ -58,9 +58,9 @@ class TestUtilsMethods(unittest.TestCase):
         old = conf("initial_config")
         new = conf("fiber2")
 
-        over = utils.override_config(new, old)
-        self.assertIn("input_transmission", over["fiber"]["variable"])
-        self.assertNotIn("input_transmission", over["fiber"])
+        over = utils.override_config(vars(new), old)
+        self.assertNotIn("input_transmission", over.variable)
+        self.assertIsNone(over.input_transmission)
 
 
 if __name__ == "__main__":