Merge in changes for v0.4.0

.pre-commit-config.yaml

@@ -16,4 +16,4 @@ repos:
   rev: v1.13.0
   hooks:
     - id: mypy
-      additional_dependencies: []
+      additional_dependencies: [types-PyYAML]

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.9"
+    python: "3.13"
     # You can also specify other tool versions:
     # nodejs: "16"
     # rust: "1.55"

data/ero_file.csv

@@ -0,0 +1,7 @@
+type,unit,duration_myr,parameter1,parameter2,parameter3
+exponential,erosion_rate,150.0,-0.030,40.0,-0.010
+exponential,erosion_rate,200.0,-0.010,50.0,0.060
+linear,erosion_rate,200.0,0.060,0.000,
+constant,erosion_rate,200.0,0.000,,
+linear,erosion_rate,100.0,0.000,0.030,
+exponential,erosion_rate,150.0,0.030,60.0,0.005

data/input_file.yaml

@@ -0,0 +1,265 @@
+# Tc1D input file (YAML)
+#
+# Goal:
+# - Replace command lines with a readable config file
+# - If a key is omitted, Tc1D falls back to tc1d-cli defaults
+#
+# IMPORTANT:
+# - YAML keys present here override argparse values (and thus override CLI flags)
+# - Avoid defining the same key twice in this file: the last occurrence wins
+#
+# ---------------------------------------------------------------------------
+# Inversion syntax (NA / MCMC)
+#
+# For any parameter you want to invert, write it as a 2-element range:
+#   param: [min, max]
+#
+# Examples:
+#   ero_option1: [0.0, 20.0]   # invert within 0..20 km for instance
+#   temp_base:   [1200, 1400] #
+#
+# For any parameter you want to fix, write it as a scalar:
+#   param: 7.0
+#
+# Notes:
+# - Ranges are equivalent to the CLI syntax:  --param min max
+# - Scalars are equivalent to the CLI syntax: --param value
+# ---------------------------------------------------------------------------
+
+# Units:
+# - time: Myr
+# - dt: years
+# - lengths/depths/thicknesses: km
+# - erosion rates: depend on ero_type (see comments below)
+
+# ==============================================================================
+# 1) General / run control
+# ==============================================================================
+general:
+  run_type: "mcmc"          # forward / batch / na / mcmc
+  batch_mode: false
+  inverse_mode: true
+  debug: false
+
+  # Screen output toggles
+  echo_inputs: false
+  no_echo_info: true
+  no_echo_thermal_info: true
+  no_echo_ages: true
+
+# ==============================================================================
+# 2) Geometry and time
+# ==============================================================================
+geometry_time:
+  length: 125.0                # --length (model depth extent)
+  nx: 251                      # --nx
+  time: 15.0                 # --time
+  dt: 10000.0                  # --dt
+
+  init_moho_depth: 50.0        # --init-moho-depth
+  crustal_uplift: false        # --crustal-uplift
+  fixed_moho: false            # --fixed-moho
+
+  removal_fraction: 0.0        # --removal-fraction
+  removal_start_time: 0.0      # --removal-start-time
+  removal_end_time: -1.0       # --removal-end-time
+
+# ==============================================================================
+# 3) Materials
+# ==============================================================================
+materials:
+  rho_crust: 2850.0
+  cp_crust: 800.0
+  k_crust: 2.75
+  heat_prod_crust: 0.5
+  heat_prod_decay_depth: -1.0
+  alphav_crust: 3.0e-5
+
+  rho_mantle: 3250.0
+  cp_mantle: 1000.0
+  k_mantle: 2.5
+  heat_prod_mantle: 0.0
+  alphav_mantle: 3.0e-5
+
+  rho_a: 3250.0
+  k_a: 20.0
+
+# ==============================================================================
+# 4) Thermal model
+# ==============================================================================
+thermal_model:
+  explicit: false              # false => implicit scheme
+  mantle_adiabat: true
+
+  temp_surf: 0.0
+  temp_base: 1300.0
+
+# ==============================================================================
+# 5) Magmatic intrusion (optional)
+# ==============================================================================
+intrusion_model:
+  intrusion_temperature: 750.0
+  intrusion_start_time: -1.0
+  intrusion_duration: -1.0
+  intrusion_thickness: -1.0
+  intrusion_base_depth: -1.0
+
+# ==============================================================================
+# 6) Erosion model
+# ==============================================================================
+erosion_model:
+  vx_init: 0.0                 # --vx-init (mm/yr)
+
+  # Select erosion model (0 to 7)
+  # 0: multi-stage erosion defined directly in YAML (ero_stages)
+  # 1: constant erosion magnitude (total thickness in km over the run)
+  # 2: stepwise thicknesses with transition times
+  # 3: exponential decay
+  # 4: thrust sheet emplacement + erosional removal
+  # 5: tectonic exhumation + erosion
+  # 6: linear change in erosion rate
+  # 7: extensional tectonics
+  ero_type: 0
+
+  # ---- Active parameters (EDIT THESE) ----------------------------------------
+  # Define only the options used by your selected ero_type.
+  # Unused options can be omitted; tc1d-cli defaults will apply.
+
+  # ero_type = 2 (example: two intervals)
+  #ero_option1: 10.0
+  #ero_option2: 5.0
+  #ero_option3: 2.0
+  #ero_option4: 10.0
+
+  # ---- Optional: ero_type = 0 (Multi-stage erosion) ---------------
+  # BG: YAML-defined multi-stage erosion/burial history
+  ero_stages:
+    # Stage 1: exponential decay
+    - type: exponential
+      unit: erosion_rate
+      duration_myr: [0.1, 5.0]
+      parameter1: [0.1, 4.0]    # r_start (km/Myr)
+      parameter2: [0.1, 3.0] # tau (Myr)
+      parameter3: 0.01 # t_target (km/Myr)
+
+    # Stage 2: constant erosion
+    - type: constant
+      unit: erosion_rate
+      duration_myr: [1.0, 10.0]
+      parameter1: 0.01
+
+    # Stage 3: linear increase
+    - type: linear
+      unit: erosion_rate
+      duration_myr: [0.1, 6.0]
+      parameter1: 0.01
+      parameter2: [0.1, 3.0]
+
+  # ---- Optional: other erosion types (examples) ------------------------------
+  # ero_type = 1 (constant magnitude over the run)
+  # ero_type: 1
+  # ero_option1: 2.0
+
+  # ero_type = 3 (exponential decay)
+  # ero_type: 3
+  # ero_option1: 15.0
+  # ero_option2: 20.0
+  # ero_option3: 0.0
+
+# ==============================================================================
+# 7) Age prediction
+# ==============================================================================
+age_prediction:
+  no_calc_ages: false
+
+  ketch_aft: true
+  madtrax_aft: false
+  madtrax_aft_kinetic_model: 1
+  madtrax_zft_kinetic_model: 1
+
+  ap_rad: 45.0
+  ap_uranium: 10.0
+  ap_thorium: 40.0
+
+  zr_rad: 60.0
+  zr_uranium: 100.0
+  zr_thorium: 40.0
+
+  pad_time: 0.0
+  past_age_increment: 0.0
+
+# ==============================================================================
+# 8) Observations and misfit
+# ==============================================================================
+observations:
+  obs_age_file: "sample_data.csv"             # CSV file containing measured ages
+
+  obs_ahe: []
+  obs_ahe_stdev: []
+  obs_aft: []
+  obs_aft_stdev: []
+  obs_zhe: []
+  obs_zhe_stdev: []
+  obs_zft: []
+  obs_zft_stdev: []
+
+  misfit_num_params: 0
+  misfit_type: 1
+
+# ==============================================================================
+# 9) Plotting
+# ==============================================================================
+plotting:
+  no_plot_results: false
+  no_display_plots: false
+
+  plot_myr: false
+  plot_depth_history: false
+  plot_fault_depth_history: false
+  invert_tt_plot: false
+
+  t_plots: [1, 3, 5, 7, 9, 10]
+
+  crust_solidus: false
+  crust_solidus_comp: "wet_intermediate"
+  mantle_solidus: false
+  mantle_solidus_xoh: 0.0
+  solidus_ranges: false
+
+# ==============================================================================
+# 10) Output
+# ==============================================================================
+output:
+  log_output: false
+  log_file: ""
+  model_id: ""
+
+  write_temps: false
+  write_past_ages: false
+  write_age_output: false
+  save_plots: true
+
+# ==============================================================================
+# 11) Advanced
+# ==============================================================================
+advanced:
+  read_temps: false
+  compare_temps: false
+
+# ==============================================================================
+# 12) Inversion hyperparameters
+# ==============================================================================
+inversion:
+  neighbourhood_algorithm:
+    na_ns: 20
+    na_nr: 5
+    na_ni: 50
+    na_n: 5
+    na_n_resample: 2000
+    na_n_walkers: 5
+
+  mcmc:
+    mcmc_nwalkers: 24
+    mcmc_nsteps: 300
+    mcmc_discard: 0
+    mcmc_thin: 3

docs/rtd-requirements.txt

@@ -1,4 +1,5 @@
 myst-nb
 numpydoc
 sphinx-book-theme
-sphinxcontrib-bibtex
+sphinxcontrib-bibtex
+tc1d

docs/source/conf.py

@@ -1,10 +1,10 @@
 # Configuration file for the Sphinx documentation builder.
 
 # -- Path setup
-from pathlib import Path
-import sys
+# from pathlib import Path
+# import sys
 
-sys.path.insert(0, str(Path("..", "..", "src").resolve()))
+# sys.path.insert(0, str(Path("..", "..", "src").resolve()))
 
 # -- Project information
 

docs/source/erosion-models.md

@@ -125,7 +125,7 @@ The maximum erosion rate $\dot{e}_{\mathrm{max}}$ is calculated as:
 
 $$
 \begin{equation}
-\dot{e}_{\mathrm{max}} = \frac{m}{\uptau - \exp{(-(t_{\mathrm{total}} - t_{\mathrm{start}}) / \uptau)}}.
+\dot{e}_{\mathrm{max}} = \frac{m}{\uptau (1 - \exp{(-(t_{\mathrm{total}} - t_{\mathrm{start}}) / \uptau))}}.
 \end{equation}
 $$
 

docs/source/index.rst

@@ -2,7 +2,7 @@ Documentation for T\ :sub:`c`\ 1D
 =================================
 
 .. image:: gif/tc1d-2025.gif
-   :width: 600
+   :width: 720
    :alt: TC1D running
 
 T\ :sub:`c`\ 1D is a one-dimensional thermal and thermochronometer age prediction model that can simulate the effects of various geodynamic and geomorphic processes on thermochronometer ages.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "tc1d"
-version = "0.3.2"
+version = "0.4.0"
 authors = [
     {name = "Dave Whipp", email = "david.whipp@helsinki.fi"},
     {name= "Benjamin Gérard", email = "benjamin.gerard@helsinki.fi"},
@@ -127,3 +127,5 @@ hatchling = ">=1.27.0,<2"
 mypy = ">=1.17.1,<2"
 pip = ">=25.2,<26"
 pre-commit = ">=4.3.0,<5"
+types-pyyaml = ">=6.0.12.20250915,<7"
+pyyaml = ">=6.0.3,<7"