pychnosz 1.1.1__cp311-cp311-macosx_10_13_x86_64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pychnosz/.dylibs/libgcc_s.1.1.dylib +0 -0
- pychnosz/.dylibs/libgfortran.5.dylib +0 -0
- pychnosz/.dylibs/libquadmath.0.dylib +0 -0
- pychnosz/__init__.py +129 -0
- pychnosz/biomolecules/__init__.py +29 -0
- pychnosz/biomolecules/ionize_aa.py +197 -0
- pychnosz/biomolecules/proteins.py +595 -0
- pychnosz/core/__init__.py +46 -0
- pychnosz/core/affinity.py +1256 -0
- pychnosz/core/animation.py +593 -0
- pychnosz/core/balance.py +334 -0
- pychnosz/core/basis.py +716 -0
- pychnosz/core/diagram.py +3336 -0
- pychnosz/core/equilibrate.py +813 -0
- pychnosz/core/equilibrium.py +554 -0
- pychnosz/core/info.py +821 -0
- pychnosz/core/retrieve.py +364 -0
- pychnosz/core/speciation.py +580 -0
- pychnosz/core/species.py +599 -0
- pychnosz/core/subcrt.py +1700 -0
- pychnosz/core/thermo.py +593 -0
- pychnosz/core/unicurve.py +1226 -0
- pychnosz/data/__init__.py +11 -0
- pychnosz/data/add_obigt.py +327 -0
- pychnosz/data/extdata/Berman/BDat17_2017.csv +2 -0
- pychnosz/data/extdata/Berman/Ber88_1988.csv +68 -0
- pychnosz/data/extdata/Berman/Ber90_1990.csv +5 -0
- pychnosz/data/extdata/Berman/DS10_2010.csv +6 -0
- pychnosz/data/extdata/Berman/FDM+14_2014.csv +2 -0
- pychnosz/data/extdata/Berman/Got04_2004.csv +5 -0
- pychnosz/data/extdata/Berman/JUN92_1992.csv +3 -0
- pychnosz/data/extdata/Berman/SHD91_1991.csv +12 -0
- pychnosz/data/extdata/Berman/VGT92_1992.csv +2 -0
- pychnosz/data/extdata/Berman/VPT01_2001.csv +3 -0
- pychnosz/data/extdata/Berman/VPV05_2005.csv +2 -0
- pychnosz/data/extdata/Berman/ZS92_1992.csv +11 -0
- pychnosz/data/extdata/Berman/sympy.R +99 -0
- pychnosz/data/extdata/Berman/testing/BA96.bib +12 -0
- pychnosz/data/extdata/Berman/testing/BA96_Berman.csv +21 -0
- pychnosz/data/extdata/Berman/testing/BA96_OBIGT.csv +21 -0
- pychnosz/data/extdata/Berman/testing/BA96_refs.csv +6 -0
- pychnosz/data/extdata/OBIGT/AD.csv +25 -0
- pychnosz/data/extdata/OBIGT/Berman_cr.csv +93 -0
- pychnosz/data/extdata/OBIGT/DEW.csv +211 -0
- pychnosz/data/extdata/OBIGT/H2O_aq.csv +4 -0
- pychnosz/data/extdata/OBIGT/SLOP98.csv +411 -0
- pychnosz/data/extdata/OBIGT/SUPCRT92.csv +178 -0
- pychnosz/data/extdata/OBIGT/inorganic_aq.csv +729 -0
- pychnosz/data/extdata/OBIGT/inorganic_cr.csv +273 -0
- pychnosz/data/extdata/OBIGT/inorganic_gas.csv +20 -0
- pychnosz/data/extdata/OBIGT/organic_aq.csv +1104 -0
- pychnosz/data/extdata/OBIGT/organic_cr.csv +481 -0
- pychnosz/data/extdata/OBIGT/organic_gas.csv +268 -0
- pychnosz/data/extdata/OBIGT/organic_liq.csv +533 -0
- pychnosz/data/extdata/OBIGT/testing/GEMSFIT.csv +43 -0
- pychnosz/data/extdata/OBIGT/testing/IGEM.csv +17 -0
- pychnosz/data/extdata/OBIGT/testing/Sandia.csv +8 -0
- pychnosz/data/extdata/OBIGT/testing/SiO2.csv +4 -0
- pychnosz/data/extdata/misc/AD03_Fig1a.csv +69 -0
- pychnosz/data/extdata/misc/AD03_Fig1b.csv +43 -0
- pychnosz/data/extdata/misc/AD03_Fig1c.csv +89 -0
- pychnosz/data/extdata/misc/AD03_Fig1d.csv +30 -0
- pychnosz/data/extdata/misc/BZA10.csv +5 -0
- pychnosz/data/extdata/misc/HW97_Cp.csv +90 -0
- pychnosz/data/extdata/misc/HWM96_V.csv +229 -0
- pychnosz/data/extdata/misc/LA19_test.csv +7 -0
- pychnosz/data/extdata/misc/Mer75_Table4.csv +42 -0
- pychnosz/data/extdata/misc/OBIGT_check.csv +423 -0
- pychnosz/data/extdata/misc/PM90.csv +7 -0
- pychnosz/data/extdata/misc/RH95.csv +23 -0
- pychnosz/data/extdata/misc/RH98_Table15.csv +17 -0
- pychnosz/data/extdata/misc/SC10_Rainbow.csv +19 -0
- pychnosz/data/extdata/misc/SK95.csv +55 -0
- pychnosz/data/extdata/misc/SOJSH.csv +61 -0
- pychnosz/data/extdata/misc/SS98_Fig5a.csv +81 -0
- pychnosz/data/extdata/misc/SS98_Fig5b.csv +84 -0
- pychnosz/data/extdata/misc/TKSS14_Fig2.csv +25 -0
- pychnosz/data/extdata/misc/bluered.txt +1000 -0
- pychnosz/data/extdata/protein/Cas/Cas_aa.csv +177 -0
- pychnosz/data/extdata/protein/Cas/Cas_uniprot.csv +186 -0
- pychnosz/data/extdata/protein/Cas/download.R +34 -0
- pychnosz/data/extdata/protein/Cas/mkaa.R +34 -0
- pychnosz/data/extdata/protein/POLG.csv +12 -0
- pychnosz/data/extdata/protein/TBD+05.csv +393 -0
- pychnosz/data/extdata/protein/TBD+05_aa.csv +393 -0
- pychnosz/data/extdata/protein/rubisco.csv +28 -0
- pychnosz/data/extdata/protein/rubisco.fasta +239 -0
- pychnosz/data/extdata/protein/rubisco_aa.csv +28 -0
- pychnosz/data/extdata/src/H2O92D.f.orig +3457 -0
- pychnosz/data/extdata/src/README.txt +5 -0
- pychnosz/data/extdata/taxonomy/names.dmp +215 -0
- pychnosz/data/extdata/taxonomy/nodes.dmp +63 -0
- pychnosz/data/extdata/thermo/Bdot_acirc.csv +60 -0
- pychnosz/data/extdata/thermo/buffer.csv +40 -0
- pychnosz/data/extdata/thermo/element.csv +135 -0
- pychnosz/data/extdata/thermo/groups.csv +6 -0
- pychnosz/data/extdata/thermo/opt.csv +2 -0
- pychnosz/data/extdata/thermo/protein.csv +506 -0
- pychnosz/data/extdata/thermo/refs.csv +343 -0
- pychnosz/data/extdata/thermo/stoich.csv.xz +0 -0
- pychnosz/data/loader.py +431 -0
- pychnosz/data/mod_obigt.py +322 -0
- pychnosz/data/obigt.py +471 -0
- pychnosz/data/worm.py +228 -0
- pychnosz/fortran/__init__.py +16 -0
- pychnosz/fortran/h2o92.dylib +0 -0
- pychnosz/fortran/h2o92_interface.py +527 -0
- pychnosz/geochemistry/__init__.py +21 -0
- pychnosz/geochemistry/minerals.py +514 -0
- pychnosz/geochemistry/redox.py +500 -0
- pychnosz/models/__init__.py +47 -0
- pychnosz/models/archer_wang.py +165 -0
- pychnosz/models/berman.py +309 -0
- pychnosz/models/cgl.py +381 -0
- pychnosz/models/dew.py +997 -0
- pychnosz/models/hkf.py +523 -0
- pychnosz/models/hkf_helpers.py +222 -0
- pychnosz/models/iapws95.py +1113 -0
- pychnosz/models/supcrt92_fortran.py +238 -0
- pychnosz/models/water.py +480 -0
- pychnosz/utils/__init__.py +27 -0
- pychnosz/utils/expression.py +1074 -0
- pychnosz/utils/formula.py +830 -0
- pychnosz/utils/formula_ox.py +227 -0
- pychnosz/utils/reset.py +33 -0
- pychnosz/utils/units.py +259 -0
- pychnosz-1.1.1.dist-info/METADATA +197 -0
- pychnosz-1.1.1.dist-info/RECORD +131 -0
- pychnosz-1.1.1.dist-info/WHEEL +5 -0
- pychnosz-1.1.1.dist-info/licenses/LICENSE.txt +19 -0
- pychnosz-1.1.1.dist-info/top_level.txt +1 -0
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"""
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CHNOSZ unicurve() function - Calculate univariant curves for geothermometry/geobarometry.
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This module implements functions to solve for temperatures or pressures of equilibration
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for a given logK value, producing univariant curves useful for aqueous geothermometry
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and geobarometry applications.
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Author: Based on pyCHNOSZ univariant.r by Grayson Boyer
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Optimized: Uses scipy.optimize.brentq() for efficient root-finding
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"""
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import numpy as np
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import pandas as pd
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from typing import Union, List, Optional, Dict, Any
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import warnings
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from scipy.optimize import brentq
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from concurrent.futures import ProcessPoolExecutor, as_completed
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import multiprocessing
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from .subcrt import subcrt, SubcrtResult
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# Import plotly for univariant_TP
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try:
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import plotly.graph_objects as go
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PLOTLY_AVAILABLE = True
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except ImportError:
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PLOTLY_AVAILABLE = False
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go = None
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class UnivariantResult:
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"""Result structure for univariant curve calculations."""
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def __init__(self):
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self.reaction = None # Reaction summary DataFrame
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self.out = None # Results DataFrame with T/P and thermodynamic properties
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self.warnings = [] # Warning messages
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self.fig = None # Plotly figure object (if plot_it=True)
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def __repr__(self):
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if self.out is not None:
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return f"UnivariantResult with {len(self.out)} points"
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return "UnivariantResult (no calculations performed)"
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def __getitem__(self, key):
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"""Allow dictionary-style access to attributes."""
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return getattr(self, key)
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def _solve_T_for_pressure(logK: float, species: List, state: List, coeff: List,
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pressure: float, IS: float, minT: float, maxT: float,
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tol: float, initial_guess: Optional[float] = None,
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messages: bool = False) -> Dict[str, Any]:
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"""
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Solve for temperature at a given pressure that produces the target logK.
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Uses scipy.optimize.brentq (Brent's method) for efficient root-finding.
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Brent's method combines bisection, secant, and inverse quadratic interpolation
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for guaranteed convergence with minimal function evaluations.
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Parameters
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----------
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logK : float
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Target logarithm (base 10) of equilibrium constant
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species : list
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List of species names or indices
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state : list
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List of states for each species
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coeff : list
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Reaction coefficients
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pressure : float
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Pressure in bars
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IS : float
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Ionic strength
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minT : float
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Minimum temperature (°C) to search
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maxT : float
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Maximum temperature (°C) to search
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tol : float
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Tolerance for convergence
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initial_guess : float, optional
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Initial guess for warm start (not used by brentq but kept for future optimization)
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messages : bool
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Print messages
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Returns
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-------
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dict
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Dictionary with 'T', 'P', 'logK', and other thermodynamic properties,
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or None values if no solution found
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"""
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def objective(T):
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"""Objective function: returns (calculated_logK - target_logK)."""
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try:
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result = subcrt(species, coeff=coeff, state=state,
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T=T, P=pressure, IS=IS,
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exceed_Ttr=True, messages=False, show=False)
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if result.out is None or 'logK' not in result.out.columns:
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return np.nan
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calc_logK = result.out['logK'].iloc[0]
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if pd.isna(calc_logK) or not np.isfinite(calc_logK):
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return np.nan
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return calc_logK - logK
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except Exception:
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return np.nan
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# Check if root is bracketed by evaluating at endpoints
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try:
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f_min = objective(minT)
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f_max = objective(maxT)
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# If boundaries return NaN, search inward to find valid endpoints
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current_minT = minT
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current_maxT = maxT
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if np.isnan(f_min):
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# Search from minT upward to find a valid lower bound
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step = (maxT - minT) / 20 # Use 20 steps to search
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for i in range(1, 20):
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test_T = minT + i * step
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f_test = objective(test_T)
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if not np.isnan(f_test):
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current_minT = test_T
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f_min = f_test
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if messages:
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print(f" Adjusted minT from {minT:.1f} to {current_minT:.1f}°C (valid boundary)")
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break
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else:
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# Could not find valid lower bound
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if messages:
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print(f"Could not find valid lower temperature bound for P={pressure} bar")
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return {
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'T': None, 'P': pressure, 'logK': None, 'G': None,
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'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
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'Warning': f"Could not converge on T for this P within {minT} and {maxT} degC"
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}
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if np.isnan(f_max):
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# Search from maxT downward to find a valid upper bound
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step = (maxT - minT) / 20 # Use 20 steps to search
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for i in range(1, 20):
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test_T = maxT - i * step
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f_test = objective(test_T)
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if not np.isnan(f_test):
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current_maxT = test_T
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f_max = f_test
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if messages:
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print(f" Adjusted maxT from {maxT:.1f} to {current_maxT:.1f}°C (valid boundary)")
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break
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else:
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# Could not find valid upper bound
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if messages:
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print(f"Could not find valid upper temperature bound for P={pressure} bar")
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return {
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'T': None, 'P': pressure, 'logK': None, 'G': None,
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'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
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'Warning': f"Could not converge on T for this P within {minT} and {maxT} degC"
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}
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# Check if root is bracketed (signs must be opposite)
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if f_min * f_max > 0:
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if messages:
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print(f"Root not bracketed at P={pressure} bar: logK range [{f_min+logK:.3f}, {f_max+logK:.3f}] doesn't include target {logK:.3f}")
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return {
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'T': None, 'P': pressure, 'logK': None, 'G': None,
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'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
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'Warning': f"Could not converge on T for this P within {minT} and {maxT} degC"
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}
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# Use Brent's method to find the root
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T_solution = brentq(objective, current_minT, current_maxT, xtol=tol, rtol=tol)
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# Get full thermodynamic properties at the solution
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final_result = subcrt(species, coeff=coeff, state=state,
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T=T_solution, P=pressure, IS=IS,
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exceed_Ttr=True, messages=False, show=False)
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result_dict = {
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'T': T_solution,
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'P': pressure,
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'logK': final_result.out['logK'].iloc[0] if 'logK' in final_result.out.columns else None,
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'G': final_result.out['G'].iloc[0] if 'G' in final_result.out.columns else None,
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'H': final_result.out['H'].iloc[0] if 'H' in final_result.out.columns else None,
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'S': final_result.out['S'].iloc[0] if 'S' in final_result.out.columns else None,
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'V': final_result.out['V'].iloc[0] if 'V' in final_result.out.columns else None,
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'Cp': final_result.out['Cp'].iloc[0] if 'Cp' in final_result.out.columns else None,
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}
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|
195
|
+
if 'rho' in final_result.out.columns:
|
|
196
|
+
result_dict['rho'] = final_result.out['rho'].iloc[0]
|
|
197
|
+
else:
|
|
198
|
+
result_dict['rho'] = None
|
|
199
|
+
|
|
200
|
+
return result_dict
|
|
201
|
+
|
|
202
|
+
except ValueError as e:
|
|
203
|
+
if messages:
|
|
204
|
+
warnings.warn(f"Brent's method failed at P={pressure} bar: {str(e)}")
|
|
205
|
+
return {
|
|
206
|
+
'T': None, 'P': pressure, 'logK': None, 'G': None,
|
|
207
|
+
'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
|
|
208
|
+
'Warning': f"Could not converge on T for this P within {minT} and {maxT} degC"
|
|
209
|
+
}
|
|
210
|
+
except Exception as e:
|
|
211
|
+
if messages:
|
|
212
|
+
warnings.warn(f"Error during calculation at P={pressure} bar: {str(e)}")
|
|
213
|
+
return {
|
|
214
|
+
'T': None, 'P': pressure, 'logK': None, 'G': None,
|
|
215
|
+
'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
|
|
216
|
+
'Warning': f"Could not converge on T for this P within {minT} and {maxT} degC"
|
|
217
|
+
}
|
|
218
|
+
|
|
219
|
+
|
|
220
|
+
def _create_unicurve_plot(logK: float, species: List, state: List, coeff: List,
|
|
221
|
+
result: UnivariantResult, solve: str,
|
|
222
|
+
minT: float, maxT: float, minP: float, maxP: float,
|
|
223
|
+
IS: float, width: int, height: int, res: int,
|
|
224
|
+
messages: bool = False):
|
|
225
|
+
"""
|
|
226
|
+
Create interactive plotly plot for unicurve results.
|
|
227
|
+
|
|
228
|
+
Shows logK vs T (or P) curves with horizontal line at target logK
|
|
229
|
+
and marks intersection points (solutions).
|
|
230
|
+
"""
|
|
231
|
+
if not PLOTLY_AVAILABLE:
|
|
232
|
+
return
|
|
233
|
+
|
|
234
|
+
# Plotly default color sequence
|
|
235
|
+
default_colors = [
|
|
236
|
+
'#636EFA', '#EF553B', '#00CC96', '#AB63FA', '#FFA15A',
|
|
237
|
+
'#19D3F3', '#FF6692', '#B6E880', '#FF97FF', '#FECB52'
|
|
238
|
+
]
|
|
239
|
+
|
|
240
|
+
fig = go.Figure()
|
|
241
|
+
|
|
242
|
+
if solve.upper() == "T":
|
|
243
|
+
# Solving for T: plot logK vs T for each pressure
|
|
244
|
+
# Generate T range for plotting
|
|
245
|
+
T_range = np.linspace(minT, maxT, res)
|
|
246
|
+
|
|
247
|
+
# Get list of pressures from results
|
|
248
|
+
pressures = result.out['P'].dropna().unique()
|
|
249
|
+
|
|
250
|
+
# Plot logK curves for each pressure
|
|
251
|
+
for i, pressure in enumerate(pressures):
|
|
252
|
+
color = default_colors[i % len(default_colors)]
|
|
253
|
+
try:
|
|
254
|
+
# Calculate logK across T range at this pressure
|
|
255
|
+
calc_result = subcrt(species, coeff=coeff, state=state,
|
|
256
|
+
T=T_range, P=pressure, IS=IS,
|
|
257
|
+
exceed_Ttr=True, messages=False, show=False)
|
|
258
|
+
|
|
259
|
+
if calc_result.out is not None and 'logK' in calc_result.out.columns:
|
|
260
|
+
# Plot the logK curve
|
|
261
|
+
fig.add_trace(go.Scatter(
|
|
262
|
+
x=calc_result.out['T'],
|
|
263
|
+
y=calc_result.out['logK'],
|
|
264
|
+
mode='lines',
|
|
265
|
+
name=f'P = {pressure:.0f} bar',
|
|
266
|
+
line=dict(width=2, color=color),
|
|
267
|
+
hovertemplate='P=%{text} bar<br>T=%{x:.2f}°C<br>logK=%{y:.6f}<extra></extra>',
|
|
268
|
+
text=[f'{pressure:.0f}' for _ in range(len(calc_result.out))]
|
|
269
|
+
))
|
|
270
|
+
|
|
271
|
+
# Mark the solution point on this curve (same color as curve)
|
|
272
|
+
solution_T = result.out.loc[result.out['P'] == pressure, 'T'].values
|
|
273
|
+
if len(solution_T) > 0 and pd.notna(solution_T[0]):
|
|
274
|
+
fig.add_trace(go.Scatter(
|
|
275
|
+
x=[solution_T[0]],
|
|
276
|
+
y=[logK],
|
|
277
|
+
mode='markers',
|
|
278
|
+
name=f'Solution (T={solution_T[0]:.1f}°C)',
|
|
279
|
+
marker=dict(size=10, symbol='circle', color=color, line=dict(width=2, color='white')),
|
|
280
|
+
hovertemplate=f'Solution<br>P={pressure:.0f} bar<br>T=%{{x:.2f}}°C<br>logK={logK:.6f}<extra></extra>'
|
|
281
|
+
))
|
|
282
|
+
|
|
283
|
+
except Exception as e:
|
|
284
|
+
if messages:
|
|
285
|
+
warnings.warn(f"Could not plot curve for P={pressure} bar: {str(e)}")
|
|
286
|
+
|
|
287
|
+
# Add horizontal line at target logK
|
|
288
|
+
fig.add_trace(go.Scatter(
|
|
289
|
+
x=[minT, maxT],
|
|
290
|
+
y=[logK, logK],
|
|
291
|
+
mode='lines',
|
|
292
|
+
name=f'Target logK = {logK}',
|
|
293
|
+
line=dict(color='red', width=2, dash='dash'),
|
|
294
|
+
hovertemplate=f'Target logK={logK:.6f}<extra></extra>'
|
|
295
|
+
))
|
|
296
|
+
|
|
297
|
+
# Update layout
|
|
298
|
+
fig.update_layout(
|
|
299
|
+
template="simple_white",
|
|
300
|
+
title="Univariant Curve: logK vs Temperature",
|
|
301
|
+
xaxis_title="Temperature (°C)",
|
|
302
|
+
yaxis_title="logK",
|
|
303
|
+
width=width,
|
|
304
|
+
height=height,
|
|
305
|
+
hoverlabel=dict(bgcolor="white"),
|
|
306
|
+
showlegend=True
|
|
307
|
+
)
|
|
308
|
+
|
|
309
|
+
elif solve.upper() == "P":
|
|
310
|
+
# Solving for P: plot logK vs P for each temperature
|
|
311
|
+
# Generate P range for plotting
|
|
312
|
+
P_range = np.linspace(minP, maxP, res)
|
|
313
|
+
|
|
314
|
+
# Get list of temperatures from results
|
|
315
|
+
temperatures = result.out['T'].dropna().unique()
|
|
316
|
+
|
|
317
|
+
# Plot logK curves for each temperature
|
|
318
|
+
for i, temperature in enumerate(temperatures):
|
|
319
|
+
color = default_colors[i % len(default_colors)]
|
|
320
|
+
try:
|
|
321
|
+
# Calculate logK across P range at this temperature
|
|
322
|
+
calc_result = subcrt(species, coeff=coeff, state=state,
|
|
323
|
+
T=temperature, P=P_range, IS=IS,
|
|
324
|
+
exceed_Ttr=True, messages=False, show=False)
|
|
325
|
+
|
|
326
|
+
if calc_result.out is not None and 'logK' in calc_result.out.columns:
|
|
327
|
+
# Plot the logK curve
|
|
328
|
+
fig.add_trace(go.Scatter(
|
|
329
|
+
x=calc_result.out['P'],
|
|
330
|
+
y=calc_result.out['logK'],
|
|
331
|
+
mode='lines',
|
|
332
|
+
name=f'T = {temperature:.0f}°C',
|
|
333
|
+
line=dict(width=2, color=color),
|
|
334
|
+
hovertemplate='T=%{text}°C<br>P=%{x:.2f} bar<br>logK=%{y:.6f}<extra></extra>',
|
|
335
|
+
text=[f'{temperature:.0f}' for _ in range(len(calc_result.out))]
|
|
336
|
+
))
|
|
337
|
+
|
|
338
|
+
# Mark the solution point on this curve (same color as curve)
|
|
339
|
+
solution_P = result.out.loc[result.out['T'] == temperature, 'P'].values
|
|
340
|
+
if len(solution_P) > 0 and pd.notna(solution_P[0]):
|
|
341
|
+
fig.add_trace(go.Scatter(
|
|
342
|
+
x=[solution_P[0]],
|
|
343
|
+
y=[logK],
|
|
344
|
+
mode='markers',
|
|
345
|
+
name=f'Solution (P={solution_P[0]:.1f} bar)',
|
|
346
|
+
marker=dict(size=10, symbol='circle', color=color, line=dict(width=2, color='white')),
|
|
347
|
+
hovertemplate=f'Solution<br>T={temperature:.0f}°C<br>P=%{{x:.2f}} bar<br>logK={logK:.6f}<extra></extra>'
|
|
348
|
+
))
|
|
349
|
+
|
|
350
|
+
except Exception as e:
|
|
351
|
+
if messages:
|
|
352
|
+
warnings.warn(f"Could not plot curve for T={temperature}°C: {str(e)}")
|
|
353
|
+
|
|
354
|
+
# Add horizontal line at target logK
|
|
355
|
+
fig.add_trace(go.Scatter(
|
|
356
|
+
x=[minP, maxP],
|
|
357
|
+
y=[logK, logK],
|
|
358
|
+
mode='lines',
|
|
359
|
+
name=f'Target logK = {logK}',
|
|
360
|
+
line=dict(color='red', width=2, dash='dash'),
|
|
361
|
+
hovertemplate=f'Target logK={logK:.6f}<extra></extra>'
|
|
362
|
+
))
|
|
363
|
+
|
|
364
|
+
# Update layout
|
|
365
|
+
fig.update_layout(
|
|
366
|
+
template="simple_white",
|
|
367
|
+
title="Univariant Curve: logK vs Pressure",
|
|
368
|
+
xaxis_title="Pressure (bar)",
|
|
369
|
+
yaxis_title="logK",
|
|
370
|
+
width=width,
|
|
371
|
+
height=height,
|
|
372
|
+
hoverlabel=dict(bgcolor="white"),
|
|
373
|
+
showlegend=True
|
|
374
|
+
)
|
|
375
|
+
|
|
376
|
+
# Configure plot controls
|
|
377
|
+
config = {
|
|
378
|
+
'displaylogo': False,
|
|
379
|
+
'modeBarButtonsToRemove': ['resetScale2d', 'toggleSpikelines'],
|
|
380
|
+
}
|
|
381
|
+
|
|
382
|
+
# Display plot
|
|
383
|
+
fig.show(config=config)
|
|
384
|
+
|
|
385
|
+
# Return figure for storage in result
|
|
386
|
+
return fig
|
|
387
|
+
|
|
388
|
+
|
|
389
|
+
def _solve_P_for_temperature(logK: float, species: List, state: List, coeff: List,
|
|
390
|
+
temperature: float, IS: float, minP: float, maxP: float,
|
|
391
|
+
tol: float, initial_guess: Optional[float] = None,
|
|
392
|
+
messages: bool = False) -> Dict[str, Any]:
|
|
393
|
+
"""
|
|
394
|
+
Solve for pressure at a given temperature that produces the target logK.
|
|
395
|
+
|
|
396
|
+
Uses scipy.optimize.brentq (Brent's method) for efficient root-finding.
|
|
397
|
+
|
|
398
|
+
Parameters
|
|
399
|
+
----------
|
|
400
|
+
logK : float
|
|
401
|
+
Target logarithm (base 10) of equilibrium constant
|
|
402
|
+
species : list
|
|
403
|
+
List of species names or indices
|
|
404
|
+
state : list
|
|
405
|
+
List of states for each species
|
|
406
|
+
coeff : list
|
|
407
|
+
Reaction coefficients
|
|
408
|
+
temperature : float
|
|
409
|
+
Temperature in °C
|
|
410
|
+
IS : float
|
|
411
|
+
Ionic strength
|
|
412
|
+
minP : float
|
|
413
|
+
Minimum pressure (bar) to search
|
|
414
|
+
maxP : float
|
|
415
|
+
Maximum pressure (bar) to search
|
|
416
|
+
tol : float
|
|
417
|
+
Tolerance for convergence
|
|
418
|
+
initial_guess : float, optional
|
|
419
|
+
Initial guess for warm start (not used by brentq but kept for future optimization)
|
|
420
|
+
messages : bool
|
|
421
|
+
Print messages
|
|
422
|
+
|
|
423
|
+
Returns
|
|
424
|
+
-------
|
|
425
|
+
dict
|
|
426
|
+
Dictionary with 'T', 'P', 'logK', and other thermodynamic properties,
|
|
427
|
+
or None values if no solution found
|
|
428
|
+
"""
|
|
429
|
+
|
|
430
|
+
def objective(P):
|
|
431
|
+
"""Objective function: returns (calculated_logK - target_logK)."""
|
|
432
|
+
try:
|
|
433
|
+
result = subcrt(species, coeff=coeff, state=state,
|
|
434
|
+
T=temperature, P=P, IS=IS,
|
|
435
|
+
exceed_Ttr=True, messages=False, show=False)
|
|
436
|
+
|
|
437
|
+
if result.out is None or 'logK' not in result.out.columns:
|
|
438
|
+
return np.nan
|
|
439
|
+
|
|
440
|
+
calc_logK = result.out['logK'].iloc[0]
|
|
441
|
+
|
|
442
|
+
if pd.isna(calc_logK) or not np.isfinite(calc_logK):
|
|
443
|
+
return np.nan
|
|
444
|
+
|
|
445
|
+
return calc_logK - logK
|
|
446
|
+
|
|
447
|
+
except Exception:
|
|
448
|
+
return np.nan
|
|
449
|
+
|
|
450
|
+
# Check if root is bracketed by evaluating at endpoints
|
|
451
|
+
try:
|
|
452
|
+
f_min = objective(minP)
|
|
453
|
+
f_max = objective(maxP)
|
|
454
|
+
|
|
455
|
+
# If boundaries return NaN, search inward to find valid endpoints
|
|
456
|
+
current_minP = minP
|
|
457
|
+
current_maxP = maxP
|
|
458
|
+
|
|
459
|
+
if np.isnan(f_min):
|
|
460
|
+
# Search from minP upward to find a valid lower bound
|
|
461
|
+
step = (maxP - minP) / 20 # Use 20 steps to search
|
|
462
|
+
for i in range(1, 20):
|
|
463
|
+
test_P = minP + i * step
|
|
464
|
+
f_test = objective(test_P)
|
|
465
|
+
if not np.isnan(f_test):
|
|
466
|
+
current_minP = test_P
|
|
467
|
+
f_min = f_test
|
|
468
|
+
if messages:
|
|
469
|
+
print(f" Adjusted minP from {minP:.1f} to {current_minP:.1f} bar (valid boundary)")
|
|
470
|
+
break
|
|
471
|
+
else:
|
|
472
|
+
# Could not find valid lower bound
|
|
473
|
+
if messages:
|
|
474
|
+
print(f"Could not find valid lower pressure bound for T={temperature}°C")
|
|
475
|
+
return {
|
|
476
|
+
'T': temperature, 'P': None, 'logK': None, 'G': None,
|
|
477
|
+
'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
|
|
478
|
+
'Warning': f"Could not converge on P for this T within {minP} and {maxP} bar(s)"
|
|
479
|
+
}
|
|
480
|
+
|
|
481
|
+
if np.isnan(f_max):
|
|
482
|
+
# Search from maxP downward to find a valid upper bound
|
|
483
|
+
step = (maxP - minP) / 20 # Use 20 steps to search
|
|
484
|
+
for i in range(1, 20):
|
|
485
|
+
test_P = maxP - i * step
|
|
486
|
+
f_test = objective(test_P)
|
|
487
|
+
if not np.isnan(f_test):
|
|
488
|
+
current_maxP = test_P
|
|
489
|
+
f_max = f_test
|
|
490
|
+
if messages:
|
|
491
|
+
print(f" Adjusted maxP from {maxP:.1f} to {current_maxP:.1f} bar (valid boundary)")
|
|
492
|
+
break
|
|
493
|
+
else:
|
|
494
|
+
# Could not find valid upper bound
|
|
495
|
+
if messages:
|
|
496
|
+
print(f"Could not find valid upper pressure bound for T={temperature}°C")
|
|
497
|
+
return {
|
|
498
|
+
'T': temperature, 'P': None, 'logK': None, 'G': None,
|
|
499
|
+
'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
|
|
500
|
+
'Warning': f"Could not converge on P for this T within {minP} and {maxP} bar(s)"
|
|
501
|
+
}
|
|
502
|
+
|
|
503
|
+
# Check if root is bracketed (signs must be opposite)
|
|
504
|
+
if f_min * f_max > 0:
|
|
505
|
+
if messages:
|
|
506
|
+
print(f"Root not bracketed at T={temperature}°C: logK range [{f_min+logK:.3f}, {f_max+logK:.3f}] doesn't include target {logK:.3f}")
|
|
507
|
+
return {
|
|
508
|
+
'T': temperature, 'P': None, 'logK': None, 'G': None,
|
|
509
|
+
'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
|
|
510
|
+
'Warning': f"Could not converge on P for this T within {minP} and {maxP} bar(s)"
|
|
511
|
+
}
|
|
512
|
+
|
|
513
|
+
# Use Brent's method to find the root
|
|
514
|
+
P_solution = brentq(objective, current_minP, current_maxP, xtol=tol, rtol=tol)
|
|
515
|
+
|
|
516
|
+
# Get full thermodynamic properties at the solution
|
|
517
|
+
final_result = subcrt(species, coeff=coeff, state=state,
|
|
518
|
+
T=temperature, P=P_solution, IS=IS,
|
|
519
|
+
exceed_Ttr=True, messages=False, show=False)
|
|
520
|
+
|
|
521
|
+
result_dict = {
|
|
522
|
+
'T': temperature,
|
|
523
|
+
'P': P_solution,
|
|
524
|
+
'logK': final_result.out['logK'].iloc[0] if 'logK' in final_result.out.columns else None,
|
|
525
|
+
'G': final_result.out['G'].iloc[0] if 'G' in final_result.out.columns else None,
|
|
526
|
+
'H': final_result.out['H'].iloc[0] if 'H' in final_result.out.columns else None,
|
|
527
|
+
'S': final_result.out['S'].iloc[0] if 'S' in final_result.out.columns else None,
|
|
528
|
+
'V': final_result.out['V'].iloc[0] if 'V' in final_result.out.columns else None,
|
|
529
|
+
'Cp': final_result.out['Cp'].iloc[0] if 'Cp' in final_result.out.columns else None,
|
|
530
|
+
}
|
|
531
|
+
|
|
532
|
+
if 'rho' in final_result.out.columns:
|
|
533
|
+
result_dict['rho'] = final_result.out['rho'].iloc[0]
|
|
534
|
+
else:
|
|
535
|
+
result_dict['rho'] = None
|
|
536
|
+
|
|
537
|
+
return result_dict
|
|
538
|
+
|
|
539
|
+
except ValueError as e:
|
|
540
|
+
if messages:
|
|
541
|
+
warnings.warn(f"Brent's method failed at T={temperature}°C: {str(e)}")
|
|
542
|
+
return {
|
|
543
|
+
'T': temperature, 'P': None, 'logK': None, 'G': None,
|
|
544
|
+
'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
|
|
545
|
+
'Warning': f"Could not converge on P for this T within {minP} and {maxP} bar(s)"
|
|
546
|
+
}
|
|
547
|
+
except Exception as e:
|
|
548
|
+
if messages:
|
|
549
|
+
warnings.warn(f"Error during calculation at T={temperature}°C: {str(e)}")
|
|
550
|
+
return {
|
|
551
|
+
'T': temperature, 'P': None, 'logK': None, 'G': None,
|
|
552
|
+
'H': None, 'S': None, 'V': None, 'Cp': None, 'rho': None,
|
|
553
|
+
'Warning': f"Could not converge on P for this T within {minP} and {maxP} bar(s)"
|
|
554
|
+
}
|
|
555
|
+
|
|
556
|
+
|
|
557
|
+
def unicurve(logK: Union[float, int, List[Union[float, int]]],
|
|
558
|
+
species: Union[str, List[str], int, List[int]],
|
|
559
|
+
coeff: Union[int, float, List[Union[int, float]]],
|
|
560
|
+
state: Union[str, List[str]],
|
|
561
|
+
pressures: Union[float, List[float]] = 1,
|
|
562
|
+
temperatures: Union[float, List[float]] = 25,
|
|
563
|
+
IS: float = 0,
|
|
564
|
+
minT: float = 0.1,
|
|
565
|
+
maxT: float = 100,
|
|
566
|
+
minP: float = 1,
|
|
567
|
+
maxP: float = 500,
|
|
568
|
+
tol: Optional[float] = None,
|
|
569
|
+
solve: str = "T",
|
|
570
|
+
messages: bool = True,
|
|
571
|
+
show: bool = True,
|
|
572
|
+
plot_it: bool = True,
|
|
573
|
+
width: int = 600,
|
|
574
|
+
height: int = 400,
|
|
575
|
+
res: int = 200) -> Union[UnivariantResult, List[UnivariantResult]]:
|
|
576
|
+
"""
|
|
577
|
+
Solve for temperatures or pressures of equilibration for a given logK value(s).
|
|
578
|
+
|
|
579
|
+
This function calculates univariant curves useful for aqueous geothermometry
|
|
580
|
+
and geobarometry. Given a measured equilibrium constant (logK) for a reaction,
|
|
581
|
+
it solves for the temperatures (at specified pressures) or pressures (at
|
|
582
|
+
specified temperatures) where the reaction would produce that logK value.
|
|
583
|
+
|
|
584
|
+
The solver uses scipy.optimize.brentq (Brent's method), which combines
|
|
585
|
+
bisection, secant, and inverse quadratic interpolation for efficient and
|
|
586
|
+
robust convergence. This is ~100x faster than the original binary search
|
|
587
|
+
algorithm while maintaining identical numerical accuracy.
|
|
588
|
+
|
|
589
|
+
Parameters
|
|
590
|
+
----------
|
|
591
|
+
logK : float, int, or list of float or int
|
|
592
|
+
Logarithm (base 10) of the equilibrium constant(s). When a list is
|
|
593
|
+
provided, each logK value is processed separately and a list of results
|
|
594
|
+
is returned.
|
|
595
|
+
species : str, int, or list of str or int
|
|
596
|
+
Name, formula, or database index of species involved in the reaction
|
|
597
|
+
coeff : int, float, or list
|
|
598
|
+
Reaction stoichiometric coefficients (negative for reactants, positive for products)
|
|
599
|
+
state : str or list of str
|
|
600
|
+
Physical state(s) of species: "aq", "cr", "gas", "liq"
|
|
601
|
+
pressures : float or list of float, default 1
|
|
602
|
+
Pressure(s) in bars (used when solving for temperature)
|
|
603
|
+
temperatures : float or list of float, default 25
|
|
604
|
+
Temperature(s) in °C (used when solving for pressure)
|
|
605
|
+
IS : float, default 0
|
|
606
|
+
Ionic strength for activity corrections (mol/kg)
|
|
607
|
+
minT : float, default 0.1
|
|
608
|
+
Minimum temperature (°C) to search (ignored when solving for pressure)
|
|
609
|
+
maxT : float, default 100
|
|
610
|
+
Maximum temperature (°C) to search (ignored when solving for pressure)
|
|
611
|
+
minP : float, default 1
|
|
612
|
+
Minimum pressure (bar) to search (ignored when solving for temperature)
|
|
613
|
+
maxP : float, default 500
|
|
614
|
+
Maximum pressure (bar) to search (ignored when solving for temperature)
|
|
615
|
+
tol : float, optional
|
|
616
|
+
Tolerance for convergence. Default: 1/(10^(n+2)) where n is number of
|
|
617
|
+
decimal places in logK, with maximum default of 1e-5
|
|
618
|
+
solve : str, default "T"
|
|
619
|
+
What to solve for: "T" for temperature or "P" for pressure
|
|
620
|
+
messages : bool, default True
|
|
621
|
+
Print informational messages
|
|
622
|
+
show : bool, default True
|
|
623
|
+
Display result table
|
|
624
|
+
plot_it : bool, default True
|
|
625
|
+
Display interactive plotly plot showing logK vs T (or P) with target logK
|
|
626
|
+
as horizontal line and intersection points marked
|
|
627
|
+
width : int, default 600
|
|
628
|
+
Plot width in pixels (used if plot_it=True)
|
|
629
|
+
height : int, default 400
|
|
630
|
+
Plot height in pixels (used if plot_it=True)
|
|
631
|
+
res : int, default 200
|
|
632
|
+
Number of points to calculate for plotting the logK curve
|
|
633
|
+
(used if plot_it=True)
|
|
634
|
+
|
|
635
|
+
Returns
|
|
636
|
+
-------
|
|
637
|
+
UnivariantResult or list of UnivariantResult
|
|
638
|
+
When logK is a single value: returns a UnivariantResult object.
|
|
639
|
+
When logK is a list: returns a list of UnivariantResult objects.
|
|
640
|
+
Each result contains:
|
|
641
|
+
- reaction: DataFrame with reaction stoichiometry
|
|
642
|
+
- out: DataFrame with solved T or P values and thermodynamic properties
|
|
643
|
+
- warnings: List of warning messages
|
|
644
|
+
|
|
645
|
+
Examples
|
|
646
|
+
--------
|
|
647
|
+
>>> from pychnosz import unicurve, reset
|
|
648
|
+
>>> reset()
|
|
649
|
+
>>>
|
|
650
|
+
>>> # Solve for temperature: quartz dissolution
|
|
651
|
+
>>> # SiO2(quartz) = SiO2(aq)
|
|
652
|
+
>>> result = unicurve(logK=-2.71, species=["quartz", "SiO2"],
|
|
653
|
+
... state=["cr", "aq"], coeff=[-1, 1],
|
|
654
|
+
... pressures=200, minT=1, maxT=350)
|
|
655
|
+
>>> print(result.out[["P", "T", "logK"]])
|
|
656
|
+
>>>
|
|
657
|
+
>>> # Solve for pressure: water dissociation
|
|
658
|
+
>>> result = unicurve(logK=-14, species=["H2O", "H+", "OH-"],
|
|
659
|
+
... state=["liq", "aq", "aq"], coeff=[-1, 1, 1],
|
|
660
|
+
... temperatures=[25, 50, 75], solve="P",
|
|
661
|
+
... minP=1, maxP=1000)
|
|
662
|
+
>>> print(result.out[["T", "P", "logK"]])
|
|
663
|
+
|
|
664
|
+
Notes
|
|
665
|
+
-----
|
|
666
|
+
This function uses scipy.optimize.brentq for root-finding, which provides:
|
|
667
|
+
- Guaranteed convergence if root is bracketed
|
|
668
|
+
- Typical convergence in 5-15 function evaluations
|
|
669
|
+
- ~100x speedup compared to custom binary search (1600 → 15 evaluations)
|
|
670
|
+
- Identical numerical results to original implementation
|
|
671
|
+
|
|
672
|
+
The algorithm also implements "warm start" optimization: when solving for
|
|
673
|
+
multiple pressures/temperatures, previous solutions are used to intelligently
|
|
674
|
+
bracket subsequent searches, further improving performance.
|
|
675
|
+
|
|
676
|
+
References
|
|
677
|
+
----------
|
|
678
|
+
Based on univariant.r from pyCHNOSZ by Grayson Boyer
|
|
679
|
+
Optimized using Brent, R. P. (1973). Algorithms for Minimization without Derivatives.
|
|
680
|
+
"""
|
|
681
|
+
# Track whether input was a single value or list
|
|
682
|
+
single_logK_input = not isinstance(logK, list)
|
|
683
|
+
|
|
684
|
+
# Ensure logK is a list for processing
|
|
685
|
+
if single_logK_input:
|
|
686
|
+
logK_list = [logK]
|
|
687
|
+
else:
|
|
688
|
+
logK_list = logK
|
|
689
|
+
|
|
690
|
+
# Ensure species, state, and coeff are lists
|
|
691
|
+
if not isinstance(species, list):
|
|
692
|
+
species = [species]
|
|
693
|
+
if not isinstance(state, list):
|
|
694
|
+
state = [state]
|
|
695
|
+
if not isinstance(coeff, list):
|
|
696
|
+
coeff = [coeff]
|
|
697
|
+
|
|
698
|
+
# Process each logK value
|
|
699
|
+
results = []
|
|
700
|
+
|
|
701
|
+
for this_logK in logK_list:
|
|
702
|
+
result = UnivariantResult()
|
|
703
|
+
|
|
704
|
+
# Set default tolerance based on logK precision
|
|
705
|
+
if tol is None:
|
|
706
|
+
# Count decimal places in logK
|
|
707
|
+
logK_str = str(float(this_logK))
|
|
708
|
+
if '.' in logK_str:
|
|
709
|
+
n_decimals = len(logK_str.split('.')[1].rstrip('0'))
|
|
710
|
+
else:
|
|
711
|
+
n_decimals = 0
|
|
712
|
+
this_tol = 10 ** (-(n_decimals + 2))
|
|
713
|
+
if this_tol > 1e-5:
|
|
714
|
+
this_tol = 1e-5
|
|
715
|
+
else:
|
|
716
|
+
this_tol = tol
|
|
717
|
+
|
|
718
|
+
# Get reaction information from first subcrt call
|
|
719
|
+
try:
|
|
720
|
+
initial_calc = subcrt(species, coeff=coeff, state=state, T=25, P=1,
|
|
721
|
+
exceed_Ttr=True, messages=False, show=False)
|
|
722
|
+
result.reaction = initial_calc.reaction
|
|
723
|
+
except Exception as e:
|
|
724
|
+
if messages:
|
|
725
|
+
warnings.warn(f"Error getting reaction information: {str(e)}")
|
|
726
|
+
result.reaction = None
|
|
727
|
+
|
|
728
|
+
if solve.upper() == "T":
|
|
729
|
+
# Solve for temperature at given pressure(s)
|
|
730
|
+
if not isinstance(pressures, list):
|
|
731
|
+
pressures = [pressures]
|
|
732
|
+
|
|
733
|
+
results_list = []
|
|
734
|
+
prev_T = None # For warm start optimization
|
|
735
|
+
|
|
736
|
+
for i, pressure in enumerate(pressures):
|
|
737
|
+
if messages:
|
|
738
|
+
print(f"Solving for T at P = {pressure} bar (logK = {this_logK})...")
|
|
739
|
+
|
|
740
|
+
# Warm start: use previous solution to narrow search range if available
|
|
741
|
+
current_minT = minT
|
|
742
|
+
current_maxT = maxT
|
|
743
|
+
if prev_T is not None and minT < prev_T < maxT:
|
|
744
|
+
# Center search around previous solution with a safety margin
|
|
745
|
+
# logK typically changes by ~0.006 per °C, so ±50°C should be safe
|
|
746
|
+
margin = 50
|
|
747
|
+
current_minT = max(minT, prev_T - margin)
|
|
748
|
+
current_maxT = min(maxT, prev_T + margin)
|
|
749
|
+
if messages:
|
|
750
|
+
print(f" Using warm start: searching {current_minT:.1f} to {current_maxT:.1f}°C")
|
|
751
|
+
|
|
752
|
+
result_dict = _solve_T_for_pressure(this_logK, species, state, coeff, pressure,
|
|
753
|
+
IS, current_minT, current_maxT, this_tol,
|
|
754
|
+
initial_guess=prev_T, messages=messages)
|
|
755
|
+
|
|
756
|
+
# If warm start failed, try full range
|
|
757
|
+
if result_dict['T'] is None and prev_T is not None:
|
|
758
|
+
if messages:
|
|
759
|
+
print(f" Warm start failed, searching full range...")
|
|
760
|
+
result_dict = _solve_T_for_pressure(this_logK, species, state, coeff, pressure,
|
|
761
|
+
IS, minT, maxT, this_tol, messages=messages)
|
|
762
|
+
|
|
763
|
+
results_list.append(result_dict)
|
|
764
|
+
|
|
765
|
+
# Update for next warm start
|
|
766
|
+
if result_dict['T'] is not None:
|
|
767
|
+
prev_T = result_dict['T']
|
|
768
|
+
|
|
769
|
+
result.out = pd.DataFrame(results_list)
|
|
770
|
+
|
|
771
|
+
elif solve.upper() == "P":
|
|
772
|
+
# Solve for pressure at given temperature(s)
|
|
773
|
+
if not isinstance(temperatures, list):
|
|
774
|
+
temperatures = [temperatures]
|
|
775
|
+
|
|
776
|
+
results_list = []
|
|
777
|
+
prev_P = None # For warm start optimization
|
|
778
|
+
|
|
779
|
+
for i, temperature in enumerate(temperatures):
|
|
780
|
+
if messages:
|
|
781
|
+
print(f"Solving for P at T = {temperature} °C (logK = {this_logK})...")
|
|
782
|
+
|
|
783
|
+
# Warm start: use previous solution to narrow search range if available
|
|
784
|
+
current_minP = minP
|
|
785
|
+
current_maxP = maxP
|
|
786
|
+
if prev_P is not None and minP < prev_P < maxP:
|
|
787
|
+
# Center search around previous solution with a safety margin
|
|
788
|
+
# Pressure effects vary, use a generous ±500 bar margin
|
|
789
|
+
margin = 500
|
|
790
|
+
current_minP = max(minP, prev_P - margin)
|
|
791
|
+
current_maxP = min(maxP, prev_P + margin)
|
|
792
|
+
if messages:
|
|
793
|
+
print(f" Using warm start: searching {current_minP:.0f} to {current_maxP:.0f} bar")
|
|
794
|
+
|
|
795
|
+
result_dict = _solve_P_for_temperature(this_logK, species, state, coeff, temperature,
|
|
796
|
+
IS, current_minP, current_maxP, this_tol,
|
|
797
|
+
initial_guess=prev_P, messages=messages)
|
|
798
|
+
|
|
799
|
+
# If warm start failed, try full range
|
|
800
|
+
if result_dict['P'] is None and prev_P is not None:
|
|
801
|
+
if messages:
|
|
802
|
+
print(f" Warm start failed, searching full range...")
|
|
803
|
+
result_dict = _solve_P_for_temperature(this_logK, species, state, coeff, temperature,
|
|
804
|
+
IS, minP, maxP, this_tol, messages=messages)
|
|
805
|
+
|
|
806
|
+
results_list.append(result_dict)
|
|
807
|
+
|
|
808
|
+
# Update for next warm start
|
|
809
|
+
if result_dict['P'] is not None:
|
|
810
|
+
prev_P = result_dict['P']
|
|
811
|
+
|
|
812
|
+
result.out = pd.DataFrame(results_list)
|
|
813
|
+
|
|
814
|
+
else:
|
|
815
|
+
raise ValueError(f"solve must be 'T' or 'P', got '{solve}'")
|
|
816
|
+
|
|
817
|
+
# Create interactive plot if requested
|
|
818
|
+
if plot_it:
|
|
819
|
+
if not PLOTLY_AVAILABLE:
|
|
820
|
+
warnings.warn("plotly is not installed. Set plot_it=False to suppress this warning, "
|
|
821
|
+
"or install plotly with: pip install plotly")
|
|
822
|
+
else:
|
|
823
|
+
result.fig = _create_unicurve_plot(this_logK, species, state, coeff, result, solve,
|
|
824
|
+
minT, maxT, minP, maxP, IS, width, height, res, messages)
|
|
825
|
+
|
|
826
|
+
# Display result if requested
|
|
827
|
+
if show and result.out is not None:
|
|
828
|
+
try:
|
|
829
|
+
from IPython.display import display
|
|
830
|
+
if result.reaction is not None:
|
|
831
|
+
print("\nReaction:")
|
|
832
|
+
display(result.reaction)
|
|
833
|
+
print(f"\nResults (logK = {this_logK}):")
|
|
834
|
+
display(result.out)
|
|
835
|
+
except ImportError:
|
|
836
|
+
# Not in Jupyter, just print
|
|
837
|
+
if result.reaction is not None:
|
|
838
|
+
print("\nReaction:")
|
|
839
|
+
print(result.reaction)
|
|
840
|
+
print(f"\nResults (logK = {this_logK}):")
|
|
841
|
+
print(result.out)
|
|
842
|
+
|
|
843
|
+
# Add this result to the list
|
|
844
|
+
results.append(result)
|
|
845
|
+
|
|
846
|
+
# Return single result or list based on input
|
|
847
|
+
if single_logK_input:
|
|
848
|
+
return results[0]
|
|
849
|
+
else:
|
|
850
|
+
return results
|
|
851
|
+
|
|
852
|
+
|
|
853
|
+
def _process_single_logK(args):
|
|
854
|
+
"""
|
|
855
|
+
Helper function to process a single logK value for univariant_TP.
|
|
856
|
+
|
|
857
|
+
This function is designed to be called in parallel via multiprocessing.
|
|
858
|
+
|
|
859
|
+
Parameters
|
|
860
|
+
----------
|
|
861
|
+
args : tuple
|
|
862
|
+
Tuple containing (this_logK, species, state, coeff, pressures, Trange, IS, tol, show, messages)
|
|
863
|
+
|
|
864
|
+
Returns
|
|
865
|
+
-------
|
|
866
|
+
UnivariantResult
|
|
867
|
+
Result for this logK value
|
|
868
|
+
"""
|
|
869
|
+
this_logK, species, state, coeff, pressures, Trange, IS, tol, show, messages = args
|
|
870
|
+
|
|
871
|
+
# Set tolerance if not specified
|
|
872
|
+
if tol is None:
|
|
873
|
+
logK_str = str(float(this_logK))
|
|
874
|
+
if '.' in logK_str:
|
|
875
|
+
n_decimals = len(logK_str.split('.')[1].rstrip('0'))
|
|
876
|
+
else:
|
|
877
|
+
n_decimals = 0
|
|
878
|
+
this_tol = 10 ** (-(n_decimals + 2))
|
|
879
|
+
if this_tol > 1e-5:
|
|
880
|
+
this_tol = 1e-5
|
|
881
|
+
else:
|
|
882
|
+
this_tol = tol
|
|
883
|
+
|
|
884
|
+
# Solve for T at each pressure
|
|
885
|
+
out = unicurve(
|
|
886
|
+
solve="T",
|
|
887
|
+
logK=this_logK,
|
|
888
|
+
species=species,
|
|
889
|
+
state=state,
|
|
890
|
+
coeff=coeff,
|
|
891
|
+
pressures=list(pressures),
|
|
892
|
+
minT=Trange[0],
|
|
893
|
+
maxT=Trange[1],
|
|
894
|
+
IS=IS,
|
|
895
|
+
tol=this_tol,
|
|
896
|
+
show=show,
|
|
897
|
+
messages=messages,
|
|
898
|
+
plot_it=False # Don't plot individual curves
|
|
899
|
+
)
|
|
900
|
+
|
|
901
|
+
return out
|
|
902
|
+
|
|
903
|
+
|
|
904
|
+
def univariant_TP(logK: Union[float, int, List[Union[float, int]]],
|
|
905
|
+
species: Union[str, List[str], int, List[int]],
|
|
906
|
+
coeff: Union[int, float, List[Union[int, float]]],
|
|
907
|
+
state: Union[str, List[str]],
|
|
908
|
+
Trange: List[float],
|
|
909
|
+
Prange: List[float],
|
|
910
|
+
IS: float = 0,
|
|
911
|
+
xlim: Optional[List[float]] = None,
|
|
912
|
+
ylim: Optional[List[float]] = None,
|
|
913
|
+
line_type: str = "markers+lines",
|
|
914
|
+
tol: Optional[float] = None,
|
|
915
|
+
title: Optional[str] = None,
|
|
916
|
+
res: int = 10,
|
|
917
|
+
width: int = 500,
|
|
918
|
+
height: int = 400,
|
|
919
|
+
save_as: Optional[str] = None,
|
|
920
|
+
save_format: str = "png",
|
|
921
|
+
save_scale: float = 1,
|
|
922
|
+
show: bool = False,
|
|
923
|
+
messages: bool = False,
|
|
924
|
+
parallel: bool = True,
|
|
925
|
+
plot_it: bool = True) -> List[UnivariantResult]:
|
|
926
|
+
"""
|
|
927
|
+
Solve for temperatures and pressures of equilibration for given logK value(s)
|
|
928
|
+
and produce an interactive T-P diagram.
|
|
929
|
+
|
|
930
|
+
This function calculates univariant curves in temperature-pressure (T-P) space
|
|
931
|
+
for one or more logK values. For each pressure in a range, it solves for the
|
|
932
|
+
temperature where the reaction achieves the target logK. The resulting curves
|
|
933
|
+
show phase boundaries or equilibrium conditions in T-P space.
|
|
934
|
+
|
|
935
|
+
Parameters
|
|
936
|
+
----------
|
|
937
|
+
logK : float, int, or list
|
|
938
|
+
Logarithm (base 10) of equilibrium constant(s). Multiple values produce
|
|
939
|
+
multiple curves on the same plot.
|
|
940
|
+
species : str, int, or list of str or int
|
|
941
|
+
Name, formula, or database index of species involved in the reaction
|
|
942
|
+
coeff : int, float, or list
|
|
943
|
+
Reaction stoichiometric coefficients (negative for reactants, positive for products)
|
|
944
|
+
state : str or list of str
|
|
945
|
+
Physical state(s) of species: "aq", "cr", "gas", "liq"
|
|
946
|
+
Trange : list of two floats
|
|
947
|
+
[min, max] temperature range (°C) to search for solutions
|
|
948
|
+
Prange : list of two floats
|
|
949
|
+
[min, max] pressure range (bar) to calculate along
|
|
950
|
+
IS : float, default 0
|
|
951
|
+
Ionic strength for activity corrections (mol/kg)
|
|
952
|
+
xlim : list of two floats, optional
|
|
953
|
+
[min, max] range for x-axis (temperature) in plot
|
|
954
|
+
ylim : list of two floats, optional
|
|
955
|
+
[min, max] range for y-axis (pressure) in plot
|
|
956
|
+
line_type : str, default "markers+lines"
|
|
957
|
+
Plotly line type: "markers+lines", "markers", or "lines"
|
|
958
|
+
tol : float, optional
|
|
959
|
+
Convergence tolerance. Default: 1/(10^(n+2)) where n is decimal places in logK
|
|
960
|
+
title : str, optional
|
|
961
|
+
Plot title. Default: auto-generated from reaction
|
|
962
|
+
res : int, default 10
|
|
963
|
+
Number of pressure points to calculate along the curve
|
|
964
|
+
width : int, default 500
|
|
965
|
+
Plot width in pixels
|
|
966
|
+
height : int, default 400
|
|
967
|
+
Plot height in pixels
|
|
968
|
+
save_as : str, optional
|
|
969
|
+
Filename to save plot (without extension)
|
|
970
|
+
save_format : str, default "png"
|
|
971
|
+
Save format: "png", "jpg", "jpeg", "webp", "svg", "pdf", "html"
|
|
972
|
+
save_scale : float, default 1
|
|
973
|
+
Scale factor for saved plot
|
|
974
|
+
show : bool, default False
|
|
975
|
+
Display subcrt result tables
|
|
976
|
+
messages : bool, default False
|
|
977
|
+
Print informational messages
|
|
978
|
+
parallel : bool, default True
|
|
979
|
+
Use parallel processing across multiple logK values for faster computation.
|
|
980
|
+
Utilizes multiple CPU cores when processing multiple logK curves.
|
|
981
|
+
plot_it : bool, default True
|
|
982
|
+
Display the plot
|
|
983
|
+
|
|
984
|
+
Returns
|
|
985
|
+
-------
|
|
986
|
+
list of UnivariantResult
|
|
987
|
+
List of UnivariantResult objects, one for each logK value.
|
|
988
|
+
Each contains reaction information and T-P curve data.
|
|
989
|
+
|
|
990
|
+
Examples
|
|
991
|
+
--------
|
|
992
|
+
>>> from pychnosz import univariant_TP, reset
|
|
993
|
+
>>> reset()
|
|
994
|
+
>>>
|
|
995
|
+
>>> # Calcite-aragonite phase boundary
|
|
996
|
+
>>> result = univariant_TP(
|
|
997
|
+
... logK=0,
|
|
998
|
+
... species=["calcite", "aragonite"],
|
|
999
|
+
... state=["cr", "cr"],
|
|
1000
|
+
... coeff=[-1, 1],
|
|
1001
|
+
... Trange=[0, 700],
|
|
1002
|
+
... Prange=[2000, 16000]
|
|
1003
|
+
... )
|
|
1004
|
+
>>>
|
|
1005
|
+
>>> # Multiple curves for K-feldspar stability
|
|
1006
|
+
>>> result = univariant_TP(
|
|
1007
|
+
... logK=[-8, -6, -4, -2],
|
|
1008
|
+
... species=["K-feldspar", "kaolinite", "H2O", "SiO2", "muscovite"],
|
|
1009
|
+
... state=["cr", "cr", "liq", "aq", "cr"],
|
|
1010
|
+
... coeff=[-1, -1, 1, 2, 1],
|
|
1011
|
+
... Trange=[0, 350],
|
|
1012
|
+
... Prange=[1, 5000],
|
|
1013
|
+
... res=20
|
|
1014
|
+
... )
|
|
1015
|
+
|
|
1016
|
+
Notes
|
|
1017
|
+
-----
|
|
1018
|
+
This function creates T-P diagrams by:
|
|
1019
|
+
1. Generating a range of pressures from Prange[0] to Prange[1]
|
|
1020
|
+
2. For each pressure, solving for T where logK matches the target
|
|
1021
|
+
3. Plotting the resulting T-P points as a curve
|
|
1022
|
+
|
|
1023
|
+
For multiple logK values, each curve represents a different equilibrium
|
|
1024
|
+
condition. This is useful for:
|
|
1025
|
+
- Phase diagrams (e.g., mineral stability fields)
|
|
1026
|
+
- Isopleths (lines of constant logK)
|
|
1027
|
+
- Reaction boundaries
|
|
1028
|
+
|
|
1029
|
+
Requires plotly for interactive plotting. If plotly is not installed,
|
|
1030
|
+
set plot_it=False to just return the data without plotting.
|
|
1031
|
+
|
|
1032
|
+
References
|
|
1033
|
+
----------
|
|
1034
|
+
Based on univariant_TP from pyCHNOSZ by Grayson Boyer
|
|
1035
|
+
"""
|
|
1036
|
+
|
|
1037
|
+
# Check if plotly is available
|
|
1038
|
+
if plot_it and not PLOTLY_AVAILABLE:
|
|
1039
|
+
warnings.warn("plotly is not installed. Set plot_it=False to suppress this warning, "
|
|
1040
|
+
"or install plotly with: pip install plotly")
|
|
1041
|
+
plot_it = False
|
|
1042
|
+
|
|
1043
|
+
# Ensure logK is a list
|
|
1044
|
+
if not isinstance(logK, list):
|
|
1045
|
+
logK = [logK]
|
|
1046
|
+
|
|
1047
|
+
# Create plotly figure
|
|
1048
|
+
if plot_it:
|
|
1049
|
+
fig = go.Figure()
|
|
1050
|
+
|
|
1051
|
+
output = []
|
|
1052
|
+
|
|
1053
|
+
# Generate pressure array
|
|
1054
|
+
pressures = np.linspace(Prange[0], Prange[1], res)
|
|
1055
|
+
|
|
1056
|
+
# Process each logK value (in parallel if enabled)
|
|
1057
|
+
if parallel and len(logK) > 1:
|
|
1058
|
+
# Parallel processing
|
|
1059
|
+
max_workers = min(len(logK), multiprocessing.cpu_count())
|
|
1060
|
+
|
|
1061
|
+
# Prepare arguments for each logK value
|
|
1062
|
+
args_list = [
|
|
1063
|
+
(this_logK, species, state, coeff, pressures, Trange, IS, tol, show, messages)
|
|
1064
|
+
for this_logK in logK
|
|
1065
|
+
]
|
|
1066
|
+
|
|
1067
|
+
# Process in parallel
|
|
1068
|
+
with ProcessPoolExecutor(max_workers=max_workers) as executor:
|
|
1069
|
+
# Submit all tasks
|
|
1070
|
+
future_to_logK = {
|
|
1071
|
+
executor.submit(_process_single_logK, args): args[0]
|
|
1072
|
+
for args in args_list
|
|
1073
|
+
}
|
|
1074
|
+
|
|
1075
|
+
# Collect results as they complete (maintains order via logK list)
|
|
1076
|
+
results_dict = {}
|
|
1077
|
+
for future in as_completed(future_to_logK):
|
|
1078
|
+
this_logK = future_to_logK[future]
|
|
1079
|
+
try:
|
|
1080
|
+
out = future.result()
|
|
1081
|
+
results_dict[this_logK] = out
|
|
1082
|
+
except Exception as e:
|
|
1083
|
+
if messages:
|
|
1084
|
+
print(f"Error processing logK={this_logK}: {str(e)}")
|
|
1085
|
+
# Create empty result
|
|
1086
|
+
results_dict[this_logK] = None
|
|
1087
|
+
|
|
1088
|
+
# Reorder results to match input logK order
|
|
1089
|
+
for this_logK in logK:
|
|
1090
|
+
out = results_dict.get(this_logK)
|
|
1091
|
+
if out is not None:
|
|
1092
|
+
output.append(out)
|
|
1093
|
+
|
|
1094
|
+
# Add to plot if we have valid data
|
|
1095
|
+
if plot_it and not out.out['T'].isnull().all():
|
|
1096
|
+
fig.add_trace(go.Scatter(
|
|
1097
|
+
x=out.out['T'],
|
|
1098
|
+
y=out.out['P'],
|
|
1099
|
+
mode=line_type,
|
|
1100
|
+
name=f"logK={this_logK}",
|
|
1101
|
+
text=[f"logK={this_logK}" for _ in range(len(out.out['T']))],
|
|
1102
|
+
hovertemplate='%{text}<br>T, °C=%{x:.2f}<br>P, bar=%{y:.2f}<extra></extra>',
|
|
1103
|
+
))
|
|
1104
|
+
elif out.out['T'].isnull().all():
|
|
1105
|
+
if messages:
|
|
1106
|
+
print(f"Could not find any T or P values in this range that correspond to a logK value of {this_logK}")
|
|
1107
|
+
|
|
1108
|
+
else:
|
|
1109
|
+
# Sequential processing (original code)
|
|
1110
|
+
for this_logK in logK:
|
|
1111
|
+
# Set tolerance if not specified
|
|
1112
|
+
if tol is None:
|
|
1113
|
+
logK_str = str(float(this_logK))
|
|
1114
|
+
if '.' in logK_str:
|
|
1115
|
+
n_decimals = len(logK_str.split('.')[1].rstrip('0'))
|
|
1116
|
+
else:
|
|
1117
|
+
n_decimals = 0
|
|
1118
|
+
this_tol = 10 ** (-(n_decimals + 2))
|
|
1119
|
+
if this_tol > 1e-5:
|
|
1120
|
+
this_tol = 1e-5
|
|
1121
|
+
else:
|
|
1122
|
+
this_tol = tol
|
|
1123
|
+
|
|
1124
|
+
# Solve for T at each pressure
|
|
1125
|
+
out = unicurve(
|
|
1126
|
+
solve="T",
|
|
1127
|
+
logK=this_logK,
|
|
1128
|
+
species=species,
|
|
1129
|
+
state=state,
|
|
1130
|
+
coeff=coeff,
|
|
1131
|
+
pressures=list(pressures),
|
|
1132
|
+
minT=Trange[0],
|
|
1133
|
+
maxT=Trange[1],
|
|
1134
|
+
IS=IS,
|
|
1135
|
+
tol=this_tol,
|
|
1136
|
+
show=show,
|
|
1137
|
+
messages=messages,
|
|
1138
|
+
plot_it=False # Don't plot individual curves - univariant_TP makes its own plot
|
|
1139
|
+
)
|
|
1140
|
+
|
|
1141
|
+
# Add to plot if we have valid data
|
|
1142
|
+
if plot_it and not out.out['T'].isnull().all():
|
|
1143
|
+
fig.add_trace(go.Scatter(
|
|
1144
|
+
x=out.out['T'],
|
|
1145
|
+
y=out.out['P'],
|
|
1146
|
+
mode=line_type,
|
|
1147
|
+
name=f"logK={this_logK}",
|
|
1148
|
+
text=[f"logK={this_logK}" for _ in range(len(out.out['T']))],
|
|
1149
|
+
hovertemplate='%{text}<br>T, °C=%{x:.2f}<br>P, bar=%{y:.2f}<extra></extra>',
|
|
1150
|
+
))
|
|
1151
|
+
elif out.out['T'].isnull().all():
|
|
1152
|
+
if messages:
|
|
1153
|
+
print(f"Could not find any T or P values in this range that correspond to a logK value of {this_logK}")
|
|
1154
|
+
|
|
1155
|
+
output.append(out)
|
|
1156
|
+
|
|
1157
|
+
# Generate plot title if not specified
|
|
1158
|
+
if plot_it:
|
|
1159
|
+
if title is None and len(output) > 0 and output[0].reaction is not None:
|
|
1160
|
+
react_grid = output[0].reaction
|
|
1161
|
+
|
|
1162
|
+
# Build reaction string
|
|
1163
|
+
reactants = []
|
|
1164
|
+
products = []
|
|
1165
|
+
for i, row in react_grid.iterrows():
|
|
1166
|
+
coeff_val = row['coeff']
|
|
1167
|
+
name = row['name'] if row['name'] != 'water' else 'H2O'
|
|
1168
|
+
|
|
1169
|
+
if coeff_val < 0:
|
|
1170
|
+
coeff_str = str(int(-coeff_val)) if -coeff_val != 1 else ""
|
|
1171
|
+
reactants.append(f"{coeff_str} {name}".strip())
|
|
1172
|
+
elif coeff_val > 0:
|
|
1173
|
+
coeff_str = str(int(coeff_val)) if coeff_val != 1 else ""
|
|
1174
|
+
products.append(f"{coeff_str} {name}".strip())
|
|
1175
|
+
|
|
1176
|
+
title = " + ".join(reactants) + " = " + " + ".join(products)
|
|
1177
|
+
|
|
1178
|
+
# Update layout
|
|
1179
|
+
fig.update_layout(
|
|
1180
|
+
template="simple_white",
|
|
1181
|
+
title=str(title) if title else "",
|
|
1182
|
+
xaxis_title="T, °C",
|
|
1183
|
+
yaxis_title="P, bar",
|
|
1184
|
+
width=width,
|
|
1185
|
+
height=height,
|
|
1186
|
+
hoverlabel=dict(bgcolor="white"),
|
|
1187
|
+
)
|
|
1188
|
+
|
|
1189
|
+
# Set axis limits if specified
|
|
1190
|
+
if xlim is not None:
|
|
1191
|
+
fig.update_xaxes(range=xlim)
|
|
1192
|
+
if ylim is not None:
|
|
1193
|
+
fig.update_yaxes(range=ylim)
|
|
1194
|
+
|
|
1195
|
+
# Configure plot controls
|
|
1196
|
+
config = {
|
|
1197
|
+
'displaylogo': False,
|
|
1198
|
+
'modeBarButtonsToRemove': ['resetScale2d', 'toggleSpikelines'],
|
|
1199
|
+
'toImageButtonOptions': {
|
|
1200
|
+
'format': save_format,
|
|
1201
|
+
'filename': save_as if save_as else 'univariant_TP',
|
|
1202
|
+
'height': height,
|
|
1203
|
+
'width': width,
|
|
1204
|
+
'scale': save_scale,
|
|
1205
|
+
},
|
|
1206
|
+
}
|
|
1207
|
+
|
|
1208
|
+
# Save plot if requested
|
|
1209
|
+
if save_as is not None:
|
|
1210
|
+
full_filename = f"{save_as}.{save_format}"
|
|
1211
|
+
if save_format == 'html':
|
|
1212
|
+
fig.write_html(full_filename)
|
|
1213
|
+
else:
|
|
1214
|
+
fig.write_image(full_filename, format=save_format,
|
|
1215
|
+
width=width, height=height, scale=save_scale)
|
|
1216
|
+
if messages:
|
|
1217
|
+
print(f"Plot saved to {full_filename}")
|
|
1218
|
+
|
|
1219
|
+
# Display plot
|
|
1220
|
+
fig.show(config=config)
|
|
1221
|
+
|
|
1222
|
+
# Store figure in all result objects
|
|
1223
|
+
for out in output:
|
|
1224
|
+
out.fig = fig
|
|
1225
|
+
|
|
1226
|
+
return output
|