complicator 0.3.0__tar.gz

complicator-0.3.0/LICENSE.txt

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+Copyright (c) 2025 Grayson Boyer and GEOPIG Lab.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

complicator-0.3.0/MANIFEST.in

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+# Include documentation
+include README.md
+include LICENSE.txt
+
+# Include HTML documentation
+recursive-include html *.html *.css *.js
+
+# Include data files in the package
+include complicator/*.csv
+
+# Exclude build artifacts and cache
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude .DS_Store

complicator-0.3.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: complicator
+Version: 0.3.0
+Summary: Estimate thermodynamic properties of aqueous metal complexes with monovalent ligands.
+Author-email: Grayson Boyer <gmboyer@asu.edu>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/gmboyer/complicator
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: pandas
+Requires-Dist: wormutils
+Requires-Dist: chemparse
+Dynamic: license-file
+
+# The Complicator
+
+Code Authors: Grayson Boyer, Everett Shock
+Data Compilers: GEOPIG Lab, Apar Prasad
+
+This is a Python package for estimating standard state thermodynamic properties and Helgeson-Kirkham-Flowers (HKF) equation of state parameters for aqueous metal complexes with monovalent ligands using published methods from [Sverjensky et al. (1997)](https://doi.org/10.1016/s0016-7037(97)00009-4) and [Shock et al. (1997)](https://doi.org/10.1016/S0016-7037(96)00339-0)
+
+## Installation
+
+This package can be installed through PyPI with:
+`pip install Complicator`
+
+## Usage
+
+The best way to learn about the Complicator is through the WORM Portal ([worm-portal.asu.edu](worm-portal.asu.edu)). Check out Jupyter notebook demo 4-2-1 in the WORM Library that is available when you log in.
+
+What follows is a brief example of how the Complicator can be used.
+
+Supply a dataframe containing names of metals, ligands, stability constants for the first through fourth association at 25 °C, and optionally, standard state entropies of association for the first through fourth association complex. An example is assigned to the variable `df_input` in the example below.
+
+```
+import pandas as pd
+from Complicator import complicate
+
+df_input = pd.DataFrame({
+        "Metal":["Ag+", "Al+3"],
+        "Ligand":["OH-", "OH-"],
+        "BETA_1":[2, 9.03], # stability constant for the first association complex
+        "BETA_2":[3.97, 17.6], # second stability constant
+        "BETA_3":[float('NaN'), 26.4], # third stability constant
+        "BETA_4":[float('NaN'), 33.8], # fourth stability constant
+        "Sass_1":[float('NaN'), 36.5], # entropy of association for the first complex (cal/mol/K)
+        })
+
+df_out, _, _, _ = complicate(df_in=df_input)
+
+df_out
+```
+
+The output is a dataframe containing estimated thermodynamic properties, parameters for the revised Helgeson Kirkham Flowers (HKF) equation of state, and more. [The format of the output is explained in more detail here](https://worm-portal.asu.edu/docs/database/). This Water-Organic-Rock-Microbe (WORM) database format is designed to be compatible with the free and open source online geochemical modeling platform [WORM Portal](https://worm-portal.asu.edu/). Estimated thermodynamic properties of complexes from the Complicator can be used in conjunction with the rest of the WORM database to:
+- calculate properties of reactions and create activity or predominance diagrams.
+- expand the number of aqueous complexes available in geochemical speciation (equilibration) and mass transfer calculations.

complicator-0.3.0/README.md

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+# The Complicator
+
+Code Authors: Grayson Boyer, Everett Shock
+Data Compilers: GEOPIG Lab, Apar Prasad
+
+This is a Python package for estimating standard state thermodynamic properties and Helgeson-Kirkham-Flowers (HKF) equation of state parameters for aqueous metal complexes with monovalent ligands using published methods from [Sverjensky et al. (1997)](https://doi.org/10.1016/s0016-7037(97)00009-4) and [Shock et al. (1997)](https://doi.org/10.1016/S0016-7037(96)00339-0)
+
+## Installation
+
+This package can be installed through PyPI with:
+`pip install Complicator`
+
+## Usage
+
+The best way to learn about the Complicator is through the WORM Portal ([worm-portal.asu.edu](worm-portal.asu.edu)). Check out Jupyter notebook demo 4-2-1 in the WORM Library that is available when you log in.
+
+What follows is a brief example of how the Complicator can be used.
+
+Supply a dataframe containing names of metals, ligands, stability constants for the first through fourth association at 25 °C, and optionally, standard state entropies of association for the first through fourth association complex. An example is assigned to the variable `df_input` in the example below.
+
+```
+import pandas as pd
+from Complicator import complicate
+
+df_input = pd.DataFrame({
+        "Metal":["Ag+", "Al+3"],
+        "Ligand":["OH-", "OH-"],
+        "BETA_1":[2, 9.03], # stability constant for the first association complex
+        "BETA_2":[3.97, 17.6], # second stability constant
+        "BETA_3":[float('NaN'), 26.4], # third stability constant
+        "BETA_4":[float('NaN'), 33.8], # fourth stability constant
+        "Sass_1":[float('NaN'), 36.5], # entropy of association for the first complex (cal/mol/K)
+        })
+
+df_out, _, _, _ = complicate(df_in=df_input)
+
+df_out
+```
+
+The output is a dataframe containing estimated thermodynamic properties, parameters for the revised Helgeson Kirkham Flowers (HKF) equation of state, and more. [The format of the output is explained in more detail here](https://worm-portal.asu.edu/docs/database/). This Water-Organic-Rock-Microbe (WORM) database format is designed to be compatible with the free and open source online geochemical modeling platform [WORM Portal](https://worm-portal.asu.edu/). Estimated thermodynamic properties of complexes from the Complicator can be used in conjunction with the rest of the WORM database to:
+- calculate properties of reactions and create activity or predominance diagrams.
+- expand the number of aqueous complexes available in geochemical speciation (equilibration) and mass transfer calculations.

complicator-0.3.0/complicator/CoCl4_activity.py

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+import pandas as pd
+import math
+from .autopp93s4 import complicate
+import plotly.express as px
+import plotly.graph_objects as go
+from ipywidgets import interactive, interact_manual
+interact_manual.opts['manual_name'] = 'Calculate'
+
+import pychnosz
+_ = pychnosz.thermo("WORM", messages=False)
+
+@interact_manual(log_beta=(-5, 5, 0.01), S=(-100, 100, 1), Cp=(-100, 100, 1), V=(-100, 150, 1))
+def CoCl4_2_activity(log_beta=0, S=0, Cp=0, V=0):
+
+    df_input = pd.DataFrame({
+            "Metal":["Co+2"],
+            "Ligand":["Cl-"],
+            "BETA_1":[0],
+            "BETA_2":[0],
+            "BETA_3":[0],
+            "BETA_4":[log_beta],
+            "S_4":[S],
+            "Cp_4":[Cp],
+            "V_4":[V],
+            })
+    
+    df_out, _, _, _ = complicate(df_in=df_input, print_warnings=False)
+
+    G = df_out[df_out["name"] == "Co(Cl)4-2"]["G"].values[0]
+    H = df_out[df_out["name"] == "Co(Cl)4-2"]["H"].values[0]
+    
+    _ = pychnosz.add_OBIGT(df_out, force=True, messages=False)
+    T = [0.01, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350]
+    out_estimate_psat = pychnosz.subcrt(["Co+2", "Cl-", "Co(Cl)4-2"], [-1, -4, 1], T=T, show=False, messages=False).out
+    out_estimate_600bars = pychnosz.subcrt(["Co+2", "Cl-", "Co(Cl)4-2"], [-1, -4, 1], T=T, P=600, show=False, messages=False).out
+
+    out_estimate_psat["type"] = "Psat (model)"
+    out_estimate_600bars["type"] = "600 bars (model)"
+    df_plot = pd.concat([out_estimate_psat, out_estimate_600bars], axis=0)
+    
+    fig = px.line(df_plot, x="T", y="logK", color="type", template="simple_white")
+
+    
+    fig.add_trace(go.Scatter(x=[25, 50, 90],
+                             y=[-2.09, -1.72, -1.41],
+                             mode='markers', name="Psat (Pan and Susak, 1990)",
+                             marker=dict(
+                                line_color='#1F77B4',
+                                color='#17BECF',
+                                size=10,
+                                symbol="circle",
+                                line_width=2,
+                                ),
+                             error_y=dict(
+                                type='data',
+                                array=[0.05, 0.05, 0.05],
+                                color='#1F77B4',
+                                visible=True)
+                             )
+                            
+                 )
+    
+    fig.add_trace(go.Scatter(x=[150, 250, 350],
+                             y=[-0.69, 2.16, 5.68],
+                             mode='markers', name="600 bars (Liu et al., 2011)",
+                             marker=dict(
+                                line_color='#FF7F0E',
+                                color='#FECB52',
+                                size=10,
+                                symbol="circle",
+                                line_width=2,
+                                ),
+                             error_y=dict(
+                                type='data',
+                                array=[0.2, 0.15, 0.6],
+                                color='#FF7F0E',
+                                visible=True)
+                             )
+                 )
+    
+
+
+    a1 = df_out[df_out["name"]=="Co(Cl)4-2"]["a1.a"].values[0]
+    a2 = df_out[df_out["name"]=="Co(Cl)4-2"]["a2.b"].values[0]
+    a3 = df_out[df_out["name"]=="Co(Cl)4-2"]["a3.c"].values[0]
+    a4 = df_out[df_out["name"]=="Co(Cl)4-2"]["a4.d"].values[0]
+    c1 = df_out[df_out["name"]=="Co(Cl)4-2"]["c1.e"].values[0]
+    c2 = df_out[df_out["name"]=="Co(Cl)4-2"]["c2.f"].values[0]
+    omega = df_out[df_out["name"]=="Co(Cl)4-2"]["omega.lambda"].values[0]
+    
+    annotation_text = ("Co<sup>2+</sup> + 4Cl<sup>-</sup> = CoCl<sub>4</sub><sup>2-</sup>"
+                       "<br>logβ<sub>4</sub> = {}".format(round(log_beta, 2))+""
+                       "<br>∆<sub>f</sub>G° = {} cal mol<sup>-1</sup>".format(int(G))+""
+                       "<br>∆<sub>f</sub>H° = {} cal mol<sup>-1</sup>".format(int(H))+""
+                       "<br>S° = {} cal mol<sup>-1</sup>K<sup>-1</sup>".format(S)+""
+                       "<br>Cp° = {} cal mol<sup>-1</sup>K<sup>-1</sup>".format(Cp)+""
+                       "<br>V° = {} cm<sup>3</sup> mol<sup>-1</sup>".format(V)+""
+                       "<br>a<sub>1</sub> × 10 = {} cal mol<sup>-1</sup> bar<sup>-1</sup>".format(a1)+""
+                       "<br>a<sub>2</sub> × 10<sup>-2</sup> = {} cal mol<sup>-1</sup>".format(a2)+""
+                       "<br>a<sub>3</sub> = {} cal K mol<sup>-1</sup> bar<sup>-1</sup>".format(a3)+""
+                       "<br>a<sub>4</sub> × 10<sup>-4</sup> = {} cal K mol<sup>-1</sup>".format(a4)+""
+                       "<br>c<sub>1</sub> = {} cal mol<sup>-1</sup>".format(c1)+""
+                       "<br>c<sub>2</sub> × 10<sup>-4</sup> = {} cal K mol<sup>-1</sup>".format(c2)+""
+                       "<br>ω × 10<sup>-5</sup> = {} cal K mol<sup>-1</sup>".format(omega)+""
+                       )
+    
+    fig.add_annotation(
+        x=0.05, y=1,
+        xref='paper', yref='paper',
+        showarrow=False,
+        text=annotation_text,
+        align="left",
+        font = dict(size = 10),
+    )
+    
+
+    fig.update_layout(
+        xaxis_title="T, °C",
+        yaxis_title="logβ<sub>4</sub>",
+        title=None,
+        width=600,
+        height=350,
+        legend_title=None,
+        font=dict(size=12),
+        title_x=0.5,
+        xaxis_range=[0, 360],
+        yaxis_range=[-4, 8],
+        margin=dict(l=50,r=50,b=0,t=1),
+    )
+    
+    config = {'toImageButtonOptions': {'format': "png", # one of png, svg, jpeg, webp
+                                      },
+             }
+    
+    
+    fig.show(config=config)

complicator-0.3.0/complicator/__init__.py

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+from .autopp93s4 import complicate