pyrolite 0.0.14__zip

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/melts.py

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+import os, sys
+import re
+import pandas as pd
+import logging
+from .util.melts import *
+from .util.pd import to_frame
+from pyrolite.geochem import common_oxides, common_elements
+from pyrolite.util.melts import MELTS_Env
+
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+logger = logging.getLogger(__name__)
+
+
+class MeltsSystem:
+
+    def __init__(self, composition):
+
+        self.composition = composition
+        self.liquid = None
+        self.solid = None
+        self.potentialSolid = None
+        self.parameters = None
+
+    def equilirate(self):
+        method = 'equilibrate'
+
+    def findLiquidus(self):
+        method = 'findLiquidus'
+
+    def findWetLiquidus(self):
+        method = 'findWetLiquidus'
+
+
+
+def from_melts_cstr(composition_str):
+    """Parses melts composition strings to dictionaries."""
+    regex = r"""(?P<el>[a-zA-Z'^.]+)(?P<num>[^a-zA-Z]+)"""
+    result = re.findall(regex, composition_str)
+    convert_element = lambda s: re.sub(r"""[\']+""",
+                                       str(s.count("""'"""))+'+',
+                                       s)
+    return {convert_element(el): float(val) for (el, val) in result}
+
+
+def to_meltsfiles(df, linesep=os.linesep, **kwargs):
+    """
+    Creates a number of melts files from a dataframe.
+    """
+
+    # Type checking such that series will be passed directly to MELTSfiles
+    if isinstance(df, pd.DataFrame):
+        for ix in range(df.index.size):
+            to_meltsfile(df.iloc[ix, :])
+    elif isinstance(df, pd.Series):
+        to_meltsfile(src, **kwargs)
+
+
+def to_meltsfile(ser, linesep=os.linesep, **kwargs):
+    lines = []
+    # majors -->  SiO2 45.7
+    # output majors to Wt% values, may need to reorder them for MELTS..
+    majors = [i for i in ser.index if i in common_oxides()]
+    for k, v in zip(majors, ser[majors].values):
+        if not pd.isnull(v): # no NaN data in MELTS files
+            lines.append('Initial Composition: {} {}'.format(k, v))
+
+    # traces --> Initial Trace: Sm 0.2
+
+    # output traces to ppm values
+    traces = [i for i in ser.index if i in common_elements()]
+    for k, v in zip(traces, ser[traces].values):
+        if not pd.isnull(v): # no NaN data in MELTS files
+            lines.append('Initial Trace: {} {}'.format(k, v))
+    # output valid kwargs
+    valid = ['Mode',
+             'Temperature',
+             'Pressure',
+             'dp/dt',
+             'log fo2 Path',
+             'Log fO2 Delta']
+
+    # potentially pass these as tuples (start, stop, increment)
+    # temperature, pressure --> Initial Temperature: 1500.0
+    # temperature, pressure --> Final Temperature: 2000.0
+    # temperature, pressure --> Increment Temperature: 3.00
+
+    # dp/dt: 0.00
+    # log fo2 Path: None
+    # Log fO2 Delta: 0.0
+    # Mode: Fractionate Solids
+    return linesep.join(lines)

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/mineral/__init__.py

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+import logging
+from .mineral import Mineral
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+logger = logging.getLogger(__name__)
+
+
+# Todo: class attributes to aggregate all collected minerals
+
+__db__ = Mineral.db

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/mineral/db.py

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+import periodictable as pt
+from .mineral import *
+from .sites import *
+# %% Generic Mineral Group Templates ---------------------------------------------------
+OLIVINE = MineralTemplate(
+    "olivine",
+    MX(
+        "M1",
+        affinities={
+            "Mg{2+}": 0,
+            "Fe{2+}": 1,
+            "Mn{2+}": 2,
+            "Li{+}": 3,
+            "Ca{2+}": 4,
+            "Na{+}": 5,
+        },
+    ),
+    MX(
+        "M2",
+        affinities={
+            "Al{3+}": 0,
+            "Fe{3+}": 1,
+            "Ti{4+}": 2,
+            "Cr{3+}": 3,
+            "V{3+}": 4,
+            "Ti{3+}": 5,
+            "Zr{4+}": 6,
+            "Sc{3+}": 7,
+            "Zn{2+}": 8,
+            "Mg{2+}": 9,
+            "Fe{2+}": 10,
+            "Mn{2+}": 11,
+        },
+    ),
+    TX(),
+    *[OX()] * 2,
+)
+
+PYROXENE = MineralTemplate(
+    "pyroxene",
+    MX(
+        "M1",
+        affinities={
+            "Mg{2+}": 0,
+            "Fe{2+}": 1,
+            "Mn{2+}": 2,
+            "Li{+}": 3,
+            "Ca{2+}": 4,
+            "Na{+}": 5,
+        },
+    ),
+    MX(
+        "M2",
+        affinities={
+            "Al{3+}": 0,
+            "Fe{3+}": 1,
+            "Ti{4+}": 2,
+            "Cr{3+}": 3,
+            "V{3+}": 4,
+            "Ti{3+}": 5,
+            "Zr{4+}": 6,
+            "Sc{3+}": 7,
+            "Zn{2+}": 8,
+            "Mg{2+}": 9,
+            "Fe{2+}": 10,
+            "Mn{2+}": 11,
+        },
+    ),
+    *[TX()] * 2,
+    *[OX()] * 6,
+)
+
+Mineral("forsterite", OLIVINE, pt.formula("Mg2SiO4"))
+Mineral("fayalite", OLIVINE, pt.formula("Fe2SiO4"))
+Mineral("tephroite", OLIVINE, pt.formula("Mn2SiO4"))
+Mineral("liebenbergite", OLIVINE, pt.formula("Ni1.5Mg0.5SiO4"))
+
+Mineral("enstatite", PYROXENE, pt.formula("Mg2Si2O6"))
+Mineral("ferrosilite", PYROXENE, pt.formula("Fe2Si2O6"))
+Mineral("diopside", PYROXENE, pt.formula("CaMgSi2O6"))
+Mineral("hedenbergite", PYROXENE, pt.formula("CaFeSi2O6"))
+Mineral("johannsenite", PYROXENE, pt.formula("CaMnSi2O6"))
+Mineral("esseneite", PYROXENE, pt.formula("Ca Al Fe{3+} SiO6"))
+Mineral("jadeite", PYROXENE, pt.formula("NaAlSi2O6"))
+Mineral("aegirine", PYROXENE, pt.formula("NaFe{3+}Si2O6"))
+Mineral("namansilite", PYROXENE, pt.formula("NaMn{3+}Si2O6"))
+Mineral("kosmochlor", PYROXENE, pt.formula("NaCrSi2O6"))
+Mineral("spodumene", PYROXENE, pt.formula("LiAlSi2O6"))

ProgramData/Anaconda3_64/Lib/site-packages/pyrolite/mineral/ions.py

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+import periodictable as pt
+from periodictable.core import Element
+from periodictable.formulas import Formula
+from collections import defaultdict
+import logging
+
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+logger = logging.getLogger(__name__)
+
+__default_charges__ = defaultdict(lambda: None)
+__default_charges__.update(
+    dict(
+        H=1,
+        Li=1,
+        Be=1,
+        B=3,
+        C=4,
+        O=-2,
+        F=-1,
+        Na=1,
+        Mg=2,
+        Al=3,
+        Si=4,
+        P=3,
+        Cl=-1,
+        K=1,
+        Ca=2,
+        Sc=3,
+        Ti=4,
+        V=3,
+        Cr=3,
+        Mn=2,
+        Fe=2,
+        Co=2,
+        Ni=2,
+        Cu=2,
+        Zn=2,
+        Br=-1,
+        Rb=1,
+        Sr=2,
+        Y=3,
+        Zr=4,
+        Nb=5,
+        Sn=4,
+        I=-1,
+        Cs=1,
+        Ba=2,
+        La=3,
+        Ce=3,
+        Pr=3,
+        Nd=3,
+        Sm=3,
+        Eu=3,
+        Gd=3,
+        Tb=3,
+        Dy=3,
+        Ho=3,
+        Er=3,
+        Tm=3,
+        Yb=3,
+        Lu=3,
+        Hf=4,
+        Pb=2,
+        Th=4,
+        U=4,
+    )
+)
+
+# Monkey patching for default charges
+
+Element.default_charge = 0
+Formula.default_charge = property(
+    lambda self: sum([m * a.default_charge for a, m in self.atoms.items()])
+)
+
+for el, c in __default_charges__.items():
+    getattr(pt, el).default_charge = c
+    assert isinstance(getattr(pt, el), Element)