pychnosz 1.1.1__cp311-cp311-macosx_10_13_x86_64.whl

pychnosz/data/__init__.py

@@ -0,0 +1,11 @@
+"""Data management and access for CHNOSZ thermodynamic database."""
+
+from .loader import DataLoader, get_default_loader
+from .obigt import OBIGTDatabase, get_default_obigt
+
+__all__ = [
+    'DataLoader',
+    'get_default_loader',
+    'OBIGTDatabase', 
+    'get_default_obigt'
+]

pychnosz/data/add_obigt.py

@@ -0,0 +1,327 @@
+"""
+Implementation of add_OBIGT() function for Python CHNOSZ.
+
+This function loads external OBIGT database files and replaces or adds
+entries to the currently loaded thermodynamic database, mimicking the
+behavior of R CHNOSZ add.OBIGT() function.
+"""
+
+import pandas as pd
+import numpy as np
+import os
+from typing import Union, List, Optional
+import warnings
+
+from ..core.thermo import thermo
+
+
+def add_OBIGT(file: Union[str, pd.DataFrame], force: bool = True, messages: bool = True) -> List[int]:
+    """
+    Add or replace entries in the thermodynamic database from external files or DataFrames.
+
+    This function replicates the behavior of R CHNOSZ add.OBIGT() by loading
+    CSV files from inst/extdata/OBIGT/ or accepting pandas DataFrames directly,
+    and replacing entries with matching names.
+
+    Parameters
+    ----------
+    file : str or pd.DataFrame
+        Either:
+        - Name of the database file to load (e.g., "SUPCRT92")
+          The function will look for file.csv in inst/extdata/OBIGT/
+        - Full path to a CSV file
+        - A pandas DataFrame containing OBIGT data
+    force : bool, default True
+        If True, proceed even if some species are not found
+    messages : bool, default True
+        If True, print informational messages about additions/replacements
+        If False, suppress all output (equivalent to R's suppressMessages())
+
+    Returns
+    -------
+    list of int
+        List of species indices (1-based) that were added or replaced
+
+    Examples
+    --------
+    >>> import pychnosz
+    >>> import pandas as pd
+    >>>
+    >>> # Example 1: Load from file name
+    >>> pychnosz.reset()
+    >>> indices = pychnosz.add_OBIGT("SUPCRT92")
+    >>>
+    >>> # Example 2: Load from DataFrame
+    >>> thermo_df = pd.read_csv("thermodata.csv")
+    >>> indices = pychnosz.add_OBIGT(thermo_df)
+    >>>
+    >>> # Example 3: Suppress messages
+    >>> indices = pychnosz.add_OBIGT(thermo_df, messages=False)
+
+    Notes
+    -----
+    This function modifies the thermo() object in place, replacing entries
+    with matching names and adding new entries for species not in the database.
+    The behavior exactly matches R CHNOSZ add.OBIGT().
+    """
+
+    # Get the thermo system
+    thermo_sys = thermo()
+
+    # Ensure the thermodynamic system is initialized
+    if not thermo_sys.is_initialized() or thermo_sys.obigt is None:
+        thermo_sys.reset()
+
+    # Handle DataFrame input
+    if isinstance(file, pd.DataFrame):
+        new_data = file.copy()
+        file_path = "<DataFrame>"
+        file_basename = None
+    else:
+        # Handle string file path
+        # If file is not an existing path, look for it in OBIGT directories
+        if not os.path.exists(file):
+            if not file.endswith('.csv'):
+                file_to_find = file + '.csv'
+            else:
+                file_to_find = file
+
+            # Look for the file in the OBIGT data directory
+            # Use package-relative path
+            base_paths = [
+                os.path.join(os.path.dirname(__file__), 'extdata', 'OBIGT'),
+            ]
+
+            file_path = None
+            for base_path in base_paths:
+                potential_path = os.path.join(base_path, file_to_find)
+                if os.path.exists(potential_path):
+                    file_path = potential_path
+                    break
+
+            if file_path is None:
+                raise FileNotFoundError(f"Could not find OBIGT file: {file}")
+        else:
+            # Use the file path as provided
+            file_path = file
+
+        # Extract the basename for source_file column
+        file_basename = os.path.basename(file_path)
+
+        # Read the CSV file
+        try:
+            new_data = pd.read_csv(file_path)
+        except Exception as e:
+            raise ValueError(f"Error reading {file_path}: {e}")
+
+    if new_data.empty:
+        raise ValueError(f"No data found in {file_path if isinstance(file, str) else 'DataFrame'}")
+
+    # Validate columns before processing
+    # Get the current OBIGT database to determine required columns
+    to1 = thermo_sys.obigt
+
+    # Define core required columns that all species must have
+    # These are the fundamental columns needed for thermodynamic calculations
+    # Model-specific columns (logK*, T*, P*, etc.) are optional
+    core_required_columns = [
+        'name', 'abbrv', 'formula', 'state', 'ref1', 'ref2', 'date', 'E_units',
+        'G', 'H', 'S', 'Cp', 'V',
+        'a1.a', 'a2.b', 'a3.c', 'a4.d', 'c1.e', 'c2.f', 'omega.lambda', 'z.T'
+    ]
+
+    # The 'model' column is optional and will be auto-generated if missing
+    # Filter to only include columns that exist in current OBIGT (for compatibility)
+    required_columns = [col for col in core_required_columns if col in to1.columns]
+
+    # Check for missing required columns
+    missing_columns = [col for col in required_columns if col not in new_data.columns]
+
+    if missing_columns:
+        raise ValueError(
+            f"Missing required columns in input data: {', '.join(missing_columns)}. "
+            f"Please ensure the CSV file contains all necessary OBIGT database columns."
+        )
+
+    # Special handling for 'model' column
+    if 'model' not in new_data.columns:
+        # Create model column with proper values
+        new_data = new_data.copy()  # Make a copy to avoid SettingWithCopyWarning
+
+        # Assign model based on state:
+        # - aqueous species (state == 'aq') get 'HKF'
+        # - non-aqueous species get 'CGL'
+        new_data['model'] = new_data['state'].apply(lambda x: 'HKF' if x == 'aq' else 'CGL')
+
+        # Issue a warning to inform the user
+        warnings.warn(
+            "The 'model' column was not found in the input data. "
+            "Auto-generating 'model' column: 'HKF' for aqueous species (state='aq'), "
+            "'CGL' for all other species.",
+            UserWarning
+        )
+
+    # Get energy units from the file (all unique values)
+    # Match R's behavior: unique values joined with " and "
+    if 'E_units' in new_data.columns:
+        unique_units = new_data['E_units'].dropna().unique().tolist()
+        # Filter out non-energy unit values like "CGL" (which is a model, not energy unit)
+        # Valid energy units are typically "cal" and "J"
+        energy_unit_names = [str(u) for u in unique_units if str(u) in ['cal', 'J']]
+        # Join in the order they appear in the file (matching R's paste(unique(...), collapse = " and "))
+        energy_units_str = ' and '.join(energy_unit_names) if energy_unit_names else 'cal'
+    else:
+        energy_units_str = 'cal'
+
+    # Create identifier strings for matching (name + state)
+    id1 = to1['name'].astype(str) + ' ' + to1['state'].astype(str)
+    id2 = new_data['name'].astype(str) + ' ' + new_data['state'].astype(str)
+
+    # Track the indices we've modified/added
+    inew = []
+
+    # Check which entries in new_data exist in current database
+    # does_exist is a boolean array indicating which id2 entries are in id1
+    does_exist = id2.isin(id1.values)
+
+    # Get the indices in to1 where matches exist (matching R's match(id2, id1))
+    # This gives us the positions in to1 for each id2 element
+    ispecies_exist = []
+    for i, id_val in enumerate(id2):
+        if does_exist.iloc[i]:
+            # Find the index in to1 where this matches
+            match_idx = id1[id1 == id_val].index[0]
+            ispecies_exist.append(match_idx)
+        else:
+            ispecies_exist.append(None)
+
+    nexist = sum(does_exist)
+
+    # Check if new_data has columns that to1 doesn't have, and add them
+    # Use object dtype for new columns to match pandas default behavior and avoid FutureWarning
+    for col in new_data.columns:
+        if col not in to1.columns:
+            # Determine dtype from new_data
+            dtype = new_data[col].dtype
+            # Use object dtype for string columns to avoid dtype incompatibility
+            if dtype == object or pd.api.types.is_string_dtype(dtype):
+                to1[col] = pd.Series(dtype=object)
+            else:
+                to1[col] = np.nan
+
+    if force:
+        # Replace existing entries
+        if nexist > 0:
+            # Update rows in to1 for species that exist
+            for i, idx in enumerate(ispecies_exist):
+                if idx is not None:
+                    # Replace the row in to1 with data from new_data
+                    for col in new_data.columns:
+                        # col should now be in to1 since we added missing columns above
+                        to1.loc[idx, col] = new_data.iloc[i][col]
+                    # Set source_file for replaced entries
+                    if file_basename is not None:
+                        to1.loc[idx, 'source_file'] = file_basename
+
+            # Add these indices to inew
+            inew.extend([idx for idx in ispecies_exist if idx is not None])
+
+            # Remove existing entries from new_data (to2 <- to2[!does.exist, ])
+            to2 = new_data[~does_exist].copy()
+        else:
+            to2 = new_data.copy()
+    else:
+        # Ignore any new entries that already exist
+        to2 = new_data[~does_exist].copy()
+        nexist = 0
+
+    # Add new entries
+    if len(to2) > 0:
+        # Store the starting index for new additions
+        len_id1 = len(id1)
+
+        # Ensure new entries have all required columns
+        # Make a proper copy to avoid SettingWithCopyWarning
+        to2 = to2.copy()
+        for col in to1.columns:
+            if col not in to2.columns:
+                to2[col] = np.nan
+
+        # Set source_file for new entries
+        if file_basename is not None:
+            to2['source_file'] = file_basename
+
+        # Reorder columns to match current OBIGT
+        to2 = to2.reindex(columns=to1.columns)
+
+        # Add to the database
+        # Use concat with explicit future behavior to avoid FutureWarning
+        to1 = pd.concat([to1, to2], ignore_index=True, sort=False)
+
+        # Add new indices: (length(id1)+1):nrow(to1)
+        new_indices = list(range(len_id1 + 1, len(to1) + 1))
+        inew.extend(new_indices)
+
+    # Reset rownames to 1:nrow (matching R's rownames(thermo$OBIGT) <- 1:nrow(thermo$OBIGT))
+    to1.index = range(1, len(to1) + 1)
+
+    # Update the thermo system with modified database
+    thermo_sys.obigt = to1
+
+    # Update formula_ox if the column exists in the database
+    if 'formula_ox' in to1.columns:
+        # Create a DataFrame with name and formula_ox columns
+        # Keep the same index as the obigt DataFrame (1-based)
+        formula_ox_df = pd.DataFrame({
+            'name': to1['name'],
+            'formula_ox': to1['formula_ox']
+        })
+        # Preserve the 1-based index
+        formula_ox_df.index = to1.index
+        thermo_sys.formula_ox = formula_ox_df
+    else:
+        # If formula_ox column doesn't exist, set to None
+        thermo_sys.formula_ox = None
+
+    # Print summary (matching R CHNOSZ output)
+    if messages:
+        print(f"add_OBIGT: read {len(new_data)} rows; made {nexist} replacements, {len(to2) if len(to2) > 0 else 0} additions [energy units: {energy_units_str}]")
+
+    return inew
+
+
+def list_OBIGT_files() -> List[str]:
+    """
+    List available OBIGT database files.
+    
+    Returns
+    -------
+    list of str
+        List of available .csv files in the OBIGT directory
+    """
+    
+    # Use package-relative path
+    base_paths = [
+        os.path.join(os.path.dirname(__file__), 'extdata', 'OBIGT'),
+    ]
+    
+    files = []
+    for base_path in base_paths:
+        if os.path.exists(base_path):
+            csv_files = [f[:-4] for f in os.listdir(base_path) if f.endswith('.csv')]
+            files.extend(csv_files)
+            break
+    
+    return sorted(list(set(files)))  # Remove duplicates and sort
+
+
+def reset_OBIGT() -> None:
+    """
+    Reset OBIGT database to default state.
+    
+    This function reloads the default thermodynamic database,
+    removing any modifications made by add_OBIGT().
+    """
+    from ..utils.reset import reset
+    reset()
+    print("OBIGT database reset to default state")

pychnosz/data/extdata/Berman/BDat17_2017.csv

@@ -0,0 +1,2 @@
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pychnosz/data/extdata/Berman/Ber88_1988.csv

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+K-feldspar,-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3738804,-3959704,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+"K-feldspar,low",-3745415,-3970791,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+prehnite,-5820154,-6198606,288.634,14.016,716.05,-6404.6,-2182500,268500000,0,0,0,0.1468,0.01128353,-0.1427,0,,,,,,,,,,,,,,
+pyrope,-5936009,-6286548,266.359,11.316,640.72,-4542.1,-4701900,0,0,0,0,2.2519,0.00037044,-0.0576,4.42E-05,,,,,,,,,,,,,,
+pyrophyllite,-5266865,-5640781,239.4,12.76,665.93,-5897.4,-4979900,661810000,0,0,0,1.2637,0.00381661,-0.1354,0,,,,,,,,,,,,,,
+quartz,-856288,-910700,41.46,2.269,80.01,-240.3,-3546700,491570000,0,0,0,2.3895,0,-0.2434,0.0010137,848,373,0.0237,-0.09187,0.00024607,0,,,,,,,,
+"quartz,beta",-855033,-908627,44.207,2.37,80.01,-240.3,-3546700,491570000,0,0,0,0,0,-0.1238,0.0007087,,,,,,,,,,,,,,
+rutile,-889497,-944750,50.46,1.882,77.84,0,-3367800,402940000,0,0,0,2.5716,0.00015409,-0.0454,5.84E-05,,,,,,,,,,,,,,
+sillimanite,-2439265,-2586091,95.93,4.983,256.73,-1887.2,-2977400,250960000,0,0,0,1.3431,0,-0.0753,0,,,,,,,,,,,,,,
+sphene,-2455134,-2596652,129.29,5.565,234.62,-1040.3,-5118300,591460000,0,0,0,2.52,0,-0.059,0,,,,,,,,,,,,,,
+spinel,-2176537,-2300313,84.535,3.977,235.9,-1766.6,-1710400,40620000,0,0,0,2.1691,0.00050528,-0.0489,0,,,,,,,,,,,,,,
+talc,-5517657,-5897387,261.24,13.61,664.11,-5187.2,-2147200,-327370000,0,0,0,2.9447,0,-0.1699,0.0005665,,,,,,,,,,,,,,
+tremolite,-11578548,-12305578,551.15,27.268,1229.36,-6401.9,-32089900,4208810000,0,0,0,2.4374,0.00098338,-0.1392,0.0003481,,,,,,,,,,,,,,
+"tridymite,low",-854026,-907750,43.77,2.675,75.37,0,-5958100,958250000,0,0,0,1.9339,0,-0.2508,0,383,298,0,0.4267,-0.00144575,130,,,,,,,,
+"tridymite,high",-853844,-907045,45.524,2.737,75.37,0,-5958100,958250000,0,0,0,0.4829,0,-0.074,0.0003735,,,,,,,,,,,,,,
+wollastonite,-1546123,-1631500,81.81,3.983,149.07,-690.3,-3659300,484350000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
+pseudowollastonite,-1543085,-1627427,85.279,4.016,141.16,-417.2,-5857600,940740000,0,0,0,2.818,0,-0.1245,0.0003113,,,,,,,,,,,,,,
+zoisite,-6494148,-6889488,297.576,13.588,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,
+clinozoisite,-6496497,-6894968,287.076,13.673,749.17,-6509.3,-2380500,124860000,0,0,0,3.467,0,-0.0515,0.0001288,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/Ber90_1990.csv

@@ -0,0 +1,5 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+almandine,-4943492,-5267216,340.007,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,1.8613,0.00074539,-0.0558,3.21E-05,,,,,,,,,,,,,,
+annite,-4793115,-5142800,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+ilmenite,-1155794,-1232448,108.628,3.17,150,-441.6,-3323700,348150000,0,0,0,2.7248,0.00029968,-0.0584,0.000123,,,,,,,,,,,,,,
+phlogopite,-5830350,-6210391,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/DS10_2010.csv

@@ -0,0 +1,6 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+hedenbergite,-2674300,-2837802.5,173.59,6.785,353.31148,-3106.646,2047911.742,-563018581,0,0,0,2.796487,0,-0.17457,0.00151,,,,,,,,,,,,,,
+andradite,-5419000,-5761985.8,316.4,13.167,569.7558,-1441.44,-22441040.802,3146543781,0,0,0,2.072525,0.000561,-0.06539136,0.0001635,,,,,,,,,,,,,,
+ferro-actinolite,-9839000,-10518042.6,685.1,28.26,1321.15758,-8966.454,-21705844.286,3236159154,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+grunerite,-8964807,-9623000,725,27.8,1347.83,-9356.91,-20228480,3039190000,0,0,0,2.84,0,-0.15,0,,,,,,,,,,,,,,
+ilvaite,-3440000,-3695605.5,291.5,10.016,682.79138,-8787.112,30183568.71,-5666432624,0,0,0,1.801543,0.001152,-0.06838,2.4E-05,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/FDM+14_2014.csv

@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-2100,-10000,220000000,0,0,0,4.18,0,-0.1345,0.00017,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/Got04_2004.csv

@@ -0,0 +1,5 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+zoisite,NA,-6891340,297.38,13.572,733.034,-5979.52,-5079660,552314000,0,0,0,3.713,0,-0.0735,0,,,,,,,,,,,,,,
+orthoepidote,NA,-6449500,340.8,13.852,728.954,-5565.32,-5937360,610589000,0,0,0,3.713,0,-0.0735,0,,,,,,,,,,,,,,
+clinozoisite,NA,-6892040,294.88,13.64,733.034,-5979.52,-5079660,552314000,0,0,0,2.95,0,-0.0649,0,,,,,,,,,,,,,,
+epidote,NA,-6462600,332.8,13.901,728.954,-5565.32,-5937360,610589000,0,0,0,2.95,0,-0.0581,0,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/JUN92_1992.csv

@@ -0,0 +1,3 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+glaucophane,-11225858,-11960500,535,26.05,1717.5,-19272,7050000,0,0,0,0,2.2,0.00088,-0.116,0.00029,,,,,,,,,,,,,,
+pumpellyite,-13448936,-14402300,584,29.55,1576,-10603.8,-28304200,3838351000,0,0,0,3.467,0,-0.051516,0.0001288,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/SHD91_1991.csv

@@ -0,0 +1,12 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+muscovite,-5603417,-5983434,293.157,14.087,651.49,-3873.2,-18523200,2742470000,0,0,0,3.3527,0,-0.1717,0.0004295,,,,,,,,,,,,,,
+phlogopite,-5837044,-6217085,334.346,14.977,610.38,-2083.8,-21533000,2841040000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,
+K-feldspar,-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,1436,298,282.98,-4830,3621000,-0.15733,3.477E-05,410630
+"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
+paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
+albite,-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
+annite,-4799809,-5149494,420,15.408,727.21,-4775.04,-13831900,2119060000,0,0,0,3.4447,0,-0.1697,0,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/VGT92_1992.csv

@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+sudoite,NA,-8655273,390.5,20.51,1115.84,-8507.5,-19777440,2959147000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/VPT01_2001.csv

@@ -0,0 +1,3 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+daphnite,NA,-7120845,559.4,21.588,1229.23,-10256.5,-12276900,2121510000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,
+Mg-amesite,NA,-9035900,403.2,20.52,1144.45,-8327.2,-20058040,2820786000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/VPV05_2005.csv

@@ -0,0 +1,2 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+Fe-amesite,NA,-7607460,514.8,20.9,1219.81,-10021.5,-14439720,2392326000,0,0,0,2.6451,0,-0.182,0,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/ZS92_1992.csv

@@ -0,0 +1,11 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+fluormuscovite,-5772803,-6111401,299.03,14.087,680.36024,-6515.743,0,110583120,0,0,0,3.35273302,0,-0.17169021,0.00042947,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorphlogopite,-6063382,-6403168,336.394,14.637,653.70816,-5175.19,0,-324594720,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorannite,-4983910,-5293254,422.291,15.075,742.82736,-6817.41,0,418441840,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluortremolite,-11782144,-12457969,570.279,27.045,1272.64728,-9493.496,0,-10517739.2,0,0,0,2.43738877,0.00098338,-0.13917727,0.00034809,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluorapatite,-6443050,-6823447,387.857,15.753,668.77056,-4534.201,0,-746341920,0,0,0,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+hydroxyapatite,-6297702,-6694689,398.735,15.822,758.81024,-6480.598,0,-447939040,0,0,0,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorapatite,-6217424,-6597260,399.907,16.403,663.87528,-4435.877,0,-690234480,0,0,0,0,0,0,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+fluortalc,-5717018,-6056244,264.052,13.33,602.74704,-4766.831,0,-292588712,0,0,0,2.94468112,0,-0.16988979,0.0005665,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorphlogopite,-5600840,-5939422,360.703,16.59,573.45904,-2063.549,-16465713.6,2105765360,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,
+chlorannite,-4582036,-4890196,449.529,17.247,690.44368,-4760.137,-8725313.6,1376828880,0,0,0,3.44473262,0,-0.16969784,0,NA,NA,NA,NA,NA,NA,NA,NA,,,,,,

pychnosz/data/extdata/Berman/sympy.R

@@ -0,0 +1,99 @@
+# integrate Berman's equations using sympy 20170930
+# add k4, k5, k6 20180328
+library(rSymPy)
+
+# create SymPy variables called T and P
+sympy("var('T')")
+sympy("var('P')")
+
+sympy("k0 = Symbol('k0', real=True)")
+sympy("k1 = Symbol('k1', real=True)")
+sympy("k2 = Symbol('k2', real=True)")
+sympy("k3 = Symbol('k3', real=True)")
+sympy("k4 = Symbol('k4', real=True)")
+sympy("k5 = Symbol('k5', real=True)")
+sympy("k6 = Symbol('k6', real=True)")
+sympy("v1 = Symbol('v1', real=True)")
+sympy("v2 = Symbol('v2', real=True)")
+sympy("v3 = Symbol('v3', real=True)")
+sympy("v4 = Symbol('v4', real=True)")
+sympy("Tr = Symbol('Tr', real=True)")
+sympy("Pr = Symbol('Pr', real=True)")
+sympy("VPrTr = Symbol('VPrTr', real=True)")
+sympy("HPrTr = Symbol('HPrTr', real=True)")
+sympy("SPrTr = Symbol('SPrTr', real=True)")
+
+# Cp and its integrals
+Cp <- "k0 + k1*T**-0.5 + k2*T**-2 + k3*T**-3 + k4*T**-1 + k5*T + k6*T**2"
+intCp <- sympy(paste("integrate(", Cp,", (T, Tr, T))"))
+message("intCp = ", intCp)
+
+Cp_T <- "k0*T**-1 + k1*T**-1.5 + k2*T**-3 + k3*T**-4 + k4*T**-2 + k5 + k6*T"
+intCp_T <- sympy(paste("integrate(", Cp_T,", (T, Tr, T))"))
+message("intCp_T = ", intCp_T)
+
+# V and its integrals
+# as written in Berman, 1988
+#V <- "VPrTr * (1 + v1*(P - Pr) + v2*(P - Pr)**2 + v3*(T- Tr) + v4*(T - Tr)**2)"
+# simplified version with Pr==1 (Anderson and Crerar, 1993, p. 175)
+V <- "VPrTr * (1 + v1*(P - 1) + v2*(P - 1)**2 + v3*(T - Tr) + v4*(T - Tr)**2)"
+intV <- sympy(paste("integrate(", V,", (P, 1, P))"))
+# check that intV is equal to the expression in Berman, 1988 and Anderson, 2005 eq. 5.36
+#refintV <- "VPrTr * ( (v1/2 - v2) * (P**2 - Pr**2) + v2/3 * (P**3 - Pr**3) + (1 - v1 + v2 + v3*(T-Tr) + v4*(T-Tr)**2) * (P - Pr) )"
+# simplified version with Pr==1
+refintV <- "VPrTr * ( (v1 / 2 - v2) * (P**2 - 1) + v2 / 3 * (P**3 - 1) + (1 - v1 + v2 + v3*(T-Tr) + v4*(T-Tr)**2) * (P - 1) )"
+# this doesn't collect and cancel terms, so we have to expand the expressions
+#sympy(paste(intV, "- (", refintV, ")"))
+expintV <- sympy(paste("expand (", intV, ")"))
+exprefintV <- sympy(paste("expand (", refintV, ")"))
+# the difference is zero!
+diffintV <- sympy(paste(expintV, "- (", exprefintV, ")"))
+message("diffintV = ", diffintV, " (should be 0)")
+
+# another way to check that the expressions are equal
+# a function to separate the terms of an expression
+septerms <- function(x) {
+  x <- paste("+", x)
+  x <- gsub("+ ", "+", x, fixed=TRUE)
+  x <- gsub("- ", "-", x, fixed=TRUE)
+  strsplit(x, " ")[[1]]
+}
+intVterms <- septerms(expintV)
+refintVterms <- septerms(exprefintV)
+equalintVterms <- setequal(intVterms, refintVterms)
+message("equalintVterms is ", equalintVterms, " (should be TRUE)")
+
+# continuing with V integrals for S and H
+dVdT <- sympy(paste("diff(", V, ", T, 1)"))
+# again, integrate using Pr==1
+intdVdT <- sympy(paste("integrate(", dVdT,", (P, 1, P))"))         # for S
+message("intdVdT = ", intdVdT)
+
+minusintdVdT <- sympy(paste("- (", intdVdT, ")"))                  # apply minus sign!
+V_TdVdT <- sympy(paste(V, " - T * (", dVdT, ")"))
+intV_TdVdT <- sympy(paste("integrate(", V_TdVdT,", (P, 1, P))"))   # for H
+message("intV_TdVdT = ", intV_TdVdT)
+
+# check that intV_TdVdT - T * minusintdVdT is equal to intV (for G)
+intV2 <- sympy(paste(intV_TdVdT, "- T * (", minusintdVdT, ")") )
+expintV2 <- sympy(paste("expand (", intV2, ")"))
+## maybe we need to expand the terms first...
+#expintV_TdVdT <- sympy(paste("expand (", intV_TdVdT, ")"))
+#TintdVdT <- sympy(paste("T * (", intdVdT, ")") )
+#expTintdVdT <- sympy(paste("expand (", TintdVdT, ")"))
+#expintV3 <- sympy(paste(expintV_TdVdT, "- (", expTintdVdT, ")"))
+# this is zero!
+diffexpintV <- sympy(paste(expintV2, "- (", expintV, ")"))
+message("diffexpintV = ", diffexpintV, " (should be 0)")
+
+# H, S and G
+#HCp <- sympy(paste("HPrTr +", intCp, "+", intV_TdVdT))
+#SCp <- sympy(paste("SPrTr +", intCp_T, "- (", intdVdT, ")"))
+#GCp <- sympy(paste(HCp, "- T * (", SCp, ")"))
+#G <- sympy(paste(GCp, "+", intV))
+
+# References
+# Anderson, G. M. (2005) \emph{Thermodynamics of Natural Systems}, 2nd ed., Cambridge University Press, 648 p. \url{http://www.worldcat.org/oclc/474880901}
+# Anderson, G. M. and Crerar, D. A. (1993) \emph{Thermodynamics in Geochemistry: The Equilibrium Model}, Oxford University Press. \url{http://www.worldcat.org/oclc/803272549}
+# Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system Na{\s2}O-K{\s2}O-CaO-MgO-FeO-Fe{\s2}O{\s3}-Al{\s2}O{\s3}-SiO{\s2}-TiO{\s2}-H{\s2}O-CO{\s2}. \emph{J. Petrol.} \bold{29}, 445-522. \url{https://doi.org/10.1093/petrology/29.2.445}
+

pychnosz/data/extdata/Berman/testing/BA96.bib

@@ -0,0 +1,12 @@
+@Article{BA96,
+  author    = {Berman, R. G. and Aranovich, L. {\relax Ya}.},
+  journal   = {Contributions to Mineralogy and Petrology},
+  title     = {{O}ptimized standard state and solution properties of minerals. {I}. {M}odel calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system {F}e{O}-{M}g{O}-{C}a{O}-{A}l$_2${O}$_3$-{T}i{O}$_2$-{S}i{O}$2$},
+  year      = {1996},
+  volume    = {126},
+  number    = {1},
+  pages     = {25--37},
+  day       = {01},
+  doi       = {10.1007/s004100050233},
+  issn      = {1432-0967},
+}

pychnosz/data/extdata/Berman/testing/BA96_Berman.csv

@@ -0,0 +1,21 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
+almandine,,-5265440,341.51,11.529,621.43,-3287.9,-15081000,2211870000,0,0,0,1.8599,0.00074711,-0.057,4.34E-05,,,,,,,,,,,,,,
+anthophyllite,,-12074470,537.4,26.33,1233.79,-7134,-22163800,2333940000,0,0,0,2.8105,0.00062894,-0.1139,0,,,,,,,,,,,,,,
+cordierite,,-9161480,416.23,23.311,954.39,-7962.3,-2317300,-370210000,0,0,0,0.3003,0.00018017,-0.1158,0,,,,,,,,,,,,,,
+Fe-cordierite,,-8430550,482.18,23.706,983.48,-8403.7,-1870300,-85680000,0,0,0,0.4265,0,-0.17,0,,,,,,,,,,,,,,
+fayalite,,-1477170,151.73,4.639,252,-2013.7,0,-62190000,0,0,0,2.621,0.00084233,-0.0822,0.0001944,,,,,,,,,,,,,,
+ferrosilite,,-1192910,96.47,3.295,174.2,-1393,-454400,-37710000,0,0,0,3.1406,0.000804,-0.0911,3.03E-05,,,,,,,,,,,,,,
+forsterite,,-2174420,94.18,4.36,233.18,-1801.6,0,-267940000,0,0,0,2.9464,0.00088633,-0.0791,0.0001351,,,,,,,,,,,,,,
+geikelite,,-1570520,74.41,3.077,146.2,-416,-3999800,402330000,0,0,0,2.3314,0.00088328,-0.0529,0,,,,,,,,,,,,,,
+hematite,,-826740,87.36,3.027,146.86,0,-5576800,525630000,0,0,0,3.831,1.65E-05,-0.0479,3.04E-05,955,298,0,-0.07403,0.00027921,1287,,,,,,,,
+hercynite,,-1945360,123.13,4.08,251.77,-2044.4,-1348300,131500000,0,0,0,1.5819,0.00096276,-0.051,0,,,,,,,,,,,,,,
+ilmenite,,-1233320,108.5,3.17,150,-441.6,-3323700,348150000,0,0,0,2.3314,0.00088328,-0.0529,0,,,,,,,,,,,,,,
+iron-a,,0,27.45,0.709,51.87,-379.4,-2543000,506800000,0,0,0,4.5071,0.00014104,-0.0602,0,1042,298,-0.00057,-0.22208,0.00034823,1000,,,,,,,,
+iron-g,,7720,35.64,0.691,66.24,-1237.1,6373300,-1060400000,0,0,0,4.7153,0.00014451,-0.0467,-0.0001445,,,,,,,,,,,,,,
+magnetite,,-1116960,146.04,4.452,207.93,0,-7243300,664360000,0,0,0,3.0291,0.0013847,-0.0582,0.0001751,848,298,0,-0.19502,0.00061037,1565,,,,,,,,
+enstatite,,-1546040,66.18,3.133,166.58,-1200.6,-2270600,279150000,0,0,0,2.4656,0.0007467,-0.0749,4.47E-05,,,,,,,,,,,,,,
+orthocorundum,,-1634950,33.93,3.123,119.38,774.8,-6509100,422880000,0,0,0,2.4656,0.0007467,-0.0749,4.47E-05,,,,,,,,,,,,,,
+pyrope,,-6284740,268.8,11.311,590.9,-2827,-13320800,1260330000,0,0,0,2.2519,0.00037044,-0.0576,4.42E-05,,,,,,,,,,,,,,
+rutile,,-944750,50.88,1.883,77.84,0,-3367800,402940000,0,0,0,2.5716,0.00015409,-0.0454,5.85E-05,,,,,,,,,,,,,,
+spinel,,-2302160,80.37,3.978,244.67,-2004,0,0,0,0,0,2.1691,0.00050528,-0.0489,0,,,,,,,,,,,,,,
+talc,,-5898960,261.21,13.61,664.11,-5187.2,-2147200,-327370000,0,0,0,2.5616,0,-0.1847,0.0005878,,,,,,,,,,,,,,

pychnosz/data/extdata/Berman/testing/BA96_OBIGT.csv

@@ -0,0 +1,21 @@
+name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+almandine,Alm,Si3Fe3Al2O12,cr,BA96.1,NA,03.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr,BA96.1,NA,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr,Ber88,BA96.2,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+enstatite,En,MgSiO3,cr,Ber88,BA96.2,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fayalite,Fa,Fe2SiO4,cr,BA96.1,NA,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ferrosilite,Fsl,SiFeO3,cr,BA96.1,NA,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+forsterite,Fo,Mg2SiO4,cr,Ber88,BA96.3,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hematite,Hm,Fe2O3,cr,Ber88,BA96.2,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ilmenite,Ilm,FeTiO3,cr,Ber88,BA96.4,03.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+magnetite,Mt,Fe3O4,cr,Ber88,BA96.2,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pyrope,Py,Mg3Al2Si3O12,cr,Ber88,BA96.3,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+rutile,Rt,TiO2,cr,Ber88,BA96.2,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+spinel,Sp,MgAl2O4,cr,Ber88,BA96.3,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+talc,Tc,Mg3Si4O12H2,cr,Ber88,BA96.4,01.Oct.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Fe-cordierite,fCd,Fe2Al4Si5O18,cr,BA96,NA,12.Dec.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+geikelite,Gk,MgTiO3,cr,BA96,NA,12.Dec.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hercynite,Hc,FeAl2O4,cr,BA96,NA,12.Dec.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-a,aFe,Fe,cr,BA96,NA,12.Dec.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-g,gFe,Fe,cr,BA96,NA,12.Dec.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+orthocorundum,Ok,Al2O3,cr,BA96,NA,12.Dec.17,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA