Welcome to Thermobar’s documentation!

Contents:

• Introduction and Citation
• Units
• Installation & Updating
  • Installation
  • Updating
• Importing Data
  • Preserving Sample Names
  • One Mineral type (e.g, just Liquids)
  • Treatment of FeO vs. Fe2O3
  • Exporting Data to Excel
• Available mineral and mineral-melt equations
• Adding new models
• FAQs and Troubleshooting
  • Thermobar doesn’t match the Putirka (2008) spreadsheets
  • My temperatures are really hot!
  • Importing Data Issues
• Change Log
  • Version 1.0.37 - Feb 26th, 2024
  • Version 1.0.36 - Jan 21st, 2024
  • Version 1.0.31 to Version 1.0.34 - Dec, 2023
  • Version 1.0.31 - November 17th, 2023
  • Version 1.0.31 - November 17th, 2023
  • Version 1.0.30 - October 6th, 2023
  • Version 1.0.28 - October 6th, 2023
  • Version 1.0.25 - July 6th, 2023
  • Version 1.0.20 Mayn 30th, 2023
  • Version 1.0.19 April 1st, 2023
  • Version 1.0.18 April 1st, 2023
  • Version 1.0.16 April 1st, 2023
  • Version 1.0.14 March 13th, 2023
  • Version 1.0.12, Feb 13th, 2023
  • Version 1.0.11, Feb 11th, 2023
  • Version 0.12 Nov 23rd, 2021
  • Version 0.11 Nov 15th, 2021
  • Previous changes before detailed change log started:
• Worked examples
  • Liquids and Olivines
  • Clinopyroxene (Cpx)
  • Orthopyroxene (Opx)
  • Two Pyroxene (Opx-Cpx)
  • Amphiboles
  • Feldspars
  • Garnet
  • Error Propagation
  • Melt inclusions
  • Plotting Mineral classification diagrams.
  • Other Useful examples

Narrated YouTube Videos

• YouTube Tutorials
  • Why did we develop Thermobar
  • Introduction to Thermobar
  • Liquid-only Thermometry
  • Olivine-Liquid Thermometry
  • Clinopyroxene-Liquid Melt Matching 1 (simpler)
  • Clinopyroxene-Liquid Melt Matching 2 (advanced)
  • Amphibole-only and Amphibole-Liquid (advanced)
  • Feldspar-Liquid thermobarometry and hygrometry
  • Two Feldspar thermometry
  • Integration with VESIcal

Introductory Examples

• A five minute intro to Thermobar
  • 1 - Introduction
  • 2 - Installing and importing Thermobar
  • 3 - Load data from an Excel file
  • 4. Inspect data
  • 5 - Getting help
  • 6 - Can perform calculations just for pressure if you know temperature
  • 7 - Similarly, for temperature at a known pressure
  • 8 - If you don’t know either P or T
  • 9 - Can plot a very simple x-y diagram using matplotlib (loaded as plt)
  • 10 - Example of warnings for incorrect inputs
  • 11 - Example of Error when you don’t have an FeOt column…
  • What about if you have FeO and Fe2O3?
  • What about loading in data from Petrolog?
• Exporting to Excel
  • Importing various python things
  • Lets load in the Cpx-Liq data from the Into example
  • Example 1: Lets calculate Cpx-Liq temps, which returns a pandas series (single column of numbers)
  • 1b - Append column in a specific position
  • Example 2: What happen if our function outputs a pandas dataframe? e.g., if we perform the same calculation using “Eq_Tests=True”
  • Example 3 - Combining seperate dataframe

Liq & Ol-Liq

• Liquid-only thermometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Inspect inputs to check you didn’t have any funny column headings.
• Olivine-Liquid thermometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • 1a - Putirka eq 22
  • 1b - Specify eq_tests=True
  • 1c - You can also overwrite the spreadsheet Fe3Fet_Liq in the function itself
  • 3a - Roeder and Emslie, 1970
  • 3b - Toplis, 2005
  • 3c - Putirka (2016)
  • 3d - All Models
• Olivine-Liquid Hygrometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Now we can filter out based on common values
  • Can filter outputs, so only get calculated H2O contents for those with delta Kd Roeder <0.1
• 1 Sample - Fe-Mg equilibrium between olivines and matrix glasses
  • Install Thermobar if you haven’t already (remove the # and press run!)
  • 1. Calculate Mg# for liquids
  • 2. Calculate Olivine Fo contents
  • 3. Calculate fields you want to plot on a Rhodes diagram
  • 4. Plot the Kd model you want, along with the olivine and glass Mg
• Multisample - Fe-Mg equilibrium between olivines and glass.
  • Install Thermobar if you haven’t already (remove # and press run)
  • 1. Calculate Mg# for liquids
  • 2. Calculate Olivine Fo contents
  • 3. Calculate fields you want to plot on a Rhodes diagram
  • 4. Plot the Kd model you want, along with the olivine and glass Mg
• CHOMPI calculations
  • If you havent already, import or upgrade Thermobar. Only in v1.0.25 onwards

Cpx & Cpx-Liq

• Clinopyroxene-only and Clinopyroxene-Liquid Thermobarometry.
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • 1a - Temperature for a known pressure and water content
  • 1b - Temperature, overwriting the spreadsheet water content in the function itself
  • 1c- Lets use the thermometer of Brugman and Till, 2019.
  • 1d - We can also specify eq_tests=True to get a full dataframe back with all the components, as well as a number of equilibrium test values
  • 2a - Pressure at fixed temperature (T=1300 K), and pressures from Neave and Putirka (2017)
  • 2b - Equation 30 from Putirka (2008), overwriting input water, return equilibrium tests
  • 2c - As above, but setting a fixed Fe3Fet_Liq ratio
  • 3a - Iterating equation 30 from Putirka (2008) for P, and equation 33 from Putirka (2008) for T
  • 3b - Same as above, but with eq_tests=True
  • 3a -Pressure only, using equation 32b (at T=1300 K), and H2O=0
  • 3b - Pressure only, using 5 wt% water
  • 3c - Temperature-only using eq 32d at 5 kbar
  • 3d - Iterating P from 32b, and T from 32d, with H2O=5
  • Step 1 - Calculate Mg# for liq and cpxs
  • Step 2 - Calculate equilibrium lines to show on the rhodes diagram
  • Step 3 - Combine these on a plot
• Machine-Learning-based Clinopyroxene-only and Clinopyroxene-Liquid Thermobarometry.
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Using saved models
  • Lets do Cpx-only
• Pyroxene Classification Diagrams
  • Load in some Cpx compositions
  • Lets transform these Cpx compositions into the 3 coordinates we need for plotting on our ternary diagrams.
  • Example 1
  • Example 1d - Lets add a grid
  • Example 2 - Lets add your data (simple to start!)
  • Example 3 - Lets color by Px Jd content
• Pyroxene Ternary Diagram Segmented by Sample
  • Import Python things
  • Set plotting parameters
  • Load in pyroxene compositions
  • Lets calculate the components we need to plot a ternary diagram.
  • First, we can plot all the samples as a single color
  • Or, we can try to segment for different samples, First, lets find how many unique samples we have
  • Now lets segment out for each sample ID
  • Plot 1
  • Plot 2
• Cpx-Liquid Melt Matching (Simple Intro)
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • We can also run calculations at a fixed temperature (1450 K)
  • Or at fixed pressure (5 kbar here)
  • We can adapt the filters to get more matches
  • We can look and see we get a lot more matches.
• This code is a more advanced example of Cpx-Liquid melt matching
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • First, lets combine these synthetic liquids with all measured liquids to get an even bigger dataset
  • Second, following Scruggs and Putirka (2018), lets allocate H2O as a function of SiO2 content in the melt
  • Third, lets do melt matching

Opx & Opx-Liq

• Orthopyroxene-only and Liquid thermobarometry.
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • 1a - Equation 28a, fixed pressure
  • 1b - As above, but overwriting the input spreadsheet water content with an integer.
  • 1c - we can also specify eq_tests=True to get a full dataframe back with all the components, as well as a number of equilibrium test values
  • 2a - Pressure using equation 29a at 1300 K
  • 2b - Overwrite input water content with zero. Return equilibrium tests.
  • 2c - Can overwrite input Fe3Fet_Liq ratio (or 0 if didnt enter one) with an integer
  • 3a - Iterating equation 29b from Putirka (2008) for P, and Beattie (1993) for temperature
  • Step 1 - calculate Mg# for opx and liquid (can either treat FeT as Fe2, or partition into Fe2 and Fe3, only calculated Kd using Fe2)
  • Step 2 - calculate rhodes diagram lines between Mg#=0.4 and Mg#=0.7
  • Step 3 - Plot these lines, along with measured opxs. Here we draw symbols where we account for Fe3+ (diamond), and just using Fet in the glas (stars)
• Pyroxene Classification Diagrams
  • Load in some Opx compositions
  • Calculate Opx components
  • Example 1 (hold on, we’ll add data in a second)
  • Example 1d - Lets add a grid
  • Example 2 - Lets add your data (simple to start!)
  • Example 3 - Lets color by Px Cr content
• Opx-Liq Matching
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Plotting these results

2 Pyroxene

• Opx-Cpx Thermobarometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • 1a - Pressures using equation 38 of Putirka (2008)
  • To get equilibrium tests, specify eq_tests=True. This also returns input compositions.
  • You can then filter this to get only ones in high T equilibrium
  • 1b - Equation 39 (T-dependent)
  • 2b - Putirka (2008) eq 36 (P-dependent).
  • 3b - Here, use equation T of T_Put2008_Eq36, and equation P of P_Put2008_eq39
  • 3c - Here, use Temp from Bray 1990 and equation 38 from Putirka (2008)
• Opx-Cpx Matching
  • Setting pretty plot parameters
  • Load in Opx compositions
  • Load in Cpx compositions
  • Example 1 - Assesing all possible combinations
  • 1b- High T Kd filter
  • 1c - User-selected KdMatch and Kd_Err
  • 1d - Calculations at a constant temperature
  • Lets save the “all matches” dataframe to excel…
  • Similary, here’s how we save the high T matches to excel…

Amp & Amp-Liq

• Amphibole Thermobarometry and Chemometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Ridolfi 2021 - Minerals algorithm
  • Mutch et al. (2016)
  • Using T_Put2016_eq4a_amp_sat.
  • Assessing equilibrium
  • Overwriting H2O_Liq.
  • Both are actually pretty sensitive to water.
  • can also specify eq_tests=True, and it calculates Kd Fe-Mg, and then classifies within this is within the suggested range of Putirka (2008)
  • Or, we can use an amphibole only thermobarometers to get temperature, to then feed into the chemometry function
• Amp-Liq Melt mathcing
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • This returns the average PT for each amphibole
  • This returns all Amp-Liq matches
  • Or, if you want to filter yourself, say return all pairs
• Amphibole Classification Diagrams
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)

Fspar-Liq & 2 Fspar

• Feldspar-liquid thermobarometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Temperature using equation 23 at 5 kbar
  • Temperature using equation 24a at 5 kbar
  • Equilibrium tests
  • Here we filter based on whether any given pair passes the An-Ab test within the values recomended by Putirka (2008) (T>1050 is 0.28+-0.11, and T<1050 is 0.1+-0.05)
  • Can also add filters based on Delta An, Ab, Or values
• Plag - Liquid hygrometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • 1a - Using equation H of Putirka (2005)
  • 1b - using hygrometer of Waters 2015
  • 1c - Can also just enter XAn and XAb rather than full plag compositions
  • 2d - Manually iterating temperature and water content for plagioclase-liquid thermobarometry.
  • Example 2e - Using Thermobar’s built in functions for iterating T and H
• Two Feldspar thermometry
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Import python things and set plotting parameters
  • Import Kspars
  • Import plags
  • Calculate T for all matches using equation 27a at 5 kbar
  • Examine equilibrium tests
  • Filtering outputs
  • Apply filters
• Plag-Liq and Kspar-Liq Matching
  • Example 1 - Plag and Liquid.
  • Please check your feldspars are actually plagioclases! If you apply plag-liq thermometers to kspars, you get stupid results, that mess up the iterative calculations
  • Lets plot to inspect and check they are actually plag, else you will have convergence issues
  • Example 1a - All possible Liq-Plag matches, An-Ab equilibrium
  • Example 1b - All possible Liq-Plag matches, no filter
  • Example 1c - Iterating T and H2O for all possible Plag-Liq matches
  • Example 2 - Kspar-Liquid calculations
• Feldspar ternary classification diagram
  • Load in data, in this case, have paired Plag and Kspar data, but could have as seperate sheets
  • Calculate compostions for each in terms of co-ordinates for ternary axis
  • Example 1 - Just the classification diagram (be patient, we will add your data in example 2)!
  • Example 2 - plotting data on top of classification
  • Example 3 - Setting symbol size by FeOt content
• Plag Ternary Diagram Segmented by Sample
  • Import Python things
  • Set plotting parameters
  • Load in plagioclase compositions
  • Lets calculate the components we need to plot a ternary diagram.
  • First, we can plot all the samples as a single color
  • Or, we can try to segment for different samples, First, lets find how many unique samples we have
  • Now lets segment out for each sample ID
  • Plot 1
  • Plot 2

Garnet and geotherms

• Garnet functions
  • Load data from Ozaydin et al. (2021)
  • Calculating T from Ryan_1996
  • Calculating P from Ryan 1996
  • Sudholz et al. 2021
  • Canil et al. 1999
  • Example of plotting functions
• Garnet Geotherms

Error Propagation

• Error Propagation - Liq Only
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Step 1 - Use function add_noise_sample_1phase() to add sample noise and make lots of synthetic liquids
  • Step 2 - input this synthetic dataframe into the functions for calculating temperature
  • Step 3 - Plot the results
  • Step 4 - Use a function to get the mean, median and standard deviation for each liquid
  • Step 1 - add errors based on the dataframe Liquid2_Err which are percentage errors.
  • Step 2 - calculating temperatures for all these synthetic liquids using equation 16 of Putirka (2008)
  • Step 3 - Calculating standard deviations, means, and medians etc
  • plot a histogram of resulting H2O distribution
  • Now feed this into a thermometer
• Error propagation - Cpx-Liquid.
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • Lets first calculate Cpx-only pressures for these synthetic noisy Cpxs
  • Lets plot the distribution of pressures for each Cpx
  • We can also calculate statistics…
  • Lets do the same but for Cpx-Liq now. Remember, only Cpx has noise added
  • Each histogram shows the pressure distribution from a single Cpx-Liquid pair resulting from adding 5% error to just Na in Cpx.
  • Calculate Statistics
  • First, load in the published 1 sigma values
  • Recreate plot shown in manuscript for just 2 cpx-liq pairs from experiments
  • Plot for 6 separate cpx-liq pairs
  • Temperature distributions for first 6 pairs
• Error propagation - Cpx-only
  • You need to install Thermobar once on your machine, if you haven’t done this yet, uncomment the line below (remove the #)
  • You will also need to install pyrolite for this example, if you haven’t done so already, uncomment the line below
  • Lets calculate the statistics for various noise simulations

Melt Inclusions

• Multisample - Fe-Mg equilibrium in ol-hosted MIs
  • Loading a dataset
  • Load in the matrix glasses
  • Load in the melt inclusion data and the olivines
  • Find each sample for Glasses
  • Workflow 1: Assess if the olivines are in equilibrium with the co-erupted matrix glass
  • Workflow 2: Assess if the olivines and their melt inclusions are in equilibrium
  • 1. Calculate melt inclusion Mg
  • 2. Plot on a rhodes diagram
• 1 Sample - Fe-Mg equilibrium in ol-hosted MIs
  • Loading a dataset
  • Load in the matrix glasses
  • Load in the melt inclusion data and the olivines
  • Workflow 1: Assess if the olivines are in equilibrium with the co-erupted matrix glass
  • Workflow 2: Assess if the olivines and their melt inclusions are in equilibrium
  • 1. Calculate melt inclusion Mg
  • 2. Plot on a rhodes diagram
• Combining Thermobar with VESIcal for Sat P at known T
  • First, load the python things you might need
  • Now import both Thermobar and VESIcal
  • Example 1 - Simple integration of thermometry and saturation pressures
  • Example 2 - Using a P-sensitive thermometer
  • Example 4 - Lets generally compare thermometer models and how much difference they make

Other Functions

• Calculating equilibrium mineral contents from a liquid line of descent
  • First, pip install Thermobar if you haven’t already
  • Import your liquid compositions extracted from Petrolog into the thermobar format
  • Check they have read in correctly
  • We need a temperature for many models
  • First, we read in the mineral data, each mineral has a sulfide next to it
  • Then we calculate An contents, Mg#s, and Fo contents for these
  • First, calculate Glass temperature, as buffer pos is T sensitive
  • Calculate Glass Fe3FeT from redox (FMQ+0.2, Bali et al. 2018)
  • Then we calculate Eq contents of each mineral for the matrix glasses
• Assessing Calibration Ranges of models
  • Step 1: Load in data from your system
  • Step 2: The two ways to use these functions
  • Example 1 - Amphibole
  • Example 2 - Cpx
  • Example 3 - Assessing matched liquid - Cpx pairs
• Calculating Viscosity from liquid compositions
  • Lets load in some melt compositions from a MELTS model published in Wieser et al. (2022)
  • Inspect the liquid data you have loaded in to make sure it makes sense
  • Lets calculate viscosity at the temperature stored in the column “Temp HT1987_K”
  • Using a different thermometer for temperature
  • With different F2O contents
• This notebook shows how to convert from Oxide wt% to element wt% and back again
  • Load in oxide wt % values (in this case, from plag)
  • Convert to element wt%
  • Lets compare this to that calculated by EPMA software
• Converting back and forth from Fe3Fet to different redox buffer positions.
  • Load in data
  • Example 1: Calculating Fe3Fet for a series of liquid compositions
  • Converting from FeO and Fe2O3 proportions to fo2
• Converting from fo2 to buffer position
  • Converting fo2 values to buffer positions
• Calculating Viscosity from liquid compositions
  • Lets load in some melt compositions from a MELTS model published in Wieser et al. (2022)
  • Inspect the liquid data you have loaded in to make sure it makes sense
  • Lets calculate viscosity at the temperature stored in the column “Temp HT1987_K”
  • Using a different thermometer for temperature
  • With different F2O contents
• Converting pressures into depths
  • Now convert pressure to depth using a variety of crustal density models
  • Density models for given densities in kg/m3
  • Now lets choose one for our samples
  • Now we can draw a histogram of depths in km
  • Or we can use a constant density

Detailed Code Documentation:

• Functions for mineral-melt calculations
  • Cpx and Cpx-Liquid functions
  • Opx and Opx-Liquid functions
  • Two Pyroxene functions
  • Amp and Amp-Liquid functions Functions
  • Feldspar Functions
  • Liquid Functions
  • Ol-Liq, Ol-Sp Functions
• Other functions
  • Core functions (e.g., cation fractions)
  • Mineral Equilibrium Functions
  • Error Propagation Functions
  • Viscosity calculator

Indices and tables

• Index

• Module Index

• Search Page