ENKI

Complete a spreadsheet for Phase Reaction

Overview

The Phase Reaction spreadsheet contains the following tabs:

  • reference - Basic reference information about the published paper
  • notes - Notes regarding any special decisions you made in transcribing the data
  • starter_phases - Description of the samples available at the start of the experiments
  • experimental_conditions - Details of the experimental setup
  • sample_material - Description of the mixture of the various starter phases used in the experiment
  • rxn - Details about the results of the experiments
  • <Phase> tabs - (If needed) Additional details on the phases in the experimental results
  • melt(if needed)
  • fluid(if needed)

General setup

  1. In the data directory, open these files:
    • vocab_key.xlsx: Vocabulary spreadsheet, which contains allowable terminology for most entries in the spreadsheets
    • phase-rxn/phase-rxn-template.xlsx: Phase Reaction template file
  2. Make a copy of the template file, and change the copy's filename to the paper's publication ID number followed by -phase-rxn; for example, Holdaway1971-phase-rxn.xlsx.
  3. If needed, set up the phase tabs (using the <Phase> tab placeholder), the same as for the EOS spreadsheet.

Fill out the tabs

reference tab

✦ Fill out the reference tab the same as for the paper's EOS spreadsheet.

notes tab

✦ On the notes tab, enter any notes such as special choices you made in recording the data. These notes help to make your work reproducible. Use whatever format you wish. This tab is to be read by humans rather than computers.

starter_phases tab

✦ Fill out the starter_phases tab the same as for the paper's EOS spreadsheet. Typically, all rows in this tab will be identical to those in its EOS counterpart. Add additional rows for new phases if needed.

This tab describes all the samples available for use at the start of the experiments.

experimental_conditions tab

This tab describes the conditions of the experiments as well as the results. Each row in this tab represents an experiment. Except where noted, make sure to use only allowable entries from the Vocabulary spreadsheet.

  1. Wherever needed, enter a unit on Row 2.
  2. Fill out the columns:

Reference information

  • index - Enter numbers to identify all the experiments. If there are, for example, 60 experiments, fill out 60 rows. The first experiment is 1; the second is 2, and so on. (This column and all its entries must be identical to the index column on the sample_material and rxn tabs.)
  • run_id - Enter a meaningful name for each experimental run. For example, use the name that appears in the table in the paper. (This column and all its entries must be identical to the run_id column on the sample_material and rxn tabs.)
  • lab_id -
  • source_pubid - The publication ID number for the paper in which the sample originated.
  • table_num - If the experiment appears in a table, enter the table number.
  • figure_num - If the experiment appears in a figure, enter the figure number.
  • page_num - Enter the page number on which the experiment is described. Use <-> to indicate a range of pages. For example, for pages 6 to 7, enter 6 <-> 7.

Equipment used

  • device
  • container
  • capsule_width
  • capsule_length

Procedural details

  • annealed
  • aneal_time
  • equil_time - Equilibration time of the experiment
  • press_medium
  • peak_oil_press

Pressure and temperature conditions

  • P_meas_method
  • T_meas_method
  • T_meas_heat_loc
  • T_meas_samp_loc
  • P - Pressure
  • P_err
  • T - Temperature
  • T_err

Oxidation state conditions

  • fO2
  • fO2_err

Confidence

  • trust - Enter Yes, No, or Maybe to indicate whether you have confidence in this experiment.
  • notes - Important: If you entered No or Maybe for trust, enter an explanation here. Also, enter any other notes related to information you entered on this row.

sample_material tab

This tab details the mixture of the samples (which are defined on the starter_phases tab) used in the experiment. That is, it describes the starter phases mixed together and heated. Each row in this tab represents an experiment, the same experiment represented on the same row in the experimental_conditions and rxn tabs.

  1. Set up the chemistry columns.

    For each element or oxide in the experiment, you need four values: composition, error, method, and standard. Therefore, you need to set up four columns for each composition reported:

    • composition
    • composition_err
    • composition_method
    • composition_std

    Use the placeholder headers to set up the columns, adding additional sets as needed. (Delete any not needed.)

Placeholder headers Usage Example
<oxide>
<oxide>_err
<oxide>_method
<oxide>_std
Use these if the phase is an oxide. Replace <oxide> with the oxide name. Fe2O3
Fe2O3_err
Fe2O3_method
Fe2O3_std
<oxide>(tot)
<oxide>(tot)_err
<oxide>(tot)_method
<oxide>(tot)_std
Use these headers if the measurement used a method that reported an element as total oxide equivalent. Replace <oxide> with the oxide name. Fe2O3(tot)
Fe2O3(tot)_err
Fe2O3(tot)_method
Fe2O3(tot)_std
* This experiment measured iron atoms, and the authors reported the results as total feric iron.
<element>/strong>
<element>_err
<element>_method
<element>_std
Use these if the phase is an element. Replace <element> with the element name. SIO2
SiO2_err
SiO2_method
SiO2_std
  1. On Row 2, add subheads for unit (usually wt%) to the first two columns (composition and composition_err columns) of each set. Refer to the Vocabulary spreadsheet for allowable entries.
  2. Fill out the columns:

Reference information

  • index, run_id - Fill out these columns the same as for the experimental_conditions tab. Each row represents an experiment, and the rows must agree across these tabs.
  • source_pubid - The publication ID number for the paper in which the sample originated.
  • sample_mix - A mixture of the sample; for example, And0 + Ky0 or And0 + Sil3 + Crn0. If the amount (in wt %) is important, include that as well.
  • contact_geom
  • contaminant phases
  • notes - Enter any notes related to information you entered on that row.

Chemistry columns

Note: You set up these columns in a previous step.

  • composition - Enter the compositional measurement.
  • composition_err - Enter the error in the amount of the composition. You can use decimal places as well as scientific notations.
  • composition_method - Enter the method used to measure the composition (for example, AAS, which indicates Atomic Absorption Spectroscopy).
  • composition_std - Enter the standard used in the method.
  • Total - Enter the total sum of the compositional values, for a sum close to 100%.

rxn tab

The rxn tab details the results of the experiments.

✦ Fill out the columns:

Reference information

  • index, run_id - Fill out these columns the same as the experimental_conditions and sample_material tabs. Each row represents an experiment, and the rows must agree across these tabs.

Notes

  • Enter any notes related to information you entered on that row.

Flux information

  • flux_type - The type of flux used, if any.
  • flux_amt - The amount of flux used, if any.

Reaction information

  • rxn_studied - The reaction that is studied. Make sure to use only valid phase names from the Vocabulary spreadsheet (pure_phases_vocab tab and solution_phases_vocab tab). No nicknames! Also, the entry must be a balanced stoichiometric equation.
  • method - The method used to determine the results. For example, weightdiff (from the Vocabulary spreadsheet) indicates that the authors measured the difference in crystal weights. If the method produces results that are quantitative (such as the weightdiff method), make sure to enter the specifics in the reaction metrics columns.

Reaction metrics

Use these columns to record metrics for results that involve quantitative data (as opposed to qualitative, observational data). These metrics help to determine in which direction the reaction moves. They also help to remove our uncertainty and to make interpretation of the data reproducible.

Column Usage Example 1

Method used: weightdiff (Change in crystal weight)
Example 2

Method used: xrd-peak-ratio (Ratio of x-ray diffraction peaks)
rxn_metric_unit Unit used to measure the phase reaction micrograms %
rxn_metric_zero Zero point of whatever the experiment uses to determine the direction of the phase reaction. 0 0.465
rxn_metric_err Error needed to identify the direction of the phase reaction. 5.8 
* Indicates an allowable error of 5.8 micrograms
20
* Indicates an allowable error of 20%
rxn_metric Reaction metric value. How much change there is. -6.3
* Indicates a change of -6.3 micrograms
3.13
* Indicates a change of 3.13%
rxn_metric_resid

Reaction metric residual. Compares the reaction metric value to the zero value and determines, within the error, if a direction is apparent. This value is expressed in sigma (the number of error bars away from zero).
Use this equation to calculate the residual:

  • In a simple linear metric (such as weight difference):
    m-(z/e)
    where m is measurement, z is the zero value, and e is the error.
  • In a non-linear metric (such as ratio of x-ray diffraction peaks): \(\log(m/z)/(0.01\cdot\epsilon)\)
    where m is measurement, z is the zero value, and \(\epsilon\) is the error in terms of percent.
-1.086206897 9.53375439

Results

  • results - Based on the reaction metrics you entered, describes the experiment's effect on each phase: no change, questionable, increase, or decrease. The results are measured in sigma. (Make sure to use only phase names from the Vocabulary spreadsheet.)
    • No Change (NC) - If the change is less than 1 sigma in either direction, there is no change. Enter NC.
    • Questionable (-? or +?) - A result between 1 and 2 sigma (more than one error bar width but less than two) is considered suggestive but inconclusive. Enter the phase name, a space, and -? or +?. For example, if Andalusite descreased 1.6 according to the metrics, enter And -?. If it increased 1.6, enter And +?.
    • Increase (+) - If a phase change is greater than 2 sigma, enter the phase name, a space, and a plus sign. For example, if Andalusite increased more than 2, enter And +.
    • Decrease (-) - If a phase change is less than 2 sigma, enter the phase name, a space, and a minus sign. For example, if Andalusite decreased more than 2, enter And -.

Multiple phasesIf more than one phase is involved, list them all. For example, Ky + And - indicates that Kyalite increased and Andalusite decreased.

  • metastable -
  • completion - (optional) How complete the reaction is, expressed as a percentage. For example, 20 indicates 20% complete.

<Phase>, melt(if needed), and fluid(if needed) tabs

Use these compositional tabs if you need to describe the bulk composition; for example, if the experiment uses solution phases and involves an unusual mixture.

If the experiments simply mix pure phases, you can leave these tabs blank.