Complete a spreadsheet for Equation of State¶

Overview¶

The Equation of State 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 - Details of the phases at the start of the experiment
• experimental_conditions - Details of the experimental setup
• <Phase> tabs - Details of the phases in the experiment results

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
• /eos/eos-template.xlsx: Equation of State 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 -eos; for example, Holdaway1971-eos.xlsx.
3. Set up the phase tabs: Using the placeholder <Phase> tab, create a tab for each phase that occurs in the experimental results. Change the header text (<Phase>) to the name of the phase. For example, if the results involve three phases—andalusite, kyanite, and sillimanite—add an And tab, a Ky tab, and a Sil tab. Make sure to use only names allowed by the Vocabulary spreadsheet.

Fill out the tabs¶

reference tab¶

The reference tab contains the basic reference information about the published paper.

✦ Fill out the columns. You can copy most of this information from the file you opened in JabRef.

• pub_id - The publication ID number for the paper
• authors - Names of author or authors
• date - Year of publication
• title - Title of paper
• journal - Journal where published
• volume - Volume number
• pages - Page numbers of published paper
• doi - Document Object Identifier for the paper
• notes - Enter any notes related to information you entered on this tab.

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¶

The starter_phases tab describes the phases at the start of the experiment. Each row represents an experiment.

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.)

<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>
<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 of each set. Refer to the Vocabulary spreadsheet for allowable entries.
2. Fill out the columns:

Sample information¶

• sample_id, sample_name - In these columns, provide a unique identifier and name for each sample. Use whatever convention you wish, but try for something meaningful. For example, you might use Sil (for sample_id) and Sillimanite (for sample_name) for a sillimanite sample. If the paper involves multiple sillimanite samples, you might use Sil1 and Sillimanite1, Sil2 and Sillimanite2, Sil3 and Sillimanite3, and so on.

Reference information¶

• source_pubid - The publication ID number for the paper in which the sample originated.
• notes - Enter any notes related to information you entered on that row.
• table_num - If the sample appears in a table, enter the table number. Otherwise, leave this field blank.
• figure_num - If the sample appears in a figure, enter the figure number. Otherwise, leave this field blank.
• page_num - Enter the page number on which the sample is described. Use <-> to indicate a range of pages. For example, for pages 6 to 7, enter 6 <-> 7.

Phase information¶

• phase - Make sure to enter the correct abbreviation listed in the Vocabulary spreadsheet (pure_phases_vocab tab). For example, enter And for Andalusite.
• synthetic - Enter Yes if the sample is synthetically created, or No if it is natural.
• grain_size
• contaminant_phases - If the sample is not pure but contains another phase, indicate what that other phase is. First, in Row 2, enter a unit of measurement. Then, in the working row, enter a value and the contaminant phase. For example, for a sillimanite sample that is 30% fibrous sillimanite, enter vol% (volume percent) in Row 2, and enter 30 fSil in the working row. Make sure to use only entries allowed by the Vocabulary spreadsheet.

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%.

experimental_conditions tab¶

The experimental_conditions tab contains the details of the experimental setup. If any of the columns do not apply, leave its fields blank. Except where noted, use only entries from the Vocabulary spreadsheet.

1. Enter a unit of measurement on Row 2 where appropriate.
2. Fill out the columns:

Reference information¶

• index - Enter numbers to identify all the experiments. If there are, for example, five experiments, fill out five rows. The first experiment is 1; the second is 2, and so on. (This column and all its entries must be identical to the corresponding index columns on the phase tabs.)
• run_id - Enter a meaningful name for each experimental run. For example, if there are two silliminate experiments, enter Sil1_0 and Sil2_0. (This column and all its entries must be identical to the corresponding run_id columns on the phase 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

• 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.

<Phase> tabs¶

The phase tabs describe the results of the experiments.

1. On each phase tab, enter the same information for the index and run_id columns as it appears on the experimental_conditions tab. Make sure that all these columns on all these tabs are identical.
2. On each phase tab, fill out the remaining columns. Fill out only those rows that involve this phase. Leave rows for other phases blank.

Sample information¶

• sample_id - Same sample_id as on the starter_phases tab.
• source_pubid - The publication ID number for the paper in which the sample originated.

Notes¶

• notes - Any notes related to information you entered on this row

Unit cell dimensions¶

• V - Volume measured
• V_err - Error of the volume measured
• a - Length of the a direction of the unit cell in the crystal
• a_err - Error in the measurement of a
• b - Length of the b direction of the unit cell in the crystal
• b_err - Error in the measurement of b
• c - Length of the c direction of the unit cell in the crystal
• c_err - Error in the measurement of c
• alpha
• alpha_err
• beta
• beta_err
• gamma
• gamma_err

• xrd_peak_num
• d(h,k,l)
• d(h,k,l)_err

Refraction data¶

• refract_idx_alpha - Measurement of the refractive index in alpha direction
• refract_idx_alpha_err - Error in the measurement of the refractive index in alpha direction
• refract_idx_beta - Measurement of the refractive index in beta direction
• refract_idx_beta_err - Error in the measurement of the refractive index in beta direction.
• refract_idx_gamma - Measurement of the refractive index in gamma direction
• refract_idx_gamma_err - Error in the measurement of the refractive index in gamma direction