This GlassyCriticalityreadme.txt file was generated on 2020-11-30 by Thomas E. Gartner III


GENERAL INFORMATION

1. Title of Dataset: Data from "Manifestations of metastable criticality in glassy water-like models detected by large-scale structural properties"

2. Author Information
	A. Principal Investigator Contact Information
		Name: Thomas E. Gartner III 
		Institution: Princeton University Department of Chemistry
		Address: Frick Chemistry Laboratory, Princeton, NJ 08540, USA
		Email: tgartner@princeton.edu

	B. Associate or Co-investigator Contact Information
		Names: Salvatore Torquato, Roberto Car, and Pablo G. Debenedetti 
		Institution: Princeton University
		Address: Princeton, NJ 08540, USA
		Emails: torquato@princeton.edu, rcar@princeton.edu, pdebene@princeton.edu

3. Date of data collection: 2019-10-01 to 2020-11-01 

4. Geographic location of data collection: Princeton, NJ, USA 

5. Information about funding sources that supported the collection of the data: The work of T.E.G., S.T., and R.C. was supported by the “Chemistry in Solution and at Interfaces” (CSI) Center funded by the U.S. Department of Energy Award DE-SC001934. Computational resources were provided by Terascale Infrastructure for Groundbreaking Research in Engineering and Science (TIGRESS) at Princeton University and the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231.

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: N/A

2. Links to publications that cite or use the data: Gartner et al. Manifestations of metastable criticality in glassy water-like models detected by large-scale structural properties (in preparation 2020). Link to the article will be added upon publication.

3. Links to other publicly accessible locations of the data: https://app.globus.org/file-manager?origin_id=dc43f461-0ca7-4203-848c-33a9fc00a464&origin_path=%2F8v5g-b259%2F

4. Links/relationships to ancillary data sets: N/A

5. Was data derived from another source? No

6. Recommended citation for this dataset: Thomas E. Gartner III, Salvatore Torquato, Roberto Car, and Pablo G. Debenedetti, Data from "Manifestations of metastable criticality in glassy water-like models detected by large-scale structural properties". Princeton DataSpace. Available at https://doi.org/10.34770/8v5g-b259. Deposited December 2020.


DATA & FILE OVERVIEW

1. File List: 
TIP4P2005 -- All simulation data and analysis scripts related to the TIP4P/2005 water model results in the manuscript
mW -- All simulation data and analysis scripts related to the mW water model results in the manuscript
Kob-Andersen -- All simulation data and analysis scripts related to the Kob-Andersen system results in the manuscript

2. Relationship between files, if important: N/A 

3. Additional related data collected that was not included in the current data package: N/A

4. Are there multiple versions of the dataset? No


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
Molecular simulations were performed using the LAMMPS molecular simulation software v7Aug19 (https://lammps.sandia.gov/) or the GROMACS molecular simulations software v2018.4 (http://www.gromacs.org/). Detailed methods are as described in Gartner et al, (in preparation 2020). Detailed installation instructions for all software are available at the above linked webpages.

2. Methods for processing the data: 
All data was analyzed with Python scripts (which are included in this dataset)

3. Instrument- or software-specific information needed to interpret the data: 
Python v2.7.17
Numpy v1.16.5
Scipy v1.2.1
Matplotlib v2.2.3
MDAnalysis v0.20.1
ipdb v0.13.1

4. Standards and calibration information, if appropriate: N/A 

5. Environmental/experimental conditions: N/A

6. Describe any quality-assurance procedures performed on the data: N/A

7. People involved with sample collection, processing, analysis and/or submission: N/A 


DATA-SPECIFIC INFORMATION FOR EACH DIRECTORY:
** OVERVIEW **
Each directory contains processed data files, python scripts, and .png files for creating the figures in the manuscript in their top-level directory. Raw simulation trajectory files and old (unused) analysis scripts are stored in sub-directories (filenames summarized below).
****

** REPRODUCING DATA FROM MANUSCRIPT **
S(k) and chi(k) are calculated via SkCalcDirect.py and ChiCalc.py codes (stored in each directory).
S(0) and chi(0) values are calculated for all simulations using TIP4P2005/SkCoolingQuadFit.py, mW/SkCoolingQuadFit.py, and Kob-Andersen/ChiCooling4ordFit.py.
Enthalpy, Volume, and Compressibility for TIP4P2005 are calculated via the gromacs energy feature using the EnthalpyAnaly.sh and KappaAnaly.sh bash scripts. For mW and Kob-Andersen, relevant thermodynamic quantities are calculated directly in the analysis python scripts by accessing the thermo.sample.out simulation output files.
Glass transition temperatures are calculated with the TgfitH.py codes contained in each directory.
The nonequilibrium index are calculated via the TIP4P2005/NonEquilPressureComp.1Kns.py, mW/NonEquil.mW.calc.py, and Kob-Andersen/NonEquil.KA.calc.py codes.

To create Figure 1 from the manuscript, run TIP4P2005/S0PressurePlot.1Kns.shade.py, mW/S0PressurePlot.py, and Kob-Andersen/ChiPressurePlot.py
To create Figure 2 from the manuscript, run TIP4P2005/S080KPlot.py
To create Figure 3 from the manuscript, run TIP4P2005/TgvsPPlot.py, mW/TgvsPPlot.py, and Kob-Andersen/TgvsPPlot.py
To create Figure 5 from the manuscript, run TIP4P2005/NonEquilPressureComp.1Kns.py, mW/NonEquil.mW.calc.py, and Kob-Andersen/NonEquil.KA.calc.py
****

** TABLE OF CONTENTS **

** TIP4P2005 **
The simulation trajectories for the isobaric glass formation simulations are contained in sub-directories named like N_molecules-start_temp-end_temp-pressure.replicate
    In all cases, N_molecules = 8192
    start_temp is either 300 or 240 K
    end_temp is always 80 K
    pressure ranges from -2000 to 10000 bar
    there are 10 replicates for each condition
For cooling rates other than -1 K/ns, the naming convention is N_molecules-start_temp-end_temp-pressure.cooling_rate.replicate
    The cooling rates are -10^4 K/ns, -100 K/ns, -10 K/ns, -1 K/ns, or -0.1 K/ns
The simulation trajectories for the isothermal pressurization simulations at T = 80 K are contained in sub-directories named N_molecules-temp-start_pressure-end_pressure-press_rate.replicate
    N_molecules = 8192
    temp = 80
    start_pressure = 1 bar
    end_pressure = 20000 bar
    press_rate = 0.01 MPa/ns
All simulations for TIP4P2005 were performed with gromacs, the above-summarized simulation directories contain gromacs input files (*.mdp) and the standard set of gromacs output files, named prd-temp.*, where temp is the temperature in K.
The simulation sub-directories also contain Skfiles and Chifiles directories, which contain the calculated S(k) and Chi(k) at each temperature for that simulation. 
Directories starting with DEV or base were used to devlop the simulation scripts used to produce the data. Analysis scripts not directly used in producing the data reported in the paper (e.g. other versions of calculations, validation tests, etc) but that might still be useful to other researchers are stored in an OldAnalysisScripts directory.
The top-level directory contains processed data files, python scripts to analyze the simulation data, and .png files that were used to create the figures in the manuscript. The most important scripts are summarized above in the "REPRODUCING DATA FROM MANUSCRIPT" section. 
    The files Sk0.direct.cooling.pressure.cooling_rate.0.2-1.0.QuadFit.txt contain the low-k limit of the total S(k) for the pressure and cooling rate defined in the filename. The files are matrices, where the rows are different temperatures (starting at the highest temperature) and the columns are different replicates.
    The files Sk0.O.direct.cooling.pressure.cooling_rate.0.2-1.0.QuadFit.txt contain the low-k limit of the oxygen-oxygen partial structure factor
    The files Sk0.H.direct.cooling.pressure.cooling_rate.0.2-1.0.QuadFit.txt contain the low-k limit of the hydrogen-hydrogen partial structure factor
    The files Tg.fitH.pressure.cooling_rate.txt contain the glass transition temperature for each replicate at the pressure and cooling rate defined in the filename 
****

** mW **
The simulation trajectories for the isobaric glass formation simulations are contained in sub-directories named like N_molecules-start_temp-end_temp-pressure.replicate
    N_molecules = 8192 or 66636
    start_temp is always 300 K
    end_temp is always 80 K
    pressure ranges from -1500 to 15000 bar
    there are 10 replicates for each condition
The simulation trajectories for the isothermal pressurization simulations at T = 80 K are contained in sub-directories named N_molecules-temp-start_pressure-end_pressure-press_rate.replicate
    N_molecules = 8192
    temp = 80
    start_pressure = 1 bar
    end_pressure = 20000 bar
    press_rate = 0.01 MPa/ns or 1 MPa/ns
All simulations for mW were performed with LAMMPS, the above-summarized simulation directories contain LAMMPS input files (lammps.*), lammps trajectory ouput files named mW.temp.lammpstrj, where temp is the temperature in K, and the thermodynamic output file thermo.sample.out
The simulation sub-directories also contain an Skfiles directory, which contains the calculated S(k) at each temperature for that simulation. 
Directories starting with DEV or base were used to devlop the simulation scripts used to produce the data. Analysis scripts not directly used in producing the data reported in the paper (e.g. other versions of calculations, validation tests, etc) but that might still be useful to other researchers are stored in an OldAnalysisScripts directory.
The top-level directory contains processed data files, python scripts to analyze the simulation data, and .png files that were used to create the figures in the manuscript. The most important scripts are summarized above in the "REPRODUCING DATA FROM MANUSCRIPT" section. 
    The files Sk0.direct.cooling.pressure.0.2-1.0.QuadFit.txt contain the low-k limit of the total S(k) for the pressure defined in the filename. The files are matrices, where the rows are different temperatures (starting at the highest temperature) and the columns are different replicates.
    The files Tg.fitH.pressure.txt contain the glass transition temperature for each replicate at the pressure defined in the filename 
****

** Kob-Andersen **
The simulation trajectories for the isobaric glass formation simulations are contained in sub-directories named like N_A-start_temp-end_temp-pressure.replicate
    N_A = 8192 A-type beads
    start_temp is either 0.65 or 0.85 in LJ reduced units
    end_temp is always 0.1 in reduced units
    pressure ranges from -0.5 to 10 in reduced units
    there are 10 replicates for each condition
All simulations for Kob-Andersen were performed with LAMMPS, the above-summarized simulation directories contain LAMMPS input files (lammps.*), lammps trajectory ouput files named ka.temp.lammpstrj, where temp is the temperature in reduced units, and the thermodynamic output file thermo.sample.out
The simulation sub-directories also contain Skfiles and Chifiles directories, which contain the calculated S(k) and chi(k) at each temperature for that simulation. 
Directories starting with DEV or base were used to devlop the simulation scripts used to produce the data. Analysis scripts not directly used in producing the data reported in the paper (e.g. other versions of calculations, validation tests, etc) but that might still be useful to other researchers are stored in an OldAnalysisScripts directory. 
The top-level directory contains processed data files, python scripts to analyze the simulation data, and .png files that were used to create the figures in the manuscript. The most important scripts are summarized above in the "REPRODUCING DATA FROM MANUSCRIPT" section. 
    The files Sk0.direct.cooling.pressure.0.6-3.0.QuadFit.txt contain the low-k limit of the total S(k) for the pressure defined in the filename. The files are matrices, where the rows are different temperatures (starting at the highest temperature) and the columns are different replicates.
    The files Sk0.A.direct.cooling.pressure.0.6-3.0.QuadFit.txt contain the low-k limit of the A-A partial S(k) for the pressure defined in the filename. The files are matrices, where the rows are different temperatures (starting at the highest temperature) and the columns are different replicates.
    The files Sk0.B.direct.cooling.pressure.0.6-3.0.QuadFit.txt contain the low-k limit of the B-B partial S(k) for the pressure defined in the filename. The files are matrices, where the rows are different temperatures (starting at the highest temperature) and the columns are different replicates.
    The files Sk0.AB.direct.cooling.pressure.0.6-3.0.QuadFit.txt contain the low-k limit of the A-B partial S(k) for the pressure defined in the filename. The files are matrices, where the rows are different temperatures (starting at the highest temperature) and the columns are different replicates.
    The files Chi0.direct.cooling.pressure.0.6-3.0.QuadFit.txt contain the low-k limit of the chi(k) for the pressure defined in the filename. The files are matrices, where the rows are different temperatures (starting at the highest temperature) and the columns are different replicates.
    The files Tg.fitH.pressure.txt contain the glass transition temperature for each replicate at the pressure defined in the filename 
****