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Molecular dynamics trajectories and portable binary run files for the self-assembly of heparin and amyloid-β(16-22) with the ProMPT forcefield
<h1>About this repository</h1> <p>Self-assembly simulations of heparin and amyloid-β(16-22) were performed at various numbers of peptides (<em>N_pep</em>), number of heparin molecules (<em>N_hep</em>), degrees of polymerization of heparin (<em>hep_dp</em>) and rigidity factors (<em>rig_f</em>) for heparin. This repository contains one folder per system, characterized by a combination of four system variables: <em>N_pep</em>, <em>N_hep</em>, <em>hep_dp</em> and <em>rig_f. </em></p> <p>The simulations were performed on the GROMACS 2019.4 molecular dynamics engine, with the ProMPT forcefield for coarse-grained molecular dynamics. Four independent trials: <em>trial_A</em>, <em>trial_B</em>, <em>trial_C</em> and <em>trial_D</em> were performed per system, each with different starting velocities. Each trial was run for 3000 ns.</p> <h1>Contents</h1> <h2><code>> heparin_abeta_trajectories.zip</code></h2> <p>The repository contains the zip file <code>heparin_abeta_trajectories.zip</code> with 13 folders named according to the convention,<code> "{<em>N_pep</em>}pep_{<em>N_hep</em>}hep_dp{<em>hep_dp</em>}_{<em>rig_f</em>}xRigid"</code>. For example, data for the system consisting of 16 peptides (<em>N_pep</em>), 1 heparin (<em>N_hep</em>), 18 monosaccharides in length (<em>hep_dp</em>) with a rigidity factor of 100 (<em>rig_f</em>) would be stored in the directory <code>16pep_1hep_dp18_100xRigid/</code>.</p> <p>If the system did not contain heparin, <em>N_hep, hep_dp</em> and <em>rig_f</em> were set to 0 by default. For example, data for the system consisting of 16 peptides (<em>N_pep</em>) and no heparin would be stored in the directory <code>16pep_0hep_dp0_0xRigid/</code>.</p> <p>A directory such as <code>16pep_1hep_dp18_100xRigid/</code> will have the following contents:</p> <ul> <li><code><strong>solute_only.ndx</strong></code><br>Contains an index group for solute molecules (peptides and/or heparin) only.</li> <li><code><strong>trial_A/</strong></code> <ul> <li><code><strong>md.tpr</strong></code> <br>Portable run file with which the current trajectory was generated. This file may be used to reproduce the trajectory as well.</li> <li><code><strong>solute_only.cluster_center.xtc </strong></code><br>A gromacs trajectory containing only the solute molecules (peptides and/or heparin), centered with the gromacs tool <em>gmx trjconv</em></li> <li><code><strong>solute_only.tpr </strong></code><br>A gromacs portable binary input file containing data for the solute molecules (peptides and/or heparin) only, generated with the <em>gmx convert-tpr</em> tool.<br>This file may be used during analysis of the solute_only.cluster_center.xtc trajectory.</li> </ul> </li> <li><code><strong>trial_B/</strong></code><br>contents same as <code><strong>trial_A/</strong></code></li> <li><strong><code>trial_C/</code><br></strong>contents same as <code><strong>trial_A/</strong></code></li> <li><strong><code>trial_D/</code><br></strong>contents same as <code><strong>trial_A/</strong></code></li> </ul> <h2><code>> psf_files_for_VMD_visualization.zip</code></h2> <p>This zip file contains thirteen .psf files, one per system, that can be used in accord with <code>solute_only.cluster_center.xtc </code>files to visualize trajectories on the Visual Molecular Dynamics (VMD) software.</p> <p><strong>Please seek out the associated publication for essential context on these trajectories. </strong></p> <p><strong>To access the source files with which these simulations were set-up, and a brief tutorial, see: </strong><a href="https://github.com/suhasgotla/heparin_amyloid_self-assembly">https://github.com/suhasgotla/heparin_amyloid_self-assembly</a></p>
Yellowstone Upper Basin Geyser binary eruption data (April 2007- October 2008; revised)
<p>Binary eruption data for 10 Geysers (Beehive, Castle, Depression, Dome, Grand, Lion, Little Squirt, Old Faithful, Plate, and Plume) over 19 consecutive months (April 2007- October 2008) at a sampling interval of 6 minutes.</p>
Data from "Crossed-state bowing and the strength of binary dislocation junctions"
<p>Contains data and analysis files used in the journal publication:</p> <p>Duan I. and Sills R. B., Crossed-state bowing and the strength of binary dislocation junctions, J. Mech. Phys. Sol., Vol. 190, 105696, 2024.</p> <p><a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jmps.2024.105696" target="_blank" rel="noreferrer noopener"><span>https://doi.org/10.1016/j.jmps.2024.105696</span></a></p>
The Symbiotic X-ray Binary IGR J16194-2810: Magellan Inamori Kyocera Echelle (MIKE) Spectra
<p>Optical high-resolution spectra taken with the Magellan Inamori Kyocera Echelle (MIKE) spectrograph for the symbiotic X-ray binary IGR J16194-2810.</p>
White-Dwarf Wide Binaries from Gaia EDR3
<p>This dataset contain the catalogs accompanying the paper "Hydrogen-Atmosphere White Dwarfs Are Less Likely To Be Found with Wide-Binary Companions" by Jeremy Heyl, submitted to Open Journal of Astrophysics in July 2024. </p> <p>There are five data files:</p> <p><strong>HAtmo.fits.gz</strong>: fits table with 53,364 rows and 160 columns</p> <p> objects in the Gentile-Fusillo catalogue best fit by hydrogen atmospheres</p> <p><strong>HAtmoBinary.fits.gz: </strong>fits table with 3,219 rows and 408 columns</p> <p> objects in HAtmo.fits.gz that match to objects in the El Badry binary catalogue (<a href="../records/4435257">https://zenodo.org/records/4435257</a>)</p> <p><strong>HeAtmo.fits.gz</strong>: fits table with 7,662 rows and 160 columns</p> <p> objects in the Gentile-Fusillo catalogue best fit by helium atmospheres</p> <p><strong>HeAtmoBinary.fits.gz: </strong>fits table with 975 rows and 408 columns</p> <p> objects in HeAtmo.fits.gz that match to objects in the El Badry binary catalogue (<a href="../records/4435257">https://zenodo.org/records/4435257</a>)</p> <p><strong>MWDDB-binary.fits.gz:</strong> fits table with 3,784 rows and 228 columns,</p> <p> contains all matches between the MWDDB and the El Badry catalogue (<a href="../records/4435257">https://zenodo.org/records/4435257</a>), not only the spectral types discussed in the paper</p>
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": IIC - simulation outcomes, fiducial 1E8
<p>This repository contains (a part) of the population synthesis outputs analysed in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. In particular, it contains the results of the subsets that compose the model fiducial2E8 (see <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>). The complete model includes also the results from the fiducial model stored in the repository <a href="https://doi.org/10.5281/zenodo.11992265" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.11992265</a></p> <h2>Content</h2> <p>Each tar file contains the outputs of a given simulation set from <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The name of the files corresponds to the name of the set as reported in Table 1 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The details of the sets can be found in Section 2.2 and Section 2.3 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The outputs stored in this repository contain only the systems that satisfy the following conditions:</p> <ul> <li>The two objects are in a binary system</li> <li>An object is a black hole and the other one is a star in any evolutionary phase prior to the ignition of the helium burning in the core</li> <li>The two objects are not currently interacting except for wind mass transfer (no ongoing Roche-Lobe overflow, common envelope or merger).</li> </ul> <p>The tar files contain three different files in gunzipped parquet format (<a href="https://parquet.apache.org">https://parquet.apache.org</a>):</p> <h3><strong>Python scripts</strong></h3> <ul> <li><em>analyse_sample.py</em>: python script we used to produce the file BHMS.pq.gz and BHMS_ic.pq.gz analysing the SEVN outputs</li> <li><em>create_aux.py</em>: python script we used to produce the file BHMS_VSNCE.pq.gz by combining the SEVN log outputs with the BHMS_ic.pq.gz file</li> </ul> <h3> </h3> <h3>BHMS.pq.gz</h3> <p><strong> </strong>File containing all the systems satisfying the above condition.</p> <p><strong>Columns:</strong></p> <ul> <li>ID: unique id of the binary (Long integer)</li> <li>name: unique name of the binary (Long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminosity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Euclidean distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p> <strong>Notice-1: </strong>in this file each system (identified by ID and name) can appear more than once. Indeed this file contains all the outputs in which a system satisfy the condition BH-star condition discussed above.</p> <p> <strong>Notice-2: </strong><em>the dataframe is sorted based on the bh3dist column,</em> so the first rows contains the objects that are closer to the properties of Gaia BH3 based on the bh3dist statistic.</p> <p> <strong>Notice-3: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_ic.pq.gz</h3> <p>File containing the initial conditions of all the systems included in the file BHMS.pq.gz</p> <p><strong>Columns:</strong></p> <p><em>Info from BHMS.pq.gz</em>:</p> <p>these columns report the same information as in the BHMS.pq.gz file, but each system (identified by ID and name) appears just once (the occurrence from the BHMS.pq.gz with the minimum bh3dist)</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminoisity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Eucledian distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p><em>Initial properties</em>:</p> <ul> <li>mzams_0: Initial (ZAMS) mass of the black hole in Msun</li> <li>mzams_1: Initial (ZAMS) mass of the star in Msun</li> <li>Semimajor_ini: Initial semimajor axis of the binary in Rsun </li> <li>Eccentricity_ini: Initial eccentricity axis of the binary </li> <li>seed: Random seed used in the SEVN simulation</li> <li>P_ini: Intial period of the binary in days </li> </ul> <p><strong> Notice: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_VSNCE.pq.gz</h3> <p>A file containing additional information about the evolutionary events of the systems stored in BHMS.pq.gz</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>time_SN: formation time of the black hole (BH) in Myr (all the simulations start from time=0)</li> <li>Vcom: Velocity magnitude of the center of mass after the formation of the BH (before the formation Vcom=0 is assumed)</li> <li>time_CE_preSN: time of the last CE before the BH formation (if empty no CE before BH formation)</li> <li>time_CE_postSN: time of the first CE after the BH formation (if empty no CE after BH formation)</li> <li>time_RL_preSN: time of the last Roche-Lobe overflow before the BH formation (if empty no RLO before BH formation)</li> <li>time_RL_postSN: time of the first Roche-Lobe overflow after the BH formation (if empty no RLO before BH formation)</li> </ul> <p><strong>Note: </strong>The file has been created by combining the file BHMS_ic.pq.gz with the main SEVN outputs using the script <em>create_aux.py </em>included in this repository</p> <h3>How to read the files</h3> <p>The parquet files can be easily read in Python by using the <a href="https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html">Pandas module</a>:</p> <pre><code>import pandas as pd df_bhms=pd.read_parquet("BHMS.pq.gz") df_bhms_ic=pd.read_parquet("BHMS_ic.pq.gz") df_bhms_vsnce=pd.read_parquet("BHMS_VSNCE.pq.gz")</code></pre> <p> </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": I - initial conditions & run scripts
<p>This repository contains the initial condition files and the run scripts to reproduce the results in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>.</p> <h2>Content</h2> <h3>Files XXX.ic</h3> <p>Ascii files containing the initial conditions of 2e7 binary systems. The files do not contain a header, and the columns report (from left to right):</p> <ol> <li>Mass of the primary [Msun]</li> <li>Absolute metallicity of the primary </li> <li>Initial spin (angular velocity over critical angular velocity)</li> <li>Supernova model for the primary</li> <li>Initial age of the star (Myr or special keywords)</li> <li>Mass of the secondary [Msun]</li> <li>Absolute metallicity of the secondary</li> <li>Initial spin (angular velocity over critical angular velocity)</li> <li>Supernova model for the secondary</li> <li>Initial age of the star (Myr or special keywords)</li> <li>Initial semimajor axis [Rsun]</li> <li>Initial Eccentricity </li> <li>Ending time or condition of the simulation [Myr or special keyword]</li> <li>Output frequency [Myr or special]</li> <li>Random seed</li> </ol> <p>Some columns contains the special placeorder keyword XXX. In this case, the values are undefined and they are set at runtime using the value on the runscripts. For additional information see the SEVN <a href="https://gitlab.com/sevncodes/sevn/-/blob/a4753f1177aab076da2641afc497a06006b30267/resources/SEVN_userguide.pdf">Userguide</a>.</p> <p>The initial conditions are:</p> <ul> <li><a href="../api/records/11617742/draft/files/SEVNIC20M_qmin0005.in/content" target="_blank" rel="noopener noreferrer">SEVNIC20M_qmin0005.in,</a> initial conditions used in all the simuations of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> except for the model fiducial_ICthermal (see Table 1) e partially for the model fiducial2E8 (see below).</li> <li><a href="../api/records/11617742/draft/files/SEVNIC20M_qmin0005_ethermal.in/content" target="_blank" rel="noopener noreferrer">SEVNIC20M_qmin0005_ethermal.in</a>, initial conditions for the simulation set fiducial_ICthermal</li> <li>SEVNIC20M_X.in (where X ranges from 1 to 9), initial conditions (split in different chuncks) used for the simulation set fiducial2e8. This set is also complemetned by the <a href="../api/records/11617742/draft/files/SEVNIC20M_qmin0005.in/content" target="_blank" rel="noopener noreferrer">SEVNIC20M_qmin0005.in</a> initial conditions. </li> </ul> <h3>Runscripts</h3> <p>The runscripts are contained in the archive runscripts.zip. See the README in the archive for additional information. </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": IIA - simulation outcomes
<p>This repository contains (a part) of the population synthesis outputs analysed in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. In particular, it contains the results of our fiducial model and of the models in which we change stellar (e.g. kicks) and binary evolutions parameters (e.g. common envelope parameters).</p> <h2>Content</h2> <p>Each tar file contains the outputs of a given simulation set from <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The name of the files corresponds to the name of the set as reported in Table 1 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The details of the sets can be found in Section 2.2 and Section 2.3 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The outputs stored in this repository contain only the systems that satisfy the following conditions:</p> <ul> <li>The two objects are in a binary system</li> <li>An object is a black hole and the other one is a star in any evolutionary phase prior to the ignition of the helium burning in the core</li> <li>The two objects are not currently interacting except for wind mass transfer (no ongoing Roche-Lobe overflow, common envelope or merger).</li> </ul> <p>The tar files contain three different files in gunzipped parquet format (<a href="https://parquet.apache.org">https://parquet.apache.org</a>):</p> <h3><strong>Python scripts</strong></h3> <ul> <li><em>analyse_sample.py</em>: python script we used to produce the file BHMS.pq.gz and BHMS_ic.pq.gz analysing the SEVN outputs</li> <li><em>create_aux.py</em>: python script we used to produce the file BHMS_VSNCE.pq.gz by combining the SEVN log outputs with the BHMS_ic.pq.gz file</li> </ul> <h3> </h3> <h3>BHMS.pq.gz</h3> <p><strong> </strong>File containing all the systems satisfying the above condition.</p> <p><strong>Columns:</strong></p> <ul> <li>ID: unique id of the binary (Long integer)</li> <li>name: unique name of the binary (Long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminosity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Euclidean distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p> <strong>Notice-1: </strong>in this file each system (identified by ID and name) can appear more than once. Indeed this file contains all the outputs in which a system satisfy the condition BH-star condition discussed above.</p> <p> <strong>Notice-2: </strong><em>the dataframe is sorted based on the bh3dist column,</em> so the first rows contains the objects that are closer to the properties of Gaia BH3 based on the bh3dist statistic.</p> <p> <strong>Notice-3: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_ic.pq.gz</h3> <p>File containing the initial conditions of all the systems included in the file BHMS.pq.gz</p> <p><strong>Columns:</strong></p> <p><em>Info from BHMS.pq.gz</em>:</p> <p>these columns report the same information as in the BHMS.pq.gz file, but each system (identified by ID and name) appears just once (the occurrence from the BHMS.pq.gz with the minimum bh3dist)</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminoisity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Eucledian distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p><em>Initial properties</em>:</p> <ul> <li>mzams_0: Initial (ZAMS) mass of the black hole in Msun</li> <li>mzams_1: Initial (ZAMS) mass of the star in Msun</li> <li>Semimajor_ini: Initial semimajor axis of the binary in Rsun </li> <li>Eccentricity_ini: Initial eccentricity axis of the binary </li> <li>seed: Random seed used in the SEVN simulation</li> <li>P_ini: Intial period of the binary in days </li> </ul> <p><strong> Notice: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_VSNCE.pq.gz</h3> <p>A file containing additional information about the evolutionary events of the systems stored in BHMS.pq.gz</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>time_SN: formation time of the black hole (BH) in Myr (all the simulations start from time=0)</li> <li>Vcom: Velocity magnitude of the center of mass after the formation of the BH (before the formation Vcom=0 is assumed)</li> <li>time_CE_preSN: time of the last CE before the BH formation (if empty no CE before BH formation)</li> <li>time_CE_postSN: time of the first CE after the BH formation (if empty no CE after BH formation)</li> <li>time_RL_preSN: time of the last Roche-Lobe overflow before the BH formation (if empty no RLO before BH formation)</li> <li>time_RL_postSN: time of the first Roche-Lobe overflow after the BH formation (if empty no RLO before BH formation)</li> </ul> <p><strong>Note: </strong>The file has been created by combining the file BHMS_ic.pq.gz with the main SEVN outputs using the script <em>create_aux.py </em>included in this repository</p> <h3>How to read the files</h3> <p>The parquet files can be easily read in Python by using the <a href="https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html">Pandas module</a>:</p> <pre><code>import pandas as pd df_bhms=pd.read_parquet("BHMS.pq.gz") df_bhms_ic=pd.read_parquet("BHMS_ic.pq.gz") df_bhms_vsnce=pd.read_parquet("BHMS_VSNCE.pq.gz")</code></pre> <p> </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": IIB - simulation outcomes, different metallicities
<p>This repository contains (a part) of the population synthesis outputs analysed in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. In particular, it contains the simulation sets with different metallicities.</p> <h2>Content</h2> <p>Each tar file contains the outputs of a given simulation set from <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The name of the files corresponds to the name of the set as reported in Table 1 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The details of the sets can be found in Section 2.2 and Section 2.3 of <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a>. The outputs stored in this repository contain only the systems that satisfy the following conditions:</p> <ul> <li>The two objects are in a binary system</li> <li>An object is a black hole and the other one is a star in any evolutionary phase prior to the ignition of the helium burning in the core</li> <li>The two objects are not currently interacting except for wind mass transfer (no ongoing Roche-Lobe overflow, common envelope or merger).</li> </ul> <p>The tar files contain three different files in gunzipped parquet format (<a href="https://parquet.apache.org">https://parquet.apache.org</a>):</p> <h3><strong>Python scripts</strong></h3> <ul> <li><em>analyse_sample.py</em>: python script we used to produce the file BHMS.pq.gz and BHMS_ic.pq.gz analysing the SEVN outputs</li> <li><em>create_aux.py</em>: python script we used to produce the file BHMS_VSNCE.pq.gz by combining the SEVN log outputs with the BHMS_ic.pq.gz file</li> </ul> <h3> </h3> <h3>BHMS.pq.gz</h3> <p><strong> </strong>File containing all the systems satisfying the above condition.</p> <p><strong>Columns:</strong></p> <ul> <li>ID: unique id of the binary (Long integer)</li> <li>name: unique name of the binary (Long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminosity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Euclidean distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p> <strong>Notice-1: </strong>in this file each system (identified by ID and name) can appear more than once. Indeed this file contains all the outputs in which a system satisfy the condition BH-star condition discussed above.</p> <p> <strong>Notice-2: </strong><em>the dataframe is sorted based on the bh3dist column,</em> so the first rows contains the objects that are closer to the properties of Gaia BH3 based on the bh3dist statistic.</p> <p> <strong>Notice-3: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_ic.pq.gz</h3> <p>File containing the initial conditions of all the systems included in the file BHMS.pq.gz</p> <p><strong>Columns:</strong></p> <p><em>Info from BHMS.pq.gz</em>:</p> <p>these columns report the same information as in the BHMS.pq.gz file, but each system (identified by ID and name) appears just once (the occurrence from the BHMS.pq.gz with the minimum bh3dist)</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>BWorldtime: simulation time in Myr (all the simulations start at BWorldtime=0) </li> <li>BTimestep: timestep of the simulation corresponding to the current binary properties in Myr. In this time range, the binary properties can be considered constant.</li> <li>ms: mass of the star in Msun</li> <li>ks: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2000MNRAS.315..543H/abstract">Hurley+2000</a> classification (integer)</li> <li>ks_sevn: stellar evolutionary phase following the <a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio+2023</a> classification (integer)</li> <li>rs: stellar radius in Rsun</li> <li>Ts: stellar effective temperature in Kelvin</li> <li>Ls: stellar luminoisity in Lsun</li> <li>mbh: mass of the black hole in Msun</li> <li>P: binary period in days</li> <li>BEvent: Event corresponding to the SEVN output (see SEVN user guide)</li> <li>Eccentricity: Eccentricity of the binary</li> <li>Semimajor: Semimajor axis of the binary in Rsun</li> <li>bh3dist: "Relative" Eucledian distance of the system from the Gaia BH3 properties:</li> </ul> <p> bh3dist = sqrt( ((ms-ms_GBH3)/(ms_GBH3))**2 + ((mbh-mbh_GBH3)/(mbh_GBH3))**2 + ((P-P_GBH3)/(P_GBH3))**2 + ((ecc-ecc_GBH3)/(ecc_GBH3))**2 )</p> <p><em>Initial properties</em>:</p> <ul> <li>mzams_0: Initial (ZAMS) mass of the black hole in Msun</li> <li>mzams_1: Initial (ZAMS) mass of the star in Msun</li> <li>Semimajor_ini: Initial semimajor axis of the binary in Rsun </li> <li>Eccentricity_ini: Initial eccentricity axis of the binary </li> <li>seed: Random seed used in the SEVN simulation</li> <li>P_ini: Intial period of the binary in days </li> </ul> <p><strong> Notice: </strong>The file has been created by analysing the main SEVN outputs using the script <em>analyse_sample.py </em>included in this repository</p> <h3>BHMS_VSNCE.pq.gz</h3> <p>A file containing additional information about the evolutionary events of the systems stored in BHMS.pq.gz</p> <ul> <li>ID: unique id of the binary (long integer)</li> <li>name: unique name of the binary (long integer)</li> <li>time_SN: formation time of the black hole (BH) in Myr (all the simulations start from time=0)</li> <li>Vcom: Velocity magnitude of the center of mass after the formation of the BH (before the formation Vcom=0 is assumed)</li> <li>time_CE_preSN: time of the last CE before the BH formation (if empty no CE before BH formation)</li> <li>time_CE_postSN: time of the first CE after the BH formation (if empty no CE after BH formation)</li> <li>time_RL_preSN: time of the last Roche-Lobe overflow before the BH formation (if empty no RLO before BH formation)</li> <li>time_RL_postSN: time of the first Roche-Lobe overflow after the BH formation (if empty no RLO before BH formation)</li> </ul> <p><strong>Note: </strong>The file has been created by combining the file BHMS_ic.pq.gz with the main SEVN outputs using the script <em>create_aux.py </em>included in this repository</p> <h3>How to read the files</h3> <p>The parquet files can be easily read in Python by using the <a href="https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html">Pandas module</a>:</p> <pre><code>import pandas as pd df_bhms=pd.read_parquet("BHMS.pq.gz") df_bhms_ic=pd.read_parquet("BHMS_ic.pq.gz") df_bhms_vsnce=pd.read_parquet("BHMS_VSNCE.pq.gz")</code></pre> <p> </p> <h2>Notes</h2> <p>The code used in <a href="https://ui.adsabs.harvard.edu/abs/2024arXiv240417568I/abstract" target="_blank" rel="noopener">Iorio et al., 2024</a> is SEVN (<a href="https://ui.adsabs.harvard.edu/abs/2023MNRAS.524..426I/abstract">Iorio et al., 2023</a>) version 2.10.1 (commit <a href="https://gitlab.com/sevncodes/sevn/-/tree/a4753f1177aab076da2641afc497a06006b30267">a4753f11</a>). </p>
Binary black-hole simulation SXS:BBH:0180
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0187
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0190
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0191
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0197
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0183
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0184
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0065
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0114
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0169
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
Binary black-hole simulation SXS:BBH:0047
Simulation of a black-hole binary system evolved by the <a href="https://www.black-holes.org/code/SpEC.html">SpEC code</a>.
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.