**************************************************************************************************** * * * aflow - STEFANO CURTAROLO Duke University 2003-2021 * * High-Throughput ab-initio Computing Project * * * **************************************************************************************************** LATEST VERSION OF THE FILE: materials.duke.edu/AFLOW/README_AFLOW_CHULL.TXT **************************************************************************************************** AFLOW-CHULL README: README written by: Corey Oses (corey.oses@duke.edu) Citation info: C. Oses, E. Gossett, D. Hicks, F. Rose, E. Perim, I. Takeuchi, S. Sanvito, O. Levy, C. Toher, and S. Curtarolo, AFLOW-CHULL: Cloud-based platform for autonomous phase stability analysis, J. Chem. Inf. Model. 58(12), 2477-2490 (2018) **************************************************************************************************** GENERAL OVERVIEW AFLOW-CHULL is an automated thermodynamic stability analysis tool. Compound data is downloaded from the AFLOW REST-API/AFLUX Search-API and the minimum energy surface is calculated using a modified variant (dimensionally-iterative) of the qhull convex hull algorithm: ACM Trans. on Mathematical Software, 22(4):469-483, Dec 1996. Various thermodynamic properties are extracted, including off-hull (full decomposition reaction, distances to the hull) and on-hull (equilibrium phases, equivalent ground state structures) features. Determination of the stability criterion is also available, which has served as a powerful screening tool for the discovery of new permanent magnets: Science Adv. 3(4), e1602241 (2017). Other important analyses running under the hood include: - structure comparison analysis via Burzlaff criteria (--readme=compare) - outlier detection and removal (interquartile range). Various output formats are provided, including plain text, json, PDF, and Jupyter. **************************************************************************************************** LIST OF AFLOW-CHULL COMMANDS: aflow --convex_hull=|--chull --alloy=MnPdPt[,AlCuZn,...] [--np=1] [chull_options] [--destination=DIRECTORY] Queries the AFLOW API for relevant entries (see --load_library), calculates the convex hull, and returns the information as a PDF (default, see --output). --chull : Necessary flag for entering mode for calculating convex hull. --alloy : Necessary argument, specifies system. This code is not dimension specific, i.e., you can calculate the convex hull for any n-ary system. There are two input modes: raw (comma-separated) and combinatorial (colon- and comma-separated). Raw input: --alloy=MnPdPt,AlCuZn. Combinatorial input: --alloy=Ag,Au:Mn. This is interpreted as --alloy=AgMn,AuMn. [--np=1] : Number of processors for multiple alloy inputs. [--destination=DIRECTORY] : Optional argument, specify the directory for the output. Default is "./". [--usage] : Returns usage commands and options. [--print=|--p=|--output=|--o=latex|pdf|png|json|text|jupyter|jupyter2|jupyter3] : Select the output format. Latex/PDF are the same (.pdf). JSON and plain text have the following extensions: .json and .txt. jupyter|jupyter2|jupyter3 creates a jupter notebook json file that plots a convex hull for the specified alloy (jupyter3 is default). Default is Latex/PDF. [--screen_only] : Output is direct to screen (stdout) instead of writing to a file. All logging output is suppressed. [--keep=tex|--keep_tex|--keeptex|--tex] : Latex/PDF output mode only. Will keep latex .tex and put it in --destination=DIRECTORY. [--keep=log|--keep_log|--keeplog|--log] : Prints a log file of relevant output. [--keep=tex,log] : Keep both. LOADING OPTIONS: [--load_library=|--loadlibrary=|--ll=icsd|lib1|lib2|lib3] : Specify libraries from which to load. Default: icsd, lib2, and lib3. [--load_API|--load_api|--loadapi|--lapi|--api] : Force loading entries from the API (default unless on nietzsche, aflowlib, or habana). [--load_entries_entry_output|--loadentriesentryoutput|--leo] : Get full output for all entries loaded from the AFLOW API. [--neglect=|--ban=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] : Ban specific entries from the convex hull calculation, done by AUID. [--see_neglect|--seeneglect|--sn] : Show why entries were neglected. [--remove_extreme_points=|--removeextremepoints=|--remove_extrema=|--removeextrema=|--rep=-1000] : Exclude points based on Hf/Ts (floor/ceiling). Units are meV/atom / K. [--entropic_temperature|--entropictemperature|--entroptemp] : Calculate the Ts convex hull (upper-half). Default is Hf hull (lower-half). [--include_paw_gga|--paw_gga] : Include calculations run with PAW_GGA. Easily coupled with default PAW_PBE (same level of theory, differently parametrized). ANALYSIS OPTIONS: [--distance_to_hull=|--distancetohull=|--distance2hull=|--dist2hull=|--d2h=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] : Calculates a structure's distance below/above (Hf/Ts) the hull. [--stability_criterion=|--stabilitycriterion=|--stable_criterion=|--scriterion=|--sc=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] : Calculates the stability criterion of the ground state structure. Will return a warning if structure is not a ground state one. It removes the point from the hull, calculates the new hull, and calculates the distance of this point from below/above (Hf/Ts) hull. [--n+1_enthalpy_gain=|--n+1_energy_gain=|--n+1enthalpygain=|--n+1energygain=|--n+1egain=|--n1egain=|--n+1_enthalpygain=|--n+1+energygain=|--n+1_egain=|--nplus1=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] : Calculates the N+1 enthalpy gain of the ground state structure. Will return a warning if structure is not a ground state one. It removes all points having the same dimensionality from the hull, calculates the new hull, and calculates the distance of this point from below/above (Hf/Ts) hull. [--hull_formation_enthalpy=|--hull_enthalpy=|--hull_energy=0.25,0.25] : Returns the value of the convex hull surface at the specified coordinate/concentration. For stoichiometric hulls, provide the reduced composition form, i.e., for the compound Mn2PdPt, use --hull_formation_enthalpy=0.5,0.25, where the composition of the last component is implicitly 1-sum(0.5+0.25). Providing an additional component (e.g., --dist2hull=0.5,0.25,0.1) results in a rigid shift in the energy axis and, thus, a constant added to the final distance calculated (0.1 is in units of eV for formation energy hulls). [--skip_structure_comparison|--skipstructruecomparison|--skipstructcomp|--ssc] : Structure comparison analysis for determination of equivalent ground state structures is skipped (can be time consuming). [--skip_stability_criterion_analysis|--skipstabilitycriterionanalysis|--skip_scriterion|--skipscriterion|--sscriterion] : Analysis of stability criterion for ground state structures is skipped (can be time consuming). [--skip_n_plus_1_enthalpy_gain_analysis|--skip_n_plus_1_energy_gain_analysis|--skipnplus1enthalpygainanalysis|--skipnplus1energygainanalysis|--skip_nplus1|--skipnplus1|--snp1|--snpo] : Analysis of N+1 enthalpy gain for ground state structures is skipped (can be time consuming). [--include_skewed_hulls|--include_skewed|--ish] : Process hull despite skewed endpoints (abs(ground state endpoint energy) < 15 meV). [--include_unreliable_hulls|--include_unreliable|--iuh] : Process hull despite poor statistics (binary hull count < 200). [--include_outliers|--io] : Include any detected outliers (output/warning is still shown). [--strict_outlier_analysis|--soa] : Terminate hull analysis if binary hull statistics not satisfied. [--force] : Force output despite warnings. LATEX/PDF/PNG OPTIONS: [--image_only|--imageonly|--image] : Latex/PDF output mode only. Similar to --document_only, but the image dimensions are not necessarily for a standard page. Preferred option for importing into papers/presentations. [--no_document|--nodocument|--no_doc|--nodoc|--full_page_image|--fullpageimage] : Latex/PDF output mode only. Generates a PDF of just the convex hull illustration (2/3D). Dimensions: 8.5x11 inches (standard page), landscape. [--document_only|--documentonly|--doc_only|--doconly|--doc] : Latex/PDF output mode only. Exclude convex hull illustration. This is the default for quaternary systems and above. [--latex_output|--latexoutput] : Latex/PDF output mode only. See full latex output. Good for troubleshooting. [--latex_interactive|--latexinteractive] : Latex/PDF output mode only. Allows you to interact with latex as it compiles. Good for troubleshooting. [--light_contrast|--lightcontrast|--lc] : Latex/PDF output mode only. Modifies the convex hull illustration color scheme to be lighter. [--large_font|--largefont|--large|--lf] : Latex/PDF output mode only. Prints a "larger" font size for convex hull illustration. [--png_resolution=|--pngresolution=|--pngr=300] : Set PNG resolution (-density in convert). [--plot_iso_max_latent_heat|--plot_isomax|--iso_max|--isomax] : Plot iso-max-latent-heat lines for ground state structures. See dx.doi.org/10.1063/1.4902865. For additional information contact: Corey Oses (corey.oses@duke.edu) **************************************************************************************************** * * * aflow - STEFANO CURTAROLO Duke University 2003-2021 * * High-Throughput ab-initio Computing Project * * * ****************************************************************************************************