3.2.14 - 2023/10/25 Location: http://materials.duke.edu/AFLOW/aflow.3.2.14.tar.xz -- patched aflow.in generation with INCAR_EXPLICIT_START_STOP (TB+RF) -- parallelized --chull --alloy (CO) -- fixed some logger, adding some QUIETs (CO) -- fixing --npmax and --np=max options (CO) -- fixed RDF function (CO) -- added RDF to pocc (CO) -- patching AddAtom() types vs. names bug (CO) -- reworked reshape, shift and stack function for xvector and xmatrix (HE) -- new JSON parser and writer added (HE) -- fixed minimum enumerated Wyckoff search to consider different lattice vector choices (DX) -- fixed printing of Wyckoff POSCAR in extended crystallographic data output (DX) -- fixed printing of Wyccar to check if the space group has been calculated (DX) -- added tie-breaker scheme to choose AFLOW prototype that is most alphabetical from left-to-right (DX) -- fixed atom decoration comparisons with new SetSpecies() function (DX) -- added univariate polynomial solver (SD) -- added univariate polynomial fit with weights (SD) -- added LUP decomposition (SD) -- updated aurostd::inverse function to be more robust (SD) -- added aurostd::condition_number (SD) -- added matrix pre-conditioner in aurostd::equilibrateMatrix (SD) -- added linspace function (SD) -- added simplistic JSON extractor for vectors and matrices (SD) -- added Newton-Raphson method to solve nonlinear square systems (SD) -- added deflation method to find multiple zeros in nonlinear square systems (SD) -- added binodal construction module for n-ary alloys (SD) -- added XtalFinder primitivization speed up for library runs (DX) -- added check for alternative lattice vector choice in tetragonal crystal system to minimize Wyckoff enumeration (DX) -- added fast parallelized POCC tile count estimation (HE+SD) -- transition to C++17 (HE+SD) -- added incbin library for easy raw file inclusion (HE) -- performance improvidence for xmatrix and xvector 3.2.13 - 2022/08/30 Location: http://materials.duke.edu/AFLOW/aflow.3.2.13.tar.xz -- implemented QH-POCC and POCC+QHA (AS) -- improved formatting of aflow.qha.thermo.out file (AS) -- fixed aurostd::getxvec() bug where lcols_out and lrows_out defaulted to AFLOW_MAX_INT (AZ) -- moved xmatrix2xvector functionality aurostd::getxvec() and use getxvec() in getmatInPlace (AZ) -- parallelized KBIN::CompressDirectory() (CO) -- generalizing DOS averaging for pocc systems with ARUNs having different numbers of atoms (CO) -- number->basis (CO) -- adding findClosedPackingPlane, to be finished (CO) -- testing new structure enumeration algorithm, to be finished (CO) -- removing whitespaces and hyphens from chull input injected from web (CO) -- patching IsDirectory() and IsFile(), used to trip over directory/file permissions (CO) -- added md5sum to --xplug (CO) -- added --itc flag for structure generation (CO+DX) -- fixing --cif with pocc structure (DX+CO) -- changed the "alpha" Wyckoff position to "A" in space group 47, fixes corner cases prototype commands (DX) -- fixed bug in matching Wyckoff positions for isopointal structures (DX) -- updated README_PROTO.TXT for correct Bixbyte prototype label (DX) -- fixed bug with printing atom mapping information in XtalFinder, reset for non-matches (DX) -- constexp variant of crc64 hashing to enable string based switch cases (HE) -- allow naming of generic hosts using --machine_name in combination with --machine (HE) -- adding basic http1.1 functions to aurostd (HE) -- added const strings variant of aurostd::StringSubst (HE) -- added non decimal bases to aurostd::string2utype (HE) -- new EntryLoader with automatic source selection (HE) -- improved speed of aurostd::file2string (HE) -- Fixed CIF parser for CIF files with oxidation states in species list (ME) -- Added fallback solutions for reading CIF files with unregonized settings (ME) -- Added poscar2aflowin for non-POSCAR input files (ME) -- improved AFLUX calls for --compare_database_entries and --compare2database (ME) -- fixed logical statements in aflow_kvasp.cpp to be linear (SD) -- fixed the LOCK file to be created atomically (SD) -- added xmatrix reshape, mod_floored functions (SD) -- added ATAT detector, reader and writer (SD) -- fixed execute2string to force bash (SD) -- added flag to CleanSpin() for reading spin from atom labels (SD) -- fixed logic bug in ProcessKill (SD) -- added temporary directory list to aflowrc (SD) -- fixed order of variable initializations in aflow_init.cpp (SD) -- removed "kill_vasp_all" and implemented a targeted kill vasp command (SD) -- added KBIN::BIN2VASPVersion (SD) -- fixed KBIN::VASPVersionString2Double, aurostd::substring2bool, aurostd::kvpairfound (SD) -- added extract POSCAR from aflowin (SD) -- improved AFLUX calls for --compare_database_entries and --compare2database (ME) -- fixed aurostd::getxvec() bug where lcols_out and lrows_out defaulted to AFLOW_MAX_INT (AZ) -- moved xmatrix2xvector functionality aurostd::getxvec() and use getxvec() in getmatInPlace (AZ) -- added --itc flag for structure generation (CO+DX) -- fixing --cif with pocc structure (DX+CO) (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_database.cpp, aflowlib_entry_loader.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, aflowlib_web_outreach.cpp, aflowrc.cpp, apennsy.cpp, avasp.cpp, bader.cpp, cce.cpp, chull.cpp, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, contrib_cormac.cpp, data.cpp, defects.cpp, gfa.cpp, iaims.cpp, ialien.cpp, ifrozsl.cpp, init.cpp, ivasp.cpp, kaims.cpp, kalien.cpp, kbin.cpp, kvasp.cpp, lattice.cpp, Makefile, Makefile.aflow, makefile.cpp, matlab.cpp, modules.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, plotter.cpp, pocc_apl.cpp, pocc.cpp, pocc.h, pocc_old.cpp, pocc_qha.cpp, pocc_thermo.cpp, pthreads.cpp, qsub.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_CHULL.TXT, README_AFLOW_EXCEPTIONS.TXT, README_AFLOW_QHA_SCQHA_QHA3P.TXT, README_AFLOW.TXT, README_PROTO.TXT, surface.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, test.cpp, unit_test.cpp, wyckoff.cpp, xatom.cpp, xclasses.cpp, xelement.cpp, xproto.cpp, xthread.cpp) (ANRL: aflow_anrl.cpp, README_AFLOW_ANRL.TXT) (AEL: ael_elasticity.cpp, pocc_ael_agl.cpp) (AGL: agl_debye.cpp, pocc_ael_agl.cpp) (APL: aapl_cluster.cpp, aapl_ifcs.cpp, aapl_tcond.cpp, apl_atomic_disp.cpp, apl_doscalc.cpp, apl_fccalc.cpp, apl.h, apl_kphonons.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_supercell.cpp, apl_thermalpc.cpp, qha.cpp, README_AFLOW_APL.TXT) (AUROSTD: argv.cpp, aurostd.cpp, aurostd.h, boot.cpp, crc64.cpp, main.cpp, xerror.cpp, xerror.h, xfit.cpp, xhttp.cpp, xhttp.h, xmatrix.cpp, xmatrix.h, xoption.cpp, xoption.h, xparser.cpp, xscalar.cpp, xscalar.h, xtensor.cpp, xvector.cpp, xvector.h) 3.2.12 - 2021/11/29 Location: http://materials.duke.edu/AFLOW/aflow.3.2.12.tar.xz -- Added python module install functionality. (ME) -- Added POCC+APL workflow (ME) -- Added LIB2RAW for APL (ME) -- added machine settings for machine004 (DX) -- added function to move aflow run to another directory (DX) -- added machine settings for machine004 (DX) -- fixed gcc warning (version 4) in SYMBOLICCPLUSPLUS/ (DX) -- patching populateXVASP() bug for BANDS_LATTICE and BANDS_GRID (CO) -- patching xoption::options2entry() clear() issues (CO) -- added swap memory check to aurostd::GetMemory() and aurostd::GetMemoryUsagePercentage() (CO) -- patched --qmvasp command (CO) -- adding --contcar_save_outcar_complete to KBIN::Clean() (CO) -- NBANDS equation typo patch, returning old NBANDS behavior (CO) -- fixing some error="NBANDS" patches (CO) -- patching GetStoich() bug with pocc structures (round-off printing errors) (CO) -- adding KPOINTS=GAMMA_ODD to NELM patches (CO) -- added dielectric analysis in POCC (CO) (AFLOW: aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, aflowlib_web_outreach.cpp, aflowrc.cpp, avasp.cpp, chull.cpp, compare_structure_function.cpp, init.cpp, ivasp.cpp, kbin.cpp, kvasp.cpp, lattice.cpp, Makefile.aflow, ovasp.cpp, pflow.h, plotter.cpp, pocc_apl.cpp, pocc.cpp, pocc.h, pthreads.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_POCC.TXT, README_AFLOW.TXT, test.cpp, xatom.cpp, xclasses.cpp) (APL: aapl_cluster.cpp, aapl_ifcs.cpp, aapl_tcond.cpp, apl_atomic_disp.cpp, apl_doscalc.cpp, apl_fccalc.cpp, apl.h, apl_kphonons.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_supercell.cpp, apl_thermalpc.cpp, qha.cpp) (SYMBOLICCPLUSPLUS: symbolic.cpp, symbolic.h) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xmatrix.cpp, xmatrix.h, xoption.cpp, xoption.h, xscalar.cpp, xscalar.h) 3.2.11 - 2021/08/02 Location: http://materials.duke.edu/AFLOW/aflow.3.2.11.tar.xz -- added plotter options for QHA (AS) -- fixed bug in range for GetBasisTransformationInternalTranslations() (DX) -- fixed coordination matching when comparing environments (DX) -- fixed bug in JSON printing of equivalent atom decorations (DX) -- fixed INCAR-MAGMOM reader for crystal-spin analysis in symmetry and XtalFinder (DX) -- fixed bug in internal translations with TransformStructures() to consider compression in one direction and expansion in another (DX) -- fixed web printing in edata/sgdata; prevent mixing of txt and json outputs (DX) -- remove control code characters from title line in geometry file (needed for web) (DX+ME) -- added --Wyckoff functionality (--print=txt|json and --web) (DX) -- added R. Friedrich prototype (DX+RF) -- moved/improved Wyccar writier to geometry file printer function (DX) -- updated README_AFLOW_SYM.TXT: added lattice data commands, tolerance spectrum, etc. (DX) -- added new options to the Pearson symbol command: tolerance, magnetic moment, tolerance spectrum, etc. (DX) -- updated README_AFLOW_COMPARE.TXT (DX) -- added aliases to symmetry commands (e.g., --sg, --space_group_number, etc.) (DX) -- fixed tolerance spectrum delimiter (colon to comma) (DX) -- updated AFLUX call via AFLOW; uses new API route (DX) -- updated space group queries via AFLUX in the XtalFinder routines (DX) -- fixed same-atom tolerance bug in new GetPrimitive() function (DX) -- fixed unaries in LIB2 errors for plot titles (DX+ME) -- Made string search in database case insensitive (ME) -- Supressed file output for interstitials calculation in web mode (ME) -- added command line plotting functionality for POCC runs using --plot_dos (CO) -- printing out ldau_type by default (0 if not calculated) (CO+ME) -- changed newlines to semi-colons in aurostd::execute() and aurostd::execute2string() and added file system IO options to aurostd::execute2string() (CO) -- extended CleanStringASCII_InPlace() to include ALL ASCII characters (CO) -- added NELM and NELM_STATIC options to VASP_FORCE_OPTIONS and aflow.rc (CO) -- added ISMEAR_SCHEME, ISMEAR_STATIC_SCHEME, and ISMEAR_STATIC_BANDS_SCHEME options to VASP_FORCE_OPTIONS and aflow.rc (CO) -- added SIGMA, SIGMA_STATIC, and SIGMA_STATIC_BANDS options to VASP_FORCE_OPTIONS and aflow.rc (CO) -- added MAX_VASP_NELM to aflow.rc and created a xwarning/xfixed scheme for NELM (CO) -- patched VASP_OSZICARUnconverged(), adding VASP_OSZICARUnconverging() (CO) -- patched generation of INCAR, removed duplicate lines like SYSTEM=XXXX (CO) -- patched removal of NELM from INCAR vs. NELMIN (CO) -- added XVASP_Afix_NELM() (CO) -- added auto-patches for EDDRMM errors (CO) -- patched SYM errors/warnings, ignoring if ISYM=0 (CO+ME) -- added NELM to xOUTCAR (CO) -- consolidated XVASP_KPOINTS_KPOINTS() overloads (CO) -- adding ISYM=-1 for magnetic systems (CO) -- added AFLOWIN_REMOVE() and AFLOWIN_ADD() (CO) -- cleanup aurostd::RemoveComments(), substring2bool(), substring2string(), substring2strings() (CO) -- added aurostd::kvpair2value() and kvpair2utype(), better than substring2string() for INCARs (CO) -- added KBIN::VASP_ApplyPatch() (CO) -- added KBIN::OUTCAR2VASPVersionString() and KBIN::INCAR_IALGO2ALGO() (CO) -- added new formatting for EXCCOR vasp error (CO) -- added aurostd::ProcessRunning(), aurostd::ProcessKill(), aurostd::ProcessRenice() (CO) -- extensive rewrite of KBIN::XVASP_INCAR_PREPARE_GENERIC(), KBIN::XVASP_KPOINTS_OPERATION(), and KBIN::XVASP_Afix_GENERIC() enabling a feedback loop of INCAR/KPOINTS updates (CO) -- adding KBIN::XVASP_KPOINTS_IncludesGamma() to check if existing xvasp is includes Gamma in the grid (CO) -- added RELAX=FORCES patch to EDDRMM patches (CO) -- added AFLOW_monitor_VASP() (CO) -- added AFLOW_monitor_VASP() support for LOCK files vs. directory input (CO+DX) -- adding GetCatCommand(file) for cat/xzcat/bzcat/etc. (CO) -- adding convergence test for --xplug (CO) -- adding aurostd::dirname() and aurostd::basename() (CO) -- adding GetVASPBinaryFromLOCK() (CO) -- adding check for vasp.out's modification time (CO) -- adding XVASP_INCAR_Read_MAGMOM to load up MAGMOM into xvasp.str (CO) -- added a faster aurostd::FileSize() approach (CO) -- added check for vasp.out's size to avoid hours delay grepping for warnings (CO) -- included beta support for --monitor_vasp (with --kill_vasp_all) (CO) -- adding NBANDS-- for ZPOTRF errors (CO) -- adding patch for EXIT CODE: 174 (MPICH174) (CO) -- adding patch for CALC_FROZEN (CO) -- patching initial NBANDS so it's commensurate with NPAR (CO) -- added REPEAT_STATIC (CO) -- adding RECYCLE_CONTCAR to list of patches for CALC_FROZEN (CO) -- patching SPIN_REMOVE_RELAX bug which was not turning off spin (CO) -- fixing UTC offset in dates (CO) -- adding DEFAULT_VASP_FORCE_OPTION_BADER_STATIC which turns on bader for any STATIC calculation (CO) -- patched KBIN::VASP_Reread_POSCAR(), added aurostd::StringstreamClean() around (CO) -- consolidating PARAMS->xvasp conversion in avasp (CO) -- adding aurostd::round() (CO) -- patching convertPOSCARFormat() for different machine inputs (CO) -- adding --contcar_save to KBIN::Clean() (CO) -- fixing missing LOCK issue with --lib2raw (CO) (AFLOW: aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_database.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_libraries_scrubber.cpp, aflowlib_web_interface.cpp, aflowrc.cpp, avasp.cpp, cce.cpp, chull.cpp, chull.h, chull_jupyter_plotter.py, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, contrib_shidong_auxiliary.cpp, defects.cpp, iaims.cpp, ialien.cpp, ifrozsl.cpp, init.cpp, ivasp.cpp, kaims.cpp, kalien.cpp, kbin.cpp, kvasp.cpp, Makefile, matlab.cpp, nomix.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, plotter.cpp, pocc.cpp, pocc.h, pocc_old.cpp, qsub.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_CCE.TXT, README_AFLOW_COMPARE.TXT, README_AFLOW_SYM.TXT, README_AFLOW.TXT, README_PROTO.TXT, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, xatom.cpp, xclasses.cpp) (ANRL: aflow_anrl.cpp, list.cpp) (AEL: ael_elasticity.cpp, ael_get_stress.cpp, pocc_ael_agl.cpp) (AGL: agl_debye.cpp, agl_get_ev.cpp, pocc_ael_agl.cpp) (APL: apl_kphonons.cpp) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xscalar.cpp, xscalar.h, xvector.cpp, xvector.h) 3.2.10 - 2021/06/25 Location: http://materials.duke.edu/AFLOW/aflow.3.2.10.tar.xz -- fixed bug in GetPrimitive() function, use more robust volume check (DX) -- fixed tolerance bug in edata if tolerance scan fails (DX) -- fixed bandgap code for metals with partially empty channels (CO) -- bypassing soft bandgap code errors for lib2raw (CO) -- fixed KBIN::ExtractAtomicSpecies(), removed unreliable system call (CO) -- patched aurostd::VASP_PseudoPotential_CleanName_InPlace() for more reliable composition extraction (CO) (AFLOW: aflowlib_libraries.cpp, bader.cpp, ivasp.cpp, Makefile, ovasp.cpp, pflow_funcs.cpp, plotter.cpp, xatom.cpp) (AUROSTD: aurostd.h, main.cpp, xparser.cpp, xparser.h) 3.2.9 - 2021/05/05 Location: http://materials.duke.edu/AFLOW/aflow.3.2.9.tar.xz -- Fixed bug with APL overwriting *.orig files. (AS) -- Fixed bugs in the electronic free energy calculation. (AS) -- Fixed bug in the fixed volume QHA method. (AS) -- Fixed determination of the required number of parameters for the EOS model. (AS) -- Extended the fixed volume QHA to include electronic contributions. (AS) -- Added method to JSONwriter: addVector() (vector of jsons) (AS) -- patched XVASP_KPOINTS_OPERATION() so a change is ensured for Xeven/Xodd etc. (CO) -- APL MINATOMS_RESTRICTED->MINATOMS_UNIFORM (CO) -- adding PAW_PBE_KIN to allowed DFT types in chull (CO) -- added AQueue, APartition, ANode, and --queue_status to aflow for auto-queue submission on qrats/quser (CO) -- patched stability criterion online plotter (CO) -- patching Egap calculations for HEX/Br2Mn1_ICSD_60250 (CO) -- Set output of symmetry groups to --quiet and --screen_only when in web mode. (ME) -- Made POCC web output more compact. (ME) -- Structure comparison takes from std::cin now in web mode. (ME) -- Fixed bug for --aflowlib that did not print original structure for different symmetries. (ME) -- Added alloy property to database (ME) -- Added functionality to convert entries to json and aflowlib entry formats (ME) -- Improved vector callback function for SQLite (ME) -- Minified database statistics file (ME) -- Updated AFLOW schema (ME) -- Added consistency checks for schema (ME) -- Fixed line breaks in stream2string method for istream. (ME) -- added rescale to sconv/sprim (DX+ME) -- added printing JSON/TXT options for --isopointal_prototypes in XtalFinder (DX) -- added --superlattice_data, --reciprocal_lattice_data, --pgroup_xtal_data, and --real_lattice_data functions, options: tolerance and format type (DX) -- fixed default titles for QE, AIMS, ELK, and CIF (DX) -- added methods to JSONwriter: addVector (with wrap option), addNull, addRawJSON (key-value variant), addVector (xvector variant), addMatrix (xmatrix variant) (DX) -- consolidated pflow::DATA(), moved SGDATA() into DATA() (DX) -- updated usage for lattice data (DX) -- added separate lattice functions for GetRealLatticeType(), GetCrystalPointGroupData(), GetSuperLatticeType() (DX) -- consolidated space group setting options into function (getSpaceGroupSetting()), fixes missing "aflow" option in --sgdata (DX) -- fixed SymbolicC++ compilation warnings with gcc 10 and later (DX) -- added faster and more robust GetPrimitive() function (DX) -- added new function to find translation/lattice vectors (DX) -- fixed bug for empty/cleared symmetry groups to prevent core files (DX) -- added sym_eps_no_scan to xstructure to pass around no tolerance scan information to different functions (DX) -- added more debugging to pflow::PerformFullSymmetry() (DX) -- suppressed/reduced output for minimumDistance() and LatticeDimensionSphere() (DX) -- fixed ELK reader to include magnetic/spin information (DX) -- added carbonitride and part 3 prototypes to README_PROTO.TXT (DX) -- added check_prototype_symmetry and check_prototype_uniqueness to makefile (DX) -- fixed issues with swapping species (atom types not updated) (DX) (AFLOW: aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_database.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, aflowrc.cpp, chull.cpp, chull.h, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, init.cpp, ivasp.cpp, lattice.cpp, Makefile, modules.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, plotter.cpp, README_AFLOW_AFLOWRC.TXT, README_AFLOW_COMPARE.TXT, README_AFLOW_EXCEPTIONS.TXT, README_AFLOW_SYM.TXT, README_AFLOW.TXT, README_PROTO.TXT, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, xatom.cpp, xproto.cpp) (ANRL: aflow_anrl.cpp, aflow_anrl.h, list.cpp, README_AFLOW_ANRL.TXT) (APL: apl.h, apl_kphonons.cpp, apl_supercell.cpp, qha.cpp, README_AFLOW_APL.TXT) (SQLITE: aflow_sqlite.cpp) (SYMBOLICCPLUSPLUS: number.cpp, number.h, symbolic.cpp, symbolic.h, symmatrix.cpp, symmatrix.h, vector.cpp, vector.h) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xerror.cpp, xerror.h, xfit.cpp, xmatrix.cpp, xparser.cpp, xparser.h, xvector.cpp, xvector.h) 3.2.8 - 2021/02/22 Location: http://materials.duke.edu/AFLOW/aflow.3.2.8.tar.xz -- improved efficiency/speed of minimizeDistanceCartesianMethod() (DX) -- improved structure conversions in space group routines (uses new transformation methods; TransformStructure()) (DX) -- improved lattice-type calculator; search lattices more efficiently (DX) -- fixed minor bugs for comparing unaries with different cell sizes in XtalFinder (DX) -- fixed minor bug in reading element names from Xstructure (DX) -- lib2raw bug fixes (CO) -- web aflowin bug fixes (SC) -- fixed typo in Wyckoff position for space group 85, setting 2 (DX) -- fixed compare2database species issue (DX) -- fixed alphabetic ordering of symbolic equations (DX) -- fixed origin shift coordinate-type in XtalFinder (DX) -- fixed LFA environment cardinality (DX) (AFLOW: aflowlib_web_interface.cpp, aflow_compare_structure.cpp, aflow_compare_structure_function.cpp, aflow_symmetry_spacegroup_ITC_library.cpp, aflow_xatom.cpp, Makefile) (ANRL: aflow_anrl.cpp) 3.2.7 - 2021/02/04 Location: http://materials.duke.edu/AFLOW/aflow.3.2.7.tar.xz -- Added additional AEL and AGL properties to the AFLOW schema. (ME) -- implemented new on-the-fly threading scheme into AAPL (ME) -- Fixed bug with assignment of normal and umklapp processes for phase space calculations. (ME) -- Added bounds to inCell() function. (ME) -- Added functionality to plot thermodynamic properties calculated by QHA with the SJ EOS model. (AS) -- Added processing of QHA data to LIB2LIB and LIB2RAW. (AS) -- Added a feature to employ fixed volume relaxation of QHA subcalculations. (AS) -- Added a JSONwriter class to output data in JSON format. (AS) -- added utype2string variant; includes print format (DX) -- added algorithm option to xcombos; added Heap's algorithm to generate permutations (DX) -- added Python modules for AFLOW-SYM and AFLOW-XtalFinder into src (DX) -- added check_prototype_generator (and --PrototypeGenerator_test) to the Makefile to ensure all AFLOW prototypes can be generated (DX) -- added --PrototypeSymmetry_test to check the symmetry of all the AFLOW prototypes, added function for special cases for the tolerance (consistent with encyclopedia comments) (DX) -- added corner-case for generating sigma_tP30_136_bf2ij; doesn't follow symbolic generator convention (DX) -- added structure transformation methods to aflow_xatom.cpp: ChangeBasis(), Rotate() (updated from previous version), TransformStructure(), and ShiftPos() (updated from previous versions) (DX) -- updated README_AFLOW_ANRL.TXT with symbolic prototype generator info (DX) -- updated README_COMPARE.TXT and --usage with new functionality (DX) -- added ternary and binary metal-nitride prototypes, updated README_PROTO.TXT (DX) -- added ternary metal prototypes, updated README_PROTO.TXT (DX) -- extended general comparison options to all main comparison functions (DX) -- added default XtalFinder options to aflowrc file (DX) -- added defaults/options for machine003 to run AFLOW+DFT (DX) -- updated XtalFinder comparison routines to use new transformation vs supercell methods; faster (DX) -- added option to toggle between transformation and supercell methods in aflowrc (DX) -- updated XtalFinder JSON keywords, consistent with article (DX) -- created XtalFinderCalculator class: reduces copying/moving/erasing of structures; inherits Xstream, passes universal variables (number of precessors, misfit thresholds, etc.) (DX) -- created XtalFinderCalculator::getOptions() to handle general options from command-line (DX) -- added --space_group=|--sg= flag to compare database entries; can handle multiple space group inputs (DX) -- grouped writing functions into writeComparisonOutputFile() (DX) -- renamed overloads of aflowCompareStructures() to be more intuitive: structuresMatch() and getMisfitBetweenStructures() (DX) -- improved and reformatted latticeSearch() procedure (DX) -- added structs to easily pass information to the functions (reduce copying and number of function inputs): _structure_representative (for structure info) and structure_misfit (for mapping info) (DX) -- added basis transformation, rotation, origin shift, and atom mapping info to the output (--print_mapping) (DX) -- removed old/obsolete comparison functions (DX) -- improved and reduced XtalFinderCalculator::findMatch() function; added mapping check functions (DX) -- added options to XtalFinder to convert structures to the primitive, Minkowski, and/or Niggli representation prior to comparing (DX) -- added options to XtalFinder to control the misfit threshold(s): misfit_match, misfit_family (DX) -- added _DEBUG_COMPARE_ to comparison functions (DX) -- fixed bug in GFA calculator: bug in macros (KbT and TEMPERATURE)(DX) -- added more debugging to GFA code (DX) -- updated database keywords in schema for prototype label, parameters, and parameter values (DX) -- fixed bug in aflow_surface.cpp: origin was not reset correctly (DX) -- removed multiple if-statements in nested atom mapping functions, improves efficiency (DX) -- fixed Wyckoff position errors for SG #164, #191, and #209: missing multiplication symbols or bad string formatting (DX) -- added functions to convert multiple structures into their Niggli, Minkowski, or primitive representation in aflow_xatom.cpp; useful for splitting on threads (DX) -- added copy vs modify-in-place functions for structure transformation methods: ChangeBasis() and Rotate() (DX) -- created function to identify the internal translations when converting to a larger unit cell: GetBasisTransformationInternalTranslations() (DX) -- added PolarDecomposition() function to separate the rotation and deformation components of a transformation (DX) -- added functions to transform structures based on transformation matrix, rotation, and origin shift: TransformStructure() (DX) -- added foldAtomsInCell() and SetNumEachType() in-place-modification overloads (DX) -- removed obsolete neighbor variables/functions, e.g., removed AFLOW_NEIGHBORS keywords in aflow.in (not used), removed unused xstructure neighbor attributes, removed aflow_neighbours.cpp (DX) -- major updates to xelement (CO) -- added xvector.resize() (CO) -- added var(), stddev(), mode(), correlation_Pearson() to xvector (CO) -- adding KBIN::WaitFinished() after VASP runs to allow NFS to catch up (CO) -- setting _KVASP_CHECK_SLEEP_ to 30 seconds (CO) -- created rc parameter VASP_CHECK_SLEEP (CO) -- checking if VASP output files printed correctly (CO) -- exiting with error if VASP output files are corrupted after full aflow run (CO) -- removing POSCAR.orig from --xplug check, it's already in the aflow.in (CO) -- adding --force to LIB2LIB (CO) -- adding max=6D for chull online (CO) -- adding --machine=x settings (CO) -- added stress tensor check in --xplug (CO) -- added --no_fancy_print flag (CO) -- redirected fancy print to appropriate stream (CO) -- added support for new pocc database entries in _aflowlib_entry (CO) -- added support for non-static pocc runs (CO) -- more robust patch to chemistry-specific UFF energies (CO) -- changing chull binary count statistics threshold to 75 (CO) -- defaulting to skipping chull statistics analysis if not enough points are present (CO) -- adding --calculate_highest_dimension_only to chull analysis (CO) -- created ChullPointLight() which reduces memory load and speeds up chull calculations (CO) -- adding bool check_present to AddAtom() for AddCorners() (CO) -- adding --vasp5 option (CO) -- added check for sublattice decorations and --force_pocc to override check (CO) -- fixed --sc and --output=web for chull (CO) -- patching loadXStructure() with vspecies entry.getSpeciesAURL() (CO) -- patching aflow.in.xz and LOCK.xz in database (CO) -- patched bug with LIB1 DOS plotter (CO) (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_database.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, aflowrc.cpp, avasp.cpp, cce.cpp, cce.h, cce_python.py, chull.cpp, chull.h, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, contrib_shidong_cluster_expansion.cpp, contrib_shidong_cluster_expansion.h, contrib_shidong.cpp, contrib_shidong_main.cpp, gfa.cpp, ifrozsl.cpp, init.cpp, ivasp.cpp, kaims.cpp, kbin.cpp, kvasp.cpp, Makefile, Makefile.aflow, modules.cpp, neighbours.cpp, pflow_funcs.cpp, pflow.h, plotter.cpp, pocc.cpp, pocc.h, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_CCE.TXT, README_AFLOW_CHULL.TXT, README_AFLOW_COMPARE.TXT, README_AFLOW.TXT, README_PROTO.TXT, surface.cpp, symbolic.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, sym_python.py, test.cpp, xatom.cpp, xclasses.cpp, xelement.cpp, xelement.h, xproto.cpp, xtalfinder_python.py) (ANRL: aflow_anrl.cpp, aflow_anrl.h, list.cpp, README_AFLOW_ANRL.TXT) (AEL: ael_get_stress.cpp) (AGL: agl_get_ev.cpp) (APL: aapl_tcond.cpp, apl_doscalc.cpp, apl.h, apl_kphonons.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, qha.cpp) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xcombos.cpp, xcombos.h, xfit.cpp, xmatrix.cpp, xmatrix.h, xparser.cpp, xparser.h, xscalar.cpp, xscalar.h, xvector.cpp, xvector.h) 3.2.6 - 2020/12/30 Location: http://materials.duke.edu/AFLOW/aflow.3.2.6.tar.xz -- Bibtex for publications - aflowlib.h aflowlib_web_outreach.cpp (SC) 3.2.5 - 2020/09/25 Location: http://materials.duke.edu/AFLOW/aflow.3.2.5.tar.xz -- patched convert issue: security policy 'PDF' blocking conversion (SC) -- adding decompositionAuids for webapp (SK) -- Implemented option (--get_num_anion_neighbors) for printing number of anion neighbors for each cation for given POSCAR (RF) -- Implemented option (--get_oxidation_numbers) for printing oxidation numbers for given POSCAR (RF) -- Separated CCE corrections listing into different anion types (RF) -- Moved CCE corrections and Bader charges to main CCE file (RF) -- fixed output printing of CCE (RF) -- fixed CCE for ICSD (RF) -- adding --lib2lib patches for AEL/AGL (CT) -- Added calculation of electronic contributions to the free energy. (AS) -- Added calculation of temperature-dependent phonon dispersions. (AS) -- Implemented QHANP method (frequency-volume dependency is extrapolated by N-order Taylor expansion). (AS) -- Removed old QHA code, related infrastructure and dependencies. (AS) -- Fixed web output for README files and AFLOW banners. (ME) -- Added patch functionality to the AflowDB database. (ME) -- Added xStream to AflowDB. (ME) -- Improved database analysis speed. (ME) -- Added UPDATE command interface to AflowDB. (ME) -- Made title property obsolete. (ME) -- Made search --aflowlib more inclusive. (ME) -- Fixed out of bounds error in init::AFLOW_Projects_Directories for missing LIB directories. (ME) -- Added aurostd::_ishex. (ME) -- Moved POCC progress bar into pflow. (ME) -- Added "Notice" from apl::Logger into pflow::logger. (ME) -- Modularized APL option parsing. (ME) -- Merged more pflow logging capabilities into APL. (ME) -- Consolidated APL classes: ShellHandle and ShellData integrated into Supercell, group velocities moved into PhononCalculator, and harmonic force constant calculations are now handled by a single class. (ME) -- APL code clean-up: removed obsolete code and moved functions into AUROSTD where appropriate. (ME) -- Added 49 new ANRL prototype files for the nitrides and oxides (DX+RF) -- Added 14 new parameter enumerations to existing ANRL labels for nitrides and oxides (DX+RF) -- Updated README_PROTO.TXT with new nitrides and oxides (DX+RF) -- Bug fixes in XtalFinder: precondition structures with BringInCell() for local geometry comparisons (DX) -- Bug fixes in XtalFinder: use more robust matching protocol; accounts for undecorated prototypes (i.e., small volumes) (DX) -- Bug fixes in XtalFinder: use more robust lattice search procedure (slower, but correct) (DX) -- Consolidated symmetry tolerance command-line code into pflow::getSymmetryTolerance() (DX) -- Added input tolerance capabilities to --lattice and --lattice_type (DX) -- Added tolerance spectrum analysis functionality to symmetry routines (--aflowSG) (DX) -- Added option to XtalFinder to ignore the atom decoration comparisons (DX) -- Created generic prototype generator: creates a geometry file regardless of whether it is located in the AFLOW Encyclopedia of Crystallographic Prototypes (DX) -- Added SYMBOLICCPLUSPLUS/ subdirectory to perform symbolic math operations (DX) -- Altered SYMBOLICCPLUSPLUS/ source code to compile with AFLOW and use in multiple files (e.g., moved function definitions from header files into cpp files) (DX) -- Created aflow_symbolic.cpp/.h files, containing functions to manipulate the symbolic math (DX) -- Created DecorateWithFakeElements() to xstructure (DX) -- Moved compare::fakeElements() to pflow::fakeElements() (DX) -- Extended aurostd::getCentroid(); added overload with weights (DX) -- Added aurostd::getCentroidPBC() for periodic systems (DX) -- Added comments to Standard_Lattice_Structure() (DX) -- Added getCentroidPBC() for periodic systems (DX) -- Added xstructure::getElements() and xstructure::GetReducedComposition() (DX) -- Added getCentroidOfStructure() and getCentroidOfStructurePBC() for periodic systems (DX) -- Added sorting functionality for Wyckoff positions (DX) -- Added ANRL prototype keywords (6) to schema (DX) -- Changed LDEBUG in xoptions and argv to VERBOSE (DX) -- Added functionality to minimize mapping distances in XtalFinder (DX) -- cleaning up all getElements() variants (CO+DX) -- adding aurostd_xparser.cpp .h (CO) -- adding enthlapy_formation_cce_300K_cell, enthlapy_formation_cce_300K_atom, enthlapy_formation_cce_0K_cell, and enthlapy_formation_cce_0K_cell to database (CO+RF) -- incorporating CCE into CHULL (CO) -- changed XHOST.vschema for aflowlib_date (CO+ME) -- changing NOTICE color blue to cyan (CO+ME) -- making /www/AFLOWDATA an .aflow.rc parameter (CO+ME) -- adding aurostd::RemoveTrailingCharacter() (CO+ME) -- patching lib2raw index issues: LIB7/LIB did not exist (CO) -- patching lib2raw index issues: string substitution of /core (CO) -- patching --run vs --run=1 bug in AEL/AGL (CO) -- cleaning up PrintMessageStream()/PrintWarningStream()/PrintErrorStream() (CO) -- creating VASP_Get_Kflags_from_AflowIN() and separating from KBIN::RUN_Directory() (CO) -- adding XHOST.ARUN_POSTPROCESS hard stop for VASP_Run() function (--postprocess) (CO) -- adding POCC postprocessing to LIB2LIB (CO) -- reading kflags and vflags options from aflow.in before processing POCC (CO) -- changing LIB2LIB() to run RUN_Directory() instead of individual post-processing functions (CO) -- adding functionality to process LIB6/POCC:OLD calculations (CO) -- adding --pocc_old2new to convert aflow.in of old pocc calculations to one that works for new pocc algorithm (CO) -- patching bug in aurostd::EFileEmpty() - remove file IFF it is a temporary file (CO) -- soft patch for FR+web: cout->cerr in aflowlib::WEB_Aflowlib_Entry() (CO) -- patching pocc_tol :TOL_0.001:0.001 -> :TOL_0.001_0.001 (CO) -- adding overloads to get_date() variants for an input time structure (CO) -- adding lock_date to aflowlib.out via aflowlib_date ([0]=lock_date_start,[1]=lock_date_end,[2]=lib2raw_date) (CO) -- cleaned up PrintMessageStream()/PrintErrorStream()/PrintWarningStream() (CO) -- included nice colors to screen for PrintMessageStream()/PrintErrorStream()/PrintWarningStream() (CO) -- integrated PrintMessageStream()/PrintErrorStream()/PrintWarningStream() with logger() (CO) -- force PrintErrorStream()/PrintWarningStream() to print to cerr for web (CO) -- cleaned up ErrorOption() and integrated with logger() (CO) -- patched StringstreamClean() which introduced junk binary characters before (CO) -- return early for --pocc_count_total command to avoid giving user too much verbosity (CO) -- added MessageOption() (vs. ErrorOption()) that does NOT throw error (CO) -- patching flow of POccCalculator() to read/load from aflow.in ALWAYS and overwrite with inputs (CO) -- created scheme for POCC auids, see POCCdirectory2MetadataAUIDjsonfile (CO) -- prepared LIB2RAW for POCC, including adding perform_POCC and aflowlib::LIB2RAW_Loop_POCC() (CO) -- added aurostd::FileExist() to all linking in LIB2RAW (CO) -- lots of cleaning of LIB2RAW, including adding CleanDirectoryLIB(), removing obsolete VOLDISTPARAMS and VOLDISTEVOLUTION functionality, and cleaning vspecies (CO) -- differentiating Egap_DOS and Egap in POCC (CO) -- removing exits from xOUTCAR which kills VASP auto-fix (CO) -- cleaning up Message() in aflow_init.cpp (CO) -- adding --aruns2skip=XX and [AFLOW_POCC]ARUNS2SKIP=XX for POCC analysis (CO) -- fixing empty ael_*_tensor appearing in aflowlib.out (CO) -- fixed _atom.CleanName() (CO) -- converted all exits to throw (CO+ME+DX) -- removing exits from: aflow.cpp,aflow_aconvasp.cpp,aflow_aconvasp_main.cpp,aflow_aflowrc.cpp,aflow_anrl.cpp,aflow_apennsy.cpp,aflow_apennsy_gndstate.cpp,aflow_apennsy_main.cpp,aflow_apennsy_vaspin.cpp,aflow_contrib_cormac.cpp,aflow_contrib_shidong.cpp,aflow_contrib_shidong_auxiliary.cpp,aflow_contrib_shidong_cluster_expansion.cpp,aflow_contrib_shidong_main.cpp,aflow_contrib_wahyu.cpp,aflow_defects.cpp,aflow_iaims.cpp,aflow_ivasp.cpp,aflow_kaims.cpp,aflow_kbin.cpp,aflow_mix.cpp,aflow_neighbours.cpp,aflow_oaims.cpp,aflow_pflow_funcs.cpp,aflow_pflow_print.cpp,aflow_pocc.cpp,aflow_pocc_ael_agl.cpp,aflow_pocc_old.cpp,aflow_surface.cpp,aflow_test.cpp,aflow_xelement.cpp,aflow_xvaspin.h (CO) -- added --force_outliers to chull (CO) -- added EFA to _aflowlib_entry (CO) -- added entropy_stabilization_coefficient to chull (CO) -- adding null_xv (CO) -- patched xvector for null_xv (CO) -- optimized stability criterion and n+1 enthalpy gain algorithms: shaved minutes off the full analysis for ternaries, even bigger gains for higher N (CO) -- added --n+1_enthalpy_gain and --skip_n_plus_1_enthalpy_gain_analysis for chull (CO) -- adding pocc_agl properties to aflowlib.out (CO) -- some cleaning of PrintData() (CO) -- added pocc_parameters to _aflowlib_entry (CO) -- added anrl parameters to pocc _aflowlib_entry (CO) -- starting to consolidate precisions and tolerances code-wide (CO) -- clearing title in qe input (CO) -- patching "[AFLOW] SYSTEM = " extraction problem (CO) -- adding --gen_ceram generating elemental combinations for --aflow_proto (CO) -- added LIB2RAW_Loop_Static() to --lib2raw (CO) -- converted CCE functions to take structure as read-in only parameter (CO) -- added enthalpy_formation to POCC structures (CO) -- adjusting aflow_max_argv for xplug (CO) -- adding --np functionality to --multi=zip (CO) -- added aurostd::meanWeighted() (CO) -- cleaned up GenerateGridAtoms() (CO) -- rewrote GetNeighbors() and GetCoordinations() function (CO) -- sped up CCE with new GetNeighbors() and GetCoordinations() functions and restructuring structural analysis (CO) (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_database.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_libraries_scrubber.cpp, aflowlib_web_interface.cpp, aflowlib_web_outreach.cpp, aflowrc.cpp, apennsy.cpp, apennsy_gndstate.cpp, apennsy_main.cpp, apennsy_vaspin.cpp, avasp.cpp, bader.cpp, bader.h, cce.cpp, cce_data.cpp, cce.h, chull.cpp, chull.h, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, contrib_cormac.cpp, contrib_shidong_auxiliary.cpp, contrib_shidong_cluster_expansion.cpp, contrib_shidong.cpp, contrib_shidong_main.cpp, contrib_wahyu.cpp, data.cpp, defects.cpp, estructure.cpp, gfa.cpp, iaims.cpp, ifrozsl.cpp, init.cpp, ivasp.cpp, kaims.cpp, kbin.cpp, kvasp.cpp, lattice.cpp, Makefile, Makefile.aflow, makefile.cpp, makefile.h, mix.cpp, modules.cpp, neighbours.cpp, oaims.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, plotter.cpp, pocc.cpp, pocc.h, pocc_old.cpp, pthreads.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_CCE.TXT, README_AFLOW_CHULL.TXT, README_AFLOW_EXCEPTIONS.TXT, README_AFLOW_SYM.TXT, README_PROTO.TXT, surface.cpp, symbolic.cpp, symbolic.h, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, test.cpp, wyckoff.cpp, xatom.cpp, xclasses.cpp, xelement.cpp, xelement.h, xproto.cpp, xproto_gus.cpp, xpseudopotentials.cpp, xvaspin.h) (ANRL: aflow_anrl.cpp, aflow_anrl.h, ANRL_CPPS_20180710/*.cpp, list.cpp, README_AFLOW_ANRL.TXT) (AEL: ael_elasticity.cpp, ael_elasticity.h, ael_get_stress.cpp, pocc_ael_agl.cpp) (AGL: agl_debye.cpp, agl_debye.h, agl_electronic.cpp, agl_get_ev.cpp, pocc_ael_agl.cpp) (APL: aapl_cluster.cpp, aapl_ifcs.cpp, aapl_tcond.cpp, apl_atomic_disp.cpp, apl_doscalc.cpp, apl_fccalc.cpp, apl_function_fitting.cpp, apl_group_velocity.cpp, apl_gsa.cpp, apl.h, apl_hsqpoints.cpp, apl_kphonons.cpp, apl_logger.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_shellhandle.cpp, apl_supercell.cpp, apl_thermalpc.cpp, qha3phonons_eos.cpp, qha_aflowin_creator.cpp, qha.cpp, qha_dm_pdos_save.cpp, qha_energies.cpp, qha_eos.cpp, qha_gruneisen.cpp, qha_operations.cpp, qha_operations.h, README_AFLOW_APL.TXT, scqha_eos.cpp, scqha_gruneisen.cpp, scqha_T_freqs.cpp) (SQLITE: aflow_sqlite.cpp, aflow_sqlite.h) (SYMBOLICCPLUSPLUS: array.cpp, array.h, cloning.cpp, cloning.h, constants.h, derive.cpp, derive.h, equation.cpp, equation.h, functions.cpp, functions.h, identity.cpp, identity.h, integrate.cpp, integrate.h, matnorm.cpp, matnorm.h, matrix.cpp, matrix.h, multinomial.cpp, multinomial.h, number.cpp, number.h, polynomial.cpp, polynomial.h, product.cpp, product.h, quatern.cpp, quatern.h, rational.cpp, rational.h, README_AFLOW_SYMBOLIC.TXT, solve.cpp, solve.h, sum.cpp, sum.h, symbol.cpp, symbol.h, symbolicc++.cpp, symbolicc++.h, symbolic.cpp, symbolic.h, symbolic_main.cpp, symbolic_main.h, symerror.cpp, symerror.h, symmatrix.cpp, symmatrix.h, vecnorm.cpp, vecnorm.h, vector.cpp, vector.h, verylong.cpp, verylong.h) (AUROSTD: argv.cpp, argv.h, aurostd.cpp, aurostd.h, boot.cpp, main.cpp, xcombos.cpp, xcomplex.h, xerror.cpp, xerror.h, xfit.cpp, xfit.h, xmatrix.cpp, xmatrix.h, xoption.cpp, xoption.h, xparser.cpp, xparser.h, xscalar.cpp, xscalar.h, xvector.cpp, xvector.h) 3.2.4b - 2020/07/19 Location: http://materials.duke.edu/AFLOW/aflow.3.2.4b.tar.xz -- Fixed xprototype class for David ANRL symbolic (SC) 3.2.4 - 2020/06/25 Location: http://materials.duke.edu/AFLOW/aflow.3.2.4.tar.xz -- Added latex->dvips->ps2pdf compilation route for pre-2010 texlive versions. (ME) -- Bug fixes to xPOTCAR (exits) (CO+ME) -- Bug fixes to Wyckoff positions (DX) -- Bug fixes for overwriting symmetry output files text/json (DX) -- adding in CHULL workshop unit tests (CO) -- adding exits to CCE unit tests (CO) -- Bug fixes to aurostd::isDirectory() and isFile() (CO) -- Bug fixes for xelement, adding populate() function for CCE (CO) -- Bug fixes in POCC: missing POTCAR suffix for LIB6 and EFileNotEmpty() cerr verbose (CO) -- Bug fixes in KBIN::getVASPVersion() (CO) -- Bug fixes in POCC: extending m_Egap.size() if metal is found among ARUNs (CO) -- Bug fixes in XHOST: adding another way to get XHOST.home, might fail on OSX (CO) (AFLOW: aconvasp_main.cpp, aflow.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, avasp.cpp, chull.cpp, chull_jupyter.json, chull_jupyter_plotter.py, chull_python.py, compare_structure_function.cpp, init.cpp, ivasp.cpp, kvasp.cpp, lattice.cpp, Makefile, Makefile.aflow, makefile.cpp, makefile.h, ovasp.cpp, plotter.cpp, pocc.cpp, README_AFLOW.TXT, symmetry_spacegroup_functions.cpp, symmetry_spacegroup_ITC_library.cpp, xelement.cpp, xelement.h) (AUROSTD: main.cpp) 3.2.3 - 2020/05/22 Location: http://materials.duke.edu/AFLOW/aflow.3.2.3.tar.xz -- Bug fixes in KBIN::ExtractSystemName() (ME) -- Fixed PID/TID and XPID XTID in aflow.h aflow_init.cpp (SC) -- added --np1 (N+1 enthalpy gain) and --sc (stability criterion) chull web functionality (SK) -- added check for broken REST-API to aflow_chull_python.py (MB) -- Fixed segmentation fault when DINEQUIV_ONLY option was used. (AS) -- Added QHA to modules. (AS) -- Fixed xEIGENVAL to work correctly with files created by vasp 5. (AS) -- Introduced a core part of the new QHA class: (AS) -- QHA-related options from aflow.in are parsed into QHA module; (AS) -- QHA options are processed and initialized inside the QHA class; (AS) -- QHA, QHA3P and SCQHA are united into one class; (AS) -- new QHA uses standard aflow infrastructure to create aflow.in files; (AS) -- new functionality: thermal properties can be derived from the temperature dependence of the free energy; (AS) -- added the possibility to calculate Grueneisen parameters using fit to frequency-volume relation. (AS) -- added POCC+AEL+AGL workflow (CT) -- updated and restructured CCE for PBE, LDA and SCAN (RF) -- added CCE functions for command line, web tool, and internal AFLOW use (RF) -- CCE can now determine oxidation numbers automatically from structure and Allen electronegativities (RF) -- added CCE function to determine oxidation numbers from Allen electronegativities (RF) -- added CCE function to get number of neighbors for all atoms (RF) -- added CCE function to get number of neighbors of a certain type for all atoms (RF) -- extended CCE scheme to PBE+U:ICSD functional and approach based on experimental formation enthalpies per bond (RF) -- extended CCE to work for general anion systems (RF) -- extended CCE to multi-anion sytems (RF) -- CCE corrections added for nitrides (RF) -- fixed bug that SPIN was switched OFF in static calc. when SPIN=ON in aflow.in and REMOVE_RELAX was set by default (ME+RF) -- Added check for required binaries to plotter. (ME) -- Canonical system name is now based on aflow.in instead of VASP output files. (ME) -- Fixed broken system name for aflow_proto. (ME) -- Fixed plotter title and file names when ANRL parameters are present. (ME) -- Fixed bug that deleted qmvasp files from previous runs instead of appending to them. (ME) -- Removed VASP k-mesh symmetry fixes when SYM=OFF. (ME) -- Changed database file name conventions. (ME) -- Redesigned mean square displacement calculations. (ME) -- Added interfaces to XCRYSDEN and V_SIM to visualize phonon displacements. (ME) -- Enhanced logger support for APL using xStream. (ME) -- Added state writer and reader for the force constant calculators. (ME) -- Added KPOINTS_GRID, KPOINTS_SHIFT, and RELAX_COMMENSURATE options to APL. (ME) -- NBANDS now scales with supercell size if set in the parent aflow.in (ME) -- Separated harmonic force constants and Born effective charges/dielectric tensor into different hibernate files. (ME) -- APL will now always read harmonic force constants when HIBERNATE=ON. (ME) -- Fixed multiplot bug in plotter. (ME) -- Added feature to plotter that allows setting the output image file name. (ME) -- Made adding directory to plot functions optional. Will take ./ as default. (ME) -- Added phonon plotter functions to APL README. (ME) -- Refactored apl::PhononCalculator into a force constant and phonon calcuator class. (ME) -- Removed apl::APLStageBreak. (ME) -- Replaced apl::Logger with pflow::logger in some classes. (ME). -- Fixed force constant reader for linear response calculations. (ME) -- Fixed signs of second order force constants. (ME) -- Sped up determination of irreducible tetrahedra for the tetrahedron method. (ME) -- Sped up APL force constant matrix calculation. (ME) -- Sped up the calculation of the dynamical matrix. (ME) -- Phonon DOS calculations can now be perfomed over an arbitrary frequency range. (ME) -- Phonon dispersions are now projected to the primitive cell when using DCPATH=LATTICE. (ME) -- Fixed behavior of non-analytical term correction at the Gamma point for phonon dispersions. (ME) -- Fixed calculation of non-analytical term correction for the Wang method. (ME) -- APL now always uses a commensurate k-point grid for relaxations. (ME) -- Fixed bug that did not set k-point mode to implicit for APL runs. (ME) -- Fixed bug for SPIN_REMOVE_RELAX_2 in APL relaxations. (ME) -- Updated KPPRA for phonons. (ME) -- APL now saves the structure for phonon calculations using PHPOSCAR. (ME) -- Refactored supercell generation code in APL. (ME) -- Added standard class methods to all APL and AAPL classes. (ME) -- Removed most reference members and replaced remaining ones with pointers for all APL and AAPL classes. (ME) -- Fixed bug in apl::ClusterSet for conventional unit cells. (ME) -- Moved calculation of little groups from TCONDCalculator to QMesh. (ME) -- Added missing function CalculateSymmetryPointGroupKCrystal. (ME) -- Simplified symmetry calculations in (A)APL. (ME) -- Changed the determination of the irreducible Brillouin zone in APL. (ME) -- Redesigned ThermalPropertiesCalculator to take temperature-dependent DOS. (ME) -- Made ZEROSTATE_CHGCAR obsolete. (ME) -- Changed getVASPVersionString function to not throw errors anymore (broke post-processing). (ME) -- added 67 structure prototypes from Y. Lederer: 58 new ANRL files (generates 60 new protos), 7 generated with existing files with different internal degrees of freedom (DX) -- updated README_PROTO.TXT with new prototypes, unique atom decorations, and supplemental notes (DX) -- clean input structure species (pseudopotentials) in compare::compare2database() (DX) -- updated README_AFLOW_COMPARE.TXT and README_AFLOW_ACONVASP.TXT with "relaxation_step" and "isopointal" comparison functionality (DX) -- added --relaxation_step flag to --compare2database and --compare_database_entries to compare original/relax1/most_relaxed geometry files (DX) -- added ABINIT detector and reader (DX) -- added atom type/element to ABINIT writer (via nuclear charge, i.e., znucl) (DX) -- added ELK detector, reader, and writer (DX) -- added ELK file format to READMEs (DX) -- moved frac2dbl from SYM to AUROSTD, and reformatted in more consistent style to AFLOW (DX) -- speed increase to GenerateGridAtoms(): move LDEBUG outside nested loop (DX) -- speed increase for comparing LFA environments: use angle tolerance of 10 degrees (DX) -- speed increase when checking for better structure matches: use the neighborhood distance information but remove the environment angle check (DX) -- speed increase for loading structures in comparison functions: cut out extra xstructure instantiation (DX) -- fixed Wyckoff position function; now displays more than just the representative position (DX) -- added overloads for running database comparison functions internally: compare2database(), isMatchingStructureInDatabase(), matchingStructuresInDatabase(), printCompare2Database() (DX) -- added FileMESSAGE and logstream to more comparison functions (DX) -- changed namespace of all comparison functions to "compare"; i.e., "pflow" -> "compare" (DX) -- added check for grouping structures based on the number of atoms in XtalMatch, must be integer multiples (DX) -- normalize environment distances when comparing environments in XtalMatch (DX) -- widened tolerances to check more lattices in XtalMatch for volume scaling comparisons only (DX) -- fixed typo in "a" Wyckoff position for space group #55 (DX) -- fixed bug in --poscar2aflowin; symmetry tolerance not propogated for tolerance scan (DX) -- added Patterson symmetry analysis; denoted "pgroupk_Patterson" (applies to reciprocal space only) (DX) -- compare Patterson point symmetry to Laue point group as consistency check (DX) -- added Patterson symmetry to full symmetry command (DX) -- added stand-alone Patterson symmetry command (DX) -- cleaned text/json if-statements in symmetry writing functions (DX) -- added Patterson symmetry usage to README_AFLOW_SYM.TXT and README_AFLOW_ACONVASP.TXT (DX) -- fixed compilation bugs with old GCC/G++ version (V4.3.4 specifically; nullptr vs NULL, assigning struct attributes, and no back() method for strings) (DX) -- added aflow_gcc_compatibility_check to Makefile (DX) -- variable name changes in structure comparison (number_of_atoms -> natoms, number_of_types -> ntypes, structure_from -> structure_source) (DX+CO) -- added error for non-standard prototypes that create structures with atoms too close (CO+DX) -- added note about 3-fold rotations requiring Gamma-centered k-meshes (CO+DX) -- throw error when lattice gives negative determinant (CO) -- fixed --kppra=XX collision with aflow_proto (CO) -- xvasp.POTCAR_TYPE_PRINT_flag==FALSE for lib2 and lib3 even for pocc structures (CO) -- added RHL to auto Gamma-centering kpoints schemes (CO) -- patched aflow.rc for AUTO kpoints generation (CO) -- patched TITEL search issue for PAW_LDA_KIN (CO) -- patched --slab_check warning with det(lattice)<0 (CO) -- added eurl2string(), eurl2stringstream(), eurl2vectorstring(), eurl2dequestring(), eurl2tokens(), eurl2string() (CO) -- added EWithinList() (CO) -- patched getPathAURL() to load from LIB if available (CO) -- patched loadXStructure() to handle compressed POSCARs (CO) -- added more POSCAR variants to loadXStructure() (CO) -- small speed-ups to N+1 calculation in chull (CO) -- changed material.php -> material dir for chull web links (CO) -- added N+1 enthalpy gain to chull pdf doc (CO) -- patched vbadness warnings with longtable in chull (CO) -- patched hull_energy sign (CO) -- added chull_check to Makefile (CO) -- patched --bandgap and --bandgapdos to work with extension-less OUTCAR/DOSCAR (CO) -- patched species-project dos plot issues: lacking species key and emax TOO high (CO) -- added logger objects to plotter functions (CO) -- patched BvolXXXX.dat increment issue (++atomCOUNT) (CO) -- patched --kapth to take default values from .aflow.rc (CO) -- changed default value for kgrid to AUTO (MP vs. Gamma) (CO) -- added secondary wget location for AFLOW3_FREE files for make (CO) -- pflow::matrix()->aurostd::matrix() to fix linking issues on nietzsche (CO) -- restructured xOUTCAR, xDOSCAR, xEIGENVAL, xPOTCAR, xQMVASP for xStream (CO + ME) -- removed error in xOUTCAR looking for irreducible kpoints, this fails for all OUTCAR.bands (CO) -- patched --bandgap function with new xOUTCAR.GetProperties() routine (CO) -- removed xOUTCAR.ERROR, xDOSCAR.ERROR, xAIMSOUT.ERROR (CO) -- unfriended effective mass functions (CO) -- including OUTCAR.bands in WEB, needed for Egap; EIGENVAL.bands does not have occupancies (CO) -- added unit test for Egap, will add to check_full once ICSD LIB2RAW is redone (CO) -- added some messaging/debug-logging to POCC+AEL+AGL workflow (CO) -- added Hmix to aflow.pocc.out (CO) -- ANOTHER patch for warnings with the aflow.rc, write to std::cerr, should fix www-data (CO) -- merging --web_mode with --www (CO) -- added --xplug_check_only() for completed runs (CO) -- patched time_delim in get_date_formatted() (CO) -- speeding up --poscar2aflowin with new AUTO settings (CO) -- adding TID (CO) -- restructured Makefile for auto-generation of dependency tree (CO) (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_database.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_libraries_scrubber.cpp, aflowlib_webapp_bands.js, aflowlib_webapp_entry.js, aflowlib_web_interface.cpp, aflowlib_web_outreach.cpp, aflowrc.cpp, apennsy.cpp, apennsy_gndstate.cpp, apennsy_main.cpp, apennsy_vaspin.cpp, avasp.cpp, bader.cpp, cce.cpp, cce_data.cpp, cce.h, chull.cpp, chull.h, chull_python.py, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, contrib_cormac.cpp, contrib_shidong_auxiliary.cpp, contrib_shidong.cpp, contrib_shidong_main.cpp, contrib_wahyu.cpp, defects.cpp, estructure.cpp, gfa.cpp, iaims.cpp, ialien.cpp, ifrozsl.cpp, init.cpp, ivasp.cpp, kaims.cpp, kalien.cpp, kbin.cpp, kvasp.cpp, lattice.cpp, Makefile, Makefile.aflow, makefile.cpp, makefile.h, matlab.cpp, mix_experiments.cpp, modules.cpp, neighbours.cpp, oaims.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, plotter.cpp, pocc.cpp, pocc.h, pocc_old.cpp, pthreads.cpp, qsub.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_CCE.TXT, README_AFLOW_COMPARE.TXT, README_AFLOW_SYM.TXT, README_PROTO.TXT, SQLITE/sqlite.cpp, surface.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, test.cpp, wyckoff.cpp, xatom.cpp, xclasses.cpp, xelement.cpp, xelement.h, xproto.cpp, xproto_gus.cpp, xproto_gus_lib.cpp, xpseudopotentials.cpp, xvaspin.h) (ANRL: aflow_anrl.cpp, ANRL, ANRL_CPPS_20180710/*.cpp, data.cpp, README_AFLOW_ANRL.TXT) (AEL: ael_elastic_fit.cpp, ael_elasticity.cpp, ael_elasticity.h, ael_get_stress.cpp, pocc_ael_agl.cpp) (AGL: agl_debye.cpp, agl_debye.h, agl_electronic.cpp, agl_eqn_state.cpp, agl_get_ev.cpp, agl_hugoniot.cpp, agl_plot_write.cpp, agl_polynomial.cpp, agl_rungibbs.cpp, agl_thermal.cpp, pocc_ael_agl.cpp) (APL: aapl_cluster.cpp, aapl_ifcs.cpp, aapl_setup.cpp, aapl_tcond.cpp, apl_atomic_disp.cpp, apl_dirphoncalc.cpp, apl_doscalc.cpp, apl_fccalc.cpp, apl_function_fitting.cpp, apl_group_velocity.cpp, apl_gsa.cpp, apl.h, apl_hsqpoints.cpp, apl_kphonons.cpp, apl_logger.cpp, apl_lrphoncalc.cpp, apl_ltet.cpp, apl_pathbuilder.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_shellhandle.cpp, apl_supercell.cpp, apl_thermalpc.cpp, qha3phonons_eos.cpp, qha_aflowin_creator.cpp, qha.cpp, qha_dm_pdos_save.cpp, qha_energies.cpp, qha_eos.cpp, qha_gruneisen.cpp, qha_operations.cpp, README_AFLOW_APL.TXT, scqha_eos.cpp, scqha_gruneisen.cpp, scqha_T_freqs.cpp) (AUROSTD: aurostd.cpp, aurostd.h, boot.cpp, main.cpp, xcombos.cpp, xcombos.h, xcomplex.cpp, xcomplex.h, xerror.cpp, xerror.h, xmatrix.cpp, xmatrix.h, xoption.cpp, xoption.h, xrandom.cpp, xscalar.cpp, xscalar.h, xtensor.cpp, xtensor.h, xvector.cpp, xvector.h) 3.2.2l - 2020/04/02 Location: http://materials.duke.edu/AFLOW/aflow.3.2.2*.tar.xz -- added PID to a bunch of messages 2l (SC) -- bug fixing aflow_avasp.cpp 2l (SC) -- added scrubber test for missing species_pp_AUID aflowlib_libraries_scrubber.cpp 2l (SC) -- added PID to LIB2LIB and LIB2RAW and --showPID 2l (SC) -- added temperature wait for LIB2LIB and fixed to 42C 2k (SC) -- bug fixes for vext,vcat,vzip 2k (SC) -- standardized vext,vcat,vzip from XHOST 2j (SC) -- accelerated lib2raw with moreauid checks 2i (SC) -- more pseudopotentials 2h (SC) -- fixed Mike reported bug in APL, from POTCAR_AUID in aflow_ivasp.cpp 2g (SC) -- test (2f) -- cleaned up vAUIDs vAURLs vLOOPs all now children of vLIBS 2e (SC) -- renaming VASP_Write_ppAUID_FILE and VASP_Write_ppAUID_AFLOWIN 2e (SC) -- adding pseudopotentials references 2d (SC) -- working on SCAN in aflowlib.h added aflowlib_enrty MEGAGGA 2d (SC) -- added some pseudopotentials references, fixed HEX/FCC and RHL into autogamma ivasp 2c (SC) -- removed EnthalpyReference 2b (SC) -- sum up all the previous updates - ready to run now 2a (SC) 3.2.2 - 2020/03/30 Location: http://materials.duke.edu/AFLOW/aflow.3.2.2.tar.xz -- sum up all the previous updates - ready to run now (SC) 3.2.1k - 2020/03/29 Location: http://materials.duke.edu/AFLOW/aflow.3.2.1*.tar.xz -- species_pp_groundstate_energy and species_pp_groundstate_structure 1k (SC) -- VASP_Write_AUID_FILE and VASP_Write_AUID_AUID in ivasp 1j (SC) -- removed vsymbol vname vdate in xPOTCAR, moved vZ into species_Z (unnecessary) -- LIB2RAW_Loop_PATCH in aflowlib* 1j (SC) -- needed RAUG too 1i (SC) -- --pseudopotentials_check for OUTCARS 1i (SC) -- operator << xOUTCAR 1i (SC) -- removed TITEL LEXCH symbol name date Z .... and made them dynamical vectors 1h (SC) -- --pseudopotentials_check --pp_check --ppk in aconvasp_main.cpp 1h (SC) -- unicity of PSEUDOPOTENTIALS nailed in xPOTCAR and xOUTCAR 1g (SC) -- wrapVecEntries and wrapDeqEntries overloads 1g (SC) -- adding pp information in aflolwib entries and AUROSTD 1g (SC) -- dealing with PP collision in aflow.h aflow_ovasp.cpp 1g (SC) -- removed WEB_Aflowlib_Entry_PHP aflowlib_web_interface.cpp 1f (SC) -- added aflowlib_libraries_scrubber.cpp aflow_xpseudopotentials.cpp (SC) -- added much to xPOTCAR (SC) -- AUROSTD deque/vector string2file (SC) -- AUROSTD bool2string file2md5sum (SC) -- modifications in aflow.h aflow_xclasses.cpp and aflow_ivasp.cpp for POTCAR_AUID (SC) 3.2.1c - 2020/03/22 Location: http://materials.duke.edu/AFLOW/aflow.3.2.1c.tar.xz -- fixes for lib2raw and and error checking in uploading calculations (SC) 3.2.1 - 2020/03/17 Location: http://materials.duke.edu/AFLOW/aflow.3.2.1.tar.xz -- Fixes times stamp in bug fixes (SC) -- Updates on pthread.cpp and libraries.cpp for error checking in uploading calculations (SC) 3.2.0 - 2020/02/10 Location: http://materials.duke.edu/AFLOW/aflow.3.2.0.tar.xz -- New release, finally aflow 3.2 (SC) 3.1.228 - 2020/01/20 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.228.tar.xz -- added schema name/unit/type to XHOST (SC) -- added file2dequestring(), string2dequestring() (SC) -- optimized NCPUS/NPAR/NCORE settings (SC) -- patched _atom() class: constructor()/copy()/free() (SC) -- updated xoptions so content can be lowercase (SC) -- added isdefined to xoption (SC) -- AFLOW DFT calculations can now read in CHGCAR files (ME) -- Improved runtimes and memory requirements for AAPL (ME) -- Switched the thermal conductivity integration method to the tetrahedron method (ME) -- Added Grueneisen parameter and phase space calculation to thermal conductivity calculations (ME) -- APL and AAPL can now use the CHGCAR file from the ZEROSTATE calculation to speed up calculations (ME) -- Replaced APLLogicError and APLRuntimeError with aurostd::xerror (ME) -- Fixed bug in APL and AAPL that did not properly process -D option (ME) -- Removed unused source files (ME) -- Added matrix norms to aurostd::xmatrix (ME) -- Fixed KPPRA for APL relaxations to use the standard density (ME) -- Added a handler for the AFLOW database (ME) -- Added an AFLOW-SQLITE interface (ME) -- Updated SQLite to version 3.30.1 (2019-10-11, https://www.sqlite.org/2019/sqlite-amalgamation-3300100.zip) (ME) -- Added additional web output for entry page generation (ME) -- Fixed bug that put NCORE into INCARs of linear response calculations (ME) -- Fixed bug that caused phonon dispersion path builder to break for some lattices (ME) -- Fixed bug in xDOSCAR reader error detection (ME) -- Additional web output for entry page applets (ME) -- Fixed bug that prevented LDA+U parameters from being passed into ARUN aflow.ins (ME) -- Added ael_stiffness_tensor and ael_compliance_tensor to aentry (ME) -- Fixed bug that prevented AGL from running during LIB2LIB (ME) -- added warnings/errors if species information missing in POSCAR for --poscar2aflowin (CO) -- tab aligning all files (CO) -- patched clang warnings for aurostd_boot.cpp (CO) -- patching warning for writing aflow.rc, only issue if it was written, should fix www-data (CO) -- added xQMVASP (CO) -- force signed distance for hull formation enthalpy (CO) -- added --geometry to get abc_angles for any input structure (CO) -- commenting out CreateSlab_RigidRotation(), it does not work, need to redefine lattice vectors (CO) -- patching CreateSlab_SurfaceLattice() lattice vector search to include explicit length/angle constraints (CO) -- patched slab_test with v3len_max_strict (CO) -- added minimumDistance() calculator for non-periodic systems like molecules or grid of atoms (CO) -- patched atoms grid generated for foldAtomsInCell(): GenerateGridAtoms() populates grid_atoms, not atoms (CO) -- added setAutoVolume() to xstructure (CO) -- added getOSS() and getOFStream() to xStream() (CO) -- added GetBandGap() to xDOSCAR: get bandgap from DOS (CO) -- added PrintBandGap_DOS() for command line access to DOS bandgap analysis (CO) -- incorporating equivalent hkl planes analysis (CO) -- patched supercell dimensions reduction for slip system analysis (CO) -- now preserving volume for slip system analysis (CO) -- added --plot_all_atoms option for DOS plotter (CO) -- added functionality for plotting species-projected DOS in plotter (CO) -- added '/' between all path separators in plotter (CO) -- added LDEBUG in plotter (CO) -- patched formatDefaultTitlePOCC() to understand pocc string in plotter (CO) -- added getAflowInFromAFlags() for pocc (CO) -- added --pocc_minimum_configuration identifying which ARUN is minimum energy (CO) -- patched FINAL volume of ordered supercells from pocc, should speed up VASP calculations (CO) -- added postprocessing workflow for pocc: performs postprocessing from input files, does NOT redo structure analysis (CO) -- added self-patch for pocc: patches structures files (all and unique) so individual POSCARs can be read by aflow (CO) -- added reader for structures file (CO) -- pocc writes out PARTCAR (CO) -- pocc calculates/writes out EFA (CO) -- pocc writes out ensemble average DOSCAR (CO) -- pocc writes out supercell probabilities to aflow.pocc.out (CO) -- pocc writes out results of ensemble average band gap to aflow.pocc.out (CO) -- pocc plots ensemble average DOS projected by orbitals and species (CO) -- added KBIN_POCC_TEMPERATURE_STRING (aflow.in) and --temperature (command line) for pocc post-processing (CO) -- avoiding NEGLECT_NOMIX for pocc, high-entropy offers increased solubility over binaries (CO) -- added option for printing ensemble average IDOS in pocc data files (aflow_pocc_old.cpp) (CO) -- added POccStructuresFile class to read post-processing files (CO) -- patched zero-padding for pocc output files (CO) -- add first POCC unit test to Makefile (CO) -- patch distinction between POTCAR_TYPE_DATE_PRINT_flag and POTCAR_TYPE_PRINT_flag in avasp (CO) -- patching xvasp.POTCAR_TYPE_PRINT_flag for LIB2/LIB3 (CO) -- added --potential_type for auto aflow.in generator (CO) -- streamlined xvector constructors and copy() methods (CO) -- added xvector constructor for xmatrix input (CO) -- added getcol(), getmat(), setrow(), setcol(), setmat() to xmatrix, with relevant unit tests called by —test_xmatrix (CO) -- added operator *=(utype r) and operator /=(utype r) to xmatrix (CO) -- added modulus(), modulussquare(), modulus2() to xmatrix (CO) -- getmat() now returns void, xmatrix is an input (CO) -- added lrows_out, lcols_out input getmat() as well as a overload for returning xvector (as input) (CO) -- added xmatrix2xvector() (CO) -- patched QRDecomposition_HouseHolder() not to assume lrows, lcols (CO) -- updated generalHouseHolderQRDecomposition()->QRDecomposition_HouseHolder() (CO) -- added EFileEmpty() and EFileNotEmpty() (CO) -- added _AFLOW_FILE_NAME_ to logger() and xerror(), and patched Makefile for some missing cpp (CO) -- added aurostd::getPWD() (CO) -- added unsigned long long to _isfloat(), _iscomplex(), _isreal(), _size(), _real(), isinteger() (CO) -- added aurostd::powint() for fast powers of integers (CO) -- added all variants of iszero() (CO) -- templated GCD(), patched for positive/negative inputs, and added Bezout coefficients as output (CO) -- adding free(), copy(), refresh() to xmatrix (CO) -- added shiftlrows, shiftlcols, shiftlrowscols to xmatrix (CO) -- added inverse of 2x2 matrix (CO) -- added xmatrixint2double() and xmatrixdouble2int() (CO) -- added right matrix division, traspInPlace(), traspSquareInPlace(), submatrixInPlace(), and getdiag() to xmatrix (CO) -- added getmatInplace() and getvec() to xmatrix (CO) -- patched inverse() for xmatrix, now uses matrix of minors (adjoint) approach which is more stable than GaussJordan (CO) -- converted bool inverse() to bool isNonInvertible() in xmatrix() (CO) -- added smith normal form calculator to xmatrix (CO) -- updated QR decomposition algorithm to avoid saving householder rotations to form Q at the end (CO) -- added xDOSCAR.convertSpinOFF2ON() for easy manipulation between SPIN-OFF/SPIN-ON POCC ARUNS (CO) -- fixed tolerance "WARNING" in symmetry screw axis determination (DX) -- added missing partial occupation value when printing CIF (DX) -- added site occupation to Wyckoff object (DX) -- used _atom copy constructor in symmetry functions instead of by-hand updates (DX) -- fixed indenting in symmetry functions (DX) -- added rescaling of structure in prototyping functionality (DX) -- added functions to extract information from certain Wyckoff positions (DX) -- added functionality to force input Wyckoff choice for structure prototyping (DX) -- added check for duplicate subdirectory in aflow zipping, removes subdirectory if found (DX+CO) -- added flags to get matching AFLOW prototypes and cast into prototype designation (DX) -- added environment analysis (isoconfigurational) to structure comparison (DX) -- fixed multiple thread calls in structure comparison and building prototype structures (DX) -- suppress permutation calculation for AFLOW prototypes in structure comparison (DX) -- replaced exit with throws in structure comparison functions (DX) -- added database comparison functionality (DX) -- added directory information to structure comparison for debugging (DX) -- multithreaded prototype casting in structure comparison (DX) -- use more robust supercell expansion method (lattice dimensions vs 3x3x3) in structure comparison (DX) -- added functionality to check for better matches (necessary for environment and permutation comparisons) (DX) -- store Wyckoff groupings for duplicates and same family structures (DX) -- added preliminary magnetic structure analysis with new functions to add spin to structure (DX) -- added consistency check in permutation comparisons (DX) -- boolean for threading safety check (save time) (DX) -- improved (speed) atom matching functionality in structure comparison (DX) -- speed increase to generateGrid function (DX) -- replace SplitAlloySpecies and compare::GetElements() with stringElements2VectorElements() in comparison functions (DX) -- added functionality to search prototype labels by symmetry without nspecies and stoichiometry (DX) -- added space group to lattice type and centering functions (DX) -- added more methods for extracting lattice parameters for prototyping (wyccar, cif, etc.) (DX) -- store Wyckoff information from CIF reader (DX) -- fixed bug in extracting Wyckoff coordinates (DX) -- allow non-standard space group symbol formats for CIF, check provided equations to verify setting (DX) -- update structure comparison class attribute names (DX) -- allow for mix of ICSD and non-ICSD structures during sorting by ICSD number for structure comparison (DX) -- created generalized function for adding magnetic information to structure (DX) -- fixed non-collinear spin lattice primitivization function (DX) -- fixed typos in README_PROTO.TXT: A2B_oP12_26_abc_ab-001 to A2B_oP12_26_abc_ab-002 and AB_oC8_67_a_g-001 to AB_oC8_67_a_g-002 (DX) -- check if tolerance input is negative for BringInCell() (DX) -- added AtomEnvironment class in aflow_xatom.cpp (DX) -- generalized inCell() and added atomInCell() (DX) -- added aurostd::GCD(), aurostd::LCM(), and aurostd::reduceByGCD(), for vector and deque (DX) -- added FileMESSAGE and logstream overloads for comparison functions (DX) -- added lattice deviation, coordinate displacement, and figure of failure (structure misfit) to the JSON output for structure comparison (DX) -- added try-catch for pflow::loadXstructure() in case URL times out or a bad structure file input (DX) -- refined magnetic misfit criteria (DX) -- added JSON output for structure prototyping (DX) -- fixed parameters for prototype=A_tI2_139_a; fct convention vs bct convention (DX) -- added unit tests in makefile for aflowSG, aflowSYM, and aflow-xtal-match (DX) -- put xstructure initialization in free() and call free() at beginning of constructors (otherwise xstructure is not always initialize) (DX) -- changed xstructure::Clear() to xstructure::clear() (DX) -- changed xstructure::Clean() to xstructure::clean() (DX) -- updated README_AFLOW_COMPARE.TXT (DX) -- use xoptions schema for property units in comparison code (DX) -- use ANRL setting as default for symmetry analysis in comparisons for quick conversion to AFLOW prototype designation (DX) -- use of xoptions throughout comparison functions (DX) (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_database.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, aflowrc.cpp, apennsy_gndstate.cpp, apennsy_main.cpp, avasp.cpp, bader.cpp, cce.cpp, chull.cpp, chull.h, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, contrib_shidong_auxiliary.cpp, gfa.cpp, iaims.cpp, init.cpp, ivasp.cpp, kbin.cpp, kvasp.cpp, lattice.cpp, Makefile, modules.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, plotter.cpp, pocc.cpp, pocc.h, pocc_old.cpp, pocc_old.h, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_COMPARE.TXT, README_AFLOW_EXCEPTIONS.TXT, README_AFLOW.TXT, README_PROTO.TXT, SQLITE/shell.c, SQLITE/sqlite3.c, SQLITE/sqlite3ext.h, SQLITE/sqlite3.h, SQLITE/sqlite.cpp, SQLITE/sqlite.h, surface.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, xatom.cpp, xclasses.cpp, xelement.cpp, xproto.cpp, xproto_gus.cpp) (ANRL: aflow_anrl.cpp, ANRL_CPPS_20180710/list.cpp) (APL: aapl_cluster.cpp, aapl_ifcs.cpp, aapl_setup.cpp, aapl_tcond.cpp, apl_atomic_disp.cpp, apl_dirphoncalc.cpp, apl_dm_pdos_save.cpp, apl_doscalc.cpp, apl_group_velocity.cpp, apl.h, apl_hsqpoints.cpp, apl_kphonons.cpp, apl_lrphoncalc.cpp, apl_ltet.cpp, apl_pathbuilder.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_shellhandle.cpp, apl_supercell.cpp, apl_thermalpc.cpp, qha3phonons_eos.cpp, qha_aflowin_creator.cpp, qha_dm_pdos_save.cpp, qha_energies.cpp, qha_eoscalc.cpp, qha_eos.cpp, qha_eosrun.cpp, qha_gruneisen.cpp, qha_operations.cpp, README_AFLOW_APL.TXT, scqha_eos.cpp, scqha_gruneisen.cpp, scqha_T_freqs.cpp) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xcombos.cpp, xcombos.h, xcomplex.cpp, xcomplex.h, xerror.cpp, xerror.h, xmatrix.cpp, xmatrix.h, xoption.cpp, xoption.h, xscalar.cpp, xscalar.h, xtensor.cpp, xvector.cpp, xvector.h) 3.1.227 - 2019/10/16 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.227.tar.xz -- Bug fixes for MPI (SC) -- Verbosity fixes (Message("")) (SC) 3.1.226 - 2019/10/01 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.226.tar.xz -- Modification on the allocation of web entries, through web cache of AUID. Speed up of 20-200 times in serving aflowlib entry pages (SC) -- Bug fixes in producing html/json for icsd# entries (SC) -- Modified aflow.in generation in AEL and AGL to use common routines in aflow_avasp.cpp and aflow_modules.cpp (CT) -- Write AGL enthalpy as a function of pressure in an AFLOW readable format for future phase diagram application (CT) -- Added --quiet option to LIB2LIB routine (CT) -- Sets the VASP symmetry to off by default for AEL calculations (CT) -- Added projected phonon DOS calculations (ME) -- Linear tetrahedron method does not reduce upon construction anymore (necessary for projected DOS) (ME) -- Cleaned up code and added more comments to QMesh and LTMethod files (ME) -- Made moveToBZ inside QMesh more robust (ME) -- Replaced all instances of exit in APL with throw APLRuntimeError (ME) -- Sped up reduction of q-mesh grid (ME) -- Added safeguards for DOSCAR readers for broken DOSCAR files (ME) -- Fixed plotter bugs for HTQC prototype names (ME) -- Added findInList function to AUROSTD (ME) -- Generalized BringInCell method (ME+DX) -- created overloads for BringInCell method (double/xvector/_atom/xstructure), along with "InPlace" variants, i.e., const input (DX) -- replaced all mod_one/mod_one_xvec/mod_one_atom for new BringInCell method (DX) -- replaced old BringInCell functions with new version (DX) -- fixed indenting in symmetry functions (DX) -- replaced all SYM::CrossPro() with aurostd::vector_product() (DX) -- replaced all SYM::normalize() with explicity division of aurostd::modulus() (DX) -- replaced SYM::extract_row() with aurostd::operator() (DX) -- fabs() -> aurostd::abs() (CO) -- changed abinit writer lattice from column-based to row-based (CO) -- updated some class definitions (free()/copy()) (CO) (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib.h, aflowlib_libraries.cpp, aflowlib_webapp_entry.js, aflowlib_web_interface.cpp, aflowrc.cpp, apennsy_gndstate.cpp, apennsy_main.cpp, apennsy_vaspin.cpp, avasp.cpp, chull.cpp, compare_structure_function.cpp, compare_structure.h, contrib_cormac.cpp, contrib_wahyu.cpp, data.cpp, init.cpp, Makefile, modules.cpp, oaims.cpp, ovasp.cpp, pflow_funcs.cpp, pflow_print.cpp, plotter.cpp, pocc.cpp, pocc.h, pocc_old.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_SYM.TXT, spacegroup.cpp, surface.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, xatom.cpp, xclasses.cpp, xproto.cpp) (AEL: ael_elastic_fit.cpp, ael_elasticity.cpp, ael_elasticity.h, ael_get_stress.cpp) (AGL: agl_debye.cpp, agl_debye.h, agl_electronic.cpp, agl_eqn_state.cpp, agl_get_ev.cpp, agl_hugoniot.cpp, agl_polynomial.cpp, agl_rungibbs.cpp, agl_thermal.cpp) (APL: apl_atomic_disp.cpp, apl_dm_pdos_save.cpp, apl_doscalc.cpp, apl_function_fitting.cpp, apl_group_velocity.cpp, apl.h, apl_hsqpoints.cpp, apl_kphonons.cpp, apl_ltet.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_shellhandle.cpp, apl_supercell.cpp, qha3phonons_eos.cpp, qha_dm_pdos_save.cpp, qha_energies.cpp, qha_eoscalc.cpp, qha_gruneisen.cpp, qha_operations.cpp, README_AFLOW_APL.TXT, scqha_eos.cpp, scqha_gruneisen.cpp) (AUROSTD: aurostd.h, main.cpp, xmatrix.cpp, xmatrix.h) 3.1.225 - 2019/07/26 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.225.tar.xz -- fixing bug with stability criterion calculation in --output=web, need structure comparison for correct stability criterion calculation (WS) -- changed output name for --output=web to aflow_ALLOY_hull_web.json (WS) -- integrated N+1_enthalpy_gain and stability criterion to --output=web (WS) -- patched web json for quaternary chull (WS) -- added CCE functionality (RF) -- added CCE readme (RF) -- added a user input cutoff energy to the GFA code (DF) -- Added vector version of RemoveComments (ME) -- RemoveControlCharactersFromStringstream now also removes carriage returns because they break string additions (ME) -- SPIN_REMOVE_RELAX_2 did not remove spin after the second relaxation; this is fixed now (ME) -- Removed bug that prevented certain NBANDS errors from being fixed while an NBANDS warning was present in vasp.out (ME) -- APL and AAPL now read forces from qmvasp file (ME) -- AAPL_KPPRA added to aflow_modules (ME) -- Minor APL code clean-ups (ME) -- Added new plotter functions for band structures, phonons, and thermal properties (ME) -- Updated numbering scheme for partial DOS from being zero-based to being one-based (ME) -- Changed xDOSCAR, xEIGENVAL, and xKPOINTS to be compatible with new plotter (ME) -- Added functionality to APL that outputs phonon DOS and dispersion in -- VASP format for new plotter functions (ME) -- Fixed bug for the path builder for path with - and | as separators (ME) -- Fixed xDOSCAR reader to be more general (ME) -- patched change_tolerance() bug for double& tolerance return (DX) -- renamed minimum distance functions, more descriptive (minimizeDistanceCartesianMethod() and minimizeDistanceFractionalMethod()) (DX) -- reduced number of inputs for minimum distance functions (DX) -- added functionality to read VASP5 format in CHGCAR (DX) -- cleaned species/atom names in xstructure2json; remove pseudopotential information, oxidation numbers, etc. (DX) -- added boolean to ignore minimum distance check in foldAtomsInCell() (DX) -- added overloads for mapping functions (DX) -- fixed bug in in xstructure2json in LIB2RAW runs; store corresponding structure from relaxations (DX) -- read species for xstructure2json in LIB2RAW runs (DX) -- added default permutation designation to ANRL prototypes for --proto and --aflow_proto, e.g., ".AB" for "AB_cF8_225_a_b.AB" (DX) -- added functionality to read "_symmetry_space_group_name_H-M" in CIF reader (DX) -- added GetSpaceGroupNumber() to get the space group number from the Hermann-Mauguin symbol (DX) -- added RemoveCharacterFromBack(), RemoveCharacterFromFront(), and RemoveCharacterFromBackandFront() to AUROSTD; useful for parsing CIF fields (DX) -- added function to compare Wyckoff position strings regardless of order, necessary for matching equations in CIF to ITC standard (DX) -- fixed bug in reading symops from CIF; check for symop_id (DX) -- fixed bug in "_space_group_name_Hall" reader in CIF (DX) -- converted exits to xerrors in GetSpaceGroup*() functions (DX) -- added DEFAULT_GFA_FORMATION_ENTHALPY_CUTOFF to aflow.rc (CO) -- added functions to find pointLineIntersection() and linePlaneIntersection() (CO) -- added function to find 3D rotation between two 3D vectors (CO) -- remapped const utype& tol -> utype tol in function inputs (CO) -- remapped const bool& -> bool in function inputs (CO) -- added check in generalHouseHolderQRDecomposition() that Q*R=A (CO) -- changed gcd() to GCD() (CO) -- added least common multiple function LCM() (CO) -- added --slab_test (CO) -- added setctau/setftau functions to _sym_op (CO) -- added ReplaceAtoms() to xstructure to safely RemoveAtom() then AddAtom() (CO) -- modified foldAtomsInCell() to remove fold_in_only complexity, this was simplified by GenerateGridAtoms() (CO) -- added check to foldAtomsInCell() that min_dist does not change (CO) -- added CreateSlab_RigidRotation(), CreateSlab_SurfaceLattice(), and associated functions (many overloads) to create slabs for surface calculations: the two functions should yield about the same structure but by two different methods (CO) -- reformulate basis in CreateSlab_RigidRotation() so k-points grid is created appropriately (K1xK2x1) (CO) -- added new modules for calculating the generalized stacking fault energy and cleavage energy (CO) -- patched bug in CHULL pdf output for missing column-types in compiling aflow_CsIPb_hull.tex (CO) -- added cout as default for ostream& oss in header files (CO) -- converted Normal2HKLPlane (CO) -- reduce total layers creation by calculating how many layers are in a cell for that particular direction (CO) -- added XHOST.WEB_MODE to reduce cluttered AFLOW-Online output (CO) -- removed pocc progress bar in web_mode (CO) -- added FPOSDistance() for skew considerations (CO) -- reduced dims considered for GetSuperCell(), RadiusSphereLattice and LatticeDimensionSphere() are enough (CO) -- added general getPeaks() function to AUROSTD (CO) -- calculated X-ray amplitude on-the-fly, no need to pass it around (CO) -- moved double lambda to end of inputs and default to 1.5418 Copper K-alpha (CO) -- patched RemoveControlCodeCharactersFromString() for carriage return (CO) -- added width_maximum to getPeaks() to resolve arbitrarily defined peaks (CO) -- made x-ray analysis code more modular (CO) -- added --plot_xray_file option (CO) -- patched moving_average function (!= convolution with box_filter) (CO) -- defaulted lambda=Cu_Ka for XRD functions (CO) -- added compareVecElements(), compareXVecElements(), and class compareVecElement(ind) to sort vector > and vector > and retire classes ids_cmp and hkl_cmp (CO) -- changed signal -> signal_input so it does not get confused with std::signal (CO) -- added --force_generic_title to PLOT_XRAY (CO) -- removed ids_cmp and hkl_cmp classes (CO) -- added filetype and vector_reduction_type enums (CO) -- patched aflags.Directory() early in kbin::KBIN_Main() (CO) -- corrected GetCompoundAttenuationLenght -> GetCompoundAttenuationLength and toogle -> toggle (CO) -- extended PARTCAR functionality for VASP5 POSCARs, including the optional Selective Dynamics tag (CO) -- patched 'make check' to return an error, instead of a string, if encountered (CO) -- patched 'S' -> 'P' conversion in --pocc_params (CO) -- incorporated some new warnings from VASP6 (CO) -- patched stringElements2VectorElements() to handle two types of compound designation: composition_string and pp_string (CO) -- added new suffixes to pseudopotential list (CO) -- address capital letters in new pp suffixes directly (CO) -- added faster (in place) routines for CleanStringASCII(), RemoveNumbers(), VASP_PseudoPotential_CleanName() (CO) -- added AFLOWIN_FLAG::NOAUTOPP (--noautopp) functionality to --aflow_proto (CO) -- converted flag PFLOW::LOAD_ENTRIES_ONLY_ALPHABETICAL to PFLOW::LOAD_ENTRIES_NON_ALPHABETICAL so the default is always OFF (CO) -- added 'make clean_autogen' to delete files that are automatically downloaded/generated by aflow during compilation (CO) -- set explicit double->int conversion for roundDouble() in chull (CO) (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, aflowrc.cpp, avasp.cpp, cce.cpp, cce.h, chull.cpp, chull.h, compare_structure_function.cpp, contrib_shidong_main.cpp, data.cpp, gfa.cpp, gfa.h, init.cpp, ivasp.cpp, kbin.cpp, kvasp.cpp, Makefile, mix.cpp, modules.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, plotter.cpp, pocc.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_CCE.TXT, README_AFLOW_GFA.TXT, surface.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, xatom.cpp, xclasses.cpp, xelement.cpp, xelement.h, xproto.cpp) (AGL: agl_electronic.cpp) (APL: aapl_cluster.cpp, aapl_tcond.cpp, apl_dirphoncalc.cpp, apl_doscalc.cpp, apl.h, apl_kphonons.cpp, apl_lrphoncalc.cpp, apl_pathbuilder.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_supercell.cpp, apl_thermalpc.cpp, README_AFLOW_APL.TXT) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xmatrix.cpp, xmatrix.h, xscalar.cpp, xscalar.h, xvector.cpp, xvector.h) 3.1.224 - 2019/05/20 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.224.tar.xz -- Fixed bug that didn't allow users to override the standard lattice phonon dispersion path (ME) -- Replaced anharmonic IFC option struct with xoption (ME) -- Simplified APL class structure: IReciprocalPointGrid, MonkhorstPackMesh, and UniformMesh are consolidated into QMesh. IDOSCalculator, DOSCalculator, RootSamplingMethod, and LinearTetrahedronMethod are now described only by the DOSCalculator and LTMethod classes (ME) -- Fixed QHA file name bugs for phonon dispersion and DOS (ME) -- Fixed bug that caused AAPL to read APL calculations even though AAPL calculations are still missing (ME) -- Fixed seg fault bug when DC=OFF and TP=ON (ME) -- Fixed bug where DOS parameters are not properly set when DOS=OFF and TP=ON (ME) -- Added KPPRA option for AAPL (ME) -- Increased number of iterations for the AAPL BTE solver (ME) -- fixed symmetry bug: if AddAtom() removes too many atoms and alters stoichiometry, then change to better tolerance (DX) -- fixed comparison bug: ordering of stoichiometry for material-type comparisons (DX) -- changed name of prototyping flag (DX) -- added --structure2json command line functionality (DX) -- cleaned/reduced comparison command line calls (DX) -- added to comparison code: JSON output, print to screen only, keep non-matching info, store comparison logs, store family properties, and speed up comparison grouping function (DX) -- removed atomic library for communicating between threads, obsolete (DX) -- removed unused line in SYM::PBC() function (DX) -- added types information in CIF reader, otherwise aflowSG fails (DX) -- alphabetize elements in CIF reader function (DX) -- fixed --machine names (DX) -- fixed removal of control code characters in aflow.in; only overwrites if invalid chars are detected and saves old version to aflow.in_old (DX) -- changed internal indexing of xvectors in CHULL/GFA code from 0 to 1 to match rest of code (CO) -- fixed bug in web-json writer for AFLOW-CHULL Online (CO) -- added function for defining 3D rotation matrix between two vectors (CO) -- added functions to convert xvector to xvector and vice versa, useful for hkl (CO) -- added functionality for generalized stacking fault calculation, alpha testing only (CO) -- added functions for HKLPlane -> direct normal vector and vice versa (CO) -- added function to find distance between HKL planes (CO) -- added function to get distance between images of atoms along particular direction (CO) -- for many sym functions, removed pointers for read-only bools and doubles, added const where possible (CO) -- updated xstructure::Rotate() (CO) -- in xclasses, stringstream.clear() -> stringstream.str("") (CO) -- removed '#' from sg specification in POSCAR, it is interpreted as comment and removed (CO) -- bug fix with AFLOWDATA path in automatic aflow.in generator (CO) -- added force_strict_pc2scMap to GetSuperCell() constraining the map to the true primitive cell and not equivalent atoms (CO) -- added general function to fix string for latex output (CO) -- added XHOST.vflag_control.flag("DIRECTORY_CLEAN") for accurate logging of current directory (CO) -- major restructuring of pocc code, consolidating classes, renaming variables, etc. (CO) -- fixed old pocc to run with any compression extension (CO) -- eliminating atom.print_RHT (CO) -- patches for xStream() (CO) -- fixed webapp_entry for displaying first bader charge isosurface online with help from Bob Hanson (CO) -- added convolution function for signal processing (CO) -- added moving average and box/gaussian filters (CO) -- added mean/stddev functions to xvector (CO) -- added plotter for XRD (CO) -- added analysis for peaks with moving average (CO) (AFLOW: aconvasp_main.cpp, aflow.cpp, aflow.h, aflowlib_libraries.cpp, aflowlib_webapp_entry.js, aflowrc.cpp, avasp.cpp, chull.cpp, chull.h, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, gfa.cpp, init.cpp, kbin.cpp, kvasp.cpp, lattice.cpp, Makefile, modules.cpp, pflow_funcs.cpp, pflow.h, pflow_print.cpp, pocc.cpp, pocc.h, pocc_old.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, symmetry.cpp, symmetry_spacegroup.cpp, xatom.cpp, xclasses.cpp, xproto.cpp) (ANRL: aflow_anrl.cpp, A10B2C_hP39_171_5c_c_a.cpp, A10B2C_hP39_172_5c_c_a.cpp, A10B3_oF52_42_2abce_ab.cpp, A12B2C_cF60_196_h_bc_a.cpp, A12B36CD12_cF488_196_2h_6h_ac_fgh.cpp, A12B36CD12_cF488_210_h_3h_a_fg.cpp, A12B6C_cF608_210_4h_2h_e.cpp, A12B7C2_hP21_174_2j2k_ajk_cf.cpp, A12BC4_cP34_195_2j_ab_2e.cpp, A12B_cF52_225_i_a.cpp, A12B_cI26_204_g_a.cpp, A12B_tI26_139_fij_a.cpp, A13B2C2_oP34_32_a6c_c_c.cpp, A14B3C5_tP44_94_c3g_ad_bg.cpp, A15B4_cI76_220_ae_c.cpp, A17B15_cP64_207_acfk_eij.cpp, A17BC4D_tP184_89_17p_p_4p_io.cpp, A23B6_cF116_225_bd2f_e.cpp, A24BC_cF104_209_j_a_b.cpp, A2B11_cP39_200_f_aghij.cpp, A2B13C4_hP57_168_d_c6d_2d.cpp, A2B2C4D_tP18_132_e_i_o_d.cpp, A2B2C7_cF88_227_c_d_af.cpp, A2B2C_oC80_64_efg_efg_df.cpp, A2B3C12D3_cI160_230_a_c_h_d.cpp, A2B3C18D6_hP58_192_c_f_lm_l.cpp, A2B3C3DE7_hP48_145_2a_3a_3a_a_7a.cpp, A2B3C6_cP264_205_2d_ab2c2d_6d.cpp, A2B3C6_cP33_221_cd_ag_fh.cpp, A2B3C7D_oP13_47_t_aq_eqrs_h.cpp, A2B3_hP20_159_bc_2c.cpp, A2B3_hP30_169_2a_3a.cpp, A2B3_hP30_170_2a_3a.cpp, A2B3_hP5_164_d_ad.cpp, A2B3_hR10_167_c_e.cpp, A2B3_hR5_166_c_ac.cpp, A2B3_oC40_39_2d_2c2d.cpp, A2B3_oP20_60_d_cd.cpp, A2B3_oP20_62_2c_3c.cpp, A2B3_oP40_33_4a_6a.cpp, A2B3_tI80_141_ceh_3h.cpp, A2B3_tP10_127_g_ah.cpp, A2B3_tP20_102_2c_b2c.cpp, A2B3_tP20_116_bci_fj.cpp, A2B3_tP20_117_i_adgh.cpp, A2B3_tP40_137_cdf_3g.cpp, A2B3_tP5_115_g_ag.cpp, A2B4C_hR42_148_2f_4f_f.cpp, A2B4C_oC28_66_l_kl_a.cpp, A2B4C_oP28_62_ac_2cd_c.cpp, A2B5C2_oC36_37_d_c2d_d.cpp, A2B5_mC28_15_f_e2f.cpp, A2B6CD7_tP64_77_2d_6d_d_ab6d.cpp, A2B7C2_tP88_78_4a_14a_4a.cpp, A2B7_cI54_229_e_afh.cpp, A2B8C2D_tP26_100_c_abcd_c_a.cpp, A2B8CD_oP24_48_k_2m_d_b.cpp, A2B8CD_tI24_97_d_k_a_b.cpp, A2B8C_oP22_34_c_4c_a.cpp, A2B_aP6_2_2i_i.cpp, A2B_aP6_2_aei_i.cpp, A2BC2_oF40_22_fi_ad_gh.cpp, A2BC2_oI20_45_c_b_c.cpp, A2BC2_tI20_79_c_2a_c.cpp, A2BC2_tP20_105_f_ac_2e.cpp, A2BC3_oC24_63_e_c_cg.cpp, A2BC4_cF56_227_d_a_e.cpp, A2BC4D_tI16_121_d_a_i_b.cpp, A2BC4_oP28_50_ij_ac_ijm.cpp, A2BC4_tI14_82_bc_a_g.cpp, A2BC4_tP28_126_cd_e_k.cpp, A2BC4_tP28_130_f_c_g.cpp, A2BC7D2_tP24_113_e_a_cef_e.cpp, A2BC8_tI176_110_2b_b_8b.cpp, A2BCD3E6_cF208_203_e_c_d_f_g.cpp, A2BCD4_tI16_82_ac_b_d_g.cpp, A2B_cF24_227_c_a.cpp, A2B_cF24_227_d_a.cpp, A2B_cI72_211_hi_i.cpp, A2BC_oC16_67_ag_b_g.cpp, A2BC_oC8_38_e_a_b.cpp, A2B_cP12_212_c_a.cpp, A2B_cP6_224_b_a.cpp, A2BC_tP16_76_2a_a_a.cpp, A2B_hP12_194_cg_f.cpp, A2B_hP18_180_fi_bd.cpp, A2B_hP18_190_gh_bf.cpp, A2B_hP36_177_j2lm_n.cpp, A2B_hP6_191_h_e.cpp, A2B_hP9_147_g_ad.cpp, A2B_hP9_150_ef_bd.cpp, A2B_hP9_152_c_a.cpp, A2B_hP9_180_j_c.cpp, A2B_hP9_181_j_c.cpp, A2B_hP9_189_fg_bc.cpp, A2B_hR18_148_2f_f.cpp, A2B_mC144_9_24a_12a.cpp, A2B_mC48_15_ae3f_2f.cpp, A2B_mP12_13_2g_ef.cpp, A2B_mP12_14_2e_e.cpp, A2B_mP12_3_bc3e_2e.cpp, A2B_mP12_7_4a_2a.cpp, A2B_mP18_7_6a_3a.cpp, A2B_mP6_10_mn_bg.cpp, A2B_mP6_14_e_a.cpp, A2B_oC12_36_2a_a.cpp, A2B_oC12_38_de_ab.cpp, A2B_oC12_63_2c_c.cpp, A2B_oC24_20_abc_c.cpp, A2B_oC24_64_2f_f.cpp, A2B_oF24_70_e_a.cpp, A2B_oI12_72_j_a.cpp, A2B_oI12_74_h_e.cpp, A2B_oP12_17_abe_e.cpp, A2B_oP12_19_2a_a.cpp, A2B_oP12_26_abc_ab.cpp, A2B_oP12_29_2a_a.cpp, A2B_oP12_62_2c_c.cpp, A2B_oP24_52_2e_cd.cpp, A2B_oP24_55_2g2h_gh.cpp, A2B_oP24_61_2c_c.cpp, A2B_oP6_58_g_a.cpp, A2B_tI12_140_h_a.cpp, A2B_tI12_141_e_a.cpp, A2B_tI12_98_f_a.cpp, A2B_tI24_141_2e_e.cpp, A2B_tI6_139_d_a.cpp, A2B_tP12_111_2n_adf.cpp, A2B_tP12_92_b_a.cpp, A2B_tP24_135_gh_h.cpp, A2B_tP30_85_ab2g_cg.cpp, A2B_tP36_96_3b_ab.cpp, A2B_tP48_77_8d_4d.cpp, A2B_tP6_129_ac_c.cpp, A2B_tP6_136_f_a.cpp, A2B_tP6_137_d_a.cpp, A3B10_cI52_229_e_fh.cpp, A3B11C6_tP40_100_ac_bc2d_cd.cpp, A3B13_oC32_38_ac_a2bcdef.cpp, A3B2_cI40_220_d_c.cpp, A3B2_hP10_176_h_bc.cpp, A3B2_hP10_176_h_bd.cpp, A3B2_hP5_164_ad_d.cpp, A3B2_hR5_155_e_c.cpp, A3B2_oP20_52_de_cd.cpp, A3B2_oP20_56_ce_e.cpp, A3B2_oP20_62_3c_2c.cpp, A3B2_tP10_83_adk_j.cpp, A3B3C_cI56_214_g_h_a.cpp, A3B3C_hP14_176_h_h_c.cpp, A3B3C_hP14_176_h_h_d.cpp, A3B4C_cP16_218_c_e_a.cpp, A3B4C_cP8_215_d_e_a.cpp, A3B4_cF56_227_ad_e.cpp, A3B4_tI28_141_ad_h.cpp, A3B5_oC16_65_ah_bej.cpp, A3B5_oC32_38_abce_abcdf.cpp, A3B5_oP16_55_ch_agh.cpp, 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ABC4_oP12_16_ag_cd_2u.cpp, ABC4_tI96_142_e_ab_2g.cpp, ABC4_tP12_125_a_b_m.cpp, ABC6D2_mC40_15_e_e_3f_f.cpp, ABC_cF12_216_b_c_a.cpp, ABC_cP12_198_a_a_a.cpp, ABCD3_oI48_73_d_e_e_ef.cpp, ABCD_cF16_216_c_d_b_a.cpp, ABCD_oP16_57_d_c_d_d.cpp, ABCD_tP8_129_c_b_a_c.cpp, AB_cF16_227_a_b.cpp, AB_cF8_216_c_a.cpp, AB_cF8_225_a_b.cpp, ABC_hP12_174_cj_fk_aj.cpp, ABC_hP3_183_a_a_a.cpp, ABC_hP3_187_a_d_f.cpp, ABC_hP36_175_jk_jk_jk.cpp, ABC_hP6_194_c_d_a.cpp, ABC_hR3_160_a_a_a.cpp, ABC_hR6_166_c_c_c.cpp, AB_cI16_199_a_a.cpp, ABC_oI12_71_h_j_g.cpp, ABC_oI36_46_ac_bc_3b.cpp, ABC_oP12_29_a_a_a.cpp, ABC_oP6_59_a_a_a.cpp, ABC_oP6_59_a_b_a.cpp, AB_cP16_205_c_c.cpp, AB_cP2_221_b_a.cpp, AB_cP6_221_c_d.cpp, AB_cP8_198_a_a.cpp, ABC_tI12_109_a_a_a.cpp, ABC_tP24_91_d_d_d.cpp, ABC_tP24_95_d_d_d.cpp, ABC_tP6_129_c_a_c.cpp, AB_hP12_156_2ab3c_2ab3c.cpp, AB_hP12_186_a2b_a2b.cpp, AB_hP12_194_af_bf.cpp, AB_hP12_194_df_ce.cpp, AB_hP2_187_d_a.cpp, AB_hP24_190_i_afh.cpp, AB_hP4_156_ab_ab.cpp, AB_hP4_156_ac_ac.cpp, AB_hP4_186_b_a.cpp, AB_hP4_186_b_b.cpp, AB_hP4_194_c_a.cpp, AB_hP4_194_c_d.cpp, AB_hP6_144_a_a.cpp, AB_hP6_154_a_b.cpp, AB_hP6_183_c_ab.cpp, AB_hP6_191_f_ad.cpp, AB_hP8_186_ab_ab.cpp, AB_hP8_194_ad_f.cpp, AB_hR10_160_5a_5a.cpp, AB_hR16_148_cf_cf.cpp, AB_hR2_166_a_b.cpp, AB_hR26_148_b2f_a2f.cpp, AB_hR6_160_3a_3a.cpp, AB_hR6_160_b_b.cpp, AB_mC8_15_c_e.cpp, AB_mP4_11_e_e.cpp, AB_mP4_6_2b_2a.cpp, AB_mP6_10_en_am.cpp, AB_oC8_36_a_a.cpp, AB_oC8_63_c_c.cpp, AB_oC8_65_j_g.cpp, AB_oC8_67_a_g.cpp, AB_oF8_22_a_c.cpp, AB_oF8_42_a_a.cpp, AB_oF8_69_a_b.cpp, AB_oI4_44_a_b.cpp, AB_oP16_61_c_c.cpp, AB_oP2_25_b_a.cpp, AB_oP4_51_e_f.cpp, AB_oP4_59_a_b.cpp, AB_oP48_61_3c_3c.cpp, AB_oP8_33_a_a.cpp, AB_oP8_57_d_d.cpp, AB_oP8_62_c_c.cpp, AB_tI16_140_ab_h.cpp, AB_tI16_141_e_e.cpp, AB_tI4_107_a_a.cpp, AB_tI4_119_c_a.cpp, AB_tI8_109_a_a.cpp, AB_tI8_139_e_e.cpp, AB_tI8_141_a_b.cpp, AB_tP16_84_cej_k.cpp, AB_tP2_123_a_d.cpp, AB_tP4_129_a_c.cpp, AB_tP4_129_c_c.cpp, AB_tP4_131_c_e.cpp, AB_tP8_111_n_n.cpp, AB_tP8_136_g_f.cpp, A_cF136_227_aeg.cpp, A_cF240_202_h2i.cpp, A_cF4_225_a.cpp, A_cF8_227_a.cpp, A_cI16_206_c.cpp, A_cI16_220_c.cpp, A_cI2_229_a.cpp, A_cI58_217_ac2g.cpp, A_cP1_221_a.cpp, A_cP20_213_cd.cpp, A_cP240_205_10d.cpp, A_cP46_223_dik.cpp, A_cP8_198_2a.cpp, A_cP8_205_c.cpp, A_hP1_191_a.cpp, A_hP2_194_c.cpp, A_hP3_152_a.cpp, A_hP4_186_ab.cpp, A_hP4_194_ac.cpp, A_hP4_194_bc.cpp, A_hP4_194_f.cpp, A_hP6_178_a.cpp, A_hP6_194_h.cpp, A_hP9_154_bc.cpp, A_hR105_166_bc9h4i.cpp, A_hR1_166_a.cpp, A_hR12_166_2h.cpp, A_hR2_166_c.cpp, A_hR3_166_ac.cpp, A_mC12_5_3c.cpp, A_mC16_12_4i.cpp, A_mC24_15_2e2f.cpp, A_mC34_12_ah3i2j.cpp, A_mC4_12_i.cpp, A_mP16_11_8e.cpp, A_mP32_14_8e.cpp, A_mP4_4_2a.cpp, A_mP64_14_16e.cpp, A_mP8_10_2m2n.cpp, A_mP84_13_21g.cpp, A_oC4_63_c.cpp, A_oC8_64_f.cpp, A_oF128_70_4h.cpp, A_oF8_70_a.cpp, A_oP16_55_2g2h.cpp, A_oP8_62_2c.cpp, A_tI16_142_f.cpp, A_tI2_139_a.cpp, A_tI4_139_e.cpp, A_tI4_141_a.cpp, A_tI8_139_h.cpp, A_tP12_138_bi.cpp, A_tP12_96_ab.cpp, A_tP16_138_j.cpp, A_tP30_136_bf2ij.cpp, A_tP4_129_ac.cpp, A_tP4_136_f.cpp, A_tP50_134_b2m2n.cpp, sigma_tP30_136_bf2ij.cpp) (APL: aapl_ifcs.cpp, aapl_setup.cpp, aapl_tcond.cpp, apl_atomic_disp.cpp, apl_dirphoncalc.cpp, apl_doscalc.cpp, apl_group_velocity.cpp, apl.h, apl_kphonons.cpp, apl_lrphoncalc.cpp, apl_ltet.cpp, apl_pathbuilder.cpp, apl_phoncalc.cpp, apl_qmesh.cpp, apl_supercell.cpp, apl_thermalpc.cpp, qha_energies.cpp, qha_eoscalc.cpp, qha_gruneisen.cpp, README_AFLOW_APL.TXT, scqha_gruneisen.cpp, scqha_T_freqs.cpp) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xmatrix.cpp, xmatrix.h, xscalar.cpp, xscalar.h, xvector.cpp, xvector.h) Deleted files: APL/apl_mpmesh.cpp, APL/apl_uniform_mesh.cpp, APL/apl_ltetdos.cpp, APL/apl_rsmdos.cpp 3.1.223 - 2019/04/18 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.223.tar.xz -- fixed logics for filename extended characters (SC) -- created compliance in aurostd for extended characters and added aurostd::LinkFile (SC) -- aurostd::RenameFile => aurostd::file2file (SC) -- aurostd::MoveFile => aurostd::file2directory (SC) -- --use_tmpfs=XXXXX (for rerouting /tmp directories, useful for [il]logical mapping) (SC) (AFLOW: aflowlib_libraries.cpp aflow_ivasp.cpp aurostd.h aurostd_main.cpp) 3.1.222 - 2019/04/01 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.222.tar.xz -- added GFA code+README (DF) -- added Cygwin support (ME) -- fixed bugs in the phonon property plotter (ME) -- added defaults/options for DoD MUSTANG machine (--machine=dod_mustang); also added in aflowrc (DX) -- remove pseudopotential information for comparing materials (DX) -- fixed comparison bugs (e.g., duplicate count, load from URL, printing properties, BrinInCell() for supercell expansion, etc.) (DX) -- fixed --aflow_proto bug when generating POCC structures with ANRL parameters (DX) -- patched GetDistMatrix() header declaration (CO) -- patched x-ray analysis for POSCARs with no atom names (CO) -- silenced cematrix::InverseMatrix (CO) -- minor patches for clang (CO) -- patched fancy print (colors) for POCC AFLOW-Online web mode (CO) -- added --scrub=LIBS for lib2raw (SC) -- added ProgressBar(std::ostream& oss,string prelim,uint j,uint jmax,bool VERBOSE_PERCENTAGE,bool VERBOSE_ROLLER,bool VERBOSE_CURSOR) in aurostd* (AFLOW: aconvasp.cpp, aconvasp_main.cpp, aflow.cpp, aflow.h, aflowrc.cpp, avasp.cpp, bader.cpp, compare_structure.cpp, compare_structure_function.cpp, data.cpp, gfa.cpp, gfa.h, init.cpp, ivasp.cpp, kbin.cpp, kvasp.cpp, Makefile, pflow_funcs.cpp, pflow.h, pflow_print.cpp, pocc.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_GFA.TXT, README_AFLOW.TXT, README_CONTRIBS.TXT, symmetry_spacegroup_ITC_library.cpp, xclasses.cpp) (AUROSTD: aurostd.h, boot.cpp, xmatrix.cpp) 3.1.221 - 2019/03/20 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.221.tar.xz -- changed the compiler for Mac OS to clang++ as g++ does not find the standard libraries on some systems (ME) -- fixed bug in VASP_Produce_POTCAR for POTCAR paths (ME) -- APL now switches RELAX to off with --generate_aflowin_only. Also does not check for the vasp binary anymore if POLAR is ON, which would break the code if no vasp binary is present (ME) -- fixed ANRL setting for symmetry cell choice (DX) -- added fast supercell function for quick expansion (DX) -- speed increase for compare functions (DX) -- fixed tolerance scan issue introduced in V3.1.220 after removing global symmetry variables (DX) -- added missing directory string in GetSpaceGroupLabel() function (DX) -- fixed primitive reduction corner case; should use PBC() instead of BringInCell() for distance vectors (DX) -- added ANRL directory name for --aflow_proto: check if ANRL proto matches to entry in library and return ANRL suffix, otherwise add parameter values to directory name (DX) -- added FileMESSAGE argument to compare functions (DX) -- patched species re-decoration for parent structure, volumes should be consistent across different decorations (CO) -- sort unique structures by HNF matrix/site configuration indices so order is always fixed (CO) -- removed file writing for command-line POCC commands, speeds up AFLOW-Online (CO) -- propagate flags into POCC structures for command-line control (CO) -- fixed AFLOW_CHULL_JUPYTER subdirectory creation (CO) (AFLOW: aconvasp_main.cpp, aflow.h, aflowlib_libraries.cpp, avasp.cpp, chull.cpp, chull.h, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, ivasp.cpp, Makefile, pflow.h, pocc.cpp, pocc.h, symmetry_spacegroup.cpp, xatom.cpp, xclasses.cpp) (ANRL: aflow_anrl.cpp, list.cpp) (APL: apl_kphonons.cpp) 3.1.220 - 2019/03/11 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.220.tar.xz -- added jupyter|jupyter2|jupyter3 functionality to chull (MB) -- added functionality to generate prototypes in CIF format (--cif flag); for --proto and --aflow_proto (DX) -- added functionality to generate prototypes in ABCCAR format (--abccar flag); for --proto and --aflow_proto (DX) -- added original crystal keywords to aflowlib entry (volume_cell_orig, volume_atom_orig, density_orig, crystal_family_orig, crystal_system_orig, point_group_Hermann_Mauguin_orig, point_group_Schoenflies_orig, point_group_orbifold_orig, point_group_type_orig, point_group_order_orig, point_group_structure_orig, Bravais_lattice_lattice_type_orig, Bravais_lattice_lattice_system_orig, Bravais_superlattice_lattice_type_orig, Bravais_superlattice_lattice_variation_type_orig, Bravais_superlattice_lattice_system_orig, Pearson_symbol_superlattice_orig, reciprocal_geometry_orig, reciprocal_volume_cell_orig, reciprocal_lattice_type_orig, reciprocal_lattice_variation_type_orig, Wyckoff_letters_orig, Wyckoff_multiplicities_orig, Wyckoff_site_symmetries_orig) (DX) -- fixed type for point_group_order in JSON; should be int, not string (DX) -- added character check when loading aflow.in, to prevent null bytes (DX) -- added function to remove null bytes in aflow.in file; rewrites cleaned aflow.in (DX) -- added defaults/options for DoD ONYX, GORDON, COPPER, GAFFNEY, and KOEHR machines (--machine=dod_onyx,dod_gordon,dod_copper,dod_gaffney,dod_koehr); also added in aflowrc (DX) -- added ANRL space group setting option; monoclinic: unique axis-b, rhombohedral: rhombohedral setting, centrosymmetric: origin centered on inversion (DX) -- added functionality to convert a structure into an ANRL designation, i.e., label, parameter list, and parameter values (DX) -- added ANRL keywords to aflowlib entry (anrl_label_orig, anrl_parameter_list_orig, anrl_parameter_values_orig, anrl_label_relax, anrl_parameter_list_relax, anrl_parameter_values_relax) (DX) -- added functions to get the Wyckoff equations for future symbolic notation (DX) -- added ANRL preset values for prototypes in getANRLParameters() (DX) -- added ANRL prototypes to README_PROTO.TXT along with unique permutation information (DX) -- updated headers for each AFLOW prototype in README_LIBRARY_HTQC.TXT to include the stoichometry, Pearson symbol, space group, and Wyckoff letters (DX) -- added functionality to search AFLOW prototypes (--proto_labels) via stoichiometry, space group, arity, etc. (DX) -- added AFLUX command line functionality (DX+FR) -- added AFLUX helper functions to run inside AFLOW and extract properties into vectors of properties (DX) -- added functionality to --wyccar, print letters/multiplicities/site symmetries as a string (DX) -- added function to perform symmetry on vector of xstructures (DX) -- added function to get enantiomophs of space group, if any exist (DX) -- added function to return list of particular element classes, e.g., alkali, transition metals, metals, non-metals, etc. (DX) -- added function to convert compound name into a stoichiometry (DX) -- updated comparison code; added new functionality to compare compounds to AFLOW database, compare compounds to AFLOW prototypes, identify unique permutations, etc. (DX) -- added options to ignore symmetry during structure comparison (DX) -- improved comparison code output, i.e., more information and cleaner (DX) -- improved multithreading of comparison code (DX) -- refactor symmetry code to remove extern variables, otherwise it breaks multithreaded symmetry analyses (DX) -- refactor symmetry code to remove global variable _SYM_TOL_, otherwise it breaks multithreaded symmetry analyses (DX) -- fixed lattice transformation in GetLatticeType(); account for unit cell orientation change using GetPrimitive() (DX) -- fixed bug in CIF writer; set VASP version booleans to false (DX) -- updated "make check" hash since Wyckoff letters are now in title line; changed from #174c76b2b2928dcdf2f3b39069a8b59 to #ffb9c5681045fb80f391e9a931f21d1 (DX) -- fixed typo in AEL/AGL json functions (CT) -- fixed zerostate for AAPL (ME) -- small bug fixes for AAPL and APL (ME) -- made changes to write(A)APL functions (ME) -- added keywords to aflowlib.out/json: title, ldau_type, ldau_l, ldau_u, ldau_j, kpoints_relax, kpoints_static, kpoints_bands_path, kpoints_bands_nkpts (ME) -- fixed type declaration bug in aurostd::StringStreamSubst (ME) -- fixed bug in QHA with uninitialized Booleans (ME) -- accelerated reading of forces from vasprun.xml files for APL and AAPL (ME) -- AFLOW not produces POSCAR in the format required by the VASP binary instead of just taking the format in the aflow.in file (ME) -- added functionality to read CHGCAR and WAVECAR files between relaxations (ME + Rico Friedrich) -- removed duplicate APL functions - apl_hroutines.cpp is now obsolete (ME) -- auto-sort by inequivalent atoms in APL (CO + Xiaoyu Wang from UBuffalo) -- added sortAtomsEquivalent() to pre-APL/POCC and CONVERT-sprim, -sconv, -niggli, -minkowski for prospective APL calculations: better to sort before relaxations and not have to sort again in the future (CO) -- patched sortAtoms*() to include basis and ensure relative order (CO) -- added switches for symmetrization of distortions (DISTORTION_SYMMETRIZE) and considering iatoms only (DISTORTION_INEQUIVONLY) in APL (CO) -- populate forceConstants matrix in iatoms-sorted-agnostic fashion as we move away from this dependence (CO) -- clear pgroupk and pgroupk_xtal symmetries before re-calculating -- bug in APL (CO) -- patching pc2scpMap in GetSuperCell() (CO) -- removed exit's from balanceChemicalEquations(), now throwing exceptions (CO) -- overloaded StringsAlphabetic (CO) -- set up Makefile with auto-alerts to AFLOW-Forum (CO) -- added ClearSymmetry() for _atom (CO) -- patched robust structure comparison in POCC (CO) -- patched --hnf/--hnfcell routines to work with new POCC (AFLOW-Online) and added --pocc_count_total and --pocc_count_unique (CO) -- pre-sort sites for --proto with POCC (CO) -- added 'S'+'P' combo functionality to --proto with POCC (CO) -- patching robust structure comparison analysis within POCC (CO) -- added counts to chull txt and json outputs (CO) -- patched logo+count centering on chull doc (CO) -- removed dependency of chull .tex on tabu, which breaks in TeX Live 2019 (CO) -- fixed image alignment in chull pdf doc (CO) -- added options for --aflow_proto, including --run_relax, --run_relax_static, --run_relax_static_bands, --run_static, --run_static_bands, --relax_count (CO) (AFLOW: aconvasp_main.cpp, aflow.h, aflowlib.h, aflowlib_libraries.cpp, aflowlib_webapp_bands.js, aflowlib_web_interface.cpp, aflowrc.cpp, avasp.cpp, bader.cpp, chull.cpp, chull.h, chull_jupyter.json, chull_jupyter_plotter.py, chull_jupyter_requirements.txt, chull_python.py, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h, init.cpp, ivasp.cpp, kaims.cpp, kalien.cpp, kbin.cpp, kvasp.cpp, lattice.cpp, Makefile, matlab.cpp, modules.cpp, ovasp.cpp, pflow_funcs.cpp, pflow.h, pocc.cpp, pocc.h, pocc_old.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_CHULL.TXT, README_AFLOW_COMPARE.TXT, README_AFLOW.TXT, README_LIBRARY_HTQC_BORIDES.TXT, README_LIBRARY_HTQC_CARBIDES.TXT, README_LIBRARY_HTQC.TXT, README_PROTO.TXT, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, xatom.cpp, xclasses.cpp, xproto.cpp, xproto_gus.cpp) (ANRL: aflow_anrl.cpp, list.cpp, README_AFLOW_ANRL.TXT) (APL: aapl_cluster.cpp, aapl_ifcs.cpp, aapl_setup.cpp, aapl_tcond.cpp, apl_dirphoncalc.cpp, apl.h, apl_kphonons.cpp, apl_lrphoncalc.cpp, apl_pathbuilder.cpp, apl_phoncalc.cpp, apl_shellhandle.cpp, apl_supercell.cpp, README_AFLOW_APL.TXT) (AUROSTD: aurostd.h, main.cpp) 3.1.219 - 2019/01/20 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.219.tar.xz -- small modifications for --aflow_proto (--generate_aflowin_only) that enable aflow.in generation on any mac (CO) -- fixed JSON output chull (CO) (AFLOW: aconvasp_main.cpp, avasp.cpp, chull.cpp, Makefile) 3.1.218 - 2019/01/14 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.218.tar.xz -- added defaults/options for CMU EULER machine (--machine=cmu_euler); also added in aflowrc (DX) -- modified AEL/AGL aflow.in keys (CT) -- aurostd::xoption: fixed bug in addattachedscheme, added additional Boolean functionality in options2entry (ME) -- Added debug options to AAPL (ME) -- Improved APL and AAPL defaults (ME) -- Integrated APL and AAPL into the standardized aflow.in creator for VASP calculations (ME) -- Updated the APL README (ME) -- Fixed bugs for APL and AAPL output file names (ME) -- Updated the PREC=PHONONS INCAR parameters (ME) -- Added RELAX feature to APL: structures can now be relaxed specifically for phonon calculations inside the APL environment (ME) -- Added features to handle NCPUS=MAX (ME) -- *NEW* automatic aflow.in generator for APL/AAPL/POCC (beta) (CO+ME) -- integrated POCC into the standardized aflow.in creator for VASP calculations (ME) -- added pocc params and tol to --proto (CO) -- added aflags to APL so sym analysis works with -D (CO) -- added SYMMETRIZE=OFF option for APL distortions (CO) -- added --aflow_proto options: --bader, --spin_remove_relax_1 _2, --kscheme _static, --kppra _static, --relax_count=XX, --run_relax_static, --run_relax_static_bands (CO) -- patched PrototypeLibrariesSpeciesNumber() to handle ANY ICSD (CO) -- added -001 for select ANRL prototypes (CO) -- added pseudopotential information to --aflow_proto directory + system name (CO) -- fixed m_initialized in chull/pocc (CO) -- added chull plotting functionality: if unstable, figure out how far above hull to plot automatically (CO) -- modified plot axes titles in chull (CO) -- added more fixes for "Reciprocal lattice and k-lattice belong to different class of lattices", off until further testing (CO) -- moved pocc settings to aflow.rc (CO) -- now write out all derivative structures, unique derivative structures, hnf matrices, and site configurations in pocc (CO) -- fixed pocc partial occupancy optimizer table settings (CO) -- added AEL/AGL settings to aflow.in generator (CO) (AFLOW: aconvasp_main.cpp, aflow.h, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, aflowrc.cpp, avasp.cpp, chull.cpp, contrib_shidong.cpp, ifrozsl.cpp, init.cpp, ivasp.cpp, kaims.cpp, kbin.cpp, kvasp.cpp, Makefile, modules.cpp, neighbours.cpp, pflow.h, pocc.cpp, pocc.h, pocc_old.cpp, pthreads.cpp, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, symmetry.cpp, xatom.cpp, xclasses.cpp, xproto.cpp) (ANRL: aflow_anrl.cpp) (AEL: ael_elasticity.cpp, README_AFLOW_AEL.TXT) (AGL: agl_debye.cpp, README_AFLOW_AGL.TXT) (APL: aapl_setup.cpp, aapl_tcond.cpp, apl_dirphoncalc.cpp, apl_doscalc.cpp, apl.h, apl_hsqpoints.cpp, apl_kphonons.cpp, apl_lrphoncalc.cpp, apl_pdisc.cpp, apl_phoncalc.cpp, apl_supercell.cpp, apl_thermalpc.cpp, qha_aflowin_creator.cpp, qha_eosrun.cpp, README_AFLOW_APL.TXT) (AUROSTD: aurostd.h, boot.cpp, main.cpp, xerror.cpp, xoption.cpp) 3.1.217 - 2018/12/13 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.217.tar.xz -- Added LIB2LIB function to automatically perform AEL and AGL post processing when running LIB2RAW (CT) -- Updated LIB2RAW and webpage generation functions to incorporate additional AEL and AGL properties (CT) -- Added conversion of pressure extracted from OUTCAR file from kB to GPa in AEL and AGL to keep units consistent (CT) -- added species scaling to volume for ANRL prototypes, if --params=-1.0,... (DX) -- added ANRL prototype for the kesterite structure (DX) -- improved CIF reader, i.e., account for different formats and partial occupation (DX) -- fixed bug in kpath determination (primitive vs original lattice) (DX) (AFLOW: aconvasp_main.cpp, anrl.cpp, xatom.cpp, AFLOW_README_PROTO.TXT, aflow.h, aconvasp_main.cpp, ael_elastic_fit.cpp, ael_elasticity.cpp, agl_debye.cpp, agl_electronic.cpp, init.cpp, xclasses.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, Makefile, README_PROTO.TXT) (ANRL: aflow_anrl_A2BCD4_tI16_82_ac_b_d_g.cpp, aflow_anrl_list.cpp) 3.1.216 - 2018/12/05 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.216.tar.xz -- fixed std in AAPL (ME) -- added seven SQS structures to ANRL prototypes (DX) -- Write Gibbs free energy as a function of pressure and temperature in AFLOW readable format for future phase diagram application (CT) -- Add option to suppress extrapolation in Hugoniot relation calculation (CT) -- Functions to extract electronic properties as a function of pressure from AGL data (CT) -- Calculate and write additional elastic properties from AEL (Young's modulus, Pugh's modulus ratio) (CT) -- Flattened JSON structure used for writing and storing elastic stiffness and compliance tensors (CT) -- fixed anisotropy spelling (CO) -- added ISMEAR/SIGMA VASP option (CO) -- rerouted GetAtomVolume() and GetAtomMass() for properly cleaning pp (CO) -- added N+1 analysis to chull (CO) -- removed _pc from QH_ENERGIES() class (CO) (AUROSTD: AUROSTD/aurostd.h, main.cpp, xcombos.cpp, xcombos.h) (ANRL: aflow_anrl_A3B13_oC32_38_ac_a2bcdef.cpp, aflow_anrl_A3B5_oC32_38_abce_abcdf.cpp, aflow_anrl_A5B11_mP16_6_2abc_2a3b3c.cpp, aflow_anrl_AB3_mC32_8_4a_12a.cpp, aflow_anrl_AB3_mC32_8_4a_4a4b.cpp, aflow_anrl_AB7_hR16_166_c_c2h.cpp, aflow_anrl_AB_aP16_2_4i_4i.cpp, aflow_anrl_list.cpp) (AFLOW: ael_elastic_fit.cpp, ael_elasticity.cpp, ael_elasticity.h, agl_debye.cpp, agl_debye.h, agl_electronic.cpp, agl_hugoniot.cpp, anrl.cpp, avasp.cpp, chull.cpp, chull.h, aflow.cpp, aflow.h, ivasp.cpp, kaims.cpp, kvasp.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, pocc.cpp, pocc.h, xatom.cpp, xclasses.cpp, xproto.cpp, xproto_gus.cpp, APL/aapl_cluster.cpp, APL/aapl_ifcs.cpp, APL/aapl_tcond.cpp, APL/apl.h, APL/apl_kphonons.cpp, APL/qha_energies.cpp, Makefile, README_AFLOW_AEL.TXT, README_AFLOW_AGL.TXT, README_AFLOW.TXT, README_CONTRIBS.TXT) 3.1.215 - 2018/12/04 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.215.tar.xz -- added machinery for vaiud (auid bytes for the AUID directory cached) (SC) aflowlib.h aflowlib_libraries.cpp aflowlib_web_interface.cpp aflow.h aflow_aflowrc.cpp aflow_init.cpp 3.1.214 - 2018/11/30 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.214.tar.xz -- added auid.out and auid.json to RAW/WEB (SC) 3.1.213 - 2018/11/27 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.213.tar.xz -- added LIB0 (a bunch of h and cpp) (SC) 3.1.212 - 2018/11/12 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.212.tar.xz -- in --bzd command, added option to transform high-symmetry kpaths to input lattice representation with [--transform2original] (DX) -- in --bzd command, added option to print transformation matrices between input lattice and AFLOW standard lattice [--print_transformation_matrix] (DX) -- store both the coordinate system and unit cell (rigid rotation) transformations in xstructure (DX) -- created _kpoints class; easier to transform and print kpoint information (DX) (AFLOW: aflow.h, aconvasp_main.cpp, lattice.cpp, pflow.h, xatom.cpp, README_AFLOW_ACONVASP.TXT) 3.1.211 - 2018/10/19 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.211.tar.xz -- added Pearson coefficient to element properties (ME) -- fixed some constants in xscalar (ME) -- Rewrote AAPL to be faster, require less DFT calculations, and include four-phonon processes (ME) -- Added more functionality to xvector and xmatrix for complex numbers (ME) -- Added ability to update progress bar using percentages instead of indices (ME) -- Redesigned xtensor to be more lightweight and faster (ME) -- Fixed bug in aurostd::xcombos::reset() (ME) -- Fixed minor typos (ME) -- Edited APL readme for grammar and clarity, and added new AAPL features (ME) -- Added APL and AAPL parameters to the aflow.rc (ME) -- Reformatted exception readme to be more consistent with other readmes and fixed typos (ME) -- updated get_datetime_formatted() and StringsAlphabetic() (CO) -- new chull date format avoids time stamp, too much resolution (CO) -- added png output option for chull and resolution option to aflowrc (CO) -- switched to tight tol spacegroups (vsg2) in chull (CO) -- centralized checking sign of distances in chull, then flipped sign of distance to hull to be positive by default (CO) -- funneled all points of facet through addVertex() (CO) -- fixed facet content tolerance scaling with increasing dimensionality, important for 6D hulls (CO) -- added default initializations to a bunch of variables in chull to avoid spurious warnings (CO) -- added polymorph case to decomposition phases and coefficients (CO) -- allow for eq_g_states to be calculated on the fly if not already calculated (CO) -- intelligently avoid printing unknown (or unset) stability criterion (CO) -- fixed unsorted directories in aflow_compare_structure (CO) -- now check for negative coefficients when balancing chemical equations, means we missed the facet (CO) -- correctBadDatabase() now checks for unaries too (as per apennsy) (CO) -- skipping ".old" prototypes (CO) -- fixed shidong warnings with strncat (CO) (AUROSTD: boot.cpp, AUROSTD/aurostd.h, main.cpp, xcombos.cpp, xcombos.h, xcomplex.cpp, xcomplex.h, xmatrix.cpp, xmatrix.h, xtensor.cpp, xtensor.h, xvector.cpp, xvector.h) (AFLOW: aconvasp_main.cpp, aflowrc.cpp, chull.cpp, chull.h, compare_structure.cpp, contrib_shidong_auxiliary.cpp, aflowlib_web_interface.cpp, pflow_funcs.cpp, APL/aapl_cluster.cpp, APL/aapl_ifcs.cpp, APL/aapl_setup.cpp, APL/aapl_tcond.cpp, APL/apl_atomic_disp.cpp, APL/apl_dirphoncalc.cpp, APL/apl_dm_pdos_save.cpp, APL/apl_doscalc.cpp, APL/apl_group_velocity.cpp, APL/apl_gsa.cpp, APL/apl.h, APL/apl_hsqpoints.cpp, APL/apl_kphonons.cpp, APL/apl_logger.cpp, APL/apl_lrphoncalc.cpp, APL/apl_pdisc.cpp, APL/apl_phoncalc.cpp, APL/apl_supercell.cpp, APL/apl_thermalpc.cpp, APL/qha3phonons_eos.cpp, APL/qha_aflowin_creator.cpp, APL/qha_dm_pdos_save.cpp, APL/qha_eosrun.cpp, APL/qha_gruneisen.cpp, APL/scqha_gruneisen.cpp, APL/scqha_T_freqs.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_APL.TXT, README_AFLOW_CHULL.TXT, README_AFLOW_EXCEPTIONS.TXT) 3.1.210 - 2018/10/01 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.210.tar.xz -- changed 8 ANRL prototype labels (part 2) to match with Wyckoff positions in reference literature (DX) -- fixed prototype names for A4BC4D_tP10_123_gh_a_i_d and AB_hP6_144_a_a in aflow_anrl_list.cpp (DX) -- added Strukturbericht designations to aflow_anrl_list.cpp (DX) -- fixed minimum enumerated Wyckoff letter determination; more robust (DX) -- cleaned workflow for Wyckoff functions (DX) -- added more debugging messages to symmetry functions (DX) (AFLOW: ANRL/aflow_anrl_list.cpp ANRL/aflow_anrl_A12B36CD12_cF488_210_h_3h_a_fg.cpp ANRL/aflow_anrl_A3B3C_hP14_176_h_h_c.cpp ANRL/aflow_anrl_A3B_hP8_176_h_c.cpp ANRL/aflow_anrl_AB3C_cP60_201_be_fh_g.cpp ANRL/aflow_anrl_A3B2_hP10_176_h_bc.cpp ANRL/aflow_anrl_A3BC_hP10_188_k_c_a.cpp ANRL/aflow_anrl_AB3C16_cF160_203_a_bc_eg.cpp ANRL/aflow_anrl_AB_hP4_156_ab_ab.cpp Makefile anrl.cpp symmetry_spacegroup.cpp symmetry_spacegroup.h symmetry_spacegroup_functions.cpp) 3.1.209 - 2018/08/31 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.209.tar.xz -- added all origin choice 2 possibilities to ITC space group list (DX) -- added all rhombohedral setting possibilities to ITC space group list (DX) -- added monoclinic unique axis choices (b or c) to ITC space group list (DX) -- added SYM::findRhombohedralSetting() in space group functions to distinguish between hexagonal and rhombohedral settings (DX) -- added other settings for Hall space group symbol (settings 1 or 2, H or R for rhombohedral, and unique axis-b or -c for monoclinic systems) (DX) -- added CIF reader; can read/expand CIFs with only representative Wyckoff position specified in settings 1 or 2 (H or R for rhombohedral systems and unique axis-b or -c for monoclinic systems) (DX) -- improved CIF writer; default functionality calculates the symmetry and prints the representative Wyckoff positions (DX) -- added symmetry tolerance option to CIF writer via --cif[=] (default: tight; other options: loose, ) (DX) -- added space group setting option to CIF writer via [--setting=1| =2] (default: 1) (DX) -- added [--no_symmetry] option to CIF writer, which returns CIF as space group 1 (DX) -- added space group setting option to --wyccar via [--setting=1| =2] (default: 1) (DX) -- added space group setting option to --sgdata and --edata via [--setting=1| =2] (default: 1) (DX) -- added [--no_scan] and [--magmom] options to --wyccar and moved function to pflow::WYCCAR() (DX) -- added more debugging messages to space group functions (ConventionalCell(), SpaceGroup_ITC(), etc.) (DX) -- changed ANRL prototype A6B2C_tP18_128_eh_d_b to A6B2C_tP18_128_eh_d_a (b vs a Wyckoff letter); consistent with reference (DX) -- fixed bug in minimumDistanceVector(); should return xvector not double (DX) (AFLOW: ANRL/aflow_anrl_list.cpp, ANRL/aflow_anrl_A6B2C_tP18_128_eh_d_a.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_SYM.TXT, aflow.h, aconvasp_main.cpp, anrl.cpp, pflow.h , pflow_print.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup.h, symmetry_spacegroup_ITC_library.cpp, symmetry_spacegroup_functions.cpp, xatom.cpp) 3.1.208 - 2018/08/27 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.208.tar.xz -- new small banner style in chull (CO) -- perform thermo loop with static run in aflowlib_libraries (CO) -- added xoption to edata and sgdata functions; stores all data (DX) -- added more keywords to aflowlib entry (crystal_family, crystal_system, point_group_Hermann_Mauguin, point_group_Schoenflies, point_group_orbifold, point_group_type, point_group_order, point_group_structure, Bravais_lattice_lattice_type, Bravais_lattice_lattice_system, Bravais_superlattice_lattice_type, Bravais_superlattice_lattice_variation_type, Bravais_superlattice_lattice_system, Pearson_symbol_superlattice, reciprocal_geometry, reciprocal_volume_cell, reciprocal_lattice_type, reciprocal_lattice_variation_type, Wyckoff_letters, Wyckoff_multiplicities, Wyckoff_site_symmetries) (DX) -- new aflowlib keywords extracted from xoption and integrated into aflowlib.out/.json (DX) -- prepared website function to read in new keywords once database is populated; currently commented out (DX) -- fixed typo in sgdata; Shoenflies is now Schoenflies (DX) -- added functions to create Wyckoff strings in aflowlib entry; ExtractWyckoffLettersString(), ExtractWyckoffMultiplicitiesString(), and ExtractWyckoffSiteSymmetriesString() (DX) (AUROSTD: xoption.cpp) (AFLOW: aconvasp_main.cpp, aflowrc.cpp, pflow.h, pflow_print.cpp, symmetry_spacegroup.h, symmetry_spacegroup_functions.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp) 3.1.207 - 2018/08/19 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.207.tar.xz -- integrated new html for entry page (JPO) -- fixed xaxis of bands plotter for entry page (PC) -- Improved distribution of APL calculations over threads (ME) -- Added function to SYM that returns the minimum distance vector (ME) -- Added docstring to xcombos (ME) -- added xvector::normalizeSumToOne() (CO) -- changed decomposition reaction to atomic concentrations (CO) -- added fractional_compound to chull output (CO) -- replaced AFLOWLogicError() and AFLOWRuntimeError() with xerror() (CO) -- added chull plot ICSD labels mode (CO) -- revamped small banner setting (CO) -- added verbose output if skipping entries above/below half hull (CO) -- added --output=png --png_resolution=500 options to chull (CO) -- added --keep=gpl to phonons gnuplot script (CO) (AUROSTD: boot.cpp, AUROSTD/aurostd.h, xcombos.cpp, xscalar.cpp, xscalar.h, xvector.cpp, xvector.h) (AFLOW: aconvasp_main.cpp, aflowrc.cpp, avasp.cpp, bader.cpp, chull.cpp, chull.h, aflow.cpp, aflow.h, aflowlib_webapp_bands.js, aflowlib_web_interface.cpp, pflow_funcs.cpp, pflow.h, pocc.cpp, symmetry.cpp, APL/aapl_tcond.cpp, APL/apl_atomic_disp.cpp, APL/apl_dm_pdos_save.cpp, APL/apl_doscalc.cpp, APL/apl_group_velocity.cpp, APL/apl.h, APL/apl_hroutines.cpp, APL/apl_pdisc.cpp, APL/qha3phonons_eos.cpp, APL/qha_dm_pdos_save.cpp, APL/qha_gruneisen.cpp, APL/scqha_eos.cpp, APL/scqha_gruneisen.cpp, APL/scqha_T_freqs.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_CHULL.TXT) 3.1.206 - 2018/08/08 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.206.tar.xz -- Fix JVXL (SC) 3.1.205 - 2018/07/27 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.205.tar.xz -- Improved destructor for xtensor (ME) -- Added function to test if xvector is a zero vector (ME) -- fixed parameter list for ANRL prototype (A_hR105_166_bc9h4i); z2 to x2 (DX) -- more rigorous check for atoms within the new cell in GetSuperCell(); check periodic images of atoms (DX) -- fixed "over-reduced" issue in primitivization routine in space group function (DX) -- added roundoff to axis and SU2 matrix in JSON output of symmetry elements (DX) -- fixed function for printing fractions in general Wyckoff positions (DX) -- created --generate_aflowin_only (CT) -- QHA3P and SCQHA conflict resolved (PN) -- reorganize QHA modes (PN) -- added four QHA3P options (PN) -- reorganize QHA, SCQHA, and QHA3P options (PN) -- filename changed and accordingly modified in QHA-README (PN) -- replaced some QHA functions with aurostd (PN) -- fixed slab AddAtom() function (CO+DU) -- added --readme=aflowrc (CO) -- fixed --readme=xaflow for local configuration (CO) -- fixed a few warnings for beta (CO) -- fixed AMIX/BMIX typo (CO) -- added defaults/options for DOD CONRAD machine (--machine=dod_conrad); also added in aflowrc (DX) (AUROSTD: xscalar.cpp, xscalar.h, xtensor.cpp, xvector.cpp, xvector.h) (AFLOW: aflowrc.cpp, avasp.cpp, chull.cpp, aflow.cpp, data.cpp, aflow.h, init.cpp, ivasp.cpp, kbin.cpp, kvasp.cpp, aflowlib_webapp_entry.js, aflowlib_web_interface.cpp, pocc_old.cpp, surface.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, xatom.cpp, xclasses.cpp, anrl_list.cpp, APL/apl_group_velocity.cpp, APL/apl.h, APL/apl_kphonons.cpp, APL/qha3phonons_eos.cpp, APL/qha_aflowin_creator.cpp, APL/qha_energies.cpp, APL/qha_eos.cpp, APL/qha_gruneisen.cpp, APL/scqha_eos.cpp, APL/scqha_gruneisen.cpp, APL/scqha_T_freqs.cpp, Makefile, README_AFLOW_AEL.TXT, README_AFLOW_AFLOWRC.TXT, README_AFLOW_AGL.TXT, README_AFLOW_POCC.TXT, README_AFLOW_QHA_SCQHA_QHA3P.TXT, README_AFLOW.TXT, README_AFLOW_XAFLOW.TXT) 3.1.204 - 2018/07/12 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.204.tar.xz -- updated QHA and added QHA3P and SCQHA functionality (PN) -- Restrucured xcombos. Added enumerations (ME) [AUROSTD/aflow_xcombos.cpp, AUROSTD/aflow_xcombos.h] -- Introduced exception handlier class aurostd::xerror (ME) -- Introduced xtensor class for tensors of arbitrary dimension. Other xtensor classes are obsolete now (ME). -- Changed all current xtensor3 instances to the new xtensor format (ME) -- Added Kronecker product to xmatrix (ME) -- Option to write and use AEL data at lowest finite pressure where the material is elastically stable (CT) -- Option to specify a separate set of finite pressures for AEL calculations than are used for AGL post-processing (CT) -- Integrated workflow option for using finite pressure Poisson ratio in AGL calculations (CT) -- Write nominal target pressure and calculated external pressure for AEL calculations in aflow.ael.out file (CT) -- Fixed keyword in JSON output file (CT) -- Increase grid for AGL DOSCAR (CT) -- cleaning up webapp_bands.js and added more mouse functionality (PC) -- added citation information to entry page (PC) -- added ANRL prototypes from part 2 of library (302 prototypes) (DX) -- added option to print symbolic math representation of ANRL prototypes (--add_equations or --equations_only) in aims and vasp formats (DX) -- updated DOI for ANRL part 1 and added arXiv for part 2 to title line of each prototype (DX) -- fixed bug with --vasp keyword, i.e., need to check if used with --proto command (DX) -- removed unused variables in standard lattice function (DX) -- added applyCombo() to xcombos (CO) -- fixed wget *.xz issue if *.xz already exists (CO) -- fixed apl2agr to handle xz compression format (CO) -- fixed --aflow_proto empty BZ issue, occurs when structure is downloaded from online (CO) -- fixed reading in forces from aims.out (CO) -- force species input for aims structure (CO) -- added checks for broken API (CO) -- added GENERATOR to aflow.in generation (CO) -- added auid to chull PDF output (CO) -- fixed bader num_each_type issue (relax2 vs. static primitivization) (CO) -- fixed command line aflow_qmvasp generation (CO) -- fixed search for ./aflow_data issue upon initial installation (CO) -- PARTCAR now handles '+' in write out (CO) -- fixed AddAtom() to handle different occupations (CO) -- added combination parameters to chull (CO) -- fixed aflowrc load issue (remove spaces between quotes and comment) (CO) (AUROSTD: boot.cpp, AUROSTD/aurostd.cpp, AUROSTD/aurostd.h, main.cpp, xcombos.cpp, xcombos.h, xerror.cpp, xerror.h, xmatrix.cpp, xmatrix.h, xtensor.cpp, xtensor.h) (AFLOW: aconvasp_main.cpp, aflowrc.cpp, anrl.cpp, avasp.cpp, bader.cpp, bader.h, chull.cpp, chull.h, aflow.cpp, data.cpp, aflow.h, init.cpp, ivasp.cpp, kbin.cpp, lattice.cpp, aflowlib_libraries.cpp, aflowlib_webapp_bands.js, aflowlib_web_interface.cpp, oaims.cpp, ovasp.cpp, pflow.h, pocc.cpp, pocc.h, surface.cpp, xatom.cpp, xclasses.cpp, xproto.cpp, ANRL_CPPS_20180710, APL/apl_atomic_disp.cpp, APL/apl_doscalc.cpp, APL/apl_group_velocity.cpp, APL/apl.h, APL/apl_hroutines.cpp, APL/apl_hsqpoints.cpp, APL/apl_kphonons.cpp, APL/apl_ltetdos.cpp, APL/apl_mpmesh.cpp, APL/apl_pdisc.cpp, APL/apl_phoncalc.cpp, APL/apl_thermalpc.cpp, APL/apl_uniform_mesh.cpp, APL/qha3phonons_eos.cpp, APL/qha_aflowin_creator.cpp, APL/qha_dm_pdos_save.cpp, APL/qha_energies.cpp, APL/qha_eoscalc.cpp, APL/qha_eos.cpp, APL/qha_gruneisen.cpp, APL/scqha_eos.cpp, APL/scqha_gruneisen.cpp, APL/scqha_T_freqs.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_AEL.TXT, README_AFLOW_AGL.TXT, README_AFLOW_ANRL.TXT, README_AFLOW_APL.TXT, README_AFLOW_CHULL.TXT, README_AFLOW_EXCEPTIONS.TXT, README_AFLOW_POCC.TXT, README_AFLOW_QHA_SCQHA_QHA3P.TXT, README_AFLOW.TXT, README_AFLOW_XAFLOW.TXT, README_CONTRIBS.TXT) 3.1.203 - 2018/06/15 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.203.tar.xz -- fixed tolerance scan issue in edata (try new tolerance from PrintSGData() on GetLatticeType() routine before changing tolerance) (DX) -- fixed primitivization routine in aflowSG functions (Minkowski/Niggli to fix left-handed candidate lattices and recheck moduli after Minkowski/Niggli) (DX) -- check all possible generator choices to match to ITC convention before changing tolerance (DX) -- added more rigorous check of tetragonal symmetry operations for determining conventional cell (DX) -- added generator information for P1 symmetry systems (DX) -- added check of Cartesian distance before removing fractional copies in GetPrimitive() (DX) (AFLOW: lattice.cpp, pflow_print.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_ITC.cpp, xatom.cpp) 3.1.202 - 2018/06/07 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.202.tar.xz -- dropping EXTRA to AFLOW3_FREE/EXTRA on local machine or wget (SC) 3.1.201 - 2018/06/04 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.201.tar.xz -- more space saving in lib2raw (linking OUTCAR.relax instead of copying) SC 3.1.200 - 2018/05/27 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.200.tar.xz -- fixed structure rescaling issue for space group determination (affecting LIB4) (DX) -- print geometry file location for errors/debug (DX) -- added more debugging messages along with file location in symmetry functions (DX) -- initialize variables for -O3 in symmetry and structure comparison routines (DX) -- speed increase for minimumDistance() function (DX) -- speed increase for primitivization routine in aflowSG functions (DX) -- fixed Wyckoff position typo for space group 62 (8d not 8e) (DX) -- fixed Wyckoff position typo for space group 89 (4i not 2i) (DX) (AFLOW: aflow.h, aconvasp_main.cpp, compare_structure.cpp, compare_structure_function.cpp, pflow_print.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_ITC_library.cpp, symmetry_spacegroup_functions.cpp, xatom.cpp, xproto.cpp, aflowlib_libraries.cpp) 3.1.199 - 2018/05/27 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.199.tar.xz -- compressing aflow.***.json/out in LIB2RAW and linking them (SC) -- removing the brainy/useless stuff about file compression in aurostd (SC) -- fighting sloppyness in aflow_libraries about aflow_pgroup[x][_xtal] (SC) -- fixed aflow_libraries about compress, delete and link files (SC) -- fixed inconsitencies in aflow_convasp_main compress (SC) -- fixed as bunch of inconsistencies in compressing and XHOST.command (SC) -- more inconsistencies RAW-WEB in aflow_libraries (SC) -- fixed removal useless files in LIB2RAW (SC) -- added BZ2XZ engine to aurostd_main (SC) -- added GZ2XZ engine to aurostd_main (SC) -- added ZIP2ZIP engine to aurostd_main (SC) 3.1.198 - 2018/05/24 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.198.tar.xz -- fixed bader extension finder for --lib2raw (CO) (AFLOW: bader.cpp, bader.h, aflowlib_libraries.cpp, Makefile) 3.1.197 - 2018/05/24 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.197.tar.xz -- updates to entry page bands plotter (PC) -- added some helpful comments for getGeneralNormal(), CMdet(), and ZVAL in bader (CO) -- check if /www directory exists for jmol display on entry page (CO) (AUROSTD: xmatrix.cpp, xvector.cpp) (AFLOW: bader.cpp, chull.cpp, aflowlib_webapp_bands.js, aflowlib_web_interface.cpp, Makefile) 3.1.196 - 2018/05/21 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.196.tar.xz -- fixed entry page property line wrapping issues (PC) -- added button for spin-polarized band structure selection in webapp (PC) -- fixed precision inconsistency printing xstr.json (FK) -- added some -O3 compatibility (FK) -- citation added to aflow_aapl_pairs.cpp (ME) -- fixed bug in aflow_kvasp.cpp that prevented the creation of the primitive cell structure for APL, AAPL, and QHA calculations (ME) -- implemented combinations with repetitions with sequence taken into account (ME) -- moved the code to check for input and output files in APL into separate functions to make them available for AAPL, remove duplicate code, and make the code more readable (ME) -- removed the ENCUT and EDIFF tags from AAPL input files as they may result in lower cut-off energies and higher energy differences (ME) -- fixed gcc8 issue in AGL (CO) -- added simplex content and hypercollinearity properties to convex hull data (CO) -- decoupled internal links between graph2doc and withindoc (CO) -- fixed site error calculation in POCC for vacancies (CO) -- added eyes/ones xmatrix constructors (CO) -- added Cayley-Menger determinant to xmatrix (CO) -- included cstdlib in aflow_data.cpp for compilation on qrats (CO) (AUROSTD: boot.cpp, xcombos.cpp, xcombos.h, xmatrix.cpp, xmatrix.h, xvector.cpp) (AFLOW: aconvasp_main.cpp, apennsy_main.cpp, chull.cpp, chull.h, contrib_shidong_auxiliary.cpp, data.cpp, aflow.h, kvasp.cpp, aflowlib.h, aflowlib_libraries.cpp, aflowlib_webapp_bands.js, aflowlib_web_interface.cpp, pflow_funcs.cpp, pflow.h, pocc.cpp, pocc.h, pocc_old.cpp, pocc_old.h, xatom.cpp, APL/aapl_tensor.cpp, APL/apl_dirphoncalc.cpp, APL/apl.h, APL/apl_phoncalc.cpp, APL/apl_thermalpc.cpp, Makefile) 3.1.195 - 2018/05/21 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.195.tar.xz -- beta of release with XZ (SC) 3.1.194 - 2018/05/16 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.194.tar.xz -- small bug fixes for g++/gcc 7 and 8 (SC) -- preparing for xz compression (SC) 194 xatom.cpp aurostd.h aurostd_main.cpp pthread.cpp README_SCRIPTING README_AFLOW init.cpp aflow.cpp aconvasp_main.cpp 194c fix aconvasp_main.cpp 194d avasp.cpp ael_elasticity.cpp ael_get_stress.cpp agl_debye.cpp agl_get_ev.cpp contrib_cormac.cpp contrib_junkai_phasediag.cpp 194e avasp.cpp xatom.cpp aurostd_main libraries.cpp ael_elasticity.cpp ael_get_stress.cpp agl_debye.cpp agl_get_ev.cpp contrib_cormac.cpp aconvasp_main.cpp pthread.cpp init.cpp aflow.cpp (heavy) 194f good bye bzip2 (SC) 194g aflow_contrib_wahyu.cpp 194h aflow.cpp aflow_estructure.cpp aflow_ifrozsl.cpp aflow_ivasp.cpp 194i aflow_pthreads.cpp 194j aflow_aflowrc.cpp 194l BASE64 for pseudopotentials and aflow_data.cpp 194m aflow_kbin.cpp aflow_kvasp.cpp 194n aflowlib_web_interface.cpp aflow_matlab_funcs.cpp (EXTRA/MATLAB/plotband.m) aflow_ovasp.cpp aflow_pocc_edos.cpp shortened aflow_xatom.cpp working on ZVAL POMASS and removing all EXT stuff. Tests work. Fixed even further aflow_pthread.cpp aflow_xproto_gus.cpp 3.1.193 - 2018/05/11 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.193.tar.xz -- extending xoptions push pop (SC) 3.1.192 - 2018/05/10 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.192.tar.xz -- extending xoptions push pop (SC) 3.1.191 - 2018/05/08 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.191.tar.xz -- rationalized orthogonality search in xmatrix (SC) aurostd_xmatrix.h aurostd_xmatrix.cpp aflow.h 3.1.190 - 2018/05/08 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.190.tar.xz -- fixed units in AGL output (CT) -- fixed permutation vector initialization in APL (required for compiling on DoD CONRAD machine) (DX) -- fixed bug in tolerance scan; was only scanning in one direction (DX) -- created faster minimum cartesian distance calculator for skewed cells; fewer duplicate operations (DX) -- fixed conflict between CUT_RAD and CUT_SHELL in AAPL (ME) -- properly added directory to bader error output (CO) -- fixed slow down with loadEntries() (stringElements2VectorElements()) (CO) -- fixed AIMS read-in issue with '#' comments (CO) -- added guard around BANDSDATA_JSON() for html generation (CO) -- fixed static compile settings (CO) -- fixed _sym_op.basis_map_calculated issue in ApplyAtom() for AAPL (CO) -- added xStream class for logging workflow updates (CO) -- fixed stability criterion vs. (Delta H) fonts in chull report (CO) -- substantial clean-up of classes in POCC in anticipation for AVASP_MakeSingleAFLOWIN integration (CO) -- added avasp function in preparation for AVASP_MakeSingleAFLOWIN integration (CO) -- added try/catches for easy debugging (CO) (AUROSTD: main.cpp) (AFLOW: aconvasp_main.cpp, aflowrc.cpp, agl_debye.cpp, avasp.cpp, bader.cpp, chull.cpp, chull.h, contrib_kesong_ipocc.cpp, aflow.cpp, aflow.h, ivasp.cpp, kbin.cpp, kvasp.cpp, aflowlib_web_interface.cpp, pflow.h, pocc.cpp, pocc.h, symmetry.cpp, xatom.cpp, xclasses.cpp, APL/aapl_pairs.cpp, APL/apl_kphonons.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_CHULL.TXT) 3.1.189 - 2018/05/04 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.189.tar.xz Moved these defaults from aflow.h to aflow_aflowrc.cpp for user tuning (SC) #define DEFAULT_AFLOW_PRESCRIPT_OUT string("aflow.prescript.out") #define DEFAULT_AFLOW_PRESCRIPT_COMMAND string("aflow.prescript.command") #define DEFAULT_AFLOW_POSTSCRIPT_OUT string("aflow.postscript.out") #define DEFAULT_AFLOW_POSTSCRIPT_COMMAND string("aflow.postscript.command") #define DEFAULT_AFLOW_PGROUP_OUT string("aflow.pgroup.out") #define DEFAULT_AFLOW_PGROUP_XTAL_OUT string("aflow.pgroup_xtal.out") #define DEFAULT_AFLOW_PGROUPK_OUT string("aflow.pgroupk.out") #define DEFAULT_AFLOW_PGROUPK_XTAL_OUT string("aflow.pgroupk_xtal.out") #define DEFAULT_AFLOW_FGROUP_OUT string("aflow.fgroup.out") #define DEFAULT_AFLOW_SGROUP_OUT string("aflow.sgroup.out") #define DEFAULT_AFLOW_AGROUP_OUT string("aflow.agroup.out") #define DEFAULT_AFLOW_IATOMS_OUT string("aflow.iatoms.out") #define DEFAULT_AFLOW_PGROUP_JSON string("aflow.pgroup.json") #define DEFAULT_AFLOW_PGROUP_XTAL_JSON string("aflow.pgroup_xtal.json") #define DEFAULT_AFLOW_PGROUPK_JSON string("aflow.pgroupk.json") #define DEFAULT_AFLOW_PGROUPK_XTAL_JSON string("aflow.pgroupk_xtal.json") #define DEFAULT_AFLOW_FGROUP_JSON string("aflow.fgroup.json") #define DEFAULT_AFLOW_SGROUP_JSON string("aflow.sgroup.json") #define DEFAULT_AFLOW_AGROUP_JSON string("aflow.agroup.json") #define DEFAULT_AFLOW_IATOMS_JSON string("aflow.iatoms.json") #define DEFAULT_AFLOW_ICAGES_OUT string("aflow.icages.out") #define DEFAULT_AFLOW_SURFACE_OUT string("aflow.surface.out") #define DEFAULT_AFLOW_QMVASP_OUT string("aflow.qmvasp.out") #define DEFAULT_AFLOW_ERVASP_OUT string("aflow.error.out") #define DEFAULT_AFLOW_IMMISCIBILITY_OUT string("aflow.immiscibility.out") #define DEFAULT_AFLOW_MEMORY_OUT string("aflow.memory.out") #define DEFAULT_AFLOW_FROZSL_INPUT_OUT string("aflow.frozsl_input.out") #define DEFAULT_AFLOW_FROZSL_POSCAR_OUT string("aflow.frozsl_poscar.out") #define DEFAULT_AFLOW_FROZSL_MODES_OUT string("aflow.frozsl_energies.out") #define DEFAULT_AFLOW_FROZSL_EIGEN_OUT string("aflow.frozsl_eigen.out") #define DEFAULT_AFLOW_END_OUT string("aflow.end.out") 3.1.188- 2018/05/03 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.188.tar.xz Fixing kvasp.cpp (SC) 3.1.187- 2018/04/26 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.187.tar.xz -- added missing scaling factor information to lattice for AIMS xstructure output (DX) -- fixed bug in edata lattice type/variation determination; accounts for lattices that do not reflect crystal symmetry (DX) -- fixed bug in edata reciprocal lattice type/variation determination; accounts for reciprocal lattices transformed from a lattice that does not reflect crystal symmetry (DX) -- added directory (pwd) information to LDEBUG/ERROR messages for symmetry functions (DX) (AFLOW: aconvasp_main.cpp, lattice.cpp, symmetry.cpp, xatom.cpp) 3.1.186- 2018/04/25 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.186.tar.xz -- fixed bug in tolerance scan; was only scanning in one direction (DX) -- created faster minimum cartesian distance calculator for skewed cells; fewer duplicate operations (DX) (AFLOW: symmetry_spacegroup.cpp, symmetry.cpp) 3.1.185- 2018/04/24 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.185.tar.xz Fixing kvasp.cpp for dying jobs (SC) 3.1.184- 2018/04/23 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.184.tar.xz Fixing ivasp.cpp for AFLOW_PSEUDOPOTENTIALS.TXT AFLOW_PSEUDOPOTENTIALS_LIST.TXT (SC) Tuning aflow_aflowrc.cpp for HYPERTHREADING in eos,draco,cobra,hydra (SC) 3.1.183- 2018/04/20 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.183.tar.xz Fixing ovasp for METAGGA/isKINETIC (SC) 3.1.182- 2018/04/19 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.182.tar.xz AFLOW_PSEUDOPOTENTIALS.TXT AFLOW_PSEUDOPOTENTIALS_LIST.TXT (SC) 3.1.181- 2018/04/17 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.181.tar.xz Creating defaults in aflow_aflowrc.cpp for HYPERTHREADING in eos,draco,cobra,hydra (SC) 3.1.180- 2018/04/16 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.180.tar.xz Creating defaults in aflow_aflowrc.cpp for NCPUS in eos,draco,cobra,hydra (SC) 3.1.179 - 2018/04/13 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.179.tar.xz -- fixed PP settings for SCAN (RF) -- fixed warning in APIget() (CO) -- added relative stability criterion and latex-formatted sg's to chull properties list (CO) -- added control.in and geometry.in file name specification in aflowrc (CO) -- --generate now applies for aims output as well (CO) -- force aflow.in generation even for MODE=AIMS (CO) -- fixed k-point mismatch for non-primitive APL runs (CO) -- added MINATOMS_RESTRICTED tag for APL (CO) -- added functionality for user-defined path in phonon dispersion, specify coords/labels in aflow.in (CO) -- swapped out quser for qflow, but maintain backwards compatibility (CO) (AUROSTD: xoption.cpp, xoption.cpp, xoption.h, xoption.h, xvector.cpp, xvector.cpp, xvector.h, xvector.h) (AFLOW: aconvasp_main.cpp, aconvasp_main.cpp, aflowrc.cpp, aflowrc.cpp, avasp.cpp, avasp.cpp, chull.cpp, chull.cpp, chull.h, chull.h, compare_structure.cpp, compare_structure.cpp, contrib_kesong_hnfcell.cpp, contrib_kesong_hnfcell.cpp, contrib_kesong_ipocc.cpp, contrib_kesong_ipocc.cpp, contrib_kesong_pocc_basic.cpp, contrib_kesong_pocc_basic.cpp, aflow.cpp, aflow.cpp, aflow.h, aflow.h, init.cpp, init.cpp, kbin.cpp, kbin.cpp, kvasp.cpp, kvasp.cpp, aflowlib.h, aflowlib.h, aflowlib_web_interface.cpp, aflowlib_web_interface.cpp, pocc.cpp, pocc.h, poccupation_forcefield.cpp, poccupation_forcefield.cpp, symmetry.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup_functions.cpp, symmetry_spacegroup.h, symmetry_spacegroup.h, xatom.cpp, xatom.cpp, xclasses.cpp, xclasses.cpp, APL/aapl_tcond.cpp, APL/aapl_tcond.cpp, APL/aapl_tensor.cpp, APL/aapl_tensor.cpp, APL/apl_dirphoncalc.cpp, APL/apl_dirphoncalc.cpp, APL/apl.h, APL/apl.h, APL/apl_kphonons.cpp, APL/apl_kphonons.cpp, APL/apl_lrphoncalc.cpp, APL/apl_lrphoncalc.cpp, APL/apl_pathbuilder.cpp, APL/apl_pathbuilder.cpp, APL/apl_pdisc.cpp, APL/apl_pdisc.cpp, APL/apl_phoncalc.cpp, APL/apl_phoncalc.cpp, APL/apl_supercell.cpp, APL/apl_supercell.cpp, APL/qha_eosrun.cpp, APL/qha_eosrun.cpp, Makefile, Makefile, README_AFLOW_APL.TXT, README_AFLOW_APL.TXT, README_AFLOW.TXT, README_AFLOW.TXT) 3.1.178 - 2018/04/13 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.178.tar.xz Moved these defaults from aflow.h to aflow_aflowrc.cpp for user tuning (SC) #define DEFAULT_FILE_AFLOWLIB_ENTRY_OUT string("aflowlib.out") #define DEFAULT_FILE_AFLOWLIB_ENTRY_JSON string("aflowlib.json") #define DEFAULT_FILE_EDATA_ORIG_OUT string("edata.orig.out") #define DEFAULT_FILE_EDATA_RELAX_OUT string("edata.relax.out") #define DEFAULT_FILE_EDATA_BANDS_OUT string("edata.bands.out") #define DEFAULT_FILE_DATA_ORIG_OUT string("data.orig.out") #define DEFAULT_FILE_DATA_RELAX_OUT string("data.relax.out") #define DEFAULT_FILE_DATA_BANDS_OUT string("data.bands.out") #define DEFAULT_FILE_EDATA_ORIG_JSON string("edata.orig.json") #define DEFAULT_FILE_EDATA_RELAX_JSON string("edata.relax.json") #define DEFAULT_FILE_EDATA_BANDS_JSON string("edata.bands.json") #define DEFAULT_FILE_DATA_ORIG_JSON string("data.orig.json") #define DEFAULT_FILE_DATA_RELAX_JSON string("data.relax.json") #define DEFAULT_FILE_DATA_BANDS_JSON string("data.bands.json") #define DEFAULT_FILE_TIME_OUT string("time") #define DEFAULT_FILE_SPACEGROUP1_OUT string("SpaceGroup") #define DEFAULT_FILE_SPACEGROUP2_OUT string("SpaceGroup2") #define DEFAULT_FILE_VOLDISTPARAMS_OUT string("VOLDISTParams") #define DEFAULT_FILE_VOLDISTEVOLUTION_OUT string("VOLDISTEvolution") 3.1.177 - 2018/04/06 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.177.tar.xz Bug fixes on autopseudootentialsl (SC) 3.1.176 - 2018/04/06 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.176.tar.xz Working PAW_PBE_KIN and PAW_LDA_KIN autopseudopotential (SC) 3.1.175 - 2018/04/06 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.175.tar.xz Working on mpcdf-cobra (SC) 3.1.174 - 2018/03/29 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.174.tar.xz -- added bands app to entry page (GG) -- fixed scaling factor type in xstructure2json() (DX) -- account for Wyckoff positions in represented as fractions (hex/rhl) in minimum enumerated Wyckoff search (DX) -- improved minimum enumerated Wyckoff search (consider combinations of origin shifts) (DX) -- fixed typo in xmatrix2json function (DX) -- limited outlier detection to binaries only, statistics not globally favorable for ternaries and above YET (CO) -- added explanatory comments in aflowrc for chull settings (CO) -- added statistics output to chull logger (CO) -- fixed Greek letter issues with Helvetica fonts in chull (CO) -- further decoupled ChullFacet() initialization from ConvexHull() with initialize() and addVertex() (CO) -- added user-defined dft_type restrictions in aflowrc (CO) -- added LIB1 to loadEntries() default (CO) -- fixed stringElements2VectorElements() bugs with LIB1 colons (CO) -- added plotting option for iso-max latent heat (CO) -- added kJ/mol axis for formation enthalpy hulls (CO) -- added logos to hull illustrations, generally fixed header/footers (CO) -- added stability criterion analysis to default routine (CO) -- fixed sign of decomposition energy/stability criterion (CO) -- added equivalent ICSD structures analysis to default routine (CO) -- fixed --readme vs. --readme=XX (CO) -- fixed superfluous output in --poscar2aflowin (CO) -- fixed bug in aconvasp's Ewald summation function as pointed out by Wei Xie (CO) -- changed generic xstructure title to include cleannames in case there is pp info (CO) (AUROSTD: AUROSTD/aurostd.h, main.cpp, xscalar.h, xvector.cpp) (AFLOW: aconvasp_main.cpp, aflowrc.cpp, chull.cpp, chull.h, init.cpp, aflowlib.h, aflowlib_web_interface.cpp, pflow_funcs.cpp, pflow.h, symmetry_spacegroup.cpp, webapp_bands.js, webapp_entry.js, xatom.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_CHULL.TXT) 3.1.173 - 2018/03/12 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.173.tar.xz -- Create LIB7/LIB8/LIB9 framework (SC) 3.1.172 - 2018/02/27 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.172.tar.xz -- Write data in JSON format in AEL/AGL (CT) -- Option to turn off VASP symmetry in AEL/AGL (CT) -- Write vibrational free energy and vibrational entropy at 300K in aflow.agl.out in AEL/AGL (CT) -- Write enthalpy (H = E + pV) in AEL/AGL (CT) -- Option to skip pressure/temperature points where no minimum Gibbs free energy is found, instead of truncating pressure/temperature range in AEL/AGL (CT) -- fixed tolerance scan counter for lib2raw runs (no longer static variable) (DX) -- edata speed increase, only calculate up to pgroup_xtal for lattice, superlattice, and reciprocal lattice (DX) -- fixed typo in Wyckoff position "b" for space group #160 (DX) -- fixed --kppra command line bug, divided by natoms twice (CO) -- added debug output to nanoparticle (CO) -- fixed --readme=chull empty string error (CO) -- automated plot_unstable with z_filter_cutoff in chull (CO) -- fixed plotting ranges with z_filter_cutoff in chull (CO) (AFLOW: aconvasp_main.cpp, ael_elastic_fit.cpp, ael_elasticity.cpp, ael_elasticity.h, ael_get_stress.cpp, agl_debye.cpp, agl_debye.h, agl_eqn_state.cpp, agl_get_ev.cpp, agl_hugoniot.cpp, agl_polynomial.cpp, agl_rungibbs.cpp, chull.cpp, data.cpp, aflow.h, lattice.cpp, aflowlib_libraries.cpp, pflow.h, pflow_print.cpp, symmetry.cpp, symmetry_spacegroup.cpp, symmetry_spacegroup_ITC_library.cpp, xatom.cpp, Makefile, README_AFLOW_AEL.TXT, README_AFLOW_AGL.TXT, README_AFLOW_SYM.TXT) 3.1.171 - 2018/02/21 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.171.tar.xz -- fixed multiple degeneracy prints in POCC (CO) -- added directory information to logging functions in bader/chull (CO) -- added --destination=|--path= flag for output of chull (CO) -- use full path (pwd) for working directory in AFLOW-SYM functions (DX) -- fixed directory flag for AFLOW-SYM functions (DX) -- fixed typo in site symmetry of Wyckoff position "a" for space group #109 (DX) (AUROSTD: aurostd.h, main.cpp) (AFLOW: aconvasp_main.cpp, bader.cpp, bader.h, chull.cpp, chull.h, poccupation_edos.cpp, symmetry_spacegroup_ITC_library.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_CHULL.TXT) 3.1.170 - 2018/02/18 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.170.tar.xz -- fixed chmod in LIB2RAW (CO) -- fixed DOS-extraction bug (exit vs. return false) in LIB2RAW for POCC+AEL/AGL runs (CO) -- fixed joinWDelimiter() xvector bug: removed erroneous delimiter at the end (CO) -- fixed DOSDATA_JSON() + BANDSDATA_JSON() amalgamation: removed erroneous wrapping brackets around DOS (CO) -- fixed misleading logging message in APL on primitivization of input (CO) (AUROSTD: main.cpp) (AFLOW: estructure.cpp, aflow.h, aflowlib_libraries.cpp, aflowlib_web_interface.cpp, poccupation_edos.cpp, APL/apl_supercell.cpp, Makefile) 3.1.169 - 2018/02/16 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.169.tar.xz -- added aflow_proto functionality: --relax_type=IONS, --module=APL, --apl_supercell=3x3x3, --no_volume_adjustment (CO) -- NCPUS in APL now respects parent aflow.in (default MAX, then looks at parent aflow.in, otherwise overrides with --np=XX) (CO) -- fixed spacegroup bug in apl post hibernation (CO) -- added --print and --screen_only options to chull for python integration (CO) -- removed extraneous ytick lines from 3D hull (CO) -- increased spacing between axes and ticklabels on hulls (CO) -- fixed bugs in entropic_temperature hull visualization (CO) -- fixed apl2agr/subst make commands (CO) -- fixed Niggli tolerance; more robust and use _ZERO_TOL_ (DX) -- fixed bug in Niggl step 6 (DX) -- fixed comparison of SU(2) to exp(theta*su(2)); parentheses issue (DX) -- fixed Quantum Espresso output to include lattice scaling factor (DX) -- fixed Quantum Espresso celldm units (Bohr) (DX) -- fixed Quantum Espresso alat flag to multiply cell parameters by celldm(1) or A parameter (DX) -- fixed tolerance issue with PrintData for lib2raw runs (DX) (AFLOW: aconvasp_main.cpp, avasp.cpp, chull.cpp, aflow.h, pflow_print.cpp, symmetry.cpp, xatom.cpp, APL/aapl_tcond.cpp, APL/apl_dm_pdos_save.cpp, APL/apl_doscalc.cpp, APL/apl.h, APL/apl_pdisc.cpp, APL/apl_phoncalc.cpp, APL/qha_gruneisen.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_CHULL.TXT) 3.1.168 - 2018/02/08 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.168.tar.xz -- fixed structure comparison bug (overwritten match) (DX) (AFLOW: aflow_compare_structure.h, aflow_compare_structure_function.cpp) 3.1.167 - 2018/02/06 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.167.tar.xz -- speed increase for structure comparison (DX) -- fixed bugs for structure comparison (DX) -- added Wyckoff position analysis to group similar structures in directory comparison (DX) -- added grouped Wyckoff position information to the JSON output (DX) -- added logger/status for directory comparisons (DX) -- added functionality to read .bz2 geometry files (DX) -- added --no_scale option for comparisons (required for chull) (CO+DX) (AFLOW: aconvasp_main.cpp, chull.cpp, symmetry_spacegroup.cpp, compare_structure.cpp, compare_structure_function.cpp, compare_structure.h) (DX) 3.1.166 - 2018/02/02 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.165.tar.xz -- fixed broken --slab commmand (CO) (AFLOW: slab.cpp) 3.1.165 - 2018/01/30 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.165.tar.xz -- integrated .aflow.rc settings into APL/QHA/AEL/AGL (CO) -- added LORBIT=10 to relaxation INCAR (spinD) (CO) -- improved magnetic properties extraction, pull from relax first, overwrite with static (CO) -- added safety hull coordinates assignment (CO) -- new default for load entries (no load xstructures) (CO) (AFLOW: aconvasp_main.cpp, ael_get_stress.cpp, agl_get_ev.cpp, chull.cpp, ivasp.cpp, aflowlib_libraries.cpp, APL/apl_phoncalc.cpp, APL/qha_eosrun.cpp, Makefile) (CO) 3.1.164 - 2018/01/25 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.164.tar.xz -- fixed minor bugs in Quantum Espresso reader -- added ibrav options to Quantum Espresso reader (ibrav2lattice function) -- added celldm and a, b, c, cosAB, cosAC, cosBC readers for Quantum Espresso -- added Bohr units reader for Quantum Espresso (AFLOW: aconvasp_main.cpp, pflow.h, xatom.cpp) (DX) 3.1.163 - 2018/01/23 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.163.tar.xz -- added --dist2hull=0.25,0.25 option for chull, which provides the value of the convex hull surface at the specified coordinate/concentration (CO) -- added separate readme for chull (--readme=chull) (CO) -- customized avasp.cpp (--proto) with options from .aflow.rc, --mpi, and --np (CO) -- fixed QHA/AAPL aflow.in keyword bug (CO) -- added ANRL modifiers to directory for --proto (Ex: label:ANRL=param1,param2,...) (DX) (AFLOW: aconvasp_main.cpp, aflowrc.cpp, avasp.cpp, chull.cpp, aflow.cpp, aflow.h, init.cpp, kbin.cpp, Makefile, README_AFLOW_ACONVASP.TXT, README_AFLOW_CHULL.TXT, README_AFLOW.TXT) (CO+DX) 3.1.162 - 2018/01/19 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.162.tar.xz -- added SU(2) complex matrix and su(2) generator coefficients representation of symmetry elements -- added SU(2) and su(2) information to .out and .json symmetry files -- extended functionality for complex matrices and vectors (trace, exponential, ostream, etc.) -- added xcomplex2json to represent complex numbers in json -- added pgroupk_xtal (dual of crystal point group operations) standalone function -- extended --proto for ANRL prototypes (to generate aflow.in) -- updated README_AFLOW_SYM.TXT (AUROSTD: aurostd.h, boot.cpp, main.cpp, xmatrix.cpp, xmatrix.h) (AFLOW: README_AFLOW_ACONVASP.TXT, README_AFLOW_SYM.TXT, aflow.h, aconvasp_main.cpp, avasp.cpp, symmetry.cpp, xatom.cpp) (DX) 3.1.161 - 2018/01/17 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.161.tar.xz -- bool xscalar and xvector gccV7 warning fixes (SC) -- double xscalar and xmatrix clang warning fixes (CO) -- uint chull gccV7 warning fix (CO) (AUROSTD: xscalar.h, xvector.h, xmatrix.h) (AFLOW: chull.cpp) Added README_AFLOW_SYM.TXT (init.cpp aflow.h aflow.cpp data.cpp) (DX+SC) 3.1.160 - 2018/01/13 Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.160.tar.xz convex hull mods: -- keep order of points (m_points) same as input from user/database -- size will only differ if there are artificial points (they go at the end of m_points) -- moved point banning to structurePoints() (i.e., m_coord_groups will only contain validated points) -- only print decomposition phases with non-zero coefficients (tie-line) -- fixed bug in initial facet.f_outside_set calculation -- fixed bug in using hull centroid vs. hull reference to align normals -- fixed bug in vcoords input (shiftlrows) (AFLOW: chull.cpp, chull.h) 3.1.159 - 2018/01/10 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.159.tar.xz MAJOR UPDATE - convex hull code rewritten, includes: (CO) -- complete generalization of input (need not be thermodynamic hull, can be ANY data) -- new major classes for naries, alloys, and coordinate (stoichiometry) groups -- for hulls with stoichiometric coordinates, the hull and properties are calculated in steps of increasing dimensionality -- automatic calculation of equivalent ground state structures, near-equivalent (by symmetry) ground state structures, equilibrium phases (by mixture) -- automatic removal of equivalent ground states for calculation of stability criterion -- automatic detection/removal of outliers (IQR/MAD) -- moved all major plotting options to .aflow.rc -- report any bugs to aflow.org/forum added xcombo class for combinations/permutations (CO) integrated roundoff/precision/format into stream2stream/utype2tring and variants (xvecDouble2String(),xmatDouble2String()) (CO) added another date format for chull (CO) added tol to isinteger (CO) added +=, -=, gcd (reduced composition), shiftlrows(), isCollinear(), getCentroid(), getGeneralAngles() (similar to Euler angles), getGeneralNormal() (n-dimensional normal), and getQuartiles()/getMAD() (outlier analysis) for xvector (CO) added general Householder QR decomposition (CO) smarter overloading of loadEntries()/loadXstructures() (CO) updated logger() to take directory (aflags) (CO) fixed Wyckoff position (a) for space group 117 (DX) fixed monoclinic space group determination with multiple unique axis choices (DX) (AUROSTD: Makefile,aurostd.cpp,aurostd.h,boot.cpp,main.cpp,xcombos.cpp,xcombos.h,xmatrix.cpp,xmatrix.h,xoption.cpp,xoption.h,xscalar.cpp,xscalar.h,xvector.cpp,xvector.h) (CO, patched SC) (AFLOW: Makefile,aflow.h,aconvasp_main.cpp,aflowrc.cpp,anrl.cpp,chull.cpp,chull.h,compare_structure.cpp,compare_structure.h,compare_structure_function.cpp,pflow.h,pflow_funcs.cpp,xatom.cpp) (CO) (AFLOWLIB: aflowlib.h,aflowlib_libraries.cpp,aflowlib_web_interface.cpp) (CO) (SYM: symmetry_spacegroup.cpp,symmetry_spacegroup_ITC_library.cpp) (CO) 3.1.158 - 2018/01/09 - Location: http://materials.duke.edu/AFLOW/HISTORIC/aflow.3.1.158.tar.xz Tentative distribution GNU (SC) 3.1.157 - 2017/12/19 - Working on mpcdf-draco (SC) Replaced pgroupk with pgroupk_xtal for resolving IBZ in APL/AAPL (CO) Fixed pgroupk_xtal flag and wyckoff position for sg133 (DX) (aflowrc.cpp,APL/apl_supercell.cpp,APL/apl_mpmesh.cpp,APL/aapl_tcond.cpp,lattice.cpp,symmetry_spacegroup_ITC_library.cpp) 3.1.156 - 2017/12/18 - Working on mpcdf-hydra (SC) 3.1.155 - 2017/12/13 - updated web component of ANRL CPP files to include the prototype generator and Jmol visualization fixed Wyckoff position for SG #171 improvement for monoclinic space group determination (consider alternative unique axis choices, if possible) added more to debug output for the space group routine (ANRL/,ANRL_CPPS_20171213/,aconvasp_main.cpp,symmetry_spacegroup.cpp,symmetry_spacegroup_ITC_library.cpp,symmetry_spacegroup_functions.cpp,xatom.cpp) (DX) 3.1.154 - 2017/12/07 - added pgroupk_xtal (dual of crystal point group operations) added magnetic symmetry analysis (crystal + spin) to edata added non-collinear magnetic symmetry analysis (crystal + spin) to edata,sgdata,aflowSG,aflowSYM,fgroup,pgroup_xtal,pgroupk_xtal,agroup,and sgroup fixed ApplyAtom (tolerance issue) fixed AFLOW-SYM printing bug (--screen_only for Python environment) changed point group matrix comparisons (uses Uf; exact) added SO(3) generator expansion coefficients onto Lx, Ly, and Lz (README_ACONVASP.TXT,aflow.h,aconvasp_main.cpp,ovasp.cpp,pflow.h,symmetry.cpp,symmetry_spacegroup.cpp,symmetry_spacegroup_functions.cpp,xatom.cpp,lattice.cpp,aflowlib_libraries.cpp) (DX) 3.1.153 - 2017/11/23 - Fixing Makefile for GNU version (SC) (fixed Library_ICSD..) (SC) Updating directories from AFLOW2 to AFLOW3 (SC) Updating directories for findsym platon frozsl (SC) 3.1.152 - 2017/11/20 - Fixing Makefile for GNU version (SC) (fixed DATA_CVs..) 3.1.151 - 2017/11/17 - Fixing Makefile for GNU version (SC) (fixed DATA_CVs..) 3.1.150 - 2017/11/06 - NFS cache-cleaning HACK (kbin.cpp) (CO) 3.1.149 - 2017/11/06 - fixed --xplug (libraries.cpp) (SC) 3.1.148 - 2017/10/27 - fixed --edata (txt + json print outs) (aconvasp_main.cpp,pflow.h,pflow_print.cpp,aflowlib_libraries.cpp) (CO+DX) 3.1.147 - 2017/10/25 - added skew test for structures (sym_eps), incorporated full symmetry analysis in more functions, improved --lib2raw_local, improved dos/bands-2json functionality, actually fixed --delta_kpoints, made min_dist (nearest neighbor distance) function more robust/faster, fixed nbondxx units, added jsons for sym/structure/bandsdata/dosdata to lib2raw, incorporated scale (ReScale()) in more functions (aurostd.h,boot.cpp,main.cpp,xmatrix.cpp,xmatrix.h,Makefile,README_AFLOW_ACONVASP.TXT,aflow.h,aconvasp_main.cpp,bader.cpp,defects.cpp,estructure.cpp,init.cpp,ovasp.cpp,pflow.h,pflow_print.cpp,surface.cpp,symmetry.cpp,symmetry_spacegroup.cpp,xatom.cpp,xclasses.cpp,xproto.cpp,aflowlib.h,aflowlib_libraries.cpp) (CO+DX) 3.1.146 - 2017/10/16 - rewritten bandgap code, added extensive FHI-AIMS support (APL), modified loadEntries() for GFA code, added new xvector operations (*=,/=), fixed delta_kpoints function, fixed bands/dos-2json functions, added local lib2raw (aapl_tensor.cpp,apl.h,apl_dirphoncalc.cpp,apl_gsa.cpp,apl_kphonons.cpp,apl_lrphoncalc.cpp,apl_phoncalc.cpp,qha_eosrun.cpp,aurostd.h,boot.cpp,main.cpp,xmatrix.cpp,xvector.cpp,xvector.h,xmatrix.h,Makefile,README_AFLOW_ACONVASP.TXT,aflow.h,aconvasp_main.cpp,aflowrc.cpp,chull.cpp,kbin.cpp,ovasp.cpp,pflow.h,poccupation_edos.cpp,xatom.cpp,xclasses.cpp,aflowlib_libraries.cpp,apl_supercell.cpp,iaims.cpp,kaims.cpp,oaims.cpp,estructure.cpp,ivasp.cpp,aflowlib.h) (CO) 3.1.145 - 2017/10/12 - fixed tolerance scan range (symmetry.cpp) (DX) 3.1.144 - 2017/10/03 - fixed bandgap type bug, fixed precision mistmatch in bands data when plotting band structure, changed misleading metric_tensor function name, fixed false positive message in structure_comparison, fixed APL bugs with reading aflow.in, avoid SYMPREC vs. PREC confusion (ovasp.cpp,estructure.cpp,xatom.cpp,aconvasp_main.cpp,pflow.h,aflow.h,aurostd.h,aflowlib_libraries.cpp,poccupation_edos.cpp,Makefile,ivasp.cpp,apl_phoncalc.cpp,qha_eosrun.cpp,apl.h,apl_kphonons.cpp,compare_structure.cpp,symmetry_spacegroup_functions.cpp,symmetry_spacegroup.h) (CO+DX) 3.1.143 - 2017/09/28 - added magnetic symmetry analysis (crystal + spin) to sgdata, aflowSG,aflowSYM,agroup,fgroup,pgroup_xtal,agroup,and sgroup; speed increase for space group routine, alter tolerance scan range (README_AFLOW_ACONVASP.TXT,aflow.h,aconvasp.cpp,aconvasp_main.cpp,lattice.cpp,pflow.h,symmetry.cpp,symmetry_spacegroup.cpp,symmetry_spacegroup_functions.cpp,xatom.cpp) (DX) 3.1.142 - 2017/09/14 - added mpcdf_eos machine, fixed proper nouns in symmetry output (aflow.cpp,kbin.cpp,aflowrc.cpp,init.cpp,kvasp.cpp,README_AFLOW.TXT,Makefile,pflow_print.cpp) (CO+DX) 3.1.141 - 2017/09/12 - fixed sgdata/wyccar issue, added space group functions to SYM namespace, more detailed warning messages (symmetry_spacegroup.h,symmetry_spacegroup.cpp,symmetry_spacegroup_function.cpp,symmetry_spacegroup_ITC_library.cpp,aconvasp_main.cpp,pflow_print.cpp,symmetry.cpp) (DX) 3.1.140 - 2017/09/05 - added sgdata function (along with options for json output), edata updated (along with options for json output), pgroupk speed up, added covalent radii info, dos/band structure gnuplot updates (main.cpp,README_AFLOW_ACONVASP.TXT,aflow.h,aconvasp_main.cpp,lattice.cpp,pflow.h,pflow_print.cpp,symmetry.cpp,symmetry_spacegroup.cpp,symmetry_spacegroup.h,symmetry_spacegroup_functions.cpp,xatom.cpp,estructure.cpp,init.cpp) (DX+CO) 3.1.139 - 2017/08/29 - fixed edata issue (agroups/iatoms were not calculated) for library runs (README_AFLOW_ACONVASP.TXT,aconvasp_main.cpp,lattice.cpp,xatom.cpp,aflow.h) (DX) 3.1.138 - 2017/08/25 - fully functional AAPL, Pearson symbol/lattice type speed up, json serializers for symmetry groups, tolerance scan implemented for separate symmetry groups, chull latex fix (chull.cpp,aconvasp_main.cpp,aflow.h,lattice.cpp,pflow.h,symmetry.cpp,xatom.cpp,xclasses.cpp,aapl_pairs.cpp,aapl_tcond.cpp,aapl_tensor.cpp,apl.h,apl_kphonons.cpp,aurostd.h,main.cpp) (JJPR+DX+CO) 3.1.137 - 2017/08/04 - incorporated aflow.Xgroup.json, json serializers for bands/dos, print to screen options for AFLOW-SYM API, xvector/xmatrix lrows/urows/lcols/ucols bug fix, APL symmetry output append to ofstream, removed validation for sgroup (NOT NEEDED) (aconvasp_main.cpp,aflow.h,pflow.h,symmetry.cpp,xatom.cpp,README_AFLOW_ACONVASP.TXT,main.cpp,aurostd.h,xvector.cpp,xmatrix.cpp,apl_supercell.cpp,Makefile,estructure.cpp) (DX+EG+CO) 3.1.136 - 2017/08/01 - speed up getFullSymBasis, fixed some Wyckoff positions, fixed printing in apl (spacegroup vs. lattice type) (apl_pdisc.cpp,apl_phoncalc.cpp,aflow.h,symmetry.cpp,symmetry_spacegroup.cpp,symmetry_spacegroup.h,symmetry_spacegroup_ITC_library.cpp,symmetry_spacegroup_functions.cpp) (DX+CO) 3.1.135 - 2017/07/25 - fixed xOUTCAR parsing issue with lattice vectors (vasp bug) (aflow.h,ovasp.cpp) (CO) 3.1.134 - 2017/07/19 - fixed symmetry for library runs (angle/vol tolerance), added directory output, removed relaxed data from orig structure section in entry page (aflowlib_web_interface.cpp,Makefile,aconvasp_main.cpp,aflow.h,lattice.cpp,aflowlib_libraries.cpp,pflow_print.cpp,symmetry.cpp,symmetry_spacegroup.cpp,xatom.cpp,xproto.cpp) (DX+GG+CO) 3.1.133 - 2017/07/19 - AEL/AGL: Hugoniots, AEL vs pressure (CT) 3.1.132 - 2017/07/14 - added full_sym output to RAW (aflowlib_libraries.cpp) (DX+CO) 3.1.131 - 2017/07/14 - allow global aflowrc in /etc/aflow.conf plus bug fixes in aflowrc (SC) 3.1.130 - 2017/07/13 - bug fixes in aflowrc (SC) 3.1.129 - 2017/07/13 - bug fixes init.cpp aflowrc.cpp xvector.cpp (SC/CO) 3.1.128 - 2017/07/12 - more ~/.aflowrc definitions and porting to MPI-DE (SC) 3.1.127 - 2017/07/11 - more ~/.aflowrc aflow.h ivasp ovasp avasp kbin init VASP_POTCAR_* AFLOW_LIBRARY AFLOW_PROJECT (SC) 3.1.126 - 2017/07/10 - more ~/.aflowrc name_dynamics aflow.h DEFAULT_DOS estructure.cpp poccupation_edos (SC) 3.1.125 - 2017/07/10 - more ~/.aflowrc aflow.h kbin.cpp apl_phoncalc.cpp apl_kphonons.cpp (SC) 3.1.124 - 2017/07/06 - quaternion representation additions, aflowSYM bug fixes (HfV2) (lattice.cpp,xatom.cpp,aflow.h,symmetry.cpp,Makefile) (GG+DX+CO) 3.1.123 - 2017/07/06 - adding flags for METAGGA and IVDW (xclasses.cpp) (SC) 3.1.122 - 2017/07/04 - aflowrc bug fixes, clean names (SC) 3.1.121 - 2017/07/04 - aflowrc bug fixes, clean names, clean METAGGA_SET, IVDW_SET (SC) 3.1.120 - 2017/07/02 - more ~/.aflowrc aflow.h init.cpp aflowrc.cpp kbin kvasp README* VASP_FORCE* PLATON/FINDSYM (SC) 3.1.119 - 2017/07/02 - more ~/.aflowrc aflow.h init.cpp aflowrc.cpp kbin kvasp README* MACHINE DEPENDENT MPI* (SC) 3.1.118 - 2017/07/02 - more ~/.aflowrc aflow.h init.cpp aflowrc.cpp kbin kvasp README* GENERIC MPI* (SC) 3.1.117 - 2017/07/02 - more ~/.aflowrc aflow.h init.cpp aflowrc.cpp README*.TXT: AFLOW_CORE_TEMPERATURE,VASP_PREC (SC) 3.1.116 - 2017/07/01 - starting ~/.aflowrc aflow.h init.cpp aflowrc.cpp xoptions.h.cpp avasp.cpp apennsy lattice README_AFLOW_ACONVASP.TXT (SC) 3.1.115 - 2017/06/29 - XVASP_INCAR_PREPARE_GENERIC aflow.h ivasp.cpp (SC) 3.1.114 - 2017/06/29 - added new Jmol js scripts, fixed DISMAG issue with APL, checkMEMORY() mostly removed from messaging (apl_dirphoncalc.cpp,apl_kphonons.cpp,aflowlib_web_interface.cpp,entry.cpp,entry.js,kvasp.cpp,kbin.cpp,init.cpp,avasp.cpp,aflow.h,README_AFLOW_POCC.TXT,README_AFLOW_APL.TXT,README_AFLOW_AGL.TXT,README_AFLOW_AEL.TXT,README_AFLOW.TXT,Makefile) (CO) 3.1.113 - 2017/06/28 - XVASP_INCAR_PREPARE_GENERIC aflow.h ivasp.cpp (SC) 3.1.112 - 2017/06/28 - added EDIFFG --ediffg aflow.h avasp aconvasp_main ivasp kvasp xclasses README_AFLOW_CONVASP README_AFLOW (SC) 3.1.111 - 2017/06/13 - SQLITE integration (avasp.cpp ow_chull,aflowlib_web_interface,aflowlib_libraries,kbin,apl_phoncalc,README_AFLOW_VERSIONS_HISTORY.TXT,pflow_print,pflow_funcs,main,aurostd.h,bader,Makefile,aflow,SQLITE) (CO) 3.1.110 - 2017/06/13 - fixed chull invalid inputs, removed exit in loadLIBX, force output for mpi settings in APL, fixed settings in CIF writer, removed aflow.end.out from CompressDirectory(), major fixes to CHGCAR/AECCAR readers for bader analysis (CO) 3.1.109 - 2017/06/06 - fixed some chull issues (CO) 3.1.108 - 2017/06/06 - individualized QHA/AAPL workflows, set reliable convex hull standard to 200 entries (binaries), updated ill-calculated systems in the database, incorporated sort for loadEntries(), fixed DPM=AUTO in APL, fixed MCL systems (APL/aapl_tensor,apl.h,apl_kphonons,apl_lrphoncalc,apl_phoncalc,qha_eosrun,apl_dirphoncalc,Makefile,README_AFLOW.TXT,README_AFLOW_ACONVASP.TXT,README_AFLOW_AEL.TXT,README_AFLOW_AGL.TXT,README_AFLOW_ APL.TXT,README_AFLOW_POCC.TXT,README_AFLOW_VERSIONS_HISTORY.TXT,aflow,aflow.h,avasp,init,kbin,kvasp,xclasses,aconvasp_main,chull,chull.h,symmetry_spacegroup,symmetry) (CO) 3.1.107 - 2017/06/05 - online pubs management curtarolo/oses/toher (SC) 3.1.106 - 2017/06/02 - added IVDW (aflow.h avasp xclasses aconvasp_main ivasp kvasp) (SC) 3.1.105 - 2017/06/01 - added METAGGA (aflow.h avasp xclasses aconvasp_main ivasp kvasp) (SC) 3.1.104 - 2017/05/30 - set reliable convex hull standard to 200 entries (CO) 3.1.103 - 2017/05/30 - added pgroup_xtal propagation in supercell creation, also fixed ".nfs*" issues in CompressDirectory() (CO) 3.1.102 - 2017/05/29 - issues with symmetry in the aflowlib.out calculation (CO) 3.1.101 - 2017/05/26 - cosmetics and added PaddedCENTER (SC) 3.1.100 - 2017/05/26 - changed numbering style + cosmetics(SC)