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*                                                                                                  *
*                        aflow - STEFANO CURTAROLO Duke University 2003-2021                       *
*                            High-Throughput ab-initio Computing Project                           *
*                                                                                                  *
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LATEST VERSION OF THE FILE:                              materials.duke.edu/AFLOW/aflow_aconvasp.pdf
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 AFLOW POSTPROCESSING MODE (formerly called aconvasp/aqe)
  aflow --help [-h]
        Gives Help information.
  aflow --version | -v
        Gives Version Information.
  aflow --machine
        Gives Machine Information.

  aflow --check_integrity | --checki
        Check the integrity of xlib functions

  aflow --abccar < POSCAR | WYCCAR
        Converts the POSCAR or WYCCAR in format.
        POSCAR is the usual VASP file
        WYCCAR is described as
        TITLE
         SCALE (positive (rescaling) negative (volume))
         A B C ALPHA BETA GAMMA SG# [OPTION#]
         #specie0 #specie1 ....
         DIRECT (or CARTESIAN)
         .. .. .. specie0
         .. .. .. specie0
          . . .
         .. .. .. specie1
         .. .. .. specie1
         and so on. (Stefano Feb 2009)
        The positions of the species will be used with the list of
        symmetry operations (aflow_wyckoff.cpp) to generate all the atoms.

  aflow --abinit                                                                    
        Transforms the POSCAR (or whicever is the input file format) to a              
        ABINIT GEOM format.                                                  
        The geometrical file follows the ABINIT convention.   

  aflow --aims                                                                    
        Transforms the POSCAR (or whicever is the input file format) to a              
        AIMS GEOM format.                                                  
        The geometrical file follows the AIMS convention.   

  aflow --ace < POSCAR
        Outputs to standard out a cell standard ASCII (ace) file
        based on the POSCAR input file.  This can be used as input
        for CaRIne.

  aflow --aflux="<summons>"
        Command line interface to use the AFLUX Search API.
        <summons> has the same syntax as described in the article (doi: 10.1016/j.commatsci.2017.04.036).
        Though not required, it is recommended to put the summons between double quotes,
        so the user does not have to escape any parentheses.
        e.g. command:
          aflow --aflux="enthalpy_formation_atom,natoms,sg2(*',Fm-3m #225'),aurl,species((Cl:Br),(Na:K)),nspecies(2),format(aflow),paging(0)"

  aflow --use_aflow.in=XXX
        Uses XXX instead of "aflow.in" in searching/running/operating directories.
        The option is very useful for compounded calculations.
	
  aflow --aflowin  < POSCAR
        Output the structure inside the strings:
        [VASP_POSCAR_MODE_EXPLICIT]START
        structure...
        [VASP_POSCAR_MODE_EXPLICIT]STOP
        which is useful if you want to recycle partially ran aflow.in !

  aflow [options] --aflow_proto=label*:speciesA*[:speciesB*][:volumeA*[:volumeB*]|:volume] [--params=..... [--hex]]
        Creates automatic aflow.in.
        OPTIONS are:
         --usage
         --potential=pot_LDA | pot_GGA | potpaw_LDA | potpaw_GGA | potpaw_PBE | potpaw_LDA_KIN | potpaw_PBE_KIN 
         --potential_complete
         --missing
         --noautopp
         --bader (default: DEFAULT_VASP_FORCE_OPTION_BADER)
         --spin_remove_relax_1 (default: DEFAULT_VASP_FORCE_OPTION_SPIN_REMOVE_RELAX_1)
         --spin_remove_relax_2 (default: DEFAULT_VASP_FORCE_OPTION_SPIN_REMOVE_RELAX_2)
         --kscheme=[M | G] (default: DEFAULT_KSCHEME in .aflow.rc) --kscheme_static=[M | G] (default: DEFAULT_KSCHEME_STATIC in .aflow.rc)
	       --kppra=NNNN (default: DEFAULT_KPPRA in .aflow.rc) --kppra_static=NNNN (default: DEFAULT_KPPRA_STATIC in .aflow.rc) --bands_grid=NNNN (default: DEFAULT_BANDS_GRID in .aflow.rc)
         --enmax_multiply=NNNN (default: DEFAULT_VASP_PREC_ENMAX_HIGH in .aflow.rc, DEFAULT_VASP_PREC_ENMAX_ACCURATE  in .aflow.rc)
         --pressure=0,1,2  (string of kB pressures separated by commas)
 	       --module=[APL | QHA | AAPL]
         --apl_supercell=NxNxN
         --potim=XXX (default: DEFAULT_VASP_PREC_POTIM in .aflow.rc)  (VASP) 
         --relax_type=[ALL | IONS | CELL_SHAPE | CELL_VOLUME | IONS_CELL_VOLUME | IONS_CELL_SHAPE] (overrides relax_mode) (VASP)
         --relax_mode=[ENERGY | FORCES | ENERGY_FORCES | FORCES_ENERGY] (default: DEFAULT_VASP_FORCE_OPTION_RELAX_MODE_SCHEME in .aflow.rc) (VASP)
         --relax_count=XX (default: DEFAULT_VASP_FORCE_OPTION_RELAX_COUNT in .aflow.rc) (VASP)
         --run_relax_static
         --run_relax_static_bands
         --precision=[(LOW | MEDIUM | NORMAL | HIGH | ACCURATE), PRESERVED] (default: DEFAULT_VASP_FORCE_OPTION_PREC_SCHEME in .aflow.rc) (VASP)
         --metagga=[TPSS | RTPSS | M06L | MBJL | SCAN | MS0 | MS1 | MS2 | NONE] (default: DEFAULT_VASP_FORCE_OPTION_METAGGA_SCHEME in .aflow.rc) (VASP)
	       --ivdw=[number_for_VASP_see_manual_for_IVDW | 0] (default: DEFAULT_VASP_FORCE_OPTION_IVDW_SCHEME in .aflow.rc) (VASP)
	       --algorithm=[(NORMAL | VERYFAST | FAST | ALL | DAMPED), PRESERVED] (default: DEFAULT_VASP_FORCE_OPTION_ALGO_SCHEME in .aflow.rc) (VASP)
         --type=[METAL | INSULATOR | SEMICONDUCTOR | DEFAULT] (default: DEFAULT_VASP_FORCE_OPTION_TYPE_SCHEME in .aflow.rc) (VASP)
         --convert_unit_cell= (SPRIM, SCONV, NIGGLI, MINK, INCELL, COMPACT, WS, CART, FRAC, PRES)
         --volume_plus_equal=XXX 
         --volume_multiply_equal=XXX
         --volume_preserved
	       --ediffg=XXX (default: DEFAULT_VASP_PREC_EDIFFG_XXXX in .aflow.rc)  (VASP) 
         --ldau2  
         --noldau2  
         --bands
         --neglect_nomix
         --stdout
         --qe
         --abinit
         --aims
         --atat
         --list
         --params=....  { check aflow --readme=anrl }
         --hex          { check aflow --readme=anrl }

        This command generates the directory: ./AFLOWDATA/speciesAspeciesB/label/
        and create an aflow.in inside with the "label" structure from
        HTQC library project, with speciesAs, speciesBs,.. and the volumes per atoms,
        volumeAs, volumeBs,.. (real in A^3).
        Aflow generates a huge number, #speciesAs*#speciesBs...*#label[*#pressures],
        of directories containing all the combinations of
        ./AFLOWDATA/speciesAspeciesB../label:pressure
        and so on. This is helpful for generating huge databases.

        Be careful to include the various "_pv,_sv, etc" in the species so that
        the POTCAR makes sense.
        HIGH-THROUGHPUT NOTE: label, speciesA, speciesB, volumeA, volumeB can be
        multiple strings separated by commas without spaces in between such as
        Note that that --aflow_proto label A B ... is not supported anymore and you now need to use
        --aflow_proto=label:A:B... et cetera.

      LABEL
	  label* = string of label1,label2,label3,... separated by commas ","
         specify which labels/prototypes to generate

      SPECIES
        speciesA* = string of speciesA1,speciesA2,speciesA3,... separated by commas ","
         specify which species in position A to consider.
        speciesB* = string of speciesB1,speciesB2,speciesB3,... separated by commas ","
         specify which species in position B to consider.
        similarily you can have speciesC*,speciesD*, and so on.

      VOLUMES
        volumeA* = string of volumeA1,volumeA2,volumeA3,... separated by commas ","
         specify the volumes of speciesAs, the number must be identical to the number
         of speciesAs otherwise you get an error.
        volumeB* = string of volumeB1,volumeB2,volumeB3,... separated by commas ","
         specify the volumes of speciesBs, the number must be identical to the number
         of speciesBs otherwise you get an error.
        similarily you can have volumeC*,volumeD*, and so on.
        If you want to set one volume per atom, identical to all the species, then
        specify only one number as species...:volume .

      USAGE
        With --usage a brief syntax help comes out.

      POTENTIALS
        The user can specify the potential type.
        --potential=pot_LDA | pot_GGA | potpaw_LDA | potpaw_GGA | potpaw_PBE | potpaw_LDA_KIN | potpaw_PBE_KIN 
        If not specified it takes potpaw_PBE and the standard default for the species.
        With --potential_complete it creates the subdirectory containing the type and
        date of the potentials: i.e. Ti_sv => Ti_sv:PAW_GGA:07Sep2000
        With the option --noautopp, then you have to be careful to include the various
        "_pv,_sv, etc" in the species so that the POTCAR makes sense.

      MISSING
        With the option --missing  it creates automatic aflow.in only for the missing .
        structures of the database. It checks on:
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB0))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB1))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB2))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB3))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB4))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB5))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB6))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB7))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB8))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB9))/LIB/        of AFLOW_MATERIALS_SERVER
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD))/LIB/        of AFLOW_MATERIALS_SERVER
    
     BADER CALCULATION
        With --bader, the proper flags are set in the INCAR to write the AECCAR's for the bader calculation.

     SPIN_REMOVE_RELAX_1 _2
        With --spin_remove_relax_1 _2, the user can indicate when to avoid a spin-polarized calculation if
        the system's magnetic moment is negligible.
       
     KPOINTS SPECIFICATION
        With --kppra=NNN the user can specify a NNN number of kpoints per reciprocal atom.
        Input KPPRA (6,000-10,000 recommended) is the lower bound of the product of the 
        (total count of k-points in the 3-D grid) and 
        (number of atoms in the cell). 
        The smallest mesh to satisfy this requirement is calculated. 
        Effectively, cells with more atoms will yield smaller grid meshes.
        The user can also specify the scheme with --kscheme=[M | G].
        The static variants can also be set via command-line.
 
     PRESSURE CALCULATIONS
        The user can run calculations under pressure by adding --pressure (kB).
        --pressure=p0[,p1][,p1]...
        Example
        --pressure=10,20,30
        Then the data will be generated as directories containing all the combinations of
        ./AFLOWDATA/specieAspecieB/label:P=p0/
        ./AFLOWDATA/specieAspecieB/label:P=p1/
        The input file aflow.in will contain the correct PSTRESS=** entry
    
      BANDS CALCULATIONS
        The user can run bands by adding --bands

      MODULE PARAMETERS
        The user can set up a module-specific run by adding --module=MODULE, where
        current options include APL (harmonic phonon analysis), QHA (quasi-harmonic phonon analysis),
        and AAPL (anharmonic phonon analysis).
        This option will, e.g., uncomment [AFLOW_APL]CALC.
        [APL | QHA | AAPL]
        
      APL MODULE PARAMETERS
        Use --apl_supercell=NxNxN to override MINATOMS tag and set the supercell size

      POTIM PARAMETER
        For some systems VASP requires POTIM smaller than the default
        0.5. See the VASP Manual.

      RELAX_TYPE
        One of the RELAX_TYPEs specified in the AFLOW manual (VASP only).
        [ALL | IONS | CELL_SHAPE | CELL_VOLUME | IONS_CELL_VOLUME | IONS_CELL_SHAPE] (overrides RELAX_MODE)

      RELAX_MODE
        One of the RELAX_MODEs specified in the AFLOW manual (VASP only).
	      [ENERGY | FORCES | ENERGY_FORCES | FORCES_ENERGY] (default: DEFAULT_VASP_FORCE_OPTION_RELAX_MODE_SCHEME in .aflow.rc)

      RELAX_COUNT
        Set the number of relaxations (VASP only).
        (default: DEFAULT_VASP_FORCE_OPTION_RELAX_MODE_SCHEME in .aflow.rc)

      RUN_RELAX_STATIC
        Run relaxation (geometry) and static (DOS) runs (VASP only).
      
      RUN_RELAX_STATIC_BANDS
        Run relaxation (geometry), static (DOS), and bands (band structure) runs (VASP only).

      PRECISION
        One of the PRECISIONs specified in the AFLOW manual (VASP only).
        [(LOW | MEDIUM | NORMAL | HIGH | ACCURATE), PRESERVED] (default: DEFAULT_VASP_FORCE_OPTION_PREC_SCHEME in .aflow.rc)

      ALGORITHM
        One of the ALGORITHMs specified in the AFLOW manual (VASP only).
        [(NORMAL | VERYFAST | FAST | ALL | DAMPED), PRESERVED] (default: DEFAULT_VASP_FORCE_OPTION_ALGO_SCHEME in .aflow.rc)
	
      TYPE
        One of the TYPEs specified in the AFLOW manual (VASP only).
        [METAL | INSULATOR | SEMICONDUCTOR | DEFAULT] (default: DEFAULT_VASP_FORCE_OPTION_TYPE_SCHEME in .aflow.rc)

      CONVERT_UNIT_CELL
        One of the CONVERSIONs specified in the AFLOW manual (VASP only).
        [SPRIM, SCONV, NIGGLI, MINK, INCELL, COMPACT, WS, CART, FRAC, PRES]
	
      VOLUME CHANGES
        Volume plus equal adds XXX to the current volume.
       	Volume multiply equal multiplies XXX to the current volume.
	      Avoid any volume changes with --volume_preserved tag


      POTIM
        --potim=XXX parameter overrides the default value (default: DEFAULT_VASP_PREC_POTIM in .aflow.rc) for appropriate ionic steps.
	
      EDIFFG
        --ediffg=XXX parameter overrides the default value (default: DEFAULT_VASP_PREC_EDIFFG_XXXX in .aflow.rc) for very precise relaxed forces calculations.
	
      LDAU CALCULATIONS (FORCING IT ON AND OFF)
        The user can run bands by adding --ldau2 and the code will take the default ldau
        parameters that are specified inside aflow_avasp.cpp.
        If you do not like them, you can modify the cpp code OR change the lines inside aflow.in
        [VASP_FORCE_OPTION]LDAU2=ON
        [VASP_FORCE_OPTION]LDAU_PARAMETERS=Bi,Li,Zn;1,-1,2;0,0,7.5;0,0,0 // species;Ls;Us;Js
        For some reference systems, LDAU is taken by default. Then the user can remove it
        with --noldau.

      MIXING (TO MIX OR NOT TO MIX)
        Some systems is known to be no-mix, and they will be skipped from the calculations.
        To override this automatism, specify --neglect_nomix .

      STDOUT output
        If you specify --stdout, aflow will not write the file but print on the screen.

      QUANTUM ESPRESSO output                                                                     
        If you specify --qe, aflow will add QUANTUM ESPRESSO code to aflow.in (experimental).   

      ABINIT output                                                                     
        If you specify --abinit, aflow will add ABINIT code to aflow.in (experimental).   

      AIMS output                                                                     
        If you specify --aims, aflow will add AIMS code to aflow.in (experimental).   

      LIST output
        If you specify --list, aflow will not generate the aflow.ins but only report the
         ones to be created (useful for scripting).

      ANRL: AFLOW NAVAL RESEARCH LAB PROTOTYPE LIBRARY
        With respect to the article:
        Mehl et al., "The AFLOW Library of Crystallographic Prototype", https://arxiv.org/abs/1607.02532
        the code gives the possibility to define the parameters of the cell --params=...
        Some rhombohedral cells can be generated in hexagonal configurations (see the article).
        The choice is performed with the flag --hex.
        Check aflow --readme=anrl 

  aflow --aflow_proto=label[:]specieA[:]specieB[:]volume
        Same as above but the volume per atoms are extracted from the
        most dense paw_pbe values (usually the ground state) and with
        the Vegard`s law  (Vegard's law is an approximate empirical rule
        which holds that a linear relation exists, at constant temperature,
        between the crystal lattice constant of an alloy and the
        concentrations of the constituent elements).
        HIGH-THROUGHPUT NOTE: label, specieA, specieB can be
        multiple strings separated by commas without spaces in between such as
        label1,label2,label3          generate all the labels
        specieA1,specieA2,specieA3    goes through all specieAs times all Bs
        specieB1,specieB2             goes through all specieBs times all As
        In this case aflow generates a huge number, #labels*#specieAs*#specieB
        of directories containing all the combinations of
        ./AFLOWDATA/specieA?specieB?/label?
        and so on. This is helpful for generating huge databases.
        PRESSURE, POTENTIALS, BANDS calculations are allowed, see above.
        STDOUT option available.

	  
  aflow --aflowSG|--space_group|--sg|--aflowSG_number|--space_group_number|--sg_number|--aflowSG_label|--space_group_label|--sg_label[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--tolerance_spectrum=start:stop:nsteps] < file
        Calculates the space group of the crystal in the ITC convention.
        This routine employs an adaptive tolerance scheme; if any symmetry 
        rules are broken, the tolerance is changed and everything is recalculated.
        The space group number and international symbol are printed by default.
        The commands "--aflowSG_number", "--space_group_number", and "--sg_number" only return the space group number.
        The commands "--aflowSG_label", "--space_group_label", and "--sg_label" only return the space group label.
        Can be called inside aflow via:
              xstructure.SpaceGroup_ITC()        (default tolerance)
              xstructure.SpaceGroup_ITC(tol)     (user defined tolerance)
        This is the AFLOW counterpart to platonSG and findsymSG.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum 
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Performs crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--tolerance_spectrum=start:stop:nsteps] : Performs symmetry analysis for a range of tolerance values
        Check aflow --readme=symmetry
 
  aflow --alphabetic < POSCAR
        Makes the structure in alphabetic order (if possible).

  aflow --alpha_compound=string1,string2,.... 
        Makes the alphabetic "compound" from the name of string. For instance
        aflow --alpha_compound=Zr15.6Ag2Mg14
        returns Ag2Mg14Zr15.6
  aflow --alpha_species=string1,string2,.... 
        Makes the alphabetic "species" from the name of string. For instance
        aflow --alpha_species=Zr15.6Ag2Mg14
        returns AgMgZr

  aflow --analyze_database
        Outputs the statistics of the AFLOW database file into a JSON file. The
        locations of the files needs to be defined in the .aflow.rc file.

  aflow --angle=cutoff < POSCAR  
        Outputs to standard out the angles for each atom triplet
        made up of neighors within a distance cutoff of each other.  
        Actually, since this can be huge, only the first MAX_NUM_ANGLE-1
        neighbors within d are used.  MAX_NUM_ANGLE=21 at present and
        can be set in aflow_pflow_print.cpp

  aflow --bader -D DIRECTORY
        options:
            [ --usage ]
            [ --critical_points|--cp ]
            [ --calculate=|--calc=bader|voronoi ]
            [ --nocalculate=|--nocalc=bader|voronoi ]
            [ --partition=|--part=neargrid|ongrid ]
            [ --refine_edge_method=|--rem=-1|-2|-3 ]
            [ --reference=|--ref=REF_FILE ]
            [ --vacuum=|--vac=off|auto|DENSITY_THRESHOLD ]
            [ --terminate=|--term=known|max ]
            [ --print_all=atom|bader|both ]
            [ --print_index=|--print_idx=atom|bader|both ]
            [ --print_select_atom=|--print_sel_atom=[LIST OR RANGE] ]
            [ --print_select_bader=|--print_sel_bader=[LIST OR RANGE] ]
            [ --print_sum_atom=[LIST OR RANGE] ]
            [ --print_sum_bader=[LIST OR RANGE] ]
            [ --quiet|--q ]
            [ --consolidate_atoms2species|--a2s ]
            [ --remove_bader_atoms|--rba ]
            [ --jvxl_all_species=|--jvxl=CUTOFF1,CUTOFF2...[::DOWNSAMPLE1,DOWNSAMPLE2,..]
                                        |CUTOFF1[,DOWNSAMPLE1:CUTOFF2,DOWNSAMPLE2:...]
                                        |CUTOFF[,DOWNSAMPLE] ]
		    [ --keep=jvxl_only|--jvxl_only ]
            [ -D DIRECTORY ]
        
        Perform Bader charge analysis by means of FORTRAN code from the Henkelman Group
        at UT, Austin. http://theory.cm.utexas.edu/bader/
        
        DIRECTORY is the path to the data from VASP. 
        If this is omitted, it will assume the desired path is the one from which the 
        command is called.
        The following files are required to be present in DIRECTORY:
            CHGCAR.static|CHGCAR
            OUTCAR.static|OUTCAR
            POSCAR.static|POSCAR
            [ AECCAR0.static|AECCAR0 ]  }   OR A CORRESPONDING REFERENCE CHARGE DENSITY FILE 
            [ AECCAR2.static|AECCAR2 ]  }   (explained below)
        though they can be compressed as .bz2, .gz or .xz files.
        
        Description of flags and, if applicable, corresponding bader code command:

            --calculate=|--calc=bader|voronoi
            --nocalculate=|--nocalc=bader|voronoi
            [ corresponding bader code command:  -c | -n  < bader | voronoi > ]
                Turn on [-c] or off [-n] the following calculations
                    bader: Bader atoms in molecules (default)
                    voronoi: population analysis based on distance
            WARNING: If you specify --nocalc=bader without a --calc command, the bader 
            code is not expected to produce any files. 
            It is sufficient to specify --calc=voronoi without --nocalc=bader.
            EXPECTED FILES: ACF.dat, AVF.dat, BCF.dat, LABEL_abader.out (net charges 
            and atomic volumes calculated from bader code).

            --partition=|--part=neargrid|ongrid
            [ corresponding bader code command -b < neargrid | ongrid > ]
                Use the default near-grid bader partitioning or the
                original on-grid based algorithm.
            
            --refine_edge_method=|--rem=-1|-2|-3
            [ corresponding bader code command -r < refine_edge_method > ]
                By default (-r -1) , only the points around reassigned
                points are checked during refinements. The old method,
                which checks every edge point during each refinement, can
                be enabled using the -r -2 switch:
                A new weight method developed by Yu and Trinkle and be
                enabled with the -r -3 switch.

            --reference=|--ref=REF_FILE
            [ corresponding bader code command -ref REF_FILE ]
                By default, AFLOW will sum the AECCAR0 and AECCAR2 to form the aflow.CHGCAR_sum file.  
                However, this can be overridden by specifying a desired reference file.
            EXPECTED FILES: aflow.CHGCAR_sum

            --vacuum=|--vac=off|auto|DENSITY_THRESHOLD
            [ corresponding bader code command -vac < off | auto | vacuum_density > ]
                Assign low density points to vacuum.
                    auto: vacuum density cutoff is 1E-3 e/Ang^3 (by default in AFLOW)
                    off: do not assign low density points to a vacuum volume
                    DENSITY_THRESHOLD: a float designating the maximum density assigned to a vacuum volume

            --terminate=|--term=known|max
            [ corresponding bader code command -m < known | max > ]
                Determine how trajectories terminate
                    known: stop when a point is surrounded by known points
                    max: stop only when a charge density maximum is reached

            --print_all=atom|bader|both
            [ corresponding bader code command -p < all_atom | all_bader > ]
                Print calculated volumes (containing charge above threshold of 0.0001 electrons)
                    atom: all atomic volumes
                    bader: all Bader volumes 
            EXPECTED FILES: BvAtxxxx.dat/Bvolxxxx.dat
        
            --print_index=|--print_idx=atom|bader|both
            [ corresponding bader code command -p < atom_index | bader_index > ]
                Print corresponding volume index
                    atom: atomic volume index
                    bader: bader volume index
            EXPECTED FILES: AtIndex.dat/BvIndex.dat

            --print_select_atom=|--print_sel_atom=[LIST OR RANGE]
            [ corresponding bader code command -p sel_atom [LIST OR RANGE] ]
                Print specified atomic volumes.  
                List or range corresponds to 1,2,3 (comma-separated) or 1-3 (hyphen-separated).
            EXPECTED FILES: BvAtxxxx.dat

            --print_select_bader=|--print_sel_bader=[LIST OR RANGE]
            [ corresponding bader code command -p sel_bader [LIST OR RANGE] ]
                Print specified bader volumes.
                List or range corresponds to 1,2,3 (comma-separated) or 1-3 (hyphen-separated).
            EXPECTED FILES: B_wexxxx.dat (artifact of bader code)

            --print_sum_atom=[LIST OR RANGE]
            [ corresponding bader code command -p sum_atom [LIST OR RANGE] ]
                Print sum of specified atomic volumes.
                Consider using aflow --chgsum command instead.    
                List or range corresponds to 1,2,3 (comma-separated) or 1-3 (hyphen-separated).
            EXPECTED FILES: BvAt_summed.at

            --print_sum_bader=[LIST OR RANGE]
            [ corresponding bader code command -p sum_bader [LIST OR RANGE] ]
                Print sum of specified bader volumes.
                Consider using aflow --chgsum command instead.    
                List or range corresponds to 1,2,3 (comma-separated) or 1-3 (hyphen-separated).
            EXPECTED FILES: Bvol_summed.at

            --quiet|--q
                No output printed to screen.

            --consolidate_atoms2species|--a2s
                Combine all atomic volumes to form species volumes.
            EXPECTED FILES: BvAt_SPECIES.dat
            
            --remove_bader_atoms|--rba
                Remove individual atomic volumes. 
                Useful if you only want to keep species volumes.
                Only read if --a2s specified.

            --jvxl_all_species=|--jvxl=CUTOFF1,CUTOFF2...[::DOWNSAMPLE1,DOWNSAMPLE2,..]
                                      |CUTOFF1[,DOWNSAMPLE1:CUTOFF2,DOWNSAMPLE2:...]
                                      |CUTOFF[,DOWNSAMPLE]
                Generate .jvxl files of all species volumes at the specified cutoffs.
                A .jvxl file is a space-efficient file format for surface charges read by Jmol.
                See http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf.
                You may also specify a downsample ratio. 
                This will reduce the number of points on the surface by the specified factor.
                You may produce multiple .jvxl files in the following ways:
                    CYCLIC MODE (::)
                        Every combination of cutoff [and downsample_ratio] will be produced
                    SETS MODE (:)
                        Provide sets of cutoff [and corresponding downsample_ratio] to be produced
                WARNING: while you may specify a cutoff of arbitrary precision, the label of the 
                         output file will only show precision to the nearest hundredth.
            EXPECTED FILES: LABEL_Bader_CUTOFF_DOWNSAMPLE_RATIO_SPECIES.jvxl

            --keep=jvxl_only|--jvxl_only
                After producing .jvxl files, remove atomic and species volume files.
                Only read if --jvxl specified.
                                        
            NOTE:  
                
                Multiple print command can be issued, with the exception of:
                --print_all=atom && --print_sel_atom=[LIST OR RANGE]
                --print_all=bader && --print_sel_bader=[LIST OR RANGE]
                By default, the program will ignore the latter command and only 
                execute the former (--print_all).

                All CHG files printed from bader code will have its header amended
                so that it may be read by Jmol.
                See --prepare_chgcar_4_jmol command for more information.
        
        Bader Charge code reference:
        http://theory.cm.utexas.edu/henkelman/code/bader/
        W. Tang, E. Sanville, and G. Henkelman. J. Phys.: Condens. Matter 21, 084204 (2009). 
        E. Sanville, S. D. Kenny, R. Smith, and G. Henkelman. J. Comp. Chem. 28, 899-908 (2007). 
        G. Henkelman, A. Arnaldsson, and H. Jonsson. Comput. Mater. Sci. 36, 254-360 (2006).

  aflow --bandgap[=bands_directory1[,bands_directory2,...]]
        Calculates the energy gap and band edges of a material by looking at the occupancies in the OUTCAR file.
        On output it produces the following background system information:
        System      : The system name, identical to the SYSTEM tag in the OUTCAR.
        Spin tag    : Whether it is a spin polarized / unpolarized calculation.
        Fermi level : Obtained from the E-fermi tag in the OUTCAR.
        -----------------------
        The energy gap (Egap) and band edges (Valence Band Top, VBT, and Conduction Band Bottom, CBB) are then
        output in table format, with 5 signficant figures.
        -----------------------
        Unpolarized example:
                          VBT           CBB           Egap         Type
        Net Result    :   0.0000e-00    0.0000e+00   +0.0000e+00   insulator_direct    
        -----------------------
        Polarized example:
                         VBT           CBB           Egap         Type
        Majority Spin :   0.0000e+00    0.0000e+00    0.0000e+00   insulator_indirect  
        Minority Spin :  -1.0000e+00   -1.0000e+00   -1.0000e+09   metal               
        Net Result    :   0.0000e+00    0.0000e+00    0.0000e+00   insulator_direct    
        -----------------------
        Special for metallic materials: the edges are arbitrarily set to -1 and the gap is arbitrarily set to
        -1.0E-09. The "Net Result" is the overall gap and edges of the system. Note that the band edges have been 
        referenced to the Fermi energy.
        -----------------------
        There are several meaningful tags (separated by "_") provided under "Type", including:
          (half-)metal:     no band gap present in at least one of the spin-channels
          insulator:        band gap present
          (in)/direct:      issued for insulators, specifies whether VBT and CBB come from the same k-point
          zero-gap:         issued for insulators with a negligible gap (tol===1e-4 eV)
          spin-polarized:   issued for spin-polarized insulators where VBT and CBB come from different spin-channels
          empty(-partial):  issued for materials where no band edge is detected for at least a single k-point (OBSOLETE, warning issued now)
        -----------------------
        Sample output for a Spin-polarized material, Cr1O2_ICSD_186838:
        System        :   Cr1O2_ICSD_186838
        Spin tag      :   2  
        Fermi level   :  +5.2091e+00
                          VBT           CBB           Egap          Egap_fit     Type
        Majority Spin :  -1.0000e+00   -1.0000e+00   -1.0000e+09   -1.0000e+09   metal
        Minority Spin :  -4.9230e-01   +2.1851e+00   +2.6774e+00   +4.5221e+00   insulator-indirect
        Net Result    :  -1.0000e+00   -1.0000e+00   -1.0000e+09   -1.0000e+09   half-metal
 
  aflow --bandgaps < dirlist
		  Similar to --bandgap, the directories of bands runs are stored in
		  file "dirlist", one directory per line
		  (see also --calculated=bandgaps)

  aflow --bands=PROOUT < POSCAR
        Outputs the up and down bands to band.up.out and band.dn.out.
        Format is
        k-space path length (true, fractional), bands (up or down),
        nkpt, kx, ky, kz
        Uses data in PROOUT file.  Uses POSCAR to get lattice to calculate
        true recipricol distances.  Must run vasp with LORBIT=2 to get
        the PROOUT file.

  aflow --bs | --band_structures
        Given a calculation with all the parts (static,bands) creates the
        subdirectory BANDS with the band structures files.

  aflow --bzdirections | --bzd < POSCAR
        Calculates lattice and print a nice looking KPOINTS in VASP format
        for the AFLOW standard lattice (Setyawan and Curtarolo, 2010). 
        Options:
          [--transform2original]: Use this option if you need consistent labels for reciprocal lattice points 
                                  of a non-standard AFLOW lattice. 
                                  For low symmetry space groups several equivalent cell choices exist 
                                  and k-point labels must be transformed accordingly. 
                                  If the metric tensor of your cell choice and the AFLOW standard lattice 
                                  differ this option will transform the AFLOW standard k-points labels/path 
                                  back to your cell choice. (addition suggested by Prof. B. Kiefer) 
          [--print_transformation_matrix]: Print the transformation matrices P and Q(=P^1) with output.
                                           (addition suggested by Prof. B. Kiefer)

  aflow --bzdirections= | --bzd=LATTICE
        Print a nice looking KPOINTS in VASP format for one of the lattices,
        where the lattices are in their conventional-primitive form (kpoints
        are fractional of the reciprical lattice of the CONVENTIONAL primitive).
LATTICES = (the ones with "") 
        1. TRI order: kalpha,kbeta,kgamma  > 90 (kgamma<kalpha, kgamma<kbeta) 
           or kalpha,kbeta,kgamma  < 90 (kgamma>kalpha, kgamma>kbeta) 
           special case when kgamma=90 
           "TRI1a" kalpha>90 kbeta>90 kgamma>90 
           "TRI1b" kalpha<90 kbeta<90 kgamma<90 
           "TRI2a" kalpha>90 kbeta>90 kgamma=90 
           "TRI2b" kalpha<90 kbeta<90 kgamma=90 
        2. "MCL" unique (order b<=c) 
        3. MCLC (order alpha<90) 
           "MCLC1"  kgamma>90 
           "MCLC2"  kgamma=90 
           "MCLC3"  kgamma<90, b*cos(alpha)/c + (b*sin(alpha)/a)^2 < 1 
           "MCLC4"  kgamma<90, b*cos(alpha)/c + (b*sin(alpha)/a)^2 = 1 
           "MCLC5"  kgamma<90, b*cos(alpha)/c + (b*sin(alpha)/a)^2 > 1 
        4. "ORC" unique (order a<b<c) 
        5. "ORCC" unique (order a<b) 
        6. ORCF (order a<b<c) 
           "ORCF1" "ORCF_invb2+invc2<inva2"  for 1/a^2 > 1/b^2 + 1/c^2 
           "ORCF2" "ORCF_inva2<invb2+invc2"  for 1/a^2 < 1/b^2 + 1/c^2 
           "ORCF3"                           for 1/a^2 = 1/b^2 + 1/c^2 
        7. "ORCI" unique (order a<b<c) 
        8. "TET" unique (order a a c) 
        9. BCT (order a a c) 
           "BCT1" "BCT_c<a" for c<a 
           "BCT2" "BCT_c>a" for c>a 
        10. "RHL1" alpha<90 
            "RHL2" alpha>90 
        11. "HEX" unique (order 60 90 90) 
        12. "CUB" unique 
        13. "FCC" unique (order 60 60 60) 
        14. "BCC" unique 

  aflow --BZmax < POSCAR
        Calculates the distance between high-symmetry K points and Gamma point
        in the reciprocal space, and sorts them.

  aflow --bzplot | --plotbz < POSCAR
        Reads POSCAR from stdin and makes brillouin zone image file "bzplot.eps" and "bzplot.png".
        The data for plotting is saved in bzplot.dat and the script to make the plot is saved in plotbz.sh.
    	plotbz.sh can be modified by hand to make further adjustment of the figure.
  aflow --bzplotdata < POSCAR > bzplot.dat
        Reads POSCAR and generates data for brillouin zone and kpath plotting.
        The data is outputted to stdout (cout).
 
  aflow --bzplotuseKPOINTS=KPOINTS < POSCAR
  aflow --bzplotdatauseKPOINTS=KPOINTS < POSCAR > bzplot.dat
        Analogous to --bzplot and --bzplotdata respectively, however the first word of the first line
        in KPOINTS file is used as the str_sp.bravais_lattice_variation_type to get the kpath (as opposed to
        doing --sp of the POSCAR).

  aflow [--np=NP] --cages[=roughness] < POSCAR
        Returns the center, radius and coordination (with atoms number)
        of the cages for interstitial defects (SC Nov07).
        It prints all the cages generated by putting spheres between
        four, three and two points, stable and metastable respectively.
        After finding all the cages (REDUCIBLE) the algorithm removes the
        ones symmetrically equivalent (by using the space group calculated
        at the beginning). The cages that are worth simulating are the
	IRREDUCIBLE ones.
 	  Radius is the radius includeing the scale.
        P is the number of points used to find the sphere.
        C is the coordination of the sphere (the number of atoms on its
        surface, from radius to radius+roughness.
        T is the label of the irreducible cage. You can see in the last
        part of the output the lables of the reduced cages.
        NOTES: If you specify "--np=NP", a concurrent number of NP posix
        threads will be started to speed the calculation in a multicpu-
        multicore environent.

  aflow --calculated=icsd --random 
       Print one of the available calculated directories (usefull for webs).
  aflow --calculated[[=]all|icsd|lib0|lib1|lib2|lib3|lib4|lib5|lib6|lib7|lib8|lib9]
       "all":  print the total number of calculations in the databases.
       "icsd": print the list of calculated ICSD-structures.
       "lib0": print the list of calculated pure isolated systems.
       "lib1": print the list of calculated pure systems.
       "lib2": print the list of calculated binary systems.
       "lib3": print the list of calculated ternary systems (magnetic, Heusler projects, etc.)
       "lib4": print the list of calculated 4-species systems (very few)
       "lib5": print the list of calculated 5-species systems (very few)
       "lib6": print the list of calculated 6-species systems (very few)
       "lib7": print the list of calculated 6-species systems (very few)
       "lib8": print the list of calculated 6-species systems (very few)
       "lib9": print the list of calculated 6-species systems (very few)
 
  aflow --cart [-c] < POSCAR
        Outputs to standard out a new POSCAR file with atom
        positions in cartesian coordinates.

  aflow --cce[=STRUCT_FILE --usage]
        Prints user instructions for CCE.
  aflow --cce|--cce_correction=STRUCT_FILE
        options:
            [ --usage ]
            [ --functionals=PBE|LDA|SCAN]
            [ --enthalpies_formation_dft|dft_formation_enthalpies=form_enthalpy_1,form_enthalpy_2,...]
            [ --oxidation_numbers=ox_num_1,ox_num_2,...]
            [ --print=json|out] (default is out)

        Prints the results of the full CCE anaysis, i.e. cation coordination numbers, oxidation numbers,
        and CCE corrections and formation enthalpies, for the given structure file. It can be in any
        structure format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF. For VASP,
        a VASP5 POSCAR is required or, if a VASP4 POSCAR is used, the species must be written on the right
        side next to the coordinates for each atom.
        Precalculated DFT formation enthalpies can be provided as a comma separated list using the option
        --enthalpies_formation_dft= in eV/cell.
        Functionals for which corrections should be returned can be provided as a comma separated list 
        using the option --functionals=. If used together with --dft_formation enthalpies, the functionals
        must be in the same sequence as the DFT formation enthalpies they correspond to. 
        Oxidation numbers can be provided as a comma separated list using the option --oxidation_numbers=
        It is assumed that: (i) one is provided for each atom of the structure and (ii) they are in the 
        same sequence as the corresponding atoms in the provided structure file.
        Output in json format can be obtained using the option --print=json

  aflow --chgcar2jvxl=|--c2j=CHGCAR11[,CHGCAR2,...]::CUTOFF1,CUTOFF2...[::DOWNSAMPLE1,DOWNSAMPLE2,...]
                              |CHGCAR1,CUTOFF1[,DOWNSAMPLE1:CHGCAR2,CUTOFF2[,DOWNSAMPLE2:...]]
                              |CHGCAR,CUTOFF[,DOWNSAMPLE]
        options:
            [ --usage ]
            [ --output=|--o=OUTPUT_FILE ]
        
        Converts a surface data file (e.g. CHGCAR file) to a .jvxl file at a specified cutoff.
        See http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf.
        You may also specify a downsample ratio. 
        This will reduce the number of points on the surface by the specified factor.
        You may produce multiple .jvxl files in the following ways:
            CYCLIC MODE (::)
                Every combination of cutoff [and downsample_ratio] will be produced
            SETS MODE (:)
                Provide sets of cutoff [and corresponding downsample_ratio] to be produced
        You may specify the name of the output file (ending with .jvxl) ONLY if sets are provided.
        WARNING: while you may specify a cutoff of arbitrary precision, the label of the 
                 output file will only show precision to the nearest hundredth.
  aflow --chgdiff=CHGCAR1,CHGCAR2 
        options:
            [ --usage ]
            [ --output=|--o=CHGCAR_OUT ]

        This takes the difference between two CHGCAR files, outputting
        CHGCAR1-CHGCAR2.  The output is in the form of a vasp46s  
        CHGCAR.  The output file is aflow_CHGDIFF.out (unless otherwise
        specified).  

  aflow --chgsum=CHGCAR1,CHGCAR2,...
        options:
            [ --usage ]
            [ --output=|--o=CHGCAR_OUT ]

        This finds the sum between two or more CHGCAR files.  The output 
        is in the form of a vasp46s CHGCAR.  
        The output file is aflow_CHGSUM.out (unless otherwise
        specified).  
  aflow --chgint CHGCAR
        Outputs to standard out the integrated charge density around  
        every atom.  The total integrated density within the Voronoi  
        volume is given for each atom.  The code also calculates  
        the integrated density in a surrounding sphere for each atom.  
        This is output as a function of radius for radii from 0 to 3  
        angstrom in steps of 0.1 angstrom.  The total,Up-Dn,Up,Dn  
        charges are all integrated although for non-spin polarized  
        calculations only the first gives new information. The code
        works on all the recent versions of vasp we have tried but they  
        seem to change the CHGCAR formatting sometimes so it may crash  
        on different versions (at least 4.4.1 and 4.4.5 (including PAW)  
        work).  For a large cell this can take a while (e.g., 80 atoms  
        might take ~20 minutes).  vasp4631 ok.
  
  aflow --cif[=<tolerance_value>|=tight|=loose] [--no_scan] [--no_symmetry] [--setting=1|2|aflow] < file
        Converts a geometry file to a Crystallographic Information File (CIF).
        By default, a symmetry analysis is performed via AFLOW-SYM; however, this can be suppresed
        with --no_symmetry, printing the positions explicitly (i.e., representing as space group 1).
        This can be used as input for Mercury, and is the preferred  
        format in Gerd's structure collection.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Space group setting:
          The space group setting can be specified with the optional flag [--setting=1| =2] (the default is setting 1).
          For rhombohedral systems, setting 1=rhl and 2=hex.
          For monoclinic systems, setting 1=unique axis-b and 2=unique axis-c.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--no_scan]                              : Suppresses tolerance scan.
          [--no_symmetry]                          : Ignores symmetry analysis and returns the CIF with space group 1.
          [--setting=1|2|aflow]                    : Specifies the space group setting. The `aflow' setting follows the choices of the AFLOW Prototype Encyclopedia.
                                                     Different settings exist for the following space groups:
                                                       - centrosymmetric space groups with two origin choices (24 space groups, e.g., sg=227):
                                                           --setting=1     : origin centered on high site symmetry (not inversion site)
                                                           --setting=2     : origin centered on inversion site
                                                           --setting=aflow : origin centered on inversion site
                                                       - rhombohedral space groups (e.g., space group 166):
                                                           --setting=1     : rhombohedral setting
                                                           --setting=2     : hexagonal setting
                                                           --setting=aflow : rhombohedral setting
                                                       - monoclinic space groups (e.g., space group 5):
                                                           --setting=1     : unique axis-b
                                                           --setting=2     : unique axis-c
                                                           --setting=aflow : unique axis-b
  
  aflow --clat=a,b,c,alpha,beta,gamma
        Outputs to standard out the cartesian lattice vectors obtained
        from the input a b c alpha beta gamma.

  aflow --clean --DIRECTORY=DIRECTORY
        Cleans the directory, like aflow --clean --DIRECTORY=DIRECTORY

  aflow --clean_all < LIST_DIRECTORIES
        Cleans all the directories. Be careful !
        (if the LIST_DIRECTORIES contain aflow.in and LOCK the substring
        gets removed to help the search).

  aflow  --cluster-expansion=... | --ce=structure_type,A,B,EA,EB
         --ce structure_type A B formation_energy_A formation_energy_B 
        Cluster expansion
        structure_type: fcc/bcc/hcp
        A, B: element names
        EA, EB: formation energy of pury element A and B

  aflow --cluster=structure_type,atom_num_min,atom_num_max,neighbour_min,neighbour_max
        Get clusters
        atom_num_min, atom_num_max : minimum and maximum numbers of atoms in a cluster
        neighbour_min, neighbour_max : minimum and maximum nearest neighbour
        pairs including in a cluster

  aflow --cmp_str POSCAR1 POSCAR2 rcut  
        This compares the characteristics of two POSCAR files and is  
        useful for determining if the files are the same.  Characteristics
        compared include number of atoms, number of types, total volume,  
        volume per atom, lattice parameters, number of neighbors of each
        pair type out to rcut, differences in bond lengths for neighbors
        of each pair type out to cutoff, and space groups.  For rcut<0 the
        cutoff is set to 4*(Wigner-Seitz radius of each atom) (this is the  
        radius such that num atom spheres occupies the whole volume).
  aflow --compare=a,b,c,d,e,f,g,h,k,j,i,l
        Outputs to standard output the % comparison between
        a#g b#h c#k d#j e#i f#l in %  
         cout << abs(a1-a7)/((a1+a7)/2.0) << ;
         cout << abs(a2-a8)/((a2+a8)/2.0) << ;
         cout << abs(a3-a9)/((a3+a9)/2.0) << ;
         cout << abs(a4-a10)/((a4+a10)/2.0) << ;
         cout << abs(a5-a11)/((a5+a11)/2.0) << ;
         cout << abs(a6-a12)/((a6+a12)/2.0) << ;
         cout << endl;
        Useful with y-ndata to compare % relaxations.

  aflow --compare2database [GENERAL_COMPARISON_OPTIONS] [COMPARE2DATABASE_OPTIONS] < file
      Compares a structure (file) to entries in the AFLOW database, returning similar 
      compounds and quantifying their levels of similarity (misfit values).
      Material properties can be extracted from the database and printed (via AFLUX), highlighting structure-property relationships.
      
      [COMPARE2DATABASE_OPTIONS] : Options specific to this command:
          [--structure_comparison] : Performs structure-type comparisons.
          [--properties=enthalpy_atom,natoms,...] : Specify the properties via their API keyword to print the corresponding 
            values with the comparison results.
          [--catalog=lib1|lib2|lib3|lib4|lib6|lib7|icsd] : Restrict the entries to compare with to a specific catalog/library 
            (e.g., `lib1', `lib2', `lib3', `icsd', etc.).
          [--geometry_file=POSCAR.relax1] : Compare geometries from a particular step in the DFT relaxation 
            (e.g., `POSCAR.relax1', `POSCAR.relax2', `POSCAR.static', etc.).
          [--relaxation_step=original|relax1|most_relaxed] : Compare geometries from a particular step in the DFT relaxation.
            Allows numeric or string input (e.g., 0->original, 1->relax1, 2->most_relaxed).
      [GENERAL_COMPARISON_OPTIONS] :
        [--np=16|--num_proc=16] : Allocate the number of processors/threads for the task.
        [--optimize_match] : Explore all lattice and origin choices to find the best matching representation, i.e., minimizes misfit value.
        [--no_scale_volume] : Suppresses volume rescaling during structure matching; identifies differences due to volume expansion or compression of a structure.
        [--ignore_symmetry] : Neglects symmetry analysis (both space group and Wyckoff positions) for grouping comparisons.
        [--ignore_Wyckoff] : Neglects Wyckoff symmetry (site symmetry) for filtering comparisons, but considers the space group number.
        [--ignore_environment] : Neglects LFA environment analysis for filtering comparisons.
        [--keep_unmatched!] : Retains misfit information of unmatched structures (i.e., misfit>0.1).
        [--match_to_aflow_prototypes!] : Identifies matching AFLOW prototypes to the representative structure.
        [--magmom=<m1,m2,...|INCAR|OUTCAR>:...] : Specifies the magnetic moment for each structure (collinear or non-collinear) delimited by colons, 
          signaling a magnetic-type comparison. The option does not apply to --compare_structures since the atom type is neglected.
          AFLOW-XtalFinder supports three input formats for the magnetic moment:
              1) explicit declaration via comma-separated string m_{1},m_{2},...m_{n} (m_{1,x},m_{1,y},m_{1,z},m_{2,x},...m_{n,z} for non-collinear) 
              2) read from a VASP INCAR, or
              3) read from a VASP OUTCAR.
            Additional magnetic moment readers for other ab initio codes will be available in future versions.
        [--add_aflow_prototype_designation] : Casts prototype structure into the AFLOW standard designation.
        [--remove_duplicate_compounds] : For structure-type comparisons, duplicate compounds are identified first 
          (via a material-type comparison without volume scaling), then remaining unique compounds are compared, removing duplicate bias.
        [--ICSD] : Only if ICSD structures: ensure the representative structure is the entry with the smallest ICSD number 
        [--print] : For comparing two structures, additional comparison information is printed, including atom mappings, distances between matched atoms, 
          and the transformed structures in the closest matching representation.
        [--print=TEXT|JSON] : For comparing multiple structures, the results printed to the relevant files are formatted into human-readable 
          text or JSON, respectively.  By default, AFLOW-XtalFinder writes the output in both formats.
        [--quiet|--q] : Suppresses the log information for the comparisons.
        [--screen_only] : Prints the comparison results to the screen and does not write to any files.
        Check aflow --readme=compare
    
    
  aflow --compare2prototypes [GENERAL_COMPARISON_OPTIONS] [COMPARE2PROTOTYPES_OPTIONS] < file
      Compares a structure (file) to the AFLOW crystallographic prototype structures, returning the similar 
      structures and quantifying their levels of similarity (misfit values).
      
      [COMPARE2PROTOTYPES_OPTIONS] : Options specific to this command:
          [--catalog=anrl|htqc|all] : Restrict the entries to compare with to a specific catalog/library (e.g., `anrl' or `htqc').
      [GENERAL_COMPARISON_OPTIONS] :
        [--np=16|--num_proc=16] : Allocate the number of processors/threads for the task.
        [--optimize_match] : Explore all lattice and origin choices to find the best matching representation, i.e., minimizes misfit value.
        [--no_scale_volume] : Suppresses volume rescaling during structure matching; identifies differences due to volume expansion or compression of a structure.
        [--ignore_symmetry] : Neglects symmetry analysis (both space group and Wyckoff positions) for grouping comparisons.
        [--ignore_Wyckoff] : Neglects Wyckoff symmetry (site symmetry) for filtering comparisons, but considers the space group number.
        [--ignore_environment] : Neglects LFA environment analysis for filtering comparisons.
        [--keep_unmatched!] : Retains misfit information of unmatched structures (i.e., misfit>0.1).
        [--magmom=<m1,m2,...|INCAR|OUTCAR>:...] : Specifies the magnetic moment for each structure (collinear or non-collinear) delimited by colons, 
          signaling a magnetic-type comparison. The option does not apply to --compare_structures since the atom type is neglected.
          AFLOW-XtalFinder supports three input formats for the magnetic moment:
              1) explicit declaration via comma-separated string m_{1},m_{2},...m_{n} (m_{1,x},m_{1,y},m_{1,z},m_{2,x},...m_{n,z} for non-collinear) 
              2) read from a VASP INCAR, or
              3) read from a VASP OUTCAR.
            Additional magnetic moment readers for other ab initio codes will be available in future versions.
        [--add_aflow_prototype_designation] : Casts prototype structure into the AFLOW standard designation.
        [--print=TEXT|JSON] : For comparing multiple structures, the results printed to the relevant files are formatted into human-readable 
          text or JSON, respectively.  By default, AFLOW-XtalFinder writes the output in both formats.
        [--quiet|--q] : Suppresses the log information for the comparisons.
        [--screen_only] : Prints the comparison results to the screen and does not write to any files.
        Check aflow --readme=compare
    

  aflow --compare_materials=<f1>,<f2>,...| -D <path> | -F=<filename> [GENERAL_COMPARISON_OPTIONS]
      Compares compounds comprised of the same atomic species and with 
      commensurate stoichiometric ratios, i.e., material-type comparison, and returns their level of similarity (misfit value).
      This method identifies unique and duplicate materials.
      There are three input types:
          aflow --compare_materials=<f1>,<f2>,...  : append geometry files (<f1>,<f2>,...) to compare,
          aflow --compare_materials -D <path>      : specify path to directory (<path>) containing geometry files to compare, and
          aflow --compare_materials -F=<filename>  : specify file (<filename>) containing compounds between delimiters 
                                                     [VASP_POSCAR_MODE_EXPLICIT]START and VASP_POSCAR_MODE_EXPLICIT]STOP.
                                                     Additional delimiters will be included in later versions.
      [GENERAL_COMPARISON_OPTIONS] :
        [--np=16|--num_proc=16] : Allocate the number of processors/threads for the task.
        [--optimize_match] : Explore all lattice and origin choices to find the best matching representation, i.e., minimizes misfit value.
        [--no_scale_volume] : Suppresses volume rescaling during structure matching; identifies differences due to volume expansion or compression of a structure.
        [--ignore_symmetry] : Neglects symmetry analysis (both space group and Wyckoff positions) for grouping comparisons.
        [--ignore_Wyckoff] : Neglects Wyckoff symmetry (site symmetry) for filtering comparisons, but considers the space group number.
        [--ignore_environment] : Neglects LFA environment analysis for filtering comparisons.
        [--keep_unmatched!] : Retains misfit information of unmatched structures (i.e., misfit>0.1).
        [--match_to_aflow_prototypes!] : Identifies matching AFLOW prototypes to the representative structure.
        [--magmom=<m1,m2,...|INCAR|OUTCAR>:...] : Specifies the magnetic moment for each structure (collinear or non-collinear) delimited by colons, 
          signaling a magnetic-type comparison. The option does not apply to --compare_structures since the atom type is neglected.
          AFLOW-XtalFinder supports three input formats for the magnetic moment:
              1) explicit declaration via comma-separated string m_{1},m_{2},...m_{n} (m_{1,x},m_{1,y},m_{1,z},m_{2,x},...m_{n,z} for non-collinear) 
              2) read from a VASP INCAR, or
              3) read from a VASP OUTCAR.
            Additional magnetic moment readers for other ab initio codes will be available in future versions.
        [--add_aflow_prototype_designation] : Casts prototype structure into the AFLOW standard designation.
        [--ICSD] : Only if ICSD structures: ensure the representative structure is the entry with the smallest ICSD number 
        [--print] : For comparing two structures, additional comparison information is printed, including atom mappings, distances between matched atoms, 
          and the transformed structures in the closest matching representation.
        [--print=TEXT|JSON] : For comparing multiple structures, the results printed to the relevant files are formatted into human-readable 
          text or JSON, respectively.  By default, AFLOW-XtalFinder writes the output in both formats.
        [--quiet|--q] : Suppresses the log information for the comparisons.
        [--screen_only] : Prints the comparison results to the screen and does not write to any files.
        Check aflow --readme=compare
    
  aflow --compare_structures=<f1>,<f2>,...| -D <path> | -F=<filename> [GENERAL_COMPARISON_OPTIONS]
      Compares compounds with commensurate stoichiometric ratios and no 
      requirement of the atomic species, i.e., structure-type comparison, and returns their level of similarity (misfit value).
      This method identifies unique and duplicate prototypes.
      There are three input types:
          aflow --compare_structures=<f1>,<f2>,...  : append geometry files (<f1>,<f2>,...) to compare,
          aflow --compare_structures -D <path>      : specify path to directory (<path>) containing geometry files to compare, and
          aflow --compare_structures -F=<filename>  : specify file (<filename>) containing compounds between delimiters 
                                                     [VASP_POSCAR_MODE_EXPLICIT]START and VASP_POSCAR_MODE_EXPLICIT]STOP.
                                                     Additional delimiters will be included in later versions.
      [GENERAL_COMPARISON_OPTIONS]:
        [--np=16|--num_proc=16] : Allocate the number of processors/threads for the task.
        [--optimize_match] : Explore all lattice and origin choices to find the best matching representation, i.e., minimizes misfit value.
        [--no_scale_volume] : Suppresses volume rescaling during structure matching; identifies differences due to volume expansion or compression of a structure.
        [--ignore_symmetry] : Neglects symmetry analysis (both space group and Wyckoff positions) for grouping comparisons.
        [--ignore_Wyckoff] : Neglects Wyckoff symmetry (site symmetry) for filtering comparisons, but considers the space group number.
        [--ignore_environment] : Neglects LFA environment analysis for filtering comparisons.
        [--keep_unmatched!] : Retains misfit information of unmatched structures (i.e., misfit>0.1).
        [--match_to_aflow_prototypes!] : Identifies matching AFLOW prototypes to the representative structure.
        [--add_aflow_prototype_designation] : Casts prototype structure into the AFLOW standard designation.
        [--remove_duplicate_compounds] : For structure-type comparisons, duplicate compounds are identified first 
          (via a material-type comparison without volume scaling), then remaining unique compounds are compared, removing duplicate bias.
        [--ICSD] : Only if ICSD structures: ensure the representative structure is the entry with the smallest ICSD number 
        [--print] : For comparing two structures, additional comparison information is printed, including atom mappings, distances between matched atoms, 
          and the transformed structures in the closest matching representation.
        [--print=TEXT|JSON] : For comparing multiple structures, the results printed to the relevant files are formatted into human-readable 
          text or JSON, respectively.  By default, AFLOW-XtalFinder writes the output in both formats.
        [--quiet|--q] : Suppresses the log information for the comparisons.
        [--screen_only] : Prints the comparison results to the screen and does not write to any files.
        Check aflow --readme=compare

  aflow --convex_hull=|--chull --alloy=MnPdPt[,AlCuZn,...] [chull_options] [--destination=[DIRECTORY]]
        Queries the AFLOW API for relevant entries (see --load_library), calculates
        the convex hull, and returns the information as a PDF (default, see --output).
        --chull : Necessary flag for entering mode for calculating convex hull.
        --alloy : Necessary argument, specifies system. This code is not dimension specific, 
              i.e., you can calculate the convex hull for any n-ary system.
              There are two input modes:  raw (comma-separated) and combinatorial (colon- and comma-separated).
              Raw input:  --alloy=MnPdPt,AlCuZn.
              Combinatorial input:  --alloy=Ag,Au:Mn.  This is interpreted as --alloy=AgMn,AuMn.
        [--destination=[DIRECTORY]] : Optional argument, specify the directory for the output.  
              Default is "./".
        [--usage] : Returns usage commands and options.
        [--print=|--p=|--output=|--o=latex|pdf|json|text] : Select the output format. Latex/PDF are the same (.pdf).
             JSON and plain text have the following extensions:  .json and .txt.
             Default is Latex/PDF.
        [--screen_only] : Output is direct to screen (stdout) instead of writing to a file. 
              All logging output is surpressed.
        [--keep=log|--keep_log|--keeplog|--log] : Prints a log file of relevant output.
        [--keep=tex,log] : Keep both.
        
        LOADING OPTIONS:
        [--load_library=|--loadlibrary=|--ll=icsd|lib1|lib2|lib3] : Specify libraries
              from which to load.  Default:  icsd, lib2, and lib3.
        [--load_API|--load_api|--loadapi|--lapi|--api] : Force loading entries from the API (default unless
              on nietzsche, aflowlib, or habana.
        [--load_entries_entry_output|--loadentriesentryoutput|--leo] : Get full output for
              all entries loaded from the AFLOW API.
        [--neglect=|--ban=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] :
              Ban specific entries from the convex hull calculation, done by AUID.
        [--see_neglect|--seeneglect| --sn] : Show why entries were neglected.
        [--remove_extreme_points=|--removeextremepoints=|--remove_extrema=|--removeextrema=|--rep=-1000] :
              Exclude points based on Hf/Ts (floor/ceiling). Units are meV/atom / K.
        [--entropic_temperature|--entropictemperature|--entroptemp] : Calculate the Ts
             convex hull (upper-half). Default is Hf hull (lower-half).  
        [--include_paw_gga|--paw_gga] : Include calculations run with PAW_GGA. Easily coupled
              with default PAW_PBE (same level of theory, differently parametrized).

        ANALYSIS OPTIONS:
        [--distance_to_hull=|--distancetohull=|--distance2hull=|--dist2hull=|--d2h=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] :
              Calculates a structure's distance below/above (Hf/Ts) the hull.
        [--stability_criterion=|--stabilitycriterion=|--stable_criterion=|--scriterion=|--sc=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] :
              Calculates the stability criterion of the ground state structure. Will return
              a warning if structure is not a ground state one. It removes the point from the 
              hull, calculates the new hull, and calculates the distance of this point from
              below/above (Hf/Ts) hull.
        [--n+1_enthalpy_gain=|--n+1_energy_gain=|--n+1enthalpygain=|--n+1energygain=|--n+1egain=|--n1egain=|--n+1_enthalpygain=|--n+1+energygain=|--n+1_egain=aflow:bb0d45ab555bc208,aflow:fb9eaa58604ce774] :
              Calculates the N+1 enthalpy gain of the ground state structure. Will return
              a warning if structure is not a ground state one. It removes all points having the 
              same dimensionality from the hull, calculates the new hull, and calculates the 
              distance of this point from below/above (Hf/Ts) hull.
        [--hull_formation_enthalpy=|--hull_energy=0.25,0.25] : Returns the value of the convex hull surface at the specified coordinate/concentration.
              For stoichiometric hulls, provide the reduced composition form, i.e., for the compound Mn2PdPt, use
              --hull_formation_enthalpy=0.5,0.25, where the composition of the last component is implicitly 1-sum(0.5+0.25).
              Providing an additional component (e.g., --dist2hull=0.5,0.25,0.1) results in a rigid shift in the energy axis and,
              thus, a constant added to the final distance calculated (0.1 is in units of eV for formation energy hulls).
        [--skip_structure_comparison|--skipstructruecomparison|--skipstructcomp|--ssc] : structure comparison analysis for determination of
              equivalent ground state structures is skipped (can be time consuming).
        [--skip_stability_criterion_analysis|--skipstabilitycriterionanalysis|--skipscriterion|--sscriterion] : analysis
              of stability criterion for ground state structures is skipped (can be time consuming).
        [--skip_n_plus_1_enthalpy_gain_analysis|--skip_n_plus_1_energy_gain_analysis|--skipnplus1enthalpygainanalysis|--skipnplus1energygainanalysis|--skipnplus1|--snp1|--snpo] : analysis
              of N+1 enthalpy gain for ground state structures is skipped (can be time consuming).
        [--include_skewed_hulls|--include_skewed|--ish] : process hull despite skewed endpoints (abs(ground state endpoint energy) < 15 meV).
        [--include_unreliable_hulls|--include_unreliable|--iuh] : process hull despite poor statistics (binary hull count < 200).
        [--include_outliers|--io] : include any detected outliers (output/warning is still shown).
        [--force] : force output despite warnings.
        [--force_outliers|--fo] : force output despite outlier warnings.

        PDF/LATEX OPTIONS:
        [--image_only|--imageonly|--image] : Latex/PDF output mode only. Similar to --document_only, 
             but the image dimensions are not necessarily for a standard page. Preferred option for 
             importing into papers/presentations.
        [--no_document|--nodocument|--no_doc|--nodoc|--full_page_image|--fullpageimage] :
              Latex/PDF output mode only. Generates a PDF of just the convex hull illustration (2/3D).
              Dimensions: 8.5x11 inches (standard page), landscape.
        [--document_only|--documentonly|--doc_only|--doconly|--doc] : Latex/PDF output mode only.
             Exclude convex hull illustration. This is the default for quaternary systems and above.
        [--keep=tex|--keep_tex|--keeptex|--tex] : Latex/PDF output mode only. Will keep latex .tex and put it in
             --destination=[DIRECTORY].
        [--latex_output|--latexoutput] : Latex/PDF output mode only. See full latex output.
              Good for troubleshooting.
        [--latex_interactive|--latexinteractive] : Latex/PDF output mode only. Allows you
              to interact with latex as it compiles. Good for troubleshooting.
        [--light_contrast|--lightcontrast|--lc] : Latex/PDF output mode only. Modifies the convex 
             hull illustration color scheme to be lighter.
        [--large_font|--largefont|--large|--lf] : Latex/PDF output mode only. Prints a "larger" font size 
             for convex hull illustration.
        [--png_resolution=|--pngresolution=|--pngr=300] : Set PNG resolution (-density in convert).
        [--plot_iso_max_latent_heat|--iso_max|--isomax] : Plot iso-max-latent-heat lines for ground state structures.
              See dx.doi.org/10.1063/1.4902865.
        
        Check aflow --readme=chull

  aflow --corners | --corner < POSCAR
        Add to the POSCAR the corner and face atoms so it looks
        good when you plot the unit cell with rasmol/jmol and so on..
        This option is just for visualization and should not be used
        to transform POSCARS to run. You will get super-imposed atoms!

  aflow --data[=tolerance| =tight| =loose] [--no_scan] [--print=txt | --print=json] < POSCAR
        Outputs to standard out basic data about the structure in the
        POSCAR input file. Output includes volume, a b c alpha beta gamma,
        reciprocal lattice, reciprocal lattice volume.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Options:
          [--no_scan] : Will not perform tolerance scan.
          [--print=txt | --print=json] : Specify output format.
  aflow --data1=rcut < POSCAR
        This is basically like cmp_str except that it works on 1 str.  
        Slightly different data is given: No space groups, All bond lengths.
  aflow --data2 < POSCAR
        Outputs to standard out basic data about the structure in the
        POSCAR input file. Similar to --data but with another style (SC).
  aflow --debye=THERMO
        Usage:  aflow --debye=THERMO[.bz2|.gz|.xz]
 	  Fits Debye temperature to heat capacity data in THERMO[.bz2|.gz|.xz] file as calculated using APL.
	  Writes results to file debye_temperature.dat and plots results in debye_temperature.png
	  Also calculates value for Debye temperature which best fits all heat capacity data in the range
          given in the THERMO file, and writes this value in the file debye_temperature.dat
    	  See Ascroft & Mermin, Solid State Physics, equation 23.26 for expression for heat capacity in terms of debye temperature.
 	  The following files must reside in DIRECTORY as in the AFLOW written form or as compressed files.
 		THERMO 
		aflow.in
	  The aflow.in file is used to determine the number of atoms per unit cell.
	  If the files are found compressed, the compressed files are preserved and temporary files are written and discarded.
 	  The generation of the THERMO file is controlled by the command
 	      [AFLOW_APL]TP
       See README_APL, especially 3). for more details.

  aflow --diff=POSCAR1,POSCAR2
        Gives the difference in energy of the two structures within the PARTIAL OCCUPATION force field.
 
  aflow --disp=cutoff < POSCAR
        Outputs to standard out the displacement from each atom to all
        neighors within a distance cutoff.  Also gives which unit cell the
        neighbour is in.
  aflow --dist=cutoff < POSCAR
        Outputs to standard out the distances for each atom to all
        neighors within a distance cutoff.  Also gives which unit cell the
        neighbour is in.
    
  aflow --delta_kpoints=number < POSCAR [or --dkpoints=number | -dkpoints=number | -dk=number]
        Gives the k1,k2,k3 so that the delta_kappa is less-equal than "number".
        Input dK is the desired smallest distance between grid points in reciprocal space. 
        The smallest mesh to satisfy this requirement is calculated.
        See also --kpoints.

  aflow --edata[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--setting=1|2|aflow] [--suppress_Wyckoff|--suppress_Wyckoff_printing] < file
        Outputs to standard the information given by --data in addition
        to lattice-, superlattice- and reciprocal-lattice types.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Space group setting:
          The space group setting can be specified with the optional flag [--setting=1| =2] (the default is setting 1).
          For rhombohedral systems, setting 1=rhl and 2=hex.
          For monoclinic systems, setting 1=unique axis-b and 2=unique axis-c.
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--setting=1|2|aflow]                    : Specifies the space group setting. The `aflow' setting follows the choices of the AFLOW Prototype Encyclopedia.
                                                     Different settings exist for the following space groups:
                                                       - centrosymmetric space groups with two origin choices (24 space groups, e.g., sg=227):
                                                           --setting=1     : origin centered on high site symmetry (not inversion site)
                                                           --setting=2     : origin centered on inversion site
                                                           --setting=aflow : origin centered on inversion site
                                                       - rhombohedral space groups (e.g., space group 166):
                                                           --setting=1     : rhombohedral setting
                                                           --setting=2     : hexagonal setting
                                                           --setting=aflow : rhombohedral setting
                                                       - monoclinic space groups (e.g., space group 5):
                                                           --setting=1     : unique axis-b
                                                           --setting=2     : unique axis-c
                                                           --setting=aflow : unique axis-b
          [--suppress_Wyckoff]                     : Suppresses Wyckoff position output (i.e., space group info only)
        Check aflow --readme=symmetry

  aflow --edos ispin
        ispin(1=nonspin,2=spin), Outputs to standard out the DOS, format:
        Energy DOSup DOSdown
        The integrated DOS is not outputted since it can be calculated from the energy bins
        and DOS. Needs DOSCAR and POSCAR files. DOS for spin down is given in (negative) sign.
        See also --kband
  aflow --edos ispin s d
  aflow --edos ispin d s
        See --edos. Outputs total DOS and DOS of orbital s and d. The sDOS or dDOS is per species
        as given in POSCAR. Output format:
        Energy DOSup DOSdown s_up_spec1 s_down_spec1...s_up_specN s_down_specN d_up_spec1 d_down_spec1...d_up_specN d_down_specN
  
  aflow --elk
        Transforms an input geometry file to the ELK format.
        The output follows the ELK conventions discussed in http://elk.sourceforge.net/elk.pdf.
  
  aflow --equivalent | --equiv | --iatoms[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] < file
        Calculate point/factor/space group and use them to label equivalent
        and inequivalent atoms. On the output, each structure atom has
        number_label_of_atom[equivalent_to_label]* (* if inequivalent).(SC201107).
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
        Check aflow --readme=symmetry

  aflow --eigcurv=bands_directory
        Perform a graph decomposition of the BZ paths found in a BANDS calculation into component vertices and edges.
        These are then organized into a data structure that contains information on the branching associated with each
        edge in the graph. Once this is in place, short walks are performed along these edges and their branches, with
        the purpose of detecting maxima and minima in the band structure, as well as their corresponding curvatures.
        The curvatures are currently calculated using the 5 point central difference approximation,
        f"(@f3) = (-f1+16f2-30f3+16f4-f5)/(12h^2)
        which has an O(4) error. Note that the curvatures are not reliable, given that angular information is lost in the
        vicinity of the vertices.

  aflow --effective-mass | --em directory_name
        Calculate the carrier effective masses.
        If the data is generated by aflow, DOSCAR.static, POSCAR.static, and EIGENVAL.static are used.
        Otherwise, DOSCAR, POSCAR, and EIGENVAL are used.
        Output format:
          compund_name
          1. Band index:
             Carrier type:
             Carrier Spin:
             Effective masses along principle axes (m0):
             Number of equivalent valleys:
             DOS effective mass (m0):
          DOS electron effective mass (m0): {me_spin_up, me_spin_down}
          DOS hole effective mass (m0): {mh_spin_up, mh_spin_down}

  aflow --enum | --multienum  < POSCAR
        Call MULTIENUM and convert a POSCAR with partial occupation into regular POSCARs.
    
  aflow --enumsort | --multienumsort  < POSCAR
        Call MULTIENUM and convert a POSCAR with partial occupation into regular POSCARs, and sort POSCARs using siplified universal force filed method.

  aflow --ewald[=eta] < POSCAR
        Finds the electrostatic energy of the POSCAR file using the  
        Ewald sum.  Charges must be entered after each atom position.
        E.g.,   Co 0.00 0.00 0.00 +2.  This is easy to do using the --names  
        option.  Eta is a real space screening parameter.  Setting  
        eta<=0 or leaving it out will cause aflow to choose it  
        automatically (and hopefully optimally).  Eta->0 is no  
        screening and the Ewald recipricol term will be zero.  Eta->inf  
        is total screening and the Ewald real term will be zero.  The  
        Ewald sum itself should always be the same and eta will only  
        affect the efficiency of the calculation.

  aflow --extract_kpoints | --xkpoints aflow.in
        Extract to stdout the kpoints embedded in the aflow.in file.
        Useful for scripting (SC200902).
  aflow --extract_incar | --xincar aflow.in
        Extract to stdout the incar embedded in the aflow.in file.
        Useful for scripting (SC200902).
  aflow --extract_poscar | --xposcar aflow.in
        Extract to stdout the poscar embedded in the aflow.in file.
        Useful for scripting (SC200902).
  aflow --extract_potcar | --xpotcar aflow.in
        Extract to stdout the potcar embedded in the aflow.in file.
        Useful for scripting (SC200902).
  aflow --extract_symmetry | --xsymmetry aflow.in
        Extract the symmetry (pgroup,fgroup,iatoms) from the poscar
        embedded in the aflow.in file. Must use this for aflow<2947
        to fix the fgroup bug.
        Useful for scripting (SC200902).
        Check aflow --readme=symmetry

  aflow --factorgroup|--fgroup[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculates factor group symmetry of the cell {R|t} and writes
        in the aflow.fgroup.out file. See documentation of aflow.
        The point group is required for the factor group, therefore
        the aflow.pgroup.out file will be generated as well.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry

  aflow --findsym[=tolerance_relative: default 1.0e-3] < POSCAR
        Runs and prints out the output of the program findsym
  aflow --findsym_print[=tolerance_relative: default 1.0e-3] < POSCAR
        This prints out the input file structure for findsym.
  aflow --findsymSG[=tolerance_relative: default 1.0e-3] < POSCAR
        This prints out the space group without bothering with wrap ups.
        findsym must be accessible on the path !	  
  aflow --findsymSG_label[=tolerance_relative: default 1.0e-3] < POSCAR
        Same as above but prints ONLY the space group name.	  
  aflow --findsymSG_number[=tolerance_relative: default 1.0e-3] < POSCAR
        Same as above but prints ONLY the space group number.	  

  aflow --fix_bands POSCAR KPOINTS.bands.old EIGENVAL.bands.old KPOINTS.bands.new EIGENVAL.bands.new
        Resample the PATH following the standard definition of the POSCAR and the standard path.
        If there are not nearby points, it will ask to redo the nbands step.

  aflow --aflow-sym|--AFLOW-SYM|--AFLOWSYM|--aflowSYM|--aflowsym|--full_symmetry|--full_sym|--fullsym[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculates the full symmetry of a crystal: point group lattice, point group crystal, factor group,
        space group, site point group, inequivalent/equivalent atoms, and the point group of the klattice.
        This routine calculates the full symmetry suite at a certain tolerance. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum 
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry


  aflow --frac [-f,-d,--fract,--fractional,--direct] < POSCAR
        Outputs to standard out a new POSCAR file with
        atom positions in direct (fractional) coordinates.

  aflow --get_cation_coordination_numbers|--get_cation_coord_nums|--poscar2cation_coord_nums < STRUC_FILE
        Determines the number of anion neighbors for each cation for the structure in file STRUC_FILE.
        It can be in any structure format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF.
        For VASP, a VASP5 POSCAR is required or, if a VASP4 POSCAR is used, the species must be written
        on the right side next to the coordinates for each atom. (RF20200820)

  aflow --get_oxidation_numbers|--get_ox_nums|--poscar2ox_nums < STRUC_FILE
        Determines the oxidation numbers for the structure in file STRUC_FILE. It can be in any structure
        format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF. For VASP, a VASP5 POSCAR
        is required or, if a VASP4 POSCAR is used, the species must be written on the right side next to
        the coordinates for each atom.

  aflow --getTEMP[s] [--runstat | --runbar | --refresh=X | --warning_beep=T | --warning_halt=T ]
        If available, the command outputs the hostname and temperatures of the machine. Useful to find hardware issues:
	          with --runstat the command continuously prints the temperature, refreshing every XX refresh seconds;
	          with --runbar the command prints a bar with the temperature, refreshing every XX refresh seconds;
        with --refresh=X you can specify the refresh time (DEFAULT below)
        with --warning_beep=T, if the max temp goes beyond T(C, DEFAULT below), the command beeps the computer speaker;
	          with --warning_halt=T, it the max temp goes beyond T(C, DEFAULT below), the command halts the computer (aflow must be run as root).
	      DEFAULT VALUES in .aflow.rc
            AFLOW_CORE_TEMPERATURE_BEEP=56.0  // Celsius
            AFLOW_CORE_TEMPERATURE_HALT=65.0  // Celsius, you need to run aflow as root to halt
            AFLOW_CORE_TEMPERATURE_REFRESH=5.0   // seconds

  aflow --gfa --alloy=CaCu [--ae_file=All_atomic_environments_read.dat]
      	Outputs the glass-forming ability of an alloy system at various stoichiometries.
      	It is optional to specify a file of atomic environments for the code to read (saves time).
      	The file must follow the format of, but not be named All_atomic_environments.dat.
        Check aflow --readme=gfa

  aflow --gulp < POSCAR
        Outputs to standard out a gulp formatted input file based on
        the POSCAR input file.  The formatting is for a distance
        calculation in gulp.  If you want atom names you must put
        them after each atom position in the POSCAR file (see --names).
        If any names are missing they are defaulted to H.

  aflow --hkl=h,k,l[,bond] < POSCAR 
        Returns the planar density and number of broken bonds per unit are
        along the Miller plane (h k l). The calculations returns also
        the bonds broken for each type and all types.
        Note: the indices are with respect to the unit cell, not the
        conventional cell, and the result is in #atoms/A^2 (scale included).
	  BOND: (default BOND_DEF):
        If you specify a "bond", all the bonds shorter than
        bond*nearest_neighbour_bond (between all types or combination
        of them) that are cut by the plane will contribute to the broken
        bond density Nb(#/AA).
        NOTE2: the 1st atom is taken to be the origin (all the other atoms
        are shifted).
  aflow --hkl_search[=khlmax[,bond[,step]]] < POSCAR	
        Returns the planar density and number of broken bonds per unit
        are along the Miller plane (h k l). The calculations returns
        also the bonds broken for each type and all types.
        Note: the indices are with respect to the unit cell, not the
        conventional cell, and the result is in #atoms/A^2 (scale included).
	  Search from -hmax<=h<=hmax, -kmax<=k<=kmax, -lmax<=l<=lmax, where
        the boundaries are (-4,-4,-4) to (4,4,4) unless the HKLMAX is specified.
        HKLMAX:
        If you specify a hklmax, then the search is  
        -hklmax<=h<=hklmax, -hklmax<=k<=hklmax, -hklmax<=l<=hklmax
	  BOND: (default 1.3):
        If you specify a "bond", all the bonds shorter than
        bond*nearest_neighbour_bond (between all types or combination
        of them) that are cut by the plane will contribute to the broken
        bond density Nb(#/AA).
	  STEP: (default 1):
        If you specify STEP then the update of h,k,l, is done in steps of step.
  aflow --hkl_search_simple[=cutoff[,bond[,khlmax[,step]]]] < POSCAR	
  aflow --hkl_search_complete[=cutoff[,bond[,khlmax[,step]]]] < POSCAR	
        Returns the planar density and number of broken bonds per unit are
        along the Miller plane (h k l). The calculations returns also the bonds
        broken for each type and all types.
        Note: the indices are with respect to the unit cell, not the
        conventional cell, and the result is in #atoms/A^2 (scale included).
        The simple search is fast but it might miss some planes!
	  The complete search should not miss planes but can be very slow!
	  CUTOFF (default 1.3):
        If you specify a cutoff, the command will look for all the
        planes generated with triplets of atoms in a radius cutoff*|a1+a2+a3|.
        The algorithm to find the density of atoms is quite complex,
        and it relies on a sum of four triangles (one triangle v1,v2,v3
        generated by hkl) plus three triangles generated by adding the v's
        and subtracting one. This guarantees that we span 2 unit cells "rhombi"
        in independent directions. The algorithm also plots the number of atoms
        in the radius, so you can choose a decent cutoff'. For bcc/fcc cutoff=1.5
        usually good. If you do not specify the cutoff, a value of 1.3 is
        take by default. Be careful with the cutoff ! The complexity grows
        as cutoff^3 !
	  BOND: (default 1.3):
        If you specify a "bond", all the bonds shorter than
        bond*nearest_neighbour_bond (between all types or combination
        of them) that are cut by the plane will contribute to the broken
        bond density Nb(#/AA).
        HKLMAX (default "dims" given by cutoff)
        If you specify a hklmax, then the search is  
        -hklmax<=h<=hklmax, -hklmax<=k<=hklmax, -hklmax<=l<=hklmax
	  STEP (detault simple: 1 complete 1/12)
        If you specify STEP then the update of h,k,l, is done in steps of step.
	  NOTE1: The algorithm will be implemented in aflow as automatic
        surfaces generation.
        NOTE2: the 1st atom is taken to be the origin (all the other atoms
        are shifted).

  aflow --hnf n < POSCAR
        Given a POSCAR and a volume 'n' (determinant of the Hermite normal form), it
        generates the set of supercells of POSCAR having volume n and being unique.
        In more details: it calculates the HNF matrices, the point group of the POSCAR lattice,
        then reduces the supercells by symmetry and print the unique POSCARs in aflow.in START/STOP format,
        ready for high-throughput calculation.
	      If the volume is chosen negative, then all the supercells with HNF from 2 to -n will be generated
        with the same algorithm.
  aflow --hnftol [eps] < PARTCAR
        Given a PARTCAR, it calculates the HNF size to get the right concentration spread of partial
        occupation within the tolerance. If eps is zero, negative or it is not given, aflow
        takes the tolerance from the PARTCAR, and if this is not available, it takes the default value. PARTCAR example:
         PARTCAR of Ag8.8Cd4Zr3.2      // EXAMPLE
          -191.600  0.02               // POSCAR scale and tolerance if>0)
         5.76 5.76 5.76 90 90 90       // usual a1,a2,a2 or ABCCAR or WYCKCAR definitions)
         8*1+1*0.7333 4*1 1*0.266+3*1  // needs keywords * and + to determine the species and the occupations)
         Direct Partial                // you need to specify Partial, the "P" is mandatory)
         0.25  0.25  0.25  Ag
         0.75  0.75  0.25  Ag
         0.75  0.25  0.75  Ag
         0.25  0.75  0.75  Ag
         0.25  0.25  0.75  Ag
         0.75  0.75  0.75  Ag
         0.25  0.75  0.25  Ag
         0.75  0.25  0.25  Ag
         0.50  0.50  0.50  Ag
         0.00  0.00  0.00  Cd
         0.00  0.50  0.50  Cd
         0.50  0.00  0.50  Cd
         0.50  0.50  0.00  Cd
         0.50  0.50  0.50  Zr
         0.50  0.00  0.00  Zr
         0.00  0.50  0.00  Zr
         0.00  0.00  0.50  Zr
  aflow --hnfcell  < POSCAR
        Convert a POSCAR with partial occupation into regular POSCARs, and genereate a LOG.POCC file in working direcotry.
        Given a PARTCAR, it calculates the HNF size and generate supercells. 
        PARTCAR Example:
        PARTCAR of Se0.75Sn1Te0.25 [Sn1Se0.75Te0.25]
        1.0  -4 (0.001)                                  //POSCAR scale and [HNF size if <0 (useful when you know the HNF size); tollerance if>0]
        0.0000000000000000    3.0268425330530309    3.0268425330530309
        -3.0268425330530309    3.0268425330530309    0.0000000000000000
        -3.0268425330530309    0.0000000000000000    3.0268425330530309
        1*0.75 1*0.25 1                                 //different species mut be separated by blank space 
        Direct Partial
        0.5000000000000000  0.5000000000000000  0.5000000000000000 Se
        0.5000000000000000  0.5000000000000000  0.5000000000000000 Te
        0.0000000000000000  0.0000000000000000  0.0000000000000000 Sn
        Another PARTCAR Example:
        Se1.75Sn2 
        1.0  -4
        2.1393597183461157   -5.9785152916018083    0.0000000000000000
        2.1393597183461157    5.9785152916018083    0.0000000000000000
        0.0000000000000000    0.0000000000000000    4.2994759406996081
        1*0.75+1  2
        Direct P
        0.6424479395478624  0.3575520604521376  0.7500000000000000   Se
        0.3575520604521376  0.6424479395478624  0.2500000000000000   Se
        0.8714903476790070  0.1285096523209930  0.7500000000000000   Sn
        0.1285096523209930  0.8714903476790070  0.2500000000000000   Sn
    
  aflow --icsd Pb Sn Se < ternary.icsd
  aflow --icsd Sn 34 Pb < ternary.icsd
  aflow --icsd 34 82 50 < ternary.icsd
        Output to standard out in "ICSD-format" (the NIST's Inorganic
        Crystal Structure Database) all Pb-Sn-Se ternary-compounds.
        The arguments for --icsd can be the elements' symbol or atomic number.
        The input is from stdin ICSD-format in this example is streamed in
        from file "ternary.icsd".
        "ICSD-format" is generated by exporting the entry (hit) in NIST's Inorganic
        Crystal Structure Databse in long format using "FindIt" software (the stand-alone ICSD browser).
        Examples are /common/NIST/binary.icsd  and /common/NIST/ternary.icsd
        More information on ICSD: http://www.nist.gov/srd/nist84.htm
      (2009, wahyu@alumni.duke.edu)
  aflow --icsd_alllessthan Ra < input.icsd
        (see --icsd). Output compounds if ALL elements in a compound have Z<Z_Ra
  aflow --icsd_allmorethan Ra < input.icsd
        (see --icsd_alllessthan).
  aflow --icsd_basislessthan 20 < input.icsd
  aflow --icsd_basismorethan 20 < input.icsd
        (see --icsd). Output all compounds having number of basis atoms in the PRIMITIVE cell
        lessthan or morethan the specified parameter.
  aflow --icsd_chem MgB4 < input.icsd
        (see icsd). Extract MgB4 compound.	
  aflow --icsd_cubic < ternary.icsd
  aflow --icsd_triclinic < ternary.icsd
  aflow --icsd_monoclinic < ternary.icsd
  aflow --icsd_orthorhombic < ternary.icsd
  aflow --icsd_tetragonal < ternary.icsd
  aflow --icsd_rhombohedral < ternary.icsd
  aflow --icsd_trigonal < ternary.icsd
  aflow --icsd_hexagonal < ternary.icsd
  aflow --icsd_cubic --icsd_orthorhombic < ternary.icsd
        (see --icsd). Output all compounds which belong to the specified system.
        If multiple options, the relational is "OR".
  aflow --icsd_tri < input.icsd
  aflow --icsd_mcl < input.icsd
  aflow --icsd_mclc < input.icsd
  aflow --icsd_orc < input.icsd
  aflow --icsd_orcc < input.icsd
  aflow --icsd_orcf < input.icsd
  aflow --icsd_orci < input.icsd
  aflow --icsd_tet < input.icsd
  aflow --icsd_bct < input.icsd
  aflow --icsd_rhl < input.icsd
  aflow --icsd_hex < input.icsd
  aflow --icsd_cub < input.icsd
  aflow --icsd_fcc < input.icsd
  aflow --icsd_bcc < input.icsd
        (see --icsd). Output compunds which belong to the specified lattice type:
        tri (trigonal)
	  mcl (monoclinic)
	  mclc (c-centered monoclinic)
	  orc (orthorhombic)
	  orcc (c-centered orthorhombic)
	  orcf (face-centered orthorhombic)
	  orci (body-centered orthorhombic)
	  tet (tetragonal)
	  bct (body-centered tetragonal)
	  rhl (rhombohedral/trigonal)
	  hex (hexagonal)
	  cub (simple cubic)
	  fcc (face-centered cubic)
	  bcc (body-centered cubic)
  aflow --icsd_denslessthan 4.5 < ternary.icsd
  aflow --icsd_densmorethan 5.5 < ternary.icsd
  aflow --icsd_densmorethan 4.5 --icsd_denslessthan 8.3 < ternary.icsd
        (see --icsd). Output all compounds with density (in g/cm^3) lessthan and/or morethan
        the specified argument.
  aflow --icsd_id 11120 < input.icsd
        (see --icsd). Extract compound with entry ID number 11120 of the original ICSD database.
  aflow --icsd_lessthan Pb < binary.icsd
  aflow --icsd_lessthan 82 < binary.icsd
        (see --icsd). Output all compounds in binary.icsd that contains AT LEAST
        ONE element with atomic number Z<Z_Pb (Z<82).
  aflow --icsd_listmetals
        Output to stdout a list of metallic elements used in the --icsd_removemetals option.
  aflow --icsd_makelabel < input.icsd
	      Output to stdout a list of labels compatible to generate aflow.in from icsd database.
		  The label uses the following format: chemicalformula_ICSD_entrynumber
		  The chemicalformula is ascendingly sorted based on the element symbol and the
		  concentration must be explicitly included eventhough it is 1.
		  The entrynumber is the entry number of the compound in the ICSD database.
		  e.g. Zn1Zr1_ICSD_106235
  aflow --icsd_morethan Pb < binary.icsd
  aflow --icsd_morethan 82 < binary.icsd
  aflow --icsd_morethan Pt --icsd_lessthan Hg < binary.icsd
  aflow --icsd_morethan 78 --icsd_lessthan 80 < binary.icsd
        (see --icsd_lessthan and --icsd).
  aflow --icsd_n_ary 2 < input.icsd
        (see --icsd). Output all binary compounds
  aflow --icsd_n_ary 3 < input.icsd
        (see --icsd). Output all ternary compounds. and so on
  aflow --icsd_nobrokenbasis < input.icsd
        (see --icsd). Some compounds reported in the ICSD database have missing wyckoff position
        of some of the constituents. This option extracts only the ones with complete wyckoff pos.
  aflow --icsd_nopartialocc < input.icsd
        (see --icsd). Output only compounds with full occupancies
  aflow --icsd_proto #Nspecies1 #Nspecies2 #Nspecies3 ... < input.icsd
  aflow --icsd_proto 2 1 7 < input.icsd
        (see icsd). Output all ternary compounds with general chemical formula A2BC7, AB2C7, A7B2C, and all
        other posible cyclic permutations.
  aflow --icsd_remove Pu < input.icsd
        (see --icsd). Remove compounds which contain Pu.
  aflow --icsd_removemetals < input.icsd
        (see --icsd). Remove compounds that are composed ENTIRELY by metallic elements.
        Metallic elements:
        Alkali metals, Alkaline earth metals, Transition metals,
        Lanthanoids, Actinoids, Other metals (Al, Ga, In, Sn, Tl, Pb, Bi).
        To list all metallic elements used in this option, use --icsd_listmetals
  aflow --icsd_sg 62 < binary.icsd
  aflow --icsd_sglessthan 62 < binary.icsd
  aflow --icsd_sgmorethan 45 < binary.icsd
  aflow --icsd_sgmorethan 194 --icsd_sglessthan 231 < binary.icsd
        (see --icsd). Output all compounds where the space group number satisfies the
        specified arguments.
  aflow --icsd_unique < input.icsd
        (see --icsd). Dicard redundant compounds based on SG# AND ChemicalFormula

  aflow --icsd_check_raw > output.dat
 	Checks the validity of the current vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/RAW/ dirs and files
        (POSCAR KPOINTS DOSCAR and EIGENVAL)
        with respect to vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/LIB/  
        output.dat will contain:
        vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/RAW/../../  OK
        vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/RAW/../../  OK
        vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/RAW/../../  ERROR file1 file2 ...
        vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/RAW/../../  NotInLIB
        vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/RAW/../../  NotInLIB
        vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/LIB/../../  NotInRAW
        vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD)/LIB/../../  NotInRAW
        and so on.
        aflow --icsd_check_raw 0 > output.dat
        same as the default --icsd_check_raw
        aflow --icsd_check_raw 1 > output.dat
        use the list of RAW and LIB dirs that have been compiled in aflow
        i.e. XHOST.vGlobal.at(X) (ICSD_LIB);  // aflow_data_calculated.cpp
             XHOST.vGlobal.at(X) (ICSD_RAW);  // aflow_data_calculated.cpp

  aflow --icsd2aflowin < input.icsd
        Convert input.icsd (ICSD-format) to aflow.in
  aflow --icsd2poscar < input.icsd
        Write output to stdout POSCAR from stdin ICSD-format
  aflow --icsd2proto < input.icsd
        Write output to stdout in ICSD_PROTO-format from stdin ICSD-format
  aflow --icsd2wyck < ternary.icsd
        Write output to file WYCKCAR  (WYCKCAR-format) from stdin ICSD-format
        in this example is streamed in from file "ternary.icsd".
        If the input contains multiple compounds, a subfolder will
        be created for each compound using the following folder name template:
            CompoundFormula_ICSD_ICSDid/
        The ICSDid is the compound id in the original ICSD database.
        ONLY compounds with elements having full occupation (sof=1) will be processed.
  aflow --icsd2wyck --sof < ternary.icsd
        (see --icsd2wyck). In this case, all compounds will be processed.
        If partial occupation is detected, the sof will be written as part of
        the label of the element and WARNING will be written in the title and cerr.
  aflow --icsdproto2aflowin < input.proto
        Convert ICSD-PROTOTYPE-format to aflow.in
        (2007-2011, wahyu@alumni.duke.edu)

  aflow --identical < POSCAR
        Makes all the atoms identical. Useful to find the properties of
        the superlattice.
  aflow --incell < POSCAR
        Outputs to standard out a POSCAR file with all
        atoms mapped to their images within the unit cell.
  aflow --incompact < POSCAR
        Similar to --incell
        Outputs to standard out a POSCAR file where all the
        atoms are mapped through the unit and neighbors cells
        to minimixe the shortest possible bond with an adjacent atom
        This option is very useful if you run big and complicate
        molecules where atoms exit of the unit cell and you have
        problems understanding where they are because visualization
        packages do not show bonds anymore ...
        Anyway, it is easier to test than to describe. (SC 6 Aug 04)
  aflow --insphere radius < POSCAR
        Similar to --incell and --incompact
        Outputs in XYZ format (rasmol standard), the
        positions of all the atoms inside a sphere of radius
        "radius" centered in the origin.
        If you want another origin, you must shift the atoms first.
        The radius is in cartesian format. (SC 6 Aug 04)
  aflow --intpol=file1,file2,nimages,nearest_image_flag
        Creates nimages image POSCAR files by interpolating linearly
        between structures in file1 and file2.  File1 and file2
        should both be POSCAR like files with corresponding atoms.  
        The nearest_image_flag is set to 'e' for exact interpolation
        and 'n' or 'N' for nearest-image interpolation.  Exact
        interpolation means that all the positions are taken exactly
        as they are input.  Nearest-image interpolation means that
        the interpolation between two corresponding atoms in file1
        and file2 is actually done between the atom in file1 and
        the nearest image of the corresponding atom in file2.  This
        is useful, e.g., if the positions (in direct coordinates)
        are 0.01 (file1) and 0.99 (file2).  These are far apart in
        exact interpolation but very close in nearest-image
        interpolation.  The POSCAR output files are numbered and
        output to the present directory.  The code also creates
        numbered subdirectories and copies the appropriate POSCAR
        files into those.  This option makes it easy to set up a rubber
        band calculation in vasp.
  aflow --inwignerseitz [--inws] < POSCAR
        Outputs to standard out a POSCAR file where all the atoms are
        mapped to their images in the Wigner-Seitz cell.(SC20100104)
  aflow --inflate_lattice=coefficient | --ilattice coefficient=coefficient < POSCAR
        Inflate/deflate POSCAR lattice of coefficient.
  aflow --inflate_volume=coefficient | --ivolume coefficient=coefficient < POSCAR
        Inflate/deflate POSCAR lattice of coefficient.
  aflow --kpath [--grid=XX] < POSCAR
        Outputs to stdout a KPOINTS in line mode useful for bandstructure
        calculations. The k-points path is chosen to cover all possible
        pair combinations of special k-points in the irreducible BZ (IRBZ).
        a special k-point is either:
        (1) a center of a face in IRBZ, or
        (2) a corner of IRBZ, or
        (3) a midpoint (say M) of a line-edge (say AB) IF the Gamma-M-A makes a 90 degrees angle.
        The coordinates are given in fractionals of the k-vectors, in which
        derived from the "standard" lattice used in AFLOW.
        To find out the standard lattice of the POSCAR, use --sp option.
        Optional: --grid=XX specifies the density of the grid, if not specified it takes --grid=16.
        NOTE. If grid is negative real number, e.g. --grid=-0.01, then its value is taken 
        as the deltaK during the path which is constructed as uniformly as possible in the k-space.
        The option works both for VASP, QE style mode inputs (ABINIT and AIMS in the future).
        Example: aflow --proto=3:Ag:Zr [--qe | --abinit | --aims] | aflow --kpath=-0.01

  aflow --kpoints=KDENS [or --kppra=KDENS,-k=KDENS] < POSCAR 
        This funtion prints a set of Monkhorst-Pack kpoint mesh values
        (divisions along each reciprical lattice parameter)
        based on the desired KDENS density and the
        lattice parameters.  The values assure the most even
        distribution of KDENS along the lattice params consistent
        with the kpt density. See --delta_kpoints

  aflow --jmol[=n1[,n2[,n3[,color[,true/false]]]]] < POSCAR
        Similar to --xyz. Starts jmol (must be available) with a file
        based on the POSCAR input file. If you want to use atom names
        you must put them after each atom  position in the POSCAR
        file (see --names). If any names are missing they are defaulted to H.
        If no numbers are specified, aflow takes "1,1,1". (SC/Dec09)
        Background color may be chosen (e.g., white, brown, beige, etc...).
        Default background color is white. The flag "true" specifies that the
        cif file is to be saved. Default is "false." (RHT/Mar11)

  aflow --jmolanimation | --animation | --print=gif [gif_file] < POSCAR
        Generate animated gif file of rotated structure from POSCAR by using
        jmol and ImageMagick. If no output gif file name is given, the default name
        "aninamtion_" + process id + ".gif" will be used. The setting parameters
        of jmol cannot be changed by users currently.
        User must have valid DISPLAY for jmol to open its window and "Convert"
        command is used to generate multi-gif by combining gif files generated by jmol.
        

  aflow --join_strlist strlist1 strlist2
        Outputs to standard out a sequence of structures in POSCAR format.
        The structures consist of those in strlist1 with the atoms from  
        strlist2 added in.  The positions are taken from strlist2,  
        transformed into Cartesian coordinates, and then inserted into
        strlist1.  All inserted atoms are added as new types.  If one
        file has more structures than the other then the shorter file
        is padded with copies of the last structure.  For more information
        on a strlist see --make_strlist.

  aflow --kband ispin
        ispin(1=nospin,2=spin). Outputs to standard out Eband vs K for band structure plot.
        Needs EIGENVAL and KPOINTS files. Format:
        Kpoint upEband1 upEband2...upEbandN downEband1 downEband2...downEbandN
        The Kpoint column is constructed by cascading each KPOINT-segment specified in KPOINT file.

  aflow --latticereduction | -latreduction POSCAR
        Lattice Reduction to Max Orthogonality (Minkowski) and then
        to Niggly Form. This procedure has been shown to give the best
        unit cell for the lattice in terms of Minkowski optimization and
        most symmetric representation.  For the bcc and fcc it gives the
        standard, most symmetric, unit vectors.
        It also helps in the primitive cell serach, as it has been
        included by default inside. (SC0902).
  
  aflow --lattice_data|--data_lattice|--real_lattice_data|--data_real_lattice[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] < file
        Returns the lattice type data, includeing the lattice vectors, lattice parameters (Angstroms/Bohrs and degrees)
        volume, c/a ratio, lattice type, lattice variation, lattice system, and Pearson symbol.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
  
  aflow --lattice_type | --lattice | --lattice_crystal[=<tolerance_value>|=tight|=loose] < file
        Returns the lattice type and the conventional lattice type of the CRYSTAL following the tables
        of Setyawayn-Curtarolo [http://dx.doi.org/10.1016/j.commatsci.2010.05.010].
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
        Check aflow --readme=symmetry
  
  aflow --lattice_lattice_type | --lattice_lattice[=<tolerance_value>|=tight|=loose] < file
        Returns the lattice type and the conventional lattice type of the LATTICE following the tables
        of Setyawayn-Curtarolo [http://dx.doi.org/10.1016/j.commatsci.2010.05.010].
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
        Check aflow --readme=symmetry
  
  aflow --latticehistogram < POSCAR
        Outputs the lattice calculated respect to tolerance of histogram of symmetry.
    
  aflow --unique_atom_decorations [GENERAL_COMPARISON_OPTIONS] < file
      Determines the unique and duplicate atom decorations for a given structure, grouping 
      equivalent decorations (if applicable).
      
      [GENERAL_COMPARISON_OPTIONS]:
        [--np=16|--num_proc=16] : Allocate the number of processors/threads for the task.
        [--optimize_match] : Explore all lattice and origin choices to find the best matching representation, i.e., minimizes misfit value.
        [--no_scale_volume] : Suppresses volume rescaling during structure matching; identifies differences due to volume expansion or compression of a structure.
        [--ignore_symmetry] : Neglects symmetry analysis (both space group and Wyckoff positions) for grouping comparisons.
        [--ignore_Wyckoff] : Neglects Wyckoff symmetry (site symmetry) for filtering comparisons, but considers the space group number.
        [--ignore_environment] : Neglects LFA environment analysis for filtering comparisons.
        [--print=TEXT|JSON] : For comparing multiple structures, the results printed to the relevant files are formatted into human-readable 
          text or JSON, respectively.  By default, AFLOW-XtalFinder writes the output in both formats.
        [--quiet|--q] : Suppresses the log information for the comparisons.
        [--screen_only] : Prints the comparison results to the screen and does not write to any files.
        Check aflow --readme=compare

  aflow --use_LOCK=XXX
        Uses XXX instead of "LOCK" in freezing/searching/operating directories.
        The option is very useful for compounded calculations.

  aflow --ltcell=a11,a12,a13,a21,a22,a23,a31,a32,a33 < POSCAR
  aflow --ltcell=a11,a22,a33 < POSCAR
  aflow --ltcell=file < POSCAR
        Outputs to standard out the linear tranform of the input
        POSCAR file.  This simpy multiplies cell parameters and
        atom positions by the 3x3 matrix values.  This can
        be used to rotate the cell, swap x and y coordinates, etc.
        This cannot create a supercell (see --supercell for that).
        The nine numbers must be separated spaces, and they form the
        nine elements a11,a12,a13,a21,a22,a23,a31,a32,a33 of the 3x3
        supercell matrix, respectively. If you specify only 3 numbers,
        the other six are taken zero. If you use the "file" syntax,
        nine numbers are read from file. They can be on one or
        multiple lines. New algorithm by SC (aug07).
        The new lattice is (by column) (a1 a2 a3)*=LT*(a1 a2 a3).
  aflow --ltcellfv=v1,v2,v3,phi < POSCAR  
        Rotates the lattice vectors and atoms by angle phi (in degrees)
        around vector (v1,v2,v3).  Outputs to standard out the new
        POSCAR.  This can be used to rotate the cell, swap x and y
        coordinates, etc. 

  aflow --magpara=directory | --magpara (./)
        Output shows the magnetic momentum, cell of volume and spin polarization around Fermi level.
        If a directory is not specified, it loads "./"
        EXAMPLE: aflow --magpara
                 MAGNETIC MOMENTUM CELL : 2.74234
                 MAGNETIC MOMENTUM ATOM : 0.685586
                 VOLUME CELL            : 53.43
                 VOLUME ATOM            : 13.3575
                 SPIN DECOMPOSITION     : 0.032,1.447,1.447,-0.062
                 POLARIZATION FERMI     : 0.755068

  aflow --slab=h,k,l[,#filled_layers[,#vacuum layers]] < POSCAR
  	Produces a slab unit cell in POSCAR format. The normal of the slab is specified
        by the Miller indices of the orthogonal plane. Thus, make sure you know how the original POSCAR is specified.
        For example, (100) is not what you think for fcc primitive.
        Each point (hkl) in the reciprocal lattice
        corresponds to a set of lattice planes (hkl) in the real space lattice.
        The reciprocal lattice vector points in a direction normal to the real space planes.      

  aflow --make_strlist OUTCAR XDATCAR
        Outputs to standard out a sequence of structures in POSCAR format.
        The strlist file created contains a list of structures, each  
        formatted exactly like a POSCAR file, with an empty line after  
        all but the last one.  The file must have no extra lines at the end
        or all routines that read it will crash.  The lattice parameters  
        are pulled out from the OUTCAR and the positions from XDATCAR.  
        If OUTCAR has too few lattice parameters then copies of the last  
        set are used for the remaining XDATCAR.
  aflow --maxatoms=N | --max_atoms=N | --atoms_max=N | --atomsmax=N < POSCAR
        Limits the input POSCAR to N atoms (it writes an error if atoms>N).
        This is an useful option for online wrappers.
  aflow --minkowski_basis_reduction | --minkowski | --mink < POSCAR
        Converts the unit cell with the Minkowski reduction
        This routine takes a set of basis vectors (that form a lattice)
        and reduces them so that they form the shortest possible basis.
        The reduction is performed so that each vector "a_i" is a close
        as possible to the origin while remaining in the affine plane which
        is defined by "a_j", "a_k" but shifted by "a_i", for any choice
        of even permutations of i,j,k in 1,2,3.
        See Lecture notes in computer science, ISSN 0302-974, ANTS - VI :
        algorithmic number theory, 2004, vol. 3076, pp. 338-357
        ISBN 3-540-22156-5
        Written by Gus Hart in F90, recoded by SC in C++ (Sep/08).
        http://www.farcaster.com/papers/sm-thesis/node6.html
  aflow --miscibility | --mix strings ..
        Tells if in the library the system (on of the strings) was found
        to be miscible, immiscible or unknown.
        aflow --mix AgMg
        returns AgMg MISCIBILITY_SYSTEM_MISCIBLE
  aflow --mom < POSCAR  
        Gets the mass moments of the POSCAR file.  Gets only the first
        (center of mass) at this point. The scale is used in the
        calculation.
  aflow --msi < POSCAR
        Outputs to standard out a msi file based on the POSCAR input
        file.  This can be used as input for cerius.
        In the functions that output the msi format I do something
        to put the lattice vectors in a form that cerius2 can read
        happily.  It involvs making the third lattice vector parallel
        to Z, the second once in the YZ plane, and the letting the
        first lattice vector have all 3 components.  It is confusing
        and probably done in a silly manner, but it seems to work.
        If you want atom names you must put them after each atom
        position in the POSCAR file (see -names).  If any names are
        missing they are defaulted to H.  For an msi file one
        needs the atomic numbers.  These are coded into the
        program for most atoms.  If you use atoms with atomic numbers
        over 86 or f-electron atoms (Lanthanides and Actinides) then
        you will have to increase the database.  For the list of all
        coded atomic numbers see the constructor for the structure
        class in structure.cc.
 
  aflow --names A1 A2 ... < POSCAR
        Outputs to standard out a POSCAR file with names
        A1,A2, ... after the atom positions.  Each name
        Ai is assigned to all atoms of type i.
 
  aflow --natoms | --numatoms < POSCAR
        Outputs to standard out the number of atoms in the POSCAR.
        Useful for scripting. (SC0902).
  aflow --nbondxx< POSCAR
        Outputs to standard out the nearest neighbor distances between all types of atoms in the POSCAR.
        Useful for scripting. (CO1017).
  aflow --nanoparticle radius distance < POSCAR
        Starting from the input poscar, aflow prints a nanoparticle
        POSCAR with the radius and appropriate lattice making the
        particles as far as "at least distance". The origin of the
        particle is taken to be point 0,0,0 in the unit cell.
        You can translate the origin before with the command --setorigin (see below)
        to an atom, a point in cartesian or fractional coordinates.
        The radius and distance are in Angstroms and not scale
        normalized (all scales are set to 1.0).
        If not specified the parameters are taken to be 10A. (SC Apr/08)
  aflow --ndata < POSCAR
        Outputs to standard output the following normalized data:
        a1 a2 a3 phi(a2,a3) phi(a3,a1) phi(a1,a2)
        a1,a2,a3 are NORMALIZED over V^1/3 and phi are in degrees.
  aflow --niggli POSCAR
        Converts the unit cell to the standardized Niggli form.  The
        form is unique (up to some signs, I think).  The transformation
        makes use of only the lattice vectors and does not depend on the
        basis atoms.  This will work on any cell, but it treats the given
        cell as primitive, and it will not reduce the cell to primitive
        if it is not primitive already.  At present the algorithm seems to
        hang if I force more than about 6 digits of accuracy so be aware that
        small errors might be introduced (these can break symmetry!).
  aflow --nn < POSCAR
        Outputs to standard out the nearest neighbour distance.
  aflow --noorderparameter < POSCAR
        Outputs to standard out a POSCAR without all the order parameter
        stuff in it. (SC0903).
  aflow --nosd < POSCAR
        Outputs to standard out a POSCAR without selective dynamics
        formatting.  Combined with the above --sd option this allows
        easy movement between POSCAR files with and without selective
        dynamics formatting.
  aflow --numnames A1 A2 ... < POSCAR
        Same as names except appends an increasing integer to
        each different atom type.  Starts counting at 1 again
        for each new atom type.
  aflow --nspecies | --numspecies < POSCAR
        Outputs to standard out the number of species in the POSCAR.
        Useful for scripting. (SC0902).

  aflow --OrthoDefect < POSCAR
        Computes the orthogonality defect of the lattice of POSCAR. 
        The orthogonality defect is defined as the ratio of the product of
        lattice vector magnitudes to the volume of the parallelpiped defined 
        by the lattice vectors. So, for three orthogonal vectors, this ratio 
        would be unity. (R. Taylor).

  aflow --patch_database --patchfiles=file1,file2,...
        Patches entries of the database file. The patch files have to be in
        jsonl format. Each json in the jsonl must contain an AUID. If an AUID
        is not found in the database, it will be skipped. Properties not in
        the schema will be ignored.

  aflow --pdb < POSCAR
        Outputs to standard out a protein database (PDB) format file
        based on the POSCAR input file.  This can be used as input
        for many viewing programs.  Note that I don't really know
        anything about PDB but it seems to be an annoyingly column
        formatted.  Therefore, all the widths I use must tbe kept as is.  
        This means that if we have width W for variable X, and prec P,
        then X takes up P+1 for for the decimal part and decimal point,
        and we have only R=W-(P+1)-1=W-P-2 remaining digits (the -1 is
        because if X takes up all of W then you run into the previous
        field).  So we have the constraints
        Cell vectors: W=9,P=3,R=4 => <=10^5
        Cell angles: W=7,P=2,R=3 => <=10^3 (which always works since
             angles are given as >=0 and <=360)
        Cartesian positions: W=12,8,P=3,R=7,3 => <=10^8,10^4 (>0)
              and <=10^7,10^3 (<0 since you need a space for the -- sign)
        This is all probably fine unless an atom makes it to more
        negative than -999.999.
  aflow --pdos pdos.in PROOUT
        Writes the projected DOS for any desired combination of atoms,
        kpoints, bands, and lm values.  The output consists of 6  
        columns, spin up, down, up-down, and the cumulative DOS for  
        each of those.  Only up spin data is given for non  
        spin-polarized calculations.  The PDOS should look like
        an equivalent vasp output but will not be identical since
        vasp uses a different smearing method to get the PDOS.  
        However, I think these PDOS are basically correct, at least
        qualitatively.  To make this work you must
           -- Use slightly altered version of vasp
           -- set LORBIT=2 in INCAR
           -- Set ISYM=0 in INCAR  
           -- Set RWIGS in INCAR (see below)
        The details explaining all this are given above in the --pocc  
        section.  The input file has the following format
        
           # Input for aflow --pdos.  
          
           # These values you supply once.
           EMIN = --20.01477264 # default: 0.5eV below lowest energy.
           EMAX = 6.90250559 # default: 0.5ev above highest energy.
           NBINS = 300 # default: 300
           SMOOTH_SIGMA = 0.1 # Gaussian smoothing of the DOS.
                              # default: 1 bin width.
           PRINT_PARAMS = 1 # 0=prints only data (easy to plot).
                               # 1=prints all the input parameters.
                            # default: 0
          
           # You can have as many cases as you want.
           # They are all added together.
            
           # case 1
           ATOMS = 1 # default: all atoms.
           KPOINTS = # default: all kpoints.  
           BANDS = # default: all bands.
           LMVALUES = # default: all s,p,d,f.
            
           # case 1
           ATOMS = 2 # default: all atoms.
           KPOINTS = 1 2 3 # default: all kpoints.  
           BANDS = 1 # default: all bands.
           LMVALUES = 3 # default: all s,p,d,f.
        
        All # denote comment lines.  Each case is started when the token
        ATOMS is used.  Following an ATOMS token, all KPOINTS, BANDS,  
        LMVALUES tokens will apply to the atoms denoted in the preceeding  
        ATOMS token until the next ATOM token.  The  KPOINTS, BANDS,  
        LMVALUES tokens can be left out in which case their default values  
        will be used.  You can have any number of cases.  The above  
        example will calculate a PDOS with projections onto atom 1
        for all kpoints, bands, and s,p,d, and f (case 1) added to the
        projection onto atom 2 for kpoints 1-3, band 1, and the Pz orbital.
        I believe you can create any desired projections with this input
        file.  The LMVALUES use the following correspondence between  
        numerical input and orbitals projected.
        
        Input number: 1 2  3  4  5    6   7   8   9   10     11    
        Orbitals:     S Py Pz Px Ptot Dxy Dyz Dz2 Dxz Dx2-y2 Dtot
        Input number: 12 13 14 15 16 17 18 19   20
        Orbitals:     F1 F2 F3 F4 F5 F6 F7 Ftot Tot
        
        I have not done the work to figure out which of the standard
        f-orbital functions correspond to F1-F7.  
        
        This is only tested for version 4.4.5.

  aflow --pearson_symbol|--pearson|--Pearson_symbol|--Pearson [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--tolerance_spectrum=start:stop:nsteps] < file
        Returns the Pearson symbol of the structure.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Performs crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--tolerance_spectrum=start:stop:nsteps] : Performs symmetry analysis for a range of tolerance values
        Check aflow --readme=symmetry

  aflow --planedens dens2d.in CHGCAR
        This finds the charge density in a plane.  The input file dens2d.in  
        has the form
           D # Coordinates for following points (Direct/Cartesian)
           scale # Scale factor - edges of plane get mult. by this (but not origin).
           x y z # origin point
           x y z # X axis
           x y z # Y axis
           Nx Ny # Number of X and Y grid points
           Middle # Location for origin (Middle/Corner).
           Ortho # Whether to use Y orthogonal to X (Ortho/Strict).
        The output consists of 4 files, dens.[tot/diff/up/dn].out.  Each  
        has the same format, consisting of rows of density values, each  
        row corresponding to a value along the X axis and each column
        to a value along the Y axis.  The format can be read directly  
        into Excel and easily into MatLab.  This routine uses the same  
        routine as --chgint to read in the CHGCAR and should work
        for the same versions of vasp (see --chgint for more information).
  aflow --platon[=EQUAL | EXACT][,ang,d1,d2,d3] < POSCAR
        This finds the space group.  aflow is creating an output
        file, which is piped into a script platonSG, which uses the
        program platon.
        Wraps input file for Platon ADDSYM package:
        CALC ADDSYM (EQUAL) (EXACT) (ang d1 d2 d3)
        where:
        EQUAL - Search with all atom type treated as equivalent.
        EXACT - All atoms should fit for given criteria.
        ang - Angle criterium in search for metrical symmetry of the
              lattice (default 1.0 degree).
        d1 - Distance criterium for coinciding atoms for non-inversion
             (pseudo)symmetry elements (default 0.25 Angstrom).
        d2 - Distance criterium for coinciding atoms for (pseudo)
             inversion symmetry (default 0.25 Angstrom).
        d3 - Distance criterium for coinciding atoms for (pseudo)
             translation symmetry (default 0.25 Angstrom).
        The defaults are specified in aflow_xatom.cpp as
         #define PLATON_TOLERANCE_ANGLE 1.0
         #define PLATON_TOLERANCE_D1 0.25
         #define PLATON_TOLERANCE_D2 0.25
         #define PLATON_TOLERANCE_D3 0.25
        To get the space group, type
           aflow -platon < POSCAR | platonSG
        To just get see the output file from aflow, type
           aflow -platon < POSCAR
        To check for errors and see output from platon, type
           aflow -platon < POSCAR | platon -o
        Note that the added flags above do not seem to work.  To change tolerance
        create output file from aflow, and then add the four tolerances
        after CALC ADDSYM (on the same line).  Then pipe this file to platonSG.
        Aflow will use your atom labels if they are there.  If you
        give no atom labels it will use defaults for each atom type,
        (these are He,Li,Be,B,C, and then W for all remaining atom types).
        WARNING: If you have more than 6 atom types the W default
        will give the wrong space group. The equal flag may not work.
        Atoms labeled with H do not get read by default in platon.
        Do not use H labels.
        SEE: http://www.cryst.chem.uu.nl/platon/pl000401.html
        Note: it works with platon.f and xdrvr.c > 51108
        platon must be accessible on the path !	  
  aflow --platonSG[=EQUAL | EXACT][,ang,d1,d2,d3] < POSCAR
        This prints out the space group without bothering with the wrap ups.
        Note: it works with platon.f and xdrvr.c > 51108
        platon must be accessible on the path !	  
  aflow --platonSG_label[=EQUAL | EXACT][,ang,d1,d2,d3] < POSCAR
        Same as above but prints ONLY the space group name.	  
  aflow --platonSG_number[=EQUAL | EXACT][,ang,d1,d2,d3] < POSCAR
        Same as above but prints ONLY the space group number.	  

  aflow --plotband|--plotbands[=directory[,Emin[,Emax]]] [--keep=gpl] [--noshift] [--print=pdf|eps|gif|jpg|png] [--title=] [--outfile=]
        Generate bandstructure plot using GNUPLOT and pdfLaTeX
        The following files must reside in the directory:
         DOSCAR.static
         EIGENVAL.bands
         KPOINTS.bands
         POSCAR.static
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value: -10
         Emax: The maximum value of the DOS plot. Default value: 10
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --noshift: do not shift the Fermi level to zero
         --print: specify the format of the output image (default: pdf)
         --title: the title of the plot in LaTeX format (default: title in EIGENVAL file)
         --outfile: the name of the output image file.
        Examples:
         aflow --plotband=/common/DATA/ZnO,-8,6
         aflow --plotband=./ --print=gpl --print=png --title=ZnO

  aflow --plotband2[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]
        In this function, the DOS is the sum of spin-up and spin-down!
        The following files must reside in the directory
	 DOSCAR.static
	 EIGENVAL.bands
	 KPOINTS.bands
	 OUTCAR.static
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value -10
         Emax: The maximum value of the DOS plot. Default value 10
         DOSSCALE: The scale value of the DOS plot. Default value 1.2
  aflow --plotband_spinsplit[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]
        This function generates spin-up and spin-down electronic band structure plots, respectively.
        The following files must reside in the directory:
         EIGENVAL.bands
         KPOINTS.bands
         OUTCAR.bands
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value -10
         Emax: The maximum value of the DOS plot. Default value 10
         DOSSCALE: The scale value of the DOS plot. Default value 1.2

  aflow --plotbanddos[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]] [--keep=gpl] [--noshift] [--print=pdf|eps|gif|jpg|png] [--projection=atoms|lm|none|orbitals] [--title=] [--outfile=]
        Generate combined bandstructure and DOS plot using GNUPLOT and pdfLaTeX
        The following files must reside in the directory
	 DOSCAR.static
	 EIGENVAL.bands
	 KPOINTS.bands
	 POSCAR.static
        NOTE: If the DOSCAR contains f-orbitals and the calculation was performed
              with LORBIT = 10 and LSORBIT = .TRUE., either INCAR.static,
              vasprun.xml.static, or OUTCAR.static are required as well.
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value: -10
         Emax: The maximum value of the DOS plot. Default value: 10
         DOSSCALE: The scale value of the DOS plot. Default value: no scaling
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --noshift: do not shift the Fermi level to zero
         --print: specify the format of the output image (default: pdf)
         --projection: Determines whether the DOS is projected along the atoms, l- or lm-resolved orbitals, or not at all (default: orbitals)
         --title: the title of the plot in LaTeX format (default: title in DOSCAR file)
         --outfile: the name of the output image file.
        Examples:
          aflow --plotbanddos=/common/DATA/ZnO,-8,6,1.5
          aflow --plotbanddos=./ --print=png --projection=atoms

  aflow --plotdos[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]] [--keep=gpl] [--noshift] [--print=pdf|eps|gif|jpg|png] [--projection=atoms|species|lm|none|orbitals] [--title=] [--outfile=]
        Generate DOS plot using GNUPLOT and pdfLaTeX
        The following file must reside in the directory:
         DOSCAR.static
         POSCAR.static (in VASP 5 format for atom-projected DOS)
        NOTE: If the DOSCAR contains f-orbitals and the calculation was performed
              with LORBIT = 10 and LSORBIT = .TRUE., either INCAR.static,
              vasprun.xml.static, or OUTCAR.static are required as well.
        If it is a POCC run, the following files are required:
         DOSCAR.pocc_TxxxxK
        NOTE: If projection==species, the ARUN.POCC_xx directories are required,
              along with the aflow.in and aflow.pocc.structures_unique.out file.
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value: -10
         Emax: The maximum value of the DOS plot. Default value: 10
         DOSSCALE: The scale value of the DOS plot. Default value: no scaling
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --noshift: do not shift the Fermi level to zero
         --print: specify the format of the output image (default: pdf)
         --projection: Determines whether the DOS is projected along the atoms, l- or lm-resolved orbitals, or not at all (default: orbitals). For POCC runs, the DOS can also be projected among the species.
         --title: the title of the plot in LaTeX format (default: title in DOSCAR file)
         --outfile: the name of the output image file.
        Examples:
         aflow --plotdos=/common/DATA/ZnO,-8,6
         aflow --plotdos=./ --print=png --projection=atoms

  aflow --plotdosweb[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]
        Generate DOS plot using GNUPLOT
        The following file must reside in the directory
         DOSCAR.static
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value: -10
         Emax: The maximum value of the DOS plot. Default value: 10
         DOSSCALE: The scale value of the DOS plot. Default value: 1.2
 
  aflow --plotpdos|--plotpedos[=directory[,number_atom[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]] [--keep=gpl] [--noshift] [--print=pdf|eps|gif|jpg|png] [--projection=lm|none|orbitals] [--title=] [--outfile=]
        Generate atom-projected DOS plot using GNUPLOT and pdfLaTeX
        The following files must reside in the directory
	  	DOSCAR.static
	  	POSCAR.static
        NOTE: If the DOSCAR contains f-orbitals and the calculation was performed
              with LORBIT = 10 and LSORBIT = .TRUE., either INCAR.static,
              vasprun.xml.static, or OUTCAR.static are required as well.
        Defaults.
         Directory: default = ./
         Number atom: The atom index. Default value -1 (plot all inequivalent)
         Emin: The minimum value of the DOS plot. Default value: -10
         Emax: The maximum value of the DOS plot. Default value: 10
         DOSSCALE: The scale value of the DOS plot. Default value: no scaling
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --noshift: do not shift the Fermi level to zero
         --print: specify the format of the output image (default: pdf)
         --projection: Determines whether the DOS is projected along the l- or lm-resolved orbitals, or not at all (default: orbitals)
         --title: the title of the plot in LaTeX format (default: AFLOW-formatted title based on title in DOSCAR file)
         --outfile: the name of the output image file.
        Examples:
         aflow --plotpdos=/common/DATA/ZnO,-1,-8,6,1.2
         aflow --plotpdos=./,2 --print=png

  aflow --plotpdosall|--plotpedosall[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]] [--keep=gpl] [--noshift] [--print=pdf|eps|gif|jpg|png] [--projection=lm|none|orbitals] [--title=] [--outfile=]
        Generate atom-projected DOS plots of all inequivalent atoms using GNUPLOT and pdfLaTeX
        The following files must reside in the directory
	  	DOSCAR.static
	  	POSCAR.static
        NOTE: If the DOSCAR contains f-orbitals and the calculation was performed
              with LORBIT = 10 and LSORBIT = .TRUE., either INCAR.static,
              vasprun.xml.static, or OUTCAR.static are required as well.
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value: -10
         Emax: The maximum value of the DOS plot. Default value: 10
         DOSSCALE: The scale value of the DOS plot. Default value: no scaling
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --noshift: do not shift the Fermi level to zero
         --print: specify the format of the output image (default: pdf)
         --projection: Determines whether the DOS is projected along the l- or lm-resolved orbitals, or not at all (default: orbitals)
         --title: the title of the plot in LaTeX format (default: AFLOW-formatted title based on title in DOSCAR file)
         --outfile: the name of the output image file.
        Examples:
         aflow --plotpdosall=/common/DATA/ZnO,-1,-8,6,1.2
         aflow --plotpdosall=./ --print=png

  aflow --plotpedosall_nonquivalent[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]
        Usage: aflow  --plotpedosall_nonquivalent[=directory[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]
        Generate PDOS plots of all the inquivalent atoms using GNUPLOT.
        The following files must reside in the directory
	  	DOSCAR.static
	  	OUTCAR.static
                POSCAR.relax1
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value -10
         Emax: The maximum value of the DOS plot. Default value 10
         DOSSCALE: The scale value of the DOS plot. Default value 1.2
        Use --keep=gnuplot (--keep=GPL) to keep the GNU plot code.

  aflow --plotphdisp|--plotphonondispersion|--pphdis[=directory,[Emin,[Emax]]] [--keep=gpl] [--print=pdf|eps|gif|jpg|png] [--title=] [--unit=THz|Hz|eV|meV|rcm|cm-1]
        Plot the phonon dispersion using GNUPLOT and pdfLaTex
        The following files must reside in the directory
                PHDOSCAR
                PHEIGENVAL
                PHKPOINTS
                PHPOSCAR
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the plot. Default value: minimum frequency
         Emax: The maximum value of the plot. Default value: maximum frequency
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --print: specify the format of the output image (default: pdf)
         --title: the title of the plot in LaTeX format (default: title in PHEIGENVAL file)
         --unit: the unit of the phonon frequencies/energies (default: THz)
        Example:
         aflow --plotphdisp=./ --print=png --unit=cm-1
        
  aflow --plotphdispdos[=directory,[Emin,[Emax[,DOSSCALE]]]] [--keep=gpl] [--print=pdf|eps|gif|jpg|png] [--title=] [--unit=THz|Hz|eV|meV|rcm|cm-1]
        Plot a combined phonon dispersion and phonon DOS plot using GNUPLOT and pdfLaTex
        The following files must reside in the directory
                PHDOSCAR
                PHEIGENVAL
                PHKPOINTS
                PHPOSCAR
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the DOS plot. Default value: minimum frequency
         Emax: The maximum value of the DOS plot. Default value: maximum frequency
         DOSSCALE: The scaling factor of the DOS plot. Default value: no scaling
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --print: specify the format of the output image (default: pdf)
         --title: the title of the plot in LaTeX format (default: title in PHDOSCAR file)
         --unit: the unit of the phonon frequencies/energies (default: THz)
         --outfile: the name of the output image file.
        Example:
         aflow --plotphdispdos=./  --print=png --unit=cm-1
 	  
  aflow --plotphdos[=directory,[Emin,[Emax[,DOSSCALE]]]] [--keep=gpl] [--print=pdf|eps|gif|jpg|png] [--title=] [--unit=THz|Hz|eV|meV|rcm|cm-1]
        Plot a combined phonon dispersion and phonon DOS plot using GNUPLOT and pdfLaTex
        The following files must reside in the directory
                PHDOSCAR
        Defaults.
         Directory: default = ./
         Emin: The minimum value of the plot. Default value: minimum frequency
         Emax: The maximum value of the plot. Default value: maximum frequency
         DOSSCALE: The scaling factor of the DOS plot. Default value: no scaling
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --print: specify the format of the output image (default: pdf)
         --title: the title of the plot in LaTeX format (default: title in PHDOSCAR file)
         --unit: the unit of the phonon frequencies/energies (default: THz)
         --outfile: the name of the output image file.
        Example:
         aflow --plotphdos=./  --print=png --unit=cm-1

  aflow --plotthermo[=directory[,Tmin[,Tmax]]] [--keep=gpl] [--print=pdf|eps|gif|jpg|png] [--title=] [--outfile=]
        Plots the APL thermal properties such as vibrational free energy, entropy, and heat capacity
        using GNUPLOT and pdfLaTeX.
        The following file must reside in the directory:
                aflow.apl.thermal_properties.out
        Defaults.
         Directory: default = ./
         Tmin: The minimum temperature of the plot. Default value: 0 K
         Tmax: The maximum temperature of the plot. Default value: maximum temperature
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --print: specify the format of the output image (default: pdf)
         --title: the title of the plot in LaTeX format (default: SYSTEM in out file)
         --outfile: the name of the output image file.
        Example:
         aflow --plotthermo=./,100,300

  aflow --plotcond|--plothermalconductivity[=directory[,Tmin[,Tmax]]] [--keep=gpl] [--print=pdf|eps|gif|jpg|png] [--title=] [--outfile=]
        Plots the AAPL thermal conductivity using GNUPLOT and pdfLaTeX.
        The following file must reside in the directory:
                aflow.aapl.thermal_conductivity.out
        Defaults.
         Directory: default = ./
         Tmin: The minimum temperature of the plot. Default value: 0 K
         Tmax: The maximum temperature of the plot. Default value: maximum temperature
        Optional arguments:
         --keep=gpl: keep the gnuplot script
         --print: specify the format of the output image (default: pdf)
         --title: the title of the plot in LaTeX format (default: SYSTEM in out file)
         --outfile: the name of the output image file.
        Example:
         aflow --plottcond=./,100,300

  aflow --pocc_dos[=directory[,T[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]]
        Generate density of states (DOS) plot at different temperature for a partial occupation structure.
        If not specified, default directory is ./, temperature is 300K, DOS_Emin=-5 eV, DOS_Emax=5 eV, and DOSSCALE=1.2.
        Example: aflow --pocc_dos=./,300
        More details about how to do this can be found in "README_AFLOW_POCC.TXT".
  aflow --pocc_mag[=directory[,T[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]]
        Calculate magnetic moment at different temperature for a partial occupation structure.
 	If not specified, default directory is ./, temperature is 300K, DOS_Emin=-5 eV, DOS_Emax=5 eV, and DOSSCALE=1.2.
        Example: aflow --pocc_mag=./,300
        More details about how to do this can be found in "README_AFLOW_POCC.TXT".
  aflow --pocc_bandgap[=directory[,T[,DOS_Emin[,DOS_Emax[,DOSSCALE]]]]]
        Calculate band gap at different temperature for a partial occupation structure.
 	If not specified, default directory is ./, temperature is 300K, DOS_Emin=-5 eV, DOS_Emax=5 eV, and DOSSCALE=1.2.
        Example: aflow --pocc_bandgap=./,300
        More details about how to do this can be found in "README_AFLOW_POCC.TXT".

  aflow --pocc PROOUT
  aflow --pocc PROOUT
        Outputs occupations calculated from projections onto spherical  
        harmonics for each ion for many combinations of L, M, bands,  
        and kpoints.  This works with version 445 and has not been tested  
        on any other version (and probably won't work).  To make this work
        you need to do the following
           -- Use slightly altered version of vasp (see below)
           -- set LORBIT=2 in INCAR (see below)
           -- Set ISYM=0 in INCAR (see below)
           -- Set RWIGS in INCAR (see below)
        Here is why you need to do these things (feel free to skip this).
        The --pocc option reads the PROOUT file, which is produced by  
        running vasp with LORBIT=2 in the INCAR file.  There is an  
        annoying subtle point here. I am not sure I totally get this  
        but here is my best understanding.  The projection onto the  
        spherical harmonics actually uses some atomic like radial  
        functions (bessel functions).  This means that for each  
        spherical harmonic there are multiple states, corresponding  
        to different atomic energy levels and radial functions.  
        Write the projection of band n, at kpt k, onto spherical harmonic  
        with angular quantum numbers l,m and energy level e as Pnklme.  
        As compiled, the vasp code outputs projections Pnklm, summing  
        over the e parameter.  This makes each projection a sum of  
        complex numbers, allowing some cancellations.  However, for  
        occupations, like those output in PROCAR (LORBIT=1) and OUTCAR,  
        the summations over e are done with the squares of the Pnklme.  
        This makes sense, since you want to add up probabilities,  
        not amplitudes, to get an occupation.  Unfortunately, from  
        the output Pnklm one cannot reconstruct the Pnklme, so the  
        ouptut in PROOUT is not enough to reproduce the occupations.
        Therefore, I suggest the following.  Recompile vasp with following
        modifications to sphpro.F
        change line 252
                   WRITE(IUP,'(9F12.6)') CSUM_PHASE
        to
                   write(IUP,'(9F12.6)') CSUM_ABS
        CSUM_ABS is a complex variable but the imaginary part is zero.  It
        is the squared amplitude for each projection.  Note that this is  
        a probability.  You use it directly (do not square it) to get  
        occupations.  Note that the augmentations are added to this real  
        number, and are therefore probablities, not amplitudes.  
        This makes sense when you look at the code in sphpro.F that  
        calculates the augmentation portion.  The augmentations can be  
        <0, which I assume corresponds to reducing the probability of  
        finding electrons.  This make me a little uncomfortable but  
        I guess it is OK.  At this point the aflow code assumes  
        the above modification and uses the magnitude of the projections
        to calculate all occupations (not the magnitude squared).  
          Also, there is another subtle point with the kpoints.  If  
        you use symmetry certain sets of symmetry equivalent kpoints  
        (a star) are represented by a single irreducible kpoint.  We  
        are used to ignoring this and simply weighting things associated  
        with the irreducible kpoint appropriately to account for the  
        whole star.  However, the projections onto different orbitals  
        are not the same for all the points in a star.  For example,  
        the kpoints (0.1,0,0),(0,0.1,0),(0,0,0.1) may all be in the  
        same star in fcc, but states associated with them will project  
        differently onto Px orbitals.  Therefore, if you use irreducible
        kpoints you will get the wrong projections (it seems like you
        do get the right totals for S,P, and D, bit I am not sure that  
        is always the case).  To be safe, don't use any symmetry -- i.e.,
        set ISYM=0 in the INCAR file.
          You must set RWIGS so that the code knows the radius of
        the spheres onto which it projects.  
          To make sure all is in order you can look at the total  
        occupations for each ion in OUTCAR.  These should match  
        the Occupations vs. ION:LM values in the output of aflow  
        (the last lines in the output).  A more detailed check is  
        to run vasp with LORBIT=1 and compare the PROCAR file with  
        the output of aflow.  I am not sure that this will all  
        work the same way with PAW potentials.  

  aflow --pointgroup | --pgroup[=<tolerance_value>|=tight|=loose] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculates the point group symmetry of the lattice {R} and writes
        it in the aflow.pgroup.out file. See documentation of aflow.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry
  
  aflow --pointgroup_crystal|--pgroup_crystal|--pgroup_xtal[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculate the point group symmetry of the crystal {R+atoms} and
        writes it the aflow.pgroup_xtal.file.  
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry

  aflow --pointgroupkcrystal|--pointgroupk_xtal[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculates the dual of the crystal point group symmetry operations and writes
        it in the aflow.pgroupk_xtal.out file. See documentation of aflow.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry
  
  aflow --pointgroupklattice|--pgroupk[=<tolerance_value>|=tight|=loose] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculates the point group symmetry of the klattice {K} and writes
        it in the aflow.pgroupk.out file. See documentation of aflow.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry

  aflow --pointgroupk_Patterson|--pgroupk_Patterson[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculates the Patterson point group symmetry operations and writes
        it in the aflow.pgroupk_Patterson.out file. See documentation of aflow.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry
  
  aflow --pgl < POSCAR
        Calculate the point group symmetry of the lattice {R} and
        prints it to stdout.
  aflow --pgx < POSCAR
        Calculate the point group symmetry of the crystal {R+atoms} and
        prints it to stdout.

  aflow --pomass[=directory]
        Outputs from the available POTCAR/OUTCAR the sum of POMASS.
  aflow --pomass_atom[=directory]
        Outputs from the available POTCAR/OUTCAR and POSCAR/CONTCAR the POMASS of the cell per atom.
  aflow --pomass_cell[=directory]
        Outputs from the available POTCAR/OUTCAR and POSCAR/CONTCAR the POMASS of the whole cell.

  aflow --poscar < ABCCAR | WYCCAR
      Converts the ABCCAR in POSCAR format.
      ABCCAR is described as:
        TITLE
         SCALE (positive (rescaling) negative (volume))
         A B C ALPHA BETA GAMMA
         #specie0 #specie1 ....
         DIRECT (or CARTESIAN)
         .. .. .. specie0
         .. .. .. specie0
          . . .
         .. .. .. specie1
         .. .. .. specie1
         and so on. (Stefano Feb 2009)
      Converts the WYCCAR IN POSCAR format.
      WYCCAR is described as
      TITLE
        SCALE (positive (rescaling) negative (volume))
        A B C ALPHA BETA GAMMA SG# [OPTION#]
        #specie0 #specie1 ....
        DIRECT (or CARTESIAN)
        .. .. .. specie0
        .. .. .. specie0
         . . .
        .. .. .. specie1
        .. .. .. specie1
        and so on. (Stefano Feb 2009)
      The positions of the species will be used with the list of
      symmetry operations (aflow_wyckoff.cpp) to generate all the atoms.

  aflow --poscar2aflowin < POSCAR
        Makes an "almost standard" aflow.in starting from the poscar.
        Useful for scripting (SC20100630).

  aflow --poscar2cce|--get_cce_correction|--get_cce_cor < STRUCT_FILE
        options:
            [ --functionals=PBE|LDA|SCAN]
            [ --enthalpies_formation_dft|dft_formation_enthalpies=form_enthalpy_1,form_enthalpy_2,...]
            [ --oxidation_numbers=ox_num_1,ox_num_2,...]
            [ --print=json|out] (default is out)

        Determines the CCE corrections for the structure in file STRUCT_FILE. It can be in any structure
        format that AFLOW supports, e.g. VASP POSCAR, QE, AIMS, ABINIT, ELK, and CIF. For VASP, a VASP5
        POSCAR is required or, if a VASP4 POSCAR is used, the species must be written on the right side
        next to the coordinates for each atom.
        Precalculated DFT formation enthalpies can be provided as a comma separated list using the option
        --enthalpies_formation_dft= in eV/cell.
        Functionals for which corrections should be returned can be provided as a comma separated list 
        using the option --functionals=. If used together with --dft_formation enthalpies, the functionals
        must be in the same sequence as the DFT formation enthalpies they correspond to. 
        Oxidation numbers can be provided as a comma separated list using the option --oxidation_numbers=
        It is assumed that: (i) one is provided for each atom of the structure and (ii) they are in the 
        same sequence as the corresponding atoms in the provided structure file.
        Output in json format can be obtained using the option --print=json

  aflow --poscar2enum < POSCAR
        Convert a POSCAR into an input format for MULTIENUM (partial occupation).
        This is useful for debuging MULTIENUM.

  aflow --poscar2gulp < POSCAR
        Convert a POSCAR into an input format for gulp program.
    
  aflow --poscar2wyckoff < POSCAR
        Outputs to Wyckoff positions using findsym.
        Note that you may find more detailed information just using aflow --findsym < POSCAR if you can not understand it very clearly.
    
  aflow --prepare_chgcar_4_jmol=|--prep4jmol=CHGCAR1[,CHGACAR2,...]

        options:
            [ --usage ]
            [ --outcar=OUTCAR ] 
            [ --zip ]

        Modify the header of a CHGCAR file so it can be read by Jmol.
        Jmol requires species to be specified in the comment line of the CHGCAR file (first line).
        This code requires an OUTCAR to read in the species.
        Unless specified, it will first look for OUTCAR file in the directory of the CHGCAR, then it will
        look in the directory from which the command is called. 
        The CHGCAR and OUTCAR files may be compressed, and the edited CHGCAR file can be recompressed 
        (if it was previously) by specifying the --zip command.
  
  aflow --prim < POSCAR
        Outputs to standard out a POSCAR file with a
        primitive unit cell.  In the primitive cell finding
        function I look for a primitive cell by considering
        as candidate cell vectors every possible triad of 3
        vectors that can be made from the original cell vectors
        or the basis vectors which translate the lattice onto
        itself.  I then take the triad with the smallest volume
        to be the primitive cell.  If there are multiple
        candidates I take the ones with the largest projections
        onto the original lattice vectors.  See the rouinte
        GetPrim.cc for more information. NOTE: the algorithm is by SC
        different from the old DM aflow approace).
    
  aflow --primr | --fastprimitivecell | --fprim < POSCAR           
        Returns the primitive, Minkowski reduced cell, using a fast(er) routine. (R. Taylor).
      
  aflow [options] --proto=label*[:specieA*[:specieB*]..[:volumeA*[:volumeB*].. | :volume]] [ --params=..... [--hex]]
        This command prints out a prototype of label="label" with speciesA,speciesB,.... (non mandatory)
        of volumes per atom "volumeA, volumeB..." (not mandatory) or with standard volume per atom = "volume".
        Note that that --proto label A B ... is not supported anymore and you now need to use
        --proto=label:A:B... et cetera.

      QUANTUM ESPRESSO output                                                                     
        If you specify --qe, aflow will add QUANTUM ESPRESSO code to aflow.in (experimental).   

      ABINIT output                                                                     
        If you specify --abinit, aflow will add ABINIT code to aflow.in (experimental).   

      AIMS output                                                                     
        If you specify --aims, aflow will add AIMS code to aflow.in (experimental).  

      AFLOW-ANRL: AFLOW NAVAL RESEARCH LAB PROTOTYPE LIBRARY
        The AFLOW-ANRL Library consists of 590 (part 1: 288, part 2: 302) crystallographic prototypes
        from the following articles:
          - M. J. Mehl, D. Hicks, C. Toher, O. Levy, R. M. Hanson, G. L. W. Hart, and S. Curtarolo,
            The AFLOW Library of Crystallographic Prototypes: Part 1, Comp. Mat. Sci. 136, S1–S828 (2017).
          - D. Hicks, M. J. Mehl, E. Gossett, C. Toher, O. Levy, R. M. Hanson, G. L. W. Hart, and S. Curtarolo,
            The AFLOW Library of Crystallographic Prototypes: Part 2, Comp. Mat. Sci. 161 Supplement, S1-S1011 (2019).
        These prototypes must be accompanied by the --params=... flag or label suffix (e.g., <label>-001) specifying
        the internal degrees of freedom for the prototype.
        Rhombohedral systems can be generated in the hexagonal setting with the flag --hex.
        Check aflow --readme=anrl for more information.
   

  aflow --prototype [--setting=1|2|anrl] < file             
      Converts a structure (file) into its corresponding standard AFLOW prototype label. 
      The parameter variables (degrees of freedom) and parameter values are also listed.
      Information about the label and parameters are described in the AFLOW Library of Crystallographic Prototypes:
      Part 1 (doi=10.1016/j.commatsci.2017.01.017), 
      Part 2 (doi=10.1016/j.commatsci.2018.10.043), 
      or README_AFLOW_ANRL.TXT.
      
      Options:
          [--setting=1|2|aflow] : Specifies the space group setting. The `aflow' setting follows the choices of the AFLOW Prototype Encyclopedia (default: aflow).
                                  Different settings exist for the following space groups:
                                    - centrosymmetric space groups with two origin choices (24 space groups, e.g., sg=227):
                                        --setting=1     : origin centered on high site symmetry (not inversion site)
                                        --setting=2     : origin centered on inversion site
                                        --setting=aflow : origin centered on inversion site
                                    - rhombohedral space groups (e.g., space group 166):
                                        --setting=1     : rhombohedral setting
                                        --setting=2     : hexagonal setting
                                        --setting=aflow : rhombohedral setting
                                    - monoclinic space groups (e.g., space group 5):
                                        --setting=1     : unique axis-b
                                        --setting=2     : unique axis-c
                                        --setting=aflow : unique axis-b
          [--print_element_names]  : Print the element names from the input structure
          [--print_atomic_numbers] : Print the atomic number for the elements in the input structure

  aflow --prototype_labels|--proto_labels [--library=htqc|anrl|all] [--arity=|--number_of_species=|--species_count=<number>] [--stoichiometry=|--stoich=<number>,<number>,...] [--space_group_number=|--space_group=|--sg=<number>] 
        Returns a list of the AFLOW prototype labels.
        The labels can be filtered by arity, stoichiometry, and space group.
        options:
          [--library] : specify library/catalog, i.e., htqc, anrl, or all (default=all)
          [--arity=<number>] : specify 1=unary, 2=binary, 3=ternary, etc.
          [--stoichiometry=<number>,<number>,...] : specify the stoichiometry
          [--space_group_number=<number>] : specify the space group number

  aflow --prototypermult | --PROTOTYPERMULT <POSCAR
        Inputs 3 to 10 ary POSCARS, outputs the first alloy of prototype
	  group, which is categoried by --protoclassify, from ICSD database.

  aflow --prototypes | --protos
        Give the list of prototypes (file LIST.txt) from the DMQC-HTQC
        project (SC oct 08)

  aflow --pseudopotentials_check=[POTCAR|OUTCAR][""|.bz2|.gz|.xz] | --pp_check= | --ppk=
       Returns unique identification information about the
       pseudopotentials used for the calculations.   
 
  aflow [--server=XXXXXXXX] --prototypes_icsd[=N] | --protos_icsd[=N]                                  
        Give the list of prototypes from the ICSD database included in the code.   
        If N is passed, then it returns ONLY the N-ary compounds.
	If the ICSD_AFLOW_LIBRARY is not available, the code switches to downloading
        information from the server=aflowlib.duke.edu database.
        You can force downloading from different servers:
        --server=aflowlib.duke.edu
        --server=materials.duke.edu
        --server=default (switches to aflowlib.duke.edu)

  aflow [--server=XXXXXXXX] [--vasp|--qe|--abinit|--aims] --proto_icsd=label                                  
        Returns the prototype labeled with the string label, from the             
        ICSD database.                                                            
        Example: aflow --proto_icsd=Ba1Ga4_ICSD_659522
        Example: aflow --aflowlib.duke.edu --proto_icsd=Ba1Ga4_ICSD_659522
	If the ICSD AFLOW_LIBRARY is not available, the code switches to downloading
        information from the  server=aflowlib.duke.edu database.
        You can force downloading from different servers:
        --server=aflowlib.duke.edu
        --server=materials.duke.edu
        --server=default (switches to aflowlib.duke.edu)
        The label can be of this type:
        --proto_icsd=ICSD_number.{ABC}[:speciesA*[:speciesB*]..[:volumeA*[:volumeB*].. | :volume]]"
        --proto_icsd=label_ICSD_number"

  aflow --python_modules[=module1,module2] | --create_python_modules[=module1,module2] [-D directory]
        Installs AFLOW python modules in the chosen directory.
        Available modules: aflow_cce, aflow_chull, aflow_chull_plotter, aflow_sym, aflow_xtal_finder
        --python_modules: A comma-separated list with the desired modules. Leave blank to install all.
        --create_python_modules: alias for --python_modules
        -D: directory in which to install the python modules. Default: ./

  aflow --qe                                                                       
        Transforms the POSCAR (or whicever is the input file format) to a              
        QUANTUM ESPRESSO GEOM format.                                                  
        The geometrical file follows the QE convention (see ibrav in QE manual).   

  aflow --qmvasp [--static] [-D directory]
        Given the current directory (or the one specified by -D), aflow
        produces the file aflow.qmvasp.out containing thermodynamic information
        from relax2 CONTCAR/OSZICAR/OUTCAR (or .static if --static is specified).

  aflow --quasi_chem_approx|--qca --plattice=|--plat=fcc --elements=|--elem=Au,Pt[,Zn] [qca_options] [--directory=[DIRECTORY]]
        Loads the alloy data from the AFLOW database, calculates the equi-concentration transition
        temperature, and returns the output as a TXT (default, see --format_data).
        --quasi_chem_approx|--qca : Necessary argument, enters the mode to use the QCA.
        --plattice|--plat : Necessary argument, specifies the parent lattice of the alloy. Argument is restricted to
            only FCC (face centered cubic), BCC (body centered cubic) and HCP (hexagonal closed pack for only binaries).
        --elements|--elem : Necessary argument, specifies the elements present in the alloy.
        [--directory=[DIRECTORY]] : Optional argument, specifies the directory where to run the
            calculation.
            Default: "./"

        GENERAL OPTIONS:
        [--usage] : Returns the usage commands and options.
            Default: OFF
        [--screen_only] : Outputs directly to screen (stdout) instead of writing to a file.
            Default: OFF
        [--image_only|--image] : Reads only the output data and plot the results. Plotting
            is only implemented for binary alloys.
            Default: OFF
        [--aflowlib_directory=|--aflowlib_dir=] : Specifies a directory (including
            its subdirectories) from where to read additional aflowlib files.
            Default: ""
        [--print=|--p=|--output=|--o=txt|json|pdf|eps|png] : Selects the output format.
            Default: txt

        BINODAL OPTIONS:
        [--binodal] : Calculates the binodal curve for the given concentration and temperature
            profiles.
            Default: OFF
        [--use_sg] : Uses the space groups for structure comparison.
            Default: OFF
        [--aflow_max_num_atoms=4] : Specifies the maximum number of atoms in the unit cell of
            the AFLOW calculations.
            Default: 4
        [--max_num_atoms=|--mna=8] : Specifies the maximum number of atoms in the alloy.
            Default: 8
        [--cv_cutoff=|--cv_cut=0.05] : Specifies the cross validation (CV) score cut-off for
            the cluster expansion. The calculation will terminate prematurely if the CV
            score is below the cut-off.
            Default: 0.05
            Units: eV
        [--conc_curve_range=|--conc_curve=0,1,1,0] : Specifies the concentration curve
            to evaluate the equilibria properties. The format of this argument is:
            <c_1i>,<c_1f>,<c_2i>,<c_2f>,...,<c_[K]i>,<c_[K]f> where K is number
            of elements, <c_[k]i> is the initial concentration and <c_[k]f> is the
            final concentration. The concentration is defined on [0,1].
            Default: NONE
        [--conc_npts=20] : Specifies the number of points used to determine the sub-division of
            the concentration profile.
            Default: 20
        [--temp_range=|--temp=300,5000] : Specifies the temperature range to evaluate the
            equilibria properties. The format of this argument is: <T_i>,<T_f>
            where <T_i> and <T_f> is the initial and final temperature, respectively.
            Default: 300,2000
            Units: K
        [--temp_npts=100] : Specifies the number of points used to determine the sub-division of
            the temperature profile.
            Default: 150

  aflow --rasmol[=n1[,n2[,n3]]] < POSCAR
        Similar to --xyz. Starts rasmol (must be available) with a file
        based on the POSCAR input file. If you want to use atom names
        you must put them after each atom  position in the POSCAR
        file (see -names). If any names are missing they are defaulted to H.
        If no numbers are specified, aflow takes "1 1 1". (SC/OCT07,OCT14)
  aflow --raytrace rtfile
        Outputs jpeg or mpeg pictures created by ray tracing.  This  
        is a rather elaborate routine.  The basic idea is that it
        takes as input a list of structures (in POSCAR like format)  
        and converts them into a dat file, inputs that into the ray  
        tracing program tachyon, then takes the tga file output by  
        tachyon and uses convert to make it a jpeg, then if needed  
        takes all the jpegs and puts them together into and mpg using  
        mpeg_encoder.  Therefore the following programs must be  
        installed and in your path: tachyon, convert, mpeg_encoder  
        (only if making a movie).  There is an input file rtfile  
        which contains tokens setting characteristics of the calculation
        and the ray traced picture.  This input file looks like the  
        following:          

           # These set the input for the ray tracing program tachyon
           CALCTYPE = 0 #0=strlist
           INFILE = strlist # For CALCTYPE=0
           OUTFILE = XXX # All ouput will have this prefix.
           RESX = 600 # X pixels in images.
           RESY = 500 # Y pixels in images.
           ZOOM = 1.5 # Like a zoom lens.
           ASPECTRATIO = 1 # Y height / X height.
           ANTIALIASING = 0 # Something to do with extra accuracy.
           RAYDEPTH = 12 # Number of reflections to keep in ray trace.
           # x,y,z of camera location.  Changes incrementally each frame  
           # from initial to final value.  format is ciX cfX ciY cfY ciZ cfZ,  
           # where i,f denote initial and final, respectively.
           # Default is displaced along -Y from structure center.
           #CENTER = 1 1 -2 -2 2 4
           #VIEWDIR = 1 0 0 # Direction of camera viewing.
            #UPDIR = 0 0 1 # Up direction for picture.
           BACKGROUND = 0.3 0.1 0.1 # Background lighting (all lights are R G B).
           LIGHT = -20 -20 -20  0.01 1.0 1.0 1.0 # Spherical light source: center(3) radius(1) color(3)
           LIGHT = 20 20 20  0.01 1.0 1.0 1.0 # Spherical light source: center(3) radius(1) color(3)
           ATOMTEXTURE = 1 0.1 0.9 0.0  1.0 # atomtype ambient diffuse specular opacity
           ATOMTEXTURE = 2 0.1 0.9 0.0  1.0 # atomtype ambient diffuse specular opacity
           ATOMTEXTURE = 3 0.1 0.9 0.0  1.0 # atomtype ambient diffuse specular opacity
           ATOMTEXTURE = 4 0.2 0.9 0.3  1.0 # atomtype ambient diffuse specular opacity
           ATOMCOLOR = 1 1.0 0.75 0.3 # atomtype(1) color(3)
           ATOMCOLOR = 2 0.2 0.4 1.0 # atomtype(1) color(3)
           ATOMCOLOR = 3 1.0 1.0 1.0 # atomtype(1) color(3)
           ATOMCOLOR = 4 1.0 0.0 0.0 # atomtype(1) color(3)
           ATOMRAD = 1 0.6 # atomtype rad
           ATOMRAD = 2 0.3 # atomtype rad
           ATOMRAD = 3 1.0 # atomtype rad
           ATOMRAD = 4 0.8 # atomtype rad
           SHADING = mediumshade # fullshade,mediumshade,lowshade,lowestshade  
           # A supercell matrix given as 9 reals:  a11 a12 a13 a21 a22 a23  
           # a31 a32 a33.  Note that using this moves all atoms into images
           # the unit cell.
           # Default = 1 0 0 0 1 0 0 0 1
           SUPERCELL = 1 0 0   0 1 0  0 0 1  
           # Rotation around x,y,z axis through structure_origin
           # (counterclockwise).  Rotation take place incrementally each
           # frame.  Rotation goes from initial to final value.  
           # format is riX ifX riY rfY riZ rfZ, where i,f denote initial
           # and final, respectively.
           # Default = 0 0 0 0 0 0
           ROTATION = 0 0 0 0 -180 180
           # The zero for the structure coordinates and lattice parameters.
           # Rotations occur around this point.
           # Default = First moment of atom positions.
           STRUCTURE_ORIGIN = 0 0 0  
           PLANE = 1 # 0 for no plane, 1 for plane.
           PLANECENTER = 0 0 -9.21016 # X Y Z for center of plane.
           PLANENORMAL = 0 0 1 # Direction of plane normal.
           PLANECOLOR = 1 1 1 # R G B for plane color.
           PLANETEXTURE = 0.3 0.6 0.8 1.0 # ambient diffuse specular opacity for plane.
        
        Tokens can be in any order, whitespace is ignored, and anything
        following a # on a line is ignored.  The CENTER, VIEDDIR, and  
        UPDIR depend on the structure and can be a pain to set by hand  
        so they have fairly elaborate defaults that seem to usually work  
        fine.  The other values are not bad places to start.  For  
        more info about these check out the tachyon documentation.
        
        For a single structure the output consists of XXX.dat, XXX.tga,
        XXX.jpg, XXX.enc, XXX.mpg.  Having all these files is useful  
        if some part of the program did not exectute properly and you  
        need to do steps by hand (tachyon XXX.dat produces XXX.tga,  
        convert XXX.tga XXX.jpg produces XXX.jpg, and mpeg_encode XXX.enc
        produces XXX.mpg).  For more than one structure the XXX.dat  
        and XXX.tga files are erased to avoid clutter.  The XXX.enc file  
        is used for the mpeg_encode programs and is totally set in  
        aflow and the user has not control over it from the rtfile.  
        If you want to alter it after it is output go ahead but I know  
        almost nothing about how it works.  To make your own mpg from  
        the jpg type:      mpeg_encode XXX.enc  
        The tga, jpg files  can be viewed with xv and the mpg with mpeg_play.XXX
        Note: this routine was written by Dane and readapted by Stefano.
        It might not work but require slightly modifications in the C++ source.
	  TACHYON WEB:  http://jedi.ks.uiuc.edu/~johns/raytracer/
        MPEG_ENCODER: http://bmrc.berkeley.edu/frame/research/mpeg/mpeg_encode.html
        CONVERT:      http://www.imagemagick.org/script/index.php
	  LINUX: Debian 4.0r1 contains convert ("imagemagick") and
	         the mpeg_encoder ("ucbmpeg").
  aflow --rbanal nim nearest_image_flag
        This is meant to allow you to analyse a rubber band calculation
        to get energy vs. distance along activation path. The distance
        is given a cumulative from the 00 to END images (a line integral),
        and also as the total distance from 00 and END for each image.
        The first is the activation path, the others are for double checking.
        The rubber band run must have had nim images.  The distance  
        between two images is defined to be the square root of the  
        sum of all the squared distances between all the atoms in the  
        two images.  The distances depend on the  
        setting of nearest_image_flag (see --intpol).  The code works  
        in two steps.  First it gets energies and distances from the  
        OSZICAR and POSCAR/CONTCAR files, respectively.  This  
        requires that it be run in the directory above all the image  
        directories.  The distances are obtained from POSCAR files  
        for the first and last images, which are not actually calculated
        so now CONTCAR files exists.  For imtermediate images the
        POSCAR files are used.  The energies are pulled from the
        OSZICAR files.  First, these do not exist in the first and  
        last image directories, so you must put them their yourself
        based on other runs (if you leave them out then no energies
        will be obtained but you can add the energies later, as described
        below).  Second, the output format for OSZICAR in a parallel
        vasp rubber band run is all messed up.  Therefore, the energies
        are not E0 values (which are not the energy values of the  
        images) but the free energy from the line just before the  
        last E0.  This numbers differ somewhat from E0 values.  This
        whole output formatting problem changes with version of vasp --  
        I set  it up for version 4.4.1 beta.  It should also work with
        v 454.   We should change it to use E0 as soon as possible.  
        Once the distances and energies have been obtained then they  
        are interpolated with a cubic spline curve.  The spline  
        interpolation assumes that the derivatives at the end points  
        are 0.  The E.vs.dist data and the spline interpolation are  
        both output to standard out.  If there is any problem with  
        the energy data (e.g., you need to add end members) then  
        you can fix it and run the spline interpolation again  
        independently (see --spline).  The spline interpolation is  
        done on 50 points by default.  This can be  
        changed by setting DEFAULT_NPT_FOR_SPLINE in aflow_pflow_funcs.cpp.
  aflow --rbdist POSCAR1 POSCAR2 n|N|e|E  
        Gets the distance between two POSCAR files.  Uses lattice params  
        of POSCAR1.  For use of n|N|e|E see --intpol.
  aflow --rdf[=rmax[,nbins[,sigma]]] < POSCAR
        Get the radial distribution function (rdf) for a POSCAR file
        rmax: The radius out to which the rdf is calculated.
        nbins:  The number of bins for the rdf.
        sigma:  The sigma of the gaussian used to smear the rdf.
        This also finds the nearest-nieghbor shells by looking at  
        where the rdf has minima.  The output gives the rdf and nn shells
        for each atom and for each type of neighbour, including a sum
        of all neighbour types.  If you want to treat all atoms as the  
        same (e.g., to look at the parent lattice) just set one
        type in the POSCAR file.  You may need to play with sigma
        and the nbins to get atoms grouped together that you want in  
        one shell but not to group atoms you want in different shells.
        One apporach is to choose enough bins to make sure to distinguish
        every shell of interest and the increase sigma until you group
        desired atoms together.
        rmax default = 5
        nbins default = 25
        sigma default = 0 (zero does no smearing).
  aflow --rdfcmp=rmax,nbins,sigma,nshmax,POSCAR1,POSCAR2
        Uses the radial distribution functions (rdf) for POSCAR 1 and 2  
        to assess how close the structures are.  For each atom the
        rdf and radial shell function (rsf - this gives the coordination
        numbers for each shell) are found for each type.  
        The shells are found by looking at the derivatives of the rdf.
        Then the atoms of the same types are compared and the rms  
        errors in the rsf for POSCAR1 and POSCAR2 are computed.  Then  
        we step through the atoms of POSCAR1, matching them up  
        with the atoms of POSCAR2, based on the minimum rms.  When a  
        POSCAR2 atom is matched it not considered for later matches.
        The total rms based on these best matches is found by averaging  
        all the individual atom RMS's.  The total RMS and the  
        rsf for the best matched atoms are output.
        rmax: The radius out to which the rdf is calculated.
        nbins:  The number of bins for the rdf.
        sigma:  The sigma of the gaussian used to smear the density.
        nshmax:  The farthest possible shell used for computing RMS  
                 with the rsf (if <nshmax shells are found then fewer
                 will be used).
        I think this works but large changes in shape give rsf that
        are too different to compare exactly and the RMS!=0.  However,
        looking at the output can make it clear how the shells are
        related.  At this point the 2 structure must have the same
        number of atoms of each type.  If you want to compare 2 POSCARs
        where one is a multiple of the other in terms of atoms of  
        each type you can create supercell (see --supercell) to make this
        function usable.

  aflow --rebuild_database [--patchfiles=file1,file2,...]
        Fetches new entries and rebuilds the AFLOW database file.
        --patchfiles can be used to patch the AFLOW database using jsonl files (see --patch_database).
   
   aflow --reciprocal_lattice_data|--reciprocallattice_data|--klattice_data|--data_reciprocal_lattice[=<tolerance_value>|=tight|=loose] [--no_scan] [--print=text|json] < file
        Returns the reciprocal lattice type data, includeing the lattice vectors, lattice parameters (Angstroms/Bohrs and degrees)
        volume, c/a ratio, lattice type, lattice variation, lattice system, and Pearson symbol.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.

  aflow --revsg [#] [n] [l] [m]
        Constructs a POSCAR of a specified space group and with specified wyckoff positions
        #  is the space group number
        n  multiplicity of wyckoff site (e.g., do position 4 g 1 twice)
        l  specifies multiplicity group (e.g., positions with multiplicity 2)
        m  position within multiplicity group (e.g., 2 would indicate the second position
           with multiplicity defined by l). (R. Taylor).

  aflow --rm_atom iatom < POSCAR
        Outputs to standard out a POSCAR where iatom has been removed.
        iatom must be between 0 to N-1.
  aflow --rm_copies < POSCAR
        Outputs to standard out a POSCAR where only the first appearance of
        each cartesian position of the same type atom has been kept.
        Useful if you have multiple copies of atoms at the same
        positions for some reason. Note. This routine does not compare
        equivalent lattice positions so you are not sure that equivalent
        atoms are not in the same place.
  aflow --rsm < POSCAR
        Outputs to standard out a Rasmol (rsm) format file based on
        the POSCAr input file. This output can be saved as .rsm file
	  and is designed to be visualized in simpler version of Rasmol
	  which is called RasTop program. It might work in Rasmol program
	  directly. The format includes the plotting of the unit cell wireframe
	  and spacefill 150 for the atomic radius. (WS Sept07)
  aflow --rsm --z z_type1 z_type2 ... z_typeNtypes < POSCAR
        Similar to aflow -rsm, with additional option of atom labeling
	  based on the atomic number (z) of each type. If --z option is not
	  used, the default is --z 1 2 3 ... Ntypes. (WS Sept07)
  aflow --sc | --std_conv | --standard_conventional | --sconv < POSCAR
    	  Output POSCAR in a standard conventional lattice
	  (use --sp | --std_prim | --standard_primitive | --sprim	
	  to output POSCAR in a standard primitive lattice) (WS & SC Nov09)
        REF: Setyawan Curtarolo, DOI: 10.1016/j.commatsci.2010.05.010
        Check aflow --readme=symmetry
  aflow --scale=s < POSCAR
        Outputs POSCAR file giving same volume as input but
        with scale = s.
  aflow --sd AA1 AA2 ... < POSCAR    
        Outputs to standard out a POSCAR with selective dynamics
        formatting.  AAi gives the selective dynamics setting for
        atoms of type i and has the form AAi=TTT,TTF,etc..  If there
        are fewer AAi than atom types then the remaining types are
        defaulted to TTT. A warning will be printed and the default
        value of TTT will be used if the AAi strings are shorters
        than three characters. (SC0907)
  aflow --setcm cm1 cm2 cm3 < POSCAR
        Sets to center of mass to (cm1,cm2,cm3) by shifting all the
        atom positions.  Use --mom to check the shift was correct.
  aflow --setorigin r1 r2 r3 | atom# < POSCAR
        With r1 r2 r3, it ets the origin to r1,r2,r3 by shifting all the
        atom positions. Coordinates (r1,r2,r3) are considered fractional
        is the POSCAR is in fractional, and cartesian otherwise.
        With atom#, it sets the origin to the position of atom# 
        (atom# goes from 0 to size-1).

  aflow --sewald eta < POSCAR
        Finds the screened electrostatic energy of the POSCAR file using a
        real space sum.  eta is now the screening length (ie, all  
        coulomb interactions are multiplied by exp(-eta*R).
        Charges must be entered after each atom position.
        E.g.,   Co 0 0 0 +2.  

  aflow --sgdata|--space_group_data[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--setting=1|2|aflow] [--suppress_Wyckoff|--suppress_Wyckoff_printing] < file
        Outputs the following space group information: space group number, space group labels 
        (Hermann Mauguin, Hall, Schoenflies), Laue class, crystal class, ITC setting, ITC origin shift, 
        general Wyckoff position, and the WYCCAR (similar to --edata).
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Space group setting:
          The space group setting can be specified with the optional flag [--setting=1| =2] (the default is setting 1).
          For rhombohedral systems, setting 1=rhl and 2=hex.
          For monoclinic systems, setting 1=unique axis-b and 2=unique axis-c.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--setting=1|2|aflow]                    : Specifies the space group setting. The `aflow' setting follows the choices of the AFLOW Prototype Encyclopedia.
                                                     Different settings exist for the following space groups:
                                                       - centrosymmetric space groups with two origin choices (24 space groups, e.g., sg=227):
                                                           --setting=1     : origin centered on high site symmetry (not inversion site)
                                                           --setting=2     : origin centered on inversion site
                                                           --setting=aflow : origin centered on inversion site
                                                       - rhombohedral space groups (e.g., space group 166):
                                                           --setting=1     : rhombohedral setting
                                                           --setting=2     : hexagonal setting
                                                           --setting=aflow : rhombohedral setting
                                                       - monoclinic space groups (e.g., space group 5):
                                                           --setting=1     : unique axis-b
                                                           --setting=2     : unique axis-c
                                                           --setting=aflow : unique axis-b
          [--suppress_Wyckoff]                     : Suppresses Wyckoff position output (i.e., space group info only)
        Check aflow --readme=symmetry

  aflow --shell=ns,r1,r2,name,dens < POSCAR
        Based on the structure in POSCAR, this outputs to standard
        out all points with ns neighbors in a shell define by inner
        radius r1 and outer radius r2 (r1<r2).  The shell is
        restricted to only consider atoms of type name (name=NONE (""))
        is unrestricted).  The dens is the linear density of
        candidate points.  So for example, to search for all sites with
        4 oxygen around them between 1.8 and 2.2 Angstron you could type
          aflow --shell=4,1.8,2.2,O,20
        This would construct a 20x20x20 grid of puts in the cell and
        print out all points that met the shell criteria.  The output
        gives all the points and their shels meeting the shell criteria.
        However, since many points are in the same shell it is
        convenient to find unique shell environments.  Therefore, aflow
        reduces the complete list to keep only one representative point
        from each unique shell. The shells are distinguished by their
        centers of mass.  The unique points and their shells are output
        as all unique points meeting the shell criteria.  The
        representative point for each shell is the shell center of mass.
        This routine is great for finding open tetrahedral and octahedral
        sites where one might put an intercalant.  This routine can
        take a while to run (usually a 20x20x20 mesh is enough, and might
        take a couple of minutes for a big cell - start small!).
  aflow --shift=Sx,Sy,Sz[,cCdD] < POSCAR
        Outputs to standard out a POSCAR with all positions shifted by  
        S=(Sx,Sy,Sz).  The shifted is added to the positions.  The shift
        is assumed to be given in Cartesian coordinates unless you specify
        c or C for Cartesian or d or D for direct at the end.
  
  aflow --sitepointgroup|--agroup[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--screen_only] < file
        Calculates the site point group symmetry for every atom in the
        unit cell and writes it in the aflow.agroup.out file.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry
  
  aflow --spacegroup[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--print=text|json] [--radius=<radius>] [--screen_only] < file
        Calculates space group symmetry of the cell {R|t+T} with
        translations as big as |T| and writes it in the aflow.sgroup.out
        file. See documentation of aflow.
        Be careful because the size of the space group increases
        as the radius^3 times the size of the factor roup.
        The point and factor groups are required for the space group,
        therefore the aflow.pgroup.out and aflow.fgroup.out files will
        be generated as well.
        This routine consists of symmetry consistency checks. If symmetry rules are broken,
        the code automatically changes tolerance and recalculates from the beginning.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
          [--radius=<radius>]                      : Specifies radius (Angstroms) to print symmetry operations out to a given distance from the origin
          [--screen_only]                          : Prints symmetry elements to string and does not write to a file.
        Check aflow --readme=symmetry

  aflow --sqs=structure_type,atom_num,neighbour_num,sl_num_min,sl_num_max,A,B | --special-quasirandom-structure=...
      Generate special-quasirandom-structure (SQS)
      structure: bcc/fcc/hcp
      atom_num : maximum number of atoms in a cluster
      neighbour_num : maximum number of nearest neighbour pairs in a cluster
      sl_num_min : minimum number of the base structure in the superlattice
      sl_num_max : maximum number of the base structure in the superlattice

      To generate sqs bcc structure, one needs first to generate a
      'cluster' file and a bcc superlattice file. Use the following commands
      to get sqs bcc from 5 to 8 atom/cell of AuCu alloy with energy
      calculated by using cluster expansion method with cluster containing up 
      to 6th nearest neighbour pairs.
      =-=-=-=-=-=-=-=-=-=-=-=
      1. Get cluster file. Number of atoms in a cluster is from 1 to 2 and
      distance of two atoms in a cluster is from the 1st to the 6th neighbour
      distance.
          aflow --cluster=bcc,1,2,1,6
      2. Get all supercell configuration. Here we get supercell with 8 atom.
      The first 5 is the smallest number of atoms in a supercell and the
      second one is the largest number.
          aflow --superlattice=bcc,6,8
      3. Get SQS. Check correlations of clusters with up to 2 atoms and 6th
      neighbour distance. You can give any two element names for the last two
      arguments.
          aflow --sqs=bcc,2,6,5,8,Au,Cu
  

  aflow --species < POSCAR
        Outputs the species names, as taken from the 1st representative
        atom of each set.

  aflow --spline npt < file
        Outputs to standard out a cubic spline interpolation of npt  
        evenly spaced points.  The infput file must be two colums  
        giving X and Y(X).  The derivatives at the endpoints are  
        assumed to be zero.  To change this, change yp1 and ypn  
        in the SetSpline function in the aflow_pflow_funcs.cpp file.
  aflow --sp | --std_prim | --standard_primitive | --sprim < POSCAR
   	  Output POSCAR in a standard primitive lattice
	  (use --sc | --std_conv | --standard_conventional | --sconv	
	  to output POSCAR in a standard conventional lattice) (WS & SC Nov09)
        REF: Setyawan Curtarolo, DOI: 10.1016/j.commatsci.2010.05.010
        Check aflow --readme=symmetry
  
  aflow --superlattice_data|--data_superlattice[=<tolerance_value>|=tight|=loose] [--no_scan] [--print=text|json] < file
        Returns the superlattice type data, includeing the lattice vectors, lattice parameters (Angstroms/Bohrs and degrees)
        volume, c/a ratio, lattice type, lattice variation, lattice system, and Pearson symbol.
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--no_scan]                              : Suppresses tolerance scan.
          [--print=text|json]                      : Outputs the results into human-readable text (default) or JSON, respectively.
  
  aflow --statdiel OUTCAR*
        Extracts and diagonalizes the static dielectric constant tensor
        from the output of a DFPT run (see the aflow "DIELECTRIC_STATIC" tag).
        The input OUTCAR can be in one of two formats: plain text (regular VASP
        output), or compressed with the appropriate utility (OUTCAR*[.bz2,.gz,.xz]). The
        routines attempt to symmetrize the tensor to within a tolerance
        (currently set to 1.0e-5) prior to diagonalization.
        The output is a single row containing 6 numbers. The first three are
        the real-valued diagonal terms of the tensor eps(xx), eps(yy), epz(zz);
        while the second set of three contain any imaginary eigenvalues that
        would result from a failure of the ad-hoc symmetrization procedure.
        Example corresponding to Al1As1_ICSD_67784:
        input:  aflow --statdiel OUTCAR.dielectric_static[.bz2,.gz,.xz]
        output: 8.772122    8.772122    8.772122    0.000000    0.000000    0.000000 

  aflow --suffix=[directory,]"from2to"
        Change the suffixes of VASP files. Easy conversion between AFLOW format and VASP format. (KESONG Dec. 22nd, 2013)
	Mnemonic: from2to with from/to =[n=none;r1=relax1;r2=relax2;r3=relax3;s=static;b=bands] or without abbreviations.
        Changes suffix of all VASPFILEs from VASPFILE*"from" to VASPFILE*"to".
        If a directory is specified (e.g. aflow --suffix=abc,n2s) 
        then it change abc/VASPFILE*"from" to abc/VASPFILE*"to"
        Example: aflow --suffix=n2s   (or --suffix=none2static)
        Change VASPFILE* to VASPFILE*.static
        Example: aflow --suffix=s2n     (or --suffix=static2none)
        Change VASPFILE*.static to VASPFILE*

  aflow --sumpdos pdos.in PROOUT
        Works for vasp.46x
        This allows you to sum up projected DOS together for convenient
        plotting.  It only works when you have run with the following  
        INCAR file settings.  LORBIT=1 or 2 and set RWIGS, or  
        LORBIT = 11 or 12 and no RWIGS (only works when using PAW PP).
        If you are running parallel you must set NPAR=1.  The
        input file is similar to --pdos above but somewhat simpler
        so I give a full example here.
        
           # Input for aflow --sumpdos.
          
           # These values you supply once.
           SPIN = 1 # 1 = non-spin polarized, 2 = spin polarized
                    # Default 1
           EFERMI = -999 # This will be subracted from the energies.
                            # Set to 0 to subtract nothing, -999 to use
                         # the E_Fermi in the DOSCAR.  Default -999.
           NLM = 9 # number of orbitals, 9 (spd:1+3+5) or 16 (spdf:1+3+5+7)
                   # Default 9
           PRINT_PARAMS = 0 # 0=prints only data (easy to plot).
                            # 1=prints all the input parameters.
                            # default: 0
        
           # You can have as many cases as you want.
           # They are all added together.
          
           # case 1: t2g on atom 1
           ATOMS = 1 # default: no atoms
           LMVALUES = 5 6 8 # default: no lm
           # case 2: eg on atoms 2 and 3
           ATOMS = 2 3 # default: no atoms
           LMVALUES = 7 9 # default: no lm
        
        All # denote comment lines and can be put anywhere.  
        Each case is started when the token ATOMS is used.  
        Following an ATOMS token, all LMVALUES tokens  
        will apply to the atoms denoted in the preceeding  
        ATOMS token until the next ATOM token. You can have any number  
        of cases, and the results for all cases are added together.  
        WARNING: make sure to use SPIN to set if it is a spin poloarized
        calculation, make sure to use EFERMI to your desired reference,
        and make sure to set NLM to 9 (spd) or 16 (spdf).
        The lm values correspond to orbitals by the following scheme.
        Input number: 1 2  3  4  5   6   7   8   9      
        Orbitals:     S Py Pz Px Dxy Dyz Dz2 Dxz Dx2-y2
        Input number: 10 11 12 13 14 15 16  
        Orbitals:     F1 F2 F3 F4 F5 F6 F7  
  aflow --supercell=a11,a12,a13,a21,a22,a23,a31,a32,a33 < POSCAR
  aflow --supercell=a11,a22,a33 < POSCAR
  aflow --supercell=file < POSCAR
        Outputs to standard out a supercell of the input POSCAR file.
        This lattice vectors of the supercell are given by multiplying
        the original cell parameters by the 3x3 matrix a_ij coefficients.
        The supercell need not be integral combinations of the original
        lattice vectors, although using fraction may cause you to end up
        with a lattice inequivalent to your original. This can be used
        to build big supercells, swap lattice vectors, etc.
        The nine numbers must be separated spaces, and they form the
        nine elements a11,a12,a13,a21,a22,a23,a31,a32,a33 of the 3x3
        supercell matrix, respectively. If you specify only 3 numbers,
        the other six are taken zero. If you use the "file" syntax,
        nine numbers are read from file. They can be on one or
        mulitple lines. New algorithm by SC (aug07).
  aflow --supercell_strlist=a11,a12,a13,a21,a22,a23,a31,a32,a33,strlist
  aflow --supercell_strlist=a11,a22,a33,strlist
  aflow --supercell_strlist=file,strlist
        Outputs to standard out a sequence of structures in POSCAR format.
        The structures are supercells formed using the supercell matrix
        a11,a12,a13,a21,a22,a23,a31,a32,a33. If only 3 values are specified
        the other are taken to be zero. If you use the "file" syntax,
        nine numbers are read from file. They can be on one or mulitple
        lines. For more information on supercells see --supercell.
        For more information on a strlist see --make_strlist.

  aflow --superlattice=structure_type,n_min,n_max < POSCAR
        --superlattice=VASP,structure_type,A,B < superlattice_name
        Generate a superlattice of base structure POSCAR
        structure_type : fcc/bcc/hcp
        n_min, n_max : minimum and maximum numbers of base structures in the superlattice
 
  aflow --swap specie1 specie2 < POSCAR
        Swap the specie number 1 with the specie number 2.
        It is useful if you forgot to put the POSCAR in alphabetic mode.

  aflow --terdata=Aa:Bb:Cc   [--fonts=XX | --keep=eps | --print=jpg | --print=gif | --print=png]
        Inputs are the elements in alphabetic order. Output is ternary convexhull named
	  "phasediagram_AaBbCc.num.pdf". The num is the calculated number of compounds.
	  EX:
	     aflow --terdata=Nb:Pt:Rh
        No matter the order of the elements, the list is alphabetized.
        Options
         --fonts=XX  specity the size of gnuplot fonts, default 50
         --keep=eps  avoid to delete the postscript before making the pdf
         --print=jpg       adds the jpg picture
         --print=gif       adds the gif picture
         --print=png       adds the png picture
 
  acovasp --terdata_exist list
        The list is the one containing each element for the systems for a certain format.
	  Each element should be alphabetical order. Put 2 strings before each elements.
	  EX:
           aflow --terdata_exist system
        
	  INPUTS EX:
           empty empty Al Co Mn
           empty empty Co Ge Mn

  aflow --terdata A B C list
  	  Inputs are the elements in alphabetic order and extra data for the list. Output is ternary convexhull named
	  "phasediagram_ABC.num.pdf". The num is the calculated number of compounds.
	  list type is:
	  ADDRESS1    COMPOUND_NAME1
	  ADDRESS2    COMPOUND_NAME2
	  ...	      ...
	  EX:
		aflow --terdata terdata Nb Pt Rh list

  aflow --uffenergy | --ue <  POSCAR
        Output the energy of the structure using the simplified Universal Force Filed (UFF) method [JACS, 114, 10024 (1992)].

  aflow --update_database [--patchfiles=file1,file2,...]
        Fetches new entries and rebuilds the AFLOW database file if new entries are available.
        --patchfiles can be used to patch the AFLOW database using jsonl files (see --patch_database).

  aflow --vasp                                                                     
        Transforms the GEOMETRICAL (or whicever is the input file format) to a        
        VASP format.                                          

  aflow --visualize_phonons --qpoint=|--qpoints=|--q= [--format=XCRYSDEN|V_SIM] [--amplitude=] [--branches=] [--periods=] [--steps=] [--scell=] -D DIRECTORY
        Outputs a phonon visualization file. Currently supported formats: xcrysden and v_sim.
        A phonon calculator state file (aflow.apl.fccalc_state.out) and a force constant
        file (aflow.apl.harmonicIFCs.xml) must reside in the directory.

        Options for all formats:
          --qpoint:    q-points for the phonons to be visualized as a comma-separated list.
                       Multiple points can be specified.

          --format:    The output file format.
                       Default: DEFAULT_APL_ADISP_SCENE_FORMAT in .aflow.rc.

          --amplitude: The amplitude of the displacements.
                       Default: DEFAULT_APL_ADISP_AMPLITUDE in .aflow.rc.


        Options for XCRYSDEN:
          --branches:  The branches of the phonon modes as a comma-separated list (1-based).
                       Default: all.

          --periods:   The number of periods displayed in the output file.
                       Default: DEFAULT_APL_ADISP_NPERIODS in .aflow.rc

          --steps:     The number of steps per period in the output file.
                       Default: DEFAULT_APL_ADISP_NSTEPS in .aflow.rc

          --scell:     The supercell to be displayed in the output file.
                       Default: unit cell.

        Examples:
          aflow --visualize_phonons --qpoint=0.5,0,0 --steps=40 --amplitude=0.3 --scell=3x3x3 -D ./
          aflow --visualize_phonons --q=0,0,0,0.5,0.5,0.5 --branches=4,5,6 --format=XCRYSDEN --scell=4x4x2
          aflow --visualize_phonons --q=0,0,0 --branches=1,2,3 --format=V_SIM --amplitude=0.2

  aflow --volume v < POSCAR
        Outputs POSCAR file having volume equal to v.
  aflow --volume*= x < POSCAR
  aflow --volume+= x < POSCAR
        Outputs POSCAR with volume changes as *=, += actor (like in c,c++).

  aflow --wyccar[=<tolerance_value>|=tight|=loose] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--no_scan] [--setting=1|2|aflow] < file
        Prints the wyccar file (the poscar file with wyckoff positions) for the input POSCAR
        The wyccar format presents the lattice in standard conventional form and the wyckoff
        positions with their associated labels and site symmetry. If variability in the
        Wyckoff positions exists, the algorithm finds the Wykoff positions with the "smallest"
        lettering scheme ("a" being the smallest).
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Space group setting:
          The space group setting can be specified with the optional flag [--setting=1|=2|=aflow] (the default is setting 1).
          For rhombohedral systems, setting 1=rhl, 2=hex, and aflow=rhl.
          For monoclinic systems, setting 1=unique axis-b, 2=unique axis-c, and aflow=unique axis-b.
          For centrosymmetric systems, setting 1=origin on high-symmetry site, 2=origin on inversion site, aflow=origin on inversion site
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--no_scan]                              : Suppresses tolerance scan.
          [--setting=1|2|aflow]                    : Specifies the space group setting. The `aflow' setting follows the choices of the AFLOW Prototype Encyclopedia.
                                                     Different settings exist for the following space groups:
                                                       - centrosymmetric space groups with two origin choices (24 space groups, e.g., sg=227):
                                                           --setting=1     : origin centered on high site symmetry (not inversion site)
                                                           --setting=2     : origin centered on inversion site
                                                           --setting=aflow : origin centered on inversion site
                                                       - rhombohedral space groups (e.g., space group 166):
                                                           --setting=1     : rhombohedral setting
                                                           --setting=2     : hexagonal setting
                                                           --setting=aflow : rhombohedral setting
                                                       - monoclinic space groups (e.g., space group 5):
                                                           --setting=1     : unique axis-b
                                                           --setting=2     : unique axis-c
                                                           --setting=aflow : unique axis-b
        Check aflow --readme=symmetry
  
  aflow --Wyckoff|--Wyckoff_positions|--wyckoff|--wyckoff_positions[=<tolerance_value>|=tight|=loose] [--letters_only] [--magmom=[m1,m2,...|INCAR|OUTCAR]] [--multiplicities_only] [--no_scan] [--setting=1|2|aflow] [--site_symmetries_only] < file
        Prints the Wyckoff positions (multiplicity, letter, site symmetry and representative
        coordinate) based on the input geometry. If variability in the Wyckoff positions exists,
        the algorithm finds the Wykoff positions with the "smallest" lettering scheme ("a" being the smallest).
        Tolerance:
           The tolerance is given in Angstroms.  There are two preset tolerances:
             tight: minimum_interatomic_distance/100.0
             loose: minimum_interatomic_distance/10.0
           The default tolerance is the "tight" tolerance value.
           A value can also be specified. (Note, it must be below the minimum
           interatomic distance, otherwise an error will be thrown.)
        Space group setting:
          The space group setting can be specified with the optional flag [--setting=1| =2] (the default is setting 1).
          For rhombohedral systems, setting 1=rhl, 2=hex, and aflow=rhl.
          For monoclinic systems, setting 1=unique axis-b, 2=unique axis-c, and aflow=unique axis-b.
          For centrosymmetric systems, setting 1=origin on high-symmetry site, 2=origin on inversion site, aflow=origin on inversion site
        Magnetic analysis:
          The magnetic tag specifies the magnetic moment on each of the atoms.
          The three possible input types are:
            1) a comma separated string of the magnetic moments (in the same order as the atoms in the geometry file)
            2) a string specifying the path to the INCAR, or
            3) a string specifying the path to the OUTCAR.
          AFLOW autodetects collinear/non-collinear magnetic moments based on the input.
        Options:
          [=<tolerance_value>|=tight|=loose]       : Specifies the symmetry tolerance: <tolerance_value>: user-input, "tight": min_interatomic_dist/100, "loose": min_interatomic_dist/10 (option is appended to command without spaces)
          [--letters_only]                         : Prints the Wyckoff letters only (colons separate elements, commas separate Wyckoff positions for a given element)
          [--magmom=[m1,m2,...|INCAR|OUTCAR]]      : Perform crystal spin symmetry analysis, where spin degree of freedom breaks symmetry
          [--multiplicities_only]                  : Prints the Wyckoff multiplicities only (colons separate elements, commas separate Wyckoff positions for a given element)
          [--no_scan]                              : Suppresses tolerance scan.
          [--setting=1|2|aflow]                    : Specifies the space group setting. The `aflow' setting follows the choices of the AFLOW Prototype Encyclopedia.
                                                     Different settings exist for the following space groups:
                                                       - centrosymmetric space groups with two origin choices (24 space groups, e.g., sg=227):
                                                           --setting=1     : origin centered on high site symmetry (not inversion site)
                                                           --setting=2     : origin centered on inversion site
                                                           --setting=aflow : origin centered on inversion site
                                                       - rhombohedral space groups (e.g., space group 166):
                                                           --setting=1     : rhombohedral setting
                                                           --setting=2     : hexagonal setting
                                                           --setting=aflow : rhombohedral setting
                                                       - monoclinic space groups (e.g., space group 5):
                                                           --setting=1     : unique axis-b
                                                           --setting=2     : unique axis-c
                                                           --setting=aflow : unique axis-b
          [--site_symmetries_only]                 : Prints the Wyckoff site symmetries only (colons separate elements, commas separate Wyckoff positions for a given element)
        Check aflow --readme=symmetry

  aflow --xray=lambda < POSCAR
        Outputs to standard out the powder xray scattering pattern for
        the structure specified in the POSCAR input file.  The
        wavelength of the scattering radiation is taken to be l.
        The xray calculation is almost nothing more that the structure
        factor, altough it includes approximate treatments of the
        Debye-Waller terms and the Lorentz-polarization.  In the xray
        calculations there are a number of terms that require a lot of
        information to really do right so I approximate them.  First,
        scattering factors default to the atomic number.  In some cases
        I coded more accurate values taken from tables for lambda=1.5418.
        No lambda dependence of the scattering factors is presently
        included.  For the list of all coded atomic scattering factors
        see the constructor for the structure class in structure.cc.
        I include the Lorentz-polarization and an approximate
        Debye-Waller factor (DWF).  The DWF is found assuming T=300,
        T_Debye=300, and within the high-temperature Debye aproximation.
        The atomic mass defaults to twice the atomic number but I
        have input a few more accurate values in the code.  For the
        list of all coded atomic masses see the constructor for the
        structure class in structure.cc.  This simulation should
        give very accurate peak locations and qualitative relative
        integrated intensities (peak heights).   I am still not
        happy with why the peak intensitities do not reproduce other
        codes better.  The output contains formats with and without
        peaks at the same 2theta grouped together.  It also contains
        data ready for plotting.  Each type of data has a keyword on
        every line so you can grep it out easily.
  aflow --xray_peaks=lambda [--threshold=threshold] < POSCAR
        Outputs the peaks in amplitude from the --xray analysis.
        The order is sorted by amplitude.
        The format is:

        X-Ray Peaks:
        Two-Theta=34.008,40.488,77.689,53.878
        Amplitude=100,50.638,24.551,17.542

  aflow --xrd_dist=h,k,l < POSCAR	
  	  Compute Miller plane distance (distance between planes of atoms). The triplet h,k,l
        defines the plane spanned by the three points a/h,b/k,c/l, where a b c
        are the CONVENTIONAL lattice vectors. You may enter h,k,l as integers
        (e.g., 1 2 3), decimal numbers (e.g., 0.56 .4 .5), or fractions (e.g., 1/2 3/4 4/5)
        or any combination of the three. The POSCAR must be in conventional form to get
        meaningful results. You may first use the aflow command "aflow --sc < POSCAR" to get
        standard conventional. For example,
        cat POSCAR | aflow --sc | aflow --xrd_dist=1,0,0   	
  aflow --xyz[=n1[,n2[,n3]]] < POSCAR
        Outputs to standard out an xyz file based on the POSCAR input
        file.  This can be used as input for rasmol, xmol, etc..
        If you want atom names you must put them after each atom
        position in the POSCAR file (see -names).  If any names are
        missing they are defaulted to H.
  aflow --xyzwignerseitz [--xyzws] < POSCAR
        Performs "aflow --xyz=1,1,1" but moves the images
        of the atoms in the Wigner-Seitz cell. This parameter
        is usefull to fight against VASP trend of moving atoms
        in different (but traslationally equivalent) positions
        of the unit cell. (SC20100104).

  aflow --zval[=directory]
        Outputs from the available POTCAR/OUTCAR the sum of ZVAL.
  aflow --zval_atom[=directory]
        Outputs from the available POTCAR/OUTCAR and POSCAR/CONTCAR the ZVAL of the cell per atom.
  aflow --zval_cell[=directory]
        Outputs from the available POTCAR/OUTCAR and POSCAR/CONTCAR the ZVAL of the whole cell.

******************************************************************************************

FROZSL MODE
  aflow --frozsl_vaspsetup_aflow | --frozsl_vaspsetup < FROZSL.output
        Takes the FROZSL.output (the one containing all representations
        and deformations) and makes the POSCAR part of the aflow.in.
        All the calculations are ready to be ran as they are enclosed
        in START.XXXX/STOP.XXXX frameworks and a AFLOW_POSTSCRIPT is
        generated to extract all the energies for the various directories.
        If another parameter is passed: i.e.
         aflow --frozsl_vaspsetup_aflow --file
        then the command used to make the POSCARs is printed.
        (Mike Mehl Dec 09).
  aflow --frozsl_vaspsetup_poscar < FROZSL.output
        Takes the FROZSL.output (the one containing all representations
        and deformations) and makes all the POSCARS.
        If another parameter is passed: i.e.
         aflow --frozsl_vaspsetup_poscar --file
        then the command used to make the POSCARs is printed.
        (Mike Mehl Dec 09).
  aflow --frozsl_analyze < aflow.frozsl.out
  aflow --frozsl_readme | --frozsl_help
        A short introduction to frozsl calculations.

******************************************************************************************

 APENNSY MODE (this routines are available only in duke.edu domine)
  aflow --xfixX system structure
        Repairs the convex-hull calculation by removing
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB2))/LIB/RAW/system/structure
        and copying
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB2))/LIB/LIB/system/structure
        into
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB2))/LIB/FIX/system/structure
        You have to go by hand and check the problem (rare) and
        probably clean and rerun the structure.
        The exact command is included in pflow::XFIXX which
        is inside aflow_pflow_main.cpp

******************************************************************************************

 ALL LIBRARIES MODES
 aflow [--force] --lib2raw=all[,directory]
        Searches all the subdirectories of 'pwd'/LIB/ and updates 'pwd'/RAW/ and 'pwd'/WEB/
        entries for the missing ones. With directory specified, it searches on directory/LIB/
        It works only on AFLOW_MATERIALS_SERVER (defined in aflow_aflowrc.cpp).
        With "--force" it overwrites the old raw files if they exist.
   
 LIBN MODE (this routines are available only in duke.edu domine)
        Scripts for the production/mantenance of the LIB* libraries.
        The "all" works  only if 'pwd' = $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB*))
  aflow [--force] --lib2raw=directory
  aflow [--force] --lib2raw=Al_h/bcc
        From the $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB*))/LIB/directory_including_lattice
        calculation generates the RAW library
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_LIB*))/RAW/directory_including_lattice
        which includes the files necessary for the LIB* project
        analisys: aflow.in LOCK
	If *static files are present, the DOS is calculated.
	If *bands files are present, the electronic structure is calculaterd.
        It works only on AFLOW_MATERIALS_SERVER (defined in aflow_aflowrc.cpp),
        and it has been written for the LIB* project.
        It can be used also for LIB* directories.
        With "--force" it overwrites the old raw files if they exist.
 
 ICSD LIBRARY MODE
        Scripts for the production/mantenance of the ICSD library.
        The "all" works only if 'pwd' = $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD))
  aflow [--force] --lib2raw=directory
  aflow [--force] --lib2raw=FCC/La1Se1_ICSD_27104
        From the $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD))/LIB/directory_including_lattice
        calculation generates the RAW library
        $(vAFLOW_PROJECTS_DIRS.at(XHOST_LIBRARY_ICSD))/RAW/directory_including_lattice
        which includes the files necessary for the ICSD project
        analisys: aflow.in LOCK DOSCAR.static. EIGENVAL.bands
        KPOINTS.bands POSCAR.bands.
        It works only on AFLOW_MATERIALS_SERVER (defined in aflow_aflowrc.cpp),
        and it has been written for the ICSD project.
        With "--force" it overwrites the old raw files if they exist.

 LIBN LIBRARY MODE
        Scripts for the production/mantenance of the LIBN library.
        The "all" works only if 'pwd' = $(vAFLOW_PROJECTS_DIRS.at(LIB*)) or  
  aflow [--force] --lib2raw=directory


 aflow --lib2scrub=[all,lib0,lib1,...,lib9,icsd]
        Goes through the LIBs and/or ICSD and try to find wrong entries.

******************************************************************************************
AFLOWLIB MODE
  aflow --aflowlib=entry [--print=txt | --print=json]
        Create the WEB/PHP page for the entry specified as auid or aurl. It works where the complete
        databases have been installed.
	Entry can be auid, directories, icsd numbers.
	OPTIONS
	--print=txt (prints aflowlib.out)
	--print=json (prints aflowlib.json)
	
  aflow --aflowlib_auid2aurl=auid1,auid2.... | --auid2aurl=...
        Searches the available AUIDs and reports the AURLs if found.
	Comp. Mat. Sci. 93, 178 (2014). [doi=10.1016/j.commatsci.2014.05.014] for more information.
	
  aflow --aflowlib_aurl2auid=aurl1,aurl2.... [ --aurl2auid=...
        Searches the available AURLs and reports the AUIDs if found.
	Comp. Mat. Sci. 93, 178 (2014). [doi=10.1016/j.commatsci.2014.05.014] for more information.
	
  aflow --aflowlib_auid2loop=auid1,auid2.... | --auid2loop=...
        Searches the available AUIDs and reports the postprocessed "loop" if found.
	Comp. Mat. Sci. 93, 178 (2014). [doi=10.1016/j.commatsci.2014.05.014] for more information.
	
  aflow --aflowlib_aurl2loop=aurl1,aurl2.... [ --aurl2loop=...
        Searches the available AURLs and reports the postprocessed "loop" if found.
	Comp. Mat. Sci. 93, 178 (2014). [doi=10.1016/j.commatsci.2014.05.014] for more information.
	
****************************************************************************************************
*                                                                                                  *
*                        aflow - STEFANO CURTAROLO Duke University 2003-2021                       *
*                            High-Throughput ab-initio Computing Project                           *
*                                                                                                  *
****************************************************************************************************