MAKE LATtice, by Axel van de Walle
Utility setting up directories with maps input files for a given alloy system
and for one or multiple lattices.

Syntax: makelat [-o] [-s=scale] atom1,atom2,... lattice1,lattice2,...

Make sure that there are commas but no spaces between atoms and similarly between the lattices.

Examples:
  makelat Al,Ni bcc,fcc
  makelat Ca,Mg:O rocksalt

  (note the : to separate sublattices)
  The default scale is 1. It can be changed to allow for units other than angstroms.
  The -o option outputs to strout.

Lattices available:
B2 bcc bcc-oct bcc-tet diamond fcc fcc-oct fcc-octtet fcc-tet hcp hcp-oct hcp-tet L11 rocksalt sc wurtzite zincblende

Other lattices can be added in the /public/software/atat/3.52/gcc-13.3/8173m/share/atat/data/ directory or
new atomic radius can be added in the /public/software/atat/3.52/gcc-13.3/8173m/share/atat/data/radii.in file.

GENerate STRuctures 3.52, by Axel van de Walle
  -n=[int]      maximum nb of atom/unit cell (Default: 0)
  -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
-sig=[int]      Number of significant digits to print in output files (Default: 6)
 -2d            Find supercells along a and b axes only (Default: Off)
  -l=[string]   Input file defining the lattice (default: lat.in)

cellcvrt 3.52, by Axel van de Walle
Performs various conversions/changes on structure (or lattices).
Reads from stdin, writes to stdout.
    -c            Use cartesian coordinates (Default: Off)
    -f            Use fractional coordinates (Default: Off)
   -cc            Find conventional cell and use it as coordinate system (Default: Off)
  -abc            Use a b c alpha beta gamma format to specify axes (Default: Off)
-noabc            Use cartesian format to specify the axes (the default) (Default: Off)
   -ro            Read fractional Occupation (Default: Off)
    -u=[string]   User-specified coordinate system input file (optional) (Default: )
  -uss=[string]   User-specified supercell (Default: )
   -ss=[int]      Simple supercell (multiple of axes in all directions) (Default: 0)
   -fc            Fix cell (to make it as symmetric as possible) (Default: Off)
    -s            Look for smaller unit cell (Default: Off)
   -sh=[string]   Shift all atoms (default 0,0,0).
   -ja=[real]     Jitter all atoms positions by a random amount less than specified (Default: 0)
   -jc=[real]     Jitter all cell parameters by a random amount less than the fraction specified (Default: 0)
   -sd=[int]      Seed for random number generation (default: use clock)
   -sg=[string]   Space group file (Default: )
  -gsg            Generate Space Group (Default: Off)
   -wi            Wrap all atoms inside unit cell (Default: Off)
  -wiu            Wrap all atoms inside unit cell and undo shift (Default: Off)
   -rr            Remove redundant atoms (Default: Off)
  -rra            Remove redundant atoms and average (Default: Off)
   -ar            Add redundant atoms (Default: Off)
  -osf=[string]   Original setting file (optional) (Default: )
  -fsf=[string]   Final setting file (optional) (Default: )
    -r            Print reciprocal unit cell (Default: Off)
   -fs=[int]      Index of first structure to process (default: 1)
   -ns=[int]      Number of structures to process (Default: 2147483647)
  -slf=[string]   Structure list file (Default: )
   -pn            Print the number of atoms in the structure only (Default: Off)
   -pv            Print volume of cell only (Default: Off)
  -sym            Print spacegroup (Default: Off)
  -ppg            Print point group name (Default: Off)
  -pbv            Print Bravais Lattice name (Default: Off)
   -sc=[real]     Scale factor (default: 1)
  -sig=[int]      Number of significant digits to print in output files (Default: 6)
    -z=[real]     Tolerance for checking overlap (Default 1e-3)

fixcell 3.52, by Axel van de Walle
  -d            Use all default values (Default: Off)
  -c            read and print cell in cartesian only (no axes specified) (Default: Off)
  -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
  -b            print bravais lattice type only and conventional (potentially not primitive) cell (Default: Off)
-sig=[int]      Number of significant digits to print in output files (Default: 6)

check cell distortion 3.52, by Axel van de Walle
-d            default (Default: Off)
-q            be quiet (Default: Off)
-p            print strain (Default: Off)

Utility to convert structure files into xyz files suitable for viewing with rasmol
Syntax: str2xyz [-v] na nb nc [scale] infile
-v (optional) calls rasmol (otherwise, xyz file is written to stdout
na nb nc define the number of periodic repetition to plot
scale (optional) scales the structure to adjust which bonds are plotted

Nearest Neighbor Shell 3.52, by Axel van de Walle and Paul Dalach
  -l=[string]   Input file defining the lattice (default: lat.in)
 -lb            List bond types in given structures (Default: Off)
-sig=[int]      Number of significant digits to print in output files (Default: 5)
  -r=[real]     Define a max radius for neighbor search (Default: 0)
  -d            Use all default values (Default: Off)

nntouch 3.52, by Axel van de Walle
 Scales a lattice so that nearest neighbor atom just touch.
  -l=[string]   Input file defining the lattice (default: lat.in) Use filename - to specify stdin
  -r=[string]   Input file defining the atomic radii (default: rad.in)
  -s=[real]     Multiplicative scaling factor (Default: 1)
-sig=[int]      Number of significant digits to print in output files (Default: 6)
  -d            Use all default values (Default: Off)

Test if MINimum DISTance between two atoms is less than a given threshold, version 3.52, by Axel van de Walle
-s=[string]   Input file defining the structure (Default: stdin)
-r=[real]     Threshold radius (Default: 0)
-e            Create error file atoms are too close (Default: Off)
-h            Display more help (Default: Off)

-d            Use all default options (Default: Off)
 -q            Quiet! (Default: Off)
 -r            Round output to next largest integer (Default: Off)
-z1            Force 1 k-point along 3rd axis (Default: Off)
 -e            Force nb of kpoints to be an even number (Default: Off)

WYCKoff position EDitor, by Axel van de Walle
Syntax:
  wycked spcgrp [-r] list_of_wyckoff_position_letter_without_seperators [species1:species2:...]
The output is meant to first be edited to set the free parameters a,b,c,alpha,beta,gamma,x,y,z,etc
in each of the lines starting with #const 
and processed by sspp to create a valid ATAT structure file.
 If the -r option is specified, then:
   the structure is relaxed using a soft-sphere model (of radius 1.5 A) by invoking the GULP code
   (multiple times (10) with randomized initial positions).
   In that case, you can also specify a colon-separated list of species that will populate each wyckoff position.
   Also, the structure will be isotropically re-scaled so that the nearest neighbor distance are consistent
   with atom radii from the atat/data/radii.in file.

ACKNOWLEDGEMENTS
This code makes use of a Wyckoff position database downloaded from the Bilbao Crystallographic Server
at http://www.cryst.ehu.es/
Accordingly, if you use this code, you should cite, in addition to the usual ATAT citations,
the following papers:
  M. I. Aroyo, J. M. Perez-Mato, D. Orobengoa, E. Tasci, G. de la Flor, A. Kirov
      "Crystallography online: Bilbao Crystallographic Server" 
      Bulg. Chem. Commun. 43(2) 183-197 (2011).
  M. I. Aroyo, J. M. Perez-Mato, C. Capillas, E. Kroumova, S. Ivantchev, G. Madariaga,
  A. Kirov and H. Wondratschek,
      "Bilbao Crystallographic Server I: Databases and crystallographic computing programs" 
      Z. Krist. 221, 1, 15-27 (2006). doi:10.1524/zkri.2006.221.1.15 
  M. I. Aroyo, A. Kirov, C. Capillas, J. M. Perez-Mato and H. Wondratschek
      "Bilbao Crystallographic Server II: Representations of crystallographic point groups and
      space groups", Acta Cryst. A62, 115-128 (2006). doi:10.1107/S0108767305040286 
If you use the -r option, you should also acknowledge the GULP code:
  "GULP - a computer program for the symmetry adapted simulation of solids", J.D. Gale, JCS Faraday Trans., 93, 629 (1997)
  "The General Utility Lattice Program", J.D. Gale and A.L. Rohl, Mol. Simul., 29, 291-341 (2003)
  "GULP: Capabilities and prospects", J.D. Gale, Z. Krist., 220, 552-554 (2005)

Point DEFect generator 3.52, by Axel van de Walle
  -l=[string]   Input file defining the lattice (default: lat.in)
  -s=[string]   Input file defining the undefected structure (default: str.out)
  -p=[string]   Prefix of the directories that will contain the defected structures (Default pdef)
 -er=[real]     Minimum distance between point defects (Default: 0.00000)
-sig=[int]      Number of significant digits printed (default: 5)
  -h            Display more help (Default: Off)

STRucture PATH generator 3.52, by Axel van de Walle
 -s1=[string]   Input file defining structure 1 (default: str1.out)
 -s2=[string]   Input file defining structure 2 (default: str2.out)
 -ni=[int]      Number of images (Default: 0)
  -f=[real]     Interpolation fraction in [0,1] (Default: 0.5)
 -df=[real]     Dimer distance [0,1] (Default: 0)
 -dp=[string]   Directory name pattern (default 00)
 -ci            Calculate inflection point (Default: Off)
-cil            Calculate inflection point location (Default: Off)
-sig=[int]      Number of significant digits printed (default: 5)
  -h            Display more help (Default: Off)
  -d            Use all default values (Default: Off)

SURFace BOND counting 3.52, by Helena Liu and Axel van de Walle
  -h            Display more help (Default: Off)
  -s=[string]   Input file defining a structure (Default: str.in)
  -m=[real],... Miller indices (Default: )
 -mm=[int]      Max Miller index (Default: 0)
  -b=[real]     max bond length (Default: 0)
-nph=[int]      Nb of mesh points along phi (Default: 24)
-nth=[int]      Nb of mesh points along theta (Default: 48)
-sig=[int]      Number of significant digits printed (Default: 5)
  -z=[real]     Tolerance for comparing coordinates (default: 1e-3)
  -a            new broken bond counting Algorithm (Default: Off)
  -d            Use all default values (Default: Off)

Usage: symbrklib [-s fraction] [element] [initial_structure] [final_structure]
Currently, the initial and final structures can be one of bcc,fcc,hcp.
The -s option (optional) indicates to just generate a small distortion (a given fraction along the instability path).
This command is intended to be run before robustrelax_xxxx

Independent Cell Approximation for MAGnetic systems 3.52, by Axel van de Walle
  -h            Display more help (Default: Off)
  -l=[string]   Input file defining the lattice (Default: lat.in)
 -nm            No Magnetism (Default: Off)
-sig=[int]      Number of significant digits printed (Default: 5)
  -d            Use all default values (Default: Off)

Monte Carlo generator of Special Quasirandom Structures 3.52, by Axel van de Walle
   -n=[int]      nb of atom/unit cell (Default: 0)
If -n is not specified, generate clusters of the following sizes:
   -2=[real]      Maximum distance between two points within a pair (Default: 0)
   -3=[real]      Maximum distance between two points within a triplet (Default: 0)
   -4=[real]      Maximum distance between two points within a quadruplet (Default: 0)
   -5=[real]      Maximum distance between two points within a quintuplet (Default: 0)
   -6=[real]      Maximum distance between two points within a sextuplet (Default: 0)
   -l=[string]   Input file defining the random structure (default: rndstr.in)
  -cf=[string]   Input file defining the clusters (default: clusters.out)
 -tcf=[string]   Input file defining the target multibody correlations (default: internally calculated values for fully disordered state)
 -tol=[real]     Tolerance for matching correlations (default: 1e-3)
  -wr=[real]     Weight assigned to range of perfect correlation match in objective function (default 1)
  -wn=[real]     Multiplicative decrease in weight per additional point in cluster (default 1)
  -wd=[real]     Exponent of decay in weight as function of cluster diameter (default 0)
   -T=[real]     Temperature (default 1)
  -pf=[string]   Input file defining the optimization parameters (default: sqsparam.in)
  -rc            Read supercells from file sqscell.out (default: generate internally and write to sqscell.out) (Default: Off)
  -ip=[int]      Index of current process (for parallel operation) (Default: -1)
-best            Collect best SQS among the outputs of prior parallel runs (Default: Off)
 -crf=[string]   Select correlation functions (default: trigo)
  -sd=[int]      Seed for random number generation (default: use clock)
  -rt=[int]      Read parameter file every (rt) step (default:10000)
  -ms=[int]      Maximum number of Monte Carlo steps (default: no limit)
  -2d            Generate only supercells in the plane of a,b axes (Default: Off)
 -sig=[int]      Number of significant digits to print in output files (default: 6)
   -h            Display more help (Default: Off)

GENerate Special Quasirandom Structures 3.52, by Axel van de Walle
  -n=[int]      nb of atom/unit cell (Default: 0)
-sig=[int]      Number of significant digits to print in output files (Default: 6)
 -cf=[string]   Input file defining the clusters (default: clusters.out)
 -tc=[string]   Input file defining the target correlations (default: tcorr.out)
-tol=[real]     Tolerance for matching correlations (default: 1e-3)
  -l=[string]   Input file defining the lattice (default: lat.in)
 -rc            Read unit cells from file (Default: Off)
 -pc            Print number of supercells only, and quit (Default: Off)
 -tp=[int]      Total number of processes (for parallel operation) (Default: 1)
 -ip=[int]      Index of current process (0,...,tp-1) (for parallel operation) (Default: 0)
-crf=[string]   Select correlation functions (default: trigo)
  -h            Display more help (Default: Off)

CORRelation DUMPer 3.52, by Axel van de Walle
    -h            Display more help (Default: Off)
    -2=[real]     Maximum distance between two points within a pair (Default: 0)
    -3=[real]     Maximum distance between two points within a triplet (Default: 0)
    -4=[real]     Maximum distance between two points within a quadruplet (Default: 0)
    -5=[real]     Maximum distance between two points within a quintuplet (Default: 0)
    -6=[real]     Maximum distance between two points within a sextuplet (Default: 0)
    -l=[string]   Input file defining the lattice   (default: lat.in)
    -s=[string]   Input file defining the structure (default: str.out)
   -pc            Print composition only (Default: Off)
  -pcm            Print composition matrix only (Default: Off)
 -fast            Use fast algo to calculate correlations of 'simple' supercells (Default: Off)
-skipr            Skip algorithm robust to relaxations (Default: Off)
  -sym            Just find space group (Default: Off)
 -clus            Just find clusters (Default: Off)
    -c            Read cluster file instead of writing it (Default: Off)
   -cf=[string]   File name of the cluster file (default: clusters.out)
    -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
  -sig=[int]      Number of significant digits printed (default: 5)
  -noe            Do not include empty cluster (Default: Off)
  -nop            Do not include point cluster(s) (Default: Off)
  -noc            Do not include any cluster(s) (Default: Off)
  -eca            Calculate Energy of Clusters of Atoms (Default: Off)
   -wu=[string]   Write Unrelaxed structure into specified file (Default: )
  -rnd            Print correlation of the random state of the same composition as the input structure (Default: Off)
  -eci=[string]   Predict quantity using ECI in specified file (Default: )
   -mi            Multiplicities are already included in ECI file (Default: Off)
  -crf=[string]   Select correlation functions (default: trigo)
   -nb            Print structure number (Default: Off)
   -ro            Read lattice file containing occupation variables (this code does not make use of them) (Default: Off)

Syntax: getclus [-e] [ecifile]
extracts, from clusters.out, the cluster sizes, lengths and multiplicities
if ecifile is given, it also prints the eci therein
if -e is specified, it prints eci from eci.out

MIT Ab initio Phase Stability (MAPS) code 3.52, by Axel van de Walle
  -h            Display more help (Default: Off)
  -l=[string]   Input file defining the lattice (default: lat.in)
  -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
  -c=[real]     Exponent of the order of complexity (default: 3)
  -t=[int]      Time between disk reads in sec (default: 10 sec)
  -m=[int]      Maximum number of points in cluster (default 4)
  -g=[int]      Extend ground state search up to structures having at least that many atoms. (Default: 0)
 -c0=[real]     [c0,c1] is the concentration range where ground states must be correct. (Default: 0)
 -c1=[real]      (Default: 1)
 -mv=[int]      Maximum volume (number of atom per unit cell) allowed when generating structures (default: no limit)
 -mw=[real]     Maximum weight allowed when try to match ground states (Default: 16)
 -2d            Find supercells along a and b axes only (Default: Off)
  -p=[string]   Predictor plugins to use (examples: -p=cs or -p=cs_es) (Default: )
 -ks=[string]   same as -p (Default: )
 -fa=[string]   Select fitting algorithm (default: built-in)
  -q            Quiet mode (do not print status to stderr) (Default: Off)
-sig=[int]      Number of significant digits to print in output files (Default: 6)
  -d            Use all default values (Default: Off)

MIT Ab initio Phase Stability (MAPS) code 3.52, by Axel van de Walle
  -h            Display more help (Default: Off)
  -l=[string]   Input file defining the lattice (default: lat.in)
  -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
  -c=[real]     Exponent of the order of complexity (default: 3)
  -t=[int]      Time between disk reads in sec (default: 10 sec)
  -m=[int]      Maximum number of points in cluster (default 4)
  -g=[int]      Extend ground state search up to structures having at least that many atoms. (Default: 0)
 -cr=[string]   Concentration region input file (Default: crange.in)
 -he=[real]     Highest predicted energy, above ground state hull, allowed when generating structures (default: no limit)
 -mv=[int]      Maximum volume (number of atom per unit cell) allowed when generating structures (default: no limit)
 -mw=[real]     Maximum weight allowed when try to match ground states (Default: 16)
 -2d            Find supercells along a and b axes only (Default: Off)
  -p=[string]   Predictor plugins to use (examples: -p=es or -p=es_cs) (Default: )
 -ks=[string]   same as -p (Default: )
 -fa=[string]   Select fitting algorithm (default: built-in, alternative: -fa=bayesian)
 -xo=[string]   input additional parameter for extension (Default: )
-crf=[string]   Select correlation functions (default: trigo)
 -pn=[string]   Property to cluster expand (default: energy)
 -ig            Ignore whether cluster expansion predicts correct ground states (Default: Off)
 -pa            Quantity to expand is already per atom (Default: Off)
  -q            Quiet mode (do not print status to stderr) (Default: Off)
-sig=[int]      Number of significant digits to print in output files (Default: 6)
  -d            Use all default values (Default: Off)

Display the output of maps in graphical form.
Syntax: mapsrep [-e]
the optional switch -e tells the code to plot structures flagged with error too.
Thanks to Ruoshi Sun and Mike Widom for updating the script for recent versions of gnuplot.

Display the output of mmaps in graphical form.
Syntax: mmapsrep [-e] c1 c2 c3
where c1,c2,c3 are the column numbers of the compositions to plot
the optional switch -e tells the code to plot structures flagged with error too.

Least-Square FIT 3.52, by Axel van de Walle
    -x=[string]   x file (Default: )
    -y=[string]   y file (Default: )
    -w=[string]   weight file (Default: )
    -r=[string]   regularization parameters file (Default: )
   -pf            Perfect Fit algorithm (Default: Off)
   -pw=[string]   number of powers of each column to regress on (Default: )
    -s=[string]   select columns to regress on (one number by column, 0: ignore, 1: use) (Default: )
    -1            add a column of ones as regressor (Default: Off)
-colin            Ignore colinear columns in x file (Default: Off)
   -cv            Print crossvalidation score (Default: Off)
   -se            Print standard errors (Default: Off)
   -ty            Print trues values of y (Default: Off)
    -p            Print predicted values of y (Default: Off)
    -e            Print prediction error (Default: Off)
  -mat            Print fitting matrix (Default: Off)
  -sig=[int]      Number of significant digits printed (default: 5)

Cross-Validation code 3.52, by Axel van de Walle
-g            Favor cluster choices where the ground state line is correct (Default: Off)
-w=[real]     Weight structures by w/(struct_energy-gs_energy+w) (Default: 1000)
-p=[real]     Penality for structures that lie below the ground state line (Default: 0)
-d            Use all default values (Default: Off)
-h            Display Help (Default: Off)

Syntax: clusterexpand [-e] [-pa] [-s "1,0,1, ..."] filename
Cluster expands the quantity stored in */filename
Uses the clusters in clusters.out
Outputs to filename.eci filename.ecimult
ecimult contains the eci multiplied by multiplicity
the option -e causes the structures flagged with an error file to be ignored
the option -pa indicates that the quantity is per atom already
   so that the code must NOT divide it by the number of atoms
the option -s lets you select which cluster to include (1) or exclude (0)
the option -g selects a generalized (tensor) cluster expansion
the -cv option prints the cv score.

Syntax: clusterpredict [-pa] file
see clusterexpand for more info.
This command is to be run from within a specific structure directory containing a str.out file.

Generalized Cluster Expansion 3.52, by Axel van de Walle
   -h            Display more help (Default: Off)
   -2=[real]     Maximum distance between two points within a pair (Default: 0)
   -3=[real]     Maximum distance between two points within a triplet (Default: 0)
   -4=[real]     Maximum distance between two points within a quadruplet (Default: 0)
   -5=[real]     Maximum distance between two points within a quintuplet (Default: 0)
   -6=[real]     Maximum distance between two points within a sextuplet (Default: 0)
   -l=[string]   Input file defining the lattice   (default: lat.in)
   -s=[string]   Input file defining the structure (default: str.out)
  -pc            Print composition only (Default: Off)
 -sym            Just find space group (Default: Off)
  -st            Symmetrize tensor given in tensor.in (Default: Off)
-clus            Just find clusters (Default: Off)
   -c            Read clusters.out file instead of writing it (Default: Off)
   -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
 -sig=[int]      Number of significant digits printed (default: 5)
 -noe            Do not include empty cluster (Default: Off)
 -nop            Do not include point cluster(s) (Default: Off)
 -rnd            Print correlation of the random state of the same composition as the input structure (Default: Off)
 -eci=[string]   Predict quantity using ECI in specified file (Default: )
  -mi            Multiplicities are already included in ECI file (Default: Off)
 -crf=[string]   Select correlation functions (default: trigo)
 -gce=[string]   Select type of Generalized Cluster Expansion (default: tensor)
  -nb            Print structure number (Default: Off)

Cluster Variation Method CLUSter generator 3.52, by Axel van de Walle
  -h            Display more help (Default: Off)
  -l=[string]   Input file defining the lattice (Default: lat.in)
  -m=[string]   Maximal cluster (Default: maxclus.in)
-sig=[int]      Number of significant digits printed (Default: 5)
-crf=[string]   Select correlation functions (default: trigo)
  -d            Use all default values (Default: Off)

Eazy Monte Carlo Code 3.52, by Axel van de Walle
     -h            Help (Default: Off)
   -mu0=[real]     initial chemical potential (Default: Off)
    -T0=[real]     initial temperature (Default: Off)
   -mu1=[real]     final chemical potential (Default: Off)
    -T1=[real]     final temperature (Default: Off)
   -dmu=[real]     chemical potential step (Default: Off)
    -dT=[real]     temperature step (Default: Off)
    -db=[real]     inverse temperature step (Default: Off)
    -cm            Set Canonical mode (Default: Off)
     -x=[real]     Set concentration (Default: Off)
   -abs            take chemical potentials as absolute quantities (as in mc.out) (Default: Off)
  -phi0=[real]     initial (grand) canonical potential (Default: Off)
    -er=[real]     set the system  size so that a sphere of that radius must fit inside the simulation cell (Default: 0)
    -eq=[int]      number of equilibration passes (Default: -1)
     -n=[int]      number of averaging passes (Default: -1)
    -dx=[real]     Target precision for the average concentration (optional, replaces -n and -eq) (Default: 0)
    -aq=[int]      Alternative quantity that must meet the tolerance specified by -dx. 0: energy, 1: concentration (default), 2: long-range order, 3- correlations
    -gs=[int]      which ground state to use as initial config (-gs=-1 to use random state, c=1/2) (Default: -2)
-innerT            inner loop over T (Default: Off)
 -tstat=[real]     Critical value of the test for discontinuity (Default: 3)
-sigdig=[int]      Number of significant digits printed (Default: 6)
     -q            Quiet (do not write to stdout) (Default: Off)
     -o=[string]   Output file (default: mc.out)
   -oss=[string]   Output snapshot file (default: mcsnapshot.out)
  -opss=[string]   Output periodic snapshot files (default: do not write)
     -k=[real]     Boltzman's constant (conversion factor from T to energy) (Default: 1)
   -keV            Set Boltzman's constant to 8.617e-5 so that temperature is in K when energy is in eV (Default: Off)
     -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
    -sd=[int]      Seed for random number generation (default: use clock)
    -dl            Drop the last data point of each inner loop (after the phase transition occured) (Default: Off)
   -g2c            Convert output to canonical rather than grand-canonical quantities (Default: Off)
    -is=[string]   File name containing a user-specified initial configuration (replaces -gs) (Default: )
    -ks=[string]   Specify how k space ECI are calculated (e.g. -ks=cs). (Default: )

Multicomponent Eazy Monte Carlo Code 3.52, by Axel van de Walle
     -h            Help (Default: Off)
    -er=[real]     Set the system  size so that a sphere of that radius must fit inside the simulation cell (Default: 0)
    -cf=[string]   Control file specifying the ranges of temperature and chem. pot. scanned (default: control.in)
    -eq=[int]      Number of equilibration passes (Default: -1)
     -n=[int]      Number of averaging passes (Default: -1)
    -tp=[real]     Target precision (optional, replaces -n and -eq) (Default: 0)
    -aq=[int]      Quantity that must meet the tolerance specified by -tp. 1: energy (default), 2: long-range order, 3-: point correlations
    -gs=[int]      which ground state to use as initial config (-gs=-1 to use random state) (Default: -2)
     -k=[real]     Boltzman's constant (conversion factor from T to energy) (Default: 1)
   -keV            Set Boltzman's constant to 8.617e-5 so that temperature is in K when energy is in eV (Default: Off)
   -g2c            Convert output to canonical rather than grand-canonical quantities (Default: Off)
  -phi0=[real]     initial (grand) canonical potential (default: from mean field approx.)
 -tstat=[real]     Critical value of the test for discontinuity (Default: 3)
   -mft=[real]     Mean field threshold (if |lte-mf|<mft, use mf values instead of mc) (Default: -1)
  -mftq=[int]      Quantity that must meet the tolerance specified by -mft.0: phi (default) , 1: energy , 2: long-range order, 3-: concentrations
-sigdig=[int]      Number of significant digits printed (Default: 6)
     -q            Quiet (do not write to stdout) (Default: Off)
     -o=[string]   Output file (default: mc.out)
   -oss=[string]   Output snapshot file (default: mcsnapshot.out)
  -opss=[string]   Output periodic snapshot files (default: do not write)
    -sd=[int]      Seed for random number generation (default: use clock)
    -dl            Drop the last data point of each inner loop (after the phase transition occured) (Default: Off)
    -is=[string]   File name containing a user-specified initial configuration (replaces -gs) (Default: )
    -hf            Shift all coordinates by half a grid point in scan (e.g. 2 steps in [0,1] give 0.25,0.75 instead of 0,0.5) (Default: Off)
    -il            Include last coordinate in scan (e.g. 3 steps in [0,1] gives 0,0.5,1 instead of 0,0.333,0.666) (Default: Off)
    -ts=[string]   Triangular scanning. Specify list of composition axes (e.g. -ts=1,2). (Default: )
   -crf=[string]   Select correlation functions (default: trigo)
    -df=[int]      Max distance between flips (in unit cells) in grand-canonical mode (Default: -1)
    -mf=[int]      Minimum number of flips in grand-canonical mode (experimental) (Default: 0)
    -rw            Use random walk algorithm (experimental) (Default: Off)
   -fdT=[real]     Temperature step for finite differences (Default: 0.01)
  -fdmu=[real]     Chemical potential step for finite differences (Default: 0.01)
    -ks=[string]   Specify how k space ECI are calculated (e.g. -ks=cs). (Default: )

PHase Boundary 3.52, by Axel van de Walle
     -h            Help (Default: Off)
    -mu=[real]     initial chemical potential (Default: Off)
     -T=[real]     initial temperature (Default: Off)
   -dmu=[real]     chemical potential adjustment step (Default: Off)
    -dT=[real]     temperature step (Default: Off)
   -mug=[real]     Gap between the mu in phase 1 and mu in phase 2 (default: 0)
  -ltep=[real]     threshold free energy precision to use MC instead of LTE (in units of T) (default: always MC)
    -er=[real]     enclosed radius (Default: 0)
   -gs1=[int]      ground state for phase #1 (Default: -2)
   -gs2=[int]      ground state for phase #2 (Default: -2)
   -is1=[string]   File name containing a user-specified initial configuration (replaces -gs1) (Default: )
   -is2=[string]   File name containing a user-specified initial configuration (replaces -gs2) (Default: )
    -d1=[string]   directory for phase #1 (default: current dir)
    -d2=[string]   directory for phase #2 (default: current dir)
   -lro            print long range order parameter (Default: Off)
 -tstat=[real]     Critical value of the test for discontinuity (Default: 3)
  -smax=[real]     Maximum step (experimental feature) (Default: 1e+50)
-sigdig=[int]      Number of significant digits printed (Default: 6)
     -q            Quiet (do not write to stdout) (Default: Off)
     -o=[string]   Output file (default: mc.out)
     -k=[real]     Boltzman's constant (conversion factor from T to energy) (Default: 1)
   -keV            Set Boltzman's constant to 8.617e-5 so that temperature is in K when energy is in eV (Default: Off)
    -sd=[int]      Seed for random number generation (default: use clock)
    -dn            Go down in temperature (Default: Off)
    -dx=[real]     Concentration Precision (Default: 0)
    -ks=[string]   Specify how k space ECI are calculated (e.g. -ks=cs). (Default: )

Constituent Strain FITter 3.52, by Axel van de Walle
  -h            Display more help (Default: Off)
 -nc=[int]      Number of points in concentration mesh (default 50)
 -ns=[int]      Number of points in mesh used to look for energy minimum (default 100)
 -np=[int]      Number of points in stretching mesh in the direction perpendicular to the k-vector(default 5)
 -nl=[int]      Number of points in stretching mesh in the direction parallel to the k-vector (default 3)
 -ml=[real]     Maximum parallel stretching (default 0.05)
  -l=[string]   Input file defining the lattice (default: lat.in)
 -pa=[string]   Directory containing the pure A calculations (default 0/)
 -pb=[string]   Directory containing the pure B calculations (default 1/)
 -ds=[string]   File containing a list of stretching directions (default: dir.in)
  -t=[int]      Time between disk reads in sec (default: 10 sec)
-sig=[int]      Number of significant digits to print in output files (Default: 6)
  -d            Use all default values (Default: Off)

Generalized Constituent Strain 3.52, by Axel van de Walle
  -h            Display more help (Default: Off)
  -l=[string]   Input file defining the lattice   (default: lat.in)
  -s            Specify point group directly via generator (in sym.in) (Default: Off)
  -z=[real]     Tolerance for finding symmetry operations (default: 2e-4)
  -r=[int]      Maximum Rank of the harmonic (Default: 1)
 -mr=[int]      Minimum Rank of the harmonic (default 1)
-sig=[int]      Number of significant digits printed (default: 5)

AntiPhase Boundary 3.52, by Ruoshi Sun and Axel van de Walle
Automating impurity-enhanced antiphase boundary energy calculations from ab initio Monte Carlo,
 Calphad 53, 20 (2016)

File options:
 -l=[string]   Input file: lattice   (Default: lat.in)
 -s=[string]             : structure (Default: str.out)
 -o=[string]   Output file: APB structure (Default: str_apb.out)
-og=[string]              : energies      (Default: gamma_apb.out)

APB options:
 -f            Generate APB structure file and exit; do not compute APB energy (Default: Off)
-sx=[real]     APB slip vector: x-component (Default: 0)
-sy=[real]                    : y-component (Default: 0)
-sz=[real]                    : z-component (Default: 0)

Monte Carlo options:
-mc            Run Monte Carlo (Default: Off)
-eq=[int]      Number of: equilibration passes (Default: -1)
 -n=[int]               : averaging passes     (Default: -1)
 -T=[real]     Temperature (Default: 0)

Other options:
 -d            Use all default values (Default: Off)
 -h            Display more help (Default: Off)

Syntax: ezvasp [-c] [-s] [-n] [-p "..."] input_file

-c: Cell patch. This option will convert the cell you entered into a cell that has the symmetry needed for
    vasp to work properly. The atom positions are altered correspondingly.

-s: Static run. After the relaxations are completed, this option makes vasp start again, turning off relaxations
    and turning on tetrahedron integration with bloech correction. Can acheive the same effect by
    including DOSTATIC in the INCAR portion of the input file.

-n: do Not run vasp. If you want to create the input files now and run them later, perhaps on another machine.

-p: name of the vasp command ("vasp" by default). You can include addition prefix such as:
    ezvasp -p "rsh remote.machine nice +5 /usr/local/bin/vasp" vasp.in

Here is an example of input file:

[INCAR]
SYSTEM = FeNi
ISPIN = 2
PREC = HIGH
ISMEAR = 1
NSW=41
SIGMA = 0.1
IBRION = 2
ISIF = 3
ENMAX = 400
EDIFF = 1e-6
EDIFFG = 1e-4
KPPRA = 1000
USEPOT = PAWGGA
DOSTATIC
SUBATOM = s/Fe$/Fe_h/g
KSCHEME = GAMMA
MAGATOM =

[POSCAR]
 SOME TITLE
 3.55
  -.500000000     -.500000000    -1.000000000   
   .500000000    -1.000000000     -.500000000   
  -.500000000      .500000000     1.000000000   
 1 2
 Direct
  .33333     .33333     .00000     Fe+5
  .00000     .00000     .00000     Vac
  .66667     .66667     .00000     Fe-5

End of example.

Note that there 6 new tokens in the INCAR section.

1) KPPRA stands for "K-Point Per Reciprocal Atom". This is a way to automatically set the k-point mesh for
   a number of similar systems. Here is how it works. If you know that you need 500 k-points for a 2-atom
   structure, then you type in 1000. If you now try a similar structure with 4 atoms, the code automatically
   use 250 k-points. The mesh along the three axes is automatically chosen to make the mesh as uniform as possible.
   (For the algorithm, see atat/src/kmesh.c++).
   You can also specify KPPRA = UPDIR which indicates that the KPOINTS file
   found one directory above should be used.
   (This is useful for cell distorsions used in elastic constant calculations of constituent strain runs).
   If this token is ommited, you need to specify a [KPOINT] section in the input file that contains what
   you want the KPOINT file to be.

2) DOSTATIC indicates that a static run must be done after the relaxation run (NSW tag is removed and the ISIF and IBRION
   token are ajusted accordingly). The output files named *.relax contain the result of the (first)
   relaxation run while the files named *.static contain the results of the (second) static run.
   When DOSTATIC is not specified, all output files are named *.static , whether the VASP input parameters
   allow relaxations or not.

3) KSCHEME specifies the type mesh to use: Gamma shift or Monkorst-Pack. The default is Gamma if KSCHEME is ommited. You can
   also specify (on a separate line) KZ1 to force one k-point along the 3rd axis, which is useful for slabs.

4) MAGATOM is similar to the usual token MAGMOM used to specify the moment on each atom. The novelty is that you specify the
   moments in the POSCAR section. (In version 3.15 and above, this token can be ommited. Having spins specified in the POSCAR
   section turns this on automatically. It also set ISPIN=2 automatically.)
   The usual MAGMOM token is still available (but you cannot use both MAGMOM and MAGATOM).

5) USEPOT 
   selects the potentials used: LDA GGA PAWLDA PAWGGA PAWPBE (or any other potential defined in .ezvasp.rc)
   By default, LDA (without PAW) is used.
   For backward compatibility, you can also use the tag DOGGA instead of USEPOT = GGA

6) The SUBATOM token lets you specify a sed-like substitution command to be
   applied to the name of the atomic species.
   For instance, SUBATOM= s/Fe$/Fe_h/g  will cause ezvasp to use the Fe_h
   pseudopotential instead of the Fe one. Multiple SUBATOM token can be given,
   one for each substitution. Don't forget the s/ and /g and the $ after the first element name
   (to avoid F matching Fe, or Y matching Yb).

There are also familiar VASP tokens that are robustified. For instance ISTART = 2 does not work unless you force
the FFT grid size to match the earlier run.
To help with this, ezvasp fetches the right NGX,NGY,NGZ from the previous run's OUTCAR or CHGCAR in the current directory.

There are new features in the POSCAR section as well.
1) The line that specify the number of atoms (here 1 2) can be ommited (it is ignored).
2) The atomic species are specified to the right of the atom positions.
   The corresponding POTCAR are automatically copied. You can specify pseudopotentials like Li_h or O_s.
3) The number following the species is the magnetic moment on the atom (if MAGMOM is in the INCAR section).
   Identical species with different moments will be considered symmetrically distinct to allow for
   symmetry-breaking relaxations.
4) Do not specify "selective dynamics". It will be written to the INCAR file
   automatically if you include T's and F's after the atom species, e.g.:
    0.5 0.5 0.5 Al T T F
5) The element "Vac" or "Va" stands for vacancy. It is ignored for everything but
   to compute the k-point mesh with the KPPRA option.

FIT Force Constants 3.52, by Axel van de Walle
   -f            Fit force constants (otherwise, generate pertubations) (Default: Off)
  -si=[string]   Input file defining the ideal structure (default: str.out)
  -sr=[string]   Input file defining the relaxed structure (default: str_relax.out)
  -er=[real]     Minimum distance between displaced atoms (Default: 0)
-ernn=[real]     Minimum distance between displaced atoms in multiple of nearest neighbor distance (Default: 0)
  -fr=[real]     Force constant range (Default: 0)
-frnn=[real]     Force constant range (in multiple of nearest neighbor distance) (Default: 0)
  -dr=[real]     Displacement of the perturbed atom (default: 0.2)
  -ms=[real]     Strain of the maximum volume sampled (default: 0.01)
  -dv            Specified strain above is volumetric (Default: Off)
  -ns=[int]      Number of volume sample (default: 2)
  -iu            Include Unperturbed structure in generated structures (Default: Off)
 -nrr            Do not rerelax structures at each new volume (Default: Off)
  -cs            Check for Singular matrix in fit (Default: Off)
 -ncs            No check for singular matrix in fit (this is the default, option included for backward compatibility) (Default: Off)
  -wm            Write fitting Matrices (Default: Off)
  -sf=[string]   Extra strain file (Default: )
   -m=[string]   Input file defining the atomic masses (default: ${atatdir}/data/masses.in)
-ccut=[string]   Character marking the species label suffix that must be cut (Default: )
  -T0=[real]     Minimum temperature (default: 0) 
  -T1=[real]     Maximum temperature (default: 2000)
  -dT=[real]     Temperature step (default: 100)
   -P=[real]     Pressure (in GPa, default: 0)
  -kp=[real]     Number of k-points per reciprocal atom (default: 1000)
  -kx=[int]      k-point mesh (along 1st recip lat. vect.) if <>0 then overrides -kp=... (Default: 0)
  -ky=[int]      k-point mesh (along 2nd recip lat. vect.) (Default: 0)
  -kz=[int]      k-point mesh (along 3rd recip lat. vect.) (Default: 0)
  -fp=[int]      Power of polynomial to fit free energy (Default: -1)
  -s0            Use a gamma-centered k-point mesh (default shift: 1/2 1/2 1/2) (Default: Off)
  -sx=[real]     k-point shift (along 1st recip lat. vect.) (Default: 0.5)
  -sy=[real]     k-point shift (along 2nd recip lat. vect.) (Default: 0.5)
  -sz=[real]     k-point shift (along 3rd recip lat. vect.) (Default: 0.5)
  -df=[string]   Phonon dispersion curve calculation input file. (Default: )
  -hp=[real]     Planck's constant (default in (eV s))
  -kb=[real]     Boltzman's constant (default in eV/K)
 -cfk=[real]     Conversion factor for force constants into energy/dist^2 (default: converts eV/A^2 into J/m^2)
  -mu=[real]     Mass units (default: converts a.u. mass into kg)
  -rl=[real]     Robust Length algorithm parameter for soft modes (beta) (Default: 0)
 -rls=[real]     Quadratic strain-dependence of robust length for positive strain (beta) (Default: 0)
  -cP=[real]     Conversion factor from pressure*volume into eV (Default: 0.00624151)
  -pa            Output free energy per atom instead of per unit cell (Default: Off)
  -pe            Print energy in 3rd column of fitfc.out (Default: Off)
  -sc=[real]     Correction factor if spectator ion are present (default: 1)
 -me0            Subtract energy at 0K (Default: Off)
  -no            Print number of atom in supercell only (Default: Off)
  -w1            Flag first perturbation wait1 instead of wait file (Default: Off)
  -w2            Flag negative perturbation directions with wait2 instead of wait file (Default: Off)
  -fn            Force continuation of calculations even if unstable (Default: Off)
  -fu            Find unstable modes (Default: Off)
  -gu=[int]      Generate unstable modes number n (Default: 0)
  -gn            Also Generate Negative displacements for mode specified by -gu=... (Default: Off)
 -mau=[int]      Maximum number of atom per supercell for unstable mode generation (Default: 64)
 -sfc=[int]      Simplify force constants: 1=streching+bending, 2=symmetric (Default: 0)
 -apd            Atom-Projected DOS (Default: Off)
 -sig=[int]      Number of significant digits printed (default: 5)
   -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
   -h            Display more help (Default: Off)

Fit Stiffness VS Length transferable force constants 3.52, by Axel van de Walle
  -f            Fit force constants (otherwise, generate pertubations) (Default: Off)
  -l=[string]   Input file defining the lattice (default: lat.in)
 -dn=[string]   Input file listing the directories containing the structures used to calculate force constants (default: strname.in)
 -er=[real]     Minimum distance between displaced atoms (Default: 0)
 -dr=[real]     Displacement of the perturbed atom (default: 0.2)
 -ms=[real]     Strain of the maximum volume sampled (default: 0.01)
 -ns=[int]      Number of volume sample (default: 2)
 -op=[int]      Order of the polynomial used to fit stiffness vs length (Default: 1)
 -dd            Use direction-dependent force constants (Default: Off)
 -pc=[int]      Maximum power of composition used in fit (default: no composition dependence)
-msl=[real]     Maximum spring length (Default: Off)
 -sf=[string]   Extra strain file (Default: )
-eqt=[real]     Tolerance for excluding force constants in plots. (Default: 2)
-sig=[int]      Number of significant digits printed (default: 5)
  -z=[real]     Tolerance for finding symmetry operations (default: 1e-3)
-ncs            No check for singular matrix in fit (Default: Off)
 -od            Use older 1-level only directory tree (Default: Off)
  -h            Display more help (Default: Off)

Vibrational free energy calculator using the Stiffness VS Length method 3.52, by Axel van de Walle
  -l=[string]   Input file defining the lattice (defaults: lat.in, ../lat.in, str.out)
 -us=[string]   Input file defining the unrelaxed structure (default: str.out)
 -rs=[string]   Input file defining the   relaxed structure (default: str_relax.out)
 -sp=[string]   Input file defining the springs (default: slspring.out)
  -m=[string]   Input file defining the atomic masses (default: ${atatdir}/data/masses.in)
  -b=[real]     Bulk modulus (Default: 0)
 -bf=[string]   Bulk modulus file (Default: )
 -ms=[real]     Maximum stretching of the lattice parameter (default: 0.05)
 -ns=[int]      Number of lattice parameter stretching step (default: 1 => harmonic approximation)
 -T0=[real]     Minimum temperature (default: 0) 
 -T1=[real]     Maximum temperature (default: 2000)
 -dT=[real]     Temperature step (default: 100)
 -kp=[real]     Number of k-points per reciprocal atom (default: 1000)
 -s0            Use a gamma-centered k-point mesh (default shift: 1/2 1/2 1/2) (Default: Off)
 -sx=[real]     k-point shift (along 1st recip lat. vect.) (Default: 0.5)
 -sy=[real]     k-point shift (along 2nd recip lat. vect.) (Default: 0.5)
 -sz=[real]     k-point shift (along 3rd recip lat. vect.) (Default: 0.5)
 -hp=[real]     Planck's constant (default in (eV s))
 -kb=[real]     Boltzman's constant (default in eV/K)
-cfk=[real]     Conversion factor for force constants into energy/dist^2 (default: converts eV/A^2 into J/m^2)
 -mu=[real]     Mass units (default: converts a.u. mass into kg)
 -rl=[real]     Robust Length algorithm parameter for soft modes (beta) (Default: 0)
 -pa            Output free energy per atom instead of per unit cell (Default: Off)
 -sc=[real]     Correction factor if spectator ion are present (default: 1)
 -fn            Force continuation of calculations even if unstable (Default: Off)
 -df=[string]   Phonon dispersion curve calculation input file. (Default: )
 -sf=[string]   Extra strain file (Default: )
-msl=[real]     Maximum spring length (Default: Off)
-sig=[int]      Number of significant digits to print in output files (Default: 5)
 -up=[string]   User-specified Potential Plug-in (optional) (Default: )
  -d            Use all default values (Default: Off)
  -h            Display more help (Default: Off)

Electronic free energy calculator 3.52, by Axel van de Walle
-dos=[string]   DOS input file name (default: dos.out)
 -T0=[real]     Minimum temperature (default: 0)
 -T1=[real]     Maximum temperature (default: 2000)
 -dT=[real]     Temperature step (default: 100)
 -kb=[real]     Boltzman's constant (default: in eV/K)
 -pa            Output free energy per atom instead of per unit cell (Default: Off)
 -sc=[real]     Correction factor if spectator ion are present (Default: 1)
 -sd=[real]     Smooth DOS with a Gaussian this width (Default: 0)
 -nf            Do not calculate free energy (Default: Off)
-sig=[int]      Number of significant digits to print in output files (Default: 5)
  -h            Display more help (Default: Off)
  -d            Use all default values (Default: Off)

Syntax: mkteci file1.eci ...
 where file1.eci etc. is a list of T-dependent eci files obtained with
 the clusterexpand command, e.g. 
 clusterexpand fvib    in the case of vibrational free energy or
 clusterexpand felec   in the case of electronic free energy.
Usually the file list is: fvib.eci felec.eci
                          ^vibrational ^electronic free energy

Calculates bulk modulus.
Syntax: calcbulk mins maxs ds runcommand
where mins and maxs are the minimum and maximum strains (e.g. 0.00 0.01)
ds is the step size (e.g. 0.005)
runcommand is the command to run the ab initio code (e.g. runstruct_vasp)

This command implements the "inflection-detection" method introduced in
A. van de Walle, Q. Hong, S. Kadkhodaei and R. Sun, "The free energy of mechanically unstable phases"
Nat. Com. 6, 7559 (2015) doi:10.1038/ncomms8559 .
and
A. van de Walle and S. Kadkhodaei and R. Sun and Q.-J. Hong, "Epicycle method for elasticity limit calculations",
Phys. Rev. B 95 144113 (2017) doi:10.1103/PhysRevB.95.144113 .

It calculates the energy of a structure that is potentially mechanically unstable.
In a nutshell: the method finds either a local minimum (for a mechanically stable phase)
or the inflection point on a path joining the unrelaxed and fully relaxed structures
(for a mechanically unstable phase).

Syntax: robustrelax_vasp [options] command_prefix
where options are
  -id             Inflection Detection method
  -idop "options" Options passed to the infdet command.
  -neb            Use the Nudged Elastic Band method to find minimum energy path
                  Otherwise: simply interpolate linearly.
  -ex             Only extract data form VASP files. Do not run anything.
  -c  [real]      Relaxation magnitude cutoff needed to activate robust relax algorithm (default: 0).
  -ni [integer]   Number of images in the minimum energy path (default: 6).
  -rc [string]    Command for full relaxation          (Default: runstruct_vasp -w vasp.wrap).
  -vc [string]    Command for volume only relaxation   (Default: runstruct_vasp -w vaspvol.wrap).
  -cc [string]    Command for chain (neb) calculations (Default: runstruct_vasp -w vaspneb.wrap).
  -sc [string]    Command for static runs              (Default: runstruct_vasp -w vaspstatic.wrap).
  -ic [string]    Command for inflection-detection runs (-id option) (Default: runstruct_vasp -p -w vaspid.wrap).
  -idf [real]     Starting point fraction for inflection detection (default: 0.5)
  -ja
  -jc             By how much to jitter atoms (-ja) and cell parameters (-jc) for the initial conditions
                  for inflection-detection method.
  -vib            Update vibrational data in svib_ht file from vol_0/svib_ht file.
  -mk             Make auxiliary vasp input files (vaspvol.wrap, vaspneb.wrap, vaspstatic.wrap, vaspf.wrap, vaspid.wrap)
                  from vasp.wrap. Does not run anything.
  -cln            clean files for a full restart.
  -cip            continue (an prior run) if possible (only implemented for -id algorithm).
  -d              Use all defaults values.
  -h              Display more help.
  command_prefix  Prefix needed for vasp to run on a remote machine or in parallel (e.g. mpirun).

Note: the commands specified by -rc,-vc,-cc,-sc can be set to empty "" to skip the corresponding
  calculation step (useful to restart an aborted run).

This command does the following:
1) Fully relax the structure (in str_hint.out or str.out) to create str_relax.out,
   just like runstruct_vasp.
2) If the relaxation cutoff (-c=...) no exceeded, stop. Typically, should be set to -c=0.05.
3) Relax the volume only of structure in str_sup.out or str.out. Results are in directory 00/
4) Do a neb (-neb) or infection detection (-id) calculation between the two structures obtained in step 1 and 3
   or just a linear interpolation between them (if no -neb or -id). Results are in directories ??/
   Note that you need VTST Tools from http://theory.cm.utexas.edu/vtsttools/ for the neb method
   with variable cell shape.
5) Do static calculations in each directory ??/
6) Find the inflection point on the path optimized in step 4. If it does not exist, find the
   minimum energy along that path.
7) Report the energy found in 6 in the file energy and the corresponding geometry in str_relax.out

Notes:
1) str_beg.out and str_end.out contain the extremities of the path.
   If you want to restart from scratch, delete these files.
2) For high symmetry phases (e.g. bcc,fcc,hcp) you may need to break the symmetry of the phase for it to relax.
   For that purpose, you can use, e.g.,
      symbrklib W fcc bcc
   or
      cellcvrt -ja=0.01 -jc=0.01 < str.out > str_hint.out .
   Sometimes a supercell is needed (a phonon analysis will tell you that - or symbrklib for bcc,fcc,hcp).

INFlection DETection method 3.52, by Axel van de Walle
  -h            Display more help (Default: Off)
-egt=[real]     Epicycle Gradient Tolerance (Default: 0.04)
-ets=[real]     Epicycle Trial Step (Default: 0.1)
-ems=[real]     Epicycle Maximum Step multiplier (Default: 5)
-eml=[real]     Epicycle Multiplier in Line minimization (Default: 2)
-ebl=[int]      Epicycle maximum number of Bracketing steps in Line minimizations (Default: 5)
-eil=[int]      Epicycle maximum number of Iterations in Line minimizations (Default: 3)
-eic=[int]      Epicycle maximum number of Iterations in Conjugate gradient (Default: 20)
-ebf=[int]      Epicycle motion Bad step Forgiveness (Default: 2)
-eir=[int]      Epicycle iterations between conjugate gradient reset (Default: 5)
 -el=[real]     Epicycle Length (Default: 0.1)
-ism=[real]     Ion motion Steepest descent Multiplier (Default: 0.003)
-isi=[int]      Ion motion Steepest maximum number of Iterations (Default: 0)
-igt=[real]     Ion motion Gradient Tolerance (Default: 0.1)
-its=[real]     Ion motion Trial Step (Default: 0.005)
-ims=[real]     Ion motion Maximum Step multiplier (Default: 5)
-iml=[real]     Ion motion Multiplier in Line minimization (Default: 2)
-ibl=[int]      Ion motion maximum number of Bracketing steps in Line minimizations (Default: 5)
-iil=[int]      Ion motion maximum number of Iterations in Line minimizations (Default: 3)
-iic=[int]      Ion motion maximum number of Iterations in Conjugate gradient (Default: 40)
-ibf=[int]      Ion motion Bad step Forgiveness (Default: 2)
-iir=[int]      Ion motion iterations between conjugate gradient reset (Default: 5)
-ics=[real]     Ion motion Curvature constraint Stiffness (0=automatic) (Default: 30)
 -ff=[real]     Force scale Factor (Default: 3)
 -ds=[int]      Dimension of the strain relaxation allowed (0: none, 1: along x, 2: along y,z, 3: along x,y,z (default)) 
 -ns            Do Not Scale tolerance with number of atoms (Default: Off)
 -st=[int]      Sleep Time between read access (Default: 5)
  -d            Use all default values (Default: Off)
 -os            Output Structure defined by epipos.out into str.out (Default: Off)
  -r            Relax to minimum (Default: Off)
For debugging only:
 -db            debug (Default: Off)
-aex            Analytical Example (for debugging) (Default: Off)
 -t1=[real]     Temp param 1 (Default: 1.9)
 -t2=[real]     Temp param 2 (Default: -2)

sqs2tdb version 3.52 by Axel van de Walle and with contributions to the SQS database
        from Ruoshi Sun, Qijun Hong and Sara Kadkhodaei.

Usage: sqs2tdb [options]    where the available options are:
-h   : More help.
-cp  : Copy SQS from the database to the current directory. Must specify:
       -lv=[level]
           level indicates how fine of composition mesh to use (0: only end members, 1: mid points, etc.)
       -l=[lattice]
          Available lattices
           AUCD_B19
           AUCD_B19.tar
           AUCU_L10
           BCC_A2
           BETASN_A5
           CDI2_C6
           CHI_A12
           CR3SI_A15
           CSCL_B2
           CUPRITE_C3
           CUPT_B22
           CUPT_L11
           DIAMOND_A4
           DUMMY
           FCC_A1
           FE3AL_D03
           FLUORITE_C1
           GA3PT5
           GAMMA_L12
           HCP_A3
           HEUSLER_D022
           HEUSLER_L21
           LIQUID
           MGCU2_C15
           MGZN2_C14
           NI3SN_D019
           NI4MO_D1A
           NIAS_D81
           OMEGA_C32
           PEROVSKITE_E21
           PYRITE_C2
           REO3_D09
           ROCKSALT_B1
           RUTILE_C4
           SIGMA_D8B
           WURTZITE_B4
           ZINCBLENDE_B3
           ZINTL_B32
           ZIRCONIA_TET

        Optional: -sp=Element,Element,...  to indicate which elements to consider
                      (otherwise read from species.in if it exists).
-fit : Fit solution model from SQS energies (to be run within the desired lattice directory)
       The -sro option can also be specified (with -fit) to include short-range order effects.
       The -ew=[real] option (default: 5) lets you set the increased weight given to endmembers in the fit.
-tdb : Combine solution models from one or multiple lattices into a single .tdb file.
       add the -oc (Open Calphad) option to generate a more portable tdb file.
-mk  : Generate input file for SQS generation with mcsqs. (Usually not needed - only for experts.)
       To be run in the SQS database directory:
       /public/software/atat/3.52/gcc-13.3/8173m/share/atat/data/sqsdb/[lattice name]
Note that -h,-mk,-cp,-fit,-tdb are mutually exclusive.


For more information see user guide published in:
  A. van de Walle, R. Sun, Q.-J. Hong, and S. Kadkhodaei.
  Software tools for high-throughput calphad from first-principles data.
  Calphad, 58:70, 2017.
  https://doi.org/10.1016/j.calphad.2017.05.005
(Also, this paper should be cited in any publication resulting from this code's use.)

EXAMPLES

-> A simple session of sqs2tdb could be:

cp ~/atat/example/vasp.wrap .
emacs vasp.wrap   #edit as needed

echo Al,Ni > species.in

sqs2tdb -cp -l=FCC_A1 -lv=1
sqs2tdb -cp -l=FCC_A1 -lv=1

cd FCC_A1
foreachfile wait pwd \; runstruct_vasp

sqs2tdb -fit

Edit the file terms.in to read
1,0
2,0

sqs2tdb -fit

cd ..

(repeat the above for other lattices if necessary)

sqs2tdb -tdb

The file AL_NI.tdb would contain a valid .tdb file.

-> In a more advanced example, the runstruct_vasp command could be replaced
by a job script submission containing the runstruct_vasp command.

-> When there are lattice instabilities, the runstruct_vasp could be replaced by 
robustrelax_vasp -mk  #this is to be run only once (see robustrelax_vasp -h for instructions)
robustrelax_vasp -id

-> If phonons are to be included (for end members) one could do:
foreachfile endmem pwd \; fitfc -si=str_relax.out -ernn=4 -ns=1 -nrr
foreachfile -d 3 wait \; runstruct_vasp -lu -w vaspf.wrap
   where vaspf.wrap contains parameters for a static run to calculate forces.
foreachfile endmem pwd \; fitfc -si=str_relax.out -f -frnn=2
foreachfile endmem pwd \; robustrelax_vasp -vib

sqs2tdb -fit

OPTIONAL input files (to placed in the topmost directory):

    exfromsgte.in : specify which phases should NOT be copied from SGTE database
                    (by default all phases for each relevant element are included,
                    but you may want to use ab initio data for virtual phase).
                    Phases are specified in the form: SGTE_[lattice]_[element]
                    e.g. SGTE_BCC_A2_AL
    subref.sed    : substitution rule (sed command to be applied to final tdb file)

OUTPUT FILES
    In addition to the *.tdb files, there is some diagnostic info available in the files fit_[property].out where property could be 
    energy, svib_ht, etc.

ADVANCED FEATURES
    In each sqs subdirectory created, there may be a file called link that contains the path to
    another directory where energy data can be found. This is useful if another structure is
    known be equivalent by symmetry. This file is created by default for equivalence within a
    given structure type can even find symmetries across structure types.
    You can also create the file yourself and the code will follow your link.

    There may also be a file called bump which indicates that a structure must be moved up in energy by the
    amount specified by the -bv option (or 5e-3 by default) to avoid degeneracy with an equivalent higher symmetry structure.
    This file is created by default (during the -cp step) when the code detects higher symmetry (e.g. a GAMMA_L12 phase with all sites occupied
    with the same type of atom is just FCC). You can delete this file if the higher-symmetry structure is not in your
    set of structures. This file is read during the -fit step.

    In summary, if you see a bump file, ask yourself if you have that structure elsewhere and put an appropriate link file.
    If you don't have that structure elsewhere, you can delete the bump file.
    The code will still work and give the right answer if you don't do this, but it will spend  more computer time.

    During the -fit step, one can specify the -sro option to include a low-order CVM approximation to the short range order.
    One can also specify the weights used to enforce better fit of the end members with the -ew option (a weight of 10 is the default).

    The default lower and upper temperature limits of 298.15K and 10000K can be changed with the -Tl=... and -Tu=... options, respectively.
    
    This code now allows for the input free energies to general CALPHAD-compatible T-dependent functions. To use this feature, place your functions
    in 'func' files and do not specify th 'energy' or 'svib_ht' files
    (or specify the -jf option to force the code to ignore the 'energy' and 'svib_ht' files).

A front-end to OpenCalphad for PLOTting Phase Diagrams.
Usage: ocplotpd [-ha] [-nt] [-tlf=fraction] [-1f] [-vtk] [-rmax=r_max] [-rmin=r_min] [-np=nb_of_proc] -tdb=tdbfile -n=nb_of_samples -T0=min_temperature -T1=max_temperature -e=element,element,...

Mandatory parameters:
 tdbfile: name of the Thermodynamic DataBase (TDB) file to use
 element,element,... : a list of the elements (and associated phases) to extract from the TDB file
 nb_of_samples: Number of phase equilibria sampled to generate the phase diagram
 min_temperature: lower bound on the temperature axis
 max_temperature: upper bound on the temperature axis (if min_temperature=max_temperature, a cross section is plotted)
 
optional parameters:
 -ha:   high accuracy calculations
 -nt:   no tie lines
 -tlf:  fraction of tie lines displayed (between 0.0 and 1.0)
 -1f:   generate a single gnuplot file
 -vtk:  generate vtk files (instead of gnuplot)
 -rmax: max distance between points in triangulation
 -rmin: discard points closer to each other than this cutoff
 -np:   launch nb_of_proc copies of opencalphad
 -noc:  do not run OpenCalphad - just create the graphs from the *.dat files
 -nd:   general n-dimensional phase diagram (generate input files for ndviewer - experimental)
 -debug:do not delete temporary files
 -mpi:  use mpi for simplexize code (experimental)

MaKe Axes 3.52, by Axel van de Walle
     -h            Display more help (Default: Off)
 -trans            Transform to coordinate system (Default: Off)
   -mat            Output transformation matrices (Default: Off)
   -tri            Gibbs triangle (Default: Off)
 -tetra            Gibbs tetrahedron (Default: Off)
 -hidim=[int]      Dimension (Default: 3)
   -col=[real]     Color (Default: 0)
   -rgb=[real],... RGB Color (Default: )
    -vl=[string]   Vertices labels (Default: )
  -zmax=[real]      (Default: 1000)
  -zmin=[real]      (Default: 0)
-zscale=[real]      (Default: 1000)
    -cs            Cross-Section (Default: Off)
    -cf=[string]   Cross section input File (Default: cut.in)
  -font=[string]   font file (Default: )
    -ef=[string]   Export format (default: vtk)
   -sig=[int]      Number of significant digits printed (Default: 5)
     -d            Use all default values (Default: Off)

Simplexize 3.52, by Axel van de Walle
   -t=[string]   Input table file (Default: tab.in)
 -col=[real]     Color (Default: 0)
 -rgb=[real],... RGB Color (Default: )
-rmax=[real]     Maximum radius of curvature (Default: 0.1)
-rmin=[real]     Minimum distance between points kept (Default: 0.001)
   -l            Plot lines (Default: Off)
 -tie            Plot tie lines (Default: Off)
-tiew=[real]     Tie line width (Default: 0.01)
 -sig=[int]      Number of significant digits printed (default: 5)
  -ef=[string]   Export format (default: vtk)
  -cs            Cross-Section (Default: Off)
  -cf=[string]   Cross section input File (Default: cut.in)
   -h            Display more help (Default: Off)
   -d            Use all default values (Default: Off)

TRIangulate PHase 3.52, by Axel van de Walle
  -t=[string]   Input table file (Default: tab.in)
 -sc=[real]     Scale for the unique axis (1st) (Default: 1000)
-col=[int]      Color (Default: 0)
-nfn            do Not fix Normal vector (Default: Off)
 -bf            generate back face (Default: Off)
-sig=[int]      Number of significant digits printed (default: 5)
 -ef=[string]   Export format (default: vtk)
  -h            Display more help (Default: Off)
  -d            Use all default values (Default: Off)

3D to GNUplot 3.52, by Axel van de Walle
 -if=[string]   Input table file (Default: tri.bi)
 -tc=[string]   set terminal command (Default: set term postscript eps color ; set out 'test.eps')
-eye=[real],... Eye position (Default: 0,-5,0)
 -at=[real],... Lookat position (Default: 0,0,0)
 -up=[real],... Up direction (Default: 0,0,1)
-fov=[real]     Field of View (in degrees) (Default: 30)
-lit=[real],... Light direction (Default: 0,0.707107,-0.707107)
-amb=[real]     Ambiant light level (Default: 0.5)
  -h            Display more help (Default: Off)
  -d            Use all default values (Default: Off)

Syntax: pollmach [-f] [-e] [-m alternate_machine_configuration_file] [-s] [-w] command_to_run

This command periodically checks the load on various machines
(specified in the file ~/.machines.rc)
and looks for subdirectories containing a file called "wait".
If the load on a machine is sufficiently low, it executes command_to_run
on that machine, in the directory where the oldest wait file lies.
A default ~/.machines.rc file is created the first time the chl command
is run. The format of the file is explained in the comments therein.
If no ~/.machines.rc file exists, command_to_run is run sequentially on
the local computer in each directory containing a "wait" file.
This is the single-machine mode.

When using this command with maps, command_to_run will typically be runstruct_vasp

The -m option overrides the default ~/.machines.rc (it is optional).

The -e option specifies that the command should terminate when no more
"wait" files are to be found (only works in single-machine (sequential) mode,
when no ~/.machines.rc file is given).

The -f option forces the command to run even if of pollmach_is_running file exists.

The -s option cause pollmach to self-manage the load (it does not poll the nodes for their loads
but instead keeps track of where it sends a job and does not send any other job to that node until it is done.
The first column in the machine_configuration_file is ignored and can be omitted.

The -w option tells pollmach to wait until all sub processes have finished before quitting.

The -il interactive loop option (beta). Here pollmach waits for a file called 'busy' to be created,
        then runs command and then deletes 'busy'.
        This repeats itself until a stop or stoppoll file is created.

The -t "command" option first runs "command" and, only if its return code is 0, runs command_to_run.

To cleanly stop this program, type
        touch stoppoll

Syntax: minload [-m alternate_machine_config_file] [-w]
Returns the command prefix needed to run a command on the remote
machine having the minimum load, among the
machines listed in the ~/.machines.rc file
(or as specified by the -m option).
A default ~/.machines.rc file is created the first time
the chl command is run and the file format is described
in the comments therein.

This command is basically like rsh, except that the command
makes sure that the current directory on the remote machine 
is the same as on the local machine.
(If the two machines do not share the same disk space, use the -r option.)

Syntax: node [-s] [-r] user@host command
 -s: use ssh instead of rsh
 -r: copy files in current directory to remote host before running command
 if user is the same on remote host, use may use
   node [-s] [-r] host command

Syntax: calc "mathematical expression"

Syntax: getvalue [label]
Script that scans standard input for a given label and
write, to standard output, the numerical value following
every occurence of that label.
Any number of : = spaces or tabs can separate the label and the number.
Example: getvalue "Final energy" < gulp.output

Syntax: getlines [-h] [ -af | -bf | -bt | -jaf | -jbf | -bt ] string1 string2
Copies selected lines of standard input to standard output.
-h   print this help.
-af  print all lines located *after* a line containing string1
-bf  print all lines located *before* a line containing string1
-bt  print all lines located between a line containing string1 and a line containing string2
     (If there are multiple blocks of lines braketed by [begin string]
      and [end string] they are all copied.)
The prefix j means "just", indicating that the line(s) containing the matching string(s) is (are) ommited.
Don't forget to quote your strings if they contain spaces.

Syntax: foreachfile [-e] [-n filename_to_skip] [-a and_filename] [-d depth] filename command
Execute the specified command in every first-level subdirectory containing the file filename.
The -e option cause foreachfile to skip directories containing the file "error".
The -n option cause foreachfile to skip directories containing the file filename_to_skip.
The -a option specifies that the file and_filename must also exist.
The -d option specifies to go down to lower level subdirectories as well (the default is 1).