ATAT VASP 与自由能命令

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)