neb.x: input description

# Input File Description ## Program: neb.x / NEB / Quantum Espresso (version: 6.6)
> > ### TABLE OF CONTENTS INTRODUCTION BEGIN BEGIN_PATH_INPUT &PATH string_method | restart_mode | nstep_path | num_of_images | opt_scheme | CI_scheme | first_last_opt | minimum_image | temp_req | ds | k_max | k_min | path_thr | use_masses | use_freezing | lfcpopt | fcp_mu | fcp_tot_charge_first | fcp_tot_charge_last CLIMBING_IMAGES index1, index2, ... indexN BEGIN_ENGINE_INPUT BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS INTERMEDIATE_IMAGE ATOMIC_POSITIONS LAST_IMAGE ATOMIC_POSITIONS ### INTRODUCTION
> >     Input data format: { } = optional, [ ] = it depends, | = or

> >     All quantities whose dimensions are not explicitly specified are in
> >     RYDBERG ATOMIC UNITS

> >     BEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE

> >     neb.x DOES NOT READ FROM STANDARD INPUT !

> >     There are two ways for running a calculation with neb.x:

> >     (1) specifying a file to parse with the ./neb.x -inp or ./neb.x -input
> >         command line option.

> >     (2) or specifying the number of copies of PWscf inputs with the ./neb.x -input_images

> >     For case (1) a file containing special KEYWORDS (aka SUPERCARDS) has to be
> >     written (see below). These KEYWORDS tell the parser which part of the file
> >     contains the neb specifics and which part contains the energy/force engine
> >     input (at the moment only PW).  After the parsing, different files are
> >     generated: neb.dat, with the neb specific variables, and a set of pw_*.in
> >     PWscf input files, i.e., one for each input position. All options for a
> >     single SCF calculation apply.

> >     The general structure of the file to be parsed is:
> >     ==================================================

> >     BEGIN
> >       BEGIN_PATH_INPUT
> >         ... neb specific namelists and cards
> >       END_PATH_INPUT

> >       BEGIN_ENGINE_INPUT
> >         ...pw specific namelists and cards
> >         BEGIN_POSITIONS
> >           FIRST_IMAGE
> >           ...pw ATOMIC_POSITIONS card
> >           INTERMEDIATE_IMAGE
> >           ...pw ATOMIC_POSITIONS card
> >           LAST_IMAGE
> >           ...pw ATOMIC_POSITIONS card
> >         END_POSITIONS
> >         ... other pw specific cards
> >       END_ENGINE_INPUT
> >     END

> >     For case (2) neb.dat and all pw_1.in, pw_2.in ... should be already present.

> >     Structure of the NEB-only input data (file neb.dat):
> >     ====================================================

> >     &PATH
> >       ...
> >     /

> >     [ CLIMBING_IMAGES
> >        list of images, separated by a comma ]
## BEGIN
Syntax of this supercard is the following:
    BEGIN
      ... content of the supercard here ...
    END
and the content is:
## BEGIN_PATH_INPUT
Syntax of this supercard is the following:
    BEGIN_PATH_INPUT
      ... content of the supercard here ...
    END_PATH_INPUT
and the content is:
## Namelist: &PATH
string_method | CHARACTER
Default: | 'neb'
>     A string describing the task to be performed. Options are:
>   `'neb' :`
>        nudget-elastic-band
>   `'smd' :`
>        string-method-dynamics
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restart_mode | CHARACTER
Default: | 'from_scratch'
>      Options are:
>   `'from_scratch' :`
>        from scratch
>   `'restart' :`
>        from previous interrupted run
[Back to Top]
nstep_path | INTEGER
Default: | 1
>     number of ionic + electronic steps
[Back to Top]
num_of_images | INTEGER
Default: | 0
>     Number of points used to discretize the path
>     (it must be larger than 3).
[Back to Top]
opt_scheme | CHARACTER
Default: | 'quick-min'
>     Specify the type of optimization scheme:
>   `'sd' :`
>       steepest descent
>   `'broyden' :`
>       quasi-Newton Broyden's second method (suggested)
>   `'broyden2' :`
>       another variant of the quasi-Newton Broyden's
>       second method to be tested and compared with the
>       previous one.
>   `'quick-min' :`
>       an optimisation algorithm based on the
>       projected velocity Verlet scheme
>   `'langevin' :`
>       finite temperature langevin dynamics of the
>       string (smd only). It is used to compute the
>       average path and the free-energy profile.
[Back to Top]
CI_scheme | CHARACTER
Default: | 'no-CI'
>     Specify the type of Climbing Image scheme:
>   `'no-CI' :`
>       climbing image is not used
>   `'auto' :`
>       original CI scheme. The image highest in energy
>       does not feel the effect of springs and is
>       allowed to climb along the path
>   `'manual' :`
>       images that have to climb are manually selected.
>       See also CLIMBING_IMAGES card
[Back to Top]
first_last_opt | LOGICAL
Default: | .FALSE.
>     Also the first and the last configurations are optimized
>     "on the fly" (these images do not feel the effect of the springs).
[Back to Top]
minimum_image | LOGICAL
Default: | .FALSE.
>     Assume a "minimum image criterion" to build the path. If an atom
>     moves by more than half the length of a crystal axis between one
>     image and the next in the input (before interpolation),
>     an appropriate periodic replica of that atom is chosen.
>     Useful to avoid jumps in the initial reaction path.
[Back to Top]
temp_req | REAL
Default: | 0.D0 Kelvin
>     Temperature used for the langevin dynamics of the string.
[Back to Top]
ds | REAL
Default: | 1.D0
>     Optimisation step length ( Hartree atomic units ).
>     If opt_scheme=="broyden", ds is used as a guess for the
>     diagonal part of the Jacobian matrix.
[Back to Top]
k_max, k_min | REAL
Default: | 0.1D0 Hartree atomic units
>     Set them to use a Variable Elastic Constants scheme
>     elastic constants are in the range [ k_min, k_max ]
>     this is useful to rise the resolution around the saddle point.
[Back to Top]
path_thr | REAL
Default: | 0.05D0 eV / Angstrom
>     The simulation stops when the error ( the norm of the force
>     orthogonal to the path in eV/A ) is less than path_thr.
[Back to Top]
use_masses | LOGICAL
Default: | .FALSE.
>     If. TRUE. the optimisation of the path is performed using
>     mass-weighted coordinates. Useful together with quick-min
>     optimization scheme, if some bonds are much stiffer than
>     others. By assigning a larger (fictitious) mass to atoms
>     with stiff bonds, one may use a longer time step "ds"
[Back to Top]
use_freezing | LOGICAL
Default: | .FALSE.
>     If. TRUE. the images are optimised according to their error:
>     only those images with an error larger than half of the largest
>     are optimised. The other images are kept frozen.
[Back to Top]
lfcpopt | LOGICAL
Default: | .FALSE.
See: | fcp_mu
>     If .TRUE. perform a constant bias potential (constant-mu)
>     calculation with ESM method (assume_isolated = 'esm' and
>     esm_bc = 'bc2' or 'bc3' must be set in SYSTEM namelist).
>     fcp_mu gives the target Fermi energy.
>     See the header of PW/src/fcp.f90 for documentation
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fcp_mu | REAL
Default: | 0.d0
See: | lfcpopt
>     If lfcpopt == .TRUE., gives the target Fermi energy [Ry].
>     One can specify the total charge of the system for the first
>     and last image by giving fcp_tot_charge_first and fcp_tot_charge_last
>     so that the Fermi energy of these systems will be the target value,
>     otherwise first_last_opt should be .TRUE.
[Back to Top]
fcp_tot_charge_first | REAL
Default: | 0.d0
See: | lfcpopt
>     Total charge of the system ('tot_charge') for the first image.
>     Initial 'tot_charge' for intermediate images will be given by
>     linear interpolation of fcp_tot_charge_first and fcp_tot_charge_last
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fcp_tot_charge_last | REAL
Default: | 0.d0
See: | lfcpopt
>     Total charge of the system ('tot_charge') for the last image.
>     Initial 'tot_charge' for intermediate images will be given by
>     linear interpolation of fcp_tot_charge_first and fcp_tot_charge_last
[Back to Top]
## Card: CLIMBING_IMAGES
Optional card, needed only if CI_scheme == 'manual', ignored otherwise ! ### Syntax: CLIMBING_IMAGES index1, index2, ... indexN
> ### Description of items:
> index1, index2, ... indexN | INTEGER
> >     index1, index2, ..., indexN are indices of the images to which the
> >     Climbing-Image procedure apply. If more than one image is specified
> >     they must be separated by a comma.
[Back to Top]
## END_PATH_INPUT
## BEGIN_ENGINE_INPUT
Syntax of this supercard is the following:
    BEGIN_ENGINE_INPUT
      ... content of the supercard here ...
    END_ENGINE_INPUT
and the content is:
    Here comes the pw.x specific namelists and cards (see file: INPUT_PW.html or INPUT_PW.txt)
    with the exception of ATOMIC_POSITIONS cards, which are specified separately within the
    BEGIN_POSITIONS/END_POSITIONS supercard as described below.

    So the input that follows here is of the following structure:

       &CONTROL
          ...
       /
       &SYSTEM
         ...
       /
       &ELECTRONS
         ...
       /
       ...
## BEGIN_POSITIONS
Syntax of this supercard is the following:
    BEGIN_POSITIONS
      ... content of the supercard here ...
    END_POSITIONS
and the content is:
    NB:
    Atomic positions for all the images are specified within the BEGIN_POSITIONS / END_POSITIONS
    supercard, where each instance of ATOMIC_POSITIONS card is prefixed either by FIRST_IMAGE,
    INTERMEDIATE_IMAGE, or LAST_IMAGE keywords.

    Note that intermediate images are optional, i.e., there can be none or any number of
    INTERMEDIATE_IMAGE images.
## FIRST_IMAGE
Syntax of this supercard is the following:
    FIRST_IMAGE
      ... content of the supercard here ...
and the content is:
## Card: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg }
    For the description of ATOMIC_POSITIONS card see file: INPUT_PW.html or INPUT_PW.txt
## INTERMEDIATE_IMAGE
Syntax of this supercard is the following:
    INTERMEDIATE_IMAGE
      ... content of the supercard here ...
and the content is:
( Remark: There can be any number (including zero) of INTERMEDIATE_IMAGE supercards. )
## Card: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg }
    For the description of ATOMIC_POSITIONS card see file: INPUT_PW.html or INPUT_PW.txt
## LAST_IMAGE
Syntax of this supercard is the following:
    LAST_IMAGE
      ... content of the supercard here ...
and the content is:
## Card: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg }
    For the description of ATOMIC_POSITIONS card see file: INPUT_PW.html or INPUT_PW.txt
## END_POSITIONS
    Here can follow other pw specific cards ...
## END_ENGINE_INPUT
## END

This file has been created by helpdoc utility on Wed Dec 02 08:04:42 CET 2020.