Input File Description

Program: neb.x / NEB / Quantum ESPRESSO (version: 7.2)

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 | lfcp | fcp_mu | fcp_thr | fcp_scheme

CLIMBING_IMAGES

index1, index2, ... indexN

BEGIN_ENGINE_INPUT

BEGIN_POSITIONS

FIRST_IMAGE

ATOMIC_POSITIONS

TOTAL_CHARGE

tot_charge

INTERMEDIATE_IMAGE

ATOMIC_POSITIONS

TOTAL_CHARGE

tot_charge

LAST_IMAGE

ATOMIC_POSITIONS

TOTAL_CHARGE

tot_charge

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
      ...pw TOTAL_CHARGE card (only for FCP)
      INTERMEDIATE_IMAGE
      ...pw ATOMIC_POSITIONS card
      ...pw TOTAL_CHARGE card (only for FCP)
      LAST_IMAGE
      ...pw ATOMIC_POSITIONS card
      ...pw TOTAL_CHARGE card (only for FCP)
    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

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nstep_path	INTEGER
Default:	1
number of ionic + electronic steps

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num_of_images	INTEGER
Default:	0
Number of points used to discretize the path (it must be larger than 3).

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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.

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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

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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).

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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.

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temp_req	REAL
Default:	0.D0 Kelvin
Temperature used for the langevin dynamics of the string.

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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.

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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.

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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.

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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"

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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.

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lfcp	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) or - ESM-RISM method (assume_isolated = 'esm' and esm_bc = 'bc1' must be set set in SYSTEM namelist, and trism = .TRUE. must be set set in CONTROL namelist). fcp_mu gives the target Fermi energy. See the header of PW/src/fcp_module.f90 for documentation

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fcp_mu	REAL
Default:	0.d0
See:	lfcp
If lfcp == .TRUE., gives the target Fermi energy [eV]. One can specify the total charge of the system for the first and last image by giving TOTAL_CHARGE cards so that the Fermi energy of these systems will be the target value, otherwise first_last_opt should be .TRUE. For the initial charge of intermediate images, the TOTAL_CHARGE is linearly interpolated between the initial and the final ones unless the TOTAL_CHARGE is given in the input file.

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fcp_thr	REAL
Default:	0.01D0 V
See:	lfcp
The simulation stops when the error ( the maximum of the force acting on the FCP in V ) is less than fcp_thr.

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fcp_scheme	CHARACTER
Default:	'lm'
See:	lfcp
Specify the type of optimization scheme for FCP: `'lm' :` Line-Minimization method. `'newton' :` Newton-Raphson method with diagonal hessian matrix. Also, coupling with DIIS. `'coupled' :` Coupled method with ionic positions. This is available only if opt_scheme == 'broyden', or 'broyden2'.

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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.

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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.
IF lfcp == .TRUE., total charges for all images have to be specified with TOTAL_CHARGE cards.

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

Card: TOTAL_CHARGE

Optional card, needed only if lfcp == .TRUE.

Syntax:

TOTAL_CHARGE
tot_charge

Description of items:

tot_charge	REAL
tot_charge is the total charge of the system.

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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

Card: TOTAL_CHARGE

Optional card, needed only if lfcp == .TRUE.

Syntax:

TOTAL_CHARGE
tot_charge

Description of items:

tot_charge	REAL
tot_charge is the total charge of the system.

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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

Card: TOTAL_CHARGE

Optional card, needed only if lfcp == .TRUE.

Syntax:

TOTAL_CHARGE
tot_charge

Description of items:

tot_charge	REAL
tot_charge is the total charge of the system.

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END_POSITIONS

Here can follow other pw specific cards ...

END_ENGINE_INPUT

END

This file has been created by helpdoc utility on Thu Mar 30 12:13:52 CEST 2023.