neb.x: input description (2024)

Table of Contents
TABLE OF CONTENTS INTRODUCTION BEGIN BEGIN_PATH_INPUT Namelist: &PATH Card: CLIMBING_IMAGES Syntax: Description of items: END_PATH_INPUT BEGIN_ENGINE_INPUT BEGIN_POSITIONS FIRST_IMAGE Card: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg } Card: TOTAL_CHARGE Syntax: Description of items: INTERMEDIATE_IMAGE Card: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg } Card: TOTAL_CHARGE Syntax: Description of items: LAST_IMAGE Card: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg } Card: TOTAL_CHARGE Syntax: Description of items: END_POSITIONS END_ENGINE_INPUT END References

TABLE OF CONTENTS

INTRODUCTION

BEGIN

BEGIN_PATH_INPUT

See Also
HtmlInputFile | BytesTommy Lee Lawsuit: Jane Doe Dismisses Helicopter Assault Claim With Hope to File Again

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, | = orAll quantities whose dimensions are not explicitly specified are inRYDBERG ATOMIC UNITSBEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLEneb.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_imagesFor case (1) a file containing special KEYWORDS (aka SUPERCARDS) has to bewritten (see below). These KEYWORDS tell the parser which part of the filecontains the neb specifics and which part contains the energy/force engineinput (at the moment only PW). After the parsing, different files aregenerated: neb.dat, with the neb specific variables, and a set of pw_*.inPWscf input files, i.e., one for each input position. All options for asingle 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_INPUTENDFor 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_methodCHARACTER
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_modeCHARACTER
Default: 'from_scratch' 
 Options are:
'from_scratch' :
 from scratch
'restart' :
 from previous interrupted run

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nstep_pathINTEGER
Default:1 
number of ionic + electronic steps

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

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opt_schemeCHARACTER
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'ssecond method to be tested and compared with theprevious one.
'quick-min' :
an optimisation algorithm based on theprojected velocity Verlet scheme
'langevin' :
finite temperature langevin dynamics of thestring (smd only). It is used to compute theaverage path and the free-energy profile.

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CI_schemeCHARACTER
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 energydoes not feel the effect of springs and isallowed 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_optLOGICAL
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_imageLOGICAL
Default: .FALSE. 
Assume a "minimum image criterion" to build the path. If an atommoves by more than half the length of a crystal axis between oneimage 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_reqREAL
Default: 0.D0 Kelvin 
Temperature used for the langevin dynamics of the string.

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dsREAL
Default: 1.D0 
Optimisation step length ( Hartree atomic units ).If opt_scheme=="broyden", ds is used as a guess for thediagonal part of the Jacobian matrix.

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k_max, k_minREAL
Default: 0.1D0 Hartree atomic units 
Set them to use a Variable Elastic Constants schemeelastic 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_thrREAL
Default: 0.05D0 eV / Angstrom 
The simulation stops when the error ( the norm of the forceorthogonal to the path in eV/A ) is less than path_thr.

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use_massesLOGICAL
Default: .FALSE. 
If. TRUE. the optimisation of the path is performed usingmass-weighted coordinates. Useful together with quick-minoptimization scheme, if some bonds are much stiffer thanothers. By assigning a larger (fictitious) mass to atomswith stiff bonds, one may use a longer time step "ds"

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use_freezingLOGICAL
Default: .FALSE. 
If. TRUE. the images are optimised according to their error:only those images with an error larger than half of the largestare optimised. The other images are kept frozen.

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lfcpLOGICAL
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_muREAL
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 firstand last image by giving TOTAL_CHARGE cardsso 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_CHARGEis linearly interpolated between the initial and the final onesunless the TOTAL_CHARGE is given in the input file.

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

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fcp_schemeCHARACTER
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 theClimbing-Image procedure apply. If more than one image is specifiedthey 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 theBEGIN_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_POSITIONSsupercard, 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 ofINTERMEDIATE_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

neb.x: input description (2024)

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