------------------------------------------------------------------------ INPUT FILE DESCRIPTION Program: neb.x / NEB / Quantum Espresso ------------------------------------------------------------------------ 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 General input file structure: =============================================================================== 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 input ./neb.x -input\_images. For case 1) a file containing KEYWORDS has to be written (see below). These KEYWORDS tells the parser which part of the file regards neb specifics and which part regards the energy/force engine (at the moment only PW). After the parsing different files are generated: neb.dat, with neb specific variables and a set of pw_*.in PWscf input files like 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 input data (file neb.dat) : =============================================================================== &PATH ... / [ CLIMBING_IMAGES list of images, separated by a comma ] ======================================================================== NAMELIST: &PATH +-------------------------------------------------------------------- Variable: string_method Type: CHARACTER Default: 'neb' Description: a string describing the task to be performed: 'neb', 'smd' +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: restart_mode Type: CHARACTER Default: 'from_scratch' Description: 'from_scratch' : from scratch 'restart' : from previous interrupted run +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: nstep_path Type: INTEGER Description: number of ionic + electronic steps Default: 1 +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: num_of_images Type: INTEGER Default: 0 Description: Number of points used to discretize the path (it must be larger than 3). +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: opt_scheme Type: CHARACTER Default: 'quick-min' Description: 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. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: CI_scheme Type: CHARACTER Default: 'no-CI' Description: 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 +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: first_last_opt Type: LOGICAL Default: .FALSE. Description: Also the first and the last configurations are optimized "on the fly" (these images do not feel the effect of the springs). +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: minimum_image Type: LOGICAL Default: .FALSE. Description: 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. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: temp_req Type: REAL Default: 0.D0 Kelvin Description: Temperature used for the langevin dynamics of the string. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: ds Type: REAL Default: 1.D0 Description: Optimisation step length ( Hartree atomic units ). If opt_scheme="broyden", ds is used as a guess for the diagonal part of the Jacobian matrix. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variables: k_max, k_min Type: REAL Default: 0.1D0 Hartree atomic units Description: 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. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: path_thr Type: REAL Default: 0.05D0 eV / Angstrom Description: The simulation stops when the error ( the norm of the force orthogonal to the path in eV/A ) is less than path_thr. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: use_masses Type: LOGICAL Default: .FALSE. Description: 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" +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: use_freezing Type: LOGICAL Default: .FALSE. Description: 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. +-------------------------------------------------------------------- ===END OF NAMELIST====================================================== ======================================================================== CARD: CLIMBING_IMAGES OPTIONAL CARD, NEEDED ONLY IF CI_SCHEME = 'MANUAL', IGNORED OTHERWISE ! ///////////////////////////////////////// // Syntax: // ///////////////////////////////////////// CLIMBING_IMAGES index1, index2, ... indexN ///////////////////////////////////////// DESCRIPTION OF ITEMS: +-------------------------------------------------------------------- Variables: index1, index2, ... indexN Type: INTEGER Description: 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. +-------------------------------------------------------------------- ===END OF CARD==========================================================