INPUT_NEB.txt 19.2 KB
Newer Older
1 2 3 4 5
*** FILE AUTOMATICALLY CREATED: DO NOT EDIT, CHANGES WILL BE LOST ***

------------------------------------------------------------------------
INPUT FILE DESCRIPTION

giannozz's avatar
giannozz committed
6
Program: neb.x / NEB / Quantum Espresso (version: 6.4)
7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472
------------------------------------------------------------------------


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 ]



########################################################################
| SUPERCARD: BEGIN/END
| this supercard is enclosed within the keywords:
|
| BEGIN
|    ... content of the supercard here ...
| END
|
| The syntax of supercard's content follows below:

   ########################################################################
   | SUPERCARD: BEGIN_PATH_INPUT/END_PATH_INPUT
   | this supercard is enclosed within the keywords:
   |
   | BEGIN_PATH_INPUT
   |    ... content of the supercard here ...
   | END_PATH_INPUT
   |
   | The syntax of supercard's content follows below:
   
      ========================================================================
      NAMELIST: &PATH
      
         +--------------------------------------------------------------------
         Variable:       string_method
         
         Type:           CHARACTER
         Default:        'neb'
         Description:   
                         A string describing the task to be performed. Options are:
          
                         'neb' :
                              nudget-elastic-band
          
                         'smd' :
                              string-method-dynamics
         +--------------------------------------------------------------------
         
         +--------------------------------------------------------------------
         Variable:       restart_mode
         
         Type:           CHARACTER
         Default:        'from_scratch'
         Description:   
                         Options are:
          
                         '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.
         +--------------------------------------------------------------------
         
         +--------------------------------------------------------------------
         Variable:       lfcpopt
         
         Type:           LOGICAL
         See:            fcp_mu
         Default:        .FALSE.
         Description:    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
         +--------------------------------------------------------------------
         
         +--------------------------------------------------------------------
         Variable:       fcp_mu
         
         Type:           REAL
         See:            lfcpopt
         Default:        0.d0
         Description:    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.
         +--------------------------------------------------------------------
         
         +--------------------------------------------------------------------
         Variable:       fcp_tot_charge_first
         
         Type:           REAL
         See:            lfcpopt
         Default:        0.d0
         Description:    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"
         +--------------------------------------------------------------------
         
         +--------------------------------------------------------------------
         Variable:       fcp_tot_charge_last
         
         Type:           REAL
         See:            lfcpopt
         Default:        0.d0
         Description:    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"
         +--------------------------------------------------------------------
         
      ===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==========================================================
      
      
   ### END OF SUPERCARD :  BEGIN_PATH_INPUT/END_PATH_INPUT ################
   
   
   ########################################################################
   | SUPERCARD: BEGIN_ENGINE_INPUT/END_ENGINE_INPUT
   | this supercard is enclosed within the keywords:
   |
   | BEGIN_ENGINE_INPUT
   |    ... content of the supercard here ...
   | END_ENGINE_INPUT
   |
   | The syntax of supercard's content follows below:
   
      Here comes the pw.x specific namelists and cards (see file: "" 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
           ...
         /
         ...
      
      ########################################################################
      | SUPERCARD: BEGIN_POSITIONS/END_POSITIONS
      | this supercard is enclosed within the keywords:
      |
      | BEGIN_POSITIONS
      |    ... content of the supercard here ...
      | END_POSITIONS
      |
      | The syntax of supercard's content follows below:
      
         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.
         
         ########################################################################
         | SUPERCARD: FIRST_IMAGE
         | this supercard starts with the keyword:
         |
         | FIRST_IMAGE
         |    ... content of the supercard here ...
         |
         | The syntax of supercard's content follows below:
         
            ========================================================================
            CARD: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg }
            
               For the description of ATOMIC_POSITIONS card see file: "" or INPUT_PW.txt
               
            ===END OF CARD==========================================================
            
            
         ### END OF SUPERCARD :  FIRST_IMAGE ####################################
         
         
         ########################################################################
         | SUPERCARD: INTERMEDIATE_IMAGE
         | this supercard starts with the keyword:
         |
         | INTERMEDIATE_IMAGE
         |    ... content of the supercard here ...
         |
         | REMARK:
         | There can be any number (including zero) of INTERMEDIATE_IMAGE supercards.
         |
         | The syntax of supercard's content follows below:
         
            ========================================================================
            CARD: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg }
            
               For the description of ATOMIC_POSITIONS card see file: "" or INPUT_PW.txt
               
            ===END OF CARD==========================================================
            
            
         ### END OF SUPERCARD :  INTERMEDIATE_IMAGE #############################
         
         
         ########################################################################
         | SUPERCARD: LAST_IMAGE
         | this supercard starts with the keyword:
         |
         | LAST_IMAGE
         |    ... content of the supercard here ...
         |
         | The syntax of supercard's content follows below:
         
            ========================================================================
            CARD: ATOMIC_POSITIONS { alat | bohr | angstrom | crystal | crystal_sg }
            
               For the description of ATOMIC_POSITIONS card see file: "" or INPUT_PW.txt
               
            ===END OF CARD==========================================================
            
            
         ### END OF SUPERCARD :  LAST_IMAGE #####################################
         
         
      ### END OF SUPERCARD :  BEGIN_POSITIONS/END_POSITIONS ##################
      
      
      Here can follow other pw specific cards ...
      
   ### END OF SUPERCARD :  BEGIN_ENGINE_INPUT/END_ENGINE_INPUT ############
   
   
### END OF SUPERCARD :  BEGIN/END ######################################


giannozz's avatar
giannozz committed
473
This file has been created by helpdoc utility on Fri Mar 01 17:56:50 CET 2019