[Pw_forum] Why the POSITION card ignored in my NEB calculation

[Paolo Giannozzi]

On Sun, Oct 22, 2017 at 7:36 AM, jibiaoli <jibiaoli at foxmail.com> wrote:


>      Reading input from standard input
>

Funny: neb.x does not read from standard input. From the documentation:

===
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 ./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.
===
Paolo


> Warning: card BEGIN_POSITIONS ignored
> Warning: card FIRST_IMAGE ignored
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%%
>      Error in routine card_atomic_positions (2):
>      two occurrences
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%%
>
>      stopping ...
>
> ...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
> my input
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
>   restart_mode      = 'from_scratch'
>   string_method     = 'neb',
>   nstep_path        = 300,
>   ds                = 1.D0,
>   opt_scheme        = "quick-min",
>   num_of_images     = 7,
>   k_max             = 0.3D0,
>   k_min             = 0.1D0,
>   CI_scheme         = "auto",
>   path_thr          = 0.1D0,
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
>   prefix         = "tri"
>   outdir         = "/home/bmllzr/calc/CO_Fe100/NEB",
>   pseudo_dir     = "/home/bmllzr/codes/pseudo/",
> /
> &SYSTEM
>                        ibrav = 6,
>                    celldm(1) = 16.270548418,
>                    celldm(3) = 2.32,
>                          nat = 54,
>                         ntyp = 3,
>                      ecutwfc = 29 ,
>                      ecutrho = 180 ,
>                  occupations = 'smearing' ,
>                      degauss = 0.05D0 ,
>                     smearing = 'methfessel-paxton' ,
>                        nspin = 2 ,
>    starting_magnetization(1) = -0.1,
>    starting_magnetization(2) = -0.1,
>    starting_magnetization(3) = 2.9,
> /
> &ELECTRONS
>                  mixing_beta = 0.2D0 ,
>              diagonalization = 'david' ,
> /
> ATOMIC_SPECIES
>     O   15.999  O.pbe-van_ak.UPF
>     C   12.001  C.pbe-van_ak.UPF
>    Fe   55.850 Fe.pbe-sp-van_ak.UPF
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS angstrom
> O       -0.000038788   1.435061950   9.445462005
> O        5.740011060   4.304997121   9.445811738
> O        2.870035088   7.174965791   9.445569579
> ...
> Fe       1.435000000   1.435000000   0.000000000    0   0   0
> Fe       4.305000000   1.435000000   0.000000000    0   0   0
> Fe       7.175000000   1.435000000   0.000000000    0   0   0
> Fe       1.435000000   4.305000000   0.000000000    0   0   0
> Fe       4.305000000   4.305000000   0.000000000    0   0   0
> Fe       7.175000000   4.305000000   0.000000000    0   0   0
> Fe       1.435000000   7.175000000   0.000000000    0   0   0
> Fe       4.305000000   7.175000000   0.000000000    0   0   0
> Fe       7.175000000   7.175000000   0.000000000    0   0   0
> LAST_IMAGE
> ATOMIC_POSITIONS angstrom
> O        0.000078345   1.434955105   7.225635830
> O        5.739958448   4.305085729   7.225477804
> O        2.869957096   7.174949092   7.226004424
> ...
> Fe       1.435000000   1.435000000   0.000000000    0   0   0
> Fe       4.305000000   1.435000000   0.000000000    0   0   0
> Fe       7.175000000   1.435000000   0.000000000    0   0   0
> Fe       1.435000000   4.305000000   0.000000000    0   0   0
> Fe       4.305000000   4.305000000   0.000000000    0   0   0
> Fe       7.175000000   4.305000000   0.000000000    0   0   0
> Fe       1.435000000   7.175000000   0.000000000    0   0   0
> Fe       4.305000000   7.175000000   0.000000000    0   0   0
> Fe       7.175000000   7.175000000   0.000000000    0   0   0
> END_POSITIONS
> K_POINTS automatic
>   3 3 1   0 0 0
> END_ENGINE_INPUT
> END
>
>
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>



-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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