For sure your structure looks much better if you set CELL_PARAMETER angstrom ... ATOMIC_POSITIONS angstrom ... You should also set K_POINTS gamma: it is faster and takes less memory
Paolo On Wed, May 4, 2016 at 10:04 AM, Paolo Giannozzi <[email protected]> wrote: > This is unfortunately a nasty error that is not easy to solve. It is > either due to pseudopotentials or to really bad structures. If the problem > arises in the first NEB step, verify that your starting positions do not > have atoms too close > > Paolo > > On Tue, May 3, 2016 at 2:48 PM, Cecil Humphrey Botchway < > [email protected]> wrote: > >> Hi There, >> I am trying to run a transition state calculation using neb.x with >> methanol C-OH bond breaking in the zeolite micro pore (the system is >> composed of 120 atoms). I have tried relaxing the whole structure with the >> adsorbate and freezing only the zeolite leaving the adsorbate. I have even >> tried increasing and decreasing the numbers of processor cores from 8-16. I >> encounter the same error (which is below) regardless . >> >> >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> task # 0 >> from rdiaghg : error # 818 >> S matrix not positive definite >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> What could be the possible cause? >> This is how my input looks like >> >> BEGIN >> BEGIN_PATH_INPUT >> &PATH >> restart_mode = 'from_scratch' >> string_method = 'neb', >> nstep_path = 20, >> ds = 2.D0, >> opt_scheme = "broyden", >> num_of_images = 7, >> k_max = 0.3D0, >> k_min = 0.2D0, >> CI_scheme = "auto", >> path_thr = 0.1D0, >> / >> END_PATH_INPUT >> BEGIN_ENGINE_INPUT >> &CONTROL >> prefix = "TS1" >> outdir = "./tmp/", >> pseudo_dir = "/home/cbotchway/Cecil", >> / >> &SYSTEM >> ibrav = 0, >> nat = 120, >> ntyp = 5, >> ecutwfc = 40.0D0, >> ecutrho = 240.0D0, >> nspin = 2, >> starting_magnetization = 0.5D0, >> occupations = "smearing", >> degauss = 0.03D0, >> / >> &ELECTRONS >> conv_thr = 1.D-6, >> mixing_beta = 0.2D0, >> electron_maxstep =1000000, >> / >> &IONS >> / >> ATOMIC_SPECIES >> O 15.99940 O.pbe-van_ak.UPF >> Si 28.0855 Si.pbe-n-van.UPF >> Al 26.98154 Al.pbe-n-van.UPF >> H 1.00794 H.pbe-van_ak.UPF >> C 12.0107 C.pbe-van_ak.UPF >> BEGIN_POSITIONS >> FIRST_IMAGE >> >> Attached to this post is a copy of my input file >> Any help or advice would be appreciated >> Thank you in advance >> -- >> Cecil Huymphrey Botchway >> Mphil. Material Science and Computational Chemistry >> Department of Chemistry >> Kwame Nkrumah University of Science and Technology >> +23329002372 >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > 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 > > -- 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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