Atoms missing from the geometry.

Clicked A Few Times

12:10:47 PM PDT - Fri, Aug 17th 2012

Here is a sample input file for a simulation I'm running. (Never mind the fact that the lattice parameters aren't right.)

title "Lithium--H_2 adsorption site optimization"
echo

permanent_dir .
scratch_dir   .

start lithium

memory 2500 mb

nwpw
  simulation_cell
    ngrid 32 32 128
  end
  mult 2
  ewald_rcut 3.0
  ewald_ncut 8
  xc pbesol
end

set nwpw:minimizer     2       # Grassman LMBFGS minimizer
set nwpw:cif_filename   li.opt  # create a CIF file containing optimization history
set nwpw:lcao_skip      .true.
set nwpw:kbpp_ray       .true.
set nwpw:kbpp_filter    .true.

geometry        center  noautosym       noautoz print
        system  crystal
                lat_a   7.01000
                lat_b   4.95682
                lat_c   39.91364
                alpha   90.0d0
                beta    90.0d0
                gamma   90.0d0
        end
        Li1     0.25000 0.00000 0.50000
        Li2     0.00000 0.50000 0.50000
        Li3     0.25000 0.50000 0.56209
        Li4     0.00000 0.00000 0.56209
        Li5     0.25000 0.00000 0.62419
        Li6     0.00000 0.50000 0.62419
        Li7     0.75000 0.00000 0.50000
        Li8     0.50000 0.50000 0.50000
        Li9     0.75000 0.50000 0.56209
        Li10    0.50000 0.00000 0.56209
        Li11    0.75000 0.00000 0.62419
        Li12    0.50000 0.50000 0.62419
        H1      0.25000 0.00000 0.65000
        H2      0.25000 0.74300 0.65000
end
task band energy ignore

The problem I am consistently running into is that when the geometry block is read, the first hydrogen atom is dropped out!

...
                             Geometry "geometry" -> ""
                             -------------------------
 
 Output coordinates in angstroms (scale by  1.889725989 to convert to a.u.)
 
  No.       Tag          Charge          X              Y              Z
 ---- ---------------- ---------- -------------- -------------- --------------
    1 Li1                  3.0000     1.75250000     0.00000000    19.95682000
    2 Li2                  3.0000     0.00000000     2.47841000    19.95682000
    3 Li3                  3.0000     1.75250000     2.47841000    22.43505791
    4 Li4                  3.0000     0.00000000     0.00000000    22.43505791
    5 Li5                  3.0000     1.75250000     0.00000000    24.91369495
    6 Li6                  3.0000     0.00000000     2.47841000    24.91369495
    7 Li7                  3.0000     5.25750000     0.00000000    19.95682000
    8 Li8                  3.0000     3.50500000     2.47841000    19.95682000
    9 Li9                  3.0000     5.25750000     2.47841000    22.43505791
   10 Li10                 3.0000     3.50500000     0.00000000    22.43505791
   11 Li11                 3.0000     5.25750000     0.00000000    24.91369495
   12 Li12                 3.0000     3.50500000     2.47841000    24.91369495
   13 H2                   1.0000     1.75250000     3.68291726    25.94386600
 
      Lattice Parameters 
...

Obviously, the simulation requires all the input atoms. How can I ensure that this atom isn't missing from the database? Thanks.

Clicked A Few Times

8:19:04 AM PDT - Mon, Aug 20th 2012
I'm going to bump this in case it just got lost in the late-Friday-afternoon rush.

Forum Vet

10:06:04 AM PDT - Mon, Aug 20th 2012
Don't use extra number on element label
Davis68, If you drop the extra number (e.g. H1 becomes H, H2 becomes H), no atoms are dropped. I do not see any reason why you need the extra number in the label, do you? Edo

Clicked A Few Times

7:19:33 AM PDT - Tue, Aug 21st 2012

Unfortunately, on the system I'm using (NCSA Ember SGI Altix UV, NCSA-provided build of 6.0), it doesn't make any difference:

    1 Li1                  3.0000     1.75250000     0.00000000    19.95682000
    2 Li2                  3.0000     0.00000000     2.47841000    19.95682000
    3 Li3                  3.0000     1.75250000     2.47841000    22.43505791
    4 Li4                  3.0000     0.00000000     0.00000000    22.43505791
    5 Li5                  3.0000     1.75250000     0.00000000    24.91369495
    6 Li6                  3.0000     0.00000000     2.47841000    24.91369495
    7 Li7                  3.0000     5.25750000     0.00000000    19.95682000
    8 Li8                  3.0000     3.50500000     2.47841000    19.95682000
    9 Li9                  3.0000     5.25750000     2.47841000    22.43505791
   10 Li10                 3.0000     3.50500000     0.00000000    22.43505791
   11 Li11                 3.0000     5.25750000     0.00000000    24.91369495
   12 Li12                 3.0000     3.50500000     2.47841000    24.91369495
   13 H                    1.0000     1.75250000     3.68291726    25.94386600

Let me try it with something besides H and I'll let you know if that impacts it at all.

Clicked A Few Times

8:31:49 AM PDT - Tue, Aug 21st 2012
The dropped atom persists if I change the species to O, if I slightly move its location (by ~0.0001 A), if I add 1.0 to the internal coordinates to periodically slide it over, if I include it twice (both are ignored), and if I include a blank line between simulations. Is this likely to be a build error more than a database error, then?

Clicked A Few Times

9:27:22 AM PDT - Tue, Aug 21st 2012
What is going on? If I change the order to put the atoms first, then one of the metal atoms is dropped. Any guesses?

Gets Around

11:02:10 AM PDT - Tue, Aug 21st 2012

Try This

Not sure what's going on. The following worked for me on my mac, Try the following input deck.....It looks like your using a 64 bit compilation, did you include the "make 64_to_32" step in the compilation.

argument  1 = li-surface.nw

3 energy calculation
- 3.1 Spin Contamination
- 3.2 Timing

======================== echo of input deck ========================

title "Lithium--H_2 adsorption site optimization"
echo

permanent_dir ./perm
scratch_dir ./perm

start lithium

memory 1900 mb

nwpw

 mult 2

 ewald_rcut 3.0

 ewald_ncut 8

 cutoff 30.0

 xc pbesol

 lmbfgs

end

set nwpw:cif_filename li.opt # create a CIF file containing optimization history
set nwpw:kbpp_ray .true.
set nwpw:kbpp_filter .true.

geometry center noautosym noautoz print

       system  crystal

               lat_a   7.01000

               lat_b   4.95682

               lat_c   39.91364

               alpha   90.0d0

               beta    90.0d0

               gamma   90.0d0

       end

       Li1     0.25000 0.00000 0.50000

       Li2     0.00000 0.50000 0.50000

       Li3     0.25000 0.50000 0.56209

       Li4     0.00000 0.00000 0.56209

       Li5     0.25000 0.00000 0.62419

       Li6     0.00000 0.50000 0.62419

       Li7     0.75000 0.00000 0.50000

       Li8     0.50000 0.50000 0.50000

       Li9     0.75000 0.50000 0.56209

       Li10    0.50000 0.00000 0.56209

       Li11    0.75000 0.00000 0.62419

       Li12    0.50000 0.50000 0.62419

       H1      0.25000 0.00000 0.65000

       H2      0.25000 0.74300 0.65000

end
task band energy

====================================================================

            Northwest Computational Chemistry Package (NWChem) 6.1.1

            --------------------------------------------------------

                   Environmental Molecular Sciences Laboratory

                      Pacific Northwest National Laboratory

                               Richland, WA 99352

                             Copyright (c) 1994-2010

                      Pacific Northwest National Laboratory

                           Battelle Memorial Institute

            NWChem is an open-source computational chemistry package

                       distributed under the terms of the

                     Educational Community License (ECL) 2.0

            A copy of the license is included with this distribution

                             in the LICENSE.TXT file

                                 ACKNOWLEDGMENT

                                 --------------

           This software and its documentation were developed at the

           EMSL at Pacific Northwest National Laboratory, a multiprogram

           national laboratory, operated for the U.S. Department of Energy

           by Battelle under Contract Number DE-AC05-76RL01830. Support

           for this work was provided by the Department of Energy Office

           of Biological and Environmental Research, Office of Basic

           Energy Sciences, and the Office of Advanced Scientific Computing.

          Job information

          ---------------

   hostname        = WE24397

   program         = nwchem

   date            = Tue Aug 21 10:51:57 2012

   compiled        = Sun_Aug_19_16:40:44_2012

   source          = /Users/bylaska/nwchem-releases/nwchem

   nwchem branch   = Development

   nwchem revision = 22741

   ga revision     = 10078M

   input           = li-surface.nw

   prefix          = lithium.

   data base       = ./perm/lithium.db

   status          = startup

   nproc           =        4

   time left       =     -1s

          Memory information

          ------------------

   heap     =   62259201 doubles =    475.0 Mbytes

   stack    =   62259201 doubles =    475.0 Mbytes

   global   =  124518400 doubles =    950.0 Mbytes (distinct from heap & stack)

   total    =  249036802 doubles =   1900.0 Mbytes

   verify   = yes

   hardfail = no

          Directory information

          ---------------------

 0 permanent = ./perm

 0 scratch   = ./perm

                               NWChem Input Module

                               -------------------

                    Lithium--H_2 adsorption site optimization

                    -----------------------------------------

 !!!!!!!!!  geom_3d NEEDS TESTING !!!!!!!!!!

                            Geometry "geometry" -> ""

                            -------------------------

Output coordinates in angstroms (scale by  1.889725989 to convert to a.u.)

 No.       Tag          Charge          X              Y              Z

---- ---------------- ---------- -------------- -------------- --------------

   1 Li1                  3.0000     1.75250000     0.00000000    19.95682000

   2 Li2                  3.0000     0.00000000     2.47841000    19.95682000

   3 Li3                  3.0000     1.75250000     2.47841000    22.43505791

   4 Li4                  3.0000     0.00000000     0.00000000    22.43505791

   5 Li5                  3.0000     1.75250000     0.00000000    24.91369495

   6 Li6                  3.0000     0.00000000     2.47841000    24.91369495

   7 Li7                  3.0000     5.25750000     0.00000000    19.95682000

   8 Li8                  3.0000     3.50500000     2.47841000    19.95682000

   9 Li9                  3.0000     5.25750000     2.47841000    22.43505791

  10 Li10                 3.0000     3.50500000     0.00000000    22.43505791

  11 Li11                 3.0000     5.25750000     0.00000000    24.91369495

  12 Li12                 3.0000     3.50500000     2.47841000    24.91369495

  13 H1                   1.0000     1.75250000     0.00000000    25.94386600

  14 H2                   1.0000     1.75250000     3.68291726    25.94386600

     Lattice Parameters 

     ------------------

     lattice vectors in angstroms (scale by  1.889725989 to convert to a.u.)

     a1=<   7.010   0.000   0.000 >

     a2=<   0.000   4.957   0.000 >

     a3=<   0.000   0.000  39.914 >

     a=       7.010 b=      4.957 c=      39.914

     alpha=  90.000 beta=  90.000 gamma=  90.000

     omega=  1386.9

     reciprocal lattice vectors in a.u.

     b1=<   0.474   0.000  -0.000 >

     b2=<  -0.000   0.671  -0.000 >

     b3=<   0.000   0.000   0.083 >

     Atomic Mass 

     -----------

     Li1                7.016000

     Li2                7.016000

     Li3                7.016000

     Li4                7.016000

     Li5                7.016000

     Li6                7.016000

     Li7                7.016000

     Li8                7.016000

     Li9                7.016000

     Li10               7.016000

     Li11               7.016000

     Li12               7.016000

     H1                 1.007825

     H2                 1.007825

==============================================================================
                               internuclear distances

------------------------------------------------------------------------------

      center one      |      center two      | atomic units |  angstroms

------------------------------------------------------------------------------

  13 H1               |   5 Li5              |     1.94674  |     1.03017

------------------------------------------------------------------------------

                        number of included internuclear distances:          1

==============================================================================

         **********************************************************

         *                                                        *

         *                   NWPW BAND Calculation                *

         *                                                        *

         *  [(bundled Grassman/Stiefel manifold implementation)]  *

         *                                                        *

         *         [ NorthWest Chemistry implementation ]         *

         *                                                        *

         *                version #1.10   01/31/03                *

         *                                                        *

         *  A pseudopotential plane-wave band structure program   *

         *  with Brillouin zone sampling for optimizing crystals, *

         *  slabs, and polymers.  Developed by Eric J. Bylaska    *

         *  , Edoardo Apra, and Patrick Nichols.                  *

         *                                                        *

         **********************************************************

    >>>  JOB STARTED       AT Tue Aug 21 10:51:57 2012  <<<

         ================ input data ========================

pseudopotential is not correctly formatted:Li.cpp

Generated formatted_filename: ./perm/Li.cpp

- Spline fitted, nray=26465 -

- filtered -

pseudopotential is not correctly formatted:H.cpp

Generated formatted_filename: ./perm/H.cpp

- Spline fitted, nray=26465 -

- filtered -

Error reading psi - bad grid

nfft :          28          20         160

ngrid:          48          36         270

Error reading psi - bad grid

nfft :          28          20         160

ngrid:          48          36         270

Error reading psi - bad grid

Grid is being converted:

------------------------

To turn off automatic grid conversion:

set nwpw:psi_nogrid .false.

old_filename: lithium.movecs                                    

new_filename: lithium.movecs                                    

converting  :  28x 20x160 -->  48x 36x270

converting .... psi:           1  spin:           1  nb:           1

converting .... psi:           2  spin:           1  nb:           1

converting .... psi:           3  spin:           1  nb:           1

converting .... psi:           4  spin:           1  nb:           1

converting .... psi:           5  spin:           1  nb:           1

converting .... psi:           6  spin:           1  nb:           1

converting .... psi:           7  spin:           1  nb:           1

converting .... psi:           1  spin:           2  nb:           1

converting .... psi:           2  spin:           2  nb:           1

converting .... psi:           3  spin:           2  nb:           1

converting .... psi:           4  spin:           2  nb:           1

converting .... psi:           5  spin:           2  nb:           1

converting .... psi:           6  spin:           2  nb:           1

converting .... psi:           7  spin:           2  nb:           1

input psi filename:./perm/lithium.movecs

number of processors used:               4

processor grid           :   4 x   1 x   1

parallel mapping         :     2d  hilbert

options:

     boundary conditions  = periodic    (version3)

     electron spin        = unrestricted

     exchange-correlation = PBEsol (White and Bird) parameterization

elements involved in the cluster:

     1: Li    core charge: 1.0  lmax=1

            comment    : Hamann pseudopotential

            pseudpotential type            :   0

            highest angular component      :   1

            local potential used           :   1

            number of non-local projections:   1

            cutoff =   1.869   1.869

     2: H     core charge: 1.0  lmax=1

            comment    : Parameterized (Chem.Phys.Lett., vol 322, page 447) Hamman psp

            pseudpotential type            :   0

            highest angular component      :   1

            local potential used           :   1

            number of non-local projections:   1

            cutoff =   0.800   0.800

total charge:   0.000

atomic composition:

    Li  : 12     H   :  2

number of electrons: spin up=    7.00  spin down=    7.00 (fourier space)

number of orbitals:  spin up=       7  spin down=       7 (fourier space)

supercell:

     lattice:    a1=<  13.247   0.000   0.000 >

                 a2=<   0.000   9.367   0.000 >

                 a3=<   0.000   0.000  75.426 >

     reciprocal: b1=<   0.474   0.000  -0.000 >

                 b2=<  -0.000   0.671  -0.000 >

                 b3=<   0.000   0.000   0.083 >

     lattice:    a=  13.247    b=   9.367     c=  75.426

             alpha=  90.000 beta=  90.000 gamma=  90.000

     volume :     9359.2

     ewald summation: cut radius=    3.00  and  8

                       madelung=-3.83603996

brillouin zone:

     number of zone points:     1

     weight=   1.000  ks=<   0.000   0.000   0.000 >, k=<   0.000   0.000   0.000>

computational grids:

     density     cutoff= 60.000  fft=  48x  36x 270(   207761 waves    51940 per task)

     wavefnc   1 cutoff= 30.000  fft=  48x  36x 270(    73475 waves    18368 per task)

technical parameters:

     time step=      5.80     ficticious mass=  400000.0

     tolerance=.100E-06 (energy)   0.100E-06 (density)

     maximum iterations =      1000 (   10 inner    100 outer )

energy calculation

         ======== bundled Grassmann lmbfgs iteration ========
    >>>  ITERATION STARTED AT Tue Aug 21 10:55:22 2012  <<<

   iter.           Energy         DeltaE       DeltaRho 

   ------------------------------------------------------

     10   -0.4153325207E+01   -0.25862E-06    0.43139E-04

     20   -0.4153326499E+01   -0.87984E-07    0.51668E-07

 *** tolerance ok.    iteration terminated.

    >>>  ITERATION ENDED   AT Tue Aug 21 10:55:57 2012  <<<

         =============  summary of results  =================

number of electrons: spin up=    7.00000  down=    7.00000 (real space)

total     energy    :  -0.4153326499E+01 (   -0.29667E+00/ion)

total orbital energy:  -0.2544232486E+01 (   -0.18173E+00/electron)

hartree   energy    :   0.3953667394E+02 (    0.28240E+01/electron)

exc-corr  energy    :  -0.2748596568E+01 (   -0.19633E+00/electron)

ion-ion   energy    :   0.3710415440E+02 (    0.26503E+01/ion)

K.S. kinetic energy :   0.2635128141E+01 (    0.18822E+00/electron)

K.S. V_l  energy    :  -0.8108210264E+02 (   -0.57916E+01/electron)

K.S. V_nl energy    :   0.4014162261E+00 (    0.28673E-01/electron)

K.S. V_Hart energy  :   0.7907334788E+02 (    0.56481E+01/electron)

K.S. V_xc energy    :  -0.3572022095E+01 (   -0.25514E+00/electron)

K.S. V_so energy    :   0.0000000000E+00 (    0.00000E+00/electron)

Virial Coefficient  :  -0.1965506173E+01

Brillouin zone point:      1

   weight=  1.000000

   k     =<   0.000   0.000   0.000> . <b1,b2,b3> 

         =<   0.000   0.000   0.000>

orbital energies:

   -0.1203746E+00 (  -3.276eV) occ=1.000    -0.1154472E+00 (  -3.142eV) occ=1.000

   -0.1285992E+00 (  -3.499eV) occ=1.000    -0.1256016E+00 (  -3.418eV) occ=1.000

   -0.1435127E+00 (  -3.905eV) occ=1.000    -0.1455777E+00 (  -3.961eV) occ=1.000

   -0.1473091E+00 (  -4.009eV) occ=1.000    -0.1470524E+00 (  -4.002eV) occ=1.000

   -0.1825473E+00 (  -4.967eV) occ=1.000    -0.1871901E+00 (  -5.094eV) occ=1.000

   -0.2265442E+00 (  -6.165eV) occ=1.000    -0.2279035E+00 (  -6.202eV) occ=1.000

   -0.3363472E+00 (  -9.153eV) occ=1.000    -0.3102258E+00 (  -8.442eV) occ=1.000

Total BAND energy   :  -0.4153326499E+01

Spin Contamination

<Sexact^2> =    0.0000000000000000     

      =    1.4506946941619141

Writing Crystallographic Information File:./perm/li.opt.cif
- cell not shifted (nwpw:cif_shift_cell .false.)

output psi filename:./perm/lithium.movecs

Timing

cputime in seconds

prologue : 0.205288E+03
main loop : 0.348505E+02
epilogue : 0.812376E+00
total : 0.240951E+03
cputime/step: 0.792057E+00 ( 44 evalulations, 20 linesearches)

Time spent doing total step

FFTs : 0.607224E+01 0.138006E+00
dot products : 0.445757E+01 0.101308E+00
geodesic : 0.278632E+01 0.633255E-01
ffm_dgemm : 0.000000E+00 0.000000E+00
fmf_dgemm : 0.000000E+00 0.000000E+00
m_diagonalize : 0.000000E+00 0.000000E+00
- m_tredq : 0.000000E+00 0.000000E+00
- m_tredq_houseq : 0.000000E+00 0.000000E+00
- m_tredq_houseq_dgemm: 0.000000E+00 0.000000E+00
- m_tredq_dgemm1 : 0.000000E+00 0.000000E+00
- m_getdiags : 0.000000E+00 0.000000E+00
- m_tqliq : 0.000000E+00 0.000000E+00
- m_eigsrt : 0.000000E+00 0.000000E+00
exchange correlation : 0.109804E+02 0.249556E+00
local pseudopotentials : 0.212901E-01 0.483865E-03
non-local pseudopotentials : 0.204364E+01 0.464464E-01
hartree potentials : 0.546095E-01 0.124113E-02
ion-ion interaction : 0.416920E-01 0.947546E-03
structure factors : 0.142439E+00 0.323725E-02
phase factors : 0.000000E+00 0.000000E+00
masking and packing : 0.239252E+01 0.543754E-01
queue fft : 0.138038E+02 0.313722E+00
queue fft (serial) : 0.355017E+01 0.806858E-01
queue fft (message passing): 0.960439E+01 0.218282E+00
HFX potential : 0.000000E+00 0.000000E+00
qmmm LJ : 0.000000E+00 0.000000E+00
qmmm residual Q : 0.000000E+00 0.000000E+00

>>> JOB COMPLETED AT Tue Aug 21 10:55:58 2012 <<<

Task times cpu: 232.3s wall: 241.0s

NWChem Input Module
-------------------

Summary of allocated global arrays

No active global arrays

GA Statistics for process 0
------------------------------

create destroy get put acc scatter gather read&inc

calls: 0 0 0 0 0 0 0 0
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
bytes total: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 0 bytes

MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:

allocation statistics:
heap stack
---- -----
current number of blocks 0 0
maximum number of blocks 284 24
current total bytes 0 0
maximum total bytes 148509360 34484616
maximum total K-bytes 148510 34485
maximum total M-bytes 149 35

CITATION
--------
Please cite the following reference when publishing
results obtained with NWChem:

M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
E. Apra, T.L. Windus, W.A. de Jong
"NWChem: a comprehensive and scalable open-source
solution for large scale molecular simulations"
Comput. Phys. Commun. 181, 1477 (2010)
doi:10.1016/j.cpc.2010.04.018

AUTHORS & CONTRIBUTORS
----------------------
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski, T. P. Straatsma,
M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus, J. Hammond,
J. Autschbach, F. Aquino, S. Hirata, M. T. Hackler, J. Mullin, P. Nichols,
R. Peverati, Y. Zhao, P.-D. Fan, R. J. Harrison, M. Dupuis, D. M. A. Smith,
J. Nieplocha, V. Tipparaju, M. Krishnan, A. Vazquez-Mayagoitia, L. Jensen,
M. Swart, Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby,
E. Brown, G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao,
R. Kendall, J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell,
D. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. Deegan,
K. Dyall, D. Elwood, E. Glendening, M. Gutowski, A. Hess, J. Jaffe,
B. Johnson, J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield,
X. Long, B. Meng, T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann,
G. Sandrone, M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe,
A. Wong, Z. Zhang.

Total times  cpu:      232.3s     wall:      241.0s

Gets Around

1:21:27 PM PDT - Tue, Aug 21st 2012

better input deck

title "Lithium--H_2 adsorption site optimization"
echo

permanent_dir ./perm
scratch_dir ./perm

start lithium

memory 1900 mb

nwpw

 mult 2

 ewald_rcut 3.0

 ewald_ncut 8

 cutoff 2.0

 xc pbesol

 lmbfgs

end

set nwpw:cif_filename li.opt # create a CIF file containing optimization history
set nwpw:kbpp_ray .true.
set nwpw:kbpp_filter .true.

geometry center noautosym noautoz print

       system  crystal

               lat_a   7.01000

               lat_b   4.95682

               lat_c   39.91364

               alpha   90.0d0

               beta    90.0d0

               gamma   90.0d0

       end

       Li1     0.25000 0.00000 0.50000

       Li2     0.00000 0.50000 0.50000

       Li3     0.25000 0.50000 0.56209

       Li4     0.00000 0.00000 0.56209

       Li5     0.25000 0.00000 0.62419

       Li6     0.00000 0.50000 0.62419

       Li7     0.75000 0.00000 0.50000

       Li8     0.50000 0.50000 0.50000

       Li9     0.75000 0.50000 0.56209

       Li10    0.50000 0.00000 0.56209

       Li11    0.75000 0.00000 0.62419

       Li12    0.50000 0.50000 0.62419

       H1      0.25000 0.00000 0.65000

       H2      0.25000 0.74300 0.65000

end
task pspw energy

nwpw; cutoff 10.0; end
task pspw energy

nwpw; cutoff 30.0; end
task pspw energy

task band energy

Clicked A Few Times

2:00:06 PM PDT - Tue, Aug 21st 2012
The problem persists with your input deck. Like I said, it's an NCSA-supplied build, so I don't know the flags used in compiling it.

Gets Around

11:31:30 AM PDT - Wed, Aug 22nd 2012
email sent to NCSA
Sudhakar, We've been getting questions from one your users using NWChem. It looks like to me that nwchem isn't compiled right on your machine. If you have a chance can you take a look. Thanks Eric Bylaska http://nwchemgit.github.io/Special_AWCforum/st/id544

Gets Around

6:09:27 PM PDT - Wed, Aug 22nd 2012
Sudhakar says you can contact him
Eric: Could you please forward the question or ask the user to contact me. Which machine is being referring to here. Thanks, Sudhakar. Original Message----- From: Bylaska, Eric J [1] Sent: Wednesday, August 22, 2012 1:30 PM To: spamidig@ncsa.illinois.edu Subject: Problem with nwchem at NCSA Sudhakar, We've been getting questions from one your users using NWChem. It looks like to me that nwchem isn't compiled right on your machine. If you have a chance can you take a look. Thanks Eric Bylaska http://nwchemgit.github.io/Special_AWCforum/st/id544

Forum >> NWChem's corner >> Running NWChem

Atoms missing from the geometry.

Contents

======================== echo of input deck ========================

====================================================================

energy calculation

Spin Contamination

Timing