Unit cell optimization trouble

From NWChem

Viewed 3169 times, With a total of 1 Posts
Jump to: navigation, search

Just Got Here
Threads 2
Posts 3
Hello I'm fairly new to NWCHEM and I am trying to optimize a metal-oxide surface. I have input the geometries of the entire unit cell using fractional coordinates, yet only six out of my initial 15 atoms are read in. Does this have to do with some inherent symmetry procedure? Please any help or suggestions. The optimization successfully completed after 121 similar steps but I am missing atoms.

Contents

======================== echo of input deck ========================
echo
start tio2test2PW
title "tio2PW surface"

scratch_dir /Volumes/Scratch
permanent_dir /Volumes/Work


geometry
O 0.2000 0.8000 0.5000
O 0.8000 0.2000 0.5000
O 0.3000 0.3000 0.0000
O 0.7000 0.7000 0.0000
O 0.3000 0.3000 1.0000
O 0.7000 0.7000 1.0000
Ti 0.5000 0.5000 0.5000
Ti 0.0000 0.0000 0.0000
Ti 1.0000 0.0000 0.0000
Ti 0.0000 1.0000 0.0000
Ti 1.0000 1.0000 0.0000
Ti 0.0000 0.0000 1.0000
Ti 1.0000 0.0000 1.0000
Ti 0.0000 1.0000 1.0000
Ti 1.0000 1.0000 1.0000

system crystal
lat_a 4.589 lat_b 4.589 lat_c 2.954
alpha 90.0 beta 90.0 gamma 90.0
end

end

nwpw
xc pbe-sic
ewald_ncut 8
ewald_rcut 3
end

Driver
 clear
maxiter 600
end

set includestrss .true.
set nwpw:zero_forces .true.
set nwpw:lcao_skip .false.
set nwpw:ci_filename tio2Periodic

task pspw optimize



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


                                        



             Northwest Computational Chemistry Package (NWChem) 6.0
------------------------------------------------------


                   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      = chemmacpro4.duq.local
program = /Applications/nwchem/bin/nwchem
date = Tue Nov 2 17:13:40 2010

   compiled      = Thu_Sep_23_10:06:43_2010
source = /Users/d3p852/Documents/nwchem-6.0
nwchem branch = 6.0
input = tio2test2PW.nw
prefix = tio2test2PW.
data base = /Volumes/Work/ngozi/tio2test2PW.db
status = startup
nproc = 1
time left = -1s



          Memory information
------------------

   heap     =   13107201 doubles =    100.0 Mbytes
stack = 13107201 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428802 doubles = 400.0 Mbytes
verify = yes
hardfail = no


          Directory information
---------------------

 0 permanent = /Volumes/Work/ngozi
0 scratch = /Volumes/Scratch/ngozi




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


                                 tio2PW surface
--------------

 !!!!!!!!!  geom_3d NEEDS TESTING !!!!!!!!!! 
Turning off AUTOSYM since
SYMMETRY directive was detected!



                            Geometry "geometry" -> ""
-------------------------

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

 No.       Tag          Charge          X              Y              Z
---- ---------------- ---------- -------------- -------------- --------------
1 O 8.0000 0.91780000 3.67120000 1.47700000
2 O 8.0000 3.67120000 0.91780000 1.47700000
3 O 8.0000 1.37670000 1.37670000 0.00000000
4 O 8.0000 3.21230000 3.21230000 0.00000000
5 Ti 22.0000 2.29450000 2.29450000 1.47700000
6 Ti 22.0000 0.00000000 0.00000000 0.00000000

     Lattice Parameters 
------------------

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

     a1=<   4.589   0.000   0.000 >
a2=< 0.000 4.589 0.000 >
a3=< 0.000 0.000 2.954 >
a= 4.589 b= 4.589 c= 2.954
alpha= 90.000 beta= 90.000 gamma= 90.000
omega= 62.2

     reciprocal lattice vectors in a.u.

     b1=<   0.725  -0.000   0.000 >
b2=< 0.000 0.725 0.000 >
b3=< -0.000 -0.000 1.126 >

     Atomic Mass 
-----------

     O                 15.994910
Ti 45.948000



           XYZ format geometry
-------------------
6
geometry
O 0.91780000 3.67120000 1.47700000
O 3.67120000 0.91780000 1.47700000
O 1.37670000 1.37670000 0.00000000
O 3.21230000 3.21230000 0.00000000
Ti 2.29450000 2.29450000 1.47700000
Ti 0.00000000 0.00000000 0.00000000

==============================================================================
                               internuclear distances
------------------------------------------------------------------------------
center one | center two | atomic units | angstroms
------------------------------------------------------------------------------
5 Ti | 1 O | 3.67920 | 1.94695
5 Ti | 2 O | 3.67920 | 1.94695
5 Ti | 3 O | 3.71572 | 1.96628
5 Ti | 4 O | 3.71572 | 1.96628
6 Ti | 3 O | 3.67920 | 1.94695
------------------------------------------------------------------------------
number of included internuclear distances: 5
==============================================================================



==============================================================================
                                internuclear angles
------------------------------------------------------------------------------
center 1 | center 2 | center 3 | degrees
------------------------------------------------------------------------------
5 Ti | 3 O | 6 Ti | 131.31
1 O | 5 Ti | 2 O | 180.00
1 O | 5 Ti | 3 O | 90.00
1 O | 5 Ti | 4 O | 90.00
2 O | 5 Ti | 3 O | 90.00
2 O | 5 Ti | 4 O | 90.00
3 O | 5 Ti | 4 O | 82.62
------------------------------------------------------------------------------
number of included internuclear angles: 7
==============================================================================




 Deleted DRIVER restart files 


...
.....

                          NWChem Geometry Optimization
----------------------------




                                 tio2PW surface


maximum gradient threshold         (gmax) =   0.000450
rms gradient threshold (grms) = 0.000300
maximum cartesian step threshold (xmax) = 0.001800
rms cartesian step threshold (xrms) = 0.001200
fixed trust radius (trust) = 0.300000
maximum step size to saddle (sadstp) = 0.100000
energy precision (eprec) = 1.0D-07
maximum number of steps (nptopt) = 600
initial hessian option (inhess) = 0
line search option (linopt) = 1
hessian update option (modupd) = 1
saddle point option (modsad) = 0
initial eigen-mode to follow (moddir) = 0
initial variable to follow (vardir) = 0
follow first negative mode (firstneg) = T
apply conjugacy (opcg) = F
source of zmatrix =


         -------------------
Energy Minimization
-------------------


Using diagonal initial Hessian 
The initial hessian

             1        2        3        4        5        6        7        8
1 37.6014 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 0.0000 37.6014 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
3 0.0000 0.0000 15.5808 0.0000 0.0000 0.0000 0.0000 0.0000
4 0.0000 0.0000 0.0000 37.6014 0.0000 0.0000 0.0000 0.0000
5 0.0000 0.0000 0.0000 0.0000 37.6014 0.0000 0.0000 0.0000
6 0.0000 0.0000 0.0000 0.0000 0.0000 15.5808 0.0000 0.0000
7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 37.6014 0.0000
8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 37.6014

             9       10       11       12       13       14       15       16
9 15.5808 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
10 0.0000 37.6014 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
11 0.0000 0.0000 37.6014 0.0000 0.0000 0.0000 0.0000 0.0000
12 0.0000 0.0000 0.0000 15.5808 0.0000 0.0000 0.0000 0.0000
13 0.0000 0.0000 0.0000 0.0000 37.6014 0.0000 0.0000 0.0000
14 0.0000 0.0000 0.0000 0.0000 0.0000 37.6014 0.0000 0.0000
15 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 15.5808 0.0000
16 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 37.6014

            17       18      
17 37.6014 0.0000
18 0.0000 15.5808

         --------
Step 0
--------


                        Geometry "geometry" -> "geometry"
---------------------------------

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

 No.       Tag          Charge          X              Y              Z
---- ---------------- ---------- -------------- -------------- --------------
1 O 8.0000 0.91780000 3.67120000 1.47700000
2 O 8.0000 3.67120000 0.91780000 1.47700000
3 O 8.0000 1.37670000 1.37670000 0.00000000
4 O 8.0000 3.21230000 3.21230000 0.00000000
5 Ti 22.0000 2.29450000 2.29450000 1.47700000
6 Ti 22.0000 0.00000000 0.00000000 0.00000000

     Lattice Parameters 
------------------

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

     a1=<   4.589   0.000   0.000 >
a2=< 0.000 4.589 0.000 >
a3=< 0.000 0.000 2.954 >
a= 4.589 b= 4.589 c= 2.954
alpha= 90.000 beta= 90.000 gamma= 90.000
omega= 62.2

     reciprocal lattice vectors in a.u.

     b1=<   0.725  -0.000   0.000 >
b2=< 0.000 0.725 0.000 >
b3=< -0.000 -0.000 1.126 >

     Atomic Mass 
-----------

     O                 15.994910
Ti 45.948000


 library name resolved from: environment
NWCHEM_NWPW_LIBRARY set to: </Applications/nwchem/usr.local.lib.nwchem/libraryps/>
library name resolved from: environment
NWCHEM_NWPW_LIBRARY set to: </Applications/nwchem/usr.local.lib.nwchem/libraryps/>
****************************************************
* *
* NWPW PSPW Calculation *
* *
* [ (Grassman/Stiefel manifold implementation) ] *
* *
* [ NorthWest Chemistry implementation ] *
* *
* version #5.10 06/12/02 *
* *
* This code was developed by Eric J. Bylaska, *
* and was based upon algorithms and code *
* developed by the group of Prof. John H. Weare *
* *
****************************************************
>>> JOB STARTED AT Tue Nov 2 17:13:40 2010 <<<
================ input data ======================== library name resolved from: environment
NWCHEM_NWPW_LIBRARY set to: </Applications/nwchem/usr.local.lib.nwchem/libraryps/>

Generated formatted atomic orbitals, filename: /Volumes/Work/ngozi/O.aorb
library name resolved from: environment
NWCHEM_NWPW_LIBRARY set to: </Applications/nwchem/usr.local.lib.nwchem/libraryps/>

Generated formatted atomic orbitals, filename: /Volumes/Work/ngozi/Ti.aorb

lcao guess, initial psi:tio2test2PW.movecs            
- spin, nalpha, nbeta: 1 16 0

input psi filename:/Volumes/Work/ngozi/tio2test2PW.movecs

Fixed ion positions:    1    2    3    4    5    6


number of processors used:         1
processor grid  : 1 x 1
parallel mapping  : slab
parallel mapping  : balanced

options:
boundary conditions = periodic (version3)
electron spin = restricted
exchange-correlation = LDA (Vosko et al) parameterization

elements involved in the cluster:
1: O core charge: 6.0000 lmax= 2
comment  : Parameterized (Chem.Phys.Lett., vol 322, page 447) Hamman psp
pseudpotential type  : 0
highest angular component  : 2
local potential used  : 2
number of non-local projections: 4
cutoff = 0.700 0.700 0.700

     2: Ti    core charge:  4.0000  lmax=  2
comment  : Troullier-Martins pseudopotential
pseudpotential type  : 0
highest angular component  : 2
local potential used  : 0
number of non-local projections: 8
semicore corrections included  : 1.980 (radius) 1.848 (charge)
cutoff = 2.420 2.993 1.933


total charge:   0.000

atomic composition:
O  : 4 Ti  : 2

number of electrons: spin up=    16 (  16 per task)  down=    16 (  16 per task) (fourier space)
number of orbitals : spin up= 16 ( 16 per task) down= 16 ( 16 per task) (fourier space)

supercell:
cell_name: cell_default
lattice: a1=< 8.672 0.000 0.000 >
a2=< 0.000 8.672 0.000 >
a3=< 0.000 0.000 5.582 >
reciprocal: b1=< 0.725 0.000 -0.000 >
b2=< -0.000 0.725 -0.000 >
b3=< 0.000 0.000 1.126 >
lattice: a= 8.672 b= 8.672 c= 5.582
alpha= 90.000 beta= 90.000 gamma= 90.000
omega= 419.8

     density cutoff=100.000  fft= 40x 40x 40(    10073 waves    10073 per task)
wavefnc cutoff= 50.000 fft= 40x 40x 40( 3541 waves 3541 per task)
ewald summation: cut radius= 3.00 and 8
madelung= 1.64052994

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



         ====== Grassmann conjugate gradient iteration ======
    >>>  ITERATION STARTED AT Tue Nov  2 17:14:05 2010  <<<
iter. Energy DeltaE DeltaRho
------------------------------------------------------
- 15 steepest descent iterations performed
10 -0.7225109252E+02 -0.15539E-02 0.34034E-04
- 10 steepest descent iterations performed
20 -0.7225773954E+02 -0.37333E-03 0.14647E-04
30 -0.7225848988E+02 -0.47569E-04 0.11040E-05
40 -0.7225888331E+02 -0.41264E-04 0.64373E-06
50 -0.7225914374E+02 -0.12823E-04 0.12799E-06
60 -0.7225932850E+02 -0.17815E-04 0.23545E-06
- 10 steepest descent iterations performed
70 -0.7225961989E+02 -0.70486E-04 0.49088E-05
- 10 steepest descent iterations performed
80 -0.7225974767E+02 -0.47649E-05 0.89869E-07
90 -0.7225978188E+02 -0.31857E-05 0.76399E-07
100 -0.7225980741E+02 -0.18898E-05 0.24590E-07
110 -0.7225982678E+02 -0.16342E-05 0.30406E-07
120 -0.7225984162E+02 -0.10353E-05 0.13521E-07
130 -0.7225985310E+02 -0.93030E-06 0.15480E-07
140 -0.7225986201E+02 -0.61094E-06 0.62932E-08
150 -0.7225986899E+02 -0.55611E-06 0.75347E-08
160 -0.7225987446E+02 -0.37551E-06 0.35111E-08
170 -0.7225987878E+02 -0.34594E-06 0.40986E-08
180 -0.7225988221E+02 -0.23734E-06 0.20480E-08
190 -0.7225988493E+02 -0.22115E-06 0.23871E-08
200 -0.7225988710E+02 -0.15299E-06 0.12740E-08
210 -0.7225988883E+02 -0.14393E-06 0.14723E-08
220 -0.7225988992E+02 -0.92256E-07 0.96634E-09
*** tolerance ok. iteration terminated
>>> ITERATION ENDED AT Tue Nov 2 17:15:37 2010 <<<


Summary Of Results


number of electrons: spin up=   16.00000  down=   16.00000 (real space)

total     energy    :  -0.7225988992E+02 (   -0.12043E+02/ion)
total orbital energy: 0.6818980553E+00 ( 0.42619E-01/electron)
hartree energy  : 0.1849915985E+02 ( 0.11562E+01/electron)
exc-corr energy  : -0.1820287669E+02 ( -0.11377E+01/electron)
ion-ion energy  : -0.5821346242E+02 ( -0.97022E+01/ion)

kinetic (planewave) :   0.5639646119E+02 (    0.35248E+01/electron)
V_local (planewave) : -0.5608491807E+02 ( -0.35053E+01/electron)
V_nl (planewave) : -0.1465425378E+02 ( -0.91589E+00/electron)
V_Coul (planewave) : 0.3699831969E+02 ( 0.23124E+01/electron)
V_xc. (planewave) : -0.2197371098E+02 ( -0.13734E+01/electron)
Virial Coefficient  : -0.9879088503E+00

orbital energies:
0.2564510E+00 ( 6.978eV)
0.2465500E+00 ( 6.709eV)
0.2465113E+00 ( 6.708eV)
0.2345154E+00 ( 6.382eV)
0.1756273E+00 ( 4.779eV)
0.1540754E+00 ( 4.193eV)
0.1540325E+00 ( 4.191eV)
0.1019030E+00 ( 2.773eV)
0.1018766E+00 ( 2.772eV)
0.4883798E-01 ( 1.329eV)
0.4472966E-01 ( 1.217eV)
0.2782909E-01 ( 0.757eV)
-0.3398758E+00 ( -9.249eV)
-0.3398848E+00 ( -9.249eV)
-0.3568405E+00 ( -9.710eV)
-0.4153893E+00 ( -11.303eV)

Total PSPW energy   :  -0.7225988992E+02


Spin Contamination


<Sexact^2> =    0.0000000000000000     
= 0.0000000000000000



Center of Charge


spin up ( 0.0000, -0.0000, 0.0000 )
spin down ( 0.0000, -0.0000, 0.0000 )
    total  (    0.0000,   -0.0000,    0.0000 )
ionic ( 0.5420, 0.5420, 1.3956 )
crystal ( 0.0000, -0.0000, 0.0000 )


Crystal Dipole


mu = ( -0.0001, 0.0000, 0.0000 ) au
|mu| = 0.0001 au, 0.0001 Debye


Molecular Dipole wrt Center of Mass


mu = ( 17.3438, 17.3439, 44.6580 ) au
|mu| = 50.9505 au, 129.4959 Debye


Translation force removed: ( 0.00000 0.00000 0.00000)


         =============  Ion Gradients =================
Ion Forces:
1 O ( 0.00000 0.00000 0.00000 )
2 O ( 0.00000 0.00000 0.00000 )
3 O ( 0.00000 0.00000 0.00000 )
4 O ( 0.00000 0.00000 0.00000 )
5 Ti ( 0.00000 0.00000 0.00000 )
6 Ti ( 0.00000 0.00000 0.00000 )
C.O.M. ( 0.00000 0.00000 0.00000 )
=============================================== |F| = 0.000000E+00
|F|/nion = 0.000000E+00
max|Fatom|= 0.000000E+00 ( 0.000eV/Angstrom)



output psi filename:/Volumes/Work/ngozi/tio2test2PW.movecs


Timing


cputime in seconds
 prologue    :   0.248338E+02
main loop  : 0.919390E+02
epilogue  : 0.569332E+00
total  : 0.117342E+03
cputime/step: 0.101478E+00 ( 906 evalulations, 217 linesearches)


Time spent doing total step
 FFTs                       :   0.492794E+01  0.543923E-02
dot products  : 0.931913E+01 0.102860E-01
geodesic  : 0.573165E+01 0.632632E-02
ffm_dgemm  : 0.159246E+01 0.175769E-02
fmf_dgemm  : 0.495302E+01 0.546691E-02
m_diagonalize  : 0.327780E-01 0.361788E-04
- m_tredq  : 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  : 0.116150E+02 0.128201E-01
local pseudopotentials  : 0.237400E-02 0.262031E-05
non-local pseudopotentials : 0.103461E+02 0.114196E-01
hartree potentials  : 0.935040E-01 0.103205E-03
ion-ion interaction  : 0.363846E+00 0.401596E-03
structure factors  : 0.150433E+02 0.166041E-01
phase factors  : 0.280000E-04 0.309051E-07
masking and packing  : 0.892788E+01 0.985418E-02
queue fft  : 0.520795E+02 0.574829E-01
queue fft (serial)  : 0.399863E+02 0.441350E-01
queue fft (message passing): 0.933832E+01 0.103072E-01
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 Nov  2 17:15:37 2010  <<<

@ Step Energy Delta E Gmax Grms Xrms Xmax Walltime
@ ---- ---------------- -------- -------- -------- -------- -------- --------
@ 0 -72.25988992 0.0D+00 0.00000 0.00000 0.00000 0.00000 117.5
                                    ok       ok       ok       ok  

 Warning ... line search gradient +ve    1.0000000000000000        0.0000000000000000

Just Got Here
Threads 2
Posts 3
Unit cell optimization fixed
I fixed the problem. NWCHEM uses the unit cell geometries not the primitive cell.


Forum >> NWChem's corner >> General Topics



Who's here now Members 0 Guests 1 Bots/Crawler 0


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC