Plane-wave DFT problem - unit cell optimization


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10:49:49 AM PST - Thu, Dec 18th 2014
I wanna self answer this question. Just convert the Cartesian coordinate to fractional coordinate. I use the website:

http://cci.lbl.gov/cctbx/frac_cart.html

to convert.

Quote:Chun-hung.wang Dec 15th 10:49 am
Hi all,

When I try to run partial unit cell optimization by plane-wave DFT calculation in NWChem 6.5 by Cascade supercomputer, the atom position is always rearranged. For example, the Zn position will "aggregate" with each other. My system has 272 atoms. In some cases the error message would be like: my atomic distance is too close. Here is my input file:



echo

title "ZIF-64"

memory stack 1800 mb heap 200 mb global 250 mb noverify

permanent_dir .

start zif64_PSPW

geometry noautoz
  system crystal

     lat_a 21.110d0

     lat_b 9.906d0

     lat_c 21.110d0

     alpha 90.0d0

     beta 90.0d0

     gamma 90.0d0

  end

C                 10.59088700    2.97180000    7.63759800

H                 11.11019300    2.57556000    6.94730100
.........
Zn                 8.91200870    4.45472820   13.76794200

Zn                 1.64299130    4.45472820   17.89705800
end

nwpw
  mult 1

  xc lda

  lmbfgs
end

driver
  maxiter 200
end

set geometry:actlist 1:2 9:10 13:14 17:18 23:24 27:28 35:36 41:42 69:74 93:98 105:110 117:122 135:140 147:152 171:176 189:194
set includestress .true.
task pspw optimize



The error message is like:
  atoms  219  and                    135  are similar

  atom    219  coordinates   8.25280109501174    2.51446878737748     27.4179707412332

  atom    135  coordinates   8.07364560376715    2.42962021218857     27.1928595327956

  atoms  221  and                    137  are similar

  atom    221  coordinates   36.0274472419937    14.4455120450660     16.8622775957722

  atom    137  coordinates   36.2066027332383    14.5303606202549     17.0873888042098

 minimum distance   0.299951707644571


I've checked my original input file that no two atoms are too close to each other. Why does this happen here? How do I fix that error? Thank you.
Chun-Hung