Decoding the content of Dump file

GULP
1

I am trying to decode the content of the dump file (for the XAZPEW MOF discussed in another topic). The target of my work is to detect why the geometry optimization generate incorrect result
(it breaks bond of a solvent under no forces influence)
Output was created by following command:
dump connect bondtest.grs
The space group is C2.
The dump contains 222 atoms (asymmetric unit cell content)
The bonds describe connectivity between 444 atoms.
So I expect GULP internally works in P2 group reducing automatically the problem complexity, Correct ?
I want to be able to draw a image directly showing the bond assignment + atom types assignment to be sure cross cell and cross/symmetry elements bonds were correctly generated …
How can I do this when GULP did not generated the 444 bonded atoms - I have no way to check the bonds are OK ?
Did GULP simply applied the 2 fold axes symmetry operation, or did it applied the 2 axis + shift back tot he unit cell ?
How can I e.g. get data for exact visualization of the atoms used in reality for the calculation with all forces and bonds assigned ? I have no idea how GULP works with symmetry …
Is it required in such a case to enter the data in P1 so GULP will not modify the coordinates ??

Btw. I had used for the problematic MOF file gaff2 force filed and replaced Zn by P to make it functional with gaff2. Atom types generated by my engine automatically … And all was working OK (so the bonds generated by GULP are probabaly OK) … The issue have something to do with UFF (normal UFF have identical problems as mofUFF I see) …

Michal

2

Here are a few point:

  1. Bonds don’t break when there is no force. If there is no force the atoms would stay exactly where they start.
  2. GULP is using symmetry, which is why there are 222 atoms in the asymmetric unit, but 444 in the unit cell under the space group specified.
  3. To see the symmetry operators used within the space group add the keyword “operator” and this outputs the roto-translation operators.
  4. If you want to see things without symmetry to avoid any transformation between the representations then just add the keyword “nosym”.