[CPMD-list] Help with molecular crystals

[mkosmows]

Dear CPMD community:
 
I'm trying to do a geometry optimization of a 
molecular crystal (with 2 molecules per cell).  I 
entered the literature data into rpluto, filled the 
unit cell, and got rid of the atoms outside the unit 
cell.  So I have one whole molecule and a bunch of 
lonely atoms due to the way the molecules pack into 
the cell.
 
I chose the cell symmetry based on the geometry of 
the cell (all angles 90 degrees, so orthorhombic) and 
the point group based on the point group of the space 
group.
 
The results were rather bizarre.  There were many 
assumed bonds that made no sense and the geometry was 
very much distorted from observed.
 
The next thing I tried was to manually CHANGE BONDS.  
This got rid of wrong bonds, but failed to add the 
right bonds that were not assumed.  These bonds are 
the bonds that end up being spread across the ends of 
the cell due to packing.  (In one cell these would be 
from two different molecules).
 
I then tried to use two whole molecules even though 
they had atoms outside of the cell but got "Failure 
to symmetrise coordinates," leading to early 
termination.  If anyone knows how to properly set up 
molecular crystals I would appreciate hearing about 
it.
 
I'm using a 40ry cutoff with the Goedecker 
pseudopotentials downloaded from CPMD.org.
 
I am also getting several ODIIS insufficient 
progress, reset messages throughout each run.  I'm 
still trying to understand what the ODIIS is and any 
assistance in how to properly set the ODIIS variable 
would be nice!
 
Thank's,
 
Mark Kosmowski

Chemistry Department
Syracuse University
mkosmows at syr.edu