rusta... at gmail.com
Wed Oct 23 06:49:46 CEST 2013
The ALMO methods need to know how your system is partitioned into
molecules. The last column in the coordinate file tells CP2K to call the
partitioning routine. Therefore, the last column is required for all ALMO
CP2K works with arbitrary molecule names (i.e. you can replace H2O with
SECRET_MOLECULAR_INGREDIENT_OF_COCA_COLA without any change in the
results). The actual partitioning is done automatically based on distances
thresholds, controlled by keywords in the following section:
CP2K_INPUT <http://manual.cp2k.org/trunk/CP2K_INPUT.html> / FORCE_EVAL<http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL.html>
/ SUBSYS <http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS.html>
As far as I understand the partitioning code collects all atoms with a
unique molecule name (e.g. all atoms with H2O) and tries to partition this
set into individual molecules based on distance thresholds. It does this
for all unique molecule names.
Therefore, if you are not satisfied with automatic partitioning:
1. assign unique molecule names (MOL1, MOL2, MOL3) to split large molecules
into smaller ones,
2. set BONDLENGTH_MAX to very large value to combine smaller molecules
within a named set to the larger molecule.
On Monday, October 21, 2013 8:45:52 PM UTC-7, Joe Greenstone wrote:
> Modifying regtest-almo/almo-d.inp by removing H2O from the end of included
> coordinate lines but no other changes causes the test to fail saying 'odd
> number of electrons'. Is there functional significance to this molecule
> name/description? If so, what molecule names are supported?
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