CPOSS Home
Project Background
Project
publications
Other project publicity
DMACRYS
The Computational Database
The Experimental
Database
Personnel
PDRA & PhD
Opportunities
UCL Home
UCL Chemistry Home
|
Worked example of a lattice energy minimisation, starting from a crystal
structure, to illustrate requirements to use DMACRYS
Programs supplied in DMACRYS package are in green,
those from other sources in red
Example files have .txt file endings, so they can be viewed with most web browsers. The example is 14.press_4FT from the test-suite.
1. Obtain crystal structure in .res (shellx) format.
Can be obtained from Cambridge Structural Database by choosing to
save in this format within Mercury.
If necessary, edit to have entire molecules in asymmetric unit. |
4FTHP.res |
2. Define covalent bonds specification.
Use a supplied bondlengths file from one of the provided test suite examples, or create your own, defining the maximum covalent bond interaction between every pair of bound atom types. |
bondlengths |
3. Define the molecular axis system.
Set up the molecular axis system as descibed in the manual. more details
|
dmacrys.mols |
4. Obtain molecular coordinates in local axis system,
using NEIGHCRYS.
Running NEIGHCRYS (if necessary adjusting the lengths of any bonds to hydrogen in X-rays structures
to standard neutron values) with these files
produces a *.dmain input file for
DMACRYS, without the intermolecular
potential. Extract the molecular structure in the correct axis system
from fort.21, by editing the section
on the molecule into *.geom, using
the co-ordinates in Angstrom. more details
Notes on using the Williams potential |
mol.geom |
5. Run ab initio calculation on the experimental molecular
structure
Edit the structure from *.geom into
a GAUSSIAN input file *.com.
Run a e.g. MP2 631G(d,p) calculation at that geometry, ensuring
that you save the charge density (*.Fchk) file. |
Density.com |
6. Analyse the charge density to obtain the distributed multipole
model. Use GDMA2 to analyse
the Test.Fchk and obtain the set
of atomic multipoles as specified by gdma2_MP2.dat
to give gdma.dma. Since GAUSSIAN
strips off the atom identifier information, it is necessary to restore
this using gdmaneighcrys and the
*.geom to create a *.dma
file containing the atom labels, coordinates and atomic multipoles
relative to the local axis system. |
gdma2_MP2.dat (notes)
gdma.dma
dmacrys.dma |
7. Set up and run the lattice energy minimisation. This
requires another run of NEIGHCRYS
to set up a *.dmain file, as in (4)
but also supplying the *.dma file
to define the electrostatic model, and a MODEL.pots
file containing the parameters for the Buckingham repulsion-dispersion
potential (parameters for both the FIT potential and the Williams01 potential are provided with the programme release). Submit DMACRYS to minimise
within the value of MAXI iterations that you specify. (Note that
to use the Williams 2001 potential, it is necessary to adapt the
procedure, including the calculation of the multipoles, to allow
for the hydrogen sites not corresponding to the proton positions.) |
pote.dat
|
8. Check the results for a true minimum. Ensure that
the minimization is VALID and that it has converged to a true minimum,
rather than a transition state. In the latter case, the minimization
should be re-run removing the symmetry element that gave rise to
the negative eigenvalue (see example 16.symmred_PAPTUX in the test suite). The minimized structure in .res format
(fort.16) can be compared with the input structure in Mercury.
|
|
9. Calculating second derivative properties.
It is important to start from an already minimized crystal structure, and run NEIGHCRYS again to generate a new *.dmain file. Then edit the *.dmain to use the STAR
PROP command and run DMACRYS for accurate second derivative properties. See examples 11.properties_CBMZPN, 12.properties_DCLBEN, and 13.properties_FINVAZ of the test suite for more details. |
|
Note that there are many possible other variations on the use of DMACRYS,
as demonstrated by publications using its predecessor DMAREL. Full specifications
and examples are given in the manuals and test suite examples.
|