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Control and Prediction of the Organic Solid State

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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 covelent 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

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 minimisation 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 minimised 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.

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