Lattice energy minimization workflow![]() |
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Workflow for minimizing the lattice energy of a crystal structureThe DMACRYS distribution includes a test suite of examples. These are available on the UCL Chemistry Clusters in /home/cposs/DMACRYS/test_suite/2.3.1.1/. Example input files should be taken from these. Automated procedureWithin the DMACRYS distribution, there is a utility called lattice_energy_minimize which is within a .tar file with an associated README. This will run on a single .res file within a folder. It automates most of the procedure. The only files you need are:
You will need to edit the start of lattice_energy_minimize to specify whether you want to standardize bonds to hydrogen and specify the level of theory for calculating the multipoles. Manual procedureIt is recommended that you work through one or more examples from the DMACRYS test suite before working on your own files.
Minimizing the experimental crystal structure with the experimental conformationThe files that you need to run DMACRYS are a *.dmain and a fort.20 file. These are generated by NEIGHCRYS, which requires the following files
Additional optional files include
The full NEIGHCRYS manual goes into great detail on how NEIGHCRYS works, and tells you what the answers should be to each of the questions. To obtain the distrubuted multipole analysis of the molecule, the molecule, within the molecular axes defined in your molecular definition file, needs to have its wavefunction generated within GAUSSIAN. If you have a .res file (when working from experimental structure)
Now you have all the files that you need to run a minimization in DMACRYS. Run NEIGHCRYS again, answering all the question in full. Then run DMACRYS on the resulting *.dmain file. Minimizing the experimental crystal structure with the gas phase optimized conformationIf you have already carried out the minimization with the experimental conformation, you already have a starting point for the optimization of the molecular conformation. Copy an example input file for GAUSSIAN from /home/cposs/GAUSSIAN/ex_input_files/ (such as CartOpt.com or ZmatOpt.com) and copy in the comformation from your *.geomG file (or edit the GAUSSIAN input file you to run a geometry optimization). Alternatively, you could draw the molecule in MOLDEN to get a reasonable starting configuration and save that as .xyz to insert into your GAUSSIAN input file. When you have run GAUSSIAN, make a note of the energy of the optimized conformation. This is needed if you have more than 1 gas phase minimum energy well, or if you are later considering carrying out CrystalOptimizer. There are instructions on how to compare energies of different conformations.
The full DMACRYS manual goes into detail on the specific instructions included in the *.dmain, and the format of the *.dmaout that results from a DMACRYS run. It is aimed at advanced users, but you might find some useful insight into a particular problem. Do your answers make sense?The fort.12 is the summary file, and contains most of the useful information from the DMACRYS minimization. This includes the energy. If you are minimizing an experimental structure with the experimental conformation, there should not be very much change in the lattice parameters. The F value is a measure of how similar the ultimate structure is to the original - for a minimization with the experimental conformation this should not be much higher than about 20. If it is higher, then perhaps the experimental structure is wrong or your potential is not appropriate for the system. When you are minmizing an experimental structure with the optimized molecular conformation, the crystal has much more scope for changing. The F value could be considerably higher, but if it is over 100 then it is likely that something has gone wrong. Maybe the conformation in the gas phase is just too different from that in the experimental crystal structure, or there was a mistake in the pasting and the atoms were not correctly ordered. Alternatively, the potential could be very bad for the system you are investigating. The fort.16 is the resulting .res file. It make life a lot simler if you change the name of this to something like fort.16.res or expminopt.res Then you can run /home/cposs/UTILITIES/Compack/compack on this with another .res file (like the original experimental one) to get an RMSD, which is another measure of the differences in the structures. You can also open the file in Mercury and overlay it with the original file, to see visually where the differences are. | |||
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