MOLPAK![]() |
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Running MOLPAK on xenonThe MOLPAK/DMACRYS process is used to calculate crystal structures for a given rigid molecular probe. MOLPAK (J. R. Holden, Z. Du and H. L. Ammon, J. Comput. Chem., 14, 422-437, 1993) performs the search for crystal structures and DMACRYS (Welch GWA, Karamertzanis PG, Price SL, Leslie M, in preparation ) performs the subsequent lattice energy minimisations on these structures. NEIGHCRYS is a program used to prepare the MOLPAK output for input into DMACRYS. The search and initial minimisation is carried out automatically. If further minimisations are required then they must be re-submitted manually. The analysis of final structures is also performed manually. Ensure .cshrc file has appropriate paths ("cd ~" then "vi .cshrc") File setupBrief descriptions of the files used are given in this webpage.
Queue Submission
*To check on a job while it is running, type "qstat -u userid" (userid is usually your initials) to see which node the job is running on, e.g. comp12. Then type "rlogin comp12", then go to your scratch area using "cd ../../scr/userid" and you will see a directory that has been created for the Molpak run, you can go into this directory and look at the results so far. Use "ls -lt" to check on search progress. Use Script postSearch to move Invalid Structures and Compile Details of Valid StructuresCopy Analysis.csh and the relevant version of Analysis from /home/cposs/ to working directory. Edit Analysis.csh to ensure that it will run the correct version of Analysis. Also, change the arguments, as necessary. The first argument is the number of iterations of DMACRYS that will be carried out. The default is 3 (0 will just discard any structures which were not tru minima in the first run of DMACRYS). The second number is the number of minima that will be kep. The default is 10,000, and this should be more than sufficient. The third number is the cutoff in kJ mol-1 and the default is 15. Of the second and third numbers, the limit that is reached first will stop further structures being kept in stable_list. In the directory, submit Analysis.csh, by typing "qsub Analysis.csh".
It will then compile details of the valid structures in a file that can be read into excel, another file, *_reducedcells, will be produced containing the reduced cell constants (calculated by nbslattice.exe). There will be files containing details for all valid structures (allreducedcells and completespreadsheet) and for each space group individually (e.g. aa_reducedcells and p1). These files will all be moved to a new subdirectory called validStrutcuresForSpreadsheet. Deal with Insufficient IterationsThe current default is to use a maximum of 1000 iterations ("MAXI 1000" in minspec). Rarely, a minimum is not reached in 1000 iterations and the output structure does not represent a lattice energy minimum and is therefore invalid. Structures affected have been moved to moreiterations by the postSearch script; the corresponding dmain files should be resubmitted to DMAREL with a greater value of MAXI, following the method given in Deal with Negative Curvature below. Deal with Negative CurvatureFor structures with negative curvature the minimisation is not valid (a minimum has not been found) and it is necessary to change the step size for the DMAREL calculation to try the minimisation again. These structures have been moved to negativecurv by the postSearch script. Copy changeStep and changeStep.csh to negativecurv. Create a new version of minspec in negativecurv with "MAXD 0.9" instead of "MAXD 0.5". Submit changeStep.csh to the queue. Check for Negative EigenvaluesThese structures have been moved to lowersymm by the postSearch script. This section will be expanded . Compiling Results into SpreadsheetSftp all files in validStructuresForSpreadsheet to your PC. They can be opened in Excel (using the space delimiter option to make sure the numbers are read into columns appropriately; File - Open - all files - click on file - click delimiter - Next - chose space - Finish). Open completespreadsheet in Excel. Then open allreducedcells onto a new worksheet in Excel. Select all (Cntrl A) in the worksheet containing allreducedcells and copy (Cntrl C), then paste (Cntrl V) onto the worksheet containing completespreadsheet. They should line up (i.e. equal numbers of structures in both files), check this is the case. A similar method can be used for each space group in turn. The structures in
each space group can then be grouped to show which are equivalent (made easier
by using the sort command in Excel to compare lattice parameters); and
each group of equivalent structures can be ordered in terms of energy. The lowest
energy structure from each group (for all space groups) can then be compiled
onto a new worksheet, and these unique structures then ordered in terms of energy.
Calculate the volume per molecule for each structure by dividing the final cell volume by the appropriate value of Z for each structure. Construct a scatterplot with final lattice energy on the y-axis and Vol/Z on the x-axis. This may help to decide on likely crystal structures; those towards the bottom left of the plot are more favourable in terms of energy and volume. Further calculations may be used to judge which of the low energy predicted crystal structures are likely to exist. Warnings and known problems
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