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Post-processing a CrystalPredictor search

This document assumes that you have run a CrystalPredictor search with either CrystalPredictor1.9 or CrystalPredictor2.2, run the relevant version of Analyse, run Imperial_Rename if necessary, and have a flder called unique_pool with a series of subfolders each containing a single crystal structure.

• unique_pool
  • 1-1
    • 1.fres
  • 2-2
    • 2.fres
  • etc

The options that you have depend on your molecule.

• If your search was carried out with a rigid molecule (or even multiple rigid molecules), you should run DMACRYS on each structure with the same multipoles file.
• If your search had one or more flexible molecules, you can
  • run a rigid molecule DMACRYS calculation with the multipoles evaluated for each crystal structure separately
  • run DMAFLEXquick on each structure
  • run CrystalOptimizer with a limited number of steps.

Sp_Dmacrys

This is located in /home/cposs/CrystalPredictor1.9/post-processing and is pretty self explanatory. You will need the Sp_Dmacrys_BA.sh submission script that defined the number of structures in each batch and the Sp_Dmacrys_for2.0.8 file, which probably needs updating for the latest version of NEIGHCRYS/DMACRYS.

You will need DMACRYS format files bondlengths, pote.dat, dmacrys.mols and dmacrys.dma, but these could be obtained by running lattice_energy_minimize (available from /home/lsp/minimize_one_crystal_structure on cposs) on one structure with just the DMACRYS release versions of fit.pots and bondlengths.

workflow

workflow is a set of scripts that are designed to run GAUSSIAN (to get the charge density), GDMA and DMACRYS on a set of crystal structures.  It is available from /home/cposs/workflow on cposs and has all the instructions in the README file. You need to check all the scripts to ensure that the calculation is doing what you want it to, because it will run properties and BZ averaged properties if you don't edit it.

lattice_energy_minimize could be used instead, but this doesn't have a built in job manager so is better suited to a single crystal structure.

DMAFLEXquick

This is currently only possible for Z'=1 single component systems.

Before CrystalOptimizer, we had a code called DMAFLEX.  The main differnce between this and CrystalOptimizer was that DMAFLEX would update the intramolecular and multipole models at each step by running GAUSSIAN in full. Now, CrystalOptimizer uses databases, which saves a lot of time.

A very approximate version of DMAFLEX was written as DMAFLEXquick.  The intramolecular changes are determined by rotating the rigid fragments of the molecule and using the intra_1_1.pot file to give the energy, in the same way as CrystalPredictor's minimizer works, and the charge density is given by rotating multipoles from a provided mult_ex.pot file.

Required files

Examples of all the DMAFLEXquick specific files are found in /home/cposs/DMAFLEXquick/files on cposs.

• crysflex
• runcrysflex.csh
• params folder
• dmaflex.input
• bondlengths
• dmacrys.mols
• mult_ex.pot
• pote.dat
• labels (optional for use with custom potentials)
• intra_1_1.pot

dmaflex.input

There is are some examples in /home/cposs/CrystalPredictor/OldVersions/CrystalPredictor1.6/post-processing/CrystalOptimizer/examples/ on cposs. The format is quite similar to the crystopt.input file, instructions for which can be found on the CrystalOptimizer webpage.

crysflex

This enters each structure directory in turn, copies all the required files and runs dmaflex. It works on batches of structures, which the user can define.  Multiple batches can be run at once, as long as the structure numbers don't overlap. It also cleans up the files that are created, but if structures fail, it is useful to run with these cleaning lines removed to facilitate finding the problem.

runcrysflex.csh

This is the submission script to run crysflex on the nodes.

dmaflex.input

This is where the parameters for the dmaflexquick minimization are set.

DMACRYS input files

bondlengths, dmacrys.mols and pote.dat are the usual format DMACRYS input files. bondlengths and pote.dat can be obtained from the DMACRYS Release bundle, and dmacrys.mols can be generated by a run of lattice_energy_minimize (see above). mult_ex.pot is the file in the format produced by gdma, and NOT with the NEIGHCRYS atom labels as written by gdmaneighcrys. THis can aso be obtained using lattice_energy_minimize.

intra_1_1.pot

This is the file used in CrystalPredictor. If you have a multicomponent system, DMAFLEXquick currently does not work. Similarly, it cannot work with multiple torsion groups. If you have split your molecule into torsion groups in order to run fewer ab initio calculations, you could combine the intra_1_1.pot and intra_1_2.pot files to one file, but only if there are 4 or fewer torsion angles in total.

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