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OrgdisordCCP-NC have developed the SOD-ORG methodology into a newer code, which is available on their GITHUB repository. It has not been used in the cposs group yet, and no instructions are available here. Using SOD-ORGThe paper describing this programme and how it works is found at http://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/C1CP20249A SOD-ORG is a programme for setting up input files for NEIGHCRYS of supercells of varying compositions. It is useful for investigating the profile of a disordered system. In a crystal structure, if some of the molecules are replaced with a different molecule, or a different conformation of the same molecule, but not in an ordered fashion, then calculating the energy of this system is difficult. To do this, one can calculate the energy of every possible configuration of a supercell of the system, and work out an overall energy for the system from this. In crystals, it is possible to take advantage of the symmetry in order to reduce the magnitude of the problem, for example, in a Z'=1 system, if any single molecule is replaced with an alternative, all the resulting crystals are identical. The energy only needs to be calculated for one of these. SOD-ORG works only for systems with 2 components of disorder. It only works for static disorder. SOD-ORG takes NEIGHCRYS input files for each of the two components, and generates supercells in the form of .res files, along with the associated .mols and .dma files. In May 2022, Jonas Nyman tried using the version of SOD-ORG provided by Louise. He encountered a lot of problems, but with examples provided by Louise and the notes below, he managed to get it working (eventually...). He wrote a summary of the problems encountered, and helpfully gave it back to us. To run SOD-ORGFor each of the components, you need the following files, all with the same stem to the name:
Once you have all your starting files together, run sodorg. An example question/answer dialogue is shown below, with annotation in italics (output that requires no reponse is in normal text)
The files that will come out of this are as follows:
When the supercell is generated, it is important to know the order in which the additional molecules are added. Firstly you have the molecule(s) that appears in the .res file, then those generated by the SYMM lines in turn (hence a different order of the SYMM lines would lead to a different order of the molecules!), then those generated by an inversion centre acting on each of the preceding molecules in turn, then those generated by centring acting on each of the preceding molecules in turn, then those generated by translation along a (if you have more than 1 multiple of the unit cell) acting on each of the preceding molecule in turn, then those generated by translation along b acting on each of the preceding molecule in turn, and finally those generated by translation along c acting on each of the preceding molecule in turn. Reading the seqlist file gives the definitions of each of the supercells generated. Each line will have a number for each molecule, with 2 denoting that the molecule is of the minor component type and 1 denoting it is of the major component type. The degeneracy file shows how many states of each type are present, and the entropy. The merge_?? directory corresponds to the lines in the seqlist and degeneracy files. You can now write a script to run NEIGHCRYS and DMACRYS in each merge_?? directory. There is a script to do this called running in the SOD-ORG directory. It does submit all the DMACRYS jobs for you, which may be a lot of jobs that take a long time, so be aware of this and check that it will be okay with everyone else before you run it. To analyze the outputYou need to write out the energies from the fort.12 files into a file called results. The easiest way is to type
Then run biprep, which gives you a new file called binp. You will need to edit this file and add three lines - one for a ratio of the components and the next two for lower and upper boundary guesses for the fuagcity. When the ratio is near zero, this will be between 0 and 1, while when it gets to near 1, it will tend to infinity. Once you have edited this file, run bisolv to generate a new file called fug (the output of this is also printed to the screen). As long as it has found the value of fugacity (and not output a lot of stars), run ratprops. This gives you 5 numbers
You can append the output of ratprops to a new file called results2, and repeat runs of bisolv and ratprops for a number of different ratios (0.05-0.95 in 0.05 steps is suggested). Then you can import this file into Excel and plot the numbers against the ratio. If you have a system where the two extrmes have the same energy, as in the case of Eniluracil in the paper, you're fine. However, if you have a combination of two different crystal structures, as in the case of the solid solution of chloro- and bromobenzene in the paper, you will need to add mixing terms. Work out what the average lattice enthalpy would be for the crystal structure of the proportions of each line, and subtract this from the actual lattice enthalpy to give the mixing lattice enthalpy. Add the configurational entropy term, TS, to give the mixing free energy. The lowest point in the free energy (or mixing free energy) is the most stable proportion. LimitationsThis cannot be run on systems where the bonds to hydrogen have been standardized in NEIGHCRYS for the charge density calculation. It is hardwired into the NEIGHCRYS run to not standardize bonds to hydrogen, and this results in the dma files having slightly different atomic positions. | |||
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