RMCProfile7 [Molecules List Setup]

[kewh5868]

Hello!

I am working in getting my first run setup in RMCProfile7 and am building my .dat file. I am particularly interested in modeling solvation (liquid) structure of various systems and am working to setup a basic use case. My plan is to fit G® 'G®_PDFGui' of liquid DMSO. My starting configuration is a structure file taken from a frozen DMSO unit cell to act as an ordered initial condition. My thought is that I could constrain the translation and rotations of the rigid DMSO molecules to fit the amorphous liquid structure.

Here is my current setup of the MOLECULE :: subsection of the .dat file:

%%%%%%%%
MOLECULE ::
  > ATOM :: O
  > ATOM :: S 1 1.3 1.6 Angstrom
  > ATOM :: C 2 1.7 1.9 Angstrom
  > ATOM :: C 2 1.7 1.9 Angstrom
  > MAXIMUM_MOVES :: 3 3 3 3    %% Not sure how to setup this condition
  > MOVE_PROBABILITIES :: 0.5
  > ROTATION_PROBABILITIES :: 0.5
  > MOLECULE_FILE :: dmso.list     %% Not sure how to format this file?
%%  > MINIMUM_ROTATION :: 0 0 0
%%  > MAXIMUM_ROTATION :: 180 180 180 
%%%%%%%%

- What is the format of the MOLECULE_FILE? Is there an example of this file format somewhere and a tool to help generate this?
Reading molecule list data file: 'dmso.list
Error  >  No atoms collections found in molecule list file!

- How should I setup the MAXIMUM_MOVES, MINIMUM_ROTATION, AND MAXIMUM_ROTATION? I am getting keyword errors for the rotation inputs:
Warning>  Unrecognised keyword: 'MINIMUM_ROTATION'Warning>  Value of unrecognised keyword: '0 0 0'
Warning>  Line number of unrecognised keyword: 28
Warning>  Unrecognised keyword: 'MAXIMUM_ROTATION'
Warning>  Value of unrecognised keyword: '180 180 180'

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RMCProfile version 7b.200
Operating System: macOS Monterey v. 12.0.1
Chip: Apple M1 Max

[y8z-admin]

You can refer to the manual here, https://pv.iris-home.net/s/E0OTM5M for references about the molecule settings.

I think the molecule list file does not have to be there -- the program will be generating the file if it cannot be found.

One thing is the Mac version is not up-to-date so we do expect issues. If you can grab a windows machine, you can use the up-to-date version available via the Dropbox folder for the total scattering school.

We will be working on compiling the program for all platforms soon and I will post a message here once it is available.