https://github.com/stefsmeets/topas_tools
Set of scripts for working with Topas
https://github.com/stefsmeets/topas_tools
powder-diffraction profile-refinement structure-refinement topas
Last synced: 4 months ago
JSON representation
Set of scripts for working with Topas
- Host: GitHub
- URL: https://github.com/stefsmeets/topas_tools
- Owner: stefsmeets
- License: mit
- Created: 2015-09-18T16:05:28.000Z (over 10 years ago)
- Default Branch: main
- Last Pushed: 2025-04-16T14:07:00.000Z (about 1 year ago)
- Last Synced: 2025-09-05T06:26:25.039Z (9 months ago)
- Topics: powder-diffraction, profile-refinement, structure-refinement, topas
- Language: Python
- Homepage:
- Size: 306 KB
- Stars: 16
- Watchers: 5
- Forks: 5
- Open Issues: 2
-
Metadata Files:
- Readme: readme.md
- Contributing: CONTRIBUTING.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://pypi.org/project/topas_tools/)
[](https://pypi.org/project/topas_tools/)
[](https://doi.org/10.5281/zenodo.4719228)
# Topas tools
These are set of small scripts and tools that were developed to help with structure refinement (of zeolites in particular) using the program [TOPAS](http://topas-academic.net/).
## topasdiff
Topasdiff is a tool to generate nice looking difference maps. First, output the observed structure factors, and structure in cif format from Topas:
Out_fobs(fobs.hkl)
Out_CIF_STR(structure.cif)
Observed structure factors can be generated using this macro (add this to `C:/topas5/local.inc`):
macro Out_fobs(file)
{
phase_out file load out_record out_fmt out_eqn
{
"%4.0f" = H;
"%4.0f" = K;
"%4.0f" = L;
'"%4.0f" = M;
"%12.4f\n" = (Iobs_no_scale_pks / M)^(0.5);
}
}
Then to calculate the difference map, run the command:
topasdiff structure.cif --diff fobs.hkl
or use the GUI, accessible available via `topasdiff.bat` (Windows). The program will ask for the scale factor provided by TOPAS, and generates an input file for the program superflip (http://superflip.fzu.cz/). Superflip is then used to perform the fourier transform, and generates an `.XPLOR` file that can be visualized using Chimera or VESTA.
Note: There is a bug in Topas where the cif files it outputs cannot be read using CCTBX, because they lack the data header. A work-around is to open `C:/topas5/topas.inc` and modify all instances of:
Out_String("\ndata_")
by:
Out_String("\ndata_topas_cif_out")
## cif2topas
cif2topas transforms a crystal structure into cif format into the corresponding TOPAS code.
Usage:
cif2topas structure.cif
## fh2topas
fh2topas is a script that converts from Fenske-Hall z-matrix to TOPAS code
Usage:
fh2topas zmatrix.fh [n]
Here, `n` is an optional parameter to give the number of molecules to generate. fh2topas will automatically number them to avoid naming conflicts.
## topasrestraints
topasrestraints is a tool that can help with the generation of bond and angle restraints for structure refinement of zeolites with TOPAS. First, generate all bonds by using the TOPAS instruction:
append_bond_lengths
to generate all bonds and angles, including their symmetry codes for the current structure. Copy everything between the curly brackets to a new file called `bonds.txt`, and run:
topasrestraints bonds.txt
This generates a file called restraints.out that contains the restraints that can be added to TOPAS. The script checks for all distances of `1.61 +- 0.4` Angstrom to identify T-O bonds. The program checks the connectivity for every atom, and reports if there is a problem (too many / not enough distances per T-atom). There is no check for symmetrically equivalent connections, so some restraints may be redundant.
## stripcif
stripcif is a tool to clean a cif file from all extra metadata. Essentially it reads a cif file and writes it back to `structure_simple.cif` with just the cell parameters and atomic coordinates.
Usage:
stripcif structure.cif
## expandcell
expandcell is a tool to take a cif file and expand the axes along different directions to form a supercell.
For example:
expandcell structure.cif -z2
will write a cif in `P1` the *z* axis doubled. You can then use a tool like [PLATON](http://www.platonsoft.nl/platon/pl000000.html) to find the right symmetry for this structure (if needed). You can use:
expandcell structure.cif -z2 -s SPGR --shift X Y Z
to force the new a new symmetry on the output. Here `SPGR` is the space group suggested by platon, and `--shift X Y Z` is the suggested origin shift.
The option `-e` can be used to exclude elements from the result.
## make_superflip
This is a very simple tool that asks a couple of questions and writes an input file for superflip.
Usage:
make_superflip
## Requirements
- Python>=3.9
- numpy
- matplotlib
- pandas
- [CCTBX](https://github.com/cctbx/cctbx_project)
- superflip ([superflip.fzu.cz/](http://superflip.fzu.cz/))
## Installation
1. Install [miniconda](https://docs.conda.io/en/latest/miniconda.html) (pick the one suitable for your platform, Python version does not matter here).
2. Install using:
```bash
conda create -n topas_tools -c conda-forge cctbx-base
conda activate topas_tools
pip install topas_tools
```
Or use the environment file:
```bash
conda env create -f environment.yml
conda activate topas_tools
pip install -e .
```
(note that every time you want to use `topas_tools`, you must always activate the environment using `conda activate topas_tools`)
## How to Cite
If you find this software useful, please consider citing it:
- Smeets, S. (2021). topas_tools (Version 1.1.0) [Computer software]. https://doi.org/10.5281/zenodo.4719229