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Merge pull request #25 from ramayo223/main
add particle_rugosity
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‎scripts/ReadMe.md‎

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@@ -26,6 +26,9 @@ This folder contains scripts submitted by users or CCDC scientists for anyone to
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### Create GAUSSIAN Input
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- Create GAUSSIAN input file (`.gjf`) for a given CSD refcode or `.mol2` file.
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### Particle Rugosity
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- Calculates the simulated BFDH particle rugosity weighted by facet area.
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## Tips
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A section for top tips in using the repository and GitHub.
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### Searching tips:

‎scripts/particle_rugosity/ReadMe.md‎

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# Particle Rugosity
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## Summary
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Simulates the particle shape of the given crystal structure using BFDH mophology
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prediction, then calculates the particle rugosity by determining the rugosity
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of the facets and calculating the weighted average (by facet area).
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### Relevance
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Rugosity is considered to be a factor in nucleation, with rougher crystal surfaces
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having higher energies and being generally less stable. This property has been used
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in rationalizing the relative stability or probability of forming one polymorph
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(or putative crystal structure from Crystal Structure Prediction, CSP) over another.
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Using a protocol similar to that reported by [Cruz-Cabeza and colleagues](https://doi.org/10.1002/anie.202006939) this script
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takes a crystal structure or refcode as an argument and will use the CCDC BFDH
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morphology module to simulate the predicted particle shape. The facet hkl planes are
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then obtained and the rugosity of these planes is calculated using the [CCDC rugosity function](https://downloads.ccdc.cam.ac.uk/documentation/API/descriptive_docs/particle.html) (including a scan of
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different offsets from the origin to identify the minimum rugosity of that crystal
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plane). Finally, the total particle rugosity is calculated by weighted average
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according to the facet surface areas.
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## Requirements
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- Tested with CSD Python API version 3.7.9 on Linux and Windows
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- ccdc.particle
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- ccdc.morphology
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## Licensing Requirements
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- CSD-Core, CSD-Particle
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## Instructions on Running
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### Linux command line
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- load the CSD Python API Miniconda environment
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- call Python to read the script, add the crystal structure refcode or filename (local file)
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~~~
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$ python particle_rugosity.py AABHTZ
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The crystal structure AABHTZ has been loaded
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Calculating particle rugosity ...
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AABHTZ particle rugosity: 1.507
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~~~
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OR
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~~~
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$ python particle_rugosity.py AABHTZ.cif
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~~~
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- results are printed and can be redirected to be saved in an output file
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~~~
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$ python particle_rugosity.py AABHTZ > AABHTZ_rugosity.out
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~~~
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### Windows CSD Python API
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- move the particle\_rugostiy.py file to the CCDC\Python\_API\_(year)\ folder
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- to determine where this is on your computer, start the CSD Python API and enter the following commands
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~~~
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>>> import os
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>>> wd = os.getcwd()
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>>> print(wd)
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C:\Program Files\CCDC\Python_API_2022\
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~~~
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the last line is the folder location where you need to move the particle\_rugostiy.py file
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- now the script can be run in the CSD Python API to calculate the rugosity of any CSD entry using:
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~~~
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>>> from particle_rugosity import particle_rugosity
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>>> particle_rugosity('AABHTZ')
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The crystal structure AABHTZ has been loaded
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Calculating particle rugosity ...
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AABHTZ particle rugosity: 1.507
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~~~
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OR
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- if you want to run your own crystal structures, make a folder (eg. rugosity_calc) in Python_API_(year), and add your
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crystal structure file to that folder
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- modify the argument to include the file path
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~~~
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>>> particle_rugosity('rugosity_calc/AABHTZ.cif')
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The crystal structure rugosity_calc/AABHTZ.cif has been loaded
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Calculating particle rugosity ...
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rugosity_calc/AABHTZ.cif particle rugosity: 1.507
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~~~
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## Author
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_R. Alex Mayo_ 2023
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> For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](mailto:support@ccdc.cam.ac.uk)

‎scripts/particle_rugosity/particle_rugosity.py‎

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# script for calculating the particle rugosity for a given crystal structure (.cif in local working directory, or refcode of a CSD entry)
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# requires a CCDC license, and loading of the CSD-python miniconda environment if run from Linux command line
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# import ccdc modules
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import os as opsys
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import argparse
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from ccdc.io import CrystalReader
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from ccdc.particle import Surface
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from ccdc.morphology import BFDHMorphology
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def particle_rugosity(xname):
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# xname is a string, either refcode (eg: 'AABHTZ') or filename (eg: 'AABHTZ.cif')
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# load structure, either (1) crystal structure file in working directory, or
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# (2) CSD refcode
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if opsys.path.isfile(xname):
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try:
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# agrument is crystal structure file
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xtal1 = CrystalReader(xname)
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xtal = xtal1[0]
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xtal1.close
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except:
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print("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file")
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input('Press ENTER to exit')
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quit()
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else:
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try:
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# agrument is a CSD refcode
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xtal = CrystalReader('CSD').crystal(xname)
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except:
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print("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file")
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input('Press ENTER to exit')
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quit()
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print(f"The crystal structure {xname} has been loaded")
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print("Calculating particle rugosity ...")
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# run BFDH morphology to determine predicted particle surface area = hkl planes, and d-spacing of the planes
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morphology = BFDHMorphology(xtal)
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facets = morphology.facets
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f = facets[0]
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all_hkl = [f.miller_indices.hkl for f in facets]
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all_mi = [f.miller_indices for f in facets]
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facets_relA = [morphology.relative_area(mi) for mi in all_mi]
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all_d_hkl = [f.miller_indices.d_spacing for f in facets]
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num_face = len(all_d_hkl)
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# generate surfaces and record rugosity, weigh by particle surface area
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w_part_rug = []
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for i in range(num_face):
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hkl = all_hkl[i]
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rug_list = []
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# check rugosity of crystal plane at 0, 0.25, 0.5, and 0.75 offset from origin
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for split in range(1,5):
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os = all_d_hkl[i] / split
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surface = Surface(xtal, hkl, offset=os)
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rug_list.append(surface.descriptors.rugosity)
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# only take the minimum rugosity value (from all offset calculations) for each hkl
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rug = min(rug_list)
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w_surf_rug = rug * facets_relA[i]
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w_part_rug.append(w_surf_rug)
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# sum weighted rugosity values and print total particle rugosity
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tot_rug = sum(w_part_rug)
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print(f'{xname} particle rugosity: ',round(tot_rug, 3))
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# ================================
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if __name__=='__main__':
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parser = argparse.ArgumentParser()
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parser.add_argument("input_x")
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args = parser.parse_args()
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crystal = args.input_x
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# run code
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particle_rugosity(crystal)
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