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pyCSH: automated generation of realistic bulk calcium silicate hydrate (C-S-H) structures.

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# pyCSH

**pyCSH** is a  Python code for the automated generation of realistic bulk calcium silicate hydrate (C-S-H) structures, based on the brick model introduced by Kunhi Mohamed et al [1].

[1] A. Kunhi Mohamed, S.C. Parker, P. Bowen, S. Galmarini. An atomistic building block description of C-S-H - Towards a realistic C-S-H model, Cement and Concrete Research 107 (2018) 221–235. https://doi.org/10.1016/j.cemconres.2018.01.007.

If you use this code, please cite the following article:

Ziga Casar, Jon López-Zorrilla, Hegoi Manzano, Eduardo Duque-Redondo, Aslam Kunhi Mohamed, Karen Scrivener, Paul Bowen. pyCSH: Automated atomic-level structure generation of bulk C-S-H and investigation of their intrinsic properties. Cement and Concrete Research 183 (2024). https://doi.org/10.1016/j.cemconres.2024.107593

# License
 
Copyright (C) 2024  Jon López-Zorrilla (jon.lopezz@ehu.eus), Ziga Casar

**pyCSH** is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, you can obtain it from https://www.gnu.org/licenses/old-licenses/gpl-2.0.html.

# Installation and usage

The only requirement for the usage of **pyCSH** is having access to Python 3, with the Numpy package installed. The executable of the code is `main_brick.py`:

python3 main_brick.py

The parameters that control the generated CSH models are defined in `parameters.py`, and are the following:

- `seed`: **Optional**. Default : 1123
   Seed for the random number generator.
   
- `shape`: **Required**
  Shape of the supercell of defective tobermorite 14 A. Tuple of the shape (Nx, Ny, Nz).
  
- `Ca_Si_ratio`: **Required**
Target Ca/Si ratio of the CSH model.

- `W_Si_ratio`: **Required**
Target water/Si ratio of the CSH model.

- `prefix`: **Optional**. Default: 'input'
  Name of the output files.
 
- `N_samples`: **Required**
Number of structures to be generated.

- `make_independent`: **Optional**. Default: False
  Whether to ensure that none of the structures are different spatial arrangement of the same unit cells or not.

- `offset_gaussian`: **Optional**. Default: False
  If True, some preliminary calculations will be done in order to impose more strictly that the amount of Ca-OH and Si-OH are closer to the experimental values.

- `width_Ca_Si`: **Optional**. Default: 0.1
Width of the gaussian used for sampling the Ca/Si ratio of each of the unit cells that compose the total supercell.  Smaller values (e.g. 0.01) will  lead to ratios closer to the target, but might cause the code to fail.

- `width_SiOH`: **Optional**. Default: 0.08
Width of the gaussian used for sampling the Si-OH/Si ratio.

- `width_CaOH`: **Optional**. Default: 0.04
Width of the gaussian used for sampling the Ca-OH/Ca ratio.

- `create`: **Required**.
True if you want to generate new structures, False, if other modes are required. See `check` and `read_structure`.

- `check`: **Optional**. Default: False
If True, a prelimilary check for a wide range of Ca/Si ratios will be performed, in order to show the accuracy of the generated models for the selected parameters with respect to the Ca/Si ratio, water/Si ratio etc.

- `read_structure`: **Optional**. Default: False
If True, handmade brick code will be read from the end of the parameters file.
	- `surface_from_bulk`: **Optional**. Default: False.
If True, the handmade structure will be transformed to a surface  in the **z** dimension by adding upper (">Lo", ">Ro") and lower ("<Lo", "<Ro") chains.
	- `surface_separation`: **Optional**. Default: False
	  Approximate distance between the layers of CSH surfaces.
	 
- `write_lammps`: **Optional**. Default: True
Write a `.data` LAMMPS data file for each of the structures.

- `write_lammps_erica`: **Optional**. Default: True
Write a `.data` LAMMPS data file for each of the structures, with core-shell, bonds and angle information to use with EricaFF.

- `write_vasp`: **Optional**. Default: True
Write a `.vasp` VASP data file for each of the structures.

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