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The computational modeling tool for custom atomistic model of calcium-silicate-hydrates (C-S-H)

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csh4lmp

A computational modeling tool for full atomistic modeling of calcium-silicate-hydrates used in the paper "Bridging the gap between NMR measured mean silicate chain length and nano-scale silicate polymorphism of calcium silicate hydrates.," Yuan Chiang, Shu-Wei Chang, Cement and Concrete Research, 140, 106268.

CSH

Calcium-silicate-hydrates (C-S-H) is the main binding materials in the cement hydrates. To date, its atomistic configuration remains a conundrum and under extensive discussion. (Qomi et al. Nat. Comm.) (Kumar et al. ACS. JPCC.) The understanding of nanoscale silicate tetrahedral vacancies in C-S-H polymorphs is absent from previous literature and lack a handy tool to build the full atomistic model of C-S-H with tailored compositions. csh4lmp realizes atomic structure modification through removing silciate monoxdide (SiO), appending hydrogen (H), and inserting water molecules (H2O) based on the anhydrous supercell of Hamid's mineral 11-Å tobermorites.

Yuan Chiang (CY) Mar/2019 @ NTUCE

relaxation

Citing

If you use this code in your work, please cite the associated paper:

Chiang, Y., & Chang, S. W. Bridging the gap between NMR measured mean silicate chain length and nano-scale silicate polymorphism of calcium silicate hydrates. Cement and Concrete Research, 140, 106268.

Or cite by BibTex:

@article{chiang140bridging,
  title={Bridging the gap between NMR measured mean silicate chain length and nano-scale silicate polymorphism of calcium silicate hydrates},
  author={Chiang, Yuan and Chang, Shu-Wei},
  journal={Cement and Concrete Research},
  volume={140},
  pages={106268},
  publisher={Elsevier}
  doi={https://doi.org/10.1016/j.cemconres.2020.106268}
}

Nomenclature and color for atoms

Type Name Element Color
1 O (oxygen) oxygen red
2 Ca (intralayer calcium) calcium blue
3 Si (silicon) silicon brown
4 H (hydrogen) hydrogen white
5 Oh (hydroxyl oxygen) oxygen yellow
6 Ow (oxygen in water) oxygen cyan
7 Cw (interlayer calcium) calcium magenta
8 Hw (hydrogen in water) hydrogen white
9 Ob (bridging oxygen) oxygen purple

Build

make -f Makefile

Command

  • I/O : input and output of LAMMPS data file

input

	< [input file name]

output

	> [output file name] hint (y/n)
  • add water : add water molecules to current model
	-aw add [#] [typeO] [typeH]        
syntax definition
# addition number of water molecules
typeO added oxygen type
typeH added hydrogen type
  • delete water : remove all of water molecules
	-dw delete [typeO] [typeH]
syntax definition
typeO removed oxygen type in water molecules
typeH removed hydrogen type in water molecules
  • remove SiO : remove a number of silicate monoxide
	-s number [typeSi] [#] [BT/PT ratio]
syntax definition
typeSi silicon type
# removal number of silicate units
α vacancy ratio of bridging tetrahedra (BT) to pairing tetrahedra (PT)
  • add H : append multiple hydrogen to undercoordinated oxygen
	-h valence (n/#) [typeO] [typeH] [typeO-H] 
syntax definition
n/# n : append hydrogen to meet electroneutrality / number of appended hydrogen
typeO atom type of oxygen to be bonded
typeH atom type of hydrogen to be added
typeO-H bond type of new bonds between O and H
  • delete atom : delete atoms with specific type
	-d delete atom type [type]
syntax definition
type atom type of atoms to be deleted
  • delete bond :
	-d delete bond type [type]                 
syntax definition
type bond type of bonds to be deleted
  • change box :
	-c boundary [pbcx] [pbcy] [pbcz]                 
syntax definition
pbcx pbcy pbcz periodic boundary condition in x y z direction = p (periodic), f (non-periodic)

This command will reset and make the image flag consistent and traslate the atoms whose bonds across boundary

License

MIT

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The computational modeling tool for custom atomistic model of calcium-silicate-hydrates (C-S-H)

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  • C++ 94.1%
  • Batchfile 5.4%
  • Makefile 0.5%