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.
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
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}
}| 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 |
make -f Makefile- 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
MIT