Calcium-silicate-hydrates (C-S-H) is the main binding materials in the cement hydrates. To date, its atomistic configuration remains uncertain and is under extensive discussion. Nat. Comm. ACS. JPCC. A straightforward model construction method is still absent and lack a handy tool to build the full atomistic C-S-H with tailored compositions. csh4lmp realized the 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
This figure shows how to achieve higer Ca/Si ratio through removing silicate units. The atoms in gray color are removed in neutral SiO2 groups including one silicon atom and two oxgygen atoms. Additional hydrogen atoms are appneded to the undercoordinated oxygen atoms. One appended hydrogen atom and one oxygen atom are bonded together and become a hydroxyl group where the oxygen atom turns into a hydroxyl oxygen atom.
| 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 SiO2 : remove multiple silicate units from current models
-s number [typeSi] [#] [BT/PT ratio]
| syntax | definition |
|---|---|
| typeSi | silicon type |
| # | removal number of silicate units |
| BT/PT ratio | ratio of removal number of bridging tetrahedra (BT) to pairing tetrahedra (PT) |
Effect of BT/PT removal ratio on the silicate connectivity indicated through Qn factors
- 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
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