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

csh4lmp

Introduction

Calcium-silicate-hydrates (C-S-H) is the main binding materials in the cement hydrates. To dates, its atomistic configuration remains uncertain and is under extensive discussion. Nat. Comm. ACS. JPCC. However, a straightforward model construction method is still absent and lack of a handy tool to build the atomic model of C-S-H with the tailored compositions. csh4lmp realized the direct modeling through removing silciate units (SiO2), appending hydrogen (H), and inserting water molecules (H2O) based on the anhydrous supercell of mineral tobermorites. This code fulfil the gap between the stoichimetry, defects distribution and topological relationship in the atomic scale.

Yuan Chiang (CY) Mar/2019 @ NTUCE

relaxation

removal regime 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.

Nomenclature and Color Convention

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 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 BT/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] [pbc] [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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