User Guide
Dependencies
ClayCode is compatible with UNIX operating systems.
It relies on the following python libraries: NumPy (1.21.2), Pandas (1.3.4) and MDAnalysis (2.0.0).
Furthermore, solvent molecules and ions are added as GROMACS subprocesses. Therefore, in order to execute builder, a local GROMACS installation is required.
Data files
The data files store information necessary to construct the clay structures for MD simulation.
The files are stored within ClayCode/data/ directory:
ClayCode
│
...
│
└── data
├── FF
│ └── ClayFF_Fe.ff
│ └── Ions.ff
├── MDP
├── UCS
│ ├── D11
│ ├── D21
│ └── LDH31
└── user
where:
data/FFcontains force fields files, as dictated by GROMACS format, currently included: - ClayFF force field12 (with added Fe parameters based on personal communication with Andrey Kalinichev) in a directoryClayFF_Fe.ff, and - Ions by Pengfei Li 34 inIons.ff, default is IOD-type, HFE and CN also included.data/UCScontains unit cell structures in .GRO format and their corresponding .ITP, topology assigned to ClayFF force field. The files are grouped per type, whereD21us dioctohedral 2:1 clay,D11is dioctohedral 1:1 andLDH31is a layered double hydroxide. To include new UCs, see Adding Unit Cells.data/MDPcontains GROMACS version-specific .MDP files for energy minimisation and equilibration.data/userreserved for user files.
Clay Composition
The file in .CSV format containing the reduced unit cell structure, including partial atomic occupancies, charge balancing ions and layer charges for each clay listed.
See full details in the Input files: CSV
It is also possible to supply clay composition within the .YAML input only. See Pyrophyllite as an example
Input Parameters
System specification for the set-up are done given in .YAML format. See full details in Input files: YAML
Parameters
Output
See Output files
Adding Unit Cells
Use of ClayCode should not be dictated only by the Unite Cells provided with this release. To add a new unit cell, one needs to:
1 - Obtain a crystal structure.
We recommend downloading .cif from the American Mineralogist Crystal Structure Database.
2 - Convert it to full occupancy expanded structure .gro (or .pdb).
We recommend using one of the the following OpenBabel, Avogadro5 (not Avogadro2) or Mercury by CCDC (licence needed). We prefer Avogadro.
3 - Manually rename the atoms in the .gro to have unique names.
4 - Create an include topology file (.itp), please reffer to GROMACS manual.
Assign each unique atom name in the .gro to an atom type, as given in the ClayFF.ff/atomtypes.atp:
hw 1.008 ; water hydrogen
ho 1.008 ; hydroxyl hydrogen
ow 16.00 ; water hydrogen
oh 16.00 ; hydroxyl oxygen
ob 16.00 ; bridging oxygen
obos 16.00 ; bridging oxygen with octahedral substitution
obts 16.00 ; bridging oxygen with tetrahedral substitution
obss 16.00 ; bridging oxygen with double substitution
ohs 16.00 ; hydroxyl oxygen with substitution
st 28.09 ; tetrahedral silicon
ao 26.98 ; octahedral aluminum
at 26.98 ; tetrahedral aluminum
mgo 24.31 ; octahedral magnesium
mgh 24.31 ; hydroxide magnesium
cao 40.08 ; octahedral calcium
cah 40.08 ; hydroxide calcium
feo 55.85 ; octahedral iron (III)
fe2 55.85 ; octahedral iron (II)
lio 6.941 ; octahedral lithium
Example UC.gro and UC.itp
A unit cell for Dioctohedral 1:1 (Kaolinite-type) with stocheometery D101.gro:
Dioctahedral 1:1 unit cell 1
34
1D101 AO1 1 0.061 0.433 0.332
1D101 AO2 2 0.321 0.283 0.332
1D101 AO3 3 0.320 0.880 0.332
1D101 AO4 4 0.064 0.730 0.332
1D101 ST1 5 0.237 0.749 0.065
1D101 ST2 6 0.500 0.594 0.067
1D101 ST3 7 0.493 0.301 0.065
1D101 ST4 8 0.244 0.147 0.067
1D101 OB1 9 0.225 0.751 0.226
1D101 OB2 10 0.255 0.135 0.227
1D101 OB3 11 0.258 0.000 0.000
1D101 OB4 12 0.359 0.651 0.021
1D101 OB5 13 0.360 0.236 0.001
1D101 OB6 14 0.480 0.304 0.226
1D101 OB7 15 0.510 0.582 0.227
1D101 OB8 16 0.002 0.447 0.000
1D101 OB9 17 0.100 0.204 0.021
1D101 OB10 18 0.104 0.683 0.001
1D101 OH1 19 0.223 0.413 0.232
1D101 OH2 20 0.123 0.581 0.433
1D101 OH3 21 0.164 0.855 0.431
1D101 OH4 22 0.162 0.306 0.434
1D101 OH5 23 0.480 0.860 0.232
1D101 OH6 24 0.379 0.134 0.433
1D101 OH7 25 0.420 0.408 0.431
1D101 OH8 26 0.420 0.753 0.434
1D101 HO1 27 0.530 0.940 0.233
1D101 HO2 28 0.410 0.129 0.527
1D101 HO3 29 0.400 0.434 0.522
1D101 HO4 30 0.137 0.264 0.519
1D101 HO5 31 0.272 0.497 0.233
1D101 HO6 32 0.150 0.576 0.527
1D101 HO7 33 0.136 0.880 0.522
1D101 HO8 34 0.400 0.712 0.519
0.51540 0.89420 0.63910
and corresponding D101.itp:
[ moleculetype ]
; name nrexcl
D101 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 KAO rtp KAO q 0.0
1 ao 1 D101 AO1 1 1.575 26.98 ;
2 ao 1 D101 AO2 2 1.575 26.98 ;
3 ao 1 D101 AO3 3 1.575 26.98 ;
4 ao 1 D101 AO4 4 1.575 26.98 ;
5 st 1 D101 ST1 5 2.1 28.09 ;
6 st 1 D101 ST2 6 2.1 28.09 ;
7 st 1 D101 ST3 7 2.1 28.09 ;
8 st 1 D101 ST4 8 2.1 28.09 ;
9 ob 1 D101 OB1 9 -1.05 16 ;
10 ob 1 D101 OB2 10 -1.05 16 ;
11 ob 1 D101 OB3 11 -1.05 16 ;
12 ob 1 D101 OB4 12 -1.05 16 ;
13 ob 1 D101 OB5 13 -1.05 16 ;
14 ob 1 D101 OB6 14 -1.05 16 ;
15 ob 1 D101 OB7 15 -1.05 16 ;
16 ob 1 D101 OB8 16 -1.05 16 ;
17 ob 1 D101 OB9 17 -1.05 16 ;
18 ob 1 D101 OB10 18 -1.05 16 ;
19 oh 1 D101 OH1 19 -0.95 16 ;
20 oh 1 D101 OH2 20 -0.95 16 ;
21 oh 1 D101 OH3 21 -0.95 16 ;
22 oh 1 D101 OH4 22 -0.95 16 ;
23 oh 1 D101 OH5 23 -0.95 16 ;
24 oh 1 D101 OH6 24 -0.95 16 ;
25 oh 1 D101 OH7 25 -0.95 16 ;
26 oh 1 D101 OH8 26 -0.95 16 ;
27 ho 1 D101 HO1 27 0.425 1.008 ;
28 ho 1 D101 HO2 28 0.425 1.008 ;
29 ho 1 D101 HO3 29 0.425 1.008 ;
30 ho 1 D101 HO4 30 0.425 1.008 ;
31 ho 1 D101 HO5 31 0.425 1.008 ;
32 ho 1 D101 HO6 32 0.425 1.008 ;
33 ho 1 D101 HO7 33 0.425 1.008 ;
34 ho 1 D101 HO8 34 0.425 1.008 ;
[ bonds ]
; i j funct length force.c.
19 31 1 0.1 463532.808
20 32 1 0.1 463532.808
21 33 1 0.1 463532.808
22 30 1 0.1 463532.808
23 27 1 0.1 463532.808
24 28 1 0.1 463532.808
25 29 1 0.1 463532.808
26 34 1 0.1 463532.808
-
Randall T. Cygan, Jian Jie Liang, and Andrey G. Kalinichev. Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field. Journal of Physical Chemistry B, 108(4):1255–1266, 1 2004. doi:10.1021/JP0363287. ↩
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Randall T. Cygan, Jeffery A. Greathouse, and Andrey G. Kalinichev. Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces. Journal of Physical Chemistry C, 125(32):17573–17589, 8 2021. doi:10.1021/ACS.JPCC.1C04600. ↩
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Pengfei Li. Advances in metal ion modeling. Michigan State University, 2016. ↩
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Madelyn Smith, Zhen Li, Luke Landry, Kenneth M Merz Jr, and Pengfei Li. Consequences of overfitting the van der waals radii of ions. Journal of Chemical Theory and Computation, 19(7):2064–2074, 2023. doi:10.1021/acs.jctc.2c01255. ↩
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