.. _data_files: Data Files =========== The data files store the information necessary to construct the clay structures for MD simulation. The files are stored in the :code:`ClayCode/package/ClayCode/data` directory: .. code-block:: bash data │ ├── user └── data ├── FF ├── MDP └── UCS Each subdirectory contains the data files of that kind where: - :code:`data/FF/` contains force field files, as dictated by GROMACS format. Currently included is: * :code:`ClayFF.ff` force fields with added Fe parameters based on personal communication with Andrey Kalinichev.\ :cite:p:`Cygan2004, Cygan2021` The interlayer water and solvent water are also included here. * :code:`Ions.ff` force fields by Pengfei Li.\ :cite:p:`Li2016, Smith2023` The default is IOD-type, with HFE and CN also included. - :code:`data/UCS/` contains unit cell structures in .GRO format and their corresponding topology in .ITP format with information taken from the ClayFF force field. Currently included is: * :code:`D21` is dioctohedral 2:1 * :code:`D11` is dioctohedral 1:1 * :code:`T21` is trioctohedral 2:1 To include new UCS data see :ref:`Adding Unit Cells `. - :code:`data/MDP/` contains version-specific GROMACS .MDP files for energy minimisation and equilibration. - :code:`user/` reserved for user files. .. _adding_ucs: Adding Unit Cells ------------------ Use of ClayCode should not be dictated only by the Unit Cells provided with this release. To add a new unit cell, one needs to: #. Obtain a crystal structure. We recommend downloading a .cif file from the `American Mineralogist Crystal Structure Database`_. #. Convert it to a full occupancy expanded structure (.gro or .pdb). We recommend using one of the the following: `OpenBabel`_, `Avogadro`_\ :cite:p:`Thanwell2012` (not Avogadro2) or `Mercury by CCDC`_ (licence needed). #. Manually rename the atoms in the .gro to have unique names. #. Create an "include topology" file (.itp). Please refer to the `GROMACS manual`_ and assign each unique atom name in the .gro to an atom type, as given in :code:`ClayFF.ff/atomtypes.atp`. .. _`American Mineralogist Crystal Structure Database`: http://rruff.geo.arizona.edu/AMS/amcsd.php .. _`OpenBabel`: http://openbabel.org/wiki/Main_Page .. _`Avogadro`: https://avogadro.cc/ .. _`Mercury by CCDC`: https://www.ccdc.cam.ac.uk/solutions/software/mercury/ .. _`GROMACS manual`: https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html ClayFF.ff/atomtypes.atp ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: bash 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: bash 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 Example UC.itp ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: bash [ 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 .. bibliography:: :style: plain :filter: False Cygan2021 Cygan2004 Li2016 Thanwell2012 Smith2023