mirror of https://github.com/lammps/lammps.git
58 lines
3.4 KiB
Plaintext
58 lines
3.4 KiB
Plaintext
# This ice (1h) unit cell is rectangular and contains 8 water molecules.
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# (Coordinates and cell dimensions converted were from a PDB file.)
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# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362
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import "spce.lt" # <-- define the "SPCE" molecule
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SpceIceRect8 {
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# Create a 3-dimensional array of 8 water molecules
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wat = new SPCE[2][2][2]
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# Array indices will be correlated with position [xindex][yindex][zindex]
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# You can overwrite coordinates of atoms after they were created this way:
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# (Order is not important)
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# atom-ID molecule-ID atomType charge newX newY newZ
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write("Data Atoms") {
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$atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381
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$atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710
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$atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710
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$atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981
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$atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970
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$atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652
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$atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300
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$atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289
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$atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971
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$atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061
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$atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391
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$atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391
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$atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381
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$atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710
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$atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710
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$atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981
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$atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970
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$atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652
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$atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300
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$atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289
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$atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971
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$atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061
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$atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391
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$atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391
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}
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} # IceRect8
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# Credit goes to Martin Chaplin.
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# These coordinates were orignally downloaded from Martin Chaplin's
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# website: http://www.btinternet.com/~martin.chaplin/ice1h.html
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# ... and then they were stretched independently in the xy and z
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# directions in order to match the lattice parameters measured by
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# Rottger et al.,
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# "Lattice constants and thermal expansion of H2O and D2O ice Ih"
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# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648
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# I am using the lattice constants measured at temperature 265K
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# (and pressure=100Torr).
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