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sjplimp
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# This file contains a unit cell for building graphene and nanotubes
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#
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#
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# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any
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# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg")
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# Surfaces constructed with this unit cell can be flat or curved into tubes.
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# The distance between nearest-neighbor carbon atoms (ie the length of a
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# carbon-carbon bond) is equal to "d" which I set to 1.420 Angstroms.
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#
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# d = length of each hexagon's side = 1.42 Angstroms
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# L = length of each hexagon = 2*d = 2.84 Angstroms
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# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms
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#
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# Consequently, the Lattice-cell vectors for singe-layer graphene are:
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# (2.4595121467478, 0, 0) (aligned with X axis)
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# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d)
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# So, to build a sheet of graphite, you could use:
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# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
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# [10].move(1.2297560733739,2.13,0)
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Graphene {
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2AtomCellAlignX
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{
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# atomID molID atomType charge x y z
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write("Data Atoms") {
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$atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0
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$atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0
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}
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}
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# Now define properties of the Carbon graphene atom
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write_once("In Init") {
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pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
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}
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write_once("Data Masses") {
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@atom:C 12.0
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}
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write_once("In Settings") {
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# i j epsilon sigma
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pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407
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# These Lennard-Jones parameters come from
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# R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
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# Chem Phys Lett, 348:187 (2001)
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# Define a group consisting of only carbon atoms in graphene molecules
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group Cgraphene type @atom:C
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}
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# Notice that the two atoms in the unit-cell above lie in the XY plane.
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# (Their z-coordinate is zero). It's also useful to have a version of
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# this object which lies in the XZ plan. So we define this below:
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2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0)
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} # Graphene
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# ------------ Graphite -----------
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#
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# Note: For graphite: sheets stacked in the Z direction are separated by a
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# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction
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# by a distance of d (1.42 Angstroms). To add additional graphene layers
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# you could use:
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# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
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# [10].move(1.2297560733739,2.13,0)
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# sheet2[*][*].move(0, 1.42, 3.35)
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# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
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# [10].move(1.2297560733739,2.13,0)
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# sheet3[*][*].move(0, -1.42, 6.70)
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# etc...
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# However, to build a thick sheet of graphite, it would
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# be more efficient to use a 4-atom unit cell:
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#
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#Graphene {
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# GraphiteCell {
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# # atomID molID atomType charge x y z
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# write("Data Atoms") {
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# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0
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# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0
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# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35
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# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35
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# }
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# } # GraphiteCell
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#}
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#
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# Then you could create a thick sheet of graphite this way:
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#
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# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0)
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# [10].move(1.2297560733739,2.13,0)
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# [5].move(0,0,6.70)
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# file "spce.lt"
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#
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# H1 H2
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# \ /
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# O
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SPCE {
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write_once("In Init") {
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# -- Default styles (for solo "SPCE" water) --
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units real
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atom_style full
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# (Hybrid force fields were not necessary but are used for portability.)
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pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
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bond_style hybrid harmonic
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angle_style hybrid harmonic
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kspace_style pppm 0.0001
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pair_modify mix arithmetic
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}
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write("Data Atoms") {
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$atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000
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$atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590
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$atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590
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}
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write_once("Data Masses") {
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@atom:O 15.9994
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@atom:H 1.008
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}
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write("Data Bonds") {
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$bond:OH1 @bond:OH $atom:O $atom:H1
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$bond:OH2 @bond:OH $atom:O $atom:H2
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}
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write("Data Angles") {
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$angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
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}
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write_once("In Settings") {
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bond_coeff @bond:OH harmonic 1000.0 1.0
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angle_coeff @angle:HOH harmonic 1000.0 109.47
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pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166
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pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058
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group spce type @atom:O @atom:H
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fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH
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# (Remember to "unfix" fSHAKE during minimization.)
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}
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} # end of definition of "SPCE" water molecule type
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# 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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@ -0,0 +1,13 @@
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This directory contains two LT files corresponding to
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different versions of TIP3P:
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tip3pcharmm.lt # The implementation of TIP3P used by CHARMM (I think).
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tip3p2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model
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# which uses long-range coulombics
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I have not tested these files so I moved them here.
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(If you have tested these files, and they work, or if you have other comments
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or suggestions, feel free to email me at jewett.aij at gmail dot com.)
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Andrew
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2012-10-20
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# file "tip3p2004.lt"
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#
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# H1 H2
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# \ /
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# O
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#
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# I think this is the TIP3P water described in the paper by
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# Daniel J. Price and Charles L. Brooks III
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# J. Chem. Phys., 121(20): 10096 (2004)
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# Specifically I think it refers to the "Model B" version of long-range TIP3P
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# described in the 3rd-to-last column of "Table I", on p.10099.
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TIP3P2004 {
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write_once("In Init") {
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# -- Default styles (for solo "TIP3P2004" water) --
|
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units real
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atom_style full
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pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5
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bond_style hybrid harmonic
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angle_style hybrid harmonic
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kspace_style pppm 0.0001
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pair_modify mix arithmetic
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}
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write("Data Atoms") {
|
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$atom:O $mol:. @atom:O -0.830 0.0000000 0.00000 0.000000
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$atom:H1 $mol:. @atom:H 0.415 0.756950327 0.00000 0.5858822766
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$atom:H2 $mol:. @atom:H 0.415 -0.756950327 0.00000 0.5858822766
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}
|
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|
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write_once("Data Masses") {
|
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@atom:O 15.9994
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@atom:H 1.008
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}
|
||||
|
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write("Data Bonds") {
|
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$bond:OH1 @bond:OH $atom:O $atom:H1
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$bond:OH2 @bond:OH $atom:O $atom:H2
|
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}
|
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|
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write("Data Angles") {
|
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$angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
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}
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write_once("In Settings") {
|
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bond_coeff @bond:OH harmonic 450.0 0.9572
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angle_coeff @angle:HOH harmonic 55.0 104.52
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#########################################################################
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#### There are two choices for for the O-O interactions
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#########################################################################
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#### O-O nonbonded interactions
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# For the 1983 Jorgensen version of TIP3P use:
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# pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507
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# For the 2004 Price & Brooks version of TIP3P use:
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pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188
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#########################################################################
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#### There are three choices for for the O-H and H-H interactions
|
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#########################################################################
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||||
#### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
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pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
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pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic
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#########################################################################
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#### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
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#### If you want to use this, uncomment the following two lines:
|
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# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
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||||
# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
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#########################################################################
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#### 3) The original Jorgensen 1983 parameterization has no OH or HH
|
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# lennard-jones interactions. For this behavior, uncomment these lines:
|
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# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000
|
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# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753
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||||
#########################################################################
|
||||
|
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# Define a group for the tip3p water molecules:
|
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group tip3p type @atom:O @atom:H
|
||||
|
||||
# Optional: Constrain the angles and distances.
|
||||
# (Most implementations use this, but it is optional.)
|
||||
fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
|
||||
# (Remember to "unfix" fSHAKE during minimization.)
|
||||
|
||||
}
|
||||
|
||||
} # "TIP3P2004" water molecule type
|
||||
|
||||
|
|
@ -0,0 +1,91 @@
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# file "tip3p_charmm.lt"
|
||||
#
|
||||
# H1 H2
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||||
# \ /
|
||||
# O
|
||||
#
|
||||
# I think this is the TIP3P water model used by CHARMM (and probably AMBER)
|
||||
# It is (mostly) based on this paper:
|
||||
# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983)
|
||||
|
||||
TIP3Pcharmm {
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles (for solo "TIP3Pcharmm" water) --
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
# I'm not sure exactly which cutoffs distances are traditionally used in
|
||||
# the TIP3P water model used by CHARMM.
|
||||
# (See the Price JCP 2004 paper for a review.)
|
||||
# pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5
|
||||
# Try this instead:
|
||||
pair_style hybrid lj/charmm/coul/charmm 10.0 10.5 10.0 10.5
|
||||
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
pair_modify mix arithmetic
|
||||
}
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000
|
||||
$atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766
|
||||
$atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:O 15.9994
|
||||
@atom:H 1.008
|
||||
}
|
||||
|
||||
write("Data Bonds") {
|
||||
$bond:OH1 @bond:OH $atom:O $atom:H1
|
||||
$bond:OH2 @bond:OH $atom:O $atom:H2
|
||||
}
|
||||
|
||||
write("Data Angles") {
|
||||
$angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:OH harmonic 450.0 0.9572
|
||||
angle_coeff @angle:HOH harmonic 55.0 104.52
|
||||
|
||||
#########################################################################
|
||||
#### There are two choices for for the O-O interactions
|
||||
#########################################################################
|
||||
#### O-O nonbonded interactions
|
||||
# For the 1983 Jorgensen version of TIP3P use:
|
||||
pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507
|
||||
# For the 2004 Price & Brooks version of TIP3P use:
|
||||
# pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188
|
||||
#########################################################################
|
||||
#### There are three choices for for the O-H and H-H interactions
|
||||
#########################################################################
|
||||
#### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter
|
||||
pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
|
||||
pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic
|
||||
#########################################################################
|
||||
#### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter,
|
||||
#### If you want to use this, uncomment the following two lines:
|
||||
# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000
|
||||
# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric
|
||||
#########################################################################
|
||||
#### 3) The original Jorgensen 1983 parameterization has no OH or HH
|
||||
# lennard-jones interactions. For this behavior, uncomment these lines:
|
||||
# pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000
|
||||
# pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753
|
||||
#########################################################################
|
||||
|
||||
# Define a group for the tip3p water molecules:
|
||||
group tip3p type @atom:O @atom:H
|
||||
|
||||
# Optional: Constrain the angles and distances.
|
||||
# (Most implementations use this, but it is optional.)
|
||||
fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH
|
||||
# (Remember to "unfix" fSHAKE during minimization.)
|
||||
|
||||
}
|
||||
|
||||
} # "TIP3Pcharmm" water molecule type
|
||||
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
# This file stores complete LAMMPS data for the TraPPE model of saturated
|
||||
# hydrocarbon chains. In this "united-atom" model, each methyl group is
|
||||
# represented by a single atom. Forces between "atoms" are taken from the
|
||||
# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577)
|
||||
|
||||
TraPPE {
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "TraPPE" --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid opls
|
||||
improper_style none
|
||||
pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:CH2 14.1707
|
||||
@atom:CH3 15.2507
|
||||
@atom:CH4 16.3307
|
||||
}
|
||||
|
||||
write_once("Data Angles By Type") {
|
||||
@angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated
|
||||
}
|
||||
|
||||
write_once("Data Dihedrals By Type") {
|
||||
@dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95
|
||||
pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75
|
||||
pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73
|
||||
bond_coeff @bond:saturated harmonic 120.0 1.54
|
||||
angle_coeff @angle:backbone harmonic 62.0022 114
|
||||
dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4
|
||||
}
|
||||
|
||||
} # class TraPPE
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
# This file stores LAMMPS data for the "mW" water model.
|
||||
# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016)
|
||||
#
|
||||
# In this model, each water molecule is represented by a single "mW" particle.
|
||||
# These particles interact with their neighbors via 3-body Stillinger-Weber
|
||||
# forces whose parameters are tuned to mimic directional hydrogen-bonding
|
||||
# in liquid water (as well as hexagonal ice, type II ice, and
|
||||
# low-density super-cooled liquid/amorphous water phases).
|
||||
|
||||
WatMW {
|
||||
write("Data Atoms") {
|
||||
$atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0
|
||||
}
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:mW 18.02
|
||||
}
|
||||
|
||||
write_once("system.in.sw") {
|
||||
mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0
|
||||
}
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "WatMW" --
|
||||
units real
|
||||
pair_style sw
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# --Now indicate which atom type(s) are simulated using the "sw" pair style
|
||||
# -- In this case only one of the atom types is used (the mW water "atom").
|
||||
|
||||
pair_coeff * * sw system.in.sw mW NULL NULL NULL
|
||||
|
||||
# -- Unfortunately LAMMPS itself does not understand molemlate syntax, so
|
||||
# -- the atoms are identified by order in the list, not by name. (The "mW"
|
||||
# -- refers to to an identifier in the system.in.sw file, not watmw.lt.)
|
||||
# -- This command says that the first atom type corresponds to the "mW"
|
||||
# -- atom in system.in.sw, and to ignore the remaining three atom types
|
||||
# -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt.
|
||||
# -- We don't want to use the "sw" force field for interactions involving
|
||||
# -- these atom types, so we put "NULL" there.)
|
||||
# -- Note: For this to work, you should probably run moltemplate this way:
|
||||
# -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt
|
||||
# -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom)
|
||||
}
|
||||
|
||||
# -- optional --
|
||||
|
||||
write_once("In Settings") {
|
||||
group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group)
|
||||
}
|
||||
|
||||
} # WatMW
|
||||
Loading…
Reference in New Issue