81 lines
2.4 KiB
Plaintext
81 lines
2.4 KiB
Plaintext
#LAMMPS input file
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#All informations can be find on http://lammps.sandia.gov/
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#choose the system of unit (real, metal, SI...)
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units real
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#define the boundary conditions, periodic here
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boundary p p p
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#define the atom style, bond style and angle style
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atom_style full
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bond_style harmonic
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angle_style harmonic
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atom_modify map array
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#comm_modify cutoff 15
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#atom_modify first water
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#neigh_modify cluster yes
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#choose the interaction between water molecules:
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pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
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pair_modify table 0
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#water model is TIP4P/2005
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#water molecules less than 1nm from each other interact via a cut lennard jones potential
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#water molecules interact via coulomb interactions calculated in real or conjugate space depending on the distance separating molecules
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#define the long-range solver (here for long range coulombic interaction)
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suffix off
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newton on
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kspace_style pppm/tip4p 1.0e-5
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suffix on
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#neighbor 5.0 bin
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#neigh_modify every 1 check yes
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#import the initial position of atoms, the coordinates of the box, etc
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read_data data.spce
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replicate 2 2 2
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#define the pair coeff for LJ interaction
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pair_coeff * * 0.0 0.0
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pair_coeff 1 1 0.1852 3.1589
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#define the coef for water molecule (distances between O-H and angle between H-O-H atoms)
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bond_coeff 1 0.0 0.9572
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angle_coeff 1 0.0 104.52
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#define groups
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group water type 1 2
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#maintain the water molecule rigid
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fix 1 water shake 1.0e-4 200 0 b 1 a 1
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#udate position and velocity each timesteps using constant NVE integration
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fix 2 water nve
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#apply Langevin thermostat on water molecules
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#fix 3 water langevin 300.0 300.0 100.0 123
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#choose how often you want thermodynamic info to be print during the computation
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thermo 1000
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thermo_modify flush yes
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thermo_style custom step etotal ke pe temp evdwl ecoul elong press
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#thermo_modify format float "%.15g"
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#give an initial random velocity to water molecule (corresponding to a temperature equal to 300K)
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velocity water create 300 123
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#print the position of atoms to visualise it with VMD for example
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#dump 4 all atom 1 dump.lammpstrj
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#dump_modify 4 flush yes
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#if $(is_active(package,gpu)) &
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# then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz"&
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# else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
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#choose the timestep, 2fs is a common choice
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timestep 1
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#run during 50000 timestep (0.1 ns)
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run 50000
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