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lammps/examples/USER/drude/toluene/in.toluene.nh
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# 250 toluene system for drude polarizability example (Nose-Hoover)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
comm_modify vel yes
group gTOLUENE molecule 1:250
group gCORES type 1 2 3 4 5 6 7
group gDRUDES type 8 9 10 11 12
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gDRUDES create ${vTEMP_D} 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude
fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fINVERSE all drude/transform/inverse
fix fMOMENTUM all momentum 100 linear 1 1 1
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000
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