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