[lammps-users] EAM syntax in data file

I am trying to use EAM with the hybrid pair_style command, but I get an
error that all pair coeffiecients are not set. I was hoping that
someone could take a quick look at my input script and data file to see
if there are any glaring mistakes. I have tried to specify the pair
coefficients within the data file and the two eam files are located in
my working directory. I am using the ptu3 and the auu3 EAM files
located in the potentials directory in the LAMMPS distribution.

Thanks,
Christina Payne
[email protected]

Here is the input file...

units real
neigh_modify delay 5 every 1
boundary p p f

atom_style hybrid full eam
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic

pair_style hybrid lj/charmm/coul/long 8 10 eam
pair_modify mix arithmetic
kspace_style pppm 1e-4
kspace_modify slab 3.0

read_data total.data

special_bonds charmm
group platinum type 38
group gold type 39
group mica type 32 33 34 35 36 37 40 41
group water type 1 23
group ions type 31
group dna id <> 1 512
group solution join water ions dna
group surface join mica platinum gold

fix 1 solution nvt 300.0 300.0 100.0
fix 2 all shake 1e-6 500 0 m 1.0 a 61

temperature mobile solution full
velocity all create 300.0 12345678 dist uniform

thermo 1
thermo_style one
thermo_modify temp mobile
timestep 0.0005

restart 10000 restart.equil.a restart.equil.b
dump equil1 all atom 500 dump.atom.equil.1
dump velo1 solution velocity 500 dump.velo.equil.1

run 50000

undump equil1
undump velo1
dump equil2 all atom 500 dump.atom.equil.2.a
dump velo2 solution velocity 500 dump.velo.equil.2.a

timestep 2.0

run 100000

And here is the first part of my data file...

Created by charmm2lammps v1.6.3 on Wed Sep 14 14:28:27 CDT 2005

      134208 atoms
       56639 bonds
       26468 angles
        1594 dihedrals
          48 impropers

          41 atom types
          41 bond types
          74 angle types
         139 dihedral types
           6 improper types

      -0.698 207.86 xlo xhi
      -0.018 144.286 ylo yhi
     -50.403 0.846 zlo zhi

Masses

       1 1.008 # HT
       2 1.008 # HN1
       3 1.008 # HN2
       4 1.008 # HN3
       5 1.008 # HN5
       6 1.008 # HN7
       7 1.008 # HN8
       8 1.008 # HN9
       9 12.011 # CN1
      10 12.011 # CN1T
      11 12.011 # CN2
      12 12.011 # CN3
      13 12.011 # CN3T
      14 12.011 # CN7
      15 12.011 # CN7B
      16 12.011 # CN8B
      17 12.011 # CN9
      18 14.007 # NN1
      19 14.007 # NN2
      20 14.007 # NN2B
      21 14.007 # NN2U
      22 14.007 # NN3
      23 15.9994 # OT
      24 15.9994 # ON1
      25 15.9994 # ON1C
      26 15.9994 # ON2
      27 15.9994 # ON3
      28 15.9994 # ON5
      29 15.9994 # ON6B
      30 30.974 # P
      31 22.98977 # SOD
      32 28.09 # SI
      33 26.98 # AT
      34 26.98 # AO
      35 16 # OB
      36 16 # OH
      37 1.008 # HO
      38 195.08 # PT
      39 196.97 # AU
      40 39.102 # POTM
      41 16 # OTT

Pair Coeffs

       1 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HT
       2 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HN1
       3 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HN2
       4 lj/charmm/coul/long 0.046 1.959977 0.046 1.959977
# HN3
       5 lj/charmm/coul/long 0.046 0.4000135 0.046 0.4000135
# HN5
       6 lj/charmm/coul/long 0.022 2.351973 0.022 2.351973
# HN7
       7 lj/charmm/coul/long 0.028 2.387609 0.028 2.387609
# HN8
       8 lj/charmm/coul/long 0.024 2.387609 0.024 2.387609
# HN9
       9 lj/charmm/coul/long 0.1 3.385415 0.1 3.385415
# CN1
      10 lj/charmm/coul/long 0.1 3.385415 0.1 3.385415
# CN1T
      11 lj/charmm/coul/long 0.1 3.385415 0.1 3.385415
# CN2
      12 lj/charmm/coul/long 0.09 3.385415 0.09 3.385415
# CN3
      13 lj/charmm/coul/long 0.09 3.385415 0.09 3.385415
# CN3T
      14 lj/charmm/coul/long 0.02 4.053589 0.01 3.385415
# CN7
      15 lj/charmm/coul/long 0.02 4.053589 0.01 3.385415
# CN7B
      16 lj/charmm/coul/long 0.056 3.581413 0.01 3.385415
# CN8B
      17 lj/charmm/coul/long 0.078 3.634867 0.01 3.385415
# CN9
      18 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN1
      19 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN2
      20 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN2B
      21 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN2U
      22 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
# NN3
      23 lj/charmm/coul/long 0.1521 3.150574 0.1521 3.150574
# OT
      24 lj/charmm/coul/long 0.12 3.029056 0.12 3.029056
# ON1
      25 lj/charmm/coul/long 0.12 3.029056 0.12 3.029056
# ON1C
      26 lj/charmm/coul/long 0.1521 3.153781 0.1521 3.153781
# ON2
      27 lj/charmm/coul/long 0.12 3.029056 0.12 3.029056
# ON3
      28 lj/charmm/coul/long 0.1521 3.153781 0.1521 3.153781
# ON5
      29 lj/charmm/coul/long 0.1521 3.153781 0.1521 3.153781
# ON6B
      30 lj/charmm/coul/long 0.585 3.830864 0.585 3.830864
# P
      31 lj/charmm/coul/long 0.0469 2.429926 0.0469 2.429926
# SOD
      32 lj/charmm/coul/long 1.8405e-06 3.302027 1.8405e-06
3.302027 # SI
      33 lj/charmm/coul/long 1.8405e-06 3.302027 1.8405e-06
3.302027 # AT
      34 lj/charmm/coul/long 1.3298e-06 4.271236 1.3298e-06
4.271236 # AO
      35 lj/charmm/coul/long 0.1554 3.165541 0.1554 3.165541
# OB
      36 lj/charmm/coul/long 0.1554 3.165541 0.1554 3.165541
# OH
      37 lj/charmm/coul/long 0.0 0.0 0.0 0.0
# HO
      38 eam ptu3
# PT
      39 eam auu3
# AU
      40 lj/charmm/coul/long 0.1 3.33401 0.1 3.33401
# POTM
      41 lj/charmm/coul/long 0.1554 3.165541 0.1554 3.165541
# OTT

Atoms

       1 1 30 1.5 29.2210000 70.6800000 -14.4440000 #
P
       2 1 27 -0.78 30.0930000 71.1100000 -14.2090000 #
ON3
       3 1 27 -0.78 28.3380000 70.8920000 -14.0260000 #
ON3
       4 1 26 -0.57 29.4670000 69.5990000 -15.5970000 #
ON2
       5 1 16 -0.08 28.5310000 68.5070000 -15.7450000 #
CN8B
..... and so on...