Bond_style command when no bonds allowed (src/input.cpp:1347) Last command: bond_style harmonic

hi, I have this problem, I’m trying to perform a simulation using LAMMPS, but I’m getting this error and i don’t know how to solve it, thank’s your help, this is the file .in and .data


data in :

log log.grafe append
units real
atom_style atomic
boundary p p p

pair_style lj/cut 12.500
bond_style harmonic
angle_style hybrid cosine/periodic fourier
dihedral_style harmonic
improper_style fourier

pair_modify tail yes mix arithmetic
special_bonds lj/coul 0.0 0.0 1.0
dielectric 1.0
box tilt large
read_data data.1

Atom Groupings

END Atom Groupings

#dump grafe_dcdmov all dcd 10 grafe_mov.dcd
min_style cg
print “MinStep,CellMinStep,AtomMinStep,FinalStep,Energy,EDiff” file grafe.min.csv screen no
variable min_eval equal 1.00e-06
variable prev_E equal 50000.00
variable iter loop 100000
label loop_min
min_style cg
fix 1 all box/relax aniso 0.0 vmax 0.01
minimize 1.0e-15 1.0e-15 10000 100000
unfix 1
min_style fire
variable tempstp equal (step) variable CellMinStep equal {tempstp}
minimize 1.0e-15 1.0e-15 10000 100000
variable AtomMinStep equal (step) variable temppe equal (pe)
variable min_E equal abs({prev_E}-{temppe})
print “{iter},{CellMinStep},{AtomMinStep},{AtomMinStep},(pe),{min_E}” append grafe.min.csv screen no
if “{min_E} < {min_eval}” then “jump SELF break_min”
variable prev_E equal {temppe} next iter jump SELF loop_min label break_min velocity all create 298.00 238681 variable dt equal 1.00 variable pdamp equal 1000*{dt}
variable tdamp equal 100*{dt} fix 2 all npt temp 298.00 298.00 {tdamp} tri 1.00 1.00 {pdamp} thermo 0 run 20000 thermo 1 run 20000 unfix 2 dump 2 all atom 500 grafe.initial_structure.dump write_data salida.data run 0 variable rs equal step variable readstep equal {rs}
variable rs delete
min_style fire
variable at equal cella
variable bt equal cellb
variable ct equal cellc
variable a equal {at} variable b equal {bt}
variable c equal {ct} variable at delete variable bt delete variable ct delete variable N equal 10 variable totDev equal 0.01000 variable sf equal {totDev}/{N}*2 print "Loop,CellScale,Vol,Pressure,E_total,E_pot,E_kin,E_bond,E_angle,E_torsion,E_imp,E_vdw,E_coul" file grafe.output.csv screen no variable do loop {N}
label loop_bulk
#read_dump grafe.initial_structure.dump {readstep} x y z box yes format native variable scaleVar equal 1.00-{totDev}+{do}*{sf}
variable scaleA equal {scaleVar}*{a}
variable scaleB equal {scaleVar}*{b}
variable scaleC equal {scaleVar}*{c}
change_box all x final 0.0 {scaleA} y final 0.0 {scaleB} z final 0.0 {scaleC} remap minimize 1.0e-15 1.0e-15 10000 50000 print "{do},{scaleVar},(vol),(press),(etotal),(pe),(ke),(ebond),(eangle),(edihed),(eimp),(evdwl),(ecoul)" append grafe.output.csv screen no
variable scaleVar delete
variable scaleA delete
variable scaleB delete
variable scaleC delete
next do
jump SELF loop_bulk
variable do delete


data file:
Created on Tue Mar 28 15:55:48 2023

      36 atoms
      24 bonds
      36 angles
      48 dihedrals
      30 impropers

       6 atom types
       7 bond types
      12 angle types
       4 dihedral types
       1 improper types
       0.000000  31.200000 xlo xhi
       0.000000  30.487707 ylo yhi
       0.000000  26.282456 zlo zhi
     -14.087298 -14.031684  -0.990170 xy xz yz

Masses

1    15.999400000 # O_3
2    12.010700000 # C_R
3    12.010700000 # C_1
4    15.999400000 # O_R
5    15.999400000 # O_2
6     1.007940000 # H_

Bond Coeffs

1      678.027898        1.291402  # O_3 C_R
2      572.510195        1.366311  # O_3 C_R
3      462.655054        1.379256  # C_R C_R
4      646.680887        1.311940  # C_R O_R
5      546.045262        1.388038  # O_R C_R
6      410.805866        1.435000  # C_R C_1
7      852.955211        1.196287  # C_1 O_2

Angle Coeffs

1                      fourier      358.960241        0.300235        0.267331        0.266745 # C_R O_3 C_R
2              cosine/periodic      196.207517              -1               3 # O_3 C_R O_3
3              cosine/periodic      147.327648              -1               3 # O_3 C_R C_R
4              cosine/periodic      111.297508              -1               3 # C_R C_R C_R
5              cosine/periodic      144.065775              -1               3 # C_R C_R O_R
6              cosine/periodic      132.610783              -1               3 # C_R C_R O_R
7              cosine/periodic      135.781731              -1               3 # O_3 C_R C_R
8              cosine/periodic      127.739968              -1               3 # O_3 C_R C_1
9              cosine/periodic      104.760596              -1               3 # C_R C_R C_1

10 cosine/periodic 80.154455 1 1 # C_R C_1 O_2
11 cosine/periodic 191.584862 -1 3 # O_3 C_R O_R
12 cosine/periodic 148.903308 -1 3 # C_R O_R C_R

Dihedral Coeffs

1        6.737110              -1               2 # C_R O_3 C_R O_3
2        2.500000              -1               2 # C_R O_3 C_R C_R
3        6.737110               1               2 # O_3 C_R O_3 C_R
4        3.368555              -1               2 # O_3 C_R C_R C_R

Improper Coeffs

1        2.000000        1.000000       -1.000000        0.000000               0 # O_3 C_R O_3 C_R

Pair Coeffs

1        0.060000        3.118146 # O_3 O_3
2        0.105000        3.430851 # C_R C_R
3        0.105000        3.430851 # C_1 C_1
4        0.060000        3.118146 # O_R O_R
5        0.060000        3.118146 # O_2 O_2
6        0.044000        2.571134 # H_ H_

Atoms

   1        1        1     0.00000    2.18082    0.93554   -0.23129
   2        1        2     0.00000    2.70675   -0.33541    0.16295
   3        2        6     0.00000    2.81841   -0.94388   -0.59924
   4        1        1     0.00000    3.91116   -0.08597    0.82527
   5        1        2     0.00000    1.75341   -0.91829    1.23002
   6        3        6     0.00000    1.69575   -0.30863    1.99326
   7        1        2     0.00000    0.39912   -1.08355    0.59924
   8        4        6     0.00000    0.45387   -1.76553   -0.10566
   9        1        2     0.00000   -0.09019    0.21401   -0.01577
  10        5        6     0.00000   -0.29608    0.83284    0.71436
  11        1        2     0.00000    0.92390    0.87612   -0.91989
  12        6        6     0.00000    1.02751    0.36174   -1.75199
  13        1        3     0.00000    0.56537    2.32722   -1.24053
  14        7        6     0.00000    0.30339    2.78440   -0.42788
  15        8        6     0.00000    1.33495    2.78278   -1.61479
  16        1        4     0.00000    2.29086   -2.17173    1.64528
  17        1        4     0.00000   -0.49930   -1.54250    1.61374
  18        1        5     0.00000   -0.49986    2.34398   -2.17093
  19        1        1     0.00000    7.38807   -0.97252    0.24180
  20        1        2     0.00000   -2.49587    0.29783   -0.13667
  21        9        6     0.00000    8.04057    0.87257    0.64707
  22        1        4     0.00000   -1.27709    0.04839   -0.79899
  23        1        2     0.00000    6.95761    0.93951   -1.14592
  24       10        6     0.00000    6.85793    0.36739   -1.93439
  25        1        2     0.00000    5.62060    1.11459   -0.45206
  26       11        6     0.00000    5.73508    1.71569    0.31171
  27        1        2     0.00000    5.10781   -0.23329    0.04205
  28       12        6     0.00000    4.91189   -0.79737   -0.73328
  29        1        2     0.00000    6.12428   -0.93709    0.91989
  30       13        6     0.00000    6.22004   -0.44622    1.76092
  31        1        3     0.00000    5.75281   -2.37501    1.21425
  32       14        6     0.00000    5.49072   -2.81974    0.39476
  33       15        6     0.00000    6.52835   -2.84097    1.57327
  34        1        4     0.00000    7.51248    2.20337   -1.51387
  35        1        4     0.00000    4.70374    1.69802   -1.37194
  36        1        5     0.00000    4.69537   -2.44074    2.14990

Bonds

   1        1        1        2
   2        2        1       11
   3        1        2        4
   4        3        2        5
   5        2        4       27
   6        3        5        7
   7        4        5       16
   8        3        7        9
   9        4        7       17
  10        3        9       11
  11        6       11       13
  12        7       13       18
  13        1       19       20
  14        2       19       29
  15        4       20       22
  16        3       20       23
  17        5       22        9
  18        3       23       25
  19        4       23       34
  20        3       25       27
  21        4       25       35
  22        3       27       29
  23        6       29       31
  24        7       31       36

Angles

   1        1        2        1       11
   2        2        1        2        4
   3        3        1        2        5
   4        3        4        2        5
   5        1        2        4       27
   6        4        2        5        7
   7        5        2        5       16
   8        5        7        5       16
   9        4        5        7        9
  10        5        5        7       17
  11        5        9        7       17
  12        4        7        9       11
  13        6        7        9       22
  14        6       11        9       22
  15        7        1       11        9
  16        8        1       11       13
  17        9        9       11       13
  18       10       11       13       18
  19        1       20       19       29
  20       11       19       20       22
  21        3       19       20       23
  22        5       22       20       23
  23       12        9       22       20
  24        4       20       23       25
  25        5       20       23       34
  26        5       25       23       34
  27        4       23       25       27
  28        5       23       25       35
  29        5       27       25       35
  30        7        4       27       25
  31        7        4       27       29
  32        4       25       27       29
  33        7       19       29       27
  34        8       19       29       31
  35        9       27       29       31
  36       10       29       31       36

Dihedrals

   1        1       11        1        2        4
   2        1       11        1        2        5
   3        2        2        1       11        9
   4        2        2        1       11       13
   5        3        1        2        4       27
   6        3        5        2        4       27
   7        4        1        2        5        7
   8        4        1        2        5       16
   9        4        4        2        5        7
  10        4        4        2        5       16
  11        2        2        4       27       25
  12        2        2        4       27       29
  13        4        2        5        7        9
  14        4        2        5        7       17
  15        4       16        5        7        9
  16        4       16        5        7       17
  17        4        5        7        9       11
  18        4        5        7        9       22
  19        4       17        7        9       11
  20        4       17        7        9       22
  21        4        7        9       11        1
  22        4        7        9       11       13
  23        4       22        9       11        1
  24        4       22        9       11       13
  25        1       29       19       20       22
  26        1       29       19       20       23
  27        2       20       19       29       27
  28        2       20       19       29       31
  29        1       19       20       22        9
  30        1       23       20       22        9
  31        4       19       20       23       25
  32        4       19       20       23       34
  33        4       22       20       23       25
  34        4       22       20       23       34
  35        2       20       22        9        7
  36        2       20       22        9       11
  37        4       20       23       25       27
  38        4       20       23       25       35
  39        4       34       23       25       27
  40        4       34       23       25       35
  41        4       23       25       27        4
  42        4       23       25       27       29
  43        4       35       25       27        4
  44        4       35       25       27       29
  45        4        4       27       29       19
  46        4        4       27       29       31
  47        4       25       27       29       19
  48        4       25       27       29       31

Impropers

   1        1        2        1        4        5
   2        1        2        4        1        5
   3        1        2        5        1        4
   4        1        5        2        7       16
   5        1        5        7        2       16
   6        1        5       16        2        7
   7        1        7        5        9       17
   8        1        7        9        5       17
   9        1        7       17        5        9
  10        1        9        7       11       22
  11        1        9       11        7       22
  12        1        9       22        7       11
  13        1       11        1        9       13
  14        1       11        9        1       13
  15        1       11       13        1        9
  16        1       20       19       22       23
  17        1       20       22       19       23
  18        1       20       23       19       22
  19        1       23       20       25       34
  20        1       23       25       20       34
  21        1       23       34       20       25
  22        1       25       23       27       35
  23        1       25       27       23       35
  24        1       25       35       23       27
  25        1       27        4       25       29
  26        1       27       25        4       29
  27        1       27       29        4       25
  28        1       29       19       27       31
  29        1       29       27       19       31
  30        1       29       31       19       27

You have the wrong atom style. Please see the documentation of the atom_style command (and that of the read_data command)

P.S.: you posted to the wrong forum category. In the future please use a suitable LAMMPS category. I’ve made the recategorization for you this time.