LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
Re: [lammps-users] Al2O3 data file using Vashishta potential
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [lammps-users] Al2O3 data file using Vashishta potential


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 15 Jul 2017 10:59:36 -0400

2017-07-15 9:43 GMT-04:00 Zeeshan Ahmed <zeeshan.ahmed@...5589...>:
> Dear All,
>
> I have built the lammps file using topo tools. But using topo tools I was
> unable to generate bonds and angles for Al2O3. It gives me the position
> only.

topotools will output the information that you feed it. topotools it
_deliberately_ has no knowlege _at all_ about chemistry. it expects
its users to know and understand what they do. that is actually its
strength, since you don't need to work around heuristics in other
tools.

> But in the Vashishta potential for Al2O3, there are details of the
> charge, bond angle , equilibrium bond distance etc. So, do I have to specify
> again the charge, angle, and bond in the lammps data file? Please see the
> generated LAMMPS data file of Al2O3.

it should be clear form the description of the potential in the
relevant publication, whether you need to specific *explicit* bonds
and angles (and then which style you would have to use for it) or
whether those are implicit in the pair style. LAMMPS doesn't care, it
will compute any syntactically correct information that you input. it
is your job to know (and learn, if you don't) what is correct and
needed or not.

axel.

> LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools
> v1.5 on Sat Jul 15 18:53:48 IST 2017
>
>  7500 atoms
>  0 bonds
>  0 angles
>  0 dihedrals
>  0 impropers
>  2 atom types
>  0 bond types
>  0 angle types
>  0 dihedral types
>  0 improper types
>  -19.660899 20.389100  xlo xhi
>  -19.999701 20.000299  ylo yhi
>  -20.000000 20.000000  zlo zhi
>
> # Pair Coeffs
> #
> # 1  Al
> # 2  O
>
>  Masses
>
>  1 26.981539 # Al
>  2 15.999400 # O
>
>  Atoms
>
> 1 1 1 1.523700 -18.690401 -18.000200 -16.674999 # Al UNK
> 2 1 2 -1.015800 -17.234400 -18.000200 -18.000000 # O UNK
> 3 1 1 1.523700 -18.690401 -18.000200 -19.325001 # Al UNK
> 4 1 2 -1.015800 -19.417400 -16.739201 -18.000000 # O UNK
> 5 1 2 -1.015800 -19.417400 -19.260201 -18.000000 # O UNK
> 6 1 1 1.523700 -18.690401 -18.000200 -12.675000 # Al UNK
> 7 1 2 -1.015800 -17.234400 -18.000200 -14.000000 # O UNK
> 8 1 1 1.523700 -18.690401 -18.000200 -15.325000 # Al UNK
> 9 1 2 -1.015800 -19.417400 -16.739201 -14.000000 # O UNK
> 10 1 2 -1.015800 -19.417400 -19.260201 -14.000000 # O UNK
> 11 1 1 1.523700 -18.690401 -18.000200 -8.675000 # Al UNK
> 12 1 2 -1.015800 -17.234400 -18.000200 -10.000000 # O UNK
> 13 1 1 1.523700 -18.690401 -18.000200 -11.325000 # Al UNK
> 14 1 2 -1.015800 -19.417400 -16.739201 -10.000000 # O UNK
> 15 1 2 -1.015800 -19.417400 -19.260201 -10.000000 # O UNK
> 16 1 1 1.523700 -18.690401 -18.000200 -4.675000 # Al UNK
> 17 1 2 -1.015800 -17.234400 -18.000200 -6.000000 # O UNK
> 18 1 1 1.523700 -18.690401 -18.000200 -7.325000 # Al UNK
> 19 1 2 -1.015800 -19.417400 -16.739201 -6.000000 # O UNK
> 20 1 2 -1.015800 -19.417400 -19.260201 -6.000000 # O UNK
> 21 1 1 1.523700 -18.690401 -18.000200 -0.675000 # Al UNK
> 22 1 2 -1.015800 -17.234400 -18.000200 -2.000000 # O UNK
> 23 1 1 1.523700 -18.690401 -18.000200 -3.325000 # Al UNK
> 24 1 2 -1.015800 -19.417400 -16.739201 -2.000000 # O UNK
> 25 1 2 -1.015800 -19.417400 -19.260201 -2.000000 # O UNK
> 26 1 1 1.523700 -18.690401 -18.000200 3.325000 # Al UNK
> 27 1 2 -1.015800 -17.234400 -18.000200 2.000000 # O UNK
> 28 1 1 1.523700 -18.690401 -18.000200 0.675000 # Al UNK
> 29 1 2 -1.015800 -19.417400 -16.739201 2.000000 # O UNK
> 30 1 2 -1.015800 -19.417400 -19.260201 2.000000 # O UNK
> 31 1 1 1.523700 -18.690401 -18.000200 7.325000 # Al UNK
> 32 1 2 -1.015800 -17.234400 -18.000200 6.000000 # O UNK
> 33 1 1 1.523700 -18.690401 -18.000200 4.675000 # Al UNK
> 34 1 2 -1.015800 -19.417400 -16.739201 6.000000 # O UNK
> 35 1 2 -1.015800 -19.417400 -19.260201 6.000000 # O UNK
> 36 1 1 1.523700 -18.690401 -18.000200 11.325000 # Al UNK
> 37 1 2 -1.015800 -17.234400 -18.000200 10.000000 # O UNK
> 38 1 1 1.523700 -18.690401 -18.000200 8.675000 # Al UNK
> 39 1 2 -1.015800 -19.417400 -16.739201 10.000000 # O UNK
> 40 1 2 -1.015800 -19.417400 -19.260201 10.000000 # O UNK
> 41 1 1 1.523700 -18.690401 -18.000200 15.325000 # Al UNK
> 42 1 2 -1.015800 -17.234400 -18.000200 14.000000 # O UNK
> 43 1 1 1.523700 -18.690401 -18.000200 12.675000 # Al UNK
> 44 1 2 -1.015800 -19.417400 -16.739201 14.000000 # O UNK
> 45 1 2 -1.015800 -19.417400 -19.260201 14.000000 # O UNK
> 46 1 1 1.523700 -18.690401 -18.000200 19.325001 # Al UNK
> 47 1 2 -1.015800 -17.234400 -18.000200 18.000000 # O UNK
> 48 1 1 1.523700 -18.690401 -18.000200 16.674999 # Al UNK
> 49 1 2 -1.015800 -19.417400 -16.739201 18.000000 # O UNK
> 50 1 2 -1.015800 -19.417400 -19.260201 18.000000 # O UNK
> 51 1 1 1.523700 -18.690401 -14.000200 -16.674999 # Al UNK
> 52 1 2 -1.015800 -17.234400 -14.000200 -18.000000 # O UNK
> 53 1 1 1.523700 -18.690401 -14.000200 -19.325001 # Al UNK
> 54 1 2 -1.015800 -19.417400 -12.739200 -18.000000 # O UNK
> 55 1 2 -1.015800 -19.417400 -15.260200 -18.000000 # O UNK
> 56 1 1 1.523700 -18.690401 -14.000200 -12.675000 # Al UNK
> 57 1 2 -1.015800 -17.234400 -14.000200 -14.000000 # O UNK
> 58 1 1 1.523700 -18.690401 -14.000200 -15.325000 # Al UNK
> 59 1 2 -1.015800 -19.417400 -12.739200 -14.000000 # O UNK
> 60 1 2 -1.015800 -19.417400 -15.260200 -14.000000 # O UNK
> 61 1 1 1.523700 -18.690401 -14.000200 -8.675000 # Al UNK
> 62 1 2 -1.015800 -17.234400 -14.000200 -10.000000 # O UNK
> 63 1 1 1.523700 -18.690401 -14.000200 -11.325000 # Al UNK
> 64 1 2 -1.015800 -19.417400 -12.739200 -10.000000 # O UNK
> 65 1 2 -1.015800 -19.417400 -15.260200 -10.000000 # O UNK
> 66 1 1 1.523700 -18.690401 -14.000200 -4.675000 # Al UNK
> 67 1 2 -1.015800 -17.234400 -14.000200 -6.000000 # O UNK
> 68 1 1 1.523700 -18.690401 -14.000200 -7.325000 # Al UNK
> 69 1 2 -1.015800 -19.417400 -12.739200 -6.000000 # O UNK
> 70 1 2 -1.015800 -19.417400 -15.260200 -6.000000 # O UNK
> 71 1 1 1.523700 -18.690401 -14.000200 -0.675000 # Al UNK
> 72 1 2 -1.015800 -17.234400 -14.000200 -2.000000 # O UNK
> 73 1 1 1.523700 -18.690401 -14.000200 -3.325000 # Al UNK
> 74 1 2 -1.015800 -19.417400 -12.739200 -2.000000 # O UNK
> 75 1 2 -1.015800 -19.417400 -15.260200 -2.000000 # O UNK
> 76 1 1 1.523700 -18.690401 -14.000200 3.325000 # Al UNK
> 77 1 2 -1.015800 -17.234400 -14.000200 2.000000 # O UNK
> 78 1 1 1.523700 -18.690401 -14.000200 0.675000 # Al UNK
> 79 1 2 -1.015800 -19.417400 -12.739200 2.000000 # O UNK
> 80 1 2 -1.015800 -19.417400 -15.260200 2.000000 # O UNK
> 81 1 1 1.523700 -18.690401 -14.000200 7.325000 # Al UNK
> 82 1 2 -1.015800 -17.234400 -14.000200 6.000000 # O UNK
> 83 1 1 1.523700 -18.690401 -14.000200 4.675000 # Al UNK
> 84 1 2 -1.015800 -19.417400 -12.739200 6.000000 # O UNK
> 85 1 2 -1.015800 -19.417400 -15.260200 6.000000 # O UNK
> 86 1 1 1.523700 -18.690401 -14.000200 11.325000 # Al UNK
> 87 1 2 -1.015800 -17.234400 -14.000200 10.000000 # O UNK
> 88 1 1 1.523700 -18.690401 -14.000200 8.675000 # Al UNK
> 89 1 2 -1.015800 -19.417400 -12.739200 10.000000 # O UNK
> 90 1 2 -1.015800 -19.417400 -15.260200 10.000000 # O UNK
> 91 1 1 1.523700 -18.690401 -14.000200 15.325000 # Al UNK
> 92 1 2 -1.015800 -17.234400 -14.000200 14.000000 # O UNK
> 93 1 1 1.523700 -18.690401 -14.000200 12.675000 # Al UNK
> 94 1 2 -1.015800 -19.417400 -12.739200 14.000000 # O UNK
> 95 1 2 -1.015800 -19.417400 -15.260200 14.000000 # O UNK
> 96 1 1 1.523700 -18.690401 -14.000200 19.325001 # Al UNK
> 97 1 2 -1.015800 -17.234400 -14.000200 18.000000 # O UNK
> 98 1 1 1.523700 -18.690401 -14.000200 16.674999 # Al UNK
> 99 1 2 -1.015800 -19.417400 -12.739200 18.000000 # O UNK
> 100 1 2 -1.015800 -19.417400 -15.260200 18.000000 # O UNK
> 101 1 1 1.523700 -18.690401 -10.000200 -16.674999 # Al UNK
> 102 1 2 -1.015800 -17.234400 -10.000200 -18.000000 # O UNK
> 103 1 1 1.523700 -18.690401 -10.000200 -19.325001 # Al UNK
> 104 1 2 -1.015800 -19.417400 -8.739200 -18.000000 # O UNK
> 105 1 2 -1.015800 -19.417400 -11.260200 -18.000000 # O UNK
> 106 1 1 1.523700 -18.690401 -10.000200 -12.675000 # Al UNK
> 107 1 2 -1.015800 -17.234400 -10.000200 -14.000000 # O UNK
> 108 1 1 1.523700 -18.690401 -10.000200 -15.325000 # Al UNK
> 109 1 2 -1.015800 -19.417400 -8.739200 -14.000000 # O UNK
> 110 1 2 -1.015800 -19.417400 -11.260200 -14.000000 # O UNK
> 111 1 1 1.523700 -18.690401 -10.000200 -8.675000 # Al UNK
> 112 1 2 -1.015800 -17.234400 -10.000200 -10.000000 # O UNK
> 113 1 1 1.523700 -18.690401 -10.000200 -11.325000 # Al UNK
> 114 1 2 -1.015800 -19.417400 -8.739200 -10.000000 # O UNK
> 115 1 2 -1.015800 -19.417400 -11.260200 -10.000000 # O UNK
> 116 1 1 1.523700 -18.690401 -10.000200 -4.675000 # Al UNK
> 117 1 2 -1.015800 -17.234400 -10.000200 -6.000000 # O UNK
> 118 1 1 1.523700 -18.690401 -10.000200 -7.325000 # Al UNK
> 119 1 2 -1.015800 -19.417400 -8.739200 -6.000000 # O UNK
> 120 1 2 -1.015800 -19.417400 -11.260200 -6.000000 # O UNK
> 121 1 1 1.523700 -18.690401 -10.000200 -0.675000 # Al UNK
> 122 1 2 -1.015800 -17.234400 -10.000200 -2.000000 # O UNK
> 123 1 1 1.523700 -18.690401 -10.000200 -3.325000 # Al UNK
> 124 1 2 -1.015800 -19.417400 -8.739200 -2.000000 # O UNK
> 125 1 2 -1.015800 -19.417400 -11.260200 -2.000000 # O UNK
> 126 1 1 1.523700 -18.690401 -10.000200 3.325000 # Al UNK
> 127 1 2 -1.015800 -17.234400 -10.000200 2.000000 # O UNK
> 128 1 1 1.523700 -18.690401 -10.000200 0.675000 # Al UNK
> 129 1 2 -1.015800 -19.417400 -8.739200 2.000000 # O UNK
> 130 1 2 -1.015800 -19.417400 -11.260200 2.000000 # O UNK
> 131 1 1 1.523700 -18.690401 -10.000200 7.325000 # Al UNK
> 132 1 2 -1.015800 -17.234400 -10.000200 6.000000 # O UNK
> 133 1 1 1.523700 -18.690401 -10.000200 4.675000 # Al UNK
> 134 1 2 -1.015800 -19.417400 -8.739200 6.000000 # O UNK
> 135 1 2 -1.015800 -19.417400 -11.260200 6.000000 # O UNK
> 136 1 1 1.523700 -18.690401 -10.000200 11.325000 # Al UNK
> 137 1 2 -1.015800 -17.234400 -10.000200 10.000000 # O UNK
> 138 1 1 1.523700 -18.690401 -10.000200 8.675000 # Al UNK
> 139 1 2 -1.015800 -19.417400 -8.739200 10.000000 # O UNK
> 140 1 2 -1.015800 -19.417400 -11.260200 10.000000 # O UNK
> 141 1 1 1.523700 -18.690401 -10.000200 15.325000 # Al UNK
> 142 1 2 -1.015800 -17.234400 -10.000200 14.000000 # O UNK
> 143 1 1 1.523700 -18.690401 -10.000200 12.675000 # Al UNK
> 144 1 2 -1.015800 -19.417400 -8.739200 14.000000 # O UNK
> 145 1 2 -1.015800 -19.417400 -11.260200 14.000000 # O UNK
> 146 1 1 1.523700 -18.690401 -10.000200 19.325001 # Al UNK
> 147 1 2 -1.015800 -17.234400 -10.000200 18.000000 # O UNK
> 148 1 1 1.523700 -18.690401 -10.000200 16.674999 # Al UNK
> 149 1 2 -1.015800 -19.417400 -8.739200 18.000000 # O UNK
> 150 1 2 -1.015800 -19.417400 -11.260200 18.000000 # O UNK
> 151 1 1 1.523700 -18.690401 -6.000200 -16.674999 # Al UNK
> 152 1 2 -1.015800 -17.234400 -6.000200 -18.000000 # O UNK
> 153 1 1 1.523700 -18.690401 -6.000200 -19.325001 # Al UNK
> 154 1 2 -1.015800 -19.417400 -4.739200 -18.000000 # O UNK
> 155 1 2 -1.015800 -19.417400 -7.260200 -18.000000 # O UNK
> 156 1 1 1.523700 -18.690401 -6.000200 -12.675000 # Al UNK
> 157 1 2 -1.015800 -17.234400 -6.000200 -14.000000 # O UNK
> 158 1 1 1.523700 -18.690401 -6.000200 -15.325000 # Al UNK
> 159 1 2 -1.015800 -19.417400 -4.739200 -14.000000 # O UNK
> 160 1 2 -1.015800 -19.417400 -7.260200 -14.000000 # O UNK
> 161 1 1 1.523700 -18.690401 -6.000200 -8.675000 # Al UNK
> 162 1 2 -1.015800 -17.234400 -6.000200 -10.000000 # O UNK
> 163 1 1 1.523700 -18.690401 -6.000200 -11.325000 # Al UNK
> 164 1 2 -1.015800 -19.417400 -4.739200 -10.000000 # O UNK
> 165 1 2 -1.015800 -19.417400 -7.260200 -10.000000 # O UNK
> 166 1 1 1.523700 -18.690401 -6.000200 -4.675000 # Al UNK
> 167 1 2 -1.015800 -17.234400 -6.000200 -6.000000 # O UNK
> 168 1 1 1.523700 -18.690401 -6.000200 -7.325000 # Al UNK
> 169 1 2 -1.015800 -19.417400 -4.739200 -6.000000 # O UNK
> 170 1 2 -1.015800 -19.417400 -7.260200 -6.000000 # O UNK
> 171 1 1 1.523700 -18.690401 -6.000200 -0.675000 # Al UNK
> 172 1 2 -1.015800 -17.234400 -6.000200 -2.000000 # O UNK
> 173 1 1 1.523700 -18.690401 -6.000200 -3.325000 # Al UNK
> 174 1 2 -1.015800 -19.417400 -4.739200 -2.000000 # O UNK
> 175 1 2 -1.015800 -19.417400 -7.260200 -2.000000 # O UNK
> 176 1 1 1.523700 -18.690401 -6.000200 3.325000 # Al UNK
> 177 1 2 -1.015800 -17.234400 -6.000200 2.000000 # O UNK
> 178 1 1 1.523700 -18.690401 -6.000200 0.675000 # Al UNK
> 179 1 2 -1.015800 -19.417400 -4.739200 2.000000 # O UNK
> 180 1 2 -1.015800 -19.417400 -7.260200 2.000000 # O UNK
> 181 1 1 1.523700 -18.690401 -6.000200 7.325000 # Al UNK
> 182 1 2 -1.015800 -17.234400 -6.000200 6.000000 # O UNK
> 183 1 1 1.523700 -18.690401 -6.000200 4.675000 # Al UNK
> 184 1 2 -1.015800 -19.417400 -4.739200 6.000000 # O UNK
> 185 1 2 -1.015800 -19.417400 -7.260200 6.000000 # O UNK
> 186 1 1 1.523700 -18.690401 -6.000200 11.325000 # Al UNK
> 187 1 2 -1.015800 -17.234400 -6.000200 10.000000 # O UNK
> 188 1 1 1.523700 -18.690401 -6.000200 8.675000 # Al UNK
> 189 1 2 -1.015800 -19.417400 -4.739200 10.000000 # O UNK
> 190 1 2 -1.015800 -19.417400 -7.260200 10.000000 # O UNK
> 191 1 1 1.523700 -18.690401 -6.000200 15.325000 # Al UNK
> 192 1 2 -1.015800 -17.234400 -6.000200 14.000000 # O UNK
> 193 1 1 1.523700 -18.690401 -6.000200 12.675000 # Al UNK
> 194 1 2 -1.015800 -19.417400 -4.739200 14.000000 # O UNK
> 195 1 2 -1.015800 -19.417400 -7.260200 14.000000 # O UNK
> 196 1 1 1.523700 -18.690401 -6.000200 19.325001 # Al UNK
> 197 1 2 -1.015800 -17.234400 -6.000200 18.000000 # O UNK
> 198 1 1 1.523700 -18.690401 -6.000200 16.674999 # Al UNK
> 199 1 2 -1.015800 -19.417400 -4.739200 18.000000 # O UNK
> 200 1 2 -1.015800 -19.417400 -7.260200 18.000000 # O UNK
> 201 1 1 1.523700 -18.690401 -2.000200 -16.674999 # Al UNK
> 202 1 2 -1.015800 -17.234400 -2.000200 -18.000000 # O UNK
> 203 1 1 1.523700 -18.690401 -2.000200 -19.325001 # Al UNK
> 204 1 2 -1.015800 -19.417400 -0.739200 -18.000000 # O UNK
> 205 1 2 -1.015800 -19.417400 -3.260200 -18.000000 # O UNK
> 206 1 1 1.523700 -18.690401 -2.000200 -12.675000 # Al UNK
> 207 1 2 -1.015800 -17.234400 -2.000200 -14.000000 # O UNK
> 208 1 1 1.523700 -18.690401 -2.000200 -15.325000 # Al UNK
> 209 1 2 -1.015800 -19.417400 -0.739200 -14.000000 # O UNK
> 210 1 2 -1.015800 -19.417400 -3.260200 -14.000000 # O UNK
> 211 1 1 1.523700 -18.690401 -2.000200 -8.675000 # Al UNK
> 212 1 2 -1.015800 -17.234400 -2.000200 -10.000000 # O UNK
> 213 1 1 1.523700 -18.690401 -2.000200 -11.325000 # Al UNK
> 214 1 2 -1.015800 -19.417400 -0.739200 -10.000000 # O UNK
> 215 1 2 -1.015800 -19.417400 -3.260200 -10.000000 # O UNK
> .
> .
> .
> .
> .
> .
> .
> .
> .
>
> Regards,
> Zeeshan Ahmed
> PhD Student (Mechanical Engineering)
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> lammps-users mailing list
> lammps-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.