Dear users,
I have prepared a structure data file for a bilayer graphene which is in attach. I used VNL to convert xyz format to lammps data format.
Ovito shows that its width, length and height are 60.17, 63.81 and 3.35 respectively.
However, the log file shows that the dimensions in x,y, and z are 83.18, 86.88 and 25.33. I have used real units and the potential is tersoff.
Here is the relevant part of log file:
Step Fmax Fnorm Press Volume sysdensi sxx syy szz syz sxz sxy PotEng cella cellb cellc cellalph cellbeta cellgamm
0 8.2048817 129.57463 636.61336 173588.33 0.34468187 -1017.6798 -892.16029 -0 -0 -0 -1.786121e-05 -23562.065 81.713176 85.350001 24.89 1.5707963 1.5707963 1.5707963
100 0.25552463 2.2234346 10.453884 182798.19 0.32731588 33.844322 -65.205975 -0 -0 -0 6.679287e-07 -23764.84 83.133465 86.833503 25.322623 1.5707963 1.5707963 1.5707963
200 0.37808138 4.0024841 3.2624665 183189.8 0.32661617 22.08661 -31.874009 -0 -0 -0 -2.2171551e-06 -23766.347 83.192788 86.895466 25.340693 1.5707963 1.5707963 1.5707963
300 0.071349298 0.55462774 -1.1272809 183164.53 0.32666123 29.585097 -26.203255 -0 -0 -0 -8.30725e-07 -23766.761 83.188962 86.891471 25.339528 1.5707963 1.5707963 1.5707963
400 0.0098842022 0.21434311 0.49075502 183132.9 0.32671764 24.866309 -26.338574 -0 -0 -0 -5.059662e-07 -23766.801 83.184175 86.88647 25.338069 1.5707963 1.5707963 1.5707963
500 0.018840409 0.16566709 0.48212972 183143.48 0.32669877 12.804229 -14.250619 -0 -0 -0 -4.0433134e-07 -23766.897 83.185776 86.888143 25.338557 1.5707963 1.5707963 1.5707963
600 0.022685048 0.17088611 0.93464057 183135.53 0.32671296 11.173392 -13.977314 -0 -0 -0 -3.6351489e-07 -23766.904 83.184572 86.886885 25.33819 1.5707963 1.5707963 1.5707963
651 0.014816564 0.12242522 0.90519467 183134.53 0.32671475 10.721737 -13.437321 -0 -0 -0 -3.1968914e-07 -23766.907 83.18442 86.886726 25.338144 1.5707963 1.5707963 1.5707963
Loop time of 19.9794 on 6 procs for 651 steps with 3000 atoms
I have two questions:
1-Is extension from ~60 to 80 for x and y directions reasonable?
2-Why the z dimension is extended so much?
Any help would be appreciated.
Best regards,
Nima Pirouzmand
twolayers.xyz (155 KB)
2layers.data (138 KB)
Dear users,
I have prepared a structure data file for a bilayer graphene which is in
attach. I used VNL to convert xyz format to lammps data format.
Ovito shows that its width, length and height are 60.17, 63.81 and 3.35
respectively.
However, the log file shows that the dimensions in x,y, and z are 83.18,
86.88 and 25.33. I have used real units and the potential is tersoff.
.xyz files have no bounding box information. if you load the file into
VMD and do a measure minmax, you can see that ovito just computed the
difference between min and maximum of x y and z. if you simulate with
periodic boundary conditions, that would be very very bad, as that would
likely put atoms on top of each other.
the converter you used, apparently just added some 20 angstrom plus a
guesstimated atom radius in each direction. that has the opposite problem.
depending on how you created your coordinates and what kind of boundaries
you want in x, y, and z, you have to figure out what are the correct box
dimensions and change the numbers in the data file accordingly.
Here is the relevant part of log file:
Step Fmax Fnorm Press Volume sysdensi sxx syy szz syz sxz sxy PotEng cella
cellb cellc cellalph cellbeta cellgamm
0 8.2048817 129.57463 636.61336 173588.33
0.34468187 -1017.6798 -892.16029 -0 -0 -0
-1.786121e-05 -23562.065 81.713176 85.350001 24.89
1.5707963 1.5707963 1.5707963
100 0.25552463 2.2234346 10.453884 182798.19
0.32731588 33.844322 -65.205975 -0 -0 -0
6.679287e-07 -23764.84 83.133465 86.833503 25.322623
1.5707963 1.5707963 1.5707963
200 0.37808138 4.0024841 3.2624665 183189.8
0.32661617 22.08661 -31.874009 -0 -0 -0
-2.2171551e-06 -23766.347 83.192788 86.895466 25.340693
1.5707963 1.5707963 1.5707963
300 0.071349298 0.55462774 -1.1272809 183164.53
0.32666123 29.585097 -26.203255 -0 -0 -0
-8.30725e-07 -23766.761 83.188962 86.891471 25.339528
1.5707963 1.5707963 1.5707963
400 0.0098842022 0.21434311 0.49075502 183132.9
0.32671764 24.866309 -26.338574 -0 -0 -0
-5.059662e-07 -23766.801 83.184175 86.88647 25.338069
1.5707963 1.5707963 1.5707963
500 0.018840409 0.16566709 0.48212972 183143.48
0.32669877 12.804229 -14.250619 -0 -0 -0
-4.0433134e-07 -23766.897 83.185776 86.888143 25.338557
1.5707963 1.5707963 1.5707963
600 0.022685048 0.17088611 0.93464057 183135.53
0.32671296 11.173392 -13.977314 -0 -0 -0
-3.6351489e-07 -23766.904 83.184572 86.886885 25.33819
1.5707963 1.5707963 1.5707963
651 0.014816564 0.12242522 0.90519467 183134.53
0.32671475 10.721737 -13.437321 -0 -0 -0
-3.1968914e-07 -23766.907 83.18442 86.886726 25.338144
1.5707963 1.5707963 1.5707963
Loop time of 19.9794 on 6 procs for 651 steps with 3000 atoms
I have two questions:
1-Is extension from ~60 to 80 for x and y directions reasonable?
depends on what you want to achieve. possibly not.
2-Why the z dimension is extended so much?
it is enlarged by about the same amount than the others...
axel.
Dear Nima,
I looked at your data file in Ovito you provided. Your box is larger than the range your atoms cover. The box you defined has sizes of ~ 81.71 in x, ~85 in y and ~25 in z. So the values you got are reasonable. If you desire smaller value you should define a smaller box.
Best regards,
Muhammad
Prof. Kohlmeyer,
Thank you for your response. So, what do you suggest to build a bilayer or trilayer graphene for lammps?
Best regards,
Nima Pirouzmand
Prof. Kohlmeyer,
Thank you for your response. So, what do you suggest to build a bilayer or
trilayer graphene for lammps?
i would use the nanotube and topotools plugins in VMD. there is no escape
from doing some more or less manual adjustment of the box dimensions and
some time on considering what this would have to be. as i already
mentioned, what those exactly have to be is something that *you* have to
decide, as this depends on the details of your research.
it appears to me, that if you would spend less effort on writing e-mails
and asking people to tell you how to fix your input for you (without them
really knowing what you need or want), and some more effort actually
thinking about what you are doing and what the tools that you use are
doing, then you would not even need to ask such questions and display
yourself in such a less than than flattering way.
axel.