Hi,
I am confused with the finite size particle volume in the simulation,i.e. in my simulation the total volume of paticles always larger than the volume of box.
For example, the following is the result from the example of Ellipsoid in LJ background. Here we have 45 ellipsoid particle (shape 3 1 1), 355 spherical particle (shape 1 1 1). In npt ensemble, with the increasing of timestep, the area of the box (2d system) decreases to 1000. While the area of the particles are about 1500, larger than the area of the box. The same thing occurs in the 3D system, i.e., the volume of the finite size particle is larger than the volume of the box. If the finite size particle is stiff, it is not reasonable in physics. Could somebody give me some comments. Thanks in advance.
LAMMPS (20 May 2010)
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
Created orthogonal box = (0 0 3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 processor grid
Created 400 atoms
Setting atom values …
45 settings made for type/fraction
Setting atom values …
400 settings made for quat/random
355 atoms in group spheroid
Setting up run …
Memory usage per processor = 2.55985 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709964 0.0005092531 2.287178 0.066789146 13689.461
500 1.9771743 0.043667903 2.030416 0.099603808 8475.4956
600 2.1056472 0.21590647 1.9341467 0.25620682 4664.3492
700 2.2591091 0.71613892 1.6064449 0.68894675 2495.8474
800 1.7733044 1.5883559 0.20924004 1.3468917 1416.9001
900 2.3681831 3.0367847 0.61651286 3.4088407 916.60516
1000 1.4504216 4.4853822 3.0017299 2.4152165 748.40795
1100 2.0290856 4.9166328 2.8483187 2.1258186 710.3309
1200 1.8636218 4.4586831 2.5381871 1.5337278 755.63189
1300 1.963823 4.0436872 2.0228794 0.65868868 838.43621
1400 2.0548769 3.7167975 1.5888041 0.71938689 928.68639
1500 1.930959 3.6866424 1.7065814 0.21196844 1013.0597
1600 2.0970402 3.5337133 1.3827531 0.84616813 1072.3599
1700 1.9719543 3.4332054 1.4094962 0.48754801 1136.7173
1800 2.0642751 3.3290013 1.2118193 0.53357896 1172.1977
1900 1.9719061 3.2767474 1.2535098 0.96503889 1168.3116
2000 1.955576 3.3968286 1.3910212 0.72582869 1142.5467

Hi,
I am confused with the finite size particle volume in the simulation,i.e. in my simulation the total volume of paticles always larger than the volume of box.
For example, the following is the result from the example of Ellipsoid in LJ background. Here we have 45 ellipsoid particle (shape 3 1 1), 355 spherical particle (shape 1 1 1). In npt ensemble, with the increasing of timestep, the area of the box (2d system) decreases to 1000. While the area of the particles are about 1500, larger than the area of the box. The same thing occurs in the 3D system, i.e., the volume of the finite size particle is larger than the volume of the box. If the finite size particle is stiff, it is not reasonable in physics. Could somebody give me some comments.
have you considered the fact that you are using a soft potential
and thus that your particle's volume is not a well defined entity?
how do you compute the volume of your ellipsoids?
cheers,
axel.
Thanks in advance.