Question about command "region block/sphere"

Hi, everyone, I have a question about initializing configurations.

In my simulations, I want to study the silicon thermal properties
(the potential file I am using is Si.sw)
First I have a input file(attached), below is part of it.

-----------------------------------------------------Input-1-----------------------------------------------------
dimension 3
boundary p p p
lattice diamond 5.430
region block1 block 0 4 0 4 0 4
neighbor 3.0 bin
neigh_modify check yes
create_box 1 block1
create_atoms 1 region block1
-----------------------------------------------------Input-1-----------------------------------------------------
atom number =512

and the output is
-----------------------------------------------------Output-1-----------------------------------------------------
Step Temp E_pair E_mol TotEng Press
       0 300 -51202.201 0 -50745.243 2564.1934
   20000 295.09734 -50760.548 0 -50311.058 4272.6702
   40000 285.39943 -50737.776 0 -50303.058 4289.7137
   60000 292.8108 -50748.322 0 -50302.314 4278.7431
   80000 304.29079 -50780.18 0 -50316.687 4273.1674
  100000 299.7897 -50716.816 0 -50260.178 4360.2537
  120000 307.21641 -50749.683 0 -50281.733 4250.0454
  140000 314.55459 -50739.021 0 -50259.894 4470.9087
  160000 298.73284 -50730.191 0 -50275.163 4160.2608
  180000 298.3894 -50713.333 0 -50258.828 4342.3659
  200000 304.3599 -50736.069 0 -50272.47 4252.1926
-----------------------------------------------------Output-1-----------------------------------------------------

However, when I edit the input file to:

-----------------------------------------------------Input-2-----------------------------------------------------
region block1 block 0 5 0 5 0 5
region sphere1 sphere 2.5 2.5 2.5 2.4
neighbor 3.0 bin
neigh_modify check yes
create_box 1 block1
create_atoms 1 region sphere1
-----------------------------------------------------Input-2-----------------------------------------------------
atom number =476 (close to input-1, 512)

the output then becomes
-----------------------------------------------------Output-2-----------------------------------------------------
Step Temp E_pair E_mol TotEng Press
       0 300 -41801.797 0 -41377.032 1189.9274
   20000 289.02479 -42836.609 0 -42427.383 -7129.2554
   40000 306.43241 -42888.055 0 -42454.182 -6970.5648
   60000 306.77556 -42899.64 0 -42465.281 -8024.4468
   80000 299.55606 -42916.291 0 -42492.154 -6668.7535
  100000 296.17049 -42895.094 0 -42475.751 -5691.9045
  120000 295.78732 -42892.669 0 -42473.868 -5966.5226
  140000 294.94105 -42883.175 0 -42465.572 -4774.5579
  160000 298.89236 -42925.26 0 -42502.063 -6285.9421
  180000 313.20756 -42954.649 0 -42511.183 -7912.634
  200000 311.18568 -42948.312 0 -42507.709 -6817.5189
-----------------------------------------------------Output-2-----------------------------------------------------

In which the pressure fluctuates a lot compared to output-1 (even
minus value). Besides the thermal properties that is calculated by
Green-Kubo method showed significant difference.
In case one the results is ~125W/m-K, while in case two, its
~0.001W/m-K, which is out of order. (The experiment value is
~120W/m-k)
Is there anything wrong with the dynamics?
I've searched for the entire mailing thread but cant find any
discussion about this kind of problem.
I attached my input file and any suggestions will be greatly appreciated.

many thanks,

Chen,

in.acftest_Si (2.1 KB)

Si.sw (655 Bytes)

This should be the right input file, sorry about that.

2012/10/15 You-Han Chen <[email protected]>:

in.acftest_Si (2.05 KB)

If I understand, in one case, you have a perfect crystal
in a periodic box. In the other case you
put a sphere of particles in a periodic box
with empty space at the corners.

Why shouldn't the dynamics be different as
well as the pressure?

Steve