There are more information you need to clarify:
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what method are you using for obtaining thermal conductivity? NEMD or EMD? If NEMD, it is fix temperture or fix heat flux? From what you described, it seems that you are using EMD and Green-Kubo method which is the command “fix thermal/conductivity” in lammps doing. You can also have a try on the NEMD method.
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You only mentioned steps, but no time step. So what’s your time step?
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If you thought it may be a bug, you’d better give the version of lammps you are using.
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“1000 W/mK should be theoretical value in case of Brenner potential”, do you mean the value for the same configuration as yours? Different directions may have different values.
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Have you ever seen the atom configuration using visualization software, such as VMD or atomeye? You may find something there.
Good luck!
Xiaopeng Huang
2010/9/28 JhonY. I. <yijhon@…8…>