The compute shc keyword

Purpose

• The compute_shc keyword is used to compute the non-equilibrium heat flux correlation function $K(t)$ for a group of atoms as defined in Eq. (18) of Ref. [1].

Grammar

• This keyword can be used in three ways, requiring 3 or 4 or 5 parameters:
 compute_shc sample_interval Nc transport_direction
compute_shc group_id sample_interval Nc transport_direction
compute_shc grouping_method group_id sample_interval Nc transport_direction

• If there are 3 parameters, it means that the SHC will be calculated for the whole system.
• If there are 4 parameters, it means that the SHC will be calculated for atoms in group group_id of grouping method 0. Here group_id should $\geq 0$ and smaller than the number of groups in grouping method 0. Also, grouping method 0 must be defined in the xyz.in file.
• If there are 5 parameters, it means that the SHC will be calculated for atoms in group group_id of grouping method grouping_method. Here group_id should $\geq 0$ and smaller than the number of groups in grouping method grouping_method. Also, grouping method grouping_method must be defined in the xyz.in file.
• In all the three ways, there are three common parameters:
• sample_interval is the sampling interval between two correlation steps. This parameter must be an integer that is $\geq 1$ and $\leq 10$. Trust me, values out of this range are bad.
• Nc is the total number of correlation steps. This parameter must be an integer that is $\geq 100$ and $\leq 1000$. Trust me, values out of this range are bad.
• transport_direction is the direction of heat transport to be measured. It can only be 0, 1, and 2, corresponding to the x, y, and z directions, respectively.

Examples

Example 1

• The command
  compute_shc 2 250 0


means that

• you want to calculate the SHC for the whole system;
• the sampling interval is 2;
• the maximum number of correlation steps is 250;
• the transport direction is $x$.

Example 2

• The command
  compute_shc 4 1 500 1


means that

• you want to calculate the SHC for atoms in group 4 defined in grouping method 0;
• the sampling interval is 1 (sample the data at each time step);
• the maximum number of correlation steps is 500;
• the transport direction is $y$.

Example 3

• The command
  compute_shc 1 4 5 100 2


means that

• you want to calculate the SHC for atoms in group 4 defined in grouping method 1;
• the sampling interval is 5;
• the maximum number of correlation steps is 100;
• the transport direction is $z$.

References

• [1] Zheyong Fan, Haikuan Dong, Ari Harju, and Tapio Ala-Nissila, Homogeneous nonequilibrium molecular dynamics method for heat transport and spectral decomposition with many-body potentials, Phys. Rev. B 99, 064308 (2019).