The compute shc keyword

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Purpose

  • The compute_shc keyword is used to compute the non-equilibrium heat flux correlation function [math]K(t)[/math] 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 [math]\geq 0[/math] 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 [math]\geq 0[/math] 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 [math]\geq 1[/math] and [math]\leq 10[/math]. 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 [math]\geq 100[/math] and [math]\leq 1000[/math]. 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 [math]x[/math].

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 [math]y[/math].

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 [math]z[/math].

Caveats

Output file

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).