My model adds an extruded gap with a single grain boundary, so orient/eco, which is designed to move grain boundaries, does not meet my needs. When I tried to modify orient/eco source, the f_eco[1] output of dump was inf or -inf, and grain boundaries did not move. Part of the dump output file is shown below.
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
40801
ITEM: BOX BOUNDS pp pp pp
-1.6138402399940688e-02 2.2396068026954168e+01
-3.4262988291089869e-01 3.8407848629979532e+02
-6.0363005801065128e-02 7.7586713364888794e+01
ITEM: ATOMS xs ys zs f_eco[1] f_eco[2]
0.119807 0.0182198 0.030867 -inf -1
0.0203263 0.0160062 0.0136767 -inf -1
0.318141 0.0184982 0.0300697 -inf -1
0.218923 0.0159543 0.0146055 -inf -1
0.420008 0.0159356 0.0145852 -inf -1
0.516368 0.0183916 0.030449 -inf -1
0.620738 0.0158537 0.0140633 -inf -1
0.719769 0.0184089 0.0297774 -inf -1
0.819209 0.0159562 0.0134935 -inf -1
0.918862 0.0184174 0.0301164 -inf -1
0.0211992 0.0230304 0.0127984 -inf -1
0.019574 0.0204918 0.0466975 inf 1
0.0216762 0.0276238 0.0462301 -inf -1
0.120676 0.0252765 0.0305172 -inf -1
0.21917 0.0229662 0.0136986 -inf -1
0.220578 0.0205573 0.0465221 inf 1
0.218916 0.0277098 0.047156 -inf -1
0.318366 0.0254132 0.0310167 -inf -1
0.418572 0.0230516 0.0140915 inf 1
0.419518 0.0204662 0.0473984 inf 1
The following code is the part I modified.
if (chi > eta) {
added_energy += half_u;
nbr[i].duchi = 0.0;
order[i][1] = sign;
} else if (chi < -eta) {
added_energy -= half_u;
nbr[i].duchi = 0.0;
order[i][1] = -sign;
} else {
//Identify the atoms at the left boundary.
if (x[i][1] < new_position_coordinate_y[0]) {
added_energy += half_u;
nbr[i].duchi = 0.0;
order[i][1] = sign;
}
//Identify the atoms at the right edge.
else if (x[i][1] > new_position_coordinate_y[new_position_coordinate_y.size() - 1]) {
added_energy -= half_u;
nbr[i].duchi = 0.0;
order[i][1] = -sign;
}
else {
if (GB_clusters[0] <= x[i][1] <= GB_clusters[GB_clusters.size() - 1]) {
omega = omega_pre * chi;
sin_om = sin(omega);
added_energy += half_u * sin_om;
nbr[i].duchi = duchi_pre * cos(omega);
order[i][1] = sign * sin_om;
}
else {
added_energy += half_u;
nbr[i].duchi = 0.0;
order[i][1] = sign;
}
}
- new_position_coordinate_y stores the y-coordinate values of atoms at the interstitial and grain boundaries.
- GB_clusters store only the y coordinate values of the atoms at the grain boundaries.
- The y coordinates in both lists have been sorted in ascending order.
With only grain boundaries, the original orient/eco command can be used to move grain boundaries in the negative Y-axis direction. I just added the judgment of the gap and grain boundary according to my own model (my model is rectangular and the Y-axis is the length of the rectangular model).