I am trying to do visualizations of the charge density for non-spin-polarized silicon nanowire. After relaxation, I try to run grid2cube with the following syntax (my input file for g2c is SiNW.g2c and for simplicity's sake, my system label will be referred to as S_L):
./grid2cube.out < SiNW.g2c S_L.XV S_L.RHO > g2c.out but when I do this, it returns that my nspin=0 and thus does not make a .cube file at all. My input file for g2c is: --------- S_L rho 0.0 0.0 0.0 1 unformatted ---------- This is the standard output of the command that I issued above: ------ Cell vectors 46.1754762584164 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 46.1754762584164 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 17.7734538727118 Grid mesh: 216 x 0 x 216 nspin = 0 ------- Something seems strange to me about that '0' in the grid mesh, too. I tried editing the fortran code for grid2cube.f, setting nspin=1 manually inside the code, recompiling and running again, but this is what I get: --------- 68 0.000000 0.000000 0.000000 216 0.213775 0.000000 0.000000 0 NaN Infinity NaN 216 0.000000 0.000000 0.082285 14 0.000000 9.433099 NaN 0.903102 14 0.000000 9.432789 NaN 5.318021 14 0.000000 13.033586 NaN 6.808950 14 0.000000 13.015757 NaN 11.235454 14 0.000000 13.015924 NaN 12.758808 14 0.000000 13.034385 NaN 17.185759 14 0.000000 16.618908 NaN 0.904276 14 0.000000 16.618154 NaN 5.315916 14 0.000000 13.005918 NaN 0.916227 14 0.000000 13.038506 NaN 5.327205 14 0.000000 16.613020 NaN 6.851160 14 0.000000 16.601408 NaN 11.252581 14 0.000000 5.860178 NaN 0.916193 14 0.000000 5.827284 NaN 5.327166 14 0.000000 9.433099 NaN 6.820480 14 0.000000 9.432860 NaN 11.246750 14 0.000000 9.432089 NaN 12.764217 14 0.000000 9.432765 NaN 17.163633 14 0.000000 2.246604 NaN 0.904218 14 0.000000 2.245486 NaN 5.316090 14 0.000000 5.830740 NaN 6.808691 14 0.000000 5.849300 NaN 11.235654 14 0.000000 5.848824 NaN 12.758320 14 0.000000 5.831752 NaN 17.185301 14 0.000000 5.828020 NaN 0.893063 14 0.000000 5.859017 NaN 5.304081 14 0.000000 9.431658 NaN 6.829797 14 0.000000 9.431909 NaN 11.229134 ---------- And this is obviously a non-result. Additionally, I read on the boards something about using a program called WSxM for visualization of SIESTA output. I downloaded the program, but could not get it to load any of my output files for plotting. Anybody use this regularly for plotting SIESTA output? I also could not find the keywords to save RHO, DRHO, etc. in formatted output. I think that may have something to do with this, at least maybe for the WSxM part. My fdf file is attached for any who wish to help me tackle my problem. Any suggestions would be appreciated, and I understand that in the past few days there has been a lot of activity in the email list. Thank you in advance for your kind help, Abraham Hmiel Research Assistant in Theoretical and Computational Nanoscience Center for Nanoscale Science and Engineering at the State University of New York at Albany
SiNW.fdf
Description: application/vnd.fdf