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Gaussian cube files and periodicity Date: 2017/11/19 18:05 Name: lzotti Hi All, we are experiencing some problems when visualizing the homo and lumo Gaussian cube files generated by Openmx. The calculation was run by the “cluster” method. When we import these files into VMD, the isosurface map appears as contained in a box (which we understand it is the cell automatically defined by OpenmX) in which the isosurface map appears broken into parts. In some of them it is perfectly aligned with the atoms the orbital is localized on, but in others it is shifted according to the periodicity defined by the size of this box. Is there any way to avoid this and to make sure the output is not broken into regions?

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Re: Gaussian cube files and periodicity ( No.1 ) Date: 2017/11/20 15:19 Name: Yung-Ting Lee  <ytlee@issp.u-tokyo.ac.jp> Dear lzotti, Could you provide some of your HOMO/LUMO cube files or any other examples (or images) for isosurface broken into regions / parts? Thank you. Yung-Ting Lee. Re: Gaussian cube files and periodicity ( No.2 ) Date: 2017/11/20 23:23 Name: lzotti Dear Yung-Ting Lee, thank you very much for offering your help but actually we've just solved the problem. It was due to having accidentally left, in the input file, the value of scf.fixed.grid resulting from a previous calculation. By deleting this line everything went back to normal.

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