Comments (3)
@tovrstra This can be also useful if we end up supporting dume_cube of non-scalar properties.
from iodata.
Is the format of a vector cube defined clearly somewhere? The description on the cubegen documentation page leaves some room for interpretation. Here is the relevant part:
Densities, the norm of the density gradient, the Laplacian of the density, and the potential are scalars (i.e. one value per point, NVal=1). A gradient cube contains the density plus the vector gradient of the density, so it has four values per point (NVal=4): i.e. the value of the density plus the X, Y, and Z components of its gradient.
Cube files have one row per record (i.e., N1*N2 records each of length N3*NVal). For formatted output, each row is written out in format (6E13.5). In this case, if N3*NVal is not a multiple of six, then there may be blank space in some lines.
Some more details can be found here, but I'm not sure if that page counts as authoritative?
from iodata.
@tovrstra This could be also useful to read the element information of different parts of the mol2 file or the pdb file (atom name or last column)
Another interesting case is when you have a certain file format which can come in a different version as the mol2 files.
from iodata.
Related Issues (20)
- Add CIF load_one HOT 2
- Add separate, more detailed section for the Input Writer? HOT 1
- Clarifications and documentation improvements in `iodata.basis`
- Functions to interpret basis sets: label-to-basis-index and basis-index-to-label
- Decontraction of basis sets
- Conversion to Cartesian basis sets
- General utility for converting between two basis sets HOT 1
- Support different types of normalization of the primitives in `iodata.basis` HOT 1
- Fix `dump_one` and `dump_many` for SDF file format HOT 6
- Support *.mol files HOT 3
- CFOUR molden files HOT 4
- Extract some information from results of `opt` and `scrf` Gaussian jobs HOT 4
- 2-electron reduced density matrices HOT 14
- PDB load_one issue with atom type CL HOT 5
- Compute electronic energy/gradient(force) in IOData
- Input writers for other quantum chemistry software HOT 2
- Install issue on Windows HOT 2
- Can I trust IOData for handling molden files generated from PySCF HOT 2
- Rename some fields read from PDB, to be more in line with PDB conventions HOT 3
- AttributeError: module 'numpy' has no attribute 'int'
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from iodata.