Status: draft. Verified steps and screenshots to come.
Contour formaldehyde's electron density and its highest occupied orbital in ParaView, at isovalues you choose. Time: 15 minutes · Program: ParaView · Also in: GaussView, ChimeraX, PyMOL
| Before this | Data | You'll need |
|---|---|---|
| Start ParaView on OnDemand | Formaldehyde's density.cube and homo.cube in ~/scratch/cubes: get the cube files |
A running ParaView session |
Note
Cluster details. Highlighted values are placeholders. AMA27's queue names, module versions, paths and addresses go in when the cluster is deployed.
Why this matters
A cube file holds a number at every point of a box drawn around a molecule: an electron density, an orbital, an electrostatic potential. ParaView treats it as an ordinary volume, so the Contour filter and the color maps from the simulation lessons work on it unchanged, and you can reuse the same pipeline on the next molecule.
Key idea
The Contour filter finds every point where the grid equals a number you type and builds a surface through them, an isosurface. That number is the only setting that matters here. Density is highest near the nuclei, so 0.05 gives a surface close to the atoms and bonds, and 0.0004 one about the size of the molecule. An orbital changes sign between lobes, so it needs two contours, 0.02 and -0.02, in different colors. The orbital here is the HOMO. The topic page works the idea through in more detail.
Steps
Step 1: Open the density
Choose File ▸ Open…, open ~/scratch/cubes/density.cube, and click Apply.
You should see: under density.cube in the Pipeline Browser, two outputs: Molecule (the atoms) and Gridded Data (the numbers). ParaView 6 splits the file this way; in ParaView 5 the reader gives the grid alone.
Screenshot: the Pipeline Browser with the Molecule and Gridded Data outputs
Screenshot to come: The Pipeline Browser showing density.cube with its two outputs, Molecule and Gridded Data
Step 2: Draw the density surface
Select Gridded Data. Choose Filters ▸ Alphabetical ▸ Contour, set Isosurfaces to 0.05, and click Apply.
You should see: a surface around the atoms. Change the value to 0.0004 and click Apply: the surface grows to about the size of the molecule. Set it back to 0.05.
Screenshot: Contour's properties, with Isosurfaces marked
Screenshot to come: The Properties panel for Contour1, with the Isosurfaces value 0.05 marked
Step 3: Show the atoms
Select Molecule. In Properties, type radius in the search box and set Atomic Radius Factor to 5.6. Then select Contour1 and set its Opacity to 0.3.
You should see: four balls inside a see-through surface: oxygen red, carbon gray, the hydrogens white. No bonds are drawn: a cube file records no bonds, and ParaView does not infer them.
Screenshot: the Properties search box finding Atomic Radius Factor
Screenshot to come: The Properties panel with radius typed in its search box, showing Atomic Radius Factor set to 5.6
Note
ParaView measures cube data in grid steps, not in bohr or ångström: about 19 steps to the ångström in these files. Atoms drawn at their usual size in ångströms are specks on that scale, so you enlarge them. The lesson's files are spaced the same along all three axes, to within about 1%, so shapes and proportions are right. A cube file with different spacing on one axis will look stretched along that axis.
Step 4: Draw the orbital
Open homo.cube, select its Gridded Data, and add a Contour with two isosurface values: 0.02 and -0.02. Tick Compute Scalars (click the gear icon to see it) and click Apply. Color the result by the orbital's values with the Cool to Warm preset, and set its Opacity to 0.6.
You should see: four lobes lying in the plane of the molecule, red and blue alternating with the orbital's sign. The pair beside the oxygen straddles the C=O bond; the pair over the hydrogens is the bigger of the two at ±0.02.
What you should see
Screenshot: Contour's properties with both values, and Compute Scalars under the gear icon
Screenshot to come: The Contour properties with the values 0.02 and -0.02, and Compute Scalars ticked, found under the gear icon
Step 5: Save a picture
Choose File ▸ Save Screenshot… and save to ~/scratch/orbitals-paraview.png at 1600 by 1200.
You should see: orbitals-paraview.png in the Files app, in your scratch folder. To make the same picture without clicking, run scripts/orbitals_paraview.py with pvbatch, from the folder holding the cube files.
Check your understanding
You raise the density isovalue from 0.0004 to 0.05. Does the surface get bigger or smaller, and why?
Smaller. A contour keeps only points where the density reaches the value you set. Density rises steeply toward the nuclei, so only points near them reach the larger value.
Why does the orbital need two isosurfaces when the density needs only one?
Because the orbital's sign flips between lobes. A contour at +0.02 catches the positive lobes, one at −0.02 the negative ones. With only the first you would see half the orbital. A density is positive everywhere, so a single contour catches all of it.
If something goes wrong
| What you see | Why | What to do |
|---|---|---|
| No surface at all | The isovalue is higher than any value in the file, or has the wrong sign | Try 0.05 for density, 0.02 and -0.02 for an orbital |
| Only one lobe of the orbital | Only one isosurface value was entered | Enter both 0.02 and -0.02 in Isosurfaces, then Apply |
| The atoms are specks | They're drawn at their size in ångströms on a ruler of grid steps | Set Atomic Radius Factor to 5.6, as in Step 3 |
| The orbital is one flat color | Compute Scalars is off, so there are no values to color by | Tick Compute Scalars under the gear icon, Apply, then color by the orbital's values |
Next
Credits
Cube files computed with PySCF (Apache-2.0) at B3LYP/6-31G(d), the level the Gaussian lessons use.