Diamond Version 5 User Manual: Building up structural parts

Pump Up or Shrink Polymeric Frameworks

Suitable for polymers: Pump up or shrink multiple coordination spheres around selected atoms

This article in brief:
- Pumping means adding directly another coordination sphere around the currently selected central atom(s), even if there are already one or more completed coordination spheres around. That means Diamond adds atoms around the atoms of the (currently) farmost coordination sphere around the central atom(s).
- Shrinking directly removes atoms from the farmost coordination sphere around the selected central atom(s).
- Available as push buttons "Pump now" and "Shrink now" from within "Coordination Spheres" dialog or to perform directly from the dropdown menu of the "Fill coordination spheres directly" button in the "Build" toolbar.

Previous article: Grow or cut molecular fragments or polymers
Next article: Using the mouse wheel

"Pump Now" and "Shrink Now" in the "Coordination Spheres" dialog
We open the sample document "PCD-1251073-unit-cell-with-Sb-polyhedra.diamdoc" and select the "Sb4" atom in the upper part of the picture. Then we open the "Coordination Spheres" dialog (command "Build"/"Coordination Spheres..."), change "Apply to" to "Selected atoms in structure picture" and set the checkmark at "Create broken-off bonds".

Note: The screenshots have been made with version 4 of Diamond.

When you press the "Pump Now" button several times, this leads to the following sequence:

Reverse function "Shrink Now" leads to the following sequence: This path is different from the "Pump Now" path. This is because the shrinking function begins with  the outmost sphere of the selected atom -- independently from what previous calls of the pumping function have created. The atoms in the bottom part of the structure picture -- created by a "fill unit cell" command before the actual pumping has begun -- are farer away from the selected "Sb4" atom than the spheres  around the "Sb4" atom created by the pumping function.

If you want to have the shrinking following the path of previous pumpings, you should use the mouse wheeling mode for pumping and shrinking. Cf. article "Mouse Wheeling".

Direct commands from the toolbar
You can perform the commands "Pump" and "Shrink" directly from the dropdown menu of the "Fill coordination spheres directly" button in the "Picture" toolbar:

"Pump and shrink" compared to "grow and cut"
"Pump and shrink" work similar to "grow and cut" (as described in the previous article). Show difference to "grow and cut" with sodium chloride, starting from Cl at (1/2, 1/2, 1/2). When no atom is selected, that means you start from "all atoms", the results are the same.

This is the sequence where we pump up the structure at Cl at 1/2,1/2,1/2, ...

... whereas "grow" with the same starting point (Cl at 1/2,1/2,1/2 in the filled unit cell) leads to that sequence:

Previous article: Grow or cut molecular fragments or polymers
Next article: Using the mouse wheel

Reference for PCD:1251073 -- Sb4F16:
Gillespie R.J., Slim D.R., Vekris J.E.; "The Crystal Structure of the 1:1 Adduct of Antimony Trifluoride and Antimony Pentafluoride"; Journal of the Chemical Society. Dalton Transactions, Inorganic Chemistry (1972-), ?, 971-974 (1977).