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fix: Creating configuration for CuBTC example (#1854) #1856

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merged 4 commits into from
Apr 15, 2024
Merged

fix: Creating configuration for CuBTC example (#1854) #1856

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792f86d
Consistency between UI control and code.
trisyoungs Apr 15, 2024
2777779
Copy box for supercell species.
trisyoungs Apr 15, 2024
069f267
Tweak UI.
trisyoungs Apr 15, 2024
c3e4a34
Update docs.
trisyoungs Apr 15, 2024
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32 changes: 24 additions & 8 deletions src/gui/importCIFDialog.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,7 @@
<rect>
<x>0</x>
<y>0</y>
<width>162</width>
<width>292</width>
<height>639</height>
</rect>
</property>
Expand Down Expand Up @@ -392,8 +392,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>407</width>
<height>675</height>
<width>296</width>
<height>625</height>
</rect>
</property>
<attribute name="icon">
Expand Down Expand Up @@ -482,7 +482,7 @@
<string>Remove any water molecules or coordinated oxygens without hydrogens</string>
</property>
<property name="text">
<string>Remove water and coordinated oxygen</string>
<string>Remove water and coordinated oxygens</string>
</property>
</widget>
</item>
Expand Down Expand Up @@ -598,8 +598,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>407</width>
<height>675</height>
<width>276</width>
<height>93</height>
</rect>
</property>
<attribute name="icon">
Expand Down Expand Up @@ -691,8 +691,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>407</width>
<height>675</height>
<width>96</width>
<height>78</height>
</rect>
</property>
<attribute name="icon">
Expand Down Expand Up @@ -728,6 +728,14 @@
</layout>
</widget>
<widget class="QWidget" name="DetectedSpeciesToolBoxPage">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>96</width>
<height>78</height>
</rect>
</property>
<attribute name="icon">
<iconset resource="main.qrc">
<normaloff>:/general/icons/threeSpecies.svg</normaloff>:/general/icons/threeSpecies.svg</iconset>
Expand Down Expand Up @@ -757,6 +765,14 @@
</layout>
</widget>
<widget class="QWidget" name="SupercellToolBoxPage">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>167</width>
<height>142</height>
</rect>
</property>
<attribute name="icon">
<iconset resource="main.qrc">
<normaloff>:/general/icons/configuration.svg</normaloff>:/general/icons/configuration.svg</iconset>
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4 changes: 3 additions & 1 deletion src/io/import/cif.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -973,12 +973,14 @@ void CIFHandler::finalise(CoreData &coreData, const Flags<OutputFlags> &flags) c
{
auto *sp = coreData.addSpecies();
sp->copyBasic(&supercellSpecies_);
if (flags.isSet(OutputFlags::OutputFramework))
if (flags.isSet(OutputFlags::OutputSupermolecule))
{
sp->removePeriodicBonds();
sp->updateIntramolecularTerms();
sp->removeBox();
}
else
sp->createBox(supercellSpecies_.box()->axisLengths(), supercellSpecies_.box()->axisAngles());

if (flags.isSet(OutputFlags::OutputConfiguration))
{
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2 changes: 1 addition & 1 deletion src/io/import/cif.h
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ class CIFHandler
// Bonding tolerance, if calculating bonding rather than using CIF definitions
double bondingTolerance_{1.1};
// Whether to prevent metallic bonding
bool preventMetallicBonds_{false};
bool preventMetallicBonds_{true};
// Whether to remove free atomic moieties in clean-up
bool removeAtomics_{false};
// Whether to remove water and coordinated oxygen atoms in clean-up
Expand Down
6 changes: 3 additions & 3 deletions web/docs/examples/cu-btc/step1.md
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Expand Up @@ -22,17 +22,17 @@ The default options get us most of the way there, but it's instructive to take a

Before we proceed, make sure that the default Cu-BTC groups (`Global/Default`, `B/Default`, and `A/1`) are the only ones enabled.

Now, if you look closely at the crystal structure you'll see "extra" oxygen atoms attached to the copper sites:
Now, if you look closely at the crystal structure you'll see some oxygen atoms floating around in space...

{{< cimage src="../cu-btc-default-zoom.png" caption="Dangling oxygens on Cu sites" >}}

These are in fact from coordinated water molecules present when the crystal structure was determined - the water hydrogen atoms are not present in the CIF data. We will remove these oxygen atoms since we want a perfectly "dry" unit cell.

{{< action type="mouse" >}}Open the {{<gui-button icon="delete" text="Structure Cleanup">}} section{{< /action >}}

The _Structure Cleanup_ page has several options for cleaning up various aspects of the structure we currently have, for example removing free atoms/ions. We want to use the option to remove water molecules, which will also remove terminal oxygen atoms based on the assumption that hydrogen positions were not available in the CIF. So:
The _Structure Cleanup_ page has several options for cleaning up various aspects of the structure we currently have, for example removing free atoms/ions. There is a specific option for removing water molecules (_Remove water and coordinated oxygens_) which will also remove terminal oxygen atoms based on the assumption that hydrogen positions were not available in the CIF. Ours are just free atoms, however, so:

{{< action type="check" >}}Enable the _Remove water and coordinated oxygen_ option{{< /action >}}
{{< action type="check" >}}Enable the _Remove unbound atoms_ option{{< /action >}}

You should see those terminal oxygen atoms disappear from the structure, leaving us with a "pure" Cu-BTC framework. There are a couple of pages left in the wizard which allow us to create a supercell from the unit cell,

Expand Down
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