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Merge branch 'v2.9'
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carlocamilloni committed Apr 27, 2023
2 parents f787e7c + 707d75b commit 79b5d9a
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2 changes: 1 addition & 1 deletion src/crystallization/EnvironmentSimilarity.cpp
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Expand Up @@ -94,7 +94,7 @@ Make sure your PDB file is correctly formatted as explained \ref pdbreader "in t
If only one reference environment is specified then the filename should be given as argument of the keyword REFERENCE.
If instead several reference environments are given, then they have to be provided in separate pdb files and given as arguments of the
keywords REFERENCE_1, REFERENCE_2, etc.
If you have a reference crystal structure configuration you can use the [Environment Finder](https://mybinder.org/v2/gh/PabloPiaggi/EnvironmentFinder/master?urlpath=apps%2FApp.ipynb) app to determine the reference environments that you should use.
If you have a reference crystal structure configuration you can use the [Environment Finder](https://github.com/PabloPiaggi/EnvironmentFinder) app to determine the reference environments that you should use.
If multiple chemical species are involved in the calculation, it is possible to provide the atom types (names) both for atoms in the reference environments and in the simulation box.
This information is provided in pdb files using the atom name field.
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Found broken examples in automatic/a-masterclass-22-09.txt
Found broken examples in automatic/a-masterclass-22-11.txt
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Found broken examples in automatic/PLUMED.tmp
Found broken examples in MiscelaneousPP.md

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