Searching by number of atoms
Structures composed of a specified number of atoms or defined by a unit cell containing a specified number of atoms can be found by numeric/range searches. For example:
- 8 will find any structures defined with exactly 8 atoms
- 3-5 will find any structures containing either 3, 4 or 5 atoms (as would [3,5])
- >2 will find any structures containing more than 2 atoms
More details on the format:
- A number matches something with that exact number of atoms in the unit cell
- x-y can be used to specify a range (inclusive), and any of the following can also be used according to their usual meaning: >x, >=x, <x, <=x, [x,y], (x,y), [x,y), (x,y]
- x~y can be used to specify a tolerance, e.g. 200~10 is the same as 190-210
- <=x is interpreted as 1-x (similarly for <)
- You should not specify <0 or <=0
Searching by compound formula
Structures of a desired compound containing a specified element(s) can be found using formula-like search terms. For example:
- C will find any structures containing Carbon
- CO will find any structures containing Carbon and Oxygen
- C2 will find any structures containing exactly 2 Carbon atoms within the chemical formula
- C2O3-5 will find any structures containing exactly 2 Carbon atoms and either 3, 4 or 5 Oxygen atoms (as would C2O[3,5]) within the chemical formula
- C2O>2 will find any structures containing exactly 2 Carbon atoms and more than 2 Oxygen atom within the chemical formula
More details on the format:
- Order of elements is unimportant
- An element followed by a * matches something with at least one atom
- An element followed by a number matches something with that exact number of atoms within the formula
- An element followed by a 0 means the element must not exist
- Multiple occurrences for the same element are added together, e.g. C2C2 is the same as C4
- An element with no number is interpreted as being followed by a 1 if any element appears multiple times, and a * otherwise, e.g. CH is the same as C*H*, but CHH is the same as C1H2
- Ranges can be specified in the same way as for number of atoms
- <1 is treated as a special case, and interpreted as 0
- You should not include an element multiple times followed by a 0 or any special characters
Searching by energy
Structures with a total energy can be found by numeric/range searches. This uses the same rules as for searching by number of atoms, with the following changes:
- You can use floating point numbers
- You can use negative numbers
- A number by itself is interpreted as "approximately equals", with tolerance defined by the number of decimal places, e.g. -200 is equivalent to -200~1 and -200.00 is equivalent to -200~0.01
- <=x and <x have their standard meaning, and both <0 and <=0 are allowed
Data retention
You may upload bulk and/or surface structure files into SAINT in order to use the SAINT tools on your project. For example, once uploaded you can generate surfaces from your bulk models (or from the bulk data already in the database). When you do so, the new model is retained on our web servers temporarily so that you can return to it if your connection to the site is temporarily broken. To return to a model at a later date, please remember to bookmark the page or otherwise save the URL. You may also find these models by selecting My Bulk Structures or My Surfaces when performing a search.
Temporary models cannot be found in searches by other users. However, they are not private - you may share the URL with any other person (whether they are a registered user of SAINT or not), and they will be able to access the model.
Models will be retained for at least one week but may be deleted at any point after that.
Uploading files
You may upload files to SAINT in order to work with your own bulk and surface models. At present, SAINT support uploads in CIF format, although some CIF features may not be supported. In particular, the space group can only be specified by number or short name (not full name), and only standard settings are supported. Uploaded files are stored on the web server for a temporary period.
Uploading grids
Trusted users can also upload grids of numerical data, representing measurements at different positions on a plane parallel to the surface, e.g. the electrostatic potential, or the interaction energy of a specified probe molecule. These grids must be in CSV format and contain no headers or row labels. Values will be interpreted as those at grid points that are evenly spaced across the surface of a single unit-cell. For example, if a surface has a 3×3 supercell, then a file with 9 rows and 9 columns should be interpreted as representing values at [x, y] fractional co-ordinates (0, 0) to (1/3, 1/3), with increments of 1/24 in both the x and y direction, as shown in the below diagram.
Due to periodic boundary conditions, the values at 00 and 80 (x,y = 0,0 and 0,1/3 respectively) would be the same due to periodic boundary conditions. This is also true of values at 00 and 08, and so on.
Searching by grid value
Structures containing a specified grid value(s) can be found by numeric/range searches. This uses the same rules as for searching by energy.
Creating surface models
From a chosen bulk phase, surface models can easily be generated. The cut for a surface can be specified by providing values for the Miller index and a location in the bulk unit cell. The latter enables the user to choose what termination is desired when there is more than one unique surface for the chosen Miller index.
When generating a new surface model, you may also request SAINT: saturate bonding (for example, for silica keep all silicon atoms four-coordinated by addition of hydrogen atoms); does not cut through molecules (as determined by comparing interatomic distances to covalent radii) for molecular crystals; or either expose or not expose metallic centres of a Metal Organic Framework. Note that these options are still under development - until complete they may return the same as the standard cut.
Please note that for ionic materials it is left for the user to ensure the surface model is appropriate (currently, SAINT does not automatically reconstruct polar surfaces – Tasker type III – in order to remove the intrinsic dipole).
Publishing models
Trusted users can publish models they have created or uploaded to SAINT. Published models will not be deleted, and will be available for all users, i.e. they can be found using the SAINT search tools.
Before publishing any model, you must ensure that you have the right to do so. Files that you have created yourself should usually be acceptable. Files that you have obtained from other databases may not be acceptable. Structural data taken from a publication can also be linked to the DOI of that paper. If in doubt, please contact the owner of the data, or contact us for assistance.
If there is data on the site that you are the owner of and feel should not be there, please contact us to discuss its removal.
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