# How to distinguish between surface and bulk calculations? **URL:** \ **Category:** New to AiiDA\ **Created:** [March 15, 2024, 6:14am UTC](https://aiida.discourse.group/t/how-to-distinguish-between-surface-and-bulk-calculations/339 "2024-03-15T06:14:41Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![un1queu5er](https://avatars.discourse-cdn.com/v4/letter/u/45deac/32.png) [@un1queu5er](https://aiida.discourse.group/u/un1queu5er)\ **Post date:** [March 15, 2024, 6:14am UTC](https://aiida.discourse.group/t/how-to-distinguish-between-surface-and-bulk-calculations/339/1 "2024-03-15T06:14:41Z")
We have tens of thousands of immigrated VASP calculations. Now we need to categorize them in surface and bulk calculations. How would you approach this task? ---
**Author:** ![sphuber](https://yyz2.discourse-cdn.com/free1/user_avatar/aiida.discourse.group/sphuber/32/6_2.png) [@sphuber](https://aiida.discourse.group/u/sphuber)\ **Post date:** [March 15, 2024, 8:00am UTC](https://aiida.discourse.group/t/how-to-distinguish-between-surface-and-bulk-calculations/339/2 "2024-03-15T08:00:23Z")
The `StructureData` nodes that represent the crystal structures have a `pbc` property which is a tuple of booleans to indicate whether there are periodic boundary conditions along each axis of the crystal cell. You could check this if any of the axes is set to `False`, which might indicate the surface normal. However, it is quite possible that the calculation is still going to be periodic even long the surface normal, so the `pbc` might still be set to `(True, True, True)` in which case it won’t be helpful. I am not a VASP user, but does it require an input in the `INCAR` to indicate the structure is a surface? If so, I believe the `INCAR` is generated based on the `parameters` input and you could query for the particular input flag. One more possibility if there are no distinghuishing features in the calculation inputs, you could analyse the structure from the `StructureData` itself. Using tools like ASE or pymatgen, you might be able to determine whether it is a surface or not. Once you have a function that can determine whether a `StructureData` is surface or not, you can “tag” it using the _extras_ of the node. Any node can have extras set, which are like tags. You can then use the `QueryBuilder` to query for them. For example: ```python structure = load_node(..) structure.base.extras('is_surface', True) QueryBuilder().append(StructureData, filters={'extras.is_surface': True}).all() ``` Another option is to use groups. You can create two groups and add the different `StructureData` nodes (or their associated VaspCalculation nodes). ```python from aiida.orm import Group bulk_structures = [load_node(), load_node()] surface_group = Group('structures/surface').store() bulk_group = Group('structures/bulk').store() bulk_group.add_nodes(bulk_structures) ``` You can then use the `Group` API to retrieve the nodes of interest, or use `verdi group list`. ---
**Author:** ![un1queu5er](https://avatars.discourse-cdn.com/v4/letter/u/45deac/32.png) [@un1queu5er](https://aiida.discourse.group/u/un1queu5er)\ **Post date:** [March 20, 2024, 4:04pm UTC](https://aiida.discourse.group/t/how-to-distinguish-between-surface-and-bulk-calculations/339/3 "2024-03-20T16:04:57Z")
Thank you for your answer. This is the query for the option based on `StructureData`: ```auto QueryBuilder().append(StructureData, filters = {"attributes.pbc1": {"==": True}, "attributes.pbc2": {"==": True}, "attributes.pbc3": {"==": False}}) ``` Not very successful in my case. For me it is often not obvious how attributes are named. Luckily, I found it in the source code. > Is there an easier way to find out what are the available attributes for the filters? Another approach utilizing kpoints: Often kpoint mesh in z direction is set to 1. ```auto QueryBuilder().append(KpointsData, filters = {"attributes.mesh.2": {"==": 1}}, tag="kpoints").append(CalcJobNode, with_incoming="kpoints", tag="calc").append(StructureData, with_outgoing="calc") ``` I’m not aware of any flag in `INCAR` indicate that a surface is calculated. Is it possible to propagate this `is_surface` property (group or extra) of the input structure automatically to the relaxed output structure of a calculation? ---
**Author:** ![sphuber](https://yyz2.discourse-cdn.com/free1/user_avatar/aiida.discourse.group/sphuber/32/6_2.png) [@sphuber](https://aiida.discourse.group/u/sphuber)\ **Post date:** [March 20, 2024, 4:40pm UTC](https://aiida.discourse.group/t/how-to-distinguish-between-surface-and-bulk-calculations/339/4 "2024-03-20T16:40:36Z")
> [@un1queu5er](#): > > Is there an easier way to find out what are the available attributes for the filters? As a matter of fact, we [just merged a PR](https://github.com/aiidateam/aiida-core/pull/6245) that provides this functionality. With that feature, you would have been able to do ```python QueryBuilder().append( StructureData, filters=(StructureData.fields.pbc1 == True) ) ``` The `StructureData.fields` is tab-completable, so in an interactive shell or IDE you can discover the fields that can be queried and projected. > Is it possible to propagate this `is_surface` property (group or extra) of the input structure automatically to the relaxed output structure of a calculation? Since the output nodes already exist, there is no automation. But you can manually propagate them. Or if you want to have them on the output structure, why not directly set the extra there or add the output structures to the group? ---
**Author:** ![un1queu5er](https://avatars.discourse-cdn.com/v4/letter/u/45deac/32.png) [@un1queu5er](https://aiida.discourse.group/u/un1queu5er)\ **Post date:** [March 20, 2024, 6:32pm UTC](https://aiida.discourse.group/t/how-to-distinguish-between-surface-and-bulk-calculations/339/5 "2024-03-20T18:32:49Z")
> [@sphuber](#): > > > [@un1queu5er](#): > > > > Is there an easier way to find out what are the available attributes for the filters? > > As a matter of fact, we [just merged a PR](https://github.com/aiidateam/aiida-core/pull/6245) that provides this functionality. With that feature, you would have been able to do > > ```auto > QueryBuilder().append( > StructureData, filters=(StructureData.fields.pbc1 == True) > ) > > ``` > > The `StructureData.fields` is tab-completable, so in an interactive shell or IDE you can discover the fields that can be queried and projected. Great! > [@sphuber](#): > > > Is it possible to propagate this `is_surface` property (group or extra) of the input structure automatically to the relaxed output structure of a calculation? > > Since the output nodes already exist, there is no automation. But you can manually propagate them. Or if you want to have them on the output structure, why not directly set the extra there or add the output structures to the group? I see. Thanks.