1

Hello.
I have a question that’s been on my mindso I’m posting it here in the community for the first time.

For the Material Projectthere are two versions: the Legacy site and the newly revamped site. I used the Legacy site firstand while using the recently updated siteI have some questionsso I’m reaching out.

  1. How to export a primitive cell
    On the Legacy sitethere was a clear button to extract the primitive cell as a cif filebut on the New siteeven when I change the crystal structure to a primitive cell and click “export as,” it seems to still give me the conventional cell structure. Additionallythe crystal structures of the cells downloaded from the Legacy site and the Renewal site look slightly different. Why is that?

  2. Different Energy Above Hull
    Of courseI understand that this issue may vary depending on the calculation process and the data that has been accumulated over time.
    HoweverI’m generally looking to check Hull Energy as a criterion for finding a stable phasebut I’m confused because the Hull Energy differs between Legacy and Newmaking it hard to determine which material has a more stable phase.
    For examplein the case of Cothe Energy Above Hull for “mp-54” and “mp-102” is different in Legacy and New.
    If Energy Above Hull = 0 indicates a more stable statethen in Legacymp-54 shows a value of 0making it appear more stablewhile in Newmp-102 shows 0indicating that it is more stable. I would appreciate it if you could explain the reason for these differences.

Best regards.

2
  1. We’re currently working on adding features to the next-gen site that were present in the legacy siteincluding a structure download - @ruoxiyang can hopefully comment if I’m wrong. For nowyou can download primitive structures through the API as follows:
from mp_api.client import MPRester

with MPRester("your_api_key") as mpr:
    # if you only need a single structure:
    structure = mpr.get_structure_by_material_id("mp-xxxxxx")
primitive_cell = structure.get_primitive_structure()

# write to filecan do something like "structure.cif""POSCAR"etc.
primitive_cell.to("structure.cif")

If you want to download larger batches of structuresuse mpr.materials.summary.search(material_ids=[<list of MP IDs>]).

Additionallythe crystal structures of the cells downloaded from the Legacy site and the Renewal site look slightly different. Why is that?

This also partly answers your second questionbut MP is in the process of recomputing all structures in our database (relaxed structures + thermodynamic + electronic properties) with a higher level of theory (r2SCAN vs. the older PBE GGA). You can find details about this here and here.

  1. The hulls in the next-gen site use a mixture of r2SCAN and PBE+U hulls (see the previous links)so they’ll differ from the legacy site. We recommend using the next-gen site for more accurate hulls/stabilities.
1 Like
3

Thank you for your reply.

First offsince it looks like the group still adding features to the next-gen siteit seems that downloading primitive cells isn’t possible on the siteright?
I’ll try downloading it using the API.

Nextyou mentioned that the results from the next-gen site are more accurate.
In the case of Coit’s known to undergo a phase transition from HCP structure at low temperatures to FCC structure at high temperatures around 825K [12].
I believe the Hull Energy calculation method is generally conducted at 0K,
so shouldn’t the HCP structuremp-54show a more stable result than the FCC structuremp-102?

image
image1628×251 11.9 KB

Best regards.

[1] First Principles Theory of the hcp-fcc Phase Transition in Cobalt | Scientific Reports (nature.com)
[2] Cobalt - Wikipedia

4

First offsince it looks like the group still adding features to the next-gen siteit seems that downloading primitive cells isn’t possible on the siteright?
I’ll try downloading it using the API.

Yes please use the API for now.

I believe the Hull Energy calculation method is generally conducted at 0K,
so shouldn’t the HCP structuremp-54show a more stable result than the FCC structuremp-102?

You’ve found an interesting edge case where r2SCAN actually predicts hcp Co to be dynamically unstableand fcc Co to be stable - see p. 024102-4 of this paper by Liu et al. I wasn’t aware of this previously.

There’s no single DFT method right now that offers universal accuracy. r2SCAN is generally more accurate but not in this specific case.

1 Like
5

According to the paper I attached earlierin the absence of magnetismCo is generally expected to have a stable phase in an FCC structure [1].

I haven’t had time to read through the link you attached yetbut here’s what I’ve roughly gathered.

  1. SCAN overstabilizes the ferromagnetic (FM) state when it has a very large local magnetic moment.
  2. In r2SCANa different approach was introduced to address this issue.
  3. The r2SCAN calculations were performed using VASPand spin-polarized calculations were conducted.
  4. At this timeCo was assumed to be ferromagnetic.

image
image520×545 106 KB

image
image526×535 106 KB

If the magnetic calculations are accurateshould we consider that the difference between the paper I presented and the one you suggested might be due to the fact thatas you mentioned earlier,

There’s no single DFT method right now that offers universal accuracy. r2SCAN is generally more accurate but not in this specific case.

there isn’t a single DFT method that provides universal accuracywhich could mean one of them might not have had an accurate calculation?

[1] First Principles Theory of the hcp-fcc Phase Transition in Cobalt | Scientific Reports (nature.com)

6

Hey.
I’d like to get some primitive cell data of Cobalt binary metals.

So I tried structure = mpr.materials.summary.search like below.

image
image836×322 10.1 KB

But this code threw an error like this.

image
image780×129 5.04 KB

It worked fine when outputting the primitive cell of a single substance.

Can you tell me how I can quickly extract the primitive cell data for multiple substances?
Even I read the MP public docsI didn’t get it as well.
Where can I find the whole codes and option list?

Thank you.

7

mpr.materials.summary.search() returns a list of structures. Run .get_primitive_structure() on the list element(s) by using an index or for loop.

1 Like
8

Hi.
Thanks for your advise.

You meanI should make an array of whole materials by using mpr.materials.summary.search()and print out those structure’s primitive cell with loop?

If socan you please tell me is the code I wrote right?

import os
from mp_api.client import MPRester

with MPRester("My API") as mpr:
    structures = mpr.materials.summary.search(
                elements = ["Co"],
                chemsys = "Co-*",
                energy_above_hull = (00),
                is_metal = True,
                is_stable = True
)

with open("2test.txt""w") as file:
    # count number of doc.
    file.write(f"Number of documents: {len(structures)}\n\n")

    if not structures:  # if nothing searched
        file.write("No results found.\n")
    else:
	for idxstructure_summary in enumerate(structures):
            # bring structure informations
            structure = mpr.get_structure_by_material_id(material_id)
            # extract primitive cell data
            primitive_cell = structure.get_primitive_structure() 

            # Save material_id and primitive cell information into test.txt file
            file.write(f"--- Document {idx + 1} ---\n")
            file.write(f"Primitive Structure:\n{primitive_cell}\n")
            file.write('-' * 40 + "\n")
            file.write("\n\n")

And my output is like below.

2test.txt

Number of documents: 110

— Document 1 —
Primitive Structure:
Full Formula (Zr6 Co23)
Reduced Formula: Zr6Co23
abc : 8.115843 8.115850 8.115907
angles: 59.999331 59.999260 59.999416
pbc : True True True
Sites (29)

SP a b c magmom

0 Zr 0.788177 0.211827 0.211805 -0.373
1 Zr 0.788195 0.788182 0.211813 -0.373
2 Zr 0.211832 0.211812 0.788177 -0.373
3 Zr 0.788179 0.211826 0.788191 -0.373
4 Zr 0.21183 0.788176 0.211802 -0.373
5 Zr 0.211829 0.788179 0.788191 -0.373
6 Co 0.499995 0.499998 0.500003 2.083
7 Co 0.500002 -3e-06 -5e-06 1.806
8 Co -7e-06 -8e-06 0.500007 1.806
9 Co 0.5 0.500003 -1e-06 1.806
10 Co -3e-06 0.500005 0.500006 1.806
11 Co -4e-06 0.500005 -8e-06 1.806
12 Co 0.500001 -1e-06 0.500005 1.806
13 Co 0.377919 0.377919 0.377934 1.63
14 Co 0.622079 0.622082 0.133761 1.63
15 Co 0.133757 0.622087 0.622077 1.63
16 Co 0.622088 0.133757 0.622078 1.63
17 Co 0.866229 0.377914 0.377928 1.63
18 Co 0.377908 0.866239 0.377926 1.63
19 Co 0.377922 0.377918 0.866226 1.63
20 Co 0.62208 0.622081 0.622079 1.629
21 Co 0.173961 0.173958 0.173965 1.457
22 Co 0.82603 0.826037 0.521902 1.457
23 Co 0.521903 0.826037 0.826028 1.457
24 Co 0.826038 0.521894 0.826032 1.457
25 Co 0.478102 0.173962 0.173971 1.457
26 Co 0.173959 0.478118 0.173964 1.457
27 Co 0.173963 0.173961 0.478113 1.457
28 Co 0.826035 0.826037 0.826029 1.457

— Document 2 —
Primitive Structure:
Full Formula (Zr6 Co23)
Reduced Formula: Zr6Co23
abc : 8.115843 8.115850 8.115907
angles: 59.999331 59.999260 59.999416
pbc : True True True
Sites (29)

SP a b c magmom

0 Zr 0.788177 0.211827 0.211805 -0.373
1 Zr 0.788195 0.788182 0.211813 -0.373
2 Zr 0.211832 0.211812 0.788177 -0.373
3 Zr 0.788179 0.211826 0.788191 -0.373
4 Zr 0.21183 0.788176 0.211802 -0.373
5 Zr 0.211829 0.788179 0.788191 -0.373
6 Co 0.499995 0.499998 0.500003 2.083
7 Co 0.500002 -3e-06 -5e-06 1.806
8 Co -7e-06 -8e-06 0.500007 1.806
9 Co 0.5 0.500003 -1e-06 1.806
10 Co -3e-06 0.500005 0.500006 1.806
11 Co -4e-06 0.500005 -8e-06 1.806
12 Co 0.500001 -1e-06 0.500005 1.806
13 Co 0.377919 0.377919 0.377934 1.63
14 Co 0.622079 0.622082 0.133761 1.63
15 Co 0.133757 0.622087 0.622077 1.63
16 Co 0.622088 0.133757 0.622078 1.63
17 Co 0.866229 0.377914 0.377928 1.63
18 Co 0.377908 0.866239 0.377926 1.63
19 Co 0.377922 0.377918 0.866226 1.63
20 Co 0.62208 0.622081 0.622079 1.629
21 Co 0.173961 0.173958 0.173965 1.457
22 Co 0.82603 0.826037 0.521902 1.457
23 Co 0.521903 0.826037 0.826028 1.457
24 Co 0.826038 0.521894 0.826032 1.457
25 Co 0.478102 0.173962 0.173971 1.457
26 Co 0.173959 0.478118 0.173964 1.457
27 Co 0.173963 0.173961 0.478113 1.457
28 Co 0.826035 0.826037 0.826029 1.457

… etc.

But I have no idea how should I make them with .cif file.

primitive_cell.to("2test.cif")

My lack of coding skill lead to be unable to make progress.
Is there any good idea?

Best regards.

9

Umm… thanks for the GPT… I mad it.

import os
from mp_api.client import MPRester

with MPRester("My_API") as mpr:
#    structure = mpr.get_structure_by_material_id("mp-149")
    structures = mpr.materials.summary.search(
#               material_ids = ["mp-149""mp-2241"])     #for multiple structure
                elements = ["Co"],
                chemsys = "Co-*",
#               formula = "AB"
#               band_gap = (0.51.0),
                energy_above_hull = (00),
                is_metal = True,
                is_stable = True
)


with open("test.txt""w") as file:
    file.write(f"Number of documents: {len(structures)}\n\n")

    if not structures:
        file.write("No results found.\n")
    else:
	for idxstructure_summary in enumerate(structures):
            material_id = structure_summary.material_id
            formula = structure_summary.formula_pretty
#            E_Hull = structure_summary.energy_above_hull
#            Is_Metal = structure_summary.is_metal
#            stable = structure_summary.is_stable
#            crystal = structure_summary.structure
            sym = structure_summary.symmetry

            structure = mpr.get_structure_by_material_id(material_id)
            primitive_cell = structure.get_primitive_structure()

            cif_filename = f"{formula}.cif"
            primitive_cell.to(filename = cif_filename)

            file.write(f"--- Document {idx + 1} ---\n")
            file.write(f"Material ID: {material_id}\n")
#            file.write(f"Chemical Formula: {formula}\n")
#            file.write(f"Energy Above Hull: {E_Hull}\n")
#            file.write(f"Is Metal: {Is_Metal}\n")
#            file.write(f"Stable: {stable}\n")
#            file.write(f"Crystal: {structure}\n")
            file.write(f"Symmetry: {sym}\n")
            file.write(f"Primitive Structure:\n{primitive_cell}\n")
            file.write('-' * 40 + "\n")
            file.write("\n\n")

First of allI’ve written it this waybut if there are any good options for optimizationplease let me know.

And there is another question.
There is another option to figure out the cell data.

crystal = structure_summary.structure

When I use this optionthe variable “crystal” include whole materials data.
It seems that the structure_summary.structure is same as structure.get_primitive_structure().

Can you tell me if I right?

   for idxstructure_summary in enumerate(structures):
           material_id = structure_summary.material_id
           formula = structure_summary.formula_pretty
           sym = structure_summary.symmetry
           structure = mpr.get_structure_by_material_id(material_id)
           primitive_cell = structure.get_primitive_structure()
           file.write(f"--- Document {idx + 1} ---\n")
           file.write(f"Material ID: {material_id}\n")
           file.write(f"Symmetry: {sym}\n")
           file.write(f"Primitive Structure:\n{primitive_cell}\n")
           file.write('-' * 40 + "\n")
           file.write("\n\n")
output by `structure.get_primitive_structure()`

Number of documents: 110

— Document 1 —
Material ID: mp-9945
Symmetry: crystal_system=<CrystalSystem.ortho: ‘Orthorhombic’> symbol=‘Pnnm’ number=58 point_group=‘mmm’ symprec=0.1 version=‘2.0.2’
Primitive Structure:
Full Formula (Co2 Te4)
Reduced Formula: CoTe2
abc : 3.936121 5.322096 6.390892
angles: 90.001887 90.000000 90.000000
pbc : True True True
Sites (6)

SP a b c magmom

0 Co -0 -0 0 1.161
1 Co 0.5 0.5 0.5 1.16
2 Te -0 0.21977 0.365541 -0.052
3 Te -0 0.78023 0.634459 -0.052
4 Te 0.5 0.719763 0.134487 -0.052
5 Te 0.5 0.280237 0.865513 -0.052

— Document 2 —
Material ID: mp-284
Symmetry: crystal_system=<CrystalSystem.cubic: ‘Cubic’> symbol=‘Pm-3m’ number=221 point_group=‘m-3m’ symprec=0.1 version=‘2.0.2’
Primitive Structure:
Full Formula (Al1 Co1)
Reduced Formula: AlCo
abc : 2.819403 2.819403 2.819403
angles: 90.000000 90.000000 90.000000
pbc : True True True
Sites (2)

SP a b c magmom

0 Al -0 -0 -0 0
1 Co 0.5 0.5 0.5 -0

        for idxstructure_summary in enumerate(structures):
            material_id = structure_summary.material_id
            sym = structure_summary.symmetry
            crystal = structure_summary.structure
            file.write(f"--- Document {idx + 1} ---\n")
            file.write(f"Material ID: {material_id}\n")
            file.write(f"Symmetry: {sym}\n")
            file.write(f"Crystal: {crystal}\n")
            file.write('-' * 40 + "\n")
            file.write("\n\n")
output by `structure_summary.structure`

Number of documents: 110

— Document 1 —
Material ID: mp-9945
Symmetry: crystal_system=<CrystalSystem.ortho: ‘Orthorhombic’> symbol=‘Pnnm’ number=58 point_group=‘mmm’ symprec=0.1 version=‘2.0.2’
Crystal: Full Formula (Co2 Te4)
Reduced Formula: CoTe2
abc : 3.936121 5.322096 6.390892
angles: 90.001887 90.000000 90.000000
pbc : True True True
Sites (6)

SP a b c magmom

0 Co -0 -0 0 1.161
1 Co 0.5 0.5 0.5 1.16
2 Te -0 0.21977 0.365541 -0.052
3 Te -0 0.78023 0.634459 -0.052
4 Te 0.5 0.719763 0.134487 -0.052
5 Te 0.5 0.280237 0.865513 -0.052

— Document 2 —
Material ID: mp-284
Symmetry: crystal_system=<CrystalSystem.cubic: ‘Cubic’> symbol=‘Pm-3m’ number=221 point_group=‘m-3m’ symprec=0.1 version=‘2.0.2’
Crystal: Full Formula (Al1 Co1)
Reduced Formula: AlCo
abc : 2.819403 2.819403 2.819403
angles: 90.000000 90.000000 90.000000
pbc : True True True
Sites (2)

SP a b c magmom

0 Al -0 -0 -0 0
1 Co 0.5 0.5 0.5 -0

10

Couple of things to consider:

  • If you’re retrieving a lot of structures or repeatedly have to run the same queriesit’s much more performant to download all structuressave them to disk and post-filter (see here for a start)
  • You don’t need to call mpr.get_structure_by_material_id(). The structure should already be in your structures list and accessible via structure_summary.structure.

HTH

1 Like
11

Thank you so much for your response.
And I’m sorry for checking late and replying now.
SomehowI managed to successfully extract the data.

I’m sorry for keeps askingbut I still don’t really get it and there are parts that keep confusing me…

  • You don’t need to call mpr.get_structure_by_material_id(). The structure should already be in your structures list and accessible via structure_summary.structure
  • Does this mean that since structure data is already inside structureswe don’t need to call structure = mpr.get_structure_by_material_id(material_id) again?
  • Sodoes that mean I can just use structures = mpr.materials.summary.search(~) to extract the data without necessarily using primitive_cell = structure.get_primitive_structure()and it will still give me the primitive cell structure?
  • I’m asking if just using the second piece of code I posted above can extract the primitive cell.

Here I have a few more questions. Regarding the indicators provided by the materials projectare the sorting results for predicted stable and Energy above Hull the same?
I looked into the cases of CuRuand Coand for metallic compounds (alloys)it seems that if Energy above Hull = 0they are all considered predicted stable.

I know that generallya state with Energy above Hull = 0 is thought as the most stable state. HoweverI’m wondering if there’s a specific reason for having those two options split into different columns.
Additionallycould you please direct me to detailed explanations for each column elements (synthesizableis metalpredicted stableformation energyetc.)? I recall finding explanations for those criteria on the site beforebut now I cannot locate them.

+ Is there any way to plot the cohesive energy of each materials?
I referred to dwinston’s answer and added the items below. (For MPResterI’m just using the mp_api.client as it is.)

from pymatgen.ext.matproj import MPRester
mpr = MPRester()
mpr.get_cohesive_energy('mp-721988'per_atom=True) # 6.73 eV/atom

My python file is below.

import os  
from mp_api.client import MPRester  

with MPRester("ZiWsNasQOf0xOblqHoCg97K6Cu2kWk7B") as mpr:  
    structures = mpr.materials.summary.search(  
                elements = ["Co"] 
                chemsys = "Co-*" 
                energy_above_hull = (00) 
                is_metal = True 
                is_stable = True  
)  

with open("test.txt""w") as file:  
    file.write(f"Number of documents: {len(structures)}\n\n")  

    if not structures:  
        file.write("No results found.\n")  
    else:  
        for idxstructure_summary in enumerate(structures):  
            material_id = structure_summary.material_id  
            formula = structure_summary.formula_pretty  
            sym = structure_summary.symmetry  

            structure = mpr.get_structure_by_material_id(material_id)  
#            cohesive = mpr.get_cohesive_energy_by_material_id(material_idper_atom = True)  
            cohesive = mpr.get_cohesive_energy(material_idper_atom = True)  
            primitive_cell = structure.get_primitive_structure()  

            cif_filename = f"{formula}.cif"  
            primitive_cell.to(filename = cif_filename)  

            file.write(f"--- Document {idx + 1} ---\n")  
            file.write(f"Material ID: {material_id}\n")  
            file.write(f"Symmetry: {sym}\n")  
            file.write(f"Cohesive: {cohesive}\n")  
            file.write(f"Primitive Structure:\n{primitive_cell}\n")  
            file.write('-' * 40 + "\n")  
            file.write("\n\n")

Howeverthe following error occurs. Is it not possible to use mpr.get_cohesive in our mp_api.client as referenced above?

Traceback (most recent call last):
File “/home/-/MP_API/API/Test_Cohesive.py”line 35in
cohesive = mpr.get_cohesive_energy(material_idper_atom = True)
^^^^^^^^^^^^^^^^^^^^^^^
File “/home/-/anaconda3/lib/python3.11/site-packages/mp_api/client/mprester.py”line 399in getattr
raise AttributeError(
AttributeError: ‘MPRester’ object has no attribute ‘get_cohesive_energy’

Best regards.

12

Hello,

I tried downloading the entire data as you mentioned in the form of documentation (mp_docs.on)but I’m not sure how to sort using the .on file. When I open this file itselfthe capacity is too large (almost 2GB) and there’s an issue where the shell itself stops.

Moreovereven if I try to extract the file to Windows for post-processingit’s difficult because the file size is too large. Can you explain again exactly how to sort using the on file?