# Interpretation of decomposition amounts

I ran an optimization of a structure with stoichiometry YBaMn2O5F, and added a powerup to check the stability. The following was written to the “launches” section of my mongo database

“action”: {

“stored_data”: {

“is_compatible”: true,

“decomposes_to”: [

{

“formula”: “BaF2”,

“amount”: 0.15000000000000002,

“material_id”: “MP#mp-1029”

},

{

“formula”: “Ba5Mn5O14”,

“amount”: 0.05714285714285694,

“material_id”: “MP#mp-763829”

},

{

“formula”: “YMnO3”,

“amount”: 0.5,

“material_id”: “MP#mp-19385”

},

{

“formula”: “Mn3O4”,

“amount”: 0.1166666666666667,

“material_id”: “MP#mp-18759”

},

{

“formula”: “Ba8Mn8O21”,

“amount”: 0.17619047619047734,

“material_id”: “MP#mp-694888”

}

],

“entry_id”: null,

“e_above_hull”: 0.10458794885714973

which would seem to give the stoichiometry

Y: 0.5

Ba: 1.85

Mn: 2.55

O: 6.47

F: 0.3

My second thought was that “amount” might mean “fraction of the cell in the referenced MP calculation”. Since Mn3O4 has 3 formula units in the MP cell, YMnO3 has 6, Ba8Mn8O21 has 1, BaF2 has 1, and Ba5Mn5O14 has 2, this would give

Y: 3

Ba: 2.13

Mn: 6.03

O: 15.7

F: 0.3

This is much closer but a couple of the species are still off by a large amount. Could someone please let me know what the amounts mean?

They seem to be created by the Simplex class in pymatgen.util.coord, then passed through several functions in pymatgen.phasediagram.analyzer, then finally to check_stability in glue_tasks.py

I am not sure what is going on. The first way you computed the stoichiometry (with Y=0.5) is what I would have expected to yield the original stoichiometry.

Can you send me the vasprun.xml and OUTCAR of the calculation somehow? The code I need to run is:

``````
vasprun, outcar = get_vasprun_outcar(self.get("calc_dir", "."),

parse_dos=False,

parse_eigen=False)

my_entry = vasprun.get_computed_entry(inc_structure=False)

stored_data = mpr.get_stability([my_entry])[0]

``````

If that is giving strange answers, I will post it to the pymatgen list since the mpr.get_stability should be in pymatgen’s domain. But first I just want to check the OUTCAR for example and also just rerun it myself.

Anubhav

···

On Tue, Jun 12, 2018 at 10:37 AM, Steven Hartman [email protected] wrote:

I ran an optimization of a structure with stoichiometry YBaMn2O5F, and added a powerup to check the stability. The following was written to the “launches” section of my mongo database

“action”: {

“stored_data”: {

“is_compatible”: true,

“decomposes_to”: [

{

“formula”: “BaF2”,

“amount”: 0.15000000000000002,

“material_id”: “MP#mp-1029”

},

{

“formula”: “Ba5Mn5O14”,

“amount”: 0.05714285714285694,

“material_id”: “MP#mp-763829”

},

{

“formula”: “YMnO3”,

“amount”: 0.5,

“material_id”: “MP#mp-19385”

},

{

“formula”: “Mn3O4”,

“amount”: 0.1166666666666667,

“material_id”: “MP#mp-18759”

},

{

“formula”: “Ba8Mn8O21”,

“amount”: 0.17619047619047734,

“material_id”: “MP#mp-694888”

}

],

“entry_id”: null,

“e_above_hull”: 0.10458794885714973

which would seem to give the stoichiometry

Y: 0.5

Ba: 1.85

Mn: 2.55

O: 6.47

F: 0.3

My second thought was that “amount” might mean “fraction of the cell in the referenced MP calculation”. Since Mn3O4 has 3 formula units in the MP cell, YMnO3 has 6, Ba8Mn8O21 has 1, BaF2 has 1, and Ba5Mn5O14 has 2, this would give

Y: 3

Ba: 2.13

Mn: 6.03

O: 15.7

F: 0.3

This is much closer but a couple of the species are still off by a large amount. Could someone please let me know what the amounts mean?

They seem to be created by the Simplex class in pymatgen.util.coord, then passed through several functions in pymatgen.phasediagram.analyzer, then finally to check_stability in glue_tasks.py

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Best,
Anubhav

This was answered on the Pymatgen user group, but I am posting the solution here in case anyone else has the same issue later.

The “amount” of Substance X is the number of atoms of that substance in the decomposition, not formula units or Materials Project supercells. For example, the decomposition produces 0.1 Y atoms because it produces 0.5 atoms of YMnO3, and it produces 0.1 F atoms from 0.15 atoms of BaF2

···

On Tuesday, June 12, 2018 at 1:12:35 PM UTC-5, Anubhav Jain wrote:

I am not sure what is going on. The first way you computed the stoichiometry (with Y=0.5) is what I would have expected to yield the original stoichiometry.

Can you send me the vasprun.xml and OUTCAR of the calculation somehow? The code I need to run is:

vasprun, outcar = get_vasprun_outcar(self.get(“calc_dir”, “.”),

parse_dos=False,

parse_eigen=False)

my_entry = vasprun.get_computed_entry(inc_structure=False)

stored_data = mpr.get_stability([my_entry])[0]

If that is giving strange answers, I will post it to the pymatgen list since the mpr.get_stability should be in pymatgen’s domain. But first I just want to check the OUTCAR for example and also just rerun it myself.

Anubhav

On Tue, Jun 12, 2018 at 10:37 AM, Steven Hartman [email protected] wrote:

I ran an optimization of a structure with stoichiometry YBaMn2O5F, and added a powerup to check the stability. The following was written to the “launches” section of my mongo database

“action”: {

“stored_data”: {

“is_compatible”: true,

“decomposes_to”: [

{

“formula”: “BaF2”,

“amount”: 0.15000000000000002,

“material_id”: “MP#mp-1029”

},

{

“formula”: “Ba5Mn5O14”,

“amount”: 0.05714285714285694,

“material_id”: “MP#mp-763829”

},

{

“formula”: “YMnO3”,

“amount”: 0.5,

“material_id”: “MP#mp-19385”

},

{

“formula”: “Mn3O4”,

“amount”: 0.1166666666666667,

“material_id”: “MP#mp-18759”

},

{

“formula”: “Ba8Mn8O21”,

“amount”: 0.17619047619047734,

“material_id”: “MP#mp-694888”

}

],

“entry_id”: null,

“e_above_hull”: 0.10458794885714973

which would seem to give the stoichiometry

Y: 0.5

Ba: 1.85

Mn: 2.55

O: 6.47

F: 0.3

My second thought was that “amount” might mean “fraction of the cell in the referenced MP calculation”. Since Mn3O4 has 3 formula units in the MP cell, YMnO3 has 6, Ba8Mn8O21 has 1, BaF2 has 1, and Ba5Mn5O14 has 2, this would give

Y: 3

Ba: 2.13

Mn: 6.03

O: 15.7

F: 0.3

This is much closer but a couple of the species are still off by a large amount. Could someone please let me know what the amounts mean?

They seem to be created by the Simplex class in pymatgen.util.coord, then passed through several functions in pymatgen.phasediagram.analyzer, then finally to check_stability in glue_tasks.py

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