From 6b29d9261afeab3e341658a2dc2b5183cb41db88 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 25 Sep 2023 19:10:51 -0700 Subject: [PATCH 01/19] feat: add 3 2D materials --- materials/Graphene.json | 85 +++++++++++++++++++++++++++ materials/WS2.json | 122 +++++++++++++++++++++++++++++++++++++++ materials/categories.yml | 18 ++++++ materials/h-BN.json | 85 +++++++++++++++++++++++++++ 4 files changed, 310 insertions(+) create mode 100644 materials/Graphene.json create mode 100644 materials/WS2.json create mode 100644 materials/h-BN.json diff --git a/materials/Graphene.json b/materials/Graphene.json new file mode 100644 index 0000000..eb4d4ea --- /dev/null +++ b/materials/Graphene.json @@ -0,0 +1,85 @@ +{ + "lattice": { + "a": 2.467291, + "b": 2.467291, + "c": 3.901537, + "alpha": 90, + "beta": 90, + "gamma": 120, + "units": { + "length": "angstrom", + "angle": "degree" + }, + "type": "HEX", + "vectors": { + "a": [ + 2.467291, + 0, + 0 + ], + "b": [ + -1.233645, + 2.136737, + 0 + ], + "c": [ + 0, + 0, + 3.901537 + ], + "alat": 1, + "units": "angstrom" + } + }, + "basis": { + "elements": [ + { + "id": 0, + "value": "C" + }, + { + "id": 1, + "value": "C" + } + ], + "coordinates": [ + { + "id": 0, + "value": [ + 0.666667, + 0.333333, + 0 + ] + }, + { + "id": 1, + "value": [ + 0.333333, + 0.666667, + 0 + ] + } + ], + "units": "crystal", + "cell": [ + [ + 2.467291, + 0, + 1.5107800128575361e-16 + ], + [ + -1.2336454999999995, + 2.136736684528712, + 1.5107800128575361e-16 + ], + [ + 0, + 0, + 3.901537 + ] + ], + "constraints": [] + }, + "name": "Graphene", + "isNonPeriodic": false +} diff --git a/materials/WS2.json b/materials/WS2.json new file mode 100644 index 0000000..45b7798 --- /dev/null +++ b/materials/WS2.json @@ -0,0 +1,122 @@ +{ + "lattice": { + "a": 3.190731, + "b": 3.19073, + "c": 14.2024, + "alpha": 90, + "beta": 90, + "gamma": 60, + "units": { + "length": "angstrom", + "angle": "degree" + }, + "type": "HEX", + "vectors": { + "a": [ + 3.190731, + 0, + 0 + ], + "b": [ + 1.595365, + 2.763253, + 0 + ], + "c": [ + 0, + 0, + 14.2024 + ], + "alat": 1, + "units": "angstrom" + } + }, + "basis": { + "elements": [ + { + "id": 0, + "value": "W" + }, + { + "id": 1, + "value": "S" + }, + { + "id": 2, + "value": "S" + } + ], + "coordinates": [ + { + "id": 0, + "value": [ + 0.3333329900432667, + 0.33333318415927227, + 0.25 + ] + }, + { + "id": 1, + "value": [ + 0.6666668718255933, + 0.6666670921030944, + 0.13924097335661575 + ] + }, + { + "id": 2, + "value": [ + 0.6666668718255933, + 0.6666670921030944, + 0.3607590266433843 + ] + } + ], + "units": "crystal", + "cell": [ + [ + 3.190731, + 0, + 1.9537592530451167E-16 + ], + [ + 1.5953650000000006, + 2.763253236617121, + 1.9537586407217172E-16 + ], + [ + 0, + 0, + 14.2024 + ] + ], + "constraints": [ + { + "id": 0, + "value": [ + true, + true, + true + ] + }, + { + "id": 1, + "value": [ + true, + true, + true + ] + }, + { + "id": 2, + "value": [ + true, + true, + true + ] + } + ] + }, + "name": "WS2", + "isNonPeriodic": false +} \ No newline at end of file diff --git a/materials/categories.yml b/materials/categories.yml index 868e567..ce59ac0 100644 --- a/materials/categories.yml +++ b/materials/categories.yml @@ -43,6 +43,18 @@ categories: - carbide entities: + - filename: Graphene.json + categories: + - 2D + - surface + - semi-metal + - non-magnetic + - filename: h-BN.json + categories: + - 2D + - surface + - insulator + - non-magnetic - filename: Na4Cl4.json categories: - 3D @@ -54,3 +66,9 @@ entities: - 3D - bulk - semiconductor + - filename: WS2.json + categories: + - 2D + - surface + - semiconductor + - non-magnetic \ No newline at end of file diff --git a/materials/h-BN.json b/materials/h-BN.json new file mode 100644 index 0000000..2d3f79f --- /dev/null +++ b/materials/h-BN.json @@ -0,0 +1,85 @@ +{ + "lattice": { + "a": 2.50899515, + "b": 2.50899515, + "c": 7.71, + "alpha": 90, + "beta": 90, + "gamma": 120, + "units": { + "length": "angstrom", + "angle": "degree" + }, + "type": "HEX", + "vectors": { + "a": [ + 2.467291, + 0, + 0 + ], + "b": [ + -1.233645, + 2.136737, + 0 + ], + "c": [ + 0, + 0, + 3.901537 + ], + "alat": 1, + "units": "angstrom" + } + }, + "basis": { + "elements": [ + { + "id": 0, + "value": "B" + }, + { + "id": 1, + "value": "N" + } + ], + "coordinates": [ + { + "id": 0, + "value": [ + 0.666667, + 0.333333, + 0 + ] + }, + { + "id": 1, + "value": [ + 0.333333, + 0.666667, + 0 + ] + } + ], + "units": "crystal", + "cell": [ + [ + 2.467291, + 0, + 1.5107800128575361e-16 + ], + [ + -1.2336454999999995, + 2.136736684528712, + 1.5107800128575361e-16 + ], + [ + 0, + 0, + 3.901537 + ] + ], + "constraints": [] + }, + "name": "h-BN", + "isNonPeriodic": false +} From 208208e52535de5cf93ac42661b5675400dac1ae Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 25 Sep 2023 19:12:40 -0700 Subject: [PATCH 02/19] feat: write tests and link fixtures --- tests/js/fixtures/Graphene.json | 1 + tests/js/fixtures/Na4Cl4.json | 1 + tests/js/fixtures/WS2.json | 1 + tests/js/fixtures/h-BN.json | 1 + tests/js/material.test.ts | 13 +++++++++++++ 5 files changed, 17 insertions(+) create mode 120000 tests/js/fixtures/Graphene.json create mode 120000 tests/js/fixtures/Na4Cl4.json create mode 120000 tests/js/fixtures/WS2.json create mode 120000 tests/js/fixtures/h-BN.json diff --git a/tests/js/fixtures/Graphene.json b/tests/js/fixtures/Graphene.json new file mode 120000 index 0000000..f34b750 --- /dev/null +++ b/tests/js/fixtures/Graphene.json @@ -0,0 +1 @@ +../../../materials/Graphene.json \ No newline at end of file diff --git a/tests/js/fixtures/Na4Cl4.json b/tests/js/fixtures/Na4Cl4.json new file mode 120000 index 0000000..0fb86d5 --- /dev/null +++ b/tests/js/fixtures/Na4Cl4.json @@ -0,0 +1 @@ +../../../materials/Na4Cl4.json \ No newline at end of file diff --git a/tests/js/fixtures/WS2.json b/tests/js/fixtures/WS2.json new file mode 120000 index 0000000..8e3772f --- /dev/null +++ b/tests/js/fixtures/WS2.json @@ -0,0 +1 @@ +../../../materials/WS2.json \ No newline at end of file diff --git a/tests/js/fixtures/h-BN.json b/tests/js/fixtures/h-BN.json new file mode 120000 index 0000000..e40fa9d --- /dev/null +++ b/tests/js/fixtures/h-BN.json @@ -0,0 +1 @@ +../../../materials/h-BN.json \ No newline at end of file diff --git a/tests/js/material.test.ts b/tests/js/material.test.ts index 0c1e744..da52fa9 100644 --- a/tests/js/material.test.ts +++ b/tests/js/material.test.ts @@ -2,6 +2,10 @@ import { expect } from "chai"; import { MaterialStandata } from "../../src/js"; import Si from "./fixtures/Si.json"; +import Na4Cl4 from "./fixtures/Na4Cl4.json"; +import Graphene from "./fixtures/Graphene.json"; +import h_BN from "./fixtures/h-BN.json"; +import WS2 from "./fixtures/WS2.json"; describe("Materials Standata", () => { it("can search materials by tags", () => { @@ -11,4 +15,13 @@ describe("Materials Standata", () => { expect(entities).to.deep.include.members([Si]); expect(entities.length).to.be.lessThan(std.entities.length); }); + + it("should return all entities with the same tag", () => { + const std = new MaterialStandata(); + const tags = ["2D"]; + const entities = std.find_entities(...tags); + expect(entities).to.deep.include.members([Graphene, h_BN, WS2]); + expect(entities).to.not.deep.include.members([Si, Na4Cl4]); + expect(entities.length).to.be.lessThan(std.entities.length); + }); }); From bdc41bfa32568bd45850ecfc30b19e720ec7fe61 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 25 Sep 2023 19:17:03 -0700 Subject: [PATCH 03/19] update: autogenerate runtime_data --- src/js/runtime_data/materials.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/js/runtime_data/materials.json b/src/js/runtime_data/materials.json index 8e28744..2502b97 100644 --- a/src/js/runtime_data/materials.json +++ b/src/js/runtime_data/materials.json @@ -1 +1 @@ -{"standataConfig":{"categories":{"type":["semiconductor","solar energy material","storage medium","organic electronics","battery/energy storage","composite","polymer","metals & alloys","solvent","catalysis","consumer packaged goods","glass","ceramic"],"form_factor":["bulk","surface","interface"],"dimensionality":["0D","1D","2D","3D","4D"],"electrical_conductivity":["metal","semi-metal","semiconductor","insulator"],"magnetism":["ferromagnetic","anti-ferromagnetic","paramagnetic","diamagnetic","non-magnetic"],"superconductivity":["type I","type II"],"composition":["oxide","nitride","carbide"]},"entities":[{"filename":"Na4Cl4.json","categories":["3D","bulk","insulator","non-magnetic"]},{"filename":"Si.json","categories":["3D","bulk","semiconductor"]}]},"filesMapByName":{"Na4Cl4.json":{"basis":{"elements":[{"id":0,"value":"Na"},{"id":1,"value":"Na"},{"id":2,"value":"Na"},{"id":3,"value":"Na"},{"id":4,"value":"Cl"},{"id":5,"value":"Cl"},{"id":6,"value":"Cl"},{"id":7,"value":"Cl"}],"coordinates":[{"id":0,"value":[0,0,0]},{"id":1,"value":[0,0.5,0.5]},{"id":2,"value":[0.5,0,0.5]},{"id":3,"value":[0.5,0.5,0]},{"id":4,"value":[0,0,0.5]},{"id":5,"value":[0,0.5,0]},{"id":6,"value":[0.5,0,0]},{"id":7,"value":[0.5,0.5,0.5]}],"units":"crystal","cell":[[1,0,6.123233995736766e-17],[1.6081226496766366e-16,1,6.123233995736766e-17],[0,0,1]]},"lattice":{"a":5.691694,"b":5.691694,"c":5.691694,"alpha":90,"beta":90,"gamma":90,"units":{"length":"angstrom","angle":"degree"},"type":"CUB","vectors":{"a":[5.691694,0,0],"b":[0,5.691694,0],"c":[0,0,5.691694],"alat":1,"units":"angstrom"}}},"Si.json":{"basis":{"elements":[{"id":0,"value":"Si"},{"id":1,"value":"Si"}],"coordinates":[{"id":0,"value":[0,0,0]},{"id":1,"value":[0.25,0.25,0.25]}]},"lattice":{"a":5,"b":5,"c":5,"alpha":90,"beta":90,"gamma":90,"type":"TRI","units":{"length":"angstrom","angle":"degree"}}}}} +{"standataConfig":{"categories":{"type":["semiconductor","solar energy material","storage medium","organic electronics","battery/energy storage","composite","polymer","metals & alloys","solvent","catalysis","consumer packaged goods","glass","ceramic"],"form_factor":["bulk","surface","interface"],"dimensionality":["0D","1D","2D","3D","4D"],"electrical_conductivity":["metal","semi-metal","semiconductor","insulator"],"magnetism":["ferromagnetic","anti-ferromagnetic","paramagnetic","diamagnetic","non-magnetic"],"superconductivity":["type I","type II"],"composition":["oxide","nitride","carbide"]},"entities":[{"filename":"Graphene.json","categories":["2D","surface","semi-metal","non-magnetic"]},{"filename":"h-BN.json","categories":["2D","surface","insulator","non-magnetic"]},{"filename":"Na4Cl4.json","categories":["3D","bulk","insulator","non-magnetic"]},{"filename":"Si.json","categories":["3D","bulk","semiconductor"]},{"filename":"WS2.json","categories":["2D","surface","semiconductor","non-magnetic"]}]},"filesMapByName":{"Graphene.json":{"lattice":{"a":2.467291,"b":2.467291,"c":3.901537,"alpha":90,"beta":90,"gamma":120,"units":{"length":"angstrom","angle":"degree"},"type":"HEX","vectors":{"a":[2.467291,0,0],"b":[-1.233645,2.136737,0],"c":[0,0,3.901537],"alat":1,"units":"angstrom"}},"basis":{"elements":[{"id":0,"value":"C"},{"id":1,"value":"C"}],"coordinates":[{"id":0,"value":[0.666667,0.333333,0]},{"id":1,"value":[0.333333,0.666667,0]}],"units":"crystal","cell":[[2.467291,0,1.5107800128575361e-16],[-1.2336454999999995,2.136736684528712,1.5107800128575361e-16],[0,0,3.901537]],"constraints":[]},"name":"Graphene","isNonPeriodic":false},"h-BN.json":{"lattice":{"a":2.50899515,"b":2.50899515,"c":7.71,"alpha":90,"beta":90,"gamma":120,"units":{"length":"angstrom","angle":"degree"},"type":"HEX","vectors":{"a":[2.467291,0,0],"b":[-1.233645,2.136737,0],"c":[0,0,3.901537],"alat":1,"units":"angstrom"}},"basis":{"elements":[{"id":0,"value":"B"},{"id":1,"value":"N"}],"coordinates":[{"id":0,"value":[0.666667,0.333333,0]},{"id":1,"value":[0.333333,0.666667,0]}],"units":"crystal","cell":[[2.467291,0,1.5107800128575361e-16],[-1.2336454999999995,2.136736684528712,1.5107800128575361e-16],[0,0,3.901537]],"constraints":[]},"name":"h-BN","isNonPeriodic":false},"Na4Cl4.json":{"basis":{"elements":[{"id":0,"value":"Na"},{"id":1,"value":"Na"},{"id":2,"value":"Na"},{"id":3,"value":"Na"},{"id":4,"value":"Cl"},{"id":5,"value":"Cl"},{"id":6,"value":"Cl"},{"id":7,"value":"Cl"}],"coordinates":[{"id":0,"value":[0,0,0]},{"id":1,"value":[0,0.5,0.5]},{"id":2,"value":[0.5,0,0.5]},{"id":3,"value":[0.5,0.5,0]},{"id":4,"value":[0,0,0.5]},{"id":5,"value":[0,0.5,0]},{"id":6,"value":[0.5,0,0]},{"id":7,"value":[0.5,0.5,0.5]}],"units":"crystal","cell":[[1,0,6.123233995736766e-17],[1.6081226496766366e-16,1,6.123233995736766e-17],[0,0,1]]},"lattice":{"a":5.691694,"b":5.691694,"c":5.691694,"alpha":90,"beta":90,"gamma":90,"units":{"length":"angstrom","angle":"degree"},"type":"CUB","vectors":{"a":[5.691694,0,0],"b":[0,5.691694,0],"c":[0,0,5.691694],"alat":1,"units":"angstrom"}}},"Si.json":{"basis":{"elements":[{"id":0,"value":"Si"},{"id":1,"value":"Si"}],"coordinates":[{"id":0,"value":[0,0,0]},{"id":1,"value":[0.25,0.25,0.25]}]},"lattice":{"a":5,"b":5,"c":5,"alpha":90,"beta":90,"gamma":90,"type":"TRI","units":{"length":"angstrom","angle":"degree"}}},"WS2.json":{"lattice":{"a":3.190731,"b":3.19073,"c":14.2024,"alpha":90,"beta":90,"gamma":60,"units":{"length":"angstrom","angle":"degree"},"type":"HEX","vectors":{"a":[3.190731,0,0],"b":[1.595365,2.763253,0],"c":[0,0,14.2024],"alat":1,"units":"angstrom"}},"basis":{"elements":[{"id":0,"value":"W"},{"id":1,"value":"S"},{"id":2,"value":"S"}],"coordinates":[{"id":0,"value":[0.3333329900432667,0.33333318415927227,0.25]},{"id":1,"value":[0.6666668718255933,0.6666670921030944,0.13924097335661575]},{"id":2,"value":[0.6666668718255933,0.6666670921030944,0.3607590266433843]}],"units":"crystal","cell":[[3.190731,0,1.9537592530451167e-16],[1.5953650000000006,2.763253236617121,1.9537586407217172e-16],[0,0,14.2024]],"constraints":[{"id":0,"value":[true,true,true]},{"id":1,"value":[true,true,true]},{"id":2,"value":[true,true,true]}]},"name":"WS2","isNonPeriodic":false}}} From bc1d738c8956e6711c2decb34b8581cf7ea60fd8 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 25 Sep 2023 19:24:18 -0700 Subject: [PATCH 04/19] fix: github workflow yaml lint --- .github/workflows/cicd.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 1b99fd4..cf15a58 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -30,6 +30,7 @@ jobs: uses: ./actions/yaml/lint with: python-version: ${{ matrix.python-version }} + targets: ./applications ./materials ./properties ./workflows - name: Run ruff linter uses: ./actions/py/lint From 9f6138975c8eaa0df8a915a3b60f610a96b4abd5 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 25 Sep 2023 19:27:33 -0700 Subject: [PATCH 05/19] chore: add a newline --- materials/WS2.json | 2 +- materials/categories.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/materials/WS2.json b/materials/WS2.json index 45b7798..2510cf0 100644 --- a/materials/WS2.json +++ b/materials/WS2.json @@ -119,4 +119,4 @@ }, "name": "WS2", "isNonPeriodic": false -} \ No newline at end of file +} diff --git a/materials/categories.yml b/materials/categories.yml index ce59ac0..906faf4 100644 --- a/materials/categories.yml +++ b/materials/categories.yml @@ -71,4 +71,4 @@ entities: - 2D - surface - semiconductor - - non-magnetic \ No newline at end of file + - non-magnetic From f5549deaa935162de0d46e26da948a45336f63db Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Sep 2023 15:31:04 -0700 Subject: [PATCH 06/19] chore: update data to be scientific correct + niggli cell --- materials/Graphene.json | 14 ++++++------ materials/Na4Cl4.json | 6 ++--- materials/Si.json | 12 +++++----- materials/WS2.json | 49 ++++++++++------------------------------- materials/h-BN.json | 10 ++++----- 5 files changed, 33 insertions(+), 58 deletions(-) diff --git a/materials/Graphene.json b/materials/Graphene.json index eb4d4ea..9105d48 100644 --- a/materials/Graphene.json +++ b/materials/Graphene.json @@ -2,7 +2,7 @@ "lattice": { "a": 2.467291, "b": 2.467291, - "c": 3.901537, + "c": 7.803074, "alpha": 90, "beta": 90, "gamma": 120, @@ -25,7 +25,7 @@ "c": [ 0, 0, - 3.901537 + 7.803074 ], "alat": 1, "units": "angstrom" @@ -46,8 +46,8 @@ { "id": 0, "value": [ - 0.666667, - 0.333333, + 0, + 0, 0 ] }, @@ -65,17 +65,17 @@ [ 2.467291, 0, - 1.5107800128575361e-16 + 0 ], [ -1.2336454999999995, 2.136736684528712, - 1.5107800128575361e-16 + 0 ], [ 0, 0, - 3.901537 + 10 ] ], "constraints": [] diff --git a/materials/Na4Cl4.json b/materials/Na4Cl4.json index af5373d..5c34b1e 100644 --- a/materials/Na4Cl4.json +++ b/materials/Na4Cl4.json @@ -105,12 +105,12 @@ [ 1, 0, - 6.123233995736766e-17 + 0 ], [ - 1.6081226496766366e-16, + 0, 1, - 6.123233995736766e-17 + 0 ], [ 0, diff --git a/materials/Si.json b/materials/Si.json index 57a08a5..74ec03a 100644 --- a/materials/Si.json +++ b/materials/Si.json @@ -30,12 +30,12 @@ ] }, "lattice": { - "a": 5, - "b": 5, - "c": 5, - "alpha": 90, - "beta": 90, - "gamma": 90, + "a": 3.867, + "b": 3.867, + "c": 3.867, + "alpha": 60, + "beta": 60, + "gamma": 60, "type": "TRI", "units": { "length": "angstrom", diff --git a/materials/WS2.json b/materials/WS2.json index 2510cf0..f3947e5 100644 --- a/materials/WS2.json +++ b/materials/WS2.json @@ -50,25 +50,25 @@ { "id": 0, "value": [ - 0.3333329900432667, - 0.33333318415927227, - 0.25 + 0.333333, + 0.333333, + 0.110759 ] }, { "id": 1, "value": [ - 0.6666668718255933, - 0.6666670921030944, - 0.13924097335661575 + 0, + 0, + 0 ] }, { "id": 2, "value": [ - 0.6666668718255933, - 0.6666670921030944, - 0.3607590266433843 + 0.0, + 0.0, + 0.221518 ] } ], @@ -77,12 +77,12 @@ [ 3.190731, 0, - 1.9537592530451167E-16 + 0 ], [ 1.5953650000000006, 2.763253236617121, - 1.9537586407217172E-16 + 0 ], [ 0, @@ -90,32 +90,7 @@ 14.2024 ] ], - "constraints": [ - { - "id": 0, - "value": [ - true, - true, - true - ] - }, - { - "id": 1, - "value": [ - true, - true, - true - ] - }, - { - "id": 2, - "value": [ - true, - true, - true - ] - } - ] + "constraints": [] }, "name": "WS2", "isNonPeriodic": false diff --git a/materials/h-BN.json b/materials/h-BN.json index 2d3f79f..5484c2e 100644 --- a/materials/h-BN.json +++ b/materials/h-BN.json @@ -46,8 +46,8 @@ { "id": 0, "value": [ - 0.666667, - 0.333333, + 0, + 0, 0 ] }, @@ -65,17 +65,17 @@ [ 2.467291, 0, - 1.5107800128575361e-16 + 0 ], [ -1.2336454999999995, 2.136736684528712, - 1.5107800128575361e-16 + 0 ], [ 0, 0, - 3.901537 + 10 ] ], "constraints": [] From ce5e719b4a63d07ab1e599c2846ce01e9bd20455 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Sep 2023 15:54:08 -0700 Subject: [PATCH 07/19] chore: run build --- src/js/runtime_data/materials.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/js/runtime_data/materials.json b/src/js/runtime_data/materials.json index 2502b97..c3030ce 100644 --- a/src/js/runtime_data/materials.json +++ b/src/js/runtime_data/materials.json @@ -1 +1 @@ -{"standataConfig":{"categories":{"type":["semiconductor","solar energy material","storage medium","organic electronics","battery/energy storage","composite","polymer","metals & alloys","solvent","catalysis","consumer packaged goods","glass","ceramic"],"form_factor":["bulk","surface","interface"],"dimensionality":["0D","1D","2D","3D","4D"],"electrical_conductivity":["metal","semi-metal","semiconductor","insulator"],"magnetism":["ferromagnetic","anti-ferromagnetic","paramagnetic","diamagnetic","non-magnetic"],"superconductivity":["type I","type 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From 77f67902ef81cc7a3bb8ceae1e7a1b3c24cbc5d0 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 27 Sep 2023 13:00:37 -0700 Subject: [PATCH 08/19] try: add include: ... *.json in tsconfig --- tsconfig.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tsconfig.json b/tsconfig.json index 6928255..358b355 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -35,7 +35,8 @@ "types": ["mocha", "node"] }, "include": [ - "./src/js" + "./src/js", + "./src/js/runtime_data/*.json" ], "exclude": [ "node_modules", From cc8574868102e4baad2ce4760a37ffe7a069bbfa Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 27 Sep 2023 13:50:37 -0700 Subject: [PATCH 09/19] try: add tsc-hook copy-files --- tsconfig.json | 1 + 1 file changed, 1 insertion(+) diff --git a/tsconfig.json b/tsconfig.json index 358b355..c5e9e5e 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -34,6 +34,7 @@ "skipLibCheck": true, "types": ["mocha", "node"] }, + "hooks": ["copy-files"], "include": [ "./src/js", "./src/js/runtime_data/*.json" From 6af0f852c592700cdb07c487137be5a4d97a8da8 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 27 Sep 2023 16:18:00 -0700 Subject: [PATCH 10/19] update: add cp to postinstall --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 0607848..8202e17 100644 --- a/package.json +++ b/package.json @@ -58,7 +58,7 @@ "lint": "eslint --cache src/js tests/js && prettier --write src/js tests/js", "lint:fix": "eslint --fix --cache src/js tests/js && prettier --write src/js tests/js", "lint:staged": "lint-staged", - "postinstall": "npm run transpile", + "postinstall": "npm run transpile && cp -r src/js/runtime_data lib/", "prepare": "node bootstrap.js", "prettier": "prettier --check src/js tests/js", "test": "mocha", From a87016035321d0a1c8a062fa6533ce5757c70418 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 27 Sep 2023 16:19:15 -0700 Subject: [PATCH 11/19] update: revert changes to tsconfig --- tsconfig.json | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tsconfig.json b/tsconfig.json index c5e9e5e..6928255 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -34,10 +34,8 @@ "skipLibCheck": true, "types": ["mocha", "node"] }, - "hooks": ["copy-files"], "include": [ - "./src/js", - "./src/js/runtime_data/*.json" + "./src/js" ], "exclude": [ "node_modules", From 2f91e9cedf57eecacf2d5e3e1b65b6195372384a Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 27 Sep 2023 18:35:23 -0700 Subject: [PATCH 12/19] update: add names to the materials --- materials/Na4Cl4.json | 4 +++- materials/Si.json | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/materials/Na4Cl4.json b/materials/Na4Cl4.json index 5c34b1e..d354daa 100644 --- a/materials/Na4Cl4.json +++ b/materials/Na4Cl4.json @@ -150,5 +150,7 @@ "alat": 1, "units": "angstrom" } - } + }, + "name": "NaCl", + "isNonPeriodic": false } diff --git a/materials/Si.json b/materials/Si.json index 74ec03a..0d8037f 100644 --- a/materials/Si.json +++ b/materials/Si.json @@ -41,5 +41,7 @@ "length": "angstrom", "angle": "degree" } - } + }, + "name": "Si", + "isNonPeriodic": false } From b0e44707584a6f0478c60ba8cc00b2ddbb7e513d Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 27 Sep 2023 20:11:28 -0700 Subject: [PATCH 13/19] chore: run build --- materials/Na4Cl4.json | 2 +- src/js/runtime_data/materials.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/materials/Na4Cl4.json b/materials/Na4Cl4.json index d354daa..c7095c6 100644 --- a/materials/Na4Cl4.json +++ b/materials/Na4Cl4.json @@ -151,6 +151,6 @@ "units": "angstrom" } }, - "name": "NaCl", + "name": "Na4Cl4", "isNonPeriodic": false } diff --git 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From 42a1dca8b07149a67afecadd830fb5a6fae728ba Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Sun, 8 Oct 2023 15:34:28 -0700 Subject: [PATCH 14/19] chore: add JSON lint to cicd.yml --- .github/workflows/cicd.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index cf15a58..68a3e9e 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -32,6 +32,12 @@ jobs: python-version: ${{ matrix.python-version }} targets: ./applications ./materials ./properties ./workflows + - name: Run JSON linter + uses: ./actions/json/lint + with: + python-version: 3.10.X + targets: ./applications ./materials ./properties ./workflows + - name: Run ruff linter uses: ./actions/py/lint with: From a6e1c0fff6cd79804945e6e8bfd6c2adb47e1e43 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 9 Oct 2023 14:22:46 -0700 Subject: [PATCH 15/19] feat: fix data according to materials-project and add source --- materials/Graphene.json | 167 ++++++++++++++++++----------------- materials/Na4Cl4.json | 19 ++-- materials/Si.json | 7 +- materials/WS2.json | 191 +++++++++++++++++++++------------------- materials/h-BN.json | 170 ++++++++++++++++++----------------- 5 files changed, 290 insertions(+), 264 deletions(-) diff --git a/materials/Graphene.json b/materials/Graphene.json index 9105d48..9a24fbd 100644 --- a/materials/Graphene.json +++ b/materials/Graphene.json @@ -1,85 +1,90 @@ { - "lattice": { - "a": 2.467291, - "b": 2.467291, - "c": 7.803074, - "alpha": 90, - "beta": 90, - "gamma": 120, - "units": { - "length": "angstrom", - "angle": "degree" + "lattice": { + "a": 2.467291, + "b": 2.467291, + "c": 20, + "alpha": 90, + "beta": 90, + "gamma": 120, + "units": { + "length": "angstrom", + "angle": "degree" + }, + "type": "HEX", + "vectors": { + "a": [ + 2.467291, + 0, + 0 + ], + "b": [ + -1.233645, + 2.136737, + 0 + ], + "c": [ + 0, + 0, + 20 + ], + "alat": 1, + "units": "angstrom" + } }, - "type": "HEX", - "vectors": { - "a": [ - 2.467291, - 0, - 0 - ], - "b": [ - -1.233645, - 2.136737, - 0 - ], - "c": [ - 0, - 0, - 7.803074 - ], - "alat": 1, - "units": "angstrom" + "basis": { + "elements": [ + { + "id": 0, + "value": "C" + }, + { + "id": 1, + "value": "C" + } + ], + "coordinates": [ + { + "id": 0, + "value": [ + 0, + 0, + 0 + ] + }, + { + "id": 1, + "value": [ + 0.333333, + 0.666667, + 0 + ] + } + ], + "units": "crystal", + "cell": [ + [ + 2.467291, + 0, + 0 + ], + [ + -1.2336454999999995, + 2.136736684528712, + 0 + ], + [ + 0, + 0, + 20 + ] + ], + "constraints": [] + }, + "name": "Graphene", + "isNonPeriodic": false, + "external": { + "id": "mp-1040425", + "source": "https://next-gen.materialsproject.org/materials/", + "origin": true } - }, - "basis": { - "elements": [ - { - "id": 0, - "value": "C" - }, - { - "id": 1, - "value": "C" - } - ], - "coordinates": [ - { - "id": 0, - "value": [ - 0, - 0, - 0 - ] - }, - { - "id": 1, - "value": [ - 0.333333, - 0.666667, - 0 - ] - } - ], - "units": "crystal", - "cell": [ - [ - 2.467291, - 0, - 0 - ], - [ - -1.2336454999999995, - 2.136736684528712, - 0 - ], - [ - 0, - 0, - 10 - ] - ], - "constraints": [] - }, - "name": "Graphene", - "isNonPeriodic": false } diff --git a/materials/Na4Cl4.json b/materials/Na4Cl4.json index c7095c6..e5c0bed 100644 --- a/materials/Na4Cl4.json +++ b/materials/Na4Cl4.json @@ -120,9 +120,9 @@ ] }, "lattice": { - "a": 5.691694, - "b": 5.691694, - "c": 5.691694, + "a": 5.58813, + "b": 5.58813, + "c": 5.58813, "alpha": 90, "beta": 90, "gamma": 90, @@ -133,24 +133,29 @@ "type": "CUB", "vectors": { "a": [ - 5.691694, + 5.58813, 0, 0 ], "b": [ 0, - 5.691694, + 5.58813, 0 ], "c": [ 0, 0, - 5.691694 + 5.58813 ], "alat": 1, "units": "angstrom" } }, "name": "Na4Cl4", - "isNonPeriodic": false + "isNonPeriodic": false, + "external": { + "id": "mp-22862", + "source": "https://next-gen.materialsproject.org/materials/", + "origin": true + } } diff --git a/materials/Si.json b/materials/Si.json index 0d8037f..e868214 100644 --- a/materials/Si.json +++ b/materials/Si.json @@ -43,5 +43,10 @@ } }, "name": "Si", - "isNonPeriodic": false + "isNonPeriodic": false, + "external": { + "id": "mp-149", + "source": "https://next-gen.materialsproject.org/materials/", + "origin": true + } } diff --git a/materials/WS2.json b/materials/WS2.json index f3947e5..9c17c38 100644 --- a/materials/WS2.json +++ b/materials/WS2.json @@ -1,97 +1,102 @@ { - "lattice": { - "a": 3.190731, - "b": 3.19073, - "c": 14.2024, - "alpha": 90, - "beta": 90, - "gamma": 60, - "units": { - "length": "angstrom", - "angle": "degree" + "lattice": { + "a": 3.190731, + "b": 3.19073, + "c": 14.2024, + "alpha": 90, + "beta": 90, + "gamma": 60, + "units": { + "length": "angstrom", + "angle": "degree" + }, + "type": "HEX", + "vectors": { + "a": [ + 3.190731, + 0, + 0 + ], + "b": [ + 1.595365, + 2.763253, + 0 + ], + "c": [ + 0, + 0, + 14.2024 + ], + "alat": 1, + "units": "angstrom" + } }, - "type": "HEX", - "vectors": { - "a": [ - 3.190731, - 0, - 0 - ], - "b": [ - 1.595365, - 2.763253, - 0 - ], - "c": [ - 0, - 0, - 14.2024 - ], - "alat": 1, - "units": "angstrom" + "basis": { + "elements": [ + { + "id": 0, + "value": "W" + }, + { + "id": 1, + "value": "S" + }, + { + "id": 2, + "value": "S" + } + ], + "coordinates": [ + { + "id": 0, + "value": [ + 0.333333, + 0.333333, + 0.110759 + ] + }, + { + "id": 1, + "value": [ + 0, + 0, + 0 + ] + }, + { + "id": 2, + "value": [ + 0.0, + 0.0, + 0.221518 + ] + } + ], + "units": "crystal", + "cell": [ + [ + 3.190731, + 0, + 0 + ], + [ + 1.5953650000000006, + 2.763253236617121, + 0 + ], + [ + 0, + 0, + 14.2024 + ] + ], + "constraints": [] + }, + "name": "WS2", + "isNonPeriodic": false, + "external": { + "id": "mp-224", + "source": "https://next-gen.materialsproject.org/materials/", + "origin": true } - }, - "basis": { - "elements": [ - { - "id": 0, - "value": "W" - }, - { - "id": 1, - "value": "S" - }, - { - "id": 2, - "value": "S" - } - ], - "coordinates": [ - { - "id": 0, - "value": [ - 0.333333, - 0.333333, - 0.110759 - ] - }, - { - "id": 1, - "value": [ - 0, - 0, - 0 - ] - }, - { - "id": 2, - "value": [ - 0.0, - 0.0, - 0.221518 - ] - } - ], - "units": "crystal", - "cell": [ - [ - 3.190731, - 0, - 0 - ], - [ - 1.5953650000000006, - 2.763253236617121, - 0 - ], - [ - 0, - 0, - 14.2024 - ] - ], - "constraints": [] - }, - "name": "WS2", - "isNonPeriodic": false } diff --git a/materials/h-BN.json b/materials/h-BN.json index 5484c2e..9faf268 100644 --- a/materials/h-BN.json +++ b/materials/h-BN.json @@ -1,85 +1,91 @@ { - "lattice": { - "a": 2.50899515, - "b": 2.50899515, - "c": 7.71, - "alpha": 90, - "beta": 90, - "gamma": 120, - "units": { - "length": "angstrom", - "angle": "degree" + "lattice": { + "a": 2.50899515, + "b": 2.50899515, + "c": 7.71, + "alpha": 90, + "beta": 90, + "gamma": 120, + "units": { + "length": "angstrom", + "angle": "degree" + }, + "type": "HEX", + "vectors": { + "a": [ + 2.467291, + 0, + 0 + ], + "b": [ + -1.233645, + 2.136737, + 0 + ], + "c": [ + 0, + 0, + 7.71 + ], + "alat": 1, + "units": "angstrom" + } }, - "type": "HEX", - "vectors": { - "a": [ - 2.467291, - 0, - 0 - ], - "b": [ - -1.233645, - 2.136737, - 0 - ], - "c": [ - 0, - 0, - 3.901537 - ], - "alat": 1, - "units": "angstrom" - } - }, - "basis": { - "elements": [ - { - "id": 0, - "value": "B" - }, - { - "id": 1, - "value": "N" - } - ], - "coordinates": [ - { - "id": 0, - "value": [ - 0, - 0, - 0 - ] - }, - { - "id": 1, - "value": [ - 0.333333, - 0.666667, - 0 - ] - } - ], - "units": "crystal", - "cell": [ - [ - 2.467291, - 0, - 0 - ], - [ - -1.2336454999999995, - 2.136736684528712, - 0 - ], - [ - 0, - 0, - 10 - ] - ], - "constraints": [] - }, - "name": "h-BN", - "isNonPeriodic": false + "basis": { + "elements": [ + { + "id": 0, + "value": "B" + }, + { + "id": 1, + "value": "N" + } + ], + "coordinates": [ + { + "id": 0, + "value": [ + 0, + 0, + 0 + ] + }, + { + "id": 1, + "value": [ + 0.333333, + 0.666667, + 0 + ] + } + ], + "units": "crystal", + "cell": [ + [ + 2.467291, + 0, + 0 + ], + [ + -1.2336454999999995, + 2.136736684528712, + 0 + ], + [ + 0, + 0, + 7.71 + ] + ], + "constraints": [] + }, + "name": "h-BN", + "isNonPeriodic": false, + "external": { + "id": "mp-984", + "source": "https://next-gen.materialsproject.org/materials/", + "origin": true + }, +} } From c0f3caac63915a184c023a8c1a5cd66fe1f8773a Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:50:13 -0700 Subject: [PATCH 16/19] chore: fix issues --- materials/WS2.json | 46 +++++++++++++++--------------- materials/h-BN.json | 3 +- src/js/runtime_data/materials.json | 2 +- 3 files changed, 25 insertions(+), 26 deletions(-) diff --git a/materials/WS2.json b/materials/WS2.json index 9c17c38..e11118e 100644 --- a/materials/WS2.json +++ b/materials/WS2.json @@ -1,11 +1,11 @@ { "lattice": { - "a": 3.190731, - "b": 3.19073, - "c": 14.2024, + "a": 3.184222, + "b": 3.184222, + "c": 12.97828, 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