From ac672c8857a84d19b9ebbc50f623c20d67db1c4d Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Thu, 30 Dec 2021 15:09:13 -0500
Subject: [PATCH 01/12] Feat: xyz file parsing - nAtoms & nLines to check
 formatting. Created functions and tests

---
 src/parsers/xyz.js     | 16 ++++++++++++++++
 tests/enums.js         |  2 ++
 tests/fixtures/CH4.xyz |  3 +++
 tests/parsers/xyz.js   | 11 ++++++++++-
 4 files changed, 31 insertions(+), 1 deletion(-)
 create mode 100644 tests/fixtures/CH4.xyz

diff --git a/src/parsers/xyz.js b/src/parsers/xyz.js
index 20da6e54..8df1ab7e 100644
--- a/src/parsers/xyz.js
+++ b/src/parsers/xyz.js
@@ -1,3 +1,4 @@
+import Integer from "lodash/string";
 import _ from "underscore";
 import s from "underscore.string";
 
@@ -140,10 +141,25 @@ function fromMaterial(materialOrConfig, fractional = false) {
     return fromBasis(basis, "%11.6f");
 }
 
+export function atomsCount(xyzFile) {
+    const xyzArray = xyzFile.split(/\r?\n/);
+    return Integer.parseInt(xyzArray[0]);
+}
+
+export function linesCount(xyzFile) {
+    const content = xyzFile.split(/\r?\n/);
+    if (!content[-1]) {
+        content.pop();
+    }
+    return content.length;
+}
+
 export default {
     validate,
     fromMaterial,
     toBasisConfig,
     fromBasis,
     CombinatorialBasis,
+    atomsCount,
+    linesCount,
 };
diff --git a/tests/enums.js b/tests/enums.js
index 1b876f27..e700d08f 100644
--- a/tests/enums.js
+++ b/tests/enums.js
@@ -31,3 +31,5 @@ export const SiPWSCFInput = readFile(path.join(FIXTURES_DIR, "Si-pwscf.in"));
 export const Zr1H23Zr1H1 = readJSONFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.json"));
 export const Zr1H23Zr1H1Poscar = readFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.poscar"));
 export const H2O = readFile(path.join(FIXTURES_DIR, "H2O.poscar"));
+
+export const CH4 = readFile(path.join(FIXTURES_DIR, "CH4.xyz"));
diff --git a/tests/fixtures/CH4.xyz b/tests/fixtures/CH4.xyz
new file mode 100644
index 00000000..e0ea7d3e
--- /dev/null
+++ b/tests/fixtures/CH4.xyz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:78e5d267cfe21a127d63beef525912bcff256e5b955c77a944b1a1c59721c989
+size 203
diff --git a/tests/parsers/xyz.js b/tests/parsers/xyz.js
index 6d685627..b086296d 100644
--- a/tests/parsers/xyz.js
+++ b/tests/parsers/xyz.js
@@ -1,5 +1,8 @@
+import { expect } from "chai";
+
 import parsers from "../../src/parsers/parsers";
-import { Si } from "../enums";
+import { atomsCount, linesCount } from "../../src/parsers/xyz";
+import { CH4, Si } from "../enums";
 import { assertDeepAlmostEqual } from "../utils";
 
 describe("Parsers:XYZ", () => {
@@ -11,4 +14,10 @@ describe("Parsers:XYZ", () => {
             "units",
         ]);
     });
+    it("should return the number of atoms for a molecule in an xyz file", () => {
+        expect(atomsCount(CH4)).to.be.equal(5);
+    });
+    it("should return the number of lines in an xyz file", () => {
+        expect(linesCount(CH4)).to.be.equal(7);
+    });
 });

From c06358a3277551b4e97e4a3dad79c62549b183fc Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Fri, 7 Jan 2022 09:15:56 -0800
Subject: [PATCH 02/12] Feat: updates to move all functions for dealing w/
 parsing xyz file and converting to poscar to made instead of web-app

---
 src/parsers/parsers.js    | 30 ++++++++++++++++++++++++++++++
 src/parsers/xyz.js        | 30 +++++++++++++++++++++++-------
 tests/enums.js            |  1 +
 tests/fixtures/CH4.poscar |  3 +++
 tests/parsers/xyz.js      |  8 ++++----
 5 files changed, 61 insertions(+), 11 deletions(-)
 create mode 100644 tests/fixtures/CH4.poscar

diff --git a/src/parsers/parsers.js b/src/parsers/parsers.js
index 2e9924c3..88215c10 100644
--- a/src/parsers/parsers.js
+++ b/src/parsers/parsers.js
@@ -1,11 +1,41 @@
 import cif from "./cif";
+// eslint-disable-next-line import/no-cycle
 import espresso from "./espresso";
 import poscar from "./poscar";
+// eslint-disable-next-line import/no-cycle
 import xyz from "./xyz";
 
+/**
+ * Function splits the contents of a string at each newline and returns the resulting array.
+ * @param fileString
+ * @returns {Array}
+ */
+export function getFileStringAsArray(fileString) {
+    return fileString.split(/\r?\n/);
+}
+
+/**
+ * Function returns the number of atoms in a file using the proper parser function based on the file extension.
+ * @param {String} fileExtension
+ * @param {String} fileContent
+ * @returns {Number}
+ */
+export function getAtomsInFileByExtension(fileExtension, fileContent) {
+    let numberOfAtoms = 0;
+    if (fileExtension === "poscar") {
+        numberOfAtoms = poscar.atomsCount(fileContent);
+    }
+    if (fileExtension === "xyz") {
+        numberOfAtoms = xyz.atomsCount(fileContent);
+    }
+    return numberOfAtoms;
+}
+
 export default {
     xyz,
     poscar,
     cif,
     espresso,
+    getFileStringAsArray,
+    getAtomsInFileByExtension,
 };
diff --git a/src/parsers/xyz.js b/src/parsers/xyz.js
index 8df1ab7e..e0390968 100644
--- a/src/parsers/xyz.js
+++ b/src/parsers/xyz.js
@@ -5,8 +5,11 @@ import s from "underscore.string";
 import { Basis } from "../basis/basis";
 import { ConstrainedBasis } from "../basis/constrained_basis";
 import { Lattice } from "../lattice/lattice";
+// eslint-disable-next-line import/no-cycle
+import { defaultMaterialConfig } from "../material";
 import math from "../math";
 import { InvalidLineError } from "./errors";
+import poscar from "./poscar";
 import { CombinatorialBasis } from "./xyz_combinatorial_basis";
 
 // Regular expression for an XYZ line with atomic constraints, eg. Si    0.000000    0.500000    0.446678 1 1 1`
@@ -141,17 +144,30 @@ function fromMaterial(materialOrConfig, fractional = false) {
     return fromBasis(basis, "%11.6f");
 }
 
+/**
+ * Function splits the xyzFile string at new lines and then returns the first element of the array.
+ * The first line of the XYZ file should contain the number of atoms in the structure.
+ * @param {String} xyzFile
+ * @returns {Number}
+ */
 export function atomsCount(xyzFile) {
     const xyzArray = xyzFile.split(/\r?\n/);
     return Integer.parseInt(xyzArray[0]);
 }
 
-export function linesCount(xyzFile) {
-    const content = xyzFile.split(/\r?\n/);
-    if (!content[-1]) {
-        content.pop();
-    }
-    return content.length;
+/**
+ * Function converts an XYZ formatted structure as a POSCAR formatted structure
+ * @param {String} xyzContent
+ * @returns {String}
+ */
+export function xyzToPoscar(xyzContent) {
+    const xyzConfig = defaultMaterialConfig;
+    const xyzArray = xyzContent.split(/\r?\n/);
+    const xyzArrayBasisOnly = xyzArray.slice(2, -1);
+    const xyzBasis = xyzArrayBasisOnly.join("\n");
+    xyzConfig.basis = toBasisConfig(xyzBasis);
+    xyzConfig.basis.units = "cartesian";
+    return poscar.toPoscar(xyzConfig);
 }
 
 export default {
@@ -161,5 +177,5 @@ export default {
     fromBasis,
     CombinatorialBasis,
     atomsCount,
-    linesCount,
+    xyzToPoscar,
 };
diff --git a/tests/enums.js b/tests/enums.js
index e700d08f..99066d6c 100644
--- a/tests/enums.js
+++ b/tests/enums.js
@@ -33,3 +33,4 @@ export const Zr1H23Zr1H1Poscar = readFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.p
 export const H2O = readFile(path.join(FIXTURES_DIR, "H2O.poscar"));
 
 export const CH4 = readFile(path.join(FIXTURES_DIR, "CH4.xyz"));
+export const CH4POSCAR = readFile(path.join(FIXTURES_DIR, "CH4.poscar"));
diff --git a/tests/fixtures/CH4.poscar b/tests/fixtures/CH4.poscar
new file mode 100644
index 00000000..025bf40a
--- /dev/null
+++ b/tests/fixtures/CH4.poscar
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7a0be33e7640e5f03bbab1c2d130eaa01f791710739919c0224593f8d9d15c95
+size 457
diff --git a/tests/parsers/xyz.js b/tests/parsers/xyz.js
index b086296d..e8150ffd 100644
--- a/tests/parsers/xyz.js
+++ b/tests/parsers/xyz.js
@@ -1,8 +1,8 @@
 import { expect } from "chai";
 
 import parsers from "../../src/parsers/parsers";
-import { atomsCount, linesCount } from "../../src/parsers/xyz";
-import { CH4, Si } from "../enums";
+import { atomsCount, xyzToPoscar } from "../../src/parsers/xyz";
+import { CH4, CH4POSCAR, Si } from "../enums";
 import { assertDeepAlmostEqual } from "../utils";
 
 describe("Parsers:XYZ", () => {
@@ -17,7 +17,7 @@ describe("Parsers:XYZ", () => {
     it("should return the number of atoms for a molecule in an xyz file", () => {
         expect(atomsCount(CH4)).to.be.equal(5);
     });
-    it("should return the number of lines in an xyz file", () => {
-        expect(linesCount(CH4)).to.be.equal(7);
+    it("should return the xyz file content in poscar file format", () => {
+        assertDeepAlmostEqual(xyzToPoscar(CH4), CH4POSCAR);
     });
 });

From e5e38b685344a785a50c202c93d3305a3c8db9ae Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Fri, 7 Jan 2022 10:04:00 -0800
Subject: [PATCH 03/12] simplified atomsCount function for xyz file and updated
 function name for getting number of atoms in parsers

---
 src/parsers/parsers.js | 8 ++++----
 src/parsers/poscar.js  | 4 ++--
 src/parsers/xyz.js     | 7 +++----
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/parsers/parsers.js b/src/parsers/parsers.js
index 88215c10..5cf21ef0 100644
--- a/src/parsers/parsers.js
+++ b/src/parsers/parsers.js
@@ -20,13 +20,13 @@ export function getFileStringAsArray(fileString) {
  * @param {String} fileContent
  * @returns {Number}
  */
-export function getAtomsInFileByExtension(fileExtension, fileContent) {
+export function getNumberOfAtomsInFileByExtension(fileExtension, fileContent) {
     let numberOfAtoms = 0;
     if (fileExtension === "poscar") {
-        numberOfAtoms = poscar.atomsCount(fileContent);
+        numberOfAtoms = poscar.poscarFileAtomsCount(fileContent);
     }
     if (fileExtension === "xyz") {
-        numberOfAtoms = xyz.atomsCount(fileContent);
+        numberOfAtoms = xyz.xyzFileAtomsCount(fileContent);
     }
     return numberOfAtoms;
 }
@@ -37,5 +37,5 @@ export default {
     cif,
     espresso,
     getFileStringAsArray,
-    getAtomsInFileByExtension,
+    getNumberOfAtomsInFileByExtension,
 };
diff --git a/src/parsers/poscar.js b/src/parsers/poscar.js
index 17e0244e..88b3b304 100644
--- a/src/parsers/poscar.js
+++ b/src/parsers/poscar.js
@@ -58,7 +58,7 @@ function toPoscar(materialOrConfig, omitConstraints = false) {
  * @param poscarFileContent
  * @returns {Number}
  */
-export function atomsCount(poscarFileContent) {
+export function poscarFileAtomsCount(poscarFileContent) {
     const atomsLine = poscarFileContent.split("\n")[6].split(" ");
     return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b);
 }
@@ -66,5 +66,5 @@ export function atomsCount(poscarFileContent) {
 export default {
     toPoscar,
     atomicConstraintsCharFromBool,
-    atomsCount,
+    poscarFileAtomsCount,
 };
diff --git a/src/parsers/xyz.js b/src/parsers/xyz.js
index e0390968..afd8a4c5 100644
--- a/src/parsers/xyz.js
+++ b/src/parsers/xyz.js
@@ -150,9 +150,8 @@ function fromMaterial(materialOrConfig, fractional = false) {
  * @param {String} xyzFile
  * @returns {Number}
  */
-export function atomsCount(xyzFile) {
-    const xyzArray = xyzFile.split(/\r?\n/);
-    return Integer.parseInt(xyzArray[0]);
+export function xyzFileAtomsCount(xyzFile) {
+    return Integer.parseInt(xyzFile.split(/\r?\n/)[0]);
 }
 
 /**
@@ -176,6 +175,6 @@ export default {
     toBasisConfig,
     fromBasis,
     CombinatorialBasis,
-    atomsCount,
+    xyzFileAtomsCount,
     xyzToPoscar,
 };

From aef4e7bcb0544e6f0eaa86dd80593c6b83aacc13 Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Fri, 7 Jan 2022 10:07:55 -0800
Subject: [PATCH 04/12] removed unused function from parsers

---
 src/parsers/parsers.js | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/src/parsers/parsers.js b/src/parsers/parsers.js
index 5cf21ef0..c2a6a2f7 100644
--- a/src/parsers/parsers.js
+++ b/src/parsers/parsers.js
@@ -5,15 +5,6 @@ import poscar from "./poscar";
 // eslint-disable-next-line import/no-cycle
 import xyz from "./xyz";
 
-/**
- * Function splits the contents of a string at each newline and returns the resulting array.
- * @param fileString
- * @returns {Array}
- */
-export function getFileStringAsArray(fileString) {
-    return fileString.split(/\r?\n/);
-}
-
 /**
  * Function returns the number of atoms in a file using the proper parser function based on the file extension.
  * @param {String} fileExtension
@@ -36,6 +27,5 @@ export default {
     poscar,
     cif,
     espresso,
-    getFileStringAsArray,
     getNumberOfAtomsInFileByExtension,
 };

From 65c6528bd79ccbeaccfe8071a2f557c25e5736b5 Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Fri, 7 Jan 2022 10:35:06 -0800
Subject: [PATCH 05/12] updated tests for new function naming

---
 tests/parsers/poscar.js | 4 ++--
 tests/parsers/xyz.js    | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/parsers/poscar.js b/tests/parsers/poscar.js
index c4642fb1..da7dc60e 100644
--- a/tests/parsers/poscar.js
+++ b/tests/parsers/poscar.js
@@ -1,7 +1,7 @@
 import { expect } from "chai";
 
 import { Material } from "../../src/material";
-import { atomsCount } from "../../src/parsers/poscar";
+import { poscarFileAtomsCount } from "../../src/parsers/poscar";
 import { H2O, Na4Cl4, Na4Cl4Poscar, Zr1H23Zr1H1, Zr1H23Zr1H1Poscar } from "../enums";
 
 describe("Parsers.POSCAR", () => {
@@ -16,6 +16,6 @@ describe("Parsers.POSCAR", () => {
     });
 
     it("should return the number of atoms for a molecule in a poscar file", () => {
-        expect(atomsCount(H2O)).to.be.equal(3);
+        expect(poscarFileAtomsCount(H2O)).to.be.equal(3);
     });
 });
diff --git a/tests/parsers/xyz.js b/tests/parsers/xyz.js
index e8150ffd..c0733b7b 100644
--- a/tests/parsers/xyz.js
+++ b/tests/parsers/xyz.js
@@ -1,7 +1,7 @@
 import { expect } from "chai";
 
 import parsers from "../../src/parsers/parsers";
-import { atomsCount, xyzToPoscar } from "../../src/parsers/xyz";
+import { xyzFileAtomsCount, xyzToPoscar } from "../../src/parsers/xyz";
 import { CH4, CH4POSCAR, Si } from "../enums";
 import { assertDeepAlmostEqual } from "../utils";
 
@@ -15,7 +15,7 @@ describe("Parsers:XYZ", () => {
         ]);
     });
     it("should return the number of atoms for a molecule in an xyz file", () => {
-        expect(atomsCount(CH4)).to.be.equal(5);
+        expect(xyzFileAtomsCount(CH4)).to.be.equal(5);
     });
     it("should return the xyz file content in poscar file format", () => {
         assertDeepAlmostEqual(xyzToPoscar(CH4), CH4POSCAR);

From 6ef320c4aa2cfc429a347528c32d6e355a375896 Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Fri, 7 Jan 2022 19:09:55 -0800
Subject: [PATCH 06/12] moved functions and updated naming based on PR comments

---
 src/parsers/parsers.js   | 24 ++++++++++++++++++++----
 src/parsers/poscar.js    |  4 ++--
 src/parsers/xyz.js       | 26 +++-----------------------
 tests/parsers/parsers.js |  9 +++++++++
 tests/parsers/poscar.js  |  4 ++--
 tests/parsers/xyz.js     |  9 +++------
 6 files changed, 39 insertions(+), 37 deletions(-)
 create mode 100644 tests/parsers/parsers.js

diff --git a/src/parsers/parsers.js b/src/parsers/parsers.js
index c2a6a2f7..32ca3e93 100644
--- a/src/parsers/parsers.js
+++ b/src/parsers/parsers.js
@@ -1,8 +1,8 @@
-import cif from "./cif";
 // eslint-disable-next-line import/no-cycle
+import { defaultMaterialConfig } from "../material";
+import cif from "./cif";
 import espresso from "./espresso";
 import poscar from "./poscar";
-// eslint-disable-next-line import/no-cycle
 import xyz from "./xyz";
 
 /**
@@ -14,18 +14,34 @@ import xyz from "./xyz";
 export function getNumberOfAtomsInFileByExtension(fileExtension, fileContent) {
     let numberOfAtoms = 0;
     if (fileExtension === "poscar") {
-        numberOfAtoms = poscar.poscarFileAtomsCount(fileContent);
+        numberOfAtoms = poscar.getAtomsCount(fileContent);
     }
     if (fileExtension === "xyz") {
-        numberOfAtoms = xyz.xyzFileAtomsCount(fileContent);
+        numberOfAtoms = xyz.getAtomsCount(fileContent);
     }
     return numberOfAtoms;
 }
 
+/**
+ * Function converts an XYZ formatted structure as a POSCAR formatted structure
+ * @param {String} xyzContent
+ * @returns {String}
+ */
+export function xyzToPoscar(xyzContent) {
+    const xyzConfig = defaultMaterialConfig;
+    const xyzArray = xyzContent.split(/\r?\n/);
+    const xyzArrayBasisOnly = xyzArray.slice(2, -1);
+    const xyzBasis = xyzArrayBasisOnly.join("\n");
+    xyzConfig.basis = xyz.toBasisConfig(xyzBasis);
+    xyzConfig.basis.units = "cartesian";
+    return poscar.toPoscar(xyzConfig);
+}
+
 export default {
     xyz,
     poscar,
     cif,
     espresso,
     getNumberOfAtomsInFileByExtension,
+    xyzToPoscar,
 };
diff --git a/src/parsers/poscar.js b/src/parsers/poscar.js
index 88b3b304..b04cb8cd 100644
--- a/src/parsers/poscar.js
+++ b/src/parsers/poscar.js
@@ -58,7 +58,7 @@ function toPoscar(materialOrConfig, omitConstraints = false) {
  * @param poscarFileContent
  * @returns {Number}
  */
-export function poscarFileAtomsCount(poscarFileContent) {
+export function getAtomsCount(poscarFileContent) {
     const atomsLine = poscarFileContent.split("\n")[6].split(" ");
     return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b);
 }
@@ -66,5 +66,5 @@ export function poscarFileAtomsCount(poscarFileContent) {
 export default {
     toPoscar,
     atomicConstraintsCharFromBool,
-    poscarFileAtomsCount,
+    getAtomsCount,
 };
diff --git a/src/parsers/xyz.js b/src/parsers/xyz.js
index afd8a4c5..070700c3 100644
--- a/src/parsers/xyz.js
+++ b/src/parsers/xyz.js
@@ -1,15 +1,11 @@
-import Integer from "lodash/string";
 import _ from "underscore";
 import s from "underscore.string";
 
 import { Basis } from "../basis/basis";
 import { ConstrainedBasis } from "../basis/constrained_basis";
 import { Lattice } from "../lattice/lattice";
-// eslint-disable-next-line import/no-cycle
-import { defaultMaterialConfig } from "../material";
 import math from "../math";
 import { InvalidLineError } from "./errors";
-import poscar from "./poscar";
 import { CombinatorialBasis } from "./xyz_combinatorial_basis";
 
 // Regular expression for an XYZ line with atomic constraints, eg. Si    0.000000    0.500000    0.446678 1 1 1`
@@ -150,23 +146,8 @@ function fromMaterial(materialOrConfig, fractional = false) {
  * @param {String} xyzFile
  * @returns {Number}
  */
-export function xyzFileAtomsCount(xyzFile) {
-    return Integer.parseInt(xyzFile.split(/\r?\n/)[0]);
-}
-
-/**
- * Function converts an XYZ formatted structure as a POSCAR formatted structure
- * @param {String} xyzContent
- * @returns {String}
- */
-export function xyzToPoscar(xyzContent) {
-    const xyzConfig = defaultMaterialConfig;
-    const xyzArray = xyzContent.split(/\r?\n/);
-    const xyzArrayBasisOnly = xyzArray.slice(2, -1);
-    const xyzBasis = xyzArrayBasisOnly.join("\n");
-    xyzConfig.basis = toBasisConfig(xyzBasis);
-    xyzConfig.basis.units = "cartesian";
-    return poscar.toPoscar(xyzConfig);
+export function getAtomsCount(xyzFile) {
+    return parseInt(xyzFile.split(/\r?\n/)[0], 10);
 }
 
 export default {
@@ -175,6 +156,5 @@ export default {
     toBasisConfig,
     fromBasis,
     CombinatorialBasis,
-    xyzFileAtomsCount,
-    xyzToPoscar,
+    getAtomsCount,
 };
diff --git a/tests/parsers/parsers.js b/tests/parsers/parsers.js
new file mode 100644
index 00000000..36d83df6
--- /dev/null
+++ b/tests/parsers/parsers.js
@@ -0,0 +1,9 @@
+import { xyzToPoscar } from "../../src/parsers/parsers";
+import { CH4, CH4POSCAR } from "../enums";
+import { assertDeepAlmostEqual } from "../utils";
+
+describe("Parsers:XYZ", () => {
+    it("should return the xyz file content in poscar file format", () => {
+        assertDeepAlmostEqual(xyzToPoscar(CH4), CH4POSCAR);
+    });
+});
diff --git a/tests/parsers/poscar.js b/tests/parsers/poscar.js
index da7dc60e..a77227b9 100644
--- a/tests/parsers/poscar.js
+++ b/tests/parsers/poscar.js
@@ -1,7 +1,7 @@
 import { expect } from "chai";
 
 import { Material } from "../../src/material";
-import { poscarFileAtomsCount } from "../../src/parsers/poscar";
+import { getAtomsCount } from "../../src/parsers/poscar";
 import { H2O, Na4Cl4, Na4Cl4Poscar, Zr1H23Zr1H1, Zr1H23Zr1H1Poscar } from "../enums";
 
 describe("Parsers.POSCAR", () => {
@@ -16,6 +16,6 @@ describe("Parsers.POSCAR", () => {
     });
 
     it("should return the number of atoms for a molecule in a poscar file", () => {
-        expect(poscarFileAtomsCount(H2O)).to.be.equal(3);
+        expect(getAtomsCount(H2O)).to.be.equal(3);
     });
 });
diff --git a/tests/parsers/xyz.js b/tests/parsers/xyz.js
index c0733b7b..fe3090e7 100644
--- a/tests/parsers/xyz.js
+++ b/tests/parsers/xyz.js
@@ -1,8 +1,8 @@
 import { expect } from "chai";
 
 import parsers from "../../src/parsers/parsers";
-import { xyzFileAtomsCount, xyzToPoscar } from "../../src/parsers/xyz";
-import { CH4, CH4POSCAR, Si } from "../enums";
+import { getAtomsCount } from "../../src/parsers/xyz";
+import { CH4, Si } from "../enums";
 import { assertDeepAlmostEqual } from "../utils";
 
 describe("Parsers:XYZ", () => {
@@ -15,9 +15,6 @@ describe("Parsers:XYZ", () => {
         ]);
     });
     it("should return the number of atoms for a molecule in an xyz file", () => {
-        expect(xyzFileAtomsCount(CH4)).to.be.equal(5);
-    });
-    it("should return the xyz file content in poscar file format", () => {
-        assertDeepAlmostEqual(xyzToPoscar(CH4), CH4POSCAR);
+        expect(getAtomsCount(CH4)).to.be.equal(5);
     });
 });

From 78572e9ad5049d6abba25f7bbfeee2bbcbf8eac7 Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Thu, 13 Jan 2022 09:16:48 -0800
Subject: [PATCH 07/12] moved defaultMaterialConfig to it's own file to avoid
 circular imports

---
 src/default_material.js | 43 ++++++++++++++++++++++++++++
 src/made.js             |  3 +-
 src/material.js         | 63 +++++++----------------------------------
 src/parsers/parsers.js  |  2 +-
 4 files changed, 56 insertions(+), 55 deletions(-)
 create mode 100644 src/default_material.js

diff --git a/src/default_material.js b/src/default_material.js
new file mode 100644
index 00000000..2b5692e3
--- /dev/null
+++ b/src/default_material.js
@@ -0,0 +1,43 @@
+import { ATOMIC_COORD_UNITS, units } from "./constants";
+import { LATTICE_TYPE } from "./lattice/types";
+
+export const defaultMaterialConfig = {
+    name: "Silicon FCC",
+    basis: {
+        elements: [
+            {
+                id: 1,
+                value: "Si",
+            },
+            {
+                id: 2,
+                value: "Si",
+            },
+        ],
+        coordinates: [
+            {
+                id: 1,
+                value: [0.0, 0.0, 0.0],
+            },
+            {
+                id: 2,
+                value: [0.25, 0.25, 0.25],
+            },
+        ],
+        units: ATOMIC_COORD_UNITS.crystal,
+    },
+    lattice: {
+        // Primitive cell for Diamond FCC Silicon at ambient conditions
+        type: LATTICE_TYPE.FCC,
+        a: 3.867,
+        b: 3.867,
+        c: 3.867,
+        alpha: 60,
+        beta: 60,
+        gamma: 60,
+        units: {
+            length: units.angstrom,
+            angle: units.degree,
+        },
+    },
+};
diff --git a/src/made.js b/src/made.js
index 6d4c1fef..299a4fb0 100644
--- a/src/made.js
+++ b/src/made.js
@@ -2,10 +2,11 @@ import { ArrayWithIds } from "./abstract/array_with_ids";
 import { Basis } from "./basis/basis";
 import { ATOMIC_COORD_UNITS, coefficients, tolerance, units } from "./constants";
 import { AtomicConstraints } from "./constraints/constraints";
+import { defaultMaterialConfig } from "./default_material";
 import { Lattice, nonPeriodicLatticeScalingFactor } from "./lattice/lattice";
 import { ReciprocalLattice } from "./lattice/reciprocal/lattice_reciprocal";
 import { DEFAULT_LATTICE_UNITS, LATTICE_TYPE_CONFIGS } from "./lattice/types";
-import { defaultMaterialConfig, Material } from "./material";
+import { Material } from "./material";
 import MadeMath from "./math";
 import parsers from "./parsers/parsers";
 import tools from "./tools/index";
diff --git a/src/material.js b/src/material.js
index 871e4b2c..469434ef 100644
--- a/src/material.js
+++ b/src/material.js
@@ -7,53 +7,10 @@ import {
     PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES,
     PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS,
 } from "./cell/conventional_cell";
-import { ATOMIC_COORD_UNITS, units } from "./constants";
 import { Lattice } from "./lattice/lattice";
-import { LATTICE_TYPE } from "./lattice/types";
 import parsers from "./parsers/parsers";
 import supercellTools from "./tools/supercell";
 
-export const defaultMaterialConfig = {
-    name: "Silicon FCC",
-    basis: {
-        elements: [
-            {
-                id: 1,
-                value: "Si",
-            },
-            {
-                id: 2,
-                value: "Si",
-            },
-        ],
-        coordinates: [
-            {
-                id: 1,
-                value: [0.0, 0.0, 0.0],
-            },
-            {
-                id: 2,
-                value: [0.25, 0.25, 0.25],
-            },
-        ],
-        units: ATOMIC_COORD_UNITS.crystal,
-    },
-    lattice: {
-        // Primitive cell for Diamond FCC Silicon at ambient conditions
-        type: LATTICE_TYPE.FCC,
-        a: 3.867,
-        b: 3.867,
-        c: 3.867,
-        alpha: 60,
-        beta: 60,
-        gamma: 60,
-        units: {
-            length: units.angstrom,
-            angle: units.degree,
-        },
-    },
-};
-
 export class Material {
     constructor(config) {
         this._json = lodash.cloneDeep(config || {});
@@ -111,7 +68,7 @@ export class Material {
      * @returns {Object}
      */
     getDerivedPropertyByName(name) {
-        return this.getDerivedProperties().find(x => x.name === name);
+        return this.getDerivedProperties().find((x) => x.name === name);
     }
 
     /**
@@ -119,7 +76,7 @@ export class Material {
      * @returns {Array}
      */
     getDerivedProperties() {
-        return this.prop('derivedProperties', []);
+        return this.prop("derivedProperties", []);
     }
 
     /**
@@ -197,12 +154,11 @@ export class Material {
      *  @returns {String}
      */
     getInchiStringForHash() {
-        const inchi = this.getDerivedPropertyByName('inchi');
+        const inchi = this.getDerivedPropertyByName("inchi");
         if (inchi) {
-            return inchi.value
-        } else {
-            throw new Error("Hash cannot be created. Missing InChI string in derivedProperties")
+            return inchi.value;
         }
+        throw new Error("Hash cannot be created. Missing InChI string in derivedProperties");
     }
 
     /**
@@ -215,10 +171,11 @@ export class Material {
      * @param salt {String} Salt for hashing, empty string by default.
      * @param isScaled {Boolean} Whether to scale the lattice parameter 'a' to 1.
      */
-    calculateHash(salt = '', isScaled = false) {
+    calculateHash(salt = "", isScaled = false) {
         let message;
         if (!this.isNonPeriodic) {
-            message = this.Basis.hashString + "#" + this.Lattice.getHashString(isScaled) + "#" + salt;
+            message =
+                this.Basis.hashString + "#" + this.Lattice.getHashString(isScaled) + "#" + salt;
         } else {
             message = this.getInchiStringForHash();
         }
@@ -226,11 +183,11 @@ export class Material {
     }
 
     set hash(hash) {
-        this.setProp('hash', hash);
+        this.setProp("hash", hash);
     }
 
     get hash() {
-        return this.prop('hash');
+        return this.prop("hash");
     }
 
     /**
diff --git a/src/parsers/parsers.js b/src/parsers/parsers.js
index 32ca3e93..4ab31fee 100644
--- a/src/parsers/parsers.js
+++ b/src/parsers/parsers.js
@@ -1,5 +1,5 @@
 // eslint-disable-next-line import/no-cycle
-import { defaultMaterialConfig } from "../material";
+import { defaultMaterialConfig } from "../default_material";
 import cif from "./cif";
 import espresso from "./espresso";
 import poscar from "./poscar";

From df3121489d8b92fe4a16cbce461dc0213f64a334 Mon Sep 17 00:00:00 2001
From: tjduigna <thomas.j.duignan@gmail.com>
Date: Thu, 13 Jan 2022 12:32:49 -0500
Subject: [PATCH 08/12] feat: git lfs pull

---
 .github/workflows/cicd.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml
index e3e6c484..62428486 100644
--- a/.github/workflows/cicd.yml
+++ b/.github/workflows/cicd.yml
@@ -18,6 +18,8 @@ jobs:
     steps:
       - name: Checkout this repository
         uses: actions/checkout@v2
+        with:
+          lfs: true
 
       - name: Checkout actions repository
         uses: actions/checkout@v2
@@ -40,6 +42,8 @@ jobs:
     steps:
       - name: Checkout this repository
         uses: actions/checkout@v2
+        with:
+          lfs: true
 
       - name: Checkout actions repository
         uses: actions/checkout@v2

From bce5e1b9fe9439eed4f5cdf4e254d597818af53e Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Thu, 13 Jan 2022 12:09:56 -0800
Subject: [PATCH 09/12] remove eslint-disable-next-line import/no-cycle

---
 src/parsers/parsers.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/parsers/parsers.js b/src/parsers/parsers.js
index 4ab31fee..9321c673 100644
--- a/src/parsers/parsers.js
+++ b/src/parsers/parsers.js
@@ -1,4 +1,3 @@
-// eslint-disable-next-line import/no-cycle
 import { defaultMaterialConfig } from "../default_material";
 import cif from "./cif";
 import espresso from "./espresso";

From d859afce1b7ee1a532622f0d0959206d153a446c Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Fri, 11 Feb 2022 18:29:48 -0800
Subject: [PATCH 10/12] updated functions for converting between formats

---
 src/parsers/parsers.js   | 17 -----------------
 src/parsers/poscar.js    | 33 +++++++++++++++++++++++++++++++++
 tests/parsers/parsers.js |  9 ---------
 tests/parsers/poscar.js  | 16 ++++++++++++++--
 4 files changed, 47 insertions(+), 28 deletions(-)
 delete mode 100644 tests/parsers/parsers.js

diff --git a/src/parsers/parsers.js b/src/parsers/parsers.js
index 9321c673..1f088fe0 100644
--- a/src/parsers/parsers.js
+++ b/src/parsers/parsers.js
@@ -1,4 +1,3 @@
-import { defaultMaterialConfig } from "../default_material";
 import cif from "./cif";
 import espresso from "./espresso";
 import poscar from "./poscar";
@@ -21,26 +20,10 @@ export function getNumberOfAtomsInFileByExtension(fileExtension, fileContent) {
     return numberOfAtoms;
 }
 
-/**
- * Function converts an XYZ formatted structure as a POSCAR formatted structure
- * @param {String} xyzContent
- * @returns {String}
- */
-export function xyzToPoscar(xyzContent) {
-    const xyzConfig = defaultMaterialConfig;
-    const xyzArray = xyzContent.split(/\r?\n/);
-    const xyzArrayBasisOnly = xyzArray.slice(2, -1);
-    const xyzBasis = xyzArrayBasisOnly.join("\n");
-    xyzConfig.basis = xyz.toBasisConfig(xyzBasis);
-    xyzConfig.basis.units = "cartesian";
-    return poscar.toPoscar(xyzConfig);
-}
-
 export default {
     xyz,
     poscar,
     cif,
     espresso,
     getNumberOfAtomsInFileByExtension,
-    xyzToPoscar,
 };
diff --git a/src/parsers/poscar.js b/src/parsers/poscar.js
index b04cb8cd..3cf274ec 100644
--- a/src/parsers/poscar.js
+++ b/src/parsers/poscar.js
@@ -2,8 +2,10 @@ import s from "underscore.string";
 
 import { ConstrainedBasis } from "../basis/constrained_basis";
 import { ATOMIC_COORD_UNITS } from "../constants";
+import { defaultMaterialConfig } from "../default_material";
 import { Lattice } from "../lattice/lattice";
 import math from "../math";
+import xyz from "./xyz";
 
 const _print = (x, printFormat = "%14.9f") => s.sprintf(printFormat, math.precise(x));
 const _latticeVectorsToString = (vectors) =>
@@ -63,8 +65,39 @@ export function getAtomsCount(poscarFileContent) {
     return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b);
 }
 
+/**
+ * Converts XYZ formated string content to POSCAR formated string content.
+ * @param xyzContent
+ * @returns {string}
+ */
+export function convertFromXyz(xyzContent) {
+    const xyzConfig = defaultMaterialConfig;
+    const xyzArray = xyzContent.split(/\r?\n/);
+    const xyzArrayBasisOnly = xyzArray.slice(2, -1);
+    const xyzBasis = xyzArrayBasisOnly.join("\n");
+    xyzConfig.basis = xyz.toBasisConfig(xyzBasis);
+    xyzConfig.basis.units = "cartesian";
+    return toPoscar(xyzConfig);
+}
+
+/**
+ * Function converts a string of content into a POSCAR formatted string of content. The function called to convert the
+ * format is determined by the format type passed to the function.
+ * @param {String} xyzContent
+ * @param {String} format
+ * @returns {String}
+ */
+export function convertFromOtherFormat(content, format) {
+    if (format === "xyz") {
+        return convertFromXyz(content);
+    }
+    return content;
+}
+
 export default {
     toPoscar,
     atomicConstraintsCharFromBool,
     getAtomsCount,
+    convertFromOtherFormat,
+    convertFromXyz,
 };
diff --git a/tests/parsers/parsers.js b/tests/parsers/parsers.js
deleted file mode 100644
index 36d83df6..00000000
--- a/tests/parsers/parsers.js
+++ /dev/null
@@ -1,9 +0,0 @@
-import { xyzToPoscar } from "../../src/parsers/parsers";
-import { CH4, CH4POSCAR } from "../enums";
-import { assertDeepAlmostEqual } from "../utils";
-
-describe("Parsers:XYZ", () => {
-    it("should return the xyz file content in poscar file format", () => {
-        assertDeepAlmostEqual(xyzToPoscar(CH4), CH4POSCAR);
-    });
-});
diff --git a/tests/parsers/poscar.js b/tests/parsers/poscar.js
index a77227b9..cf61664c 100644
--- a/tests/parsers/poscar.js
+++ b/tests/parsers/poscar.js
@@ -1,8 +1,17 @@
 import { expect } from "chai";
 
 import { Material } from "../../src/material";
-import { getAtomsCount } from "../../src/parsers/poscar";
-import { H2O, Na4Cl4, Na4Cl4Poscar, Zr1H23Zr1H1, Zr1H23Zr1H1Poscar } from "../enums";
+import { convertFromOtherFormat, getAtomsCount } from "../../src/parsers/poscar";
+import {
+    CH4,
+    CH4POSCAR,
+    H2O,
+    Na4Cl4,
+    Na4Cl4Poscar,
+    Zr1H23Zr1H1,
+    Zr1H23Zr1H1Poscar,
+} from "../enums";
+import { assertDeepAlmostEqual } from "../utils";
 
 describe("Parsers.POSCAR", () => {
     it("should return a valid poscar", () => {
@@ -18,4 +27,7 @@ describe("Parsers.POSCAR", () => {
     it("should return the number of atoms for a molecule in a poscar file", () => {
         expect(getAtomsCount(H2O)).to.be.equal(3);
     });
+    it("should return the xyz file content in poscar file format", () => {
+        assertDeepAlmostEqual(convertFromOtherFormat(CH4, "xyz"), CH4POSCAR);
+    });
 });

From 8750daec4fecfd3c5abd35a65a0dced18a0ab4e5 Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Wed, 16 Feb 2022 10:07:33 -0800
Subject: [PATCH 11/12] updated how we copy the default material in converting
 other formats to poscar

---
 src/parsers/poscar.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/parsers/poscar.js b/src/parsers/poscar.js
index 3cf274ec..50b6e288 100644
--- a/src/parsers/poscar.js
+++ b/src/parsers/poscar.js
@@ -1,5 +1,6 @@
 import s from "underscore.string";
 
+import { Material } from "../../lib/material";
 import { ConstrainedBasis } from "../basis/constrained_basis";
 import { ATOMIC_COORD_UNITS } from "../constants";
 import { defaultMaterialConfig } from "../default_material";
@@ -71,7 +72,8 @@ export function getAtomsCount(poscarFileContent) {
  * @returns {string}
  */
 export function convertFromXyz(xyzContent) {
-    const xyzConfig = defaultMaterialConfig;
+    const newMaterial = new Material(defaultMaterialConfig).clone();
+    const xyzConfig = newMaterial._json;
     const xyzArray = xyzContent.split(/\r?\n/);
     const xyzArrayBasisOnly = xyzArray.slice(2, -1);
     const xyzBasis = xyzArrayBasisOnly.join("\n");

From 431a26933ac7405ed96f78ed4d421f236570e58e Mon Sep 17 00:00:00 2001
From: adewyer <adewyer@umich.edu>
Date: Wed, 16 Feb 2022 15:19:29 -0800
Subject: [PATCH 12/12] updates for converting xyz --> poscar without altering
 default material

---
 src/default_material.js | 13 +++++++++++++
 src/made.js             |  3 ++-
 src/parsers/poscar.js   |  6 ++----
 3 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/src/default_material.js b/src/default_material.js
index 2b5692e3..7b5736f7 100644
--- a/src/default_material.js
+++ b/src/default_material.js
@@ -41,3 +41,16 @@ export const defaultMaterialConfig = {
         },
     },
 };
+
+/*
+ * Function returns the defaultMaterial object.
+ * @returns {Object}
+ */
+export function getDefaultMaterialConfig() {
+    return defaultMaterialConfig;
+}
+
+export default {
+    defaultMaterialConfig,
+    getDefaultMaterialConfig,
+};
diff --git a/src/made.js b/src/made.js
index 299a4fb0..022e408d 100644
--- a/src/made.js
+++ b/src/made.js
@@ -2,7 +2,7 @@ import { ArrayWithIds } from "./abstract/array_with_ids";
 import { Basis } from "./basis/basis";
 import { ATOMIC_COORD_UNITS, coefficients, tolerance, units } from "./constants";
 import { AtomicConstraints } from "./constraints/constraints";
-import { defaultMaterialConfig } from "./default_material";
+import { defaultMaterialConfig, getDefaultMaterialConfig } from "./default_material";
 import { Lattice, nonPeriodicLatticeScalingFactor } from "./lattice/lattice";
 import { ReciprocalLattice } from "./lattice/reciprocal/lattice_reciprocal";
 import { DEFAULT_LATTICE_UNITS, LATTICE_TYPE_CONFIGS } from "./lattice/types";
@@ -20,6 +20,7 @@ export const Made = {
 
     Material,
     defaultMaterialConfig,
+    getDefaultMaterialConfig,
     Lattice,
     nonPeriodicLatticeScalingFactor,
     ReciprocalLattice,
diff --git a/src/parsers/poscar.js b/src/parsers/poscar.js
index 50b6e288..4b991fb2 100644
--- a/src/parsers/poscar.js
+++ b/src/parsers/poscar.js
@@ -1,9 +1,8 @@
 import s from "underscore.string";
 
-import { Material } from "../../lib/material";
 import { ConstrainedBasis } from "../basis/constrained_basis";
 import { ATOMIC_COORD_UNITS } from "../constants";
-import { defaultMaterialConfig } from "../default_material";
+import { getDefaultMaterialConfig } from "../default_material";
 import { Lattice } from "../lattice/lattice";
 import math from "../math";
 import xyz from "./xyz";
@@ -72,8 +71,7 @@ export function getAtomsCount(poscarFileContent) {
  * @returns {string}
  */
 export function convertFromXyz(xyzContent) {
-    const newMaterial = new Material(defaultMaterialConfig).clone();
-    const xyzConfig = newMaterial._json;
+    const xyzConfig = { ...getDefaultMaterialConfig() };
     const xyzArray = xyzContent.split(/\r?\n/);
     const xyzArrayBasisOnly = xyzArray.slice(2, -1);
     const xyzBasis = xyzArrayBasisOnly.join("\n");