matsci-parse 0.3.0 → 0.3.1

package/dist/main.js

@@ -1,4 +1,4 @@
-class v {
+class S {
   constructor(s, e, t = {}) {
     this.speciesIndex = s, this.cart = e, this.props = t;
   }
@@ -9,34 +9,53 @@ class v {
     this.props[s] = e;
   }
 }
-function B(m) {
-  return m.sites.some((s) => Array.isArray(s.props.selectiveDynamics));
+function B(i) {
+  return i.sites.some((s) => Array.isArray(s.props.selectiveDynamics));
 }
-function M(m) {
-  return m * Math.PI / 180;
+function M(i) {
+  return i * Math.PI / 180;
 }
-function j(m, s) {
-  return m.map(
+function O(i, s) {
+  return i.map(
     (e) => e[0] * s[0] + e[1] * s[1] + e[2] * s[2]
   );
 }
-function k(m, s, e, t, i, o) {
-  const a = M(t), b = M(i), n = M(o), u = [m, 0, 0], h = [
-    s * Math.cos(n),
-    s * Math.sin(n),
+function k(i, s, e, t, m, o) {
+  const n = M(t), u = M(m), a = M(o), b = [i, 0, 0], h = [
+    s * Math.cos(a),
+    s * Math.sin(a),
     0
-  ], c = e * Math.cos(b), l = e * (Math.cos(a) - Math.cos(b) * Math.cos(n)) / Math.sin(n), f = Math.sqrt(e * e - c * c - l * l);
-  return [u, h, [c, l, f]];
+  ], r = e * Math.cos(u), l = e * (Math.cos(n) - Math.cos(u) * Math.cos(a)) / Math.sin(a), y = Math.sqrt(e * e - r * r - l * l);
+  return [b, h, [r, l, y]];
 }
-function U(m, s) {
-  const [e, t, i] = s;
+function U(i, s) {
+  const [e, t, m] = s;
   return [
-    m[0] * e[0] + m[1] * t[0] + m[2] * i[0],
-    m[0] * e[1] + m[1] * t[1] + m[2] * i[1],
-    m[0] * e[2] + m[1] * t[2] + m[2] * i[2]
+    i[0] * e[0] + i[1] * t[0] + i[2] * m[0],
+    i[0] * e[1] + i[1] * t[1] + i[2] * m[1],
+    i[0] * e[2] + i[1] * t[2] + i[2] * m[2]
   ];
 }
-class I {
+function X(i) {
+  const [[s, e, t], [m, o, n], [u, a, b]] = i, h = o * b - n * a, r = -(m * b - n * u), l = m * a - o * u, y = -(e * b - t * a), c = s * b - t * u, p = -(s * a - e * u), N = e * n - t * o, g = -(s * n - t * m), _ = s * o - e * m, v = s * h + e * r + t * l;
+  if (Math.abs(v) < 1e-12)
+    throw new Error("Matrix is singular and cannot be inverted");
+  const f = 1 / v;
+  return [
+    [h * f, y * f, N * f],
+    [r * f, c * f, g * f],
+    [l * f, p * f, _ * f]
+  ];
+}
+function J(i, s) {
+  const [e, t, m] = s, o = [
+    [e[0], t[0], m[0]],
+    [e[1], t[1], m[1]],
+    [e[2], t[2], m[2]]
+  ], n = X(o);
+  return O(n, i);
+}
+class F {
   /**
    * Creates a new CrystalStructure.
    *
@@ -93,9 +112,9 @@ class I {
    * @param position - Optional index at which to insert the site. Defaults to appending at the end.
    */
   addSite(s, e, t) {
-    let i = this.species.indexOf(s);
-    i === -1 && (this.species.push(s), i = this.species.length - 1);
-    const o = new v(i, e);
+    let m = this.species.indexOf(s);
+    m === -1 && (this.species.push(s), m = this.species.length - 1);
+    const o = new S(m, e);
     t === void 0 || t >= this.sites.length ? this.sites.push(o) : t < 0 ? this.sites.unshift(o) : this.sites.splice(t, 0, o);
   }
   /**
@@ -167,18 +186,18 @@ class I {
         "Scale must be a number, a 3-element array, or a 3x3 matrix"
       );
     const t = this.lattice.map(
-      (o) => j(e, o)
-    ), i = this.sites.map((o) => {
-      const a = j(
+      (o) => O(e, o)
+    ), m = this.sites.map((o) => {
+      const n = O(
         e,
         o.cart
       );
-      return new v(o.speciesIndex, a, o.props);
+      return new S(o.speciesIndex, n, o.props);
     });
-    return new I({
+    return new F({
       lattice: t,
       species: [...this.species],
-      sites: i
+      sites: m
     });
   }
   // ---------- Internal validation ----------
@@ -212,9 +231,9 @@ class I {
   _validateSites(s) {
     if (!Array.isArray(s)) throw new Error("Sites must be an array");
     return s.map((e) => {
-      if (e instanceof v) return e;
+      if (e instanceof S) return e;
       if (typeof e == "object" && typeof e.speciesIndex == "number" && Array.isArray(e.cart) && e.cart.length === 3)
-        return this._validateSpeciesIndex(e.speciesIndex), new v(
+        return this._validateSpeciesIndex(e.speciesIndex), new S(
           e.speciesIndex,
           e.cart,
           e.props ?? {}
@@ -233,27 +252,27 @@ class I {
       throw new Error("speciesIndex out of bounds");
   }
 }
-class X {
+class Z {
   constructor(s) {
     this.spatialUnits = "angstrom", this._invalid = !0;
-    const { origin: e, basis: t, shape: i, values: o, components: a = 1, units: b } = s, [n, u, h] = i;
-    if (o.length !== n * u * h * a)
+    const { origin: e, basis: t, shape: m, values: o, components: n = 1, units: u } = s, [a, b, h] = m;
+    if (o.length !== a * b * h * n)
       throw new Error(
-        `Invalid values length: expected ${n * u * h * a}, got ${o.length}`
+        `Invalid values length: expected ${a * b * h * n}, got ${o.length}`
       );
-    this.origin = e, this.basis = t, this.shape = i, this.values = o, this.components = a, this.units = b;
+    this.origin = e, this.basis = t, this.shape = m, this.values = o, this.components = n, this.units = u;
   }
   invalidate() {
     this._invalid = !0;
   }
   map(s) {
-    const [e, t, i] = this.shape;
-    for (let o = 0; o < i; o++)
-      for (let a = 0; a < t; a++)
-        for (let b = 0; b < e; b++)
-          for (let n = 0; n < this.components; n++) {
-            const u = this.index(b, a, o, n);
-            this.values[u] = s(this.values[u], b, a, o, n);
+    const [e, t, m] = this.shape;
+    for (let o = 0; o < m; o++)
+      for (let n = 0; n < t; n++)
+        for (let u = 0; u < e; u++)
+          for (let a = 0; a < this.components; a++) {
+            const b = this.index(u, n, o, a);
+            this.values[b] = s(this.values[b], u, n, o, a);
           }
     this.invalidate();
   }
@@ -266,15 +285,15 @@ class X {
   mean() {
     return (this._invalid || this._mean === void 0) && this.computeStats(), this._mean;
   }
-  index(s, e, t, i = 0) {
-    const [o, a] = this.shape;
-    return (s + o * (e + a * t)) * this.components + i;
+  index(s, e, t, m = 0) {
+    const [o, n] = this.shape;
+    return (s + o * (e + n * t)) * this.components + m;
   }
-  get(s, e, t, i = 0) {
-    return this.values[this.index(s, e, t, i)];
+  get(s, e, t, m = 0) {
+    return this.values[this.index(s, e, t, m)];
   }
-  set(s, e, t, i, o) {
-    this.values[this.index(s, e, t, i)] = o, this.invalidate();
+  set(s, e, t, m, o = 0) {
+    this.values[this.index(s, e, t, o)] = m, this.invalidate();
   }
   normalize() {
     const s = this.min(), e = this.max();
@@ -282,11 +301,11 @@ class X {
   }
   /** Convert grid index → Cartesian position */
   position(s, e, t) {
-    const [i, o, a] = this.basis;
+    const [m, o, n] = this.basis;
     return [
-      this.origin[0] + s * i[0] + e * o[0] + t * a[0],
-      this.origin[1] + s * i[1] + e * o[1] + t * a[1],
-      this.origin[2] + s * i[2] + e * o[2] + t * a[2]
+      this.origin[0] + s * m[0] + e * o[0] + t * n[0],
+      this.origin[1] + s * m[1] + e * o[1] + t * n[1],
+      this.origin[2] + s * m[2] + e * o[2] + t * n[2]
     ];
   }
   voxelVolume() {
@@ -300,114 +319,114 @@ class X {
   }
   computeStats() {
     const s = this.values.length;
-    let e = 1 / 0, t = -1 / 0, i = 0;
+    let e = 1 / 0, t = -1 / 0, m = 0;
     for (let o = 0; o < s; o++) {
-      const a = this.values[o];
-      a < e && (e = a), a > t && (t = a), i += a;
+      const n = this.values[o];
+      n < e && (e = n), n > t && (t = n), m += n;
     }
-    this._min = e, this._max = t, this._mean = i / s, this._invalid = !1;
+    this._min = e, this._max = t, this._mean = m / s, this._invalid = !1;
   }
 }
-function F(m) {
-  return m.split(/\r?\n/).map((s) => s.trim()).filter(Boolean);
+function I(i) {
+  return i.split(/\r?\n/).map((s) => s.trim()).filter(Boolean);
 }
-function K(m, s = 6) {
-  const e = [], t = B(m);
-  e.push("Generated by matsci-parse"), e.push("1.0"), m.lattice.forEach((a) => {
-    e.push(a.map((b) => b.toFixed(s)).join(" "));
+function Q(i, s = 6) {
+  const e = [], t = B(i);
+  e.push("Generated by matsci-parse"), e.push("1.0"), i.lattice.forEach((n) => {
+    e.push(n.map((u) => u.toFixed(s)).join(" "));
   });
-  const i = Array.from(
-    new Set(m.sites.map((a) => m.species[a.speciesIndex]))
-  ), o = i.map(
-    (a) => m.sites.filter((b) => m.species[b.speciesIndex] === a).length
+  const m = Array.from(
+    new Set(i.sites.map((n) => i.species[n.speciesIndex]))
+  ), o = m.map(
+    (n) => i.sites.filter((u) => i.species[u.speciesIndex] === n).length
   );
-  return e.push(i.join(" ")), e.push(o.join(" ")), t && e.push("Selective dynamics"), e.push("Cartesian"), i.forEach((a) => {
-    m.sites.filter((b) => m.species[b.speciesIndex] === a).forEach((b) => {
-      const n = b.cart.map((u) => u.toFixed(s)).join(" ");
+  return e.push(m.join(" ")), e.push(o.join(" ")), t && e.push("Selective dynamics"), e.push("Cartesian"), m.forEach((n) => {
+    i.sites.filter((u) => i.species[u.speciesIndex] === n).forEach((u) => {
+      const a = u.cart.map((b) => b.toFixed(s)).join(" ");
       if (t) {
-        const h = (Array.isArray(b.props?.selectiveDynamics) ? b.props.selectiveDynamics : [!0, !0, !0]).map((c) => c ? "T" : "F").join(" ");
-        e.push(`${n} ${h}`);
+        const h = (Array.isArray(u.props?.selectiveDynamics) ? u.props.selectiveDynamics : [!0, !0, !0]).map((r) => r ? "T" : "F").join(" ");
+        e.push(`${a} ${h}`);
       } else
-        e.push(n);
+        e.push(a);
     });
   }), e.join(`
 `);
 }
-function Z(m) {
+function z(i) {
   let s = 0;
   s++;
-  const e = parseFloat(m[s++]), t = [];
-  for (let c = 0; c < 3; c++)
+  const e = parseFloat(i[s++]), t = [];
+  for (let r = 0; r < 3; r++)
     t.push(
-      m[s++].split(/\s+/).map((l) => parseFloat(l) * e)
+      i[s++].split(/\s+/).map((l) => parseFloat(l) * e)
     );
-  let i = m[s].trim(), o;
-  /^[A-Za-z]/.test(i) && (o = i.split(/\s+/), s++);
-  const a = m[s++].split(/\s+/).map(Number);
-  o || (o = a.map((c, l) => `X${l + 1}`));
-  let b = !1;
-  m[s]?.toLowerCase().startsWith("s") && (b = !0, s++);
-  const u = m[s++].toLowerCase().startsWith("d"), h = [];
-  return o.forEach((c, l) => {
-    for (let f = 0; f < a[l]; f++) {
-      const r = m[s++].split(/\s+/).map(Number);
+  let m = i[s].trim(), o;
+  /^[A-Za-z]/.test(m) && (o = m.split(/\s+/), s++);
+  const n = i[s++].split(/\s+/).map(Number);
+  o || (o = n.map((r, l) => `X${l + 1}`));
+  let u = !1;
+  i[s]?.toLowerCase().startsWith("s") && (u = !0, s++);
+  const b = i[s++].toLowerCase().startsWith("d"), h = [];
+  return o.forEach((r, l) => {
+    for (let y = 0; y < n[l]; y++) {
+      const c = i[s++].split(/\s+/).map(Number);
       let p;
-      u ? p = [
-        r[0] * t[0][0] + r[1] * t[1][0] + r[2] * t[2][0],
-        r[0] * t[0][1] + r[1] * t[1][1] + r[2] * t[2][1],
-        r[0] * t[0][2] + r[1] * t[1][2] + r[2] * t[2][2]
-      ] : p = r.slice(0, 3);
+      b ? p = [
+        c[0] * t[0][0] + c[1] * t[1][0] + c[2] * t[2][0],
+        c[0] * t[0][1] + c[1] * t[1][1] + c[2] * t[2][1],
+        c[0] * t[0][2] + c[1] * t[1][2] + c[2] * t[2][2]
+      ] : p = c.slice(0, 3);
       const N = {};
-      if (b) {
-        const g = r.slice(3, 6).map((_) => _ === 1);
+      if (u) {
+        const g = c.slice(3, 6).map((_) => _ === 1);
         g.length === 3 && (N.selectiveDynamics = g);
       }
-      h.push(new v(l, p, N));
+      h.push(new S(l, p, N));
     }
   }), {
-    structure: new I({ lattice: t, species: o, sites: h }),
+    structure: new F({ lattice: t, species: o, sites: h }),
     linesConsumed: s
   };
 }
-function J(m) {
-  const s = F(m);
-  return Z(s).structure;
+function ss(i) {
+  const s = I(i);
+  return z(s).structure;
 }
-function Q(m, s = 6) {
+function es(i, s = 6) {
   const e = [];
-  return e.push("CRYSTAL"), e.push("PRIMVEC"), m.lattice.forEach((t) => {
-    e.push(t.map((i) => i.toFixed(s)).join(" "));
-  }), e.push("PRIMCOORD"), e.push(`${m.numSites} 1`), m.sites.forEach((t) => {
-    const i = m.species[t.speciesIndex];
+  return e.push("CRYSTAL"), e.push("PRIMVEC"), i.lattice.forEach((t) => {
+    e.push(t.map((m) => m.toFixed(s)).join(" "));
+  }), e.push("PRIMCOORD"), e.push(`${i.numSites} 1`), i.sites.forEach((t) => {
+    const m = i.species[t.speciesIndex];
     e.push(
-      `${i} ${t.cart.map((o) => o.toFixed(s)).join(" ")}`
+      `${m} ${t.cart.map((o) => o.toFixed(s)).join(" ")}`
     );
   }), e.join(`
 `);
 }
-function ss(m) {
-  const s = F(m), e = [], t = [], i = [];
+function ts(i) {
+  const s = I(i), e = [], t = [], m = [];
   let o = 0;
   for (; o < s.length && s[o].toUpperCase() !== "PRIMVEC"; ) o++;
   if (o === s.length) throw new Error("PRIMVEC block not found in XSF");
   o++;
-  for (let b = 0; b < 3; b++)
+  for (let u = 0; u < 3; u++)
     e.push(s[o++].split(/\s+/).map(Number));
   for (; o < s.length && s[o].toUpperCase() !== "PRIMCOORD"; ) o++;
   if (o === s.length) throw new Error("PRIMCOORD block not found in XSF");
   o++;
-  const [a] = s[o++].split(/\s+/).map(Number);
-  for (let b = 0; b < a; b++) {
-    const n = s[o++].split(/\s+/), u = n[0], h = n.slice(1, 4).map(Number);
-    let c = t.indexOf(u);
-    c === -1 && (t.push(u), c = t.length - 1), i.push(new v(c, h));
+  const [n] = s[o++].split(/\s+/).map(Number);
+  for (let u = 0; u < n; u++) {
+    const a = s[o++].split(/\s+/), b = a[0], h = a.slice(1, 4).map(Number);
+    let r = t.indexOf(b);
+    r === -1 && (t.push(b), r = t.length - 1), m.push(new S(r, h));
   }
-  return new I({ lattice: e, species: t, sites: i });
+  return new F({ lattice: e, species: t, sites: m });
 }
-function es(m, s = 6) {
-  const e = [], t = m.sites.length;
+function os(i, s = 6) {
+  const e = [], t = i.sites.length;
   e.push(String(t));
-  const i = B(m), o = m.lattice, a = [
+  const m = B(i), o = i.lattice, n = [
     o[0][0],
     o[1][0],
     o[2][0],
@@ -417,115 +436,115 @@ function es(m, s = 6) {
     o[0][2],
     o[1][2],
     o[2][2]
-  ].join(" "), b = [
+  ].join(" "), u = [
     "species:S:1",
     "pos:R:3",
-    i ? "selectiveDynamics:L:3" : null
+    m ? "selectiveDynamics:L:3" : null
   ].filter(Boolean).join(":");
-  e.push(`Lattice="${a}" Properties=${b}`);
-  for (const n of m.sites) {
-    const u = m.species[n.speciesIndex], [h, c, l] = n.cart;
-    let f = `${u} ${h.toFixed(s)} ${c.toFixed(s)} ${l.toFixed(s)}`;
-    if (i) {
-      const r = Array.isArray(n.props?.selectiveDynamics) ? n.props.selectiveDynamics : [!0, !0, !0];
-      f += " " + r.map((p) => p ? "T" : "F").join(" ");
+  e.push(`Lattice="${n}" Properties=${u}`);
+  for (const a of i.sites) {
+    const b = i.species[a.speciesIndex], [h, r, l] = a.cart;
+    let y = `${b} ${h.toFixed(s)} ${r.toFixed(s)} ${l.toFixed(s)}`;
+    if (m) {
+      const c = Array.isArray(a.props?.selectiveDynamics) ? a.props.selectiveDynamics : [!0, !0, !0];
+      y += " " + c.map((p) => p ? "T" : "F").join(" ");
     }
-    e.push(f);
+    e.push(y);
   }
   return e.join(`
 `);
 }
-function ts(m) {
-  const s = F(m);
+function is(i) {
+  const s = I(i);
   let e = 0;
   const t = parseInt(s[e++], 10);
   if (!Number.isFinite(t))
     throw new Error("Invalid XYZ: first line must be atom count");
-  const i = s[e++], o = {}, a = /(\w+)=(".*?"|\S+)/g;
-  for (const r of i.matchAll(a)) {
-    let p = r[2];
-    p.startsWith('"') && (p = p.slice(1, -1)), o[r[1]] = p;
+  const m = s[e++], o = {}, n = /(\w+)=(".*?"|\S+)/g;
+  for (const c of m.matchAll(n)) {
+    let p = c[2];
+    p.startsWith('"') && (p = p.slice(1, -1)), o[c[1]] = p;
   }
-  let b;
+  let u;
   if (o.Lattice) {
-    const r = o.Lattice.split(/\s+/).map(Number);
-    if (r.length !== 9) throw new Error("Invalid Lattice in extended XYZ");
-    b = [
-      [r[0], r[3], r[6]],
-      [r[1], r[4], r[7]],
-      [r[2], r[5], r[8]]
+    const c = o.Lattice.split(/\s+/).map(Number);
+    if (c.length !== 9) throw new Error("Invalid Lattice in extended XYZ");
+    u = [
+      [c[0], c[3], c[6]],
+      [c[1], c[4], c[7]],
+      [c[2], c[5], c[8]]
     ];
   } else
     throw new Error("Lattice must be present in extended XYZ format");
-  let n = 0, u = 1, h = null;
+  let a = 0, b = 1, h = null;
   if (o.Properties) {
-    const r = o.Properties.split(":");
+    const c = o.Properties.split(":");
     let p = 0;
-    for (let N = 0; N < r.length; N += 3) {
-      const g = r[N], _ = parseInt(r[N + 2], 10);
-      g === "species" && (n = p), g === "pos" && (u = p), g === "selectiveDynamics" && (h = p), p += _;
+    for (let N = 0; N < c.length; N += 3) {
+      const g = c[N], _ = parseInt(c[N + 2], 10);
+      g === "species" && (a = p), g === "pos" && (b = p), g === "selectiveDynamics" && (h = p), p += _;
     }
   }
-  const c = [], l = /* @__PURE__ */ new Map(), f = [];
-  for (let r = 0; r < t; r++) {
-    const p = s[e++].split(/\s+/), N = p[n];
-    l.has(N) || (l.set(N, c.length), c.push(N));
-    const g = l.get(N), _ = p.slice(u, u + 3).map(Number), S = {};
+  const r = [], l = /* @__PURE__ */ new Map(), y = [];
+  for (let c = 0; c < t; c++) {
+    const p = s[e++].split(/\s+/), N = p[a];
+    l.has(N) || (l.set(N, r.length), r.push(N));
+    const g = l.get(N), _ = p.slice(b, b + 3).map(Number), v = {};
     if (h !== null) {
-      const y = p.slice(h, h + 3).map((d) => d.toUpperCase() === "T");
-      y.length === 3 && (S.selectiveDynamics = y);
+      const f = p.slice(h, h + 3).map((d) => d.toUpperCase() === "T");
+      f.length === 3 && (v.selectiveDynamics = f);
     }
-    f.push(new v(g, _, S));
+    y.push(new S(g, _, v));
   }
-  return new I({ lattice: b, species: c, sites: f });
+  return new F({ lattice: u, species: r, sites: y });
 }
-function C(m, s) {
-  return m[0] * s[0] + m[1] * s[1] + m[2] * s[2];
+function C(i, s) {
+  return i[0] * s[0] + i[1] * s[1] + i[2] * s[2];
 }
-function L(m) {
-  return Math.sqrt(C(m, m));
+function L(i) {
+  return Math.sqrt(C(i, i));
 }
-function P(m) {
-  return m * 180 / Math.PI;
+function P(i) {
+  return i * 180 / Math.PI;
 }
-function z(m, s) {
-  const [e, t, i] = s, o = e[0] * (t[1] * i[2] - t[2] * i[1]) - e[1] * (t[0] * i[2] - t[2] * i[0]) + e[2] * (t[0] * i[1] - t[1] * i[0]);
+function G(i, s) {
+  const [e, t, m] = s, o = e[0] * (t[1] * m[2] - t[2] * m[1]) - e[1] * (t[0] * m[2] - t[2] * m[0]) + e[2] * (t[0] * m[1] - t[1] * m[0]);
   if (Math.abs(o) < 1e-12)
     throw new Error("Singular lattice matrix");
-  const a = [
+  const n = [
     [
-      (t[1] * i[2] - t[2] * i[1]) / o,
-      (e[2] * i[1] - e[1] * i[2]) / o,
+      (t[1] * m[2] - t[2] * m[1]) / o,
+      (e[2] * m[1] - e[1] * m[2]) / o,
       (e[1] * t[2] - e[2] * t[1]) / o
     ],
     [
-      (t[2] * i[0] - t[0] * i[2]) / o,
-      (e[0] * i[2] - e[2] * i[0]) / o,
+      (t[2] * m[0] - t[0] * m[2]) / o,
+      (e[0] * m[2] - e[2] * m[0]) / o,
       (e[2] * t[0] - e[0] * t[2]) / o
     ],
     [
-      (t[0] * i[1] - t[1] * i[0]) / o,
-      (e[1] * i[0] - e[0] * i[1]) / o,
+      (t[0] * m[1] - t[1] * m[0]) / o,
+      (e[1] * m[0] - e[0] * m[1]) / o,
       (e[0] * t[1] - e[1] * t[0]) / o
     ]
   ];
   return [
-    m[0] * a[0][0] + m[1] * a[1][0] + m[2] * a[2][0],
-    m[0] * a[0][1] + m[1] * a[1][1] + m[2] * a[2][1],
-    m[0] * a[0][2] + m[1] * a[1][2] + m[2] * a[2][2]
+    i[0] * n[0][0] + i[1] * n[1][0] + i[2] * n[2][0],
+    i[0] * n[0][1] + i[1] * n[1][1] + i[2] * n[2][1],
+    i[0] * n[0][2] + i[1] * n[1][2] + i[2] * n[2][2]
   ];
 }
-function ms(m, s = 6) {
-  const [e, t, i] = m.lattice, o = L(e), a = L(t), b = L(i), n = P(Math.acos(C(t, i) / (a * b))), u = P(Math.acos(C(e, i) / (o * b))), h = P(Math.acos(C(e, t) / (o * a)));
-  let c = `data_made_with_matsci-parse
+function ms(i, s = 6) {
+  const [e, t, m] = i.lattice, o = L(e), n = L(t), u = L(m), a = P(Math.acos(C(t, m) / (n * u))), b = P(Math.acos(C(e, m) / (o * u))), h = P(Math.acos(C(e, t) / (o * n)));
+  let r = `data_made_with_matsci-parse
     _symmetry_space_group_name_H-M   'P 1'
     _symmetry_Int_Tables_number    1
 
     _cell_length_a   ${o.toFixed(s)}
-    _cell_length_b   ${a.toFixed(s)}
-    _cell_length_c   ${b.toFixed(s)}
-    _cell_angle_alpha   ${n.toFixed(s)}
-    _cell_angle_beta    ${u.toFixed(s)}
+    _cell_length_b   ${n.toFixed(s)}
+    _cell_length_c   ${u.toFixed(s)}
+    _cell_angle_alpha   ${a.toFixed(s)}
+    _cell_angle_beta    ${b.toFixed(s)}
     _cell_angle_gamma   ${h.toFixed(s)}
 
     loop_
@@ -535,73 +554,73 @@ function ms(m, s = 6) {
     _atom_site_fract_y
     _atom_site_fract_z
 `;
-  return m.sites.forEach((l, f) => {
-    const r = m.species[l.speciesIndex], p = z(l.cart, m.lattice);
-    c += `${r}${f + 1} ${r} ${p[0].toFixed(s)} ${p[1].toFixed(
+  return i.sites.forEach((l, y) => {
+    const c = i.species[l.speciesIndex], p = G(l.cart, i.lattice);
+    r += `${c}${y + 1} ${c} ${p[0].toFixed(s)} ${p[1].toFixed(
       6
     )} ${p[2].toFixed(s)}
 `;
-  }), c;
+  }), r;
 }
-function os(m) {
-  const s = F(m);
-  let e = 0, t = 0, i = 0, o = 0, a = 0, b = 0, n = [];
-  const u = [];
-  let h = !1, c = [], l = !1;
-  for (const y of s) {
-    const d = y.trim();
+function ns(i) {
+  const s = I(i);
+  let e = 0, t = 0, m = 0, o = 0, n = 0, u = 0, a = [];
+  const b = [];
+  let h = !1, r = [], l = !1;
+  for (const f of s) {
+    const d = f.trim();
     if (d) {
       if (d.startsWith("_cell_length_a")) e = parseFloat(d.split(/\s+/)[1]);
       else if (d.startsWith("_cell_length_b"))
         t = parseFloat(d.split(/\s+/)[1]);
       else if (d.startsWith("_cell_length_c"))
-        i = parseFloat(d.split(/\s+/)[1]);
+        m = parseFloat(d.split(/\s+/)[1]);
       else if (d.startsWith("_cell_angle_alpha"))
         o = parseFloat(d.split(/\s+/)[1]);
       else if (d.startsWith("_cell_angle_beta"))
-        a = parseFloat(d.split(/\s+/)[1]);
+        n = parseFloat(d.split(/\s+/)[1]);
       else if (d.startsWith("_cell_angle_gamma"))
-        b = parseFloat(d.split(/\s+/)[1]);
+        u = parseFloat(d.split(/\s+/)[1]);
       else if (d.startsWith("loop_")) {
-        h = !0, c = [], l = !1;
+        h = !0, r = [], l = !1;
         continue;
       }
       if (h && d.startsWith("_")) {
-        c.push(d), d.includes("_atom_site_") && (l = !0);
+        r.push(d), d.includes("_atom_site_") && (l = !0);
         continue;
       }
       if (h && !d.startsWith("_")) {
-        l && (n.length === 0 && (n = [...c]), u.push(d.split(/\s+/)));
+        l && (a.length === 0 && (a = [...r]), b.push(d.split(/\s+/)));
         continue;
       }
     }
   }
-  if (n.length === 0)
+  if (a.length === 0)
     throw new Error("No _atom_site loop found in CIF");
-  const f = k(e, t, i, o, a, b), r = [], p = [], N = n.findIndex((y) => y.includes("fract_x")), g = n.findIndex((y) => y.includes("fract_y")), _ = n.findIndex((y) => y.includes("fract_z")), S = n.findIndex((y) => y.includes("type_symbol"));
-  if (N < 0 || g < 0 || _ < 0 || S < 0)
+  const y = k(e, t, m, o, n, u), c = [], p = [], N = a.findIndex((f) => f.includes("fract_x")), g = a.findIndex((f) => f.includes("fract_y")), _ = a.findIndex((f) => f.includes("fract_z")), v = a.findIndex((f) => f.includes("type_symbol"));
+  if (N < 0 || g < 0 || _ < 0 || v < 0)
     throw new Error("CIF missing required _atom_site columns");
-  for (const y of u) {
+  for (const f of b) {
     const d = [
-      parseFloat(y[N]),
-      parseFloat(y[g]),
-      parseFloat(y[_])
-    ], w = U(d, f);
-    let x = r.indexOf(y[S]);
-    x === -1 && (x = r.length, r.push(y[S])), p.push(new v(x, w));
-  }
-  return new I({ lattice: f, species: r, sites: p });
+      parseFloat(f[N]),
+      parseFloat(f[g]),
+      parseFloat(f[_])
+    ], w = U(d, y);
+    let x = c.indexOf(f[v]);
+    x === -1 && (x = c.length, c.push(f[v])), p.push(new S(x, w));
+  }
+  return new F({ lattice: y, species: c, sites: p });
 }
-function G(m) {
+function Y(i) {
   let s = [];
   const e = [];
-  for (let n = 0; n < m.length; n++) {
-    const u = m[n].trim();
-    if (!(!u || u.startsWith("&")) && /^CELL_PARAMETERS/i.test(u)) {
-      let h = 0, c = n + 1;
-      for (; h < 3 && c < m.length; ) {
-        const l = m[c].trim();
-        l !== "" && (s.push(l.split(/\s+/).map(Number)), h++), c++;
+  for (let a = 0; a < i.length; a++) {
+    const b = i[a].trim();
+    if (!(!b || b.startsWith("&")) && /^CELL_PARAMETERS/i.test(b)) {
+      let h = 0, r = a + 1;
+      for (; h < 3 && r < i.length; ) {
+        const l = i[r].trim();
+        l !== "" && (s.push(l.split(/\s+/).map(Number)), h++), r++;
       }
       if (h < 3) throw new Error("Incomplete CELL_PARAMETERS block");
       break;
@@ -609,49 +628,49 @@ function G(m) {
   }
   if (s.length !== 3)
     throw new Error("CELL_PARAMETERS block not found or incomplete");
-  let t = !1, i = "angstrom";
-  for (let n = 0; n < m.length; n++) {
-    const u = m[n].trim();
-    if (!(!u || u.startsWith("&"))) {
-      if (/^ATOMIC_POSITIONS/i.test(u)) {
+  let t = !1, m = "angstrom";
+  for (let a = 0; a < i.length; a++) {
+    const b = i[a].trim();
+    if (!(!b || b.startsWith("&"))) {
+      if (/^ATOMIC_POSITIONS/i.test(b)) {
         t = !0;
-        const h = u.match(/^ATOMIC_POSITIONS\s+(\w+)/i);
-        i = h ? h[1].toLowerCase() : "angstrom";
+        const h = b.match(/^ATOMIC_POSITIONS\s+(\w+)/i);
+        m = h ? h[1].toLowerCase() : "angstrom";
         continue;
       }
       if (t) {
-        const h = u.split(/\s+/);
-        if (h.length < 4 || !/^[A-Za-z]/.test(h[0]) || h.slice(1, 4).some((c) => Number.isNaN(Number(c))))
+        const h = b.split(/\s+/);
+        if (h.length < 4 || !/^[A-Za-z]/.test(h[0]) || h.slice(1, 4).some((r) => Number.isNaN(Number(r))))
           break;
-        e.push(u);
+        e.push(b);
       }
     }
   }
   if (e.length === 0)
     throw new Error("ATOMIC_POSITIONS block not found");
-  const o = i === "crystal", a = [];
-  for (const n of e) {
-    const u = n.split(/\s+/)[0];
-    a.includes(u) || a.push(u);
+  const o = m === "crystal", n = [];
+  for (const a of e) {
+    const b = a.split(/\s+/)[0];
+    n.includes(b) || n.push(b);
   }
-  const b = [];
-  for (const n of e) {
-    const u = n.split(/\s+/), h = u[0], c = u.slice(1, 4).map(Number);
+  const u = [];
+  for (const a of e) {
+    const b = a.split(/\s+/), h = b[0], r = b.slice(1, 4).map(Number);
     let l;
     o ? l = [
-      c[0] * s[0][0] + c[1] * s[1][0] + c[2] * s[2][0],
-      c[0] * s[0][1] + c[1] * s[1][1] + c[2] * s[2][1],
-      c[0] * s[0][2] + c[1] * s[1][2] + c[2] * s[2][2]
-    ] : l = c, b.push(new v(a.indexOf(h), l));
+      r[0] * s[0][0] + r[1] * s[1][0] + r[2] * s[2][0],
+      r[0] * s[0][1] + r[1] * s[1][1] + r[2] * s[2][1],
+      r[0] * s[0][2] + r[1] * s[1][2] + r[2] * s[2][2]
+    ] : l = r, u.push(new S(n.indexOf(h), l));
   }
   return {
-    structure: new I({ lattice: s, species: a, sites: b }),
-    linesConsumed: m.length
+    structure: new F({ lattice: s, species: n, sites: u }),
+    linesConsumed: i.length
   };
 }
-function is(m) {
-  const s = F(m);
-  return G(s).structure;
+function as(i) {
+  const s = I(i);
+  return Y(s).structure;
 }
 const D = {
   1: { atomicNumber: 1, symbol: "H", name: "Hydrogen", mass: 1.008 },
@@ -772,7 +791,7 @@ const D = {
   116: { atomicNumber: 116, symbol: "Lv", name: "Livermorium", mass: 293 },
   117: { atomicNumber: 117, symbol: "Ts", name: "Tennessine", mass: 294 },
   118: { atomicNumber: 118, symbol: "Og", name: "Oganesson", mass: 294 }
-}, Y = {
+}, q = {
   angstrom: 1,
   // canonical
   bohr: 0.529177,
@@ -782,70 +801,70 @@ const D = {
   cm: 1e8,
   m: 1e10,
   fm: 1e-5
-}, q = {
+}, K = {
   Å: "angstrom",
   μm: "um"
-}, R = {
-  conversions: Y,
-  aliases: q,
-  convert(m, s, e) {
-    const t = (a) => this.aliases[a] ?? a, i = t(s), o = t(e);
-    return i === o ? m : m * this.conversions[i] / this.conversions[o];
+}, $ = {
+  conversions: q,
+  aliases: K,
+  convert(i, s, e) {
+    const t = (n) => this.aliases[n] ?? n, m = t(s), o = t(e);
+    return m === o ? i : i * this.conversions[m] / this.conversions[o];
   },
-  convertArray(m, s, e) {
-    return m.map((t) => this.convert(t, s, e));
+  convertArray(i, s, e) {
+    return i.map((t) => this.convert(t, s, e));
   }
-}, $ = 1.8897268;
-function as(m, s) {
+}, R = 1.8897268;
+function rs(i, s) {
   const e = [];
   e.push("Generated by matsci-parse"), e.push("Volumetric data export");
-  const i = [...s.origin].map((l) => l * $);
+  const m = [...s.origin].map((l) => l * R);
   e.push(
-    `${m.numSites} ${i.map((l) => l.toFixed(6)).join(" ")}`
+    `${i.numSites} ${m.map((l) => l.toFixed(6)).join(" ")}`
   );
-  const o = s.shape, a = s.basis;
+  const o = s.shape, n = s.basis;
   for (let l = 0; l < 3; l++) {
-    a[l];
-    const f = a[l].map((r) => r * $);
-    e.push(`${o[l]} ${f.map((r) => r.toFixed(6)).join(" ")}`);
+    n[l];
+    const y = n[l].map((c) => c * R);
+    e.push(`${o[l]} ${y.map((c) => c.toFixed(6)).join(" ")}`);
   }
-  for (const l of m.sites) {
-    const f = m.species[l.speciesIndex], r = Object.values(D).find(
-      (g) => g.symbol === f
+  for (const l of i.sites) {
+    const y = i.species[l.speciesIndex], c = Object.values(D).find(
+      (g) => g.symbol === y
     )?.atomicNumber;
-    if (!r)
-      throw new Error(`Unknown element symbol: ${f}`);
+    if (!c)
+      throw new Error(`Unknown element symbol: ${y}`);
     [...l.cart];
-    const p = l.cart.map((g) => g * $), N = (l.getProp("charge") ?? 0).toFixed(6);
+    const p = l.cart.map((g) => g * R), N = (l.getProp("charge") ?? 0).toFixed(6);
     e.push(
-      `${r} ${N} ${p.map((g) => g.toFixed(6)).join(" ")}`
+      `${c} ${N} ${p.map((g) => g.toFixed(6)).join(" ")}`
     );
   }
-  const b = s.values, [n, u, h] = o;
-  let c = [];
+  const u = s.values, [a, b, h] = o;
+  let r = [];
   for (let l = 0; l < h; l++)
-    for (let f = 0; f < u; f++)
-      for (let r = 0; r < n; r++) {
-        const p = s.index(r, f, l);
-        c.push(b[p].toExponential(8)), c.length === 6 && (e.push(c.join(" ")), c = []);
+    for (let y = 0; y < b; y++)
+      for (let c = 0; c < a; c++) {
+        const p = s.index(c, y, l);
+        r.push(u[p].toExponential(8)), r.length === 6 && (e.push(r.join(" ")), r = []);
       }
-  return c.length > 0 && e.push(c.join(" ")), e.join(`
+  return r.length > 0 && e.push(r.join(" ")), e.join(`
 `);
 }
-function V(m, s = "bohr", e = "bohr", t = "bohr") {
-  let i = 0;
-  i += 2;
-  const o = m[i].split(/\s+/), a = parseInt(o[0]);
-  let b = [
+function H(i, s = "bohr", e = "bohr", t = "bohr") {
+  let m = 0;
+  m += 2;
+  const o = i[m].split(/\s+/), n = parseInt(o[0]);
+  let u = [
     parseFloat(o[1]),
     parseFloat(o[2]),
     parseFloat(o[3])
   ];
-  i++;
-  const n = m[i++].split(/\s+/), u = m[i++].split(/\s+/), h = m[i++].split(/\s+/);
-  let c = [
-    [parseFloat(n[1]), parseFloat(n[2]), parseFloat(n[3])],
-    [parseFloat(u[1]), parseFloat(u[2]), parseFloat(u[3])],
+  m++;
+  const a = i[m++].split(/\s+/), b = i[m++].split(/\s+/), h = i[m++].split(/\s+/);
+  let r = [
+    [parseFloat(a[1]), parseFloat(a[2]), parseFloat(a[3])],
+    [parseFloat(b[1]), parseFloat(b[2]), parseFloat(b[3])],
     [
       parseFloat(h[1]),
       parseFloat(h[2]),
@@ -853,87 +872,89 @@ function V(m, s = "bohr", e = "bohr", t = "bohr") {
     ]
   ];
   const l = [
-    parseInt(n[0], 10),
-    parseInt(u[0], 10),
+    parseInt(a[0], 10),
+    parseInt(b[0], 10),
     parseInt(h[0], 10)
-  ], f = [], r = /* @__PURE__ */ new Map(), p = [];
-  for (let w = 0; w < a; w++, i++) {
-    const x = m[i].trim().split(/\s+/);
-    if (x.length < 5) throw new Error(`Malformed atom line: "${m[i]}"`);
-    const A = parseInt(x[0], 10), H = parseFloat(x[1]), W = [
+  ], y = [], c = /* @__PURE__ */ new Map(), p = [];
+  for (let w = 0; w < n; w++, m++) {
+    const x = i[m].trim().split(/\s+/);
+    if (x.length < 5) throw new Error(`Malformed atom line: "${i[m]}"`);
+    const A = parseInt(x[0], 10), V = parseFloat(x[1]), W = [
       parseFloat(x[2]),
       parseFloat(x[3]),
       parseFloat(x[4])
-    ], O = D[A];
-    if (!O) throw new Error(`Unknown atomic number: ${A}`);
-    const E = O.symbol;
-    let T = r.get(E);
-    T === void 0 && (T = f.length, f.push(E), r.set(E, T)), p.push(new v(T, W, { charge: H }));
-  }
-  b = R.convertArray(
-    b,
+    ], j = D[A];
+    if (!j) throw new Error(`Unknown atomic number: ${A}`);
+    const E = j.symbol;
+    let T = c.get(E);
+    T === void 0 && (T = y.length, y.push(E), c.set(E, T)), p.push(new S(T, W, { charge: V }));
+  }
+  u = $.convertArray(
+    u,
     s,
     "angstrom"
-  ), c = c.map(
-    (w) => R.convertArray(
+  ), r = r.map(
+    (w) => $.convertArray(
       w,
       t,
       "angstrom"
     )
   ), p.forEach((w) => {
-    w.cart = R.convertArray(
+    w.cart = $.convertArray(
       w.cart,
       e,
       "angstrom"
     );
   });
-  const N = c.map(
+  const N = r.map(
     (w, x) => w.map((A) => A * l[x])
-  ), g = new I({
+  ), g = new F({
     lattice: N,
-    species: f,
+    species: y,
     sites: p
-  }), _ = l[0] * l[1] * l[2], S = new Float32Array(_);
-  let y = 0;
-  for (; i < m.length && y < _; ) {
-    const w = m[i++].trim().split(/\s+/);
+  }), _ = l[0] * l[1] * l[2], v = new Float32Array(_);
+  let f = 0;
+  for (; m < i.length && f < _; ) {
+    const w = i[m++].trim().split(/\s+/);
     for (const x of w)
-      x && y < _ && (S[y] = parseFloat(x), y++);
+      x && f < _ && (v[f] = parseFloat(x), f++);
   }
-  if (console.log("numVals", _), y !== _)
-    throw new Error(`Cube file truncated: expected ${_}, got ${y}`);
-  const d = new X({
-    origin: b,
-    basis: c,
+  if (f !== _)
+    throw new Error(`Cube file truncated: expected ${_}, got ${f}`);
+  const d = new Z({
+    origin: u,
+    basis: r,
     shape: l,
-    values: S,
+    values: v,
     units: "e/ų"
   });
-  return { structure: g, volumetricData: d, linesConsumed: i };
+  return { structure: g, volumetricData: d, linesConsumed: m };
 }
-function ns(m) {
-  const s = F(m);
-  return V(s).volumetricData;
+function cs(i) {
+  const s = I(i);
+  return H(s).volumetricData;
 }
-function rs(m) {
-  const s = F(m);
-  return V(s).structure;
+function ls(i) {
+  const s = I(i);
+  return H(s).structure;
 }
 export {
-  I as CrystalStructure,
-  v as Site,
-  X as VolumetricData,
-  os as cifToStructure,
-  rs as cubeToStructure,
-  ns as cubeToVolumetric,
-  V as parseCube,
-  J as poscarToStructure,
-  is as pwToStructure,
+  F as CrystalStructure,
+  S as Site,
+  Z as VolumetricData,
+  J as cartesianToFractional,
+  ns as cifToStructure,
+  ls as cubeToStructure,
+  cs as cubeToVolumetric,
+  U as fractionalToCartesian,
+  H as parseCube,
+  ss as poscarToStructure,
+  as as pwToStructure,
   ms as structureToCif,
-  K as structureToPoscar,
-  Q as structureToXsf,
-  es as structureToXyz,
-  as as volumetricToCube,
-  ss as xsfToStructure,
-  ts as xyzToStructure
+  Q as structureToPoscar,
+  es as structureToXsf,
+  os as structureToXyz,
+  rs as volumetricToCube,
+  ts as xsfToStructure,
+  is as xyzToStructure
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matsci-parse",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "type": "module",
   "main": "dist/main.js",
   "module": "dist/main.js",