matsci-parse 0.1.2 → 0.2.0

package/dist/main.js

@@ -1,42 +1,42 @@
 class x {
-  constructor(e, t, n = {}) {
-    this.speciesIndex = e, this.cart = t, this.props = n;
+  constructor(t, e, i = {}) {
+    this.speciesIndex = t, this.cart = e, this.props = i;
   }
-  getProp(e) {
-    return this.props[e];
+  getProp(t) {
+    return this.props[t];
   }
-  setProp(e, t) {
-    this.props[e] = t;
+  setProp(t, e) {
+    this.props[t] = e;
   }
 }
 function C(s) {
-  return s.sites.some((e) => Array.isArray(e.props.selectiveDynamics));
+  return s.sites.some((t) => Array.isArray(t.props.selectiveDynamics));
 }
-function E(s) {
+function F(s) {
   return s * Math.PI / 180;
 }
-function $(s, e) {
+function M(s, t) {
   return s.map(
-    (t) => t[0] * e[0] + t[1] * e[1] + t[2] * e[2]
+    (e) => e[0] * t[0] + e[1] * t[1] + e[2] * t[2]
   );
 }
-function T(s, e, t, n, o, i) {
-  const a = E(n), c = E(o), h = E(i), m = [s, 0, 0], p = [
-    e * Math.cos(h),
-    e * Math.sin(h),
+function P(s, t, e, i, o, n) {
+  const a = F(i), h = F(o), l = F(n), p = [s, 0, 0], f = [
+    t * Math.cos(l),
+    t * Math.sin(l),
     0
-  ], u = t * Math.cos(c), l = t * (Math.cos(a) - Math.cos(c) * Math.cos(h)) / Math.sin(h), d = Math.sqrt(t * t - u * u - l * l);
-  return [m, p, [u, l, d]];
+  ], r = e * Math.cos(h), u = e * (Math.cos(a) - Math.cos(h) * Math.cos(l)) / Math.sin(l), g = Math.sqrt(e * e - r * r - u * u);
+  return [p, f, [r, u, g]];
 }
-function L(s, e) {
-  const [t, n, o] = e;
+function O(s, t) {
+  const [e, i, o] = t;
   return [
-    s[0] * t[0] + s[1] * n[0] + s[2] * o[0],
-    s[0] * t[1] + s[1] * n[1] + s[2] * o[1],
-    s[0] * t[2] + s[1] * n[2] + s[2] * o[2]
+    s[0] * e[0] + s[1] * i[0] + s[2] * o[0],
+    s[0] * e[1] + s[1] * i[1] + s[2] * o[1],
+    s[0] * e[2] + s[1] * i[2] + s[2] * o[2]
   ];
 }
-class w {
+class S {
   /**
    * Creates a new CrystalStructure.
    *
@@ -48,11 +48,11 @@ class w {
    * @throws Will throw an error if lattice is not 3x3, species is not an array of strings, or sites are invalid
    */
   constructor({
-    lattice: e,
-    species: t,
-    sites: n
+    lattice: t,
+    species: e,
+    sites: i
   }) {
-    this.lattice = this._validateLattice(e), this.species = this._validateSpecies(t), this.sites = this._validateSites(n);
+    this.lattice = this._validateLattice(t), this.species = this._validateSpecies(e), this.sites = this._validateSites(i);
   }
   // ---------- Simple methods ----------
   /** Number of sites in the structure */
@@ -63,22 +63,22 @@ class w {
    * Returns the site at the specified index.
    * @param i - Site index
    */
-  site(e) {
-    return this.sites[e];
+  site(t) {
+    return this.sites[t];
   }
   /**
    * Returns the Cartesian coordinates of a site.
    * @param i - Site index
    */
-  cartCoords(e) {
-    return this.sites[e].cart;
+  cartCoords(t) {
+    return this.sites[t].cart;
   }
   /**
    * Returns the chemical species of a site.
    * @param i - Site index
    */
-  siteSpecies(e) {
-    return this.species[this.sites[e].speciesIndex];
+  siteSpecies(t) {
+    return this.species[this.sites[t].speciesIndex];
   }
   /** Returns the array of elements (species) in the structure */
   get elements() {
@@ -92,11 +92,11 @@ class w {
    * @param cart - Cartesian coordinates of the new site
    * @param position - Optional index at which to insert the site. Defaults to appending at the end.
    */
-  addSite(e, t, n) {
-    let o = this.species.indexOf(e);
-    o === -1 && (this.species.push(e), o = this.species.length - 1);
-    const i = new x(o, t);
-    n === void 0 || n >= this.sites.length ? this.sites.push(i) : n < 0 ? this.sites.unshift(i) : this.sites.splice(n, 0, i);
+  addSite(t, e, i) {
+    let o = this.species.indexOf(t);
+    o === -1 && (this.species.push(t), o = this.species.length - 1);
+    const n = new x(o, e);
+    i === void 0 || i >= this.sites.length ? this.sites.push(n) : i < 0 ? this.sites.unshift(n) : this.sites.splice(i, 0, n);
   }
   /**
    * Removes a site from the crystal.
@@ -107,14 +107,14 @@ class w {
    *
    * @throws Will throw an error if index is out of bounds
    */
-  removeSite(e) {
-    if (e < 0 || e >= this.sites.length)
+  removeSite(t) {
+    if (t < 0 || t >= this.sites.length)
       throw new Error("siteIndex out of bounds");
-    const n = this.sites.splice(e, 1)[0].speciesIndex;
+    const i = this.sites.splice(t, 1)[0].speciesIndex;
     this.sites.some(
-      (i) => i.speciesIndex === n
-    ) || (this.species.splice(n, 1), this.sites.forEach((i) => {
-      i.speciesIndex > n && (i.speciesIndex -= 1);
+      (n) => n.speciesIndex === i
+    ) || (this.species.splice(i, 1), this.sites.forEach((n) => {
+      n.speciesIndex > i && (n.speciesIndex -= 1);
     }));
   }
   /**
@@ -127,11 +127,11 @@ class w {
    *
    * @throws Will throw an error if siteIndex is out of bounds
    */
-  replaceSite(e, t) {
-    if (e < 0 || e >= this.sites.length)
+  replaceSite(t, e) {
+    if (t < 0 || t >= this.sites.length)
       throw new Error("siteIndex out of bounds");
-    const n = [...this.sites[e].cart];
-    this.removeSite(e), this.addSite(t, n, e);
+    const i = [...this.sites[t].cart];
+    this.removeSite(t), this.addSite(e, i, t);
   }
   /**
    * Returns a new CrystalStructure transformed by a linear matrix.
@@ -146,37 +146,37 @@ class w {
    *
    * @throws Will throw an error if scale is not a number, a 3-element array, or a 3x3 matrix
    */
-  applyLatticeTransformation(e) {
-    let t;
-    if (typeof e == "number")
-      t = [
-        [e, 0, 0],
-        [0, e, 0],
-        [0, 0, e]
+  applyLatticeTransformation(t) {
+    let e;
+    if (typeof t == "number")
+      e = [
+        [t, 0, 0],
+        [0, t, 0],
+        [0, 0, t]
       ];
-    else if (Array.isArray(e) && e.length === 3 && e.every((i) => typeof i == "number"))
-      t = [
-        [e[0], 0, 0],
-        [0, e[1], 0],
-        [0, 0, e[2]]
+    else if (Array.isArray(t) && t.length === 3 && t.every((n) => typeof n == "number"))
+      e = [
+        [t[0], 0, 0],
+        [0, t[1], 0],
+        [0, 0, t[2]]
       ];
-    else if (Array.isArray(e) && e.length === 3 && e.every((i) => Array.isArray(i) && i.length === 3))
-      t = e;
+    else if (Array.isArray(t) && t.length === 3 && t.every((n) => Array.isArray(n) && n.length === 3))
+      e = t;
     else
       throw new Error(
         "Scale must be a number, a 3-element array, or a 3x3 matrix"
       );
-    const n = this.lattice.map(
-      (i) => $(t, i)
-    ), o = this.sites.map((i) => {
-      const a = $(
-        t,
-        i.cart
+    const i = this.lattice.map(
+      (n) => M(e, n)
+    ), o = this.sites.map((n) => {
+      const a = M(
+        e,
+        n.cart
       );
-      return new x(i.speciesIndex, a, i.props);
+      return new x(n.speciesIndex, a, n.props);
     });
-    return new w({
-      lattice: n,
+    return new S({
+      lattice: i,
       species: [...this.species],
       sites: o
     });
@@ -186,38 +186,38 @@ class w {
    * Validates that the lattice is a 3x3 array of Cartesian vectors.
    * @throws Will throw an error if lattice is invalid
    */
-  _validateLattice(e) {
-    if (!Array.isArray(e) || e.length !== 3)
+  _validateLattice(t) {
+    if (!Array.isArray(t) || t.length !== 3)
       throw new Error("Lattice must be a 3x3 matrix");
-    return e.forEach((t) => {
-      if (!Array.isArray(t) || t.length !== 3)
+    return t.forEach((e) => {
+      if (!Array.isArray(e) || e.length !== 3)
         throw new Error("Lattice vectors must be length 3");
-    }), e;
+    }), t;
   }
   /**
    * Validates that species is an array of strings.
    * @throws Will throw an error if species array is invalid
    */
-  _validateSpecies(e) {
-    if (!Array.isArray(e)) throw new Error("Species must be an array");
-    return e.forEach((t) => {
-      if (typeof t != "string")
+  _validateSpecies(t) {
+    if (!Array.isArray(t)) throw new Error("Species must be an array");
+    return t.forEach((e) => {
+      if (typeof e != "string")
         throw new Error("Species entries must be strings");
-    }), e;
+    }), t;
   }
   /**
    * Validates the sites array, ensuring each site is a Site instance or a valid object.
    * @throws Will throw an error if sites array is invalid
    */
-  _validateSites(e) {
-    if (!Array.isArray(e)) throw new Error("Sites must be an array");
-    return e.map((t) => {
-      if (t instanceof x) return t;
-      if (typeof t == "object" && typeof t.speciesIndex == "number" && Array.isArray(t.cart) && t.cart.length === 3)
-        return this._validateSpeciesIndex(t.speciesIndex), new x(
-          t.speciesIndex,
-          t.cart,
-          t.props ?? {}
+  _validateSites(t) {
+    if (!Array.isArray(t)) throw new Error("Sites must be an array");
+    return t.map((e) => {
+      if (e instanceof x) return e;
+      if (typeof e == "object" && typeof e.speciesIndex == "number" && Array.isArray(e.cart) && e.cart.length === 3)
+        return this._validateSpeciesIndex(e.speciesIndex), new x(
+          e.speciesIndex,
+          e.cart,
+          e.props ?? {}
         );
       throw new Error(
         "Each site must be a Site instance or a valid site object"
@@ -228,210 +228,210 @@ class w {
    * Validates that a species index is within bounds.
    * @throws Will throw an error if index is out of range
    */
-  _validateSpeciesIndex(e) {
-    if (e < 0 || e >= this.species.length)
+  _validateSpeciesIndex(t) {
+    if (t < 0 || t >= this.species.length)
       throw new Error("speciesIndex out of bounds");
   }
 }
-function F(s) {
-  return s.split(/\r?\n/).map((e) => e.trim()).filter(Boolean);
+function E(s) {
+  return s.split(/\r?\n/).map((t) => t.trim()).filter(Boolean);
 }
-function P(s, e = 6) {
-  const t = [], n = C(s);
-  t.push("Generated by matsci-parse"), t.push("1.0"), s.lattice.forEach((a) => {
-    t.push(a.map((c) => c.toFixed(e)).join(" "));
+function D(s, t = 6) {
+  const e = [], i = C(s);
+  e.push("Generated by matsci-parse"), e.push("1.0"), s.lattice.forEach((a) => {
+    e.push(a.map((h) => h.toFixed(t)).join(" "));
   });
   const o = Array.from(
     new Set(s.sites.map((a) => s.species[a.speciesIndex]))
-  ), i = o.map(
-    (a) => s.sites.filter((c) => s.species[c.speciesIndex] === a).length
+  ), n = o.map(
+    (a) => s.sites.filter((h) => s.species[h.speciesIndex] === a).length
   );
-  return t.push(o.join(" ")), t.push(i.join(" ")), n && t.push("Selective dynamics"), t.push("Cartesian"), o.forEach((a) => {
-    s.sites.filter((c) => s.species[c.speciesIndex] === a).forEach((c) => {
-      const h = c.cart.map((m) => m.toFixed(e)).join(" ");
-      if (n) {
-        const p = (Array.isArray(c.props?.selectiveDynamics) ? c.props.selectiveDynamics : [!0, !0, !0]).map((u) => u ? "T" : "F").join(" ");
-        t.push(`${h} ${p}`);
+  return e.push(o.join(" ")), e.push(n.join(" ")), i && e.push("Selective dynamics"), e.push("Cartesian"), o.forEach((a) => {
+    s.sites.filter((h) => s.species[h.speciesIndex] === a).forEach((h) => {
+      const l = h.cart.map((p) => p.toFixed(t)).join(" ");
+      if (i) {
+        const f = (Array.isArray(h.props?.selectiveDynamics) ? h.props.selectiveDynamics : [!0, !0, !0]).map((r) => r ? "T" : "F").join(" ");
+        e.push(`${l} ${f}`);
       } else
-        t.push(h);
+        e.push(l);
     });
-  }), t.join(`
+  }), e.join(`
 `);
 }
-function j(s) {
-  let e = 0;
-  e++;
-  const t = parseFloat(s[e++]), n = [];
-  for (let u = 0; u < 3; u++)
-    n.push(
-      s[e++].split(/\s+/).map((l) => parseFloat(l) * t)
+function R(s) {
+  let t = 0;
+  t++;
+  const e = parseFloat(s[t++]), i = [];
+  for (let r = 0; r < 3; r++)
+    i.push(
+      s[t++].split(/\s+/).map((u) => parseFloat(u) * e)
     );
-  let o = s[e].trim(), i;
-  /^[A-Za-z]/.test(o) && (i = o.split(/\s+/), e++);
-  const a = s[e++].split(/\s+/).map(Number);
-  i || (i = a.map((u, l) => `X${l + 1}`));
-  let c = !1;
-  s[e]?.toLowerCase().startsWith("s") && (c = !0, e++);
-  const m = s[e++].toLowerCase().startsWith("d"), p = [];
-  return i.forEach((u, l) => {
-    for (let d = 0; d < a[l]; d++) {
-      const r = s[e++].split(/\s+/).map(Number);
-      let f;
-      m ? f = [
-        r[0] * n[0][0] + r[1] * n[1][0] + r[2] * n[2][0],
-        r[0] * n[0][1] + r[1] * n[1][1] + r[2] * n[2][1],
-        r[0] * n[0][2] + r[1] * n[1][2] + r[2] * n[2][2]
-      ] : f = r.slice(0, 3);
-      const g = {};
-      if (c) {
-        const y = r.slice(3, 6).map((_) => _ === 1);
-        y.length === 3 && (g.selectiveDynamics = y);
+  let o = s[t].trim(), n;
+  /^[A-Za-z]/.test(o) && (n = o.split(/\s+/), t++);
+  const a = s[t++].split(/\s+/).map(Number);
+  n || (n = a.map((r, u) => `X${u + 1}`));
+  let h = !1;
+  s[t]?.toLowerCase().startsWith("s") && (h = !0, t++);
+  const p = s[t++].toLowerCase().startsWith("d"), f = [];
+  return n.forEach((r, u) => {
+    for (let g = 0; g < a[u]; g++) {
+      const c = s[t++].split(/\s+/).map(Number);
+      let m;
+      p ? m = [
+        c[0] * i[0][0] + c[1] * i[1][0] + c[2] * i[2][0],
+        c[0] * i[0][1] + c[1] * i[1][1] + c[2] * i[2][1],
+        c[0] * i[0][2] + c[1] * i[1][2] + c[2] * i[2][2]
+      ] : m = c.slice(0, 3);
+      const w = {};
+      if (h) {
+        const y = c.slice(3, 6).map((b) => b === 1);
+        y.length === 3 && (w.selectiveDynamics = y);
       }
-      p.push(new x(l, f, g));
+      f.push(new x(u, m, w));
     }
   }), {
-    structure: new w({ lattice: n, species: i, sites: p }),
-    linesConsumed: e
+    structure: new S({ lattice: i, species: n, sites: f }),
+    linesConsumed: t
   };
 }
-function R(s) {
-  const e = F(s);
-  return j(e).structure;
+function W(s) {
+  const t = E(s);
+  return R(t).structure;
 }
-function W(s, e = 6) {
-  const t = [];
-  return t.push("CRYSTAL"), t.push("PRIMVEC"), s.lattice.forEach((n) => {
-    t.push(n.map((o) => o.toFixed(e)).join(" "));
-  }), t.push("PRIMCOORD"), t.push(`${s.numSites} 1`), s.sites.forEach((n) => {
-    const o = s.species[n.speciesIndex];
-    t.push(
-      `${o} ${n.cart.map((i) => i.toFixed(e)).join(" ")}`
+function k(s, t = 6) {
+  const e = [];
+  return e.push("CRYSTAL"), e.push("PRIMVEC"), s.lattice.forEach((i) => {
+    e.push(i.map((o) => o.toFixed(t)).join(" "));
+  }), e.push("PRIMCOORD"), e.push(`${s.numSites} 1`), s.sites.forEach((i) => {
+    const o = s.species[i.speciesIndex];
+    e.push(
+      `${o} ${i.cart.map((n) => n.toFixed(t)).join(" ")}`
     );
-  }), t.join(`
+  }), e.join(`
 `);
 }
-function O(s) {
-  const e = F(s), t = [], n = [], o = [];
-  let i = 0;
-  for (; i < e.length && e[i].toUpperCase() !== "PRIMVEC"; ) i++;
-  if (i === e.length) throw new Error("PRIMVEC block not found in XSF");
-  i++;
-  for (let c = 0; c < 3; c++)
-    t.push(e[i++].split(/\s+/).map(Number));
-  for (; i < e.length && e[i].toUpperCase() !== "PRIMCOORD"; ) i++;
-  if (i === e.length) throw new Error("PRIMCOORD block not found in XSF");
-  i++;
-  const [a] = e[i++].split(/\s+/).map(Number);
-  for (let c = 0; c < a; c++) {
-    const h = e[i++].split(/\s+/), m = h[0], p = h.slice(1, 4).map(Number);
-    let u = n.indexOf(m);
-    u === -1 && (n.push(m), u = n.length - 1), o.push(new x(u, p));
+function X(s) {
+  const t = E(s), e = [], i = [], o = [];
+  let n = 0;
+  for (; n < t.length && t[n].toUpperCase() !== "PRIMVEC"; ) n++;
+  if (n === t.length) throw new Error("PRIMVEC block not found in XSF");
+  n++;
+  for (let h = 0; h < 3; h++)
+    e.push(t[n++].split(/\s+/).map(Number));
+  for (; n < t.length && t[n].toUpperCase() !== "PRIMCOORD"; ) n++;
+  if (n === t.length) throw new Error("PRIMCOORD block not found in XSF");
+  n++;
+  const [a] = t[n++].split(/\s+/).map(Number);
+  for (let h = 0; h < a; h++) {
+    const l = t[n++].split(/\s+/), p = l[0], f = l.slice(1, 4).map(Number);
+    let r = i.indexOf(p);
+    r === -1 && (i.push(p), r = i.length - 1), o.push(new x(r, f));
   }
-  return new w({ lattice: t, species: n, sites: o });
+  return new S({ lattice: e, species: i, sites: o });
 }
-function X(s, e = 6) {
-  const t = [], n = s.sites.length;
-  t.push(String(n));
-  const o = C(s), i = s.lattice, a = [
-    i[0][0],
-    i[1][0],
-    i[2][0],
-    i[0][1],
-    i[1][1],
-    i[2][1],
-    i[0][2],
-    i[1][2],
-    i[2][2]
-  ].join(" "), c = [
+function z(s, t = 6) {
+  const e = [], i = s.sites.length;
+  e.push(String(i));
+  const o = C(s), n = s.lattice, a = [
+    n[0][0],
+    n[1][0],
+    n[2][0],
+    n[0][1],
+    n[1][1],
+    n[2][1],
+    n[0][2],
+    n[1][2],
+    n[2][2]
+  ].join(" "), h = [
     "species:S:1",
     "pos:R:3",
     o ? "selectiveDynamics:L:3" : null
   ].filter(Boolean).join(":");
-  t.push(`Lattice="${a}" Properties=${c}`);
-  for (const h of s.sites) {
-    const m = s.species[h.speciesIndex], [p, u, l] = h.cart;
-    let d = `${m} ${p.toFixed(e)} ${u.toFixed(e)} ${l.toFixed(e)}`;
+  e.push(`Lattice="${a}" Properties=${h}`);
+  for (const l of s.sites) {
+    const p = s.species[l.speciesIndex], [f, r, u] = l.cart;
+    let g = `${p} ${f.toFixed(t)} ${r.toFixed(t)} ${u.toFixed(t)}`;
     if (o) {
-      const r = Array.isArray(h.props?.selectiveDynamics) ? h.props.selectiveDynamics : [!0, !0, !0];
-      d += " " + r.map((f) => f ? "T" : "F").join(" ");
+      const c = Array.isArray(l.props?.selectiveDynamics) ? l.props.selectiveDynamics : [!0, !0, !0];
+      g += " " + c.map((m) => m ? "T" : "F").join(" ");
     }
-    t.push(d);
+    e.push(g);
   }
-  return t.join(`
+  return e.join(`
 `);
 }
-function N(s) {
-  const e = F(s);
-  let t = 0;
-  const n = parseInt(e[t++], 10);
-  if (!Number.isFinite(n))
+function Z(s) {
+  const t = E(s);
+  let e = 0;
+  const i = parseInt(t[e++], 10);
+  if (!Number.isFinite(i))
     throw new Error("Invalid XYZ: first line must be atom count");
-  const o = e[t++], i = {}, a = /(\w+)=(".*?"|\S+)/g;
-  for (const r of o.matchAll(a)) {
-    let f = r[2];
-    f.startsWith('"') && (f = f.slice(1, -1)), i[r[1]] = f;
+  const o = t[e++], n = {}, a = /(\w+)=(".*?"|\S+)/g;
+  for (const c of o.matchAll(a)) {
+    let m = c[2];
+    m.startsWith('"') && (m = m.slice(1, -1)), n[c[1]] = m;
   }
-  let c;
-  if (i.Lattice) {
-    const r = i.Lattice.split(/\s+/).map(Number);
-    if (r.length !== 9) throw new Error("Invalid Lattice in extended XYZ");
-    c = [
-      [r[0], r[3], r[6]],
-      [r[1], r[4], r[7]],
-      [r[2], r[5], r[8]]
+  let h;
+  if (n.Lattice) {
+    const c = n.Lattice.split(/\s+/).map(Number);
+    if (c.length !== 9) throw new Error("Invalid Lattice in extended XYZ");
+    h = [
+      [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 h = 0, m = 1, p = null;
-  if (i.Properties) {
-    const r = i.Properties.split(":");
-    let f = 0;
-    for (let g = 0; g < r.length; g += 3) {
-      const y = r[g], _ = parseInt(r[g + 2], 10);
-      y === "species" && (h = f), y === "pos" && (m = f), y === "selectiveDynamics" && (p = f), f += _;
+  let l = 0, p = 1, f = null;
+  if (n.Properties) {
+    const c = n.Properties.split(":");
+    let m = 0;
+    for (let w = 0; w < c.length; w += 3) {
+      const y = c[w], b = parseInt(c[w + 2], 10);
+      y === "species" && (l = m), y === "pos" && (p = m), y === "selectiveDynamics" && (f = m), m += b;
     }
   }
-  const u = [], l = /* @__PURE__ */ new Map(), d = [];
-  for (let r = 0; r < n; r++) {
-    const f = e[t++].split(/\s+/), g = f[h];
-    l.has(g) || (l.set(g, u.length), u.push(g));
-    const y = l.get(g), _ = f.slice(m, m + 3).map(Number), S = {};
-    if (p !== null) {
-      const I = f.slice(p, p + 3).map((b) => b.toUpperCase() === "T");
-      I.length === 3 && (S.selectiveDynamics = I);
+  const r = [], u = /* @__PURE__ */ new Map(), g = [];
+  for (let c = 0; c < i; c++) {
+    const m = t[e++].split(/\s+/), w = m[l];
+    u.has(w) || (u.set(w, r.length), r.push(w));
+    const y = u.get(w), b = m.slice(p, p + 3).map(Number), I = {};
+    if (f !== null) {
+      const _ = m.slice(f, f + 3).map((d) => d.toUpperCase() === "T");
+      _.length === 3 && (I.selectiveDynamics = _);
     }
-    d.push(new x(y, _, S));
+    g.push(new x(y, b, I));
   }
-  return new w({ lattice: c, species: u, sites: d });
+  return new S({ lattice: h, species: r, sites: g });
 }
-function v(s, e) {
-  return s[0] * e[0] + s[1] * e[1] + s[2] * e[2];
+function A(s, t) {
+  return s[0] * t[0] + s[1] * t[1] + s[2] * t[2];
 }
-function A(s) {
-  return Math.sqrt(v(s, s));
+function T(s) {
+  return Math.sqrt(A(s, s));
 }
-function M(s) {
+function L(s) {
   return s * 180 / Math.PI;
 }
-function D(s, e) {
-  const [t, n, o] = e, i = t[0] * (n[1] * o[2] - n[2] * o[1]) - t[1] * (n[0] * o[2] - n[2] * o[0]) + t[2] * (n[0] * o[1] - n[1] * o[0]);
-  if (Math.abs(i) < 1e-12)
+function j(s, t) {
+  const [e, i, o] = t, n = e[0] * (i[1] * o[2] - i[2] * o[1]) - e[1] * (i[0] * o[2] - i[2] * o[0]) + e[2] * (i[0] * o[1] - i[1] * o[0]);
+  if (Math.abs(n) < 1e-12)
     throw new Error("Singular lattice matrix");
   const a = [
     [
-      (n[1] * o[2] - n[2] * o[1]) / i,
-      (t[2] * o[1] - t[1] * o[2]) / i,
-      (t[1] * n[2] - t[2] * n[1]) / i
+      (i[1] * o[2] - i[2] * o[1]) / n,
+      (e[2] * o[1] - e[1] * o[2]) / n,
+      (e[1] * i[2] - e[2] * i[1]) / n
     ],
     [
-      (n[2] * o[0] - n[0] * o[2]) / i,
-      (t[0] * o[2] - t[2] * o[0]) / i,
-      (t[2] * n[0] - t[0] * n[2]) / i
+      (i[2] * o[0] - i[0] * o[2]) / n,
+      (e[0] * o[2] - e[2] * o[0]) / n,
+      (e[2] * i[0] - e[0] * i[2]) / n
     ],
     [
-      (n[0] * o[1] - n[1] * o[0]) / i,
-      (t[1] * o[0] - t[0] * o[1]) / i,
-      (t[0] * n[1] - t[1] * n[0]) / i
+      (i[0] * o[1] - i[1] * o[0]) / n,
+      (e[1] * o[0] - e[0] * o[1]) / n,
+      (e[0] * i[1] - e[1] * i[0]) / n
     ]
   ];
   return [
@@ -440,18 +440,18 @@ function D(s, e) {
     s[0] * a[0][2] + s[1] * a[1][2] + s[2] * a[2][2]
   ];
 }
-function z(s, e = 6) {
-  const [t, n, o] = s.lattice, i = A(t), a = A(n), c = A(o), h = M(Math.acos(v(n, o) / (a * c))), m = M(Math.acos(v(t, o) / (i * c))), p = M(Math.acos(v(t, n) / (i * a)));
-  let u = `data_made_with_matsci-parse
+function V(s, t = 6) {
+  const [e, i, o] = s.lattice, n = T(e), a = T(i), h = T(o), l = L(Math.acos(A(i, o) / (a * h))), p = L(Math.acos(A(e, o) / (n * h))), f = L(Math.acos(A(e, i) / (n * a)));
+  let r = `data_made_with_matsci-parse
     _symmetry_space_group_name_H-M   'P 1'
     _symmetry_Int_Tables_number    1
 
-    _cell_length_a   ${i.toFixed(e)}
-    _cell_length_b   ${a.toFixed(e)}
-    _cell_length_c   ${c.toFixed(e)}
-    _cell_angle_alpha   ${h.toFixed(e)}
-    _cell_angle_beta    ${m.toFixed(e)}
-    _cell_angle_gamma   ${p.toFixed(e)}
+    _cell_length_a   ${n.toFixed(t)}
+    _cell_length_b   ${a.toFixed(t)}
+    _cell_length_c   ${h.toFixed(t)}
+    _cell_angle_alpha   ${l.toFixed(t)}
+    _cell_angle_beta    ${p.toFixed(t)}
+    _cell_angle_gamma   ${f.toFixed(t)}
 
     loop_
     _atom_site_label
@@ -460,70 +460,134 @@ function z(s, e = 6) {
     _atom_site_fract_y
     _atom_site_fract_z
 `;
-  return s.sites.forEach((l, d) => {
-    const r = s.species[l.speciesIndex], f = D(l.cart, s.lattice);
-    u += `${r}${d + 1} ${r} ${f[0].toFixed(e)} ${f[1].toFixed(
+  return s.sites.forEach((u, g) => {
+    const c = s.species[u.speciesIndex], m = j(u.cart, s.lattice);
+    r += `${c}${g + 1} ${c} ${m[0].toFixed(t)} ${m[1].toFixed(
       6
-    )} ${f[2].toFixed(e)}
+    )} ${m[2].toFixed(t)}
 `;
-  }), u;
+  }), r;
+}
+function U(s) {
+  const t = E(s);
+  let e = 0, i = 0, o = 0, n = 0, a = 0, h = 0, l = [];
+  const p = [];
+  let f = !1, r = [], u = !1;
+  for (const _ of t) {
+    const d = _.trim();
+    if (d) {
+      if (d.startsWith("_cell_length_a")) e = parseFloat(d.split(/\s+/)[1]);
+      else if (d.startsWith("_cell_length_b"))
+        i = parseFloat(d.split(/\s+/)[1]);
+      else if (d.startsWith("_cell_length_c"))
+        o = parseFloat(d.split(/\s+/)[1]);
+      else if (d.startsWith("_cell_angle_alpha"))
+        n = parseFloat(d.split(/\s+/)[1]);
+      else if (d.startsWith("_cell_angle_beta"))
+        a = parseFloat(d.split(/\s+/)[1]);
+      else if (d.startsWith("_cell_angle_gamma"))
+        h = parseFloat(d.split(/\s+/)[1]);
+      else if (d.startsWith("loop_")) {
+        f = !0, r = [], u = !1;
+        continue;
+      }
+      if (f && d.startsWith("_")) {
+        r.push(d), d.includes("_atom_site_") && (u = !0);
+        continue;
+      }
+      if (f && !d.startsWith("_")) {
+        u && (l.length === 0 && (l = [...r]), p.push(d.split(/\s+/)));
+        continue;
+      }
+    }
+  }
+  if (l.length === 0)
+    throw new Error("No _atom_site loop found in CIF");
+  const g = P(e, i, o, n, a, h), c = [], m = [], w = l.findIndex((_) => _.includes("fract_x")), y = l.findIndex((_) => _.includes("fract_y")), b = l.findIndex((_) => _.includes("fract_z")), I = l.findIndex((_) => _.includes("type_symbol"));
+  if (w < 0 || y < 0 || b < 0 || I < 0)
+    throw new Error("CIF missing required _atom_site columns");
+  for (const _ of p) {
+    const d = [
+      parseFloat(_[w]),
+      parseFloat(_[y]),
+      parseFloat(_[b])
+    ], $ = O(d, g);
+    let v = c.indexOf(_[I]);
+    v === -1 && (v = c.length, c.push(_[I])), m.push(new x(v, $));
+  }
+  return new S({ lattice: g, species: c, sites: m });
 }
-function V(s) {
-  const e = F(s);
-  let t = 0, n = 0, o = 0, i = 0, a = 0, c = 0;
-  const h = [], m = [];
-  let p = 0;
-  for (; p < e.length; ) {
-    const l = e[p].trim();
-    if (l.startsWith("_cell_length_a")) t = parseFloat(l.split(/\s+/)[1]);
-    else if (l.startsWith("_cell_length_b"))
-      n = parseFloat(l.split(/\s+/)[1]);
-    else if (l.startsWith("_cell_length_c"))
-      o = parseFloat(l.split(/\s+/)[1]);
-    else if (l.startsWith("_cell_angle_alpha"))
-      i = parseFloat(l.split(/\s+/)[1]);
-    else if (l.startsWith("_cell_angle_beta"))
-      a = parseFloat(l.split(/\s+/)[1]);
-    else if (l.startsWith("_cell_angle_gamma"))
-      c = parseFloat(l.split(/\s+/)[1]);
-    else if (l.startsWith("loop_")) {
-      p++;
-      const d = [];
-      for (; p < e.length && e[p].trim().startsWith("_"); )
-        d.push(e[p].trim()), p++;
-      if (d.some((r) => r.includes("_atom_site_"))) {
-        const r = d.findIndex((_) => _.includes("fract_x")), f = d.findIndex((_) => _.includes("fract_y")), g = d.findIndex((_) => _.includes("fract_z")), y = d.findIndex((_) => _.includes("type_symbol"));
-        if (r < 0 || f < 0 || g < 0 || y < 0)
-          throw new Error("CIF missing required _atom_site columns");
-        for (; p < e.length && e[p].trim() && !e[p].trim().startsWith("_") && !e[p].trim().startsWith("loop_"); ) {
-          const _ = e[p].trim().split(/\s+/), S = [
-            parseFloat(_[r]),
-            parseFloat(_[f]),
-            parseFloat(_[g])
-          ], I = L(
-            S,
-            T(t, n, o, i, a, c)
-          );
-          let b = h.indexOf(_[y]);
-          b === -1 && (b = h.length, h.push(_[y])), m.push(new x(b, I)), p++;
-        }
+function N(s) {
+  let t = [];
+  const e = [];
+  for (let l = 0; l < s.length; l++) {
+    const p = s[l].trim();
+    if (!(!p || p.startsWith("&")) && /^CELL_PARAMETERS/i.test(p)) {
+      let f = 0, r = l + 1;
+      for (; f < 3 && r < s.length; ) {
+        const u = s[r].trim();
+        u !== "" && (t.push(u.split(/\s+/).map(Number)), f++), r++;
+      }
+      if (f < 3) throw new Error("Incomplete CELL_PARAMETERS block");
+      break;
+    }
+  }
+  if (t.length !== 3)
+    throw new Error("CELL_PARAMETERS block not found or incomplete");
+  let i = !1, o = "angstrom";
+  for (let l = 0; l < s.length; l++) {
+    const p = s[l].trim();
+    if (!(!p || p.startsWith("&"))) {
+      if (/^ATOMIC_POSITIONS/i.test(p)) {
+        i = !0;
+        const f = p.match(/^ATOMIC_POSITIONS\s+(\w+)/i);
+        o = f ? f[1].toLowerCase() : "angstrom";
         continue;
       }
+      if (i) {
+        const f = p.split(/\s+/);
+        if (f.length < 4 || !/^[A-Za-z]/.test(f[0]) || f.slice(1, 4).some((r) => Number.isNaN(Number(r))))
+          break;
+        e.push(p);
+      }
     }
-    p++;
   }
-  const u = T(t, n, o, i, a, c);
-  return new w({ lattice: u, species: h, sites: m });
+  if (e.length === 0)
+    throw new Error("ATOMIC_POSITIONS block not found");
+  const n = o === "crystal", a = [];
+  for (const l of e) {
+    const p = l.split(/\s+/)[0];
+    a.includes(p) || a.push(p);
+  }
+  const h = [];
+  for (const l of e) {
+    const p = l.split(/\s+/), f = p[0], r = p.slice(1, 4).map(Number);
+    let u;
+    n ? u = [
+      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]
+    ] : u = r, h.push(new x(a.indexOf(f), u));
+  }
+  return {
+    structure: new S({ lattice: t, species: a, sites: h }),
+    linesConsumed: s.length
+  };
+}
+function Y(s) {
+  const t = E(s);
+  return N(t).structure;
 }
 export {
-  w as CrystalStructure,
+  S as CrystalStructure,
   x as Site,
-  V as cifToStructure,
-  R as poscarToStructure,
-  z as structureToCif,
-  P as structureToPoscar,
-  W as structureToXsf,
-  X as structureToXyz,
-  O as xsfToStructure,
-  N as xyzToStructure
+  U as cifToStructure,
+  W as poscarToStructure,
+  Y as pwToStructure,
+  V as structureToCif,
+  D as structureToPoscar,
+  k as structureToXsf,
+  z as structureToXyz,
+  X as xsfToStructure,
+  Z as xyzToStructure
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matsci-parse",
-  "version": "0.1.2",
+  "version": "0.2.0",
   "type": "module",
   "main": "dist/main.js",
   "module": "dist/main.js",