matsci-parse 0.1.0 → 0.1.2

package/dist/main.js

@@ -9,7 +9,7 @@ class x {
     this.props[e] = t;
   }
 }
-function T(s) {
+function C(s) {
   return s.sites.some((e) => Array.isArray(e.props.selectiveDynamics));
 }
 function E(s) {
@@ -20,15 +20,15 @@ function $(s, e) {
     (t) => t[0] * e[0] + t[1] * e[1] + t[2] * e[2]
   );
 }
-function L(s, e, t, n, o, i) {
-  const c = E(n), l = E(o), f = E(i), d = [s, 0, 0], u = [
-    e * Math.cos(f),
-    e * Math.sin(f),
+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),
     0
-  ], p = t * Math.cos(l), m = t * (Math.cos(c) - Math.cos(l) * Math.cos(f)) / Math.sin(f), _ = Math.sqrt(t * t - p * p - m * m);
-  return [d, u, [p, m, _]];
+  ], 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]];
 }
-function C(s, e) {
+function L(s, e) {
   const [t, n, o] = e;
   return [
     s[0] * t[0] + s[1] * n[0] + s[2] * o[0],
@@ -169,11 +169,11 @@ class w {
     const n = this.lattice.map(
       (i) => $(t, i)
     ), o = this.sites.map((i) => {
-      const c = $(
+      const a = $(
         t,
         i.cart
       );
-      return new x(i.speciesIndex, c, i.props);
+      return new x(i.speciesIndex, a, i.props);
     });
     return new w({
       lattice: n,
@@ -237,23 +237,23 @@ function F(s) {
   return s.split(/\r?\n/).map((e) => e.trim()).filter(Boolean);
 }
 function P(s, e = 6) {
-  const t = [], n = T(s);
-  t.push("Generated by matsci-parse"), t.push("1.0"), s.lattice.forEach((c) => {
-    t.push(c.map((l) => l.toFixed(e)).join(" "));
+  const t = [], n = C(s);
+  t.push("Generated by matsci-parse"), t.push("1.0"), s.lattice.forEach((a) => {
+    t.push(a.map((c) => c.toFixed(e)).join(" "));
   });
   const o = Array.from(
-    new Set(s.sites.map((c) => s.species[c.speciesIndex]))
+    new Set(s.sites.map((a) => s.species[a.speciesIndex]))
   ), i = o.map(
-    (c) => s.sites.filter((l) => s.species[l.speciesIndex] === c).length
+    (a) => s.sites.filter((c) => s.species[c.speciesIndex] === a).length
   );
-  return t.push(o.join(" ")), t.push(i.join(" ")), n && t.push("Selective dynamics"), t.push("Cartesian"), o.forEach((c) => {
-    s.sites.filter((l) => s.species[l.speciesIndex] === c).forEach((l) => {
-      const f = l.cart.map((d) => d.toFixed(e)).join(" ");
+  return t.push(o.join(" ")), t.push(i.join(" ")), n && t.push("Selective dynamics"), t.push("Cartesian"), o.forEach((a) => {
+    s.sites.filter((c) => s.species[c.speciesIndex] === a).forEach((c) => {
+      const h = c.cart.map((m) => m.toFixed(e)).join(" ");
       if (n) {
-        const u = (Array.isArray(l.props?.selectiveDynamics) ? l.props.selectiveDynamics : [!0, !0, !0]).map((p) => p ? "T" : "F").join(" ");
-        t.push(`${f} ${u}`);
+        const p = (Array.isArray(c.props?.selectiveDynamics) ? c.props.selectiveDynamics : [!0, !0, !0]).map((u) => u ? "T" : "F").join(" ");
+        t.push(`${h} ${p}`);
       } else
-        t.push(f);
+        t.push(h);
     });
   }), t.join(`
 `);
@@ -262,35 +262,35 @@ function j(s) {
   let e = 0;
   e++;
   const t = parseFloat(s[e++]), n = [];
-  for (let p = 0; p < 3; p++)
+  for (let u = 0; u < 3; u++)
     n.push(
-      s[e++].split(/\s+/).map((m) => parseFloat(m) * t)
+      s[e++].split(/\s+/).map((l) => parseFloat(l) * t)
     );
   let o = s[e].trim(), i;
   /^[A-Za-z]/.test(o) && (i = o.split(/\s+/), e++);
-  const c = s[e++].split(/\s+/).map(Number);
-  i || (i = c.map((p, m) => `X${m + 1}`));
-  let l = !1;
-  s[e]?.toLowerCase().startsWith("s") && (l = !0, e++);
-  const d = s[e++].toLowerCase().startsWith("d"), u = [];
-  return i.forEach((p, m) => {
-    for (let _ = 0; _ < c[m]; _++) {
+  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 h;
-      d ? h = [
+      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]
-      ] : h = r.slice(0, 3);
-      const y = {};
-      if (l) {
-        const g = r.slice(3, 6).map((a) => a === 1);
-        g.length === 3 && (y.selectiveDynamics = g);
+      ] : f = r.slice(0, 3);
+      const g = {};
+      if (c) {
+        const y = r.slice(3, 6).map((_) => _ === 1);
+        y.length === 3 && (g.selectiveDynamics = y);
       }
-      u.push(new x(m, h, y));
+      p.push(new x(l, f, g));
     }
   }), {
-    structure: new w({ lattice: n, species: i, sites: u }),
+    structure: new w({ lattice: n, species: i, sites: p }),
     linesConsumed: e
   };
 }
@@ -298,7 +298,7 @@ function R(s) {
   const e = F(s);
   return j(e).structure;
 }
-function O(s, e = 6) {
+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(" "));
@@ -310,29 +310,29 @@ function O(s, e = 6) {
   }), t.join(`
 `);
 }
-function W(s) {
+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 l = 0; l < 3; l++)
+  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 [c] = e[i++].split(/\s+/).map(Number);
-  for (let l = 0; l < c; l++) {
-    const f = e[i++].split(/\s+/), d = f[0], u = f.slice(1, 4).map(Number);
-    let p = n.indexOf(d);
-    p === -1 && (n.push(d), p = n.length - 1), o.push(new x(p, u));
+  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));
   }
   return new w({ lattice: t, species: n, sites: o });
 }
 function X(s, e = 6) {
   const t = [], n = s.sites.length;
   t.push(String(n));
-  const o = T(s), i = s.lattice, c = [
+  const o = C(s), i = s.lattice, a = [
     i[0][0],
     i[1][0],
     i[2][0],
@@ -342,20 +342,20 @@ function X(s, e = 6) {
     i[0][2],
     i[1][2],
     i[2][2]
-  ].join(" "), l = [
+  ].join(" "), c = [
     "species:S:1",
     "pos:R:3",
     o ? "selectiveDynamics:L:3" : null
   ].filter(Boolean).join(":");
-  t.push(`Lattice="${c}" Properties=${l}`);
-  for (const f of s.sites) {
-    const d = s.species[f.speciesIndex], [u, p, m] = f.cart;
-    let _ = `${d} ${u.toFixed(e)} ${p.toFixed(e)} ${m.toFixed(e)}`;
+  t.push(`Lattice="${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)}`;
     if (o) {
-      const r = Array.isArray(f.props?.selectiveDynamics) ? f.props.selectiveDynamics : [!0, !0, !0];
-      _ += " " + r.map((h) => h ? "T" : "F").join(" ");
+      const r = Array.isArray(h.props?.selectiveDynamics) ? h.props.selectiveDynamics : [!0, !0, !0];
+      d += " " + r.map((f) => f ? "T" : "F").join(" ");
     }
-    t.push(_);
+    t.push(d);
   }
   return t.join(`
 `);
@@ -366,43 +366,43 @@ function N(s) {
   const n = parseInt(e[t++], 10);
   if (!Number.isFinite(n))
     throw new Error("Invalid XYZ: first line must be atom count");
-  const o = e[t++], i = {}, c = /(\w+)=(".*?"|\S+)/g;
-  for (const r of o.matchAll(c)) {
-    let h = r[2];
-    h.startsWith('"') && (h = h.slice(1, -1)), i[r[1]] = h;
+  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;
   }
-  let l;
+  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");
-    l = [
+    c = [
       [r[0], r[3], r[6]],
       [r[1], r[4], r[7]],
       [r[2], r[5], r[8]]
     ];
   } else
     throw new Error("Lattice must be present in extended XYZ format");
-  let f = 0, d = 1, u = null;
+  let h = 0, m = 1, p = null;
   if (i.Properties) {
     const r = i.Properties.split(":");
-    let h = 0;
-    for (let y = 0; y < r.length; y += 3) {
-      const g = r[y], a = parseInt(r[y + 2], 10);
-      g === "species" && (f = h), g === "pos" && (d = h), g === "selectiveDynamics" && (u = h), h += a;
+    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 += _;
     }
   }
-  const p = [], m = /* @__PURE__ */ new Map(), _ = [];
+  const u = [], l = /* @__PURE__ */ new Map(), d = [];
   for (let r = 0; r < n; r++) {
-    const h = e[t++].split(/\s+/), y = h[f];
-    m.has(y) || (m.set(y, p.length), p.push(y));
-    const g = m.get(y), a = h.slice(d, d + 3).map(Number), S = {};
-    if (u !== null) {
-      const I = h.slice(u, u + 3).map((b) => b.toUpperCase() === "T");
+    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);
     }
-    _.push(new x(g, a, S));
+    d.push(new x(y, _, S));
   }
-  return new w({ lattice: l, species: p, sites: _ });
+  return new w({ lattice: c, species: u, sites: d });
 }
 function v(s, e) {
   return s[0] * e[0] + s[1] * e[1] + s[2] * e[2];
@@ -417,7 +417,7 @@ 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)
     throw new Error("Singular lattice matrix");
-  const c = [
+  const a = [
     [
       (n[1] * o[2] - n[2] * o[1]) / i,
       (t[2] * o[1] - t[1] * o[2]) / i,
@@ -435,23 +435,23 @@ function D(s, e) {
     ]
   ];
   return [
-    s[0] * c[0][0] + s[1] * c[1][0] + s[2] * c[2][0],
-    s[0] * c[0][1] + s[1] * c[1][1] + s[2] * c[2][1],
-    s[0] * c[0][2] + s[1] * c[1][2] + s[2] * c[2][2]
+    s[0] * a[0][0] + s[1] * a[1][0] + s[2] * a[2][0],
+    s[0] * a[0][1] + s[1] * a[1][1] + s[2] * a[2][1],
+    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), c = A(n), l = A(o), f = M(Math.acos(v(n, o) / (c * l))), d = M(Math.acos(v(t, o) / (i * l))), u = M(Math.acos(v(t, n) / (i * c)));
-  let p = `data_made_with_matsci-parse
+  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
     _symmetry_space_group_name_H-M   'P 1'
     _symmetry_Int_Tables_number    1
 
     _cell_length_a   ${i.toFixed(e)}
-    _cell_length_b   ${c.toFixed(e)}
-    _cell_length_c   ${l.toFixed(e)}
-    _cell_angle_alpha   ${f.toFixed(e)}
-    _cell_angle_beta    ${d.toFixed(e)}
-    _cell_angle_gamma   ${u.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)}
 
     loop_
     _atom_site_label
@@ -460,34 +460,60 @@ function z(s, e = 6) {
     _atom_site_fract_y
     _atom_site_fract_z
 `;
-  return s.sites.forEach((m, _) => {
-    const r = s.species[m.speciesIndex], h = D(m.cart, s.lattice);
-    p += `${r}${_ + 1} ${r} ${h[0].toFixed(e)} ${h[1].toFixed(
+  return s.sites.forEach((l, d) => {
+    const r = s.species[l.speciesIndex], f = D(l.cart, s.lattice);
+    u += `${r}${d + 1} ${r} ${f[0].toFixed(e)} ${f[1].toFixed(
       6
-    )} ${h[2].toFixed(e)}
+    )} ${f[2].toFixed(e)}
 `;
-  }), p;
+  }), u;
 }
 function V(s) {
   const e = F(s);
-  let t = 0, n = 0, o = 0, i = 0, c = 0, l = 0;
-  const f = [];
-  let d = !1, u = [];
-  for (const a of e)
-    a.startsWith("_cell_length_a") ? t = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_length_b") ? n = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_length_c") ? o = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_angle_alpha") ? i = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_angle_beta") ? c = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_angle_gamma") ? l = parseFloat(a.split(/\s+/)[1]) : a.startsWith("loop_") ? (d = !0, u = []) : d && a.startsWith("_") ? u.push(a) : d && a && !a.startsWith("_") && f.push(a.split(/\s+/));
-  const p = L(t, n, o, i, c, l), m = [], _ = [], r = u.findIndex((a) => a.includes("fract_x")), h = u.findIndex((a) => a.includes("fract_y")), y = u.findIndex((a) => a.includes("fract_z")), g = u.findIndex((a) => a.includes("type_symbol"));
-  if (r < 0 || h < 0 || y < 0 || g < 0)
-    throw new Error("CIF missing required _atom_site columns");
-  for (const a of f) {
-    const S = [
-      parseFloat(a[r]),
-      parseFloat(a[h]),
-      parseFloat(a[y])
-    ], I = C(S, p);
-    let b = m.indexOf(a[g]);
-    b === -1 && (b = m.length, m.push(a[g])), _.push(new x(b, I));
+  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++;
+        }
+        continue;
+      }
+    }
+    p++;
   }
-  return new w({ lattice: p, species: m, sites: _ });
+  const u = T(t, n, o, i, a, c);
+  return new w({ lattice: u, species: h, sites: m });
 }
 export {
   w as CrystalStructure,
@@ -496,8 +522,8 @@ export {
   R as poscarToStructure,
   z as structureToCif,
   P as structureToPoscar,
-  O as structureToXsf,
+  W as structureToXsf,
   X as structureToXyz,
-  W as xsfToStructure,
+  O as xsfToStructure,
   N as xyzToStructure
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matsci-parse",
-  "version": "0.1.0",
+  "version": "0.1.2",
   "type": "module",
   "main": "dist/main.js",
   "module": "dist/main.js",