ATAT SQS file converter

mctools/sqs_read.py

@@ -0,0 +1,67 @@
+#! /usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import numpy as np
+import ase.atoms
+import ase.build
+import ase.visualize
+
+def atoms_from_sqs(filename):
+
+    with open(filename, 'r') as f:
+        lines = f.readlines()
+    lines = [line.split() for line in lines]
+
+    basis = np.matrix([list(map(float, line)) for line in lines[:3]])
+    scell = np.matrix([list(map(float, line)) for line in lines[3:6]])
+
+    spositions = [np.matrix(list(map(float, line[:3]))) for line in lines[6:]]
+    symbols = [line[-1] for line in lines[6:]]
+
+    supercell = scell * basis
+    positions = spositions * basis
+    atoms = ase.atoms.Atoms(symbols=symbols, 
+                            cell=supercell,
+                            positions=positions,
+                            pbc=True)
+
+    return atoms
+
+def txt_display(atoms):
+    print("Unit cell:")
+    print(atoms.cell)
+    print("Positions")
+    atoms = ase.build.sort(atoms)
+    for atom in atoms:
+
+        print(atom.position, atom.symbol)
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('filename', nargs='?', default='bestsqs.out',
+                        help="Input file generated by ATAT")
+    parser.add_argument('--output', '-o', default=None,
+                        help="If specified, write to this filename")
+    parser.add_argument('--gui', '-g', action='store_true',
+                        help="Show structure in ASE-GUI")
+
+    args = parser.parse_args()
+
+    atoms = atoms_from_sqs(args.filename)
+
+    if args.output is not None:
+        # Write file with vasp5 flag if supported
+        try:
+            atoms.write(args.output, sort=True, vasp5=True)
+        except TypeError:
+            atoms = ase.build.sort(atoms)
+            atoms.write(args.output)
+    else:
+        txt_display(atoms)
+
+    if args.gui:
+        ase.visualize.view(atoms)
+
+if __name__ == '__main__':
+    main()

setup.py

@@ -37,6 +37,7 @@
             'get-primitive = mctools.get_primitive:main',
             'get-spacegroup = mctools.get_spacegroup:main',
             'get-vbm = mctools.get_vbm:main',
+            'sqs-read = mctools.sqs_read:main',
             'sendto = mctools.sendto:main',
             'vasp-charge = mctools.vasp_charge:main',
             'vectors = mctools.vectors:main'