Merge pull request #10 from PytLab/fix-lammps-format-bug

Add basis info in LAMMPS data conversion

Author: PytLab

README.rst

@@ -17,7 +17,7 @@ VASPy
     :target: https://www.python.org/downloads/release/python-351/
     :alt: platform
 
-.. image:: https://img.shields.io/badge/pypi-v0.8.11-blue.svg
+.. image:: https://img.shields.io/badge/pypi-v0.8.12-blue.svg
     :target: https://pypi.python.org/pypi/vaspy/
     :alt: versions
 

setup.py

@@ -30,7 +30,7 @@
     :target: https://www.python.org/downloads/release/python-351/
     :alt: platform
 
-.. image:: https://img.shields.io/badge/pypi-v0.8.11-blue.svg
+.. image:: https://img.shields.io/badge/pypi-v0.8.12-blue.svg
     :target: https://pypi.python.org/pypi/vaspy/
     :alt: versions
 

vaspy/__init__.py

@@ -8,7 +8,7 @@
     PY2 = True
 
 
-__version__ = '0.8.11'
+__version__ = '0.8.12'
 __all__ = ['atomco', 'electro', 'iter', 'matstudio', 'plotter', 'incar']
 
 

vaspy/atomco.py

@@ -229,16 +229,24 @@ def get_cif_content(self):
 
         return content
 
-    def get_reaxff_content(self):
+    def get_lmp_content(self):
         """
-        Get ReaxFF data file content
+        Get lammps data file content
         """
         content = '# Created by VASPy\n\n'
 
         # Info
         content += '{} atoms\n{} atom types\n\n'.format(len(self.data),
                                                         len(self.atom_types))
-        content += '0 25.000 xlo xhi\n0 25.000 ylo yhi\n0 25.000 zlo zhi\n\n'
+
+        # Basis info
+        x, y, z = self.bases
+        xhi, yhi, zhi = [np.linalg.norm(i) for i in self.bases]
+        content += '0 {:.9f} xlo xhi\n0 {:.9f} ylo yhi\n0 {:.9f} zlo zhi\n'.format(xhi, yhi, zhi)
+        xy = np.dot(x, y)/np.linalg.norm(x)
+        xz = np.dot(x, z)/np.linalg.norm(x)
+        yz = np.dot(y, z)/np.linalg.norm(y)
+        content += '{}   {}   {} xy xz yz\n\n'.format(xy, xz, yz)
 
         # Masses
         content += 'Masses\n\n'