bug: fixed sort and dynamic together

Signed-off-by: Nick Papior <[email protected]>

Author: zerothi

sisl/io/vasp/car.py

@@ -50,12 +50,15 @@ def write_geometry(self, geometry, dynamic=None, sort=False):
         --------
         geometry_sort: method used to sort atoms in geometry
         """
-        if sort:
-            geometry = self.geometry_sort(geometry)
-
         # Check that we can write to the file
         sile_raise_write(self)
 
+        if sort:
+            geometry, idx = self.geometry_sort(geometry, ret_index=True)
+        else:
+            # small hack to allow dynamic
+            idx = _a.arangei(len(geometry))
+
         # LABEL
         self._write('sisl output\n')
 
@@ -107,7 +110,7 @@ def todyn(fix):
 
         fmt = '{:18.9f}' * 3
         for ia in geometry:
-            self._write(fmt.format(*geometry.xyz[ia, :]) + todyn(dynamic[ia]))
+            self._write(fmt.format(*geometry.xyz[ia, :]) + todyn(dynamic[idx[ia]]))
 
     @sile_fh_open(True)
     def read_supercell(self):

sisl/io/vasp/sile.py

@@ -8,7 +8,7 @@
 __all__ = ['SileVASP', 'SileCDFVASP', 'SileBinVASP']
 
 
-def _geometry_sort(geometry):
+def _geometry_sort(geometry, ret_index=False):
     r""" Order atoms in geometry according to species such that all of one specie is consecutive
 
     When creating VASP input files (`poscarSileVASP` for instance) the equivalent
@@ -28,6 +28,8 @@ def _geometry_sort(geometry):
     ----------
     geometry : Geometry
        geometry to be re-ordered
+    ret_index : bool, optional
+       return sorted indices
 
     Returns
     -------
@@ -43,6 +45,8 @@ def _geometry_sort(geometry):
 
     assert ia == na
 
+    if ret_index:
+        return geometry.sub(idx), idx
     return geometry.sub(idx)