Merge branch 'master' of https://github.com/dimonaks/siman

siman/analysis.py

@@ -1,3 +1,4 @@
+
 # -*- coding: utf-8 -*- 
 #Copyright Aksyonov D.A
 from __future__ import division, unicode_literals, absolute_import 
@@ -68,7 +69,7 @@ def calc_oxidation_states(cl = None, st = None, silent = 1):
         z_vals.append(ox)
         if not silent:
             ''
-            print(el, '{:3.1f}'.format(ox))
+            print(j, st.xred[j][2], el, '{:3.1f}'.format(ox))
     # print(list(zip(z_vals, self.end.get_elements())))
     # print(z_vals)
     return z_vals
@@ -1559,7 +1560,6 @@ def suf_en(cl1, cl2, silent = 0, chem_pot = None, return_diff_energy = False, ev
     else:
         return gamma
 
-
 def suf_en_polar_layered(formula, cl_surf, dmu_a = 0, dmu_b = 0, dmu_c = 0, printlog = True):
     #This function calculates an energy of polar surface using chemical potentials for every elements
     #Ef = Etot(AxByCz) - (xμA + yμB + zμC)

siman/classes.py

@@ -48,7 +48,7 @@
     get_from_server, push_to_server, run_on_server, smoother, file_exists_on_server, check_output)
 from siman.inout import write_xyz, write_lammps, read_xyz, read_poscar, write_geometry_aims, read_aims_out, read_vasp_out
 from siman.geo import (image_distance, replic, calc_recip_vectors, calc_kspacings, xred2xcart, xcart2xred, 
-local_surrounding, local_surrounding2, determine_symmetry_positions, )
+local_surrounding, local_surrounding2, determine_symmetry_positions, remove_closest, remove_vacuum, make_neutral)
 from siman.set_functions import InputSet, aims_keys
 
 
@@ -1049,6 +1049,11 @@ def order(ls, i):
             # print(oxi_state[0:8])
         return oxi_states
 
+
+    def make_neutral(self, *args, **kwargs):
+        return make_neutral(self, *args, **kwargs)
+
+
     def get_conventional_cell(self):
         """
         return conventional cell 
@@ -1247,11 +1252,11 @@ def get_surface_area(self):
         return np.linalg.norm( np.cross(st.rprimd[0] , st.rprimd[1]) )
 
 
-
     def printme(self):
         print(self.convert2pymatgen())
         return 
 
+
     def get_space_group_info(self, symprec = None):
 
         default = 0.01
@@ -1329,6 +1334,7 @@ def get_transition_elements(self, fmt = 'names'):
             tra = ns
         return tra
 
+
     def get_specific_elements(self, required_elements = None, fmt = 'n', z_range = None, zr_range = None):
         """Returns list of specific elements (chemical names. z, or numbers from 0) in the structure
         required_elements - list of elements z of interest
@@ -1380,7 +1386,6 @@ def additional_condition(xr):
         return tra
 
 
-
     def get_dipole(self, ox_states = None, chg_type = 'ox'):
         """ Return dipole moment in e*A calculated by pymatgen
         ox_states (dict) - oxidation states of elements
@@ -1392,8 +1397,6 @@ def get_dipole(self, ox_states = None, chg_type = 'ox'):
         return slab.dipole
 
 
-
-
     def add_atoms(self, atoms_xcart = None, element = 'Pu', return_ins = False, selective = None, atoms_xred = None, mag = None):
         """
         appends at the end if element is new. Other case insertered according to VASP conventions
@@ -2173,7 +2176,6 @@ def add_vacuum(self, vector_i, thickness):
 
 
 
-
     # def sum_of_coord(self):
     #     sumx = 0
     #     for x in self.xcart:
@@ -2365,7 +2367,7 @@ def find_atom_num_by_xcart(self, x_tar, prec = 1e-6, search_by_xred = 1 ):
     def shift_atoms(self, vector_red = None, vector_cart = None, return2cell = 1):
         """
         Shift all atoms according to *vector_red* or *vector_cart*
-		Use *return2cell* if atoms coordinates should be inside cell
+        Use *return2cell* if atoms coordinates should be inside cell
         """
         st = copy.deepcopy(self)
         if vector_cart is not None:
@@ -2586,13 +2588,13 @@ def remove_close_lying2(self, tol = 0.4):
         return st
 
 
+    def remove_closest(self, *args, **kwargs):
+        return remove_closest(self, *args, **kwargs)
 
 
 
-
-
-
-
+    def remove_vacuum(self, *args, **kwargs):
+        return remove_vacuum(self, *args, **kwargs)
 
 
     def find_closest_atom(self, xc = None, xr = None):
@@ -3169,15 +3171,16 @@ def ewald(self, ox_st = None, site = None):
         # site if provided (from 0), than site energy is printed
         from pymatgen.analysis.ewald import EwaldSummation
         # from siman.analysis import set_oxidation_states
-        st = self
+
+        st = copy.deepcopy(self)
+
         if ox_st == 1:
             # st = set_oxidation_states(st)
-            # st.printme()
+            #st.printme()
             stpm = st.convert2pymatgen(chg_type = 'pm')
             # print('The following oxi states were set', st.oxi_state)
-        if ox_st == 2:
+        elif ox_st == 2:
             stpm = st.convert2pymatgen(chg_type = 'pot')
-
         else:
             stpm = st.convert2pymatgen()
 
@@ -7285,6 +7288,3 @@ def calc_ec_es(self, ev = 0):
         except AttributeError:
             self.ec_es = None
 
-
-
-