Merge pull request #43 from pyscal/update_cna_ids

Update cna ids

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.3
+current_version = 3.2.4
 commit = True
 tag = True
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='pyscal3',
-    version='3.2.3',
+    version='3.2.4',
     author='Sarath Menon',
     author_email='[email protected]',
     description='Python library written in C++ for calculation of local atomic structural environment',

src/pyscal3/cna.cpp

@@ -551,47 +551,48 @@ void identify_diamond_cna(py::dict& atoms,
     vector<int> structure = atoms[py::str("structure")].cast<vector<int>>();
 
     for (int ti=0; ti<nop; ti++){
-        if (structure[ti] == 1){
-            structure[ti] = 5;
-        }
-        else if (structure[ti] == 2){
-            structure[ti] = 8;
+        if (structure[ti] == 2){
+            structure[ti] = 4;
         }
     }
 
-    //second pass
-    for (int ti=0; ti<nop; ti++){
-        if (structure[ti] < 5){
+    for(int ti=0; ti<nop; ti++){
+        if (structure[ti] == 1) continue;
+        else if (structure[ti] == 4) continue;
+        else {
             for(int i=0; i<4; i++){
-                if(structure[first_shell[ti][i]] == 5){
-                    structure[ti] = 6;
+                if(structure[first_shell[ti][i]] == 1){
+                    structure[ti] = 2;
                     break;
                 }
-                else if(structure[first_shell[ti][i]] == 8){
-                    structure[ti] = 9;
+                else if(structure[first_shell[ti][i]] == 4){
+                    structure[ti] = 5;
                     break;
-                } 
+                }
             }
-        }     
+        }
+
     }
 
-    for (int ti=0; ti<nop; ti++){
-        if (structure[ti] < 5){
-            //still unassigned
+    for(int ti=0; ti<nop; ti++){
+        if (structure[ti] == 1) continue;
+        else if (structure[ti] == 2) continue;
+        else if (structure[ti] == 4) continue;
+        else if (structure[ti] == 5) continue;
+        else {
             for (int j=0; j<neighbors[ti].size(); j++){
                 int tj = neighbors[ti][j];
-                if (structure[tj] == 5){
-                    structure[ti] = 7;
+                if (structure[tj] == 1){
+                    structure[ti] = 3;
                     break;
                 }
-                else if (structure[tj] == 8){
-                    structure[ti] = 10;
+                else if (structure[tj] == 4){
+                    structure[ti] = 6;
                     break;
-                } 
+                }
             }
         }
     }
-
     atoms[py::str("structure")] = structure;     
 
 }

src/pyscal3/operations/cna.py

@@ -91,11 +91,11 @@ def identify_diamond(system):
     Notes
     -----
     Identify diamond structure using the algorithm mentioned in [1]. It is an
-    extended CNA method. The integers 5, 6, 7, 8, 9 and 10 are assigned to the
-    structure variable of the atom. 5 stands for cubic diamond, 6 stands for first
-    nearest neighbors of cubic diamond and 7 stands for second nearest neighbors
-    of cubic diamond. 8 signifies hexagonal diamond, the first nearest neighbors
-    are marked with 9 and second nearest neighbors with 10.
+    extended CNA method. The integers 1, 2, 3, 4, 5 and 6 are assigned to the
+    structure variable of the atom. 1 stands for cubic diamond, 2 stands for first
+    nearest neighbors of cubic diamond and 3 stands for second nearest neighbors
+    of cubic diamond. 4 signifies hexagonal diamond, the first nearest neighbors
+    are marked with 5 and second nearest neighbors with 6.
 
     References
     ----------
@@ -110,11 +110,11 @@ def identify_diamond(system):
 
     res_dict = {
     "others": len([x for x in system.atoms.structure if x==0]),
-    "cubic diamond": len([x for x in system.atoms.structure if x==5]),
-    "cubic diamond 1NN": len([x for x in system.atoms.structure if x==6]),
-    "cubic diamond 2NN": len([x for x in system.atoms.structure if x==7]),
-    "hex diamond": len([x for x in system.atoms.structure if x==8]),
-    "hex diamond 1NN": len([x for x in system.atoms.structure if x==9]),
-    "hex diamond 2NN": len([x for x in system.atoms.structure if x==10]),
+    "cubic diamond": len([x for x in system.atoms.structure if x==1]),
+    "cubic diamond 1NN": len([x for x in system.atoms.structure if x==2]),
+    "cubic diamond 2NN": len([x for x in system.atoms.structure if x==3]),
+    "hex diamond": len([x for x in system.atoms.structure if x==4]),
+    "hex diamond 1NN": len([x for x in system.atoms.structure if x==5]),
+    "hex diamond 2NN": len([x for x in system.atoms.structure if x==6]),
     }
     return res_dict    

tests/test_cna.py

@@ -54,4 +54,4 @@ def test_ase_bulks():
 def test_cna_diamond():
     sys = pc.System.create.lattice.diamond(repetitions=(7,7,7), lattice_constant=4.00)
     sys.calculate.diamond_structure()
-    assert sys.atoms.structure[0] == 5
+    assert sys.atoms.structure[0] == 1