Merge pull request #44 from pyscal/update_cna_ids

Update cna ids

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.4
+current_version = 3.2.5
 commit = True
 tag = True
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='pyscal3',
-    version='3.2.4',
+    version='3.2.5',
     author='Sarath Menon',
     author_email='[email protected]',
     description='Python library written in C++ for calculation of local atomic structural environment',

src/pyscal3/cna.cpp

@@ -551,48 +551,69 @@ 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] == 2){
-            structure[ti] = 4;
+        if (structure[ti] == 1){
+            structure[ti] = 5;
+        }
+        else if (structure[ti] == 2){
+            structure[ti] = 8;
         }
     }
 
-    for(int ti=0; ti<nop; ti++){
-        if (structure[ti] == 1) continue;
-        else if (structure[ti] == 4) continue;
-        else {
+    //second pass
+    for (int ti=0; ti<nop; ti++){
+        if (structure[ti] < 5){
             for(int i=0; i<4; i++){
-                if(structure[first_shell[ti][i]] == 1){
-                    structure[ti] = 2;
+                if(structure[first_shell[ti][i]] == 5){
+                    structure[ti] = 6;
                     break;
                 }
-                else if(structure[first_shell[ti][i]] == 4){
-                    structure[ti] = 5;
+                else if(structure[first_shell[ti][i]] == 8){
+                    structure[ti] = 9;
                     break;
-                }
+                } 
             }
-        }
-
+        }     
     }
 
-    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 ti=0; ti<nop; ti++){
+        if (structure[ti] < 5){
+            //still unassigned
             for (int j=0; j<neighbors[ti].size(); j++){
                 int tj = neighbors[ti][j];
-                if (structure[tj] == 1){
-                    structure[ti] = 3;
+                if (structure[tj] == 5){
+                    structure[ti] = 7;
                     break;
                 }
-                else if (structure[tj] == 4){
-                    structure[ti] = 6;
+                else if (structure[tj] == 8){
+                    structure[ti] = 10;
                     break;
-                }
+                } 
             }
         }
     }
+
+    //map ids
+    for (int ti=0; ti<nop; ti++){
+        if (structure[ti] == 5){
+            structure[ti] = 1;
+        }
+        else if (structure[ti] == 6){
+            structure[ti] = 2;
+        }
+        else if (structure[ti] == 7){
+            structure[ti] = 3;
+        }
+        else if (structure[ti] == 8){
+            structure[ti] = 4;
+        }
+        else if (structure[ti] == 9){
+            structure[ti] = 5;
+        }
+        else if (structure[ti] == 10){
+            structure[ti] = 6;
+        }
+    }
+
     atoms[py::str("structure")] = structure;     
 
 }