Polymer implementation

MolAdsPy/__atom__.py

@@ -1,4 +1,4 @@
-from MolAdsPy.__exception__ import BasicException
+from __exception__ import BasicException
 from numpy import array,ndarray
 
 class AtomError(BasicException):

MolAdsPy/__atomcollection__.py

@@ -1,5 +1,5 @@
-from MolAdsPy.__atom__ import Atom,Species
-from MolAdsPy.__exception__ import BasicException
+from __atom__ import Atom,Species
+from __exception__ import BasicException
 from multipledispatch import dispatch
 from numpy import array,ndarray,dot,sqrt
 from copy import copy
@@ -14,8 +14,9 @@ class AtomCollection(ABC):
     _instances=None     # List of atom collection objects created so far
     __slots__=["_ucell","_atoms","_loc","_species","_a0","_latvec","_n","_m","_l",
                "_maxn","_maxm","_maxl","_id","_origin","_belongs_to","_label"]
-
-    def __init__(self):
+    _verbose = 1        # Level of verbose during usage of the lib
+
+    def __init__(self,**kwargs):
         '''
         Object initialization.
         '''
@@ -33,6 +34,7 @@ def __init__(self):
         self._maxn=self._maxm=self._maxl=0      # Maximum number of translations for resizing purposes
         self._origin=array([0.0,0.0,0.0])       # Position with minimum values of X, Y, and Z coordinates of the structure.        
 
+        self._verbose = kwargs.get("verbose",False)
         type(self)._append(self)
 
     @dispatch(int,loc=(tuple,list),update=bool)
@@ -260,7 +262,7 @@ def write_xyz(self,file_name="coords.xyz",ucell=False):
         n=self._n+1 if not ucell else 1
         m=self._m+1 if not ucell else 1
         l=self._l+1 if not ucell else 1
-        
+
         for atom in self._atoms:
             i,j,k=self._loc[atom._id]
 
@@ -558,8 +560,14 @@ def write_pw_input(self,file_name="pw.in",ucell=False,pseudopotentials={},
 
         with open(file_name,"w") as f:
             f.write(inpstr)
-
+
+    # TODO: Rename to replicate.
     def resize(self,n,m,l):
+        #print("max")
+        #print(self._maxn, self._maxm,self._maxl)
+        #print("input")
+        #print(n,m,l)
+        print(n,m,l)
         '''
         Resizes the atom collection structure.
 
@@ -579,9 +587,12 @@ def resize(self,n,m,l):
                 and n>=0 and m>=0 and l>=0):
             raise AtomCollectionError("'n', 'm' and 'l' values must be integers greater than or equal to zero!")            
         elif n==self._n and m==self._m and l==self._l:
-            raise AtomCollectionError("The current structure size was not changed!")
-        elif n>self._maxn or m>self._maxm and l>self._maxl:
-            print("WARNING: Atoms newly created will not be removed if the supercell is subsequently reduced!")
+            if(self._verbose):
+                print("The current structure size was not changed!")
+            return
+        elif n>self._maxn or m>self._maxm or l>self._maxl:
+            if(self._verbose):
+                print("WARNING: Atoms newly created will not be removed if the supercell is subsequently reduced!")
 
             for i in range(n+1):
                 for j in range(m+1):
@@ -602,11 +613,12 @@ def resize(self,n,m,l):
             self._maxn=max([self._maxn,n])
             self._maxm=max([self._maxm,m])
             self._maxl=max([self._maxl,l])
-                
+
         self._n=n
         self._m=m
         self._l=l
-
+        print()
+        print(self._n)
         self._update()
 
     def copy(self):
@@ -698,6 +710,7 @@ def _read_xyz(self,file_name):
               % (len(self._atoms),file_name))
 
         self._update()
+        f.close()
 
     def __getitem__(self,idx):
         '''
@@ -716,11 +729,13 @@ def __getitem__(self,idx):
             atom list.
         '''
         maxidx=len(self._atoms)
+        if not isinstance(idx,int):
+            raise AtomCollectionError("Index is not int!")
 
-        if isinstance(idx,int) and idx>=-maxidx and idx<maxidx:
+        if idx>=-maxidx and idx<maxidx:
             return self._atoms[idx]
         else:
-            raise AtomCollectionError("Invalid index!")
+            raise AtomCollectionError("Invalid index in get item!")
 
     @dispatch(int,int)
     def __setitem__(self,idx,atomid):
@@ -766,7 +781,7 @@ def __setitem__(self,idx,atomid):
             else:
                 raise AtomCollectionError("'atomid' must be an integer greater than or equal to zero!")            
         else:
-            raise AtomCollectionError("Invalid index!")
+            raise AtomCollectionError("Invalid index in set item!")
 
     @dispatch(int,Atom)
     def __setitem__(self,idx,atom):
@@ -804,7 +819,7 @@ def __setitem__(self,idx,atom):
             else:
                 raise AtomCollectionError("Atom already belongs to another structure!")
         else:
-            raise AtomCollectionError("Invalid index!")
+            raise AtomCollectionError("Invalid index in set item Atom dispatch!")
 
     def __len__(self):
         '''
@@ -949,6 +964,7 @@ def lattice_vectors(self,val):
         else:
             raise AtomCollectionError("Lattice vectors must be a Numpy array with three vectors!")
 
+
     @property
     def origin(self):
         return self._origin

MolAdsPy/__hybrid__.py

@@ -1,6 +1,6 @@
 from __future__ import print_function
-from MolAdsPy.__atomcollection__ import AtomCollection
-from MolAdsPy.__exception__ import BasicException
+from __atomcollection__ import AtomCollection
+from __exception__ import BasicException
 from abc import ABC,abstractmethod
 from numpy import array
 
@@ -11,10 +11,11 @@ class Hybrid(AtomCollection,ABC):
     __slots__=["_components","_a0","_latvec","_n","_m","_l","_maxn","_maxm",
                "_maxl","_origin"]
 
-    def __init__(self):
+    def __init__(self,**kwargs):
         '''
         Object initialization.
         '''
+
         self._components={}                     # Dictionary of objects that are put together to form the hybrid system
         self._a0=1.0                            # Lattice constant
         self._latvec=array([[1.0,0.0,0.0],
@@ -24,6 +25,7 @@ def __init__(self):
         self._maxn=self._maxm=self._maxl=0      # Maximum number of translations for resizing purposes
         self._origin=array([0.0,0.0,0.0])       # Position with minimum values of X, Y, and Z coordinates of the structure.
 
+        self._verbose = kwargs.get("verbose",False)
         type(self)._append(self)
 
     @abstractmethod
@@ -42,6 +44,22 @@ def remove_component(self,*args):
         '''        
         pass    
 
+    @abstractmethod
+    def beginHandler(self,obj,method,**kwargs):
+        '''
+        To be implemented in a derived hybrid structure, this method is expected 
+        to make the hybrid structure reconsntruct itself when an object is realigned inside it.
+        '''  
+        pass
+
+    @abstractmethod
+    def endHandler(self,obj,method,**kwargs):
+        '''
+        To be implemented in a derived hybrid structure, this method is expected 
+        to make the hybrid structure reconsntruct itself when an object is realigned inside it.
+        '''  
+        pass
+
     def force_update(self):
         '''
         Forces the hybrid system's attributes to be updated if there is a change 

MolAdsPy/__init__.py

@@ -1,3 +1,3 @@
-from .core import Atom,Molecule,Slab,Adsorption
+from .core import Atom,Molecule,Slab,Adsorption,Polymer
 
 __version__="1.0.0"

MolAdsPy/__molecule__.py

@@ -1,7 +1,7 @@
 from __future__ import print_function
-from MolAdsPy.__atom__ import Atom
-from MolAdsPy.__atomcollection__ import AtomCollection
-from MolAdsPy.__exception__ import BasicException
+from __atom__ import Atom
+from __atomcollection__ import AtomCollection
+from __exception__ import BasicException
 from numpy import array,ndarray,min,max,sum,cos,sin,radians,dot
 from copy import deepcopy
 from multipledispatch import dispatch
@@ -13,7 +13,7 @@ class Molecule(AtomCollection):
     __slots__=["_vaccuum","_maxx","_maxy","_maxz","_minx","_miny","_minz","_anchors"]
 
     @dispatch(str,vaccuum=(int,float))
-    def __init__(self,label,vaccuum=10.0):
+    def __init__(self,label,vaccuum=10.0,**kwargs):
         '''
         Object initialization.
 
@@ -27,7 +27,7 @@ def __init__(self,label,vaccuum=10.0):
             boundary conditions scheme. The default is 10.0 Angstroms.
 
         '''
-        super().__init__()
+        super().__init__(**kwargs)
 
         if len(label)>0:
             self._label=label
@@ -122,7 +122,8 @@ def __init__(self,label,atom_list,vaccuum=10.0):
                 if isinstance(atom,(Atom,int)):
                     self.add_atom(atom,loc=(0,0,0),update=False)
                 else:
-                    print("WARNING! An element in the atom list must be either an Atom object or an atom ID!")
+                    if(self.verbose):
+                        print("WARNING! An element in the atom list must be either an Atom object or an atom ID!")
         else:
             raise MoleculeError("'atom_list' must be a non-empyt list!")