Change filename -> __filename & add query function.

Change filename to private member and add corresponding query function.

Author: PytLab

vaspy/atomco.py

@@ -4,7 +4,7 @@
 Provide coordinate file class which do operations on these files.
 ===================================================================
 Written by PytLab <shaozhengjiang@gmail.com>, November 2014
-Updated by PytLab <shaozhengjiang@gmail.com>, November 2015
+Updated by PytLab <shaozhengjiang@gmail.com>, May 2016
 
 ==============================================================
 
@@ -18,13 +18,13 @@
 class AtomCo(VasPy):
     "Base class to be inherited by atomco classes."
     def __init__(self, filename):
-        VasPy.__init__(self, filename)
+        super(self.__class__, self).__init__(filename)
 
     def __repr__(self):
         if hasattr(self, 'get_content'):
             return self.get_content()
         else:
-            return self.filename
+            return self.filename()
 
     def __str__(self):
         return self.__repr__()
@@ -177,13 +177,13 @@ class XyzFile(AtomCo):
       ============  =======================================================
     """
     def __init__(self, filename):
-        AtomCo.__init__(self, filename)
+        super(self.__class__, self).__init__(filename)
         self.load()
         self.verify()
 
     def load(self):
         "加载文件内容"
-        with open(self.filename, 'r') as f:
+        with open(self.filename(), 'r') as f:
             content_list = f.readlines()
         ntot = int(content_list[0].strip())  # total atom number
         step = int(str2list(content_list[1])[-1])  # iter step number
@@ -269,7 +269,7 @@ def __init__(self, filename='POSCAR'):
     def load(self):
         "获取文件数据信息"
         "Load all information in POSCAR."
-        with open(self.filename, 'r') as f:
+        with open(self.filename(), 'r') as f:
             content_list = f.readlines()
         #get scale factor
         bases_const = float(content_list[1])
@@ -415,7 +415,7 @@ def __init__(self, filename='XDATCAR'):
         self.load()
 
     def load(self):
-        with open(self.filename, 'r') as f:
+        with open(self.filename(), 'r') as f:
             # read lattice info
             self.system = f.readline().strip()
             self.bases_const = float(f.readline().strip())
@@ -432,7 +432,7 @@ def load(self):
 
     def __iter__(self):
         "generator which yield step number and iterative data."
-        with open(self.filename, 'r') as f:
+        with open(self.filename(), 'r') as f:
             # pass info lines
             for i in xrange(self.info_nline):
                 f.readline()

vaspy/electro.py

@@ -4,7 +4,7 @@
 Provide electro-related file class which do operations on these files.
 ========================================================================
 Written by PytLab <shaozhengjiang@gmail.com>, September 2015
-Updated by PytLab <shaozhengjiang@gmail.com>, October 2015
+Updated by PytLab <shaozhengjiang@gmail.com>, May 2016
 ========================================================================
 
 """
@@ -131,7 +131,7 @@ def tofile(self):
         content = ''
         for datalist in data:
             content += ('%12.8f'*ndata + '\n') % tuple(datalist)
-        with open(self.filename, 'w') as f:
+        with open(self.filename(), 'w') as f:
             f.write(content)
 
         return
@@ -189,12 +189,12 @@ def __init__(self, filename='ELFCAR'):
           plot_field       method, plot scalar field for elf data
           ==============  =============================================
         """
-        PosCar.__init__(self, filename=filename)
+        super(self.__class__, self).__init__(filename)
 
     def load(self):
         "Rewrite load method"
         PosCar.load(self)
-        with open(self.filename, 'r') as f:
+        with open(self.filename(), 'r') as f:
             for i in xrange(self.totline):
                 f.readline()
             #get dimension of 3d array

vaspy/incar.py

@@ -27,13 +27,14 @@ def __init__(self, filename='INCAR'):
           filename       string, name of INCAR file
           ============  =======================================
         """
-        VasPy.__init__(self, filename)
+        super(self.__class__, self).__init__(filename)
+        self.__filename = filename
         self.load()
 
     def load(self):
         "Load all data in INCAR."
         tot_pnames, tot_datas = [], []
-        with open(self.filename, 'r') as f:
+        with open(self.__filename, 'r') as f:
             for line in f:
                 matched = self.rdata(line)
                 if matched:
@@ -43,10 +44,22 @@ def load(self):
         # set attrs
         for pname, data in zip(tot_pnames, tot_datas):
             setattr(self, pname, data)
-        self.pnames = tot_pnames
+        self.__pnames = tot_pnames
 
         return
 
+    def pnames(self):
+        """
+        Query function for all parameter names.
+        """
+        return self.__pnames
+
+    def file_name(self):
+        """
+        Query function for all INCAR path names.
+        """
+        return self.__filename
+
     @staticmethod
     def rdata(line):
         "Get INCAR data(s) in a line."
@@ -75,7 +88,7 @@ def rdata(line):
 
     def set(self, pname, data):
         """
-        Set a named property of InCar object.
+        Set a named parameter of InCar object.
 
         Example:
         --------
@@ -89,7 +102,7 @@ def set(self, pname, data):
 
     def add(self, pname, data):
         """
-        Add a new property name to InCar object.
+        Add a new parameter name to InCar object.
 
         Example:
         --------
@@ -100,20 +113,20 @@ def add(self, pname, data):
             print ("Waring: %s is already in INCAR, " +
                    "set to %s" % (pname, data))
         else:
-            self.pnames.append(pname)
+            self.__pnames.append(pname)
         setattr(self, pname, data)
 
         return
 
     def tofile(self):
         "Create INCAR file."
         content = '# Created by VASPy\n'
-        for pname in self.pnames:
+        for pname in self.__pnames:
             if not hasattr(self, pname):
                 raise ValueError('Unknown parameter: %s' % pname)
             data = str(getattr(self, pname))
             content += '%s = %s\n' % (pname, data)
-        with open('INCAR', 'w') as f:
+        with open(self.__filename, 'w') as f:
             f.write(content)
 
         return

vaspy/iter.py

@@ -4,7 +4,7 @@
 Provide iteration-related file class which do operations on these files.
 ========================================================================
 Written by PytLab <shaozhengjiang@gmail.com>, August 2015
-Updated by PytLab <shaozhengjiang@gmail.com>, September 2015
+Updated by PytLab <shaozhengjiang@gmail.com>, May 2016
 ========================================================================
 
 """
@@ -36,7 +36,7 @@ def __init__(self, filename='OSZICAR'):
           plot()         method, 对数据绘图
           ============  =======================================
         """
-        VasPy.__init__(self, filename)
+        super(self.__class__, self).__init__(filename)
 
         #set regex patterns
         float_regex = r'[\+|-]?\d*\.\d*(?:[e|E][\+|-]?\d+)?'
@@ -69,7 +69,7 @@ def match(self, line):
 
     def load(self):
         "加载文件数据信息"
-        with open(self.filename, 'r') as f:
+        with open(self.filename(), 'r') as f:
             content = ''
             for line in f:
                 eq_tuples = self.match(line)
@@ -156,7 +156,7 @@ def __init__(self, filename='OUTCAR'):
 
     def load(self):
         #locate informations
-        with open(self.filename, 'r') as f:
+        with open(self.filename(), 'r') as f:
             total_forces = []
             tforce_regex = \
                 re.compile(r'FORCES: max atom, RMS\s+(\d+\.\d+)\s+\d+\.\d+\s*')
@@ -180,7 +180,7 @@ def load(self):
             total_forces = np.array(total_forces)
             #atom forces
             atom_forces = []
-            with open(self.filename, 'r') as f:
+            with open(self.filename(), 'r') as f:
                 for i, line in enumerate(f):
                     if i > fbegin+1:
                         if '-'*10 in line:

vaspy/matstudio.py

@@ -4,7 +4,7 @@
 Provide Material Studio markup file class which do operations on these files.
 =============================================================================
 Written by PytLab <shaozhengjiang@gmail.com>, August 2015
-Updated by PytLab <shaozhengjiang@gmail.com>, September 2015
+Updated by PytLab <shaozhengjiang@gmail.com>, May 2016
 ==============================================================
 
 """
@@ -43,12 +43,12 @@ def __init__(self, filename):
           bases          np.array, basis vectors of space, dtype=np.float64
           ============  =======================================================
         """
-        AtomCo.__init__(self, filename)
+        super(self.__class__, self).__init__(filename)
         self.load()
 
     def load(self):
         # get element tree
-        tree = ET.ElementTree(file=self.filename)
+        tree = ET.ElementTree(file=self.filename())
         self.tree = tree
         # MS version info
         root = tree.getroot()