Merge dev to master.

Author: PytLab

.gitattributes

@@ -1,3 +1,3 @@
 # Enforces LF line endings
-eol=crlf
+* text eol=crlf
 

.gitignore

@@ -65,4 +65,8 @@ MANIFEST
 vaspy/*CAR
 vaspy/*.xsd
 OUTCAR
-vaspy/DOS/*
+vaspy/DOS/*
+
+# Vim temp files
+*.swp
+*.swo

scripts/change_incar_parameters.py

@@ -0,0 +1,47 @@
+'''
+Modify recursively parameters in all INCAR file.
+'''
+
+import argparse
+import commands
+import logging
+
+
+from vaspy.incar import InCar
+
+SHELL_COMMAND = "find ./ -name 'INCAR'"
+
+if "__main__" == __name__:
+
+    # Check command validity.
+    status, output = commands.getstatusoutput(SHELL_COMMAND)
+    if status:
+        raise SystemExit("Invalid shell commands - '{}'".format(SHELL_COMMAND))
+
+    # Get InCar objects.
+    incar_paths = (incar_path.strip() for incar_path in output.split('\n'))
+    incars = [InCar(incar_path) for incar_path in incar_paths]
+
+    # Get all possible arguments.
+    set_list = [set(incar.pnames()) for incar in incars]
+    possible_args = set.intersection(*set_list)
+
+    # Set arguments for this script.
+    parser = argparse.ArgumentParser()
+    for arg in possible_args:
+        arg_str = "--{}".format(arg)
+        parser.add_argument(arg_str, help="set {} INCAR parameter".format(arg))
+    args_space = parser.parse_args()
+
+    # Change parameters for all incars.
+    for pname, value in args_space.__dict__.iteritems():
+        if value is None:
+            continue
+
+        for incar in incars:
+            logging.info("{} --> {} in {}.".format(pname, value, incar.filename()))
+            incar.set(pname, value)
+            incar.tofile()
+
+    logging.info("{} INCAR files ... ok.".format(len(incars)))
+

scripts/create_xsd.py

@@ -4,51 +4,60 @@
 import sys
 import re
 import commands
+import argparse
 
-import vaspy
+from vaspy import atomco, matstudio
 
-if len(sys.argv) > 1:
-    # extract certain step data to .xyz file
-    step = sys.argv[1]
-    step_regex = re.compile(r'^STEP\s+=\s+' + step + r'$')
-    with open('OUT.ANI', 'r') as f:
-        natom = int(f.readline().strip())
-        # match step
-        content = ''
-        count = 0
-        line = f.readline()
-        while line:
-            if step_regex.match(line):
-                # get data content
-                for i in xrange(natom):
-                    content += f.readline()
-                break
+if "__main__" == __name__:
+
+    # Set argument parser.
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-s", "--step",
+                        help="step number on which the data is extracted.")
+    args = parser.parse_args()
+
+    if args.step:
+        # extract certain step data to .xyz file
+        step = args.step
+        step_regex = re.compile(r'^STEP\s+=\s+' + step + r'$')
+        with open('OUT.ANI', 'r') as f:
+            natom = int(f.readline().strip())
+            # match step
+            content = ''
+            count = 0
             line = f.readline()
-        if not content:
-            print 'Step: %s is out of range.' % step
-            sys.exit(1)
-    # write to .xyz file
-    with open('ts.xyz', 'w') as f:
-        head = '%12d\nSTEP = %8s\n' % (natom, step)
-        content = head + content
-        f.write(content)
+            while line:
+                if step_regex.match(line):
+                    # get data content
+                    for i in xrange(natom):
+                        content += f.readline()
+                    break
+                line = f.readline()
+            if not content:
+                print 'Step: %s is out of range.' % step
+                sys.exit(1)
+        # write to .xyz file
+        with open('ts.xyz', 'w') as f:
+            head = '%12d\nSTEP = %8s\n' % (natom, step)
+            content = head + content
+            f.write(content)
 
-    # coordinate transformation
-    xyz = vaspy.atomco.XyzFile('ts.xyz')
-    poscar = vaspy.atomco.PosCar()
-    direct_coordinates = xyz.coordinate_transform(poscar.bases)
-    suffix = '-' + step + '.xsd'
-else:  # the last step data
-    contcar = vaspy.atomco.ContCar()
-    direct_coordinates = contcar.data
-    suffix = '-y.xsd'
+        # coordinate transformation
+        xyz = atomco.XyzFile('ts.xyz')
+        poscar = atomco.PosCar()
+        direct_coordinates = xyz.coordinate_transform(poscar.bases)
+        suffix = '-' + step + '.xsd'
+    else:  # the last step data
+        contcar = atomco.ContCar()
+        direct_coordinates = contcar.data
+        suffix = '-y.xsd'
 
 # create .xsd file
 status, output = commands.getstatusoutput('ls *.xsd | head -1')
 if not output.endswith('.xsd'):
     print "No .xsd file in current directory."
     sys.exit(1)
-xsd = vaspy.matstudio.XsdFile(filename=output)
+xsd = matstudio.XsdFile(filename=output)
 xsd.data = direct_coordinates
 
 jobname = output.split('.')[0]

vaspy/__init__.py

@@ -1,11 +1,15 @@
-__version__ = '0.4.3'
-__all__ = ['atomco', 'electro', 'iter', 'matstudio', 'plotter']
+__version__ = '0.5.3'
+__all__ = ['atomco', 'electro', 'iter', 'matstudio', 'plotter', 'incar']
 
 
 class VasPy(object):
     def __init__(self, filename):
         "Base class to be inherited by all classes in VASPy."
-        self.filename = filename
+        self.__filename = filename
+
+    def filename(self):
+        " Query function for bounded filename."
+        return self.__filename
 
 
 class CarfileValueError(Exception):

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
 
 ==============================================================
 
@@ -24,7 +24,7 @@ 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__()
@@ -38,7 +38,7 @@ def __getattribute__(self, attr):
         elif attr == 'tf_dict':
             return self.get_tf_dict(self.tf)
         else:
-            return object.__getattribute__(self, attr)
+            return VasPy.__getattribute__(self, attr)
 
     def verify(self):
         if len(self.data) != self.ntot:
@@ -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."
@@ -74,32 +87,46 @@ def rdata(line):
             return pnames, datas
 
     def set(self, pname, data):
+        """
+        Set a named parameter of InCar object.
+
+        Example:
+        --------
+        >>> incar_obj.set("ISIF", 2)
+        """
         if not hasattr(self, pname):
             raise ValueError('%s is not in INCAR, ' +
                              'Use add() instead.' % pname)
         setattr(self, pname, str(data))
         return
 
     def add(self, pname, data):
+        """
+        Add a new parameter name to InCar object.
+
+        Example:
+        --------
+        >>> incar_obj.add("ISIF", 2)
+        """
         data = str(data)
         if hasattr(self, pname):
             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