Python Version.write方法代码示例

# 需要导入模块: from version import Version [as 别名]
# 或者: from version.Version import write [as 别名]
class ParamFile(object):
    """
    Hold the data in a PSCF parameter file.

    The constructor reads a PSCF parameter file and stores the values of
    parameters as attributes with names that are the same as the variable
    names in the parameter file. Parameters that are stored in PSCF as
    1D arrays are stored in list parameters of the same name. Parameters
    that are stored in PSCF as matrices are stored as lists of lists. 

    Note that list indices are numbered from 0 (C/python convention), 
    rather than from 1 as in PSCF (Fortran convention), so all indices
    are off by one relative to the values used in the PSCF source code.

    Construction: To construct an object from a param file named 'param':

        > param = ParamFile('param')

    Attributes: After construction, param.kuhn[2] is the statistical 
    segment length of the third monomer type, and param.block_length[0][1] 
    is the length of the 2nd block of the first chain species. 

    An instance of the ParamFile class can be used to edit values of 
    parameters by reading one parameter file, modifying one or more 
    parameters, and then write the object to another file. 
    """

    def __init__(self,filename):
        """
        Read and parse a PSCF parameter file, create an object to hold data.

        The file with specified filename is opened and closed within body 
        of the constructor method

        Argument:
        filename - name of PSCF parameter file (string)
        """
        self.file = open(filename, 'r')
        self._io   = IO()
        file = self.file
        self.N_chain   = 0
        self.N_solvent = 0

        # Dictionary flags indicates which sections are present
        # Keys are flag string values ('MONOMERS' etc.), values are all 1
        self.flags = {}

        # List sections lists section names (flags) in order read
        self.sections = []

        # Read version line
        self.version = Version(self.file)

        # Read input script section
        next = 1
        while next:
            next = self.read_param_section(file)

        self.file.close()
        self.file = None

        # Make sorted list of attribute names
        self.att_names = self.__dict__.keys()
        self.att_names.sort()

    def write(self, file, major=1, minor=0):
        '''
        Write a parameter file, in the format used by PSCF.

        If the "file" argument is a file object, it must be opened
        for writing. If it is a file name string, a file of that
        name will be opened and written to. In either case, the file
        is closed upon return. 

        Argument:
        file - output file object or file name.
        '''
        # If file argument is a string, open a file of that name
        if type(file) == type('thing'):
            temp = open(file,'w')
            file = temp
        self.file = file
        self.version.major = major
        self.version.minor = minor
        self.version.write(file)
        if self.flags.has_key('MONOMERS'):
            file.write("\n%-20s\n" % 'MONOMERS')
            self.output_monomers()
        if self.flags.has_key('CHAINS'):
            file.write("\n%-20s\n" % 'CHAINS')
            self.output_chains()
        if self.flags.has_key('SOLVENTS'):
            file.write("\n%-20s\n" % 'SOLVENTS')
            self.output_solvents()
        if self.flags.has_key('COMPOSITION'):
            file.write("\n%-20s\n" % 'COMPOSITION')
            self.output_composition()
        if self.flags.has_key('INTERACTION'):
            file.write("\n%-20s\n" % 'INTERACTION')
            self.output_interaction()
#.........这里部分代码省略.........

# 需要导入模块: from version import Version [as 别名]
# 或者: from version.Version import write [as 别名]
class OutFile(ParamFile):
    """
    Hold the data in a PSCF output summary file.

    The constructor reads an output file and holds the data in
    attributes with names that are the same as the names of the
    variables in the output file. 

    Class Outfile is derived from ParamFile because the output 
    file format begins with a parameter file section, to which 
    a few output sections are added. 
    """
   
    def __init__(self,filename):
        """
        Read and parse an output file, and create a corresponding object.

        A file named file is opened, read, and closed within the method.

        Argument:
        filename -- name of PSCF output summary file (string)
        """
        self.file = open(filename, 'r')
        self._io = IO()
        file = self.file
        self.N_chain   = 0
        self.N_solvent = 0

        # Dictionary flags indicates which sections are present
        # Keys are flag string values ('MONOMERS' etc.), values are all 1
        self.flags = {}

        # List sections lists section names (flags) in order read
        self.sections = []

        # Read version line
        self.version = Version(self.file)

        # Read input parameter file sections
        next = 1
        while next:
            next = self.read_param_section(file)

        # Read additional output sections
        next = 1
        while next :
            next = self.read_output_section()

        self.file.close()
        self.file = None

        # Make sorted list of attribute names
        self.att_names = self.__dict__.keys()
        self.att_names.sort()

    def write(self, file, major=1, minor=0):
        """
        Write an output file.

        Argument:
        file -- file object or name of file.

        If file is a file object, it must be opened for writing.
        If file is a string, a file of that name is opened. In
        either case, the file is closed upon return.
        """
        # If file argument is a string, open a file of that name
        if type(file) == type('thing'):
            temp = open(file,'w')
            file = temp
        self.file = file
        self.version.major = major
        self.version.minor = minor

        # Parameter file sections
        self.version.write(file)
        if self.flags.has_key('MONOMERS'):
            file.write("\n%-15s\n" % 'MONOMERS')
            self.output_monomers()
        if self.flags.has_key('CHAINS'):
            file.write("\n%-15s\n" % 'CHAINS')
            self.output_chains()
        if self.flags.has_key('SOLVENTS'):
            file.write("\n%-15s\n" % 'SOLVENTS')
            self.output_solvents()
        if self.flags.has_key('COMPOSITION'):
            file.write("\n%-15s\n" % 'COMPOSITION')
            self.output_composition()
        if self.flags.has_key('INTERACTION'):
            file.write("\n%-15s\n" % 'INTERACTION')
            self.output_interaction()
        if self.flags.has_key('UNIT_CELL'):
            file.write("\n%-15s\n" % 'UNIT_CELL')
            self.output_unit_cell()
        if self.flags.has_key('DISCRETIZATION'):
            file.write("\n%-15s\n" % 'DISCRETIZATION')
            self._output_vec( 'int', 'ngrid', self.dim)
            self._output_var( 'real', 'chain_step')
            #self._output_var( 'int', 'extrapolation_order')
        if self.flags.has_key('BASIS'):
#.........这里部分代码省略.........

# 需要导入模块: from version import Version [as 别名]
# 或者: from version.Version import write [as 别名]
class FieldFile(object):
    '''
    Hold data in a PSCF field file. 

    A FieldFile object contains the data in a field file in the PSCF
    symmetry-adapted Fourier expansion format (see web user manual).
    It can be used to represent either omega (chemical potential) or
    rho (volume fraction) fields. a

    The constructor reads a field file, creates a FieldFile object to store
    the data, and stores all of the parameters and field coefficients in 
    attributes of the object.

    Attributes:
    dim            -- [int] number of periodic spatial directions
    crystal_system -- [string] label of Bravais crystal system
    N_cell_param   -- [int] number of unit cell parameters
    cell_param     -- [list] list of real unit cell parameters
    group          -- [string] name of space group
    N_monomer      -- [int] number of monomer types
    N_star         -- [int] number of basis functions (or stars)
    fields         -- [list] list of list of coefficients

    The attribute field[i] is is a list (or array) of coefficients
    for a field associated with monomer type number i. The element
    field[i][j] is the coefficient of basis function j in the field
    associated with monomer type i. 
    '''

    # "Public" methods

    def __init__(self,filename):
        '''
        Read a PSCF symmetry-adapted field file, and create a new object.

        Argument:
        filename -- name of file

        The file named filename is opened and closed within this function.
        '''
        self.file = open(filename, 'r')
	self._io   = IO()
	file = self.file

        # Read version line
	self.version = Version(self.file)

        self._input_unit_cell()
        self.group_name = self._input_var('char')
        self.N_monomer = self._input_var('int')
        self.N_star = self._input_var('int')

        # Define empty lists
        self.fields = []
        self.waves = []
        self.counts = []

        for i in range(self.N_star):

            data = file.readline().split()
            if len(data) != self.N_monomer + self.dim + 1:
                raise IoException('Incorrect number of elements in field line')
            j = 0

            # Read field coefficients
            self.fields.append([])
            for k in range(self.N_monomer):
                value = float(data[j])
                self.fields[i].append(value)
                j += 1

            # Read field coefficients
            self.waves.append([])
            for k in range(self.dim):
                value = int(data[j])
                self.waves[i].append(value)
                j += 1

            # Read star_count
            self.counts.append(int(data[j]))

        self.file.close()
	self.file = None

    def write(self, file, major=1, minor=0):
        '''
        PURPOSE
           Write field to file in PSCF symmetry-adapted format.
        ARGUMENTS
           file  - file object or file name string
           major - major file format version number
           minor - minor file format version number
        COMMENT
           if file is a field object, it must be open for writing
        '''

        # If file argument is a string, open a file of that name
        if type(file) == type('thing'):
            temp = open(file,'w')
            file = temp
#.........这里部分代码省略.........