Source code for CDTK.Tools.Inputfile

#*  **************************************************************************
#*
#*  CDTK, Chemical Dynamics Toolkit
#*  A modular system for chemical dynamics applications and more
#*
#*  Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016
#*  Oriol Vendrell, DESY, <oriol.vendrell@desy.de>
#*
#*  Copyright (C) 2017, 2018, 2019
#*  Ralph Welsch, DESY, <ralph.welsch@desy.de>
#*
#*  Copyright (C) 2020, 2021, 2022, 2023
#*  Ludger Inhester, DESY, ludger.inhester@cfel.de
#*
#*  This file is part of CDTK.
#*
#*  CDTK is free software: you can redistribute it and/or modify
#*  it under the terms of the GNU General Public License as published by
#*  the Free Software Foundation, either version 3 of the License, or
#*  (at your option) any later version.
#*
#*  This program is distributed in the hope that it will be useful,
#*  but WITHOUT ANY WARRANTY; without even the implied warranty of
#*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#*  GNU General Public License for more details.
#*
#*  You should have received a copy of the GNU General Public License
#*  along with this program.  If not, see <http://www.gnu.org/licenses/>.
#*
#*  **************************************************************************

import sys



class Inputfile(object):
    """
    Read and store the contents of an input file
    """

    def __init__(self,fname=None,**args):
        self.filename = fname
        self.sections = {}
        self._readfile()


    def _readfile(self,**args):
        if self.filename is None:
            raise ValueError('Inputfile: no file to read')
        else:
            self._openfile()
            self._read_sections()
        for sect in self._sections:
            name = sect[0]
            if name[0:4] == 'cart' or name[0:4] == 'nmco': # process Cartesian geometry
                process_func = self._process_cart
            else:
                try:
                    process_func = getattr(self,'_process_'+name)
                except:
                    process_func = self._process_default
            self.sections[name] = process_func(sect[1:])


    def _openfile(self,**args):
        try:
            self.fileunit = open(self.filename,'r')
        except:
            sys.stderr.write('\n Inputfile: could not open '  + self.filename)
            sys.exit(1)


    def _read_sections(self):
        self.fileunit.seek(0)
        self._sections = []
        line = self.fileunit.readline()
        while line:
            if line[0] == '#':
                line = self.fileunit.readline()
                continue
            if line.split() == []: # detects empty lines
                line = self.fileunit.readline()
                continue
            if line[0] == '$':
                sec = _cleanstr(line[1:]).lower()
                if sec != 'end':
                    self._sections.append([sec]+self._section_list())
            line = self.fileunit.readline()


    def _section_list(self):
        seclist = []
        line = self.fileunit.readline()
        while line:
            if line[0] == '#':
                line = self.fileunit.readline()
                continue
            if line.split() == []: # detects empty lines
                line = self.fileunit.readline()
                continue
            if line[0] == '$':
                sec = _cleanstr(line[1:]).lower()
                if sec == 'end':
                    return seclist
                else:
                    raise ValueError('$end forgotten at end of section?')
            seclist.append(line)
            line = self.fileunit.readline()
        raise ValueError('$end forgotten at end of section?')


    def _process_default(self,seclist):
        dsection = {}
        for line in seclist:
            ls = line.split('=')
            keyword = ls[0].strip().lower()
            try:
                value = ls[1].split()
            except:
                value = None
            if value:
                vlist = []
                for v in value:
                    vlist.append(v.strip())
                value = vlist
            dsection[keyword] = value
        return dsection


    def _process_cart(self,seclist):
        dsection = {}
        atomlist = []
        coordinates = []
        for line in seclist:
            ls = line.split()
            atomlist.append(ls[0])
            for x in ls[1:]:
                coordinates.append( float(x) )
        dsection['atomlist'] = atomlist
        dsection['coordinates'] = coordinates
        return dsection


    def _process_secname(self,seclist):
        # modify this function to read a specific input section.
        # The section must be called "secname", where secname is a
        # name of your choice.
        # Alternatively one can specialize this class through inheritance.
        dsection = {}
        for line in seclist:
            ls = line.split('=')
            keyword = _cleanstr(ls[0]).lower()
            try:
                value = _cleanstr(ls[1])
            except:
                value = None
            dsection[keyword] = value
        return dsection



def _cleanstr(s):
    """
    remove blanks around 1st word in string
    """
    return s.split()[0]