Merge branch 'parse-CRLF-YAML' into 'development'
Stop if YAML contains CRLF line endings See merge request damask/DAMASK!333
This commit is contained in:
Franz Roters
commit
e96352b0ea
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit d90babadfb0a33afa1b793044cc4efd4d7430731
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Subproject commit 5d27d879abaeb1542e3f9f3065172be740af2899
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@ -223,25 +223,46 @@ class Colormap(mpl.colors.ListedColormap):
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return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
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def _get_file_handle(self,fname,extension):
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"""
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Provide file handle.
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Parameters
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----------
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fname : file, str, pathlib.Path, or None
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Filename or filehandle, will be name of the colormap+extension if None.
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extension: str
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Extension of the filename.
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Returns
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-------
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f
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File handle
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"""
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if fname is None:
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fhandle = open(self.name.replace(' ','_')+'.'+extension,'w',newline='\n')
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else:
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try:
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fhandle = open(fname,'w',newline='\n')
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except TypeError:
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fhandle = fname
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return fhandle
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def save_paraview(self,fname=None):
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"""
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Save as JSON file for use in Paraview.
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Parameters
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----------
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fname : file, str, or pathlib.Path, optional.
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fname : file, str, or pathlib.Path, optional
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Filename to store results. If not given, the filename will
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consist of the name of the colormap and extension '.json'.
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"""
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if fname is None:
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fhandle = None
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else:
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try:
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fhandle = open(fname,'w')
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except TypeError:
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fhandle = fname
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colors = []
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for i,c in enumerate(np.round(self.colors,6).tolist()):
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colors+=[i]+c
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@ -254,8 +275,7 @@ class Colormap(mpl.colors.ListedColormap):
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'RGBPoints':colors
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}]
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with open(self.name.replace(' ','_')+'.json', 'w') if fhandle is None else fhandle as f:
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json.dump(out, f,indent=4)
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json.dump(out,self._get_file_handle(fname,'json'),indent=4)
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def save_ASCII(self,fname=None):
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@ -264,24 +284,14 @@ class Colormap(mpl.colors.ListedColormap):
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Parameters
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----------
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fname : file, str, or pathlib.Path, optional.
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fname : file, str, or pathlib.Path, optional
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Filename to store results. If not given, the filename will
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consist of the name of the colormap and extension '.txt'.
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"""
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if fname is None:
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fhandle = None
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else:
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try:
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fhandle = open(fname,'w')
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except TypeError:
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fhandle = fname
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labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
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t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
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with open(self.name.replace(' ','_')+'.txt', 'w') if fhandle is None else fhandle as f:
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t.save(f)
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t.save(self._get_file_handle(fname,'txt'))
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def save_GOM(self,fname=None):
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@ -290,26 +300,19 @@ class Colormap(mpl.colors.ListedColormap):
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Parameters
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----------
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fname : file, str, or pathlib.Path, optional.
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fname : file, str, or pathlib.Path, optional
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Filename to store results. If not given, the filename will
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consist of the name of the colormap and extension '.legend'.
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"""
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if fname is None:
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fhandle = None
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else:
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try:
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fhandle = open(fname,'w')
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except TypeError:
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fhandle = fname
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# ToDo: test in GOM
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GOM_str = '1 1 {name} 9 {name} '.format(name=self.name.replace(" ","_")) \
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+ '0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 ' \
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+ f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(self.colors)}' \
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+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
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+ '\n'
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with open(self.name.replace(' ','_')+'.legend', 'w') if fhandle is None else fhandle as f:
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f.write(GOM_str)
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self._get_file_handle(fname,'legend').write(GOM_str)
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def save_gmsh(self,fname=None):
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@ -318,24 +321,16 @@ class Colormap(mpl.colors.ListedColormap):
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Parameters
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----------
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fname : file, str, or pathlib.Path, optional.
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fname : file, str, or pathlib.Path, optional
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Filename to store results. If not given, the filename will
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consist of the name of the colormap and extension '.msh'.
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"""
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if fname is None:
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fhandle = None
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else:
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try:
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fhandle = open(fname,'w')
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except TypeError:
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fhandle = fname
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# ToDo: test in gmsh
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gmsh_str = 'View.ColorTable = {\n' \
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+'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
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+'\n}\n'
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with open(self.name.replace(' ','_')+'.msh', 'w') if fhandle is None else fhandle as f:
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f.write(gmsh_str)
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self._get_file_handle(fname,'msh').write(gmsh_str)
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@staticmethod
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@ -75,7 +75,7 @@ class Config(dict):
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"""
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try:
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fhandle = open(fname,'w')
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fhandle = open(fname,'w',newline='\n')
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except TypeError:
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fhandle = fname
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@ -1287,7 +1287,7 @@ class Result:
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np.prod(shape))}
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data_items[-1].text=f'{os.path.split(self.fname)[1]}:{name}'
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with open(self.fname.with_suffix('.xdmf').name,'w') as f:
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with open(self.fname.with_suffix('.xdmf').name,'w',newline='\n') as f:
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f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
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@ -26,7 +26,7 @@ class Table:
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comments_ = [comments] if isinstance(comments,str) else comments
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self.comments = [] if comments_ is None else [c for c in comments_]
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self.data = pd.DataFrame(data=data)
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self.shapes = { k:(v,) if isinstance(v,(np.int,int)) else v for k,v in shapes.items() }
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self.shapes = { k:(v,) if isinstance(v,(np.int64,np.int32,int)) else v for k,v in shapes.items() }
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self._label_uniform()
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def __repr__(self):
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@ -380,7 +380,7 @@ class Table:
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[f'# {comment}' for comment in self.comments]
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try:
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fhandle = open(fname,'w')
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fhandle = open(fname,'w',newline='\n')
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except TypeError:
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fhandle = fname
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@ -66,7 +66,7 @@ class Marc:
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if logfile is not None:
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try:
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f = open(logfile,'w+')
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f = open(logfile,'w+',newline='\n')
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except TypeError:
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f = logfile
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else:
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27
src/IO.f90
27
src/IO.f90
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@ -65,8 +65,8 @@ end subroutine IO_init
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function IO_readlines(fileName) result(fileContent)
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character(len=*), intent(in) :: fileName
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character(len=pStringLen), dimension(:), allocatable :: fileContent !< file content, separated per lines
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character(len=pStringLen) :: line
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character(len=:), allocatable :: rawData
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integer :: &
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@ -75,6 +75,7 @@ function IO_readlines(fileName) result(fileContent)
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l
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logical :: warned
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rawData = IO_read(fileName)
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!--------------------------------------------------------------------------------------------------
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@ -112,16 +113,21 @@ end function IO_readlines
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!--------------------------------------------------------------------------------------------------
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!> @brief Read whole file.
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!> @details ensures that the string ends with a new line (expected UNIX behavior)
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!> @details ensures that the string ends with a new line (expected UNIX behavior) and rejects
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! windows (CRLF) line endings
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!--------------------------------------------------------------------------------------------------
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function IO_read(fileName) result(fileContent)
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character(len=*), intent(in) :: fileName
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character(len=:), allocatable :: fileContent
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integer :: &
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fileLength, &
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fileUnit, &
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myStat
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myStat, &
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firstEOL
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character, parameter :: CR = achar(13)
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inquire(file = fileName, size=fileLength)
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open(newunit=fileUnit, file=fileName, access='stream',&
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@ -137,8 +143,12 @@ function IO_read(fileName) result(fileContent)
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if(myStat /= 0) call IO_error(102,ext_msg=trim(fileName))
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close(fileUnit)
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if(fileContent(fileLength:fileLength) /= IO_EOL) fileContent = fileContent//IO_EOL ! ensure EOL@EOF
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firstEOL = index(fileContent,IO_EOL)
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if(scan(fileContent(firstEOL:firstEOL),CR) /= 0) call IO_error(115)
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end function IO_read
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@ -151,6 +161,7 @@ logical pure function IO_isBlank(string)
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integer :: posNonBlank
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posNonBlank = verify(string,IO_WHITESPACE)
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IO_isBlank = posNonBlank == 0 .or. posNonBlank == scan(string,IO_COMMENT)
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@ -170,6 +181,7 @@ pure function IO_stringPos(string)
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integer :: left, right
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allocate(IO_stringPos(1), source=0)
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right = 0
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@ -249,6 +261,7 @@ pure function IO_lc(string)
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integer :: i,n
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do i=1,len(string)
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n = index(UPPER,string(i:i))
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if(n/=0) then
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@ -271,6 +284,7 @@ function IO_rmComment(line)
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character(len=:), allocatable :: IO_rmComment
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integer :: split
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split = index(line,IO_COMMENT)
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if (split == 0) then
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@ -292,6 +306,7 @@ integer function IO_stringAsInt(string)
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integer :: readStatus
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character(len=*), parameter :: VALIDCHARS = '0123456789+- '
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valid: if (verify(string,VALIDCHARS) == 0) then
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read(string,*,iostat=readStatus) IO_stringAsInt
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if (readStatus /= 0) call IO_error(111,ext_msg=string)
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@ -313,6 +328,7 @@ real(pReal) function IO_stringAsFloat(string)
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integer :: readStatus
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character(len=*), parameter :: VALIDCHARS = '0123456789eE.+- '
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valid: if (verify(string,VALIDCHARS) == 0) then
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read(string,*,iostat=readStatus) IO_stringAsFloat
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if (readStatus /= 0) call IO_error(112,ext_msg=string)
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@ -331,6 +347,7 @@ logical function IO_stringAsBool(string)
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character(len=*), intent(in) :: string !< string for conversion to int value
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if (trim(adjustl(string)) == 'True' .or. trim(adjustl(string)) == 'true') then
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IO_stringAsBool = .true.
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elseif (trim(adjustl(string)) == 'False' .or. trim(adjustl(string)) == 'false') then
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@ -356,6 +373,7 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
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character(len=:), allocatable :: msg
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character(len=pStringLen) :: formatString
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select case (error_ID)
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!--------------------------------------------------------------------------------------------------
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@ -382,6 +400,9 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
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msg = 'invalid character for logical:'
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case (114)
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msg = 'cannot decode base64 string:'
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case (115)
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msg = 'found CR. Windows file endings (CRLF) are not supported.'
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!--------------------------------------------------------------------------------------------------
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! lattice error messages
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