reverts previous commit & append adds new attribute to single xdmf file!
This commit is contained in:
Tiago Pestana
parent
abd7b0c4f5
commit
fcadbd2e5d
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@ -417,11 +417,6 @@ class ibmppp:
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ioflag = 'a'
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else:
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ioflag = 'w'
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# get information about origin and grid spacing
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delta = [self.__dx[key], self.__dx[key], self.__dx[key]]
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origin = [self.grid[key][0][ib-1]-nghx*dx, \
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self.grid[key][1][jb-1]-nghy*dx, \
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self.grid[key][2][kb-1]-nghz*dx]
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# Open the file and write data, then close it because we are done
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fid = h5py.File(file_chunk,ioflag)
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if not append:
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@ -432,8 +427,6 @@ class ibmppp:
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fid.create_dataset('nxproc',data=self.__nxp)
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fid.create_dataset('nyproc',data=self.__nyp)
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fid.create_dataset('nzproc',data=self.__nzp)
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fid.create_dataset('origin',data=origin)
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fid.create_dataset('delta',data=delta)
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gid = fid.create_group('/'+key)
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gid.create_dataset('ib',data=self.__localChunkBounds[key][0])
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gid.create_dataset('ie',data=self.__localChunkBounds[key][1])
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@ -455,16 +448,18 @@ class ibmppp:
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did.attrs['F_CONTIGUOUS'] = 1
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did.attrs['DIM'] = (self.__localChunkSize[key][0]+2*nghx,self.__localChunkSize[key][1]+2*nghy,self.__localChunkSize[key][2]+2*nghz)
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fid.close()
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# Create an XDMF file for the field
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# Create an XDMF file for the field --> if append write only attribute
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if xdmf and self.__rank==0:
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# Construct XDMF filename
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file_xdmf = filename+'_'+key+'.xdmf'
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# Open file and write header
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fid = open(file_xdmf,'w')
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fid.write('<?xml version="1.0"?>\n')
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fid.write('<Xdmf Version="2.0">\n')
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fid.write(' <Domain>\n')
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fid.write(' <Grid Name="{}" GridType="Collection" CollectionType="Spatial">\n'.format(key))
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# file_xdmf = filename+'_'+key+'.xdmf'
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file_xdmf = filename+'.xdmf'
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# Open file and write header; or skip if appending
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if not append:
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fid = open(file_xdmf,'w')
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fid.write('<?xml version="1.0"?>\n')
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fid.write('<Xdmf Version="2.0">\n')
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fid.write(' <Domain>\n')
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fid.write(' <Grid Name="{}" GridType="Collection" CollectionType="Spatial">\n'.format(key))
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#fid.write(' <Time Value="%.2f" />\n',params.general.simtime)
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# Get ghost cell setup
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if keepAllGhost:
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@ -491,22 +486,43 @@ class ibmppp:
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nxl = ie-ib+1+2*nghx
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nyl = je-jb+1+2*nghy
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nzl = ke-kb+1+2*nghz
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# Write XDMF for this processor
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fid.write(' <Grid Name="rank {:5d} position {:3d},{:3d},{:3d}">\n'.format(iprank,iproc,jproc,kproc))
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fid.write(' <Topology TopologyType="3DCORECTMesh" NumberOfElements="{:d} {:d} {:d}"/>\n'.format(nzl,nyl,nxl))
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fid.write(' <Geometry Origin="" Type="ORIGIN_DXDYDZ">\n')
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fid.write(' <DataItem DataType="Float" Dimensions="3" Format="XML" Precision="8"> {:12f} {:12f} {:12f}</DataItem>\n'.format(z0,y0,x0))
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fid.write(' <DataItem DataType="Float" Dimensions="3" Format="XML" Precision="8"> {:12f} {:12f} {:12f}</DataItem>\n'.format(dx,dx,dx))
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fid.write(' </Geometry>\n')
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fid.write(' <Attribute Name="{}" Dimensions="{:d} {:d} {:d}">\n'.format(key,nzl,nyl,nxl))
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fid.write(' <DataItem Format="HDF5" DataType="Float" Dimensions="{:d} {:d} {:d}">\n'.format(nzl,nyl,nxl))
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fid.write(' {}:/{}/data </DataItem>\n'.format(subfile,key))
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fid.write(' </Attribute>\n')
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fid.write(' </Grid>\n')
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# Write footer and close file
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fid.write(' </Grid>\n')
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fid.write(' </Domain>\n')
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fid.write('</Xdmf> \n')
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if append:
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#find where the Geometry ends... and add new attribute
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fid = open(file_xdmf,'r')
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lines = fid.readlines()
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fid.close()
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lnb=0
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for i in lines:
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logical = "</Geometry>" in i
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if logical:
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newAttrb = ' <Attribute Name="{}" Dimensions="{:d} {:d} {:d}">\n'.format(key,nzl,nyl,nxl)
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newAttrb += ' <DataItem Format="HDF5" DataType="Float" Dimensions="{:d} {:d} {:d}">\n'.format(nzl,nyl,nxl)
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newAttrb += ' {}:/{}/data </DataItem>\n'.format(subfile,key)
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newAttrb += ' </Attribute>\n'
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break
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lnb+=1
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fid = open(file_xdmf,'w')
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fid.writelines(lines[0:lnb+1])
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fid.write(newAttrb)
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fid.writelines(lines[lnb+1:])
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fid.close()
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else:
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# Write XDMF for this processor
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fid.write(' <Grid Name="rank {:5d} position {:3d},{:3d},{:3d}">\n'.format(iprank,iproc,jproc,kproc))
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fid.write(' <Topology TopologyType="3DCORECTMesh" NumberOfElements="{:d} {:d} {:d}"/>\n'.format(nzl,nyl,nxl))
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fid.write(' <Geometry Origin="" Type="ORIGIN_DXDYDZ">\n')
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fid.write(' <DataItem DataType="Float" Dimensions="3" Format="XML" Precision="8"> {:12f} {:12f} {:12f}</DataItem>\n'.format(z0,y0,x0))
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fid.write(' <DataItem DataType="Float" Dimensions="3" Format="XML" Precision="8"> {:12f} {:12f} {:12f}</DataItem>\n'.format(dx,dx,dx))
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fid.write(' </Geometry>\n')
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fid.write(' <Attribute Name="{}" Dimensions="{:d} {:d} {:d}">\n'.format(key,nzl,nyl,nxl))
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fid.write(' <DataItem Format="HDF5" DataType="Float" Dimensions="{:d} {:d} {:d}">\n'.format(nzl,nyl,nxl))
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fid.write(' {}:/{}/data </DataItem>\n'.format(subfile,key))
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fid.write(' </Attribute>\n')
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fid.write(' </Grid>\n')
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# Write footer and close file
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fid.write(' </Grid>\n')
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fid.write(' </Domain>\n')
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fid.write('</Xdmf> \n')
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fid.close()
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def saveFieldOriginal(self,filename,key,append=False,xdmf=False):
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