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Remane PDF files not to contain "$"
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tools/plot-tools/examples/Si/PBAND1_FIG/atom_index-1/atom_index-1-$p_x$.pdf renamed to tools/plot-tools/examples/Si/PBAND1_FIG/atom_index-1/atom_index-1-p_x.pdf

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tools/plot-tools/examples/Si/PBAND1_FIG/atom_index-1/atom_index-1-$p_y$.pdf renamed to tools/plot-tools/examples/Si/PBAND1_FIG/atom_index-1/atom_index-1-p_y.pdf

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