Compiling the document, the tilde and P lie seperately under the \sum operator, but as the command superimpose would suggest, I would like them to be superimposed. Works just fine when using \textsuperimposetilde{P} as subscript for alphabetical characters.
\documentclass[11pt]{article}
\usepackage{geometry}
\geometry{letterpaper}
\usepackage{graphicx}
\usepackage{amssymb}
\usepackage{epstopdf}
\usepackage{amsmath}
\usepackage{tikz-cd}
\usepackage{tikz}
\usetikzlibrary{matrix,arrows,decorations.pathmorphing}
\newcounter{qcounter}
\usepackage{fontenc}
\usepackage{marvosym}
\usepackage{wrapfig}
\usepackage{harpoon}
\usepackage{textcomp}
\usepackage{MnSymbol}
\usepackage{mathtools}
\usepackage{xfrac}
\usepackage[safe]{tipa}
\newcommand\sit[1]{%
\textsuperimposetilde{#1}}
\begin{document}
\[
\not{\text{S}}_{hkl}\, =\, \sum_{\sit{P}}\, f_{{\sit{P}}_{a}}\, e^{[-i2\pi (hu_{p}+kv_{p}+ lw_{p}]}
\]
\end{document}
