In the Heston (1993) model, the stock price is defined by the SDE system
\begin{align*}
\mathrm{d}S_t&=(r-q) S_t \mathrm{d}t+\sqrt{v_t} S_t \mathrm{d}W_{1,t}, \\
\mathrm{d}v_t&=\kappa(\theta-v_t) \mathrm{d}t+\xi \sqrt{v_t} \mathrm{d}W_{2,t},
\end{align*}
where $\mathbb{E}^\mathbb{Q}[\mathrm{d}W_{1,t}\mathrm{d}W_{2,t}]=\rho\mathrm{d}t$. So, I assume all parameter are given under the risk-neutral measure, The characteristic function of the log stock price $\ln(S_t)$ under the risk-neutral measure $\mathbb{Q}$ is given by
\begin{align*}
\varphi_t^\text{Heston}(u) &= \exp\big( \ln\big(S_0e^{(r-q)t}\big)iu + C_t(u) + D_t(u)\cdot v_0 \big),
\end{align*}
where
\begin{align*}
C_t(u) &= \frac{\kappa\theta}{\xi^2} \left(\big( h(u)+d(u)\big) t - 2\ln\left(\frac{1-g(u)e^{d(u)t}}{1-g(u)}\right) \right),\\
D_t(u) &= \frac{h(u)+d(u)}{\xi^2}\cdot\frac{1-e^{d(u)t}}{1-g(u)e^{d(u)t}}, \\
g(u) &= \frac{h(u) + d(u)}{h(u)-d(u)}, \\
h(u) &= \kappa - \rho\xi \cdot i u, \\
d(u) &= \sqrt{h(u)^2+\xi^2\big(i u + u^2\big)}.
\end{align*}
There are some numerical issues about the Heston chararcteristic function. Just google ``little Heston trap''. The author of the paper in your question, Roger Lord, alongside Kahl and Jäckel, did some research on this. The simplest case seems to be the adjustment from Albrecher et al. (2007) and Gatheral (2006).