求助Pt55-C6F12模型中氢迁移能垒模型问题

Fluorophore

各位老师前辈们好，我在实验中发现FC涂层加快了Pt催化的WO3的气相氢注入过程。因此试图计算氢吸附至Pt表面/亚表面过程的能量变化，希望能发现氢扩散能垒的减小。
由于本人没有计算经验，组内以结构材料为研究重点，因此希望老师们指点迷津！万分感谢~
一、计算的目标：
H2, Pt55, H*surf@Pt55, H@Oh subsurf. Pt55(亚表面间隙点位), H*surf@Pt55-C6F12, H@Oh subsurf. Pt55-C6F12的总能量
二、计算参考的文献：https://doi.org/10.1038/s41563-019-0325-4 （Pd55的相同体系，结果和模型图见附件）
计算方法：All the modelled structures were optimized within the DFT framework. The cluster models were optimized using the PBE functional while van der Waals contributions were included for the polymer and polymer–H2 systems by using the vdW-CX functional. Geometry optimizations were performed using the Vienna ab initio simulation package, VASP. Projector augmented waves (PAW) were used, with a plane-wave kinetic energy cutoff of 500 eV. To avoid artificial interaction due to the periodic boundary conditions, a 30 × 30 × 31 Å3 supercell was used, ensuring at least 16 Å of vacuum between  two successive images. Γ-centered calculations were performed with a Gaussian smearing, σ, of 0.02 eV, with the energies extrapolated to σ = 0.00 eV. The atom positions were optimized until meeting the criterion of the residual forces on any direction being less than 0.02 eV Å−1.
三、计算遇到的问题：

1. 想确认下文献中的计算是不涉及过渡态NEB计算的吗？仅是得到有/无聚合物分子的各三个状态的能量？
2. 请问设定SIGMA=0.02, EDIFF=1E-06, EDIFFG=-2E-02后力很难收敛应该放宽条件吗？怎样的精度是合适的呢？
3. 结构优化达到什么精度后进行ENCUT收敛测试呢？收敛测试需要测到多少eV呢？
3. 计算中提示“The distance between some ions is very small. Please check the nearest-neighbor list in the OUTCAR file.” 中止后观察到CONTCAR结果Pd, F原子跑远了（如下图），这种情况应怎样调整MS中的模型吗？（模型是用MS的build-nanostructure-nanocluster得到纳米团簇在添加C6F12，加两个Pd-C键后clean所得，未在MS中进行结构优化）
抑或者，计算过程中是否应该以及如何选择固定原子呢？
4. 程序提示超大晶胞，LREAL改为AUTO，改动后是否需要各个模型都一致？
5. INCAR中ENCUT，SIGMA，EDIFF，EDIFFG值如果有变化了，还能使用已有CHGCAR，WAVECAR等接着算吗？
6. （使用默认PBE泛函）添加vdW-DF-CX非局域范德瓦尔斯密度泛函后，VASP的OUTCAR提示“You enforced a specific xc type in the INCAR file but a different type was found in the POTCAR file.” 该提示是否可以忽略？