Handle single MD trajectory from multiple job submission

[robinzyb]

Description

Submit MD simulation with cp2k will write -pos-, -frc-, -1.cell, and output files for storing the positions, forces, cells and output(stresses) information. but Most HPCs have time limits for single submission. This causes the MD run cannot be finished in one submission and restart will be required. When restarted or submited again, the MD run will append positions, forces, and cell information to corresponding files. However, this is not the case for the output file.

In general, there are two ways to handle the output. The first one is appending new output to old one. The second one is write into new output file. Usually, I will take the second method with job ID as file suffix, such as output_1, output_2.

For the time beining, cp2kdata cannot handle both cases.

TODO

• prepare one test case
• fix this problem in cp2kdata code.