Fix for implementing the high-spin NAMD in step2&3

[Xuyanma05]

Separate variable names are provided for calculating the alpha channel and beta channel, respectively. Fixed the bug that cp2k reads log file with misplaced energy.

[alexvakimov]

@MohammadShakiba , please review to ensure correctness; when do - let me know, so I could merge

[alexvakimov]

also, @Xuyanma05 please prepare a minimalistic test case for the new capability - with all the needed files (again, not too large - just sufficient to run small number of steps), including python and data files.