Add some assertions that are helpful for trouble shooting. #22
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1. add check.py in utils: parse the input cv files with PLUMED before running the workflow. 2. add assertions in submit.py and run_select.py to ensure the trust_lvl_1 and std_threshold to be suitable.
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1. Checking input CV files
If there got a problem in the input CV files, these commits allow rid-kit to transmit the raw error messages produced by PLUMED to users for debug.
Rid-kit provides little corresponding information in the workflow log file and only records a "CUDA error #1" in the gmx log. The check.py called by the newly added assertion parses the CV files with PLUMED in advance to ensure their validity and facilitating trouble-shooting.
2. Assertions about trust_lvl_1 and std_threshold
Too large trust_lvl_1 and too small std_threshold may emit all the data points from the training set and interrupt the workflow. When this happens, these assertions allow rid-kit to inform users to adjust the parameters.