Log file recomendations for py-mcmd

[bc118]

Log file recommendations:

1. At the beginning of the log file, print the GOMC and NAMD simulation parameters.
2. We don't need to print the energy tolerance calculation every cycle unless it's out of tolerance.
3. Maybe we should write an update every 10 cycles or so? Or make the update (to log file) frequency a user-defined parameter?
4. The estimated time to completion should be printed, as we do with GOMC.

[jpotoff]

Even if we print every step, we can considerably reduce the size of the log file by removing extraneous characters. For example, we could print data like this:
Cycle Number: Pot Eng Error Frac: PASSED/FAILED

Text like this could be printed once at the beginning of the log file. We don't need to print it every cycle. At least in the current form of py-MCMD, I don't envision us changing the chemical potential during a simulation.

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GOMC GCMC simulation is using ChemPot --> Residues and values = {'SPCE': -4210}
GOMC simulation data for simulation number 7 is completed.

[jpotoff]

Additionally, we should create a "debug mode," which would include a lot of the current information printed to the log file, such as start and stop times of the NAMD and GOMC simulation components. During a normal simulation, this information is not needed.

[jpotoff]

We need to create a title header for timing stats data. It is unclear what these data are from just looking at the console output:

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TIME_STATS_DATA: 3 9.541171 0.881118 0.01111 10.433399

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