Setting Up a Calculation: HXSettings.json

For version 0.1.4.0, makePol commands will use a set of default parameters, such as the number of conformations and iterations during optimization of polymer structures.

To view these default parameters, input HXSettings -s or HXSettings --show into the powershell prompt.

To change parameters, input HXSettings -w or HXSettings --write to create a HXSettings.json file in the working directory. Usually, the working directory is C:\Users\user_ID.

If the program detects a HXSettings.json file in the working directory, then the default parameters will be replaced with numerical values in HXSettings.json.

For version 0.1.3.4 (and older versions), input mhpSettings -w or mhpSettings --write in the powershell prompt to create a mhpSettings.json file in the working directory. Here are the default numerical values in mhpSettings.json. Additional comments on each parameter are also shown:

 {    "opt_numConfs":5, #The number of conformations that will be generated. As number of monomer units increases, increase value.

"opt_numThreads":0, #The number of threads you would like to use for the optimization and conf generation. 0 means maximum possible.

"opt_maxIters":1500, #The number of iterations used in optimization of each conformation. Increase this if a job fails to optimize.

"drawing_subImgSize_edge":250, #The side length of a subimage when saved. 

"drawing_default":"polymer.png", #The name of an image saved by default (verbosity turned on with no image name specified.)

"MV_gridSpacing":0.2, #Used for molar volume calculation.

"MV_boxMargin" :2.0, #Used for molar volume calculation.

"plot_dataPoint":"o", #Matplotlib argument to change plot point appearance.

"plot_Filename":"Size-dependent-stats.png" #name of plot. Change to the name of experiment. 

}

Construct the command line. See wiki page on Homopolymers for more details.

Run the calculation.

Consider moving the saved files to another folder.

More information is forthcoming.