Add JSON input file

[ericchansen]

Many parameters i.e. input settings are hard coded in constants.py.

• Type of Gaussian energy to use (up for debate---might not be important enough to move).

  q2mm/q2mm/constants.py

  Lines 7 to 8 in 32307ab

  	#GAUSSIAN_ENERGIES = ['HF', 'ZeroPoint']
  	GAUSSIAN_ENERGIES = ['HF']

• Log settings (also up for debate).

  q2mm/q2mm/constants.py

  Lines 14 to 62 in 32307ab

  	LOG_SETTINGS = {
  	'version': 1,
  	'disable_existing_loggers': False,
  	'formatters': {
  	'bare': {'format': '%(message)s'},
  	'basic': {'format': '%(name)s %(message)s'},
  	'simple': {'format': '%(asctime)s:%(name)s:%(levelname)s %(message)s'}
  	},
  	'handlers': {
  	'console': {
  	'class': 'logging.StreamHandler', 'formatter': 'bare',
  	'level': 'NOTSET'},
  	# 'class': 'logging.StreamHandler', 'formatter': 'basic',
  	# 'level': 'NOTSET'},
  	'root_file_handler': {
  	'class': 'logging.FileHandler', 'filename': 'root.log',
  	'formatter': 'bare', 'level': 'NOTSET'}
  	# 'class': 'logging.FileHandler', 'filename': 'root.log',
  	# 'formatter': 'basic', 'level': 'NOTSET'}
  	},
  	'loggers': {'__main__': {'level': 5, 'propagate': True},
  	'calculate': {'level': 20, 'propagate': True},
  	'compare': {'level': 10, 'propagate': True},
  	'constants': {'level': 20, 'propagate': True},
  	'datatypes': {'level': 20,' propagate': True},
  	'filetypes': {'level': 20, 'propagate': True},
  	'gradient': {'level': 20, 'propagate': True},
  	'loop': {'level': 5, 'propagate': True},
  	'opt': {'level': 5, 'propagate': True},
  	'parameters': {'level': 20, 'propagate': True},
  	'simplex': {'level': 5, 'propagate': True}
  	},
  	# 'loggers': {'__main__': {'level': 'NOTSET', 'propagate': True},
  	# 'calculate': {'level': 'NOTSET', 'propagate': True},
  	# 'compare': {'level': 'NOTSET', 'propagate': True},
  	# 'constants': {'level': 'NOTSET', 'propagate': True},
  	# 'datatypes': {'level': 'NOTSET',' propagate': True},
  	# 'filetypes': {'level': 'NOTSET', 'propagate': True},
  	# 'gradient': {'level': 'NOTSET', 'propagate': True},
  	# 'loop': {'level': 'NOTSET', 'propagate': True},
  	# 'opt': {'level': 'NOTSET', 'propagate': True},
  	# 'parameters': {'level': 'NOTSET', 'propagate': True},
  	# 'simplex': {'level': 'NOTSET', 'propagate': True}
  	# },
  	'root': {
  	'level': 'NOTSET',
  	'propagate': True,
  	'handlers': ['console', 'root_file_handler']}
  	}

• Step sizes.

  q2mm/q2mm/constants.py

  Lines 77 to 90 in 32307ab

  	STEPS = {'ae': 1.0,
  	'af': 0.1,
  	'be': 0.02,
  	'bf': 0.1,
  	'df': 0.1,
  	'imp1': 0.2,
  	'imp2': 0.2,
  	'op_b': 0.2,
  	'sb': 0.2,
  	'q': 0.1,
  	'q_p': 0.05,
  	'vdwr': 0.1,
  	'vdwfc': 0.02
  	}

• Data weights.

  q2mm/q2mm/constants.py

  Lines 93 to 115 in 32307ab

  	WEIGHTS = {'a': 2.00,
  	'b': 100.00,
  	't': 1.00,
  	'h': 0.031,
  	'h12': 0.031,
  	'h13': 0.031,
  	'h14': 0.31,
  	'eig_i': 0.00, # Weight of 1st eigenvalue.
  	'eig_d_low': 0.10, # Weight of low mode diagonal elements
  	'eig_d_high': 0.10, # Weight of high mode diagonal elemetns
  	'eig_o': 0.05, # Weight of off diagonals in eigenmatrix.
  	'e': 20.00,
  	'e1': 20.00,
  	'eo': 100.00,
  	'e1o': 100.00,
  	'ea': 20.00,
  	'eao': 100.00,
  	'q': 10.00,
  	'qh': 10.00,
  	'qa': 10.00,
  	'esp': 10.00,
  	'p': 10.00
  	}

The values mentioned here are all adjustable and should be thought about by the user before executing an optimization. In order to encourage this behavior, I think that we should create a JSON input file for Q2MM.

It would be nice to be able to specify QM vs MM data here as well.

Key features to add below.

• A means to provide a JSON input file to start an optimization procedure.
  • Reads JSON.
  • Validates JSON.
• Examples of various JSON inputs and an associated README.md.
  • I think it would really be nice if we restructured our base README.md to read more like a book.