kevincorcor / pim

This is a short and simple Javascript script that uses Regex on a supplied log file in order to find Normal Mode Tables. These Tables are then processed by 1. First, converting `center numbers` to `atom symbols`. This is done by using an array of element symbols in order of atomic number and using another table within the log file for `center number` to `atomic number` mappings. Then, merging rows with the same mode and atoms (up to the first 3 positions of their definitons) 1. here, the `relative weights` of the matching rows are summed 2. we also catalogue the names of all merged rows in order to support observing what rows were merged to produce each process row. 2. We print out that new processed tables.

Process Internal Modes (PIM)

About

This is a short and simple Javascript script that uses Regex on a supplied log file in order to find Normal Mode Tables. These Tables are then processed by

1. First, converting center numbers to atom symbols. This is done by using an array of element symbols in order of atomic number and using another table within the log file for center number to atomic number mappings. Then, merging rows with the same mode and atoms (up to the first 3 positions of their definitons)
   1. here, the relative weights of the matching rows are summed
   2. we also catalogue the names of all merged rows in order to support observing what rows were merged to produce each process row.
2. We print out that new processed tables.

Note

• MathJS is used to ensure no floating point arithmetic errors ocurr. See here for a simple example

Install NodeJs

1. Install NodeJs > v15.0.0

Literally just download and install NodeJs

2. Confirm installation Open a fresh terminal(powershell/cmd for windows) and run

node -v

you should get the version number of your installation returned. Note: Make sure it is 15 or greater.

3. Install PIM

you can save this to whatever folder you like but I would recommend placing it somewhere near the log files you aim to process. This way you paths can be nice and short.

npm install -g git+https://github.com/KevinCorcor/PIM.git

Execution

To run this script all you need is the path to the log file you wish to process. This can be a relative of full path.

Follow this structure,

pim --target PATH/TO/LOG/FILE.log

For Example, if my script is in the same location as my log file and my terminal is already in that location I could just run the following.

pim --target ./BeTAP_Int.log

CLI Options

key	Alias	Type	Description	Required
target	t	some/path/to/target.file	The path (absolute or relative) of the file we want to process	true
output	o	some/path/to/output.file	The path (absolute or relative) to save the results. This will replace an existing file of the same name or create a new file if none exist.	false
silent	s		hide the console output of results	false
no-prettyPrint			log the results to the console in json	false

Examples

Output

if the output fie does not exist one will be created.

pim -t ./normalModes.log -o ./results_15052022.json
# .
# ..
# ...
# (R)	0.80000%	C - H          	Stretch		R23,R28
# --------------------------------------------------------------------------
# NORMAL MODE: 93
# --------------------------------------------------------------------------
# (R)	80.80000%	C - H          	Stretch		R8,R10,R23,R28,R29,R37,R39,R40
# (R)	4.80000%	C - C          	Stretch		R7,R22,R27,R36
# (R)	4.00000%	C - C          	Stretch		R1,R4,R9,R13,R18,R20,R24,R38
# (A)	2.40000%	C - C - H      	Bend		A8,A12,A26,A32,A35,A53,A57,A62
# --------------------------------------------------------------------------
# Saved results to /user/Documants/res.json

If you want to save the prettyPrint console text to a file, try the following

pim -t ./normalModes.log > path/to/save/console/output.log

No-prettyPrint

pim -t ./normalModes.log --no-prettyPrint
# .
# ..
# ...
#       'A(CCN) 0.0142': [Object],
#       'A(CCN) 0.0156': [Object],
#       'A(CCC) 0.0149': [Object],
#       'A(CCH) 0.017': [Object]
#     }
#   },
#   {
#     rows: {
#       'R(CC) 0.0181': [Object],
#       'R(CC) 0.0467': [Object],
#       'R(CH) 0.3854': [Object],
#       'A(CCH) 0.012': [Object]
#     }
#   }
# ]

Silent

pim -t ./normalModes.log -o ./results_15052022.json -s
# Saved results to /user/Documants/res.json