Remote-learning

Final version of the Remote Learning subject program. It takes a .mol2 file from the /inputs directory as input and generates 3 output files in the /results directory:

• .out1: Prints energy contribution of each bond, angle and dihedral. Also prints the gradient in cartesian coordinates and the contribution of each set of internals to the gradient.
• .out2: Log of the optimization in cartesian coordinates using the BGFS Quasi-Newton optimization algorithm.
• .out3: Log of the optimization in internal coordinates using the BGFS Quasi-Newton optimization algorithm.

Execution

The program can be executed from the terminal as:

python3 geom_optimizer.py inputs/filename.mol2

Or by modifying in the script file the variable default_filename:

default_filename = os.getcwd() + "/inputs/methane.mol2"

Results

Cartesian optimization

Filename	Cartesian opt. ref. energy / $kcal · mol^{-1}$	Cartesian opt. energy / $kcal · mol^{-1}$	Deviation / $kcal · mol^{-1}$
Ethane	$-0.18518363$	$-0.18518368$	$0.00000005$
Ethane_dist	$-0.18343836$	$-0.18518367$	$0.00174531$
Isobutane	$0.27391887$	$0.27391883$	$0.00000004$
Methane	$0.00005305$	$0.00005299$	$0.00000006$
Methylcyclohexane	$3.49862154$	$3.49862132$	$0.00000022$
n_Butane	$-0.08747283$	$-0.08747224$	$0.00000059$
Pinane	$80.28771004$	$80.28770984$	$0.0000002$
Cholestane	$-$	$50.31436993$	$-$
Cholestane_reordered	$-$	$50.31436993$	$-$
Methylcyclohexane_reordered	$-$	$3.49862132$	$-$
n_Butane_reordered	$-$	$-0.08747224$	$-$
Pinane_reordered	$-$	$80.28770984$	$-$

Internal optimization

Filename	Internal opt. ref. energy / $kcal · mol^{-1}$	Internal opt. energy / $kcal · mol^{-1}$	Deviation / $kcal · mol^{-1}$
Ethane	$-0.18518368$	$-0.18518368$	$0$
Ethane_dist	$-0.18486694$	$-0.18518367$	$0.00031673$
Isobutane	$0.27391876$	$0.27391883$	$0.0000007$
Methane	$0.00005298$	$0.00005299$	$0.00000001$
Methylcyclohexane	$3.49862132$	$3.49862132$	$0$
n_Butane	$-0.08747223$	$-0.08747224$	$0.00000001$
Cholestane	$-$	$50.31436632$	$-$
Cholestane_reordered	$-$	$50.31436632$	$-$
Methylcyclohexane_reordered	$-$	$3.49862132$	$-$
n_Butane_reordered	$-$	$-0.08747224$	$-$
Pinane_reordered	$-$	$80.28770984$	$-$
Pinane	$-$	$80.28770984$	$-$