3-parameter Pinned H2O

[siuwuncheung]

This PR sets up the parametric case of Pinned H2O, with 3 parameters (2 bondlengths and 1 bondangle).
Future PR will do parametric ROM.

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3 samples of 1331 coords.in files from generate_coords_simple.py

coords_1.00_1.00_0.0.in (Bondlength = {1.83, 1.83}, Bondangle = 104.5)
O1 1 0.00 0.00 0.00 0
H1 2 1.12 1.45 0.00 1
H2 2 1.12 -1.45 0.00 1

coords_1.00_1.00_5.0.in (Bondlength = {1.83, 1.83}, Bondangle = 109.5)
O1 1 0.00 0.00 0.00 0
H1 2 1.06 1.49 0.00 1
H2 2 1.06 -1.49 0.00 1

coords_1.05_0.95_0.0.in (Bondlength = {1.9215, 1.7385}, Bondangle = 104.5)
O1 1 0.00 0.00 0.00 0
H1 2 1.18 1.52 0.00 1
H2 2 1.06 -1.37 0.00 1

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Experiments on rotating a general molecule to the 3-parameter space. Outputs of rotation_test.py

Original system
H1 = [-0.45 1.42 -1.07]
H2 = [-0.45 -1.48 -0.97]
Bondlength of O1-H1 = 1.8340665200586372
Bondlength of O1-H2 = 1.8258696558078837
Angle between O1-H1 and O1-H2 = 104.90216602748386
Aligned system
H1 = [ 1.19062568e+00 1.39506648e+00 -2.18622350e-16]
H2 = [ 1.03729618e+00 -1.50260329e+00 -2.15581121e-16]
Bondlength of O1-H1 = 1.8340665200586375
Bondlength of O1-H2 = 1.825869655807884
Angle between O1-H1 and O1-H2 = 104.90216602748387