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Update plots, add new calculations, bugfixes
1 parent 81020f9 commit 2eee205

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lines changed

‎examples/ac-ala-ome/ac-ala-ome-ab.png

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‎examples/ac-ala-ome/ac-ala-ome-ac.png

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‎examples/ac-ala-ome/ac-ala-ome-bc.png

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‎examples/ac-ala-ome/ac-ala-ome-moments.csv

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param,value,unit,comment
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,examples/ac-ala-ome/ac-ala-ome.xyz,,
3+
A,2858.247979027603,MHz,PAM Rotational Constant
4+
B,631.6126884936764,MHz,PAM Rotational Constant
5+
C,561.0998168907669,MHz,PAM Rotational Constant
6+
A,0.0953408900976289,cm-1,PAM Rotational Constant
7+
B,0.02106833149530654,cm-1,PAM Rotational Constant
8+
C,0.018716275273701743,cm-1,PAM Rotational Constant
9+
Paa,762.0100067023552,amu A^2,PAM Second Moment
10+
Pbb,138.68358457682666,amu A^2,PAM Second Moment
11+
Pcc,38.13067816372461,amu A^2,PAM Second Moment
12+
Delta,-76.26135632744922,amu A^2,PAM Intertial Defect
13+
Rotor,"[0, 1, 2, 3]",,Atoms in rotor
14+
A (rotor),137318.3659162818,MHz,Rotational Constant of Rotor Atoms
15+
B (rotor),134013.511160247,MHz,Rotational Constant of Rotor Atoms
16+
C (rotor),80283.00269134458,MHz,Rotational Constant of Rotor Atoms
17+
A (rotor),4.58044764809533,cm-1,Rotational Constant of Rotor Atoms
18+
B (rotor),4.470209559449524,cm-1,Rotational Constant of Rotor Atoms
19+
C (rotor),2.677952715252916,cm-1,Rotational Constant of Rotor Atoms
20+
I_alpha,6.294968949833785,amu A^2,Rotor Moment of Inertia
21+
lambda_a,-0.7346007226780092,,Direction Cosine of Rotor
22+
lambda_b,0.6629608055501782,,Direction Cosine of Rotor
23+
lambda_c,-0.1443771053360101,,Direction Cosine of Rotor
24+
rho_a,-0.02615336946301094,,Component of rho Axis
25+
rho_b,0.005215729889542682,,Component of rho Axis
26+
rho_c,-0.0010090550259898043,,Component of rho Axis
27+
r,0.9771842069591267,,r Parameter for F Calculation
28+
rho_Ra,-0.0,rad,Rotation Angle for PAM-RAM Transformation
29+
rho_Rb,0.03781007460465342,rad,Rotation Angle for PAM-RAM Transformation
30+
rho_Rc,0.19543744509659888,rad,Rotation Angle for PAM-RAM Transformation
31+
rho_Ra,-0.0,deg,Rotation Angle for PAM-RAM Transformation
32+
rho_Rb,2.1663576979214154,deg,Rotation Angle for PAM-RAM Transformation
33+
rho_Rc,11.197740762854862,deg,Rotation Angle for PAM-RAM Transformation
34+
theta_a,0.6784996523513822,rad,Total Rotaton Angle between Rotor and Principal Axis
35+
theta_b,0.7486541059155813,rad,Total Rotaton Angle between Rotor and Principal Axis
36+
theta_c,0.9895227392307843,rad,Total Rotaton Angle between Rotor and Principal Axis
37+
theta_a,38.87516648082781,deg,Total Rotaton Angle between Rotor and Principal Axis
38+
theta_b,42.89472058410293,deg,Total Rotaton Angle between Rotor and Principal Axis
39+
theta_c,56.69547669014827,deg,Total Rotaton Angle between Rotor and Principal Axis
40+
rho,0.026687464559131454,,Magnitude of rho Vector
41+
F,82157.49100282238,MHz,Torsion-Rotational Constant
42+
A_ram,2801.805124753998,MHz,RAM Rotational Constant
43+
B_ram,619.5899932461896,MHz,RAM Rotational Constant
44+
C_ram,560.7000649000946,MHz,RAM Rotational Constant
45+
D_ab,554.9268030733303,MHz,RAM Off-Diagonal Rotational Constant
46+
D_bc,2.3259565434443856,MHz,RAM Off-Diagonal Rotational Constant
47+
D_ac,-107.3582588738496,MHz,RAM Off-Diagonal Rotational Constant
48+
F,2.7404789150106765,cm-1,Torsion-Rotational Constant
49+
A_ram,0.09345815913601128,cm-1,RAM Rotational Constant
50+
B_ram,0.020667297549099437,cm-1,RAM Rotational Constant
51+
C_ram,0.018702940982594517,cm-1,RAM Rotational Constant
52+
D_ab,0.018510365696835854,cm-1,RAM Off-Diagonal Rotational Constant
53+
D_bc,7.758555898842477e-05,cm-1,RAM Off-Diagonal Rotational Constant
54+
D_ac,-0.0035810860483304623,cm-1,RAM Off-Diagonal Rotational Constant
55+
C0,13.00335483534,amu,"3.26002281,-1.03923327,0.06897338"
56+
H1,2.014101777844,amu,"4.02786868,-0.61037148,0.70809529"
57+
H2,2.014101777844,amu,"2.86987948,-1.94234290,0.53140325"
58+
H3,2.014101777844,amu,"3.72536335,-1.29185979,-0.88076597"
59+
C4,12.0,amu,"2.20202543,0.00798631,-0.17950039"
60+
N5,14.00307400425,amu,"0.94206942,-0.33380347,0.19719354"
61+
H6,1.007825031898,amu,"0.72214271,-1.26028836,0.52505907"
62+
O7,15.99491461926,amu,"2.45939472,1.09626078,-0.68167535"
63+
C8,12.0,amu,"-0.16911652,0.55241039,-0.04645307"
64+
H9,1.007825031898,amu,"-0.06781681,0.98716028,-1.04168240"
65+
C10,12.0,amu,"-1.42922668,-0.27969545,-0.00158294"
66+
O11,15.99491461926,amu,"-1.48483724,-1.43165925,0.37591782"
67+
O12,15.99491461926,amu,"-2.49009160,0.43037986,-0.40594868"
68+
C13,12.0,amu,"-3.73355566,-0.28716483,-0.34730453"
69+
H14,1.007825031898,amu,"-4.48518948,0.40904535,-0.69843663"
70+
H15,1.007825031898,amu,"-3.94188179,-0.59753734,0.67266696"
71+
H16,1.007825031898,amu,"-3.69253167,-1.16471817,-0.98614146"
72+
C17,12.0,amu,"-0.23942245,1.68446630,0.97829571"
73+
H18,1.007825031898,amu,"0.68913334,2.24721785,0.93564400"
74+
H19,1.007825031898,amu,"-0.36283246,1.27360262,1.97949861"
75+
H20,1.007825031898,amu,"-1.07221039,2.34822395,0.75810724"

‎examples/ac-ala-ome/ac-ala-ome-output.txt

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Initial coordinates
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Atom Mass X (A) Y (A) Z (A)
3+
C 13.003355 -3.24962974 -1.06846312 0.10394692
4+
H 2.014102 -4.02487674 -0.61775012 0.71863092
5+
H 2.014102 -2.85261474 -1.94455012 0.61041592
6+
H 2.014102 -3.70776574 -1.37063112 -0.83476108
7+
C 12.000000 -2.20109474 -0.02331212 -0.18931108
8+
N 14.003074 -0.93958874 -0.33380712 0.20868792
9+
H 1.007825 -0.71188874 -1.24138212 0.58110992
10+
O 15.994915 -2.46702574 1.03721088 -0.74368608
11+
C 12.000000 0.16373826 0.55130688 -0.07187508
12+
H 1.007825 0.06288126 0.93731488 -1.08704808
13+
C 12.000000 1.43197626 -0.26465612 0.01794592
14+
O 15.994915 1.49741226 -1.39679112 0.44992792
15+
O 15.994915 2.48755026 0.43638688 -0.41501508
16+
C 12.000000 3.73791626 -0.26466912 -0.31694508
17+
H 1.007825 4.48416026 0.42184988 -0.69742808
18+
H 1.007825 3.94441326 -0.52416612 0.71750792
19+
H 1.007825 3.70888626 -1.17189912 -0.91359108
20+
C 12.000000 0.21759526 1.73133788 0.89829492
21+
H 1.007825 -0.71639274 2.28179888 0.82492292
22+
H 1.007825 0.34029026 1.36969988 1.91839792
23+
H 1.007825 1.04468026 2.39248988 0.65050192
24+
25+
Principal Axis Coordinates
26+
Atom Mass a (A) b (A) c (A)
27+
C 13.003355 3.26002281 -1.03923327 0.06897338
28+
H 2.014102 4.02786868 -0.61037148 0.70809529
29+
H 2.014102 2.86987948 -1.94234290 0.53140325
30+
H 2.014102 3.72536335 -1.29185979 -0.88076597
31+
C 12.000000 2.20202543 0.00798631 -0.17950039
32+
N 14.003074 0.94206942 -0.33380347 0.19719354
33+
H 1.007825 0.72214271 -1.26028836 0.52505907
34+
O 15.994915 2.45939472 1.09626078 -0.68167535
35+
C 12.000000 -0.16911652 0.55241039 -0.04645307
36+
H 1.007825 -0.06781681 0.98716028 -1.04168240
37+
C 12.000000 -1.42922668 -0.27969545 -0.00158294
38+
O 15.994915 -1.48483724 -1.43165925 0.37591782
39+
O 15.994915 -2.49009160 0.43037986 -0.40594868
40+
C 12.000000 -3.73355566 -0.28716483 -0.34730453
41+
H 1.007825 -4.48518948 0.40904535 -0.69843663
42+
H 1.007825 -3.94188179 -0.59753734 0.67266696
43+
H 1.007825 -3.69253167 -1.16471817 -0.98614146
44+
C 12.000000 -0.23942245 1.68446630 0.97829571
45+
H 1.007825 0.68913334 2.24721785 0.93564400
46+
H 1.007825 -0.36283246 1.27360262 1.97949861
47+
H 1.007825 -1.07221039 2.34822395 0.75810724
48+
49+
Interatomic Distance Matrix (A)
50+
51+
C0 H1 H2 H3 C4 N5 H6 O7 C8 H9
52+
C0 0.000 1.087 1.087 1.087 1.509 2.426 2.588 2.401 3.782 4.051
53+
H1 1.087 0.000 1.774 1.755 2.122 3.140 3.374 2.703 4.420 4.732
54+
H2 1.087 1.774 0.000 1.775 2.181 2.533 2.253 3.297 3.974 4.437
55+
H3 1.087 1.755 1.775 0.000 2.122 3.135 3.316 2.710 4.389 4.428
56+
C4 1.509 2.122 2.181 2.122 0.000 1.359 2.072 1.226 2.436 2.618
57+
N5 2.426 3.140 2.533 3.135 1.359 0.000 1.007 2.263 1.442 2.074
58+
H6 2.588 3.374 2.253 3.316 2.072 1.007 0.000 3.167 2.099 2.851
59+
O7 2.401 2.703 3.297 2.710 1.226 2.263 3.167 0.000 2.758 2.555
60+
C8 3.782 4.420 3.974 4.389 2.436 1.442 2.099 2.758 0.000 1.091
61+
H9 4.051 4.732 4.437 4.428 2.618 2.074 2.851 2.555 1.091 0.000
62+
C10 4.751 5.513 4.640 5.326 3.647 2.380 2.422 4.181 1.511 2.131
63+
O11 4.771 5.583 4.387 5.361 3.997 2.670 2.219 4.803 2.418 3.141
64+
O12 5.954 6.694 5.936 6.467 4.717 3.568 3.747 5.002 2.352 2.565
65+
C13 7.046 7.840 6.864 7.545 5.945 4.707 4.643 6.354 3.674 3.943
66+
H14 7.917 8.688 7.819 8.387 6.719 5.551 5.604 6.979 4.367 4.468
67+
H15 7.241 7.970 6.945 7.854 6.232 4.914 4.713 6.759 4.009 4.523
68+
H16 7.033 7.924 6.780 7.420 6.064 4.855 4.667 6.561 4.031 4.216
69+
C17 4.527 4.853 4.798 5.295 3.180 2.466 3.131 3.223 1.529 2.144
70+
H18 4.262 4.401 4.740 5.004 2.923 2.696 3.532 2.660 2.139 2.464
71+
H19 4.704 4.944 4.784 5.610 3.584 2.732 3.117 3.883 2.159 3.049
72+
H20 5.542 5.896 5.831 6.241 4.132 3.401 4.037 4.014 2.165 2.470
73+
74+
C10 O11 O12 C13 H14 H15 H16 C17 H18 H19
75+
C0 4.751 4.771 5.954 7.046 7.917 7.241 7.033 4.527 4.262 4.704
76+
H1 5.513 5.583 6.694 7.840 8.688 7.970 7.924 4.853 4.401 4.944
77+
H2 4.640 4.387 5.936 6.864 7.819 6.945 6.780 4.798 4.740 4.784
78+
H3 5.326 5.361 6.467 7.545 8.387 7.854 7.420 5.295 5.004 5.610
79+
C4 3.647 3.997 4.717 5.945 6.719 6.232 6.064 3.180 2.923 3.584
80+
N5 2.380 2.670 3.568 4.707 5.551 4.914 4.855 2.466 2.696 2.732
81+
H6 2.422 2.219 3.747 4.643 5.604 4.713 4.667 3.131 3.532 3.117
82+
O7 4.181 4.803 5.002 6.354 6.979 6.759 6.561 3.223 2.660 3.883
83+
C8 1.511 2.418 2.352 3.674 4.367 4.009 4.031 1.529 2.139 2.159
84+
H9 2.131 3.141 2.565 3.943 4.468 4.523 4.216 2.144 2.464 3.049
85+
C10 0.000 1.214 1.339 2.330 3.209 2.621 2.622 2.497 3.428 2.734
86+
O11 1.214 0.000 2.256 2.625 3.680 2.612 2.608 3.409 4.310 3.339
87+
O12 1.339 2.256 0.000 1.437 2.017 2.080 2.080 2.925 3.900 3.306
88+
C13 2.330 2.625 1.437 0.000 1.083 1.086 1.086 4.225 5.256 4.383
89+
H14 3.209 3.680 2.017 1.083 0.000 1.786 1.785 4.740 5.729 4.991
90+
H15 2.621 2.612 2.080 1.086 1.786 0.000 1.771 4.360 5.441 4.245
91+
H16 2.622 2.608 2.080 1.086 1.785 1.771 0.000 4.889 5.877 5.082
92+
C17 2.497 3.409 2.925 4.225 4.740 4.360 4.889 0.000 1.087 1.089
93+
H18 3.428 4.310 3.900 5.256 5.729 5.441 5.877 1.087 0.000 1.773
94+
H19 2.734 3.339 3.306 4.383 4.991 4.245 5.082 1.089 1.773 0.000
95+
H20 2.759 3.821 2.654 3.905 4.187 4.113 4.717 1.087 1.773 1.775
96+
97+
H20
98+
C0 5.542
99+
H1 5.896
100+
H2 5.831
101+
H3 6.241
102+
C4 4.132
103+
N5 3.401
104+
H6 4.037
105+
O7 4.014
106+
C8 2.165
107+
H9 2.470
108+
C10 2.759
109+
O11 3.821
110+
O12 2.654
111+
C13 3.905
112+
H14 4.187
113+
H15 4.113
114+
H16 4.717
115+
C17 1.087
116+
H18 1.773
117+
H19 1.775
118+
H20 0.000
119+
120+
Principal Axis Rotational Constants
121+
A 2858.2480 MHz
122+
B 631.6127 MHz
123+
C 561.0998 MHz
124+
------------------------
125+
A 0.095340890 cm-1
126+
B 0.021068331 cm-1
127+
C 0.018716275 cm-1
128+
129+
Second moments and Inertial Defect
130+
Paa 762.010006702 amu A^2
131+
Pbb 138.683584577 amu A^2
132+
Pcc 38.130678164 amu A^2
133+
Delta -76.261356327 amu A^2
134+
135+
Rotor atoms: [0 1 2 3]
136+
137+
Rotor Rotational Constants
138+
A 137318.3659 MHz
139+
B 134013.5112 MHz
140+
C 80283.0027 MHz
141+
------------------------
142+
A 4.580447648 cm-1
143+
B 4.470209559 cm-1
144+
C 2.677952715 cm-1
145+
146+
I_alpha = 6.294969
147+
148+
Rotor Axis
149+
lambda_a -0.7346007
150+
lambda_b 0.6629608
151+
lambda_c -0.1443771
152+
153+
Rotor Axis angle with respect to principal axes
154+
theta_a 0.6784997 rad
155+
theta_b 0.7486541 rad
156+
theta_c 0.9895227 rad
157+
------------------------
158+
theta_a 38.87517 deg
159+
theta_b 42.89472 deg
160+
theta_c 56.69548 deg
161+
162+
rho Axis
163+
rho_a -0.0261534
164+
rho_b 0.0052157
165+
rho_c -0.0010091
166+
r 0.9771842
167+
168+
RAM Rotation Vector
169+
Ra -0.0000000 rad
170+
Rb 0.0378101 rad
171+
Rc 0.1954374 rad
172+
------------------------
173+
Ra -0.00000 deg
174+
Rb 2.16636 deg
175+
Rc 11.19774 deg
176+
177+
Rho Axis System Parameters
178+
rho 0.026687465
179+
F 82157.4910 MHz
180+
A_ram 2801.8051 MHz
181+
B_ram 619.5900 MHz
182+
C_ram 560.7001 MHz
183+
D_ab 554.9268 MHz
184+
D_bc 2.3260 MHz
185+
D_ac -107.3583 MHz
186+
------------------------
187+
F 2.740478915 cm-1
188+
A_ram 0.093458159 cm-1
189+
B_ram 0.020667298 cm-1
190+
C_ram 0.018702941 cm-1
191+
D_ab 0.018510366 cm-1
192+
D_bc 0.000077586 cm-1
193+
D_ac -0.003581086 cm-1

‎examples/ac-ala-ome/ac-ala-ome.xyz

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C -3.348876 -1.104102 0.092003 13
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H -4.124123 -0.653389 0.706687 2
5+
H -2.951861 -1.980189 0.598472 2
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H -3.807012 -1.406270 -0.846705 2
7+
C -2.300341 -0.058951 -0.201255
8+
N -1.038835 -0.369446 0.196744
9+
H -0.811135 -1.277021 0.569166
10+
O -2.566272 1.001572 -0.755630
11+
C 0.064492 0.515668 -0.083819
12+
H -0.036365 0.901676 -1.098992
13+
C 1.33273 -0.300295 0.006002
14+
O 1.398166 -1.432430 0.437984
15+
O 2.388304 0.400748 -0.426959
16+
C 3.638670 -0.300308 -0.328889
17+
H 4.384914 0.386211 -0.709372
18+
H 3.845167 -0.559805 0.705564
19+
H 3.60964 -1.207538 -0.925535
20+
C 0.118349 1.695699 0.886351
21+
H -0.815639 2.246160 0.812979
22+
H 0.241044 1.334061 1.906454
23+
H 0.945434 2.356851 0.638558

‎examples/acetaldehyde.xyz-coords.png

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‎examples/acetaldehyde.xyz-moments.csv

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‎examples/acetaldehyde/acetaldehyde-ab.png

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‎examples/acetaldehyde/acetaldehyde-ac.png

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‎examples/acetaldehyde/acetaldehyde-bc.png

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