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‎README.md

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,8 @@ Supports nonstandard isotopologues and will calculate internal rotation paramete
55
[![DOI](https://zenodo.org/badge/674807150.svg)](https://zenodo.org/badge/latestdoi/674807150)
66

77
<p align="center">
8-
<img src="https://github.com/kncrabtree/moments/assets/20146313/338e14c3-1f8c-48c7-9d61-010cb9c6c4ed" width=400 align="center"/>
9-
<img src="https://github.com/kncrabtree/moments/assets/20146313/01777d01-63fa-4aaf-95ef-6b2ffb5ee255" width=400 align="center"/>
8+
<img src="https://github.com/kncrabtree/moments/assets/20146313/8bf65ebd-7a60-4003-afd7-ae760d98e372" width=400 align="center"/>
9+
<img src="https://github.com/kncrabtree/moments/assets/20146313/c1c41434-18c4-4f5a-abb6-becde3c578d6" width=400 align="center"/>
1010
</p>
1111

1212
### Installation and Requirements

‎examples/ac-ala-ome-3d/ac-ala-ome-r0123-ab.png

-5.24 KB
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‎examples/ac-ala-ome-3d/ac-ala-ome-r0123-ac.png

29.9 KB
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‎examples/ac-ala-ome-3d/ac-ala-ome-r0123-bc.png

-29.8 KB
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‎examples/ac-ala-ome-3d/ac-ala-ome-r0123-moments.csv

Lines changed: 63 additions & 63 deletions
Original file line numberDiff line numberDiff line change
@@ -20,93 +20,93 @@ C (rotor),5.3517401665872555,cm-1,Rotational Constant of Rotor Atoms (F0)
2020
I_alpha,3.149934164757872,amu A^2,Rotor Moment of Inertia
2121
lambda_a,-0.7414279636568041,,Direction Cosine of Rotor
2222
lambda_b,-0.6419992958396471,,Direction Cosine of Rotor
23-
lambda_c,0.1952472249460211,,Direction Cosine of Rotor
23+
lambda_c,-0.1952472249460211,,Direction Cosine of Rotor
2424
rho_a,-0.013930557014382075,,Component of rho Axis
2525
rho_b,-0.00270187566099468,,Component of rho Axis
26-
rho_c,0.000729545695646099,,Component of rho Axis
26+
rho_c,-0.000729545695646099,,Component of rho Axis
2727
r,0.9877944514358706,,r Parameter for F Calculation
2828
rho,0.014208898188827339,,Magnitude of rho Vector
2929
F,162423.60308729514,MHz,RAM Torsion-Rotational Constant
3030
A_ram,2955.448000498272,MHz,RAM Rotational Constant
3131
B_ram,571.1262829965254,MHz,RAM Rotational Constant
3232
C_ram,518.8148052134344,MHz,RAM Rotational Constant
3333
D_ab,-444.8225038779008,MHz,RAM Off-Diagonal Rotational Constant
34-
D_bc,635.3202661014982,MHz,RAM Off-Diagonal Rotational Constant
35-
D_ac,123.99684188895648,MHz,RAM Off-Diagonal Rotational Constant
34+
D_bc,-635.3202661014982,MHz,RAM Off-Diagonal Rotational Constant
35+
D_ac,-123.99684188895648,MHz,RAM Off-Diagonal Rotational Constant
3636
F,5.417868220263737,cm-1,RAM Torsion-Rotational Constant
3737
A_ram,0.09858313381913937,cm-1,RAM Rotational Constant
3838
B_ram,0.019050722183161974,cm-1,RAM Rotational Constant
3939
C_ram,0.017305799107642475,cm-1,RAM Rotational Constant
4040
D_ab,-0.014837681602980844,cm-1,RAM Off-Diagonal Rotational Constant
41-
D_bc,0.021192002972319542,cm-1,RAM Off-Diagonal Rotational Constant
42-
D_ac,0.004136089437211808,cm-1,RAM Off-Diagonal Rotational Constant
41+
D_bc,-0.021192002972319542,cm-1,RAM Off-Diagonal Rotational Constant
42+
D_ac,-0.004136089437211808,cm-1,RAM Off-Diagonal Rotational Constant
4343
dIr,2.405992200635814,rad,CAM delta angle (Ir representation)
44-
eIr,2.8463569212408975,rad,CAM epsilon angle (Ir representation)
45-
gIr,2.943332681073779,rad,CAM gamma angle (Ir representation)
46-
bIr,2.8778672733638926,rad,CAM beta angle (Ir representation)
44+
eIr,0.29523573234889566,rad,CAM epsilon angle (Ir representation)
45+
bIr,2.943332681073779,rad,CAM beta angle (Ir representation)
46+
gIr,0.2637253802259007,rad,CAM gamma angle (Ir representation)
4747
dIr,137.85319863782533,deg,CAM delta angle (Ir representation)
48-
eIr,163.0842385749543,deg,CAM epsilon angle (Ir representation)
49-
gIr,168.64054032845272,deg,CAM gamma angle (Ir representation)
50-
bIr,164.88964876257302,deg,CAM beta angle (Ir representation)
48+
eIr,16.915761425045712,deg,CAM epsilon angle (Ir representation)
49+
bIr,168.64054032845272,deg,CAM beta angle (Ir representation)
50+
gIr,15.110351237427007,deg,CAM gamma angle (Ir representation)
5151
dIIr,2.267899400683646,rad,CAM delta angle (IIr representation)
52-
eIIr,1.8282898215763084,rad,CAM epsilon angle (IIr representation)
53-
gIIr,1.762115106103761,rad,CAM gamma angle (IIr representation)
54-
bIIr,1.6231187020642595,rad,CAM beta angle (IIr representation)
52+
eIIr,1.313302832013485,rad,CAM epsilon angle (IIr representation)
53+
bIIr,1.762115106103761,rad,CAM beta angle (IIr representation)
54+
gIIr,1.5184739515255339,rad,CAM gamma angle (IIr representation)
5555
dIIr,129.94106401942173,deg,CAM delta angle (IIr representation)
56-
eIIr,104.75329050304879,deg,CAM epsilon angle (IIr representation)
57-
gIIr,100.96175859599276,deg,CAM gamma angle (IIr representation)
58-
bIIr,92.99785127703417,deg,CAM beta angle (IIr representation)
59-
dIIIr,1.3742868065594143,rad,CAM delta angle (IIIr representation)
56+
eIIr,75.24670949695123,deg,CAM epsilon angle (IIr representation)
57+
bIIr,100.96175859599276,deg,CAM beta angle (IIr representation)
58+
gIIr,87.00214872296586,deg,CAM gamma angle (IIr representation)
59+
dIIIr,1.767305847030379,rad,CAM delta angle (IIIr representation)
6060
eIIIr,0.7136502656394681,rad,CAM epsilon angle (IIIr representation)
61-
gIIIr,1.5194294573040092,rad,CAM gamma angle (IIIr representation)
62-
bIIIr,0.19157459478543404,rad,CAM beta angle (IIIr representation)
63-
dIIIr,78.74083385636622,deg,CAM delta angle (IIIr representation)
61+
bIIIr,1.622163196285784,rad,CAM beta angle (IIIr representation)
62+
gIIIr,0.19157459478543404,rad,CAM gamma angle (IIIr representation)
63+
dIIIr,101.25916614363379,deg,CAM delta angle (IIIr representation)
6464
eIIIr,40.889148269531596,deg,CAM epsilon angle (IIIr representation)
65-
gIIIr,87.05689517137284,deg,CAM gamma angle (IIIr representation)
66-
bIIIr,10.97641574313432,deg,CAM beta angle (IIIr representation)
65+
bIIIr,92.94310482862717,deg,CAM beta angle (IIIr representation)
66+
gIIIr,10.97641574313432,deg,CAM gamma angle (IIIr representation)
6767
dIl,2.405992200635814,rad,CAM delta angle (Il representation)
68-
eIl,1.8660320591437927,rad,CAM epsilon angle (Il representation)
69-
gIl,2.943332681073779,rad,CAM gamma angle (Il representation)
70-
bIl,1.834521707020797,rad,CAM beta angle (Il representation)
68+
eIl,1.2755605944460007,rad,CAM epsilon angle (Il representation)
69+
bIl,2.943332681073779,rad,CAM beta angle (Il representation)
70+
gIl,1.307070946568996,rad,CAM gamma angle (Il representation)
7171
dIl,137.85319863782533,deg,CAM delta angle (Il representation)
72-
eIl,106.91576142504574,deg,CAM epsilon angle (Il representation)
73-
gIl,168.64054032845272,deg,CAM gamma angle (Il representation)
74-
bIl,105.110351237427,deg,CAM beta angle (Il representation)
72+
eIl,73.08423857495428,deg,CAM epsilon angle (Il representation)
73+
bIl,168.64054032845272,deg,CAM beta angle (Il representation)
74+
gIl,74.889648762573,deg,CAM gamma angle (Il representation)
7575
dIIl,2.267899400683646,rad,CAM delta angle (IIl representation)
76-
eIIl,2.884099158808381,rad,CAM epsilon angle (IIl representation)
77-
gIIl,1.762115106103761,rad,CAM gamma angle (IIl representation)
78-
bIIl,3.089270278320431,rad,CAM beta angle (IIl representation)
76+
eIIl,0.2574934947814122,rad,CAM epsilon angle (IIl representation)
77+
bIIl,1.762115106103761,rad,CAM beta angle (IIl representation)
78+
gIIl,0.05232237526936205,rad,CAM gamma angle (IIl representation)
7979
dIIl,129.94106401942173,deg,CAM delta angle (IIl representation)
80-
eIIl,165.24670949695118,deg,CAM epsilon angle (IIl representation)
81-
gIIl,100.96175859599276,deg,CAM gamma angle (IIl representation)
82-
bIIl,177.0021487229659,deg,CAM beta angle (IIl representation)
83-
dIIIl,1.3742868065594143,rad,CAM delta angle (IIIl representation)
80+
eIIl,14.753290503048808,deg,CAM epsilon angle (IIl representation)
81+
bIIl,100.96175859599276,deg,CAM beta angle (IIl representation)
82+
gIIl,2.9978512770341195,deg,CAM gamma angle (IIl representation)
83+
dIIIl,1.767305847030379,rad,CAM delta angle (IIIl representation)
8484
eIIIl,0.8571460611554287,rad,CAM epsilon angle (IIIl representation)
85-
gIIIl,1.5194294573040092,rad,CAM gamma angle (IIIl representation)
86-
bIIIl,1.3792217320094626,rad,CAM beta angle (IIIl representation)
87-
dIIIl,78.74083385636622,deg,CAM delta angle (IIIl representation)
85+
bIIIl,1.622163196285784,rad,CAM beta angle (IIIl representation)
86+
gIIIl,1.3792217320094626,rad,CAM gamma angle (IIIl representation)
87+
dIIIl,101.25916614363379,deg,CAM delta angle (IIIl representation)
8888
eIIIl,49.11085173046842,deg,CAM epsilon angle (IIIl representation)
89-
gIIIl,87.05689517137284,deg,CAM gamma angle (IIIl representation)
90-
bIIIl,79.02358425686569,deg,CAM beta angle (IIIl representation)
91-
C0,12.0,amu,"-3.36632102,-1.03556563,0.12894092"
92-
H1,1.007825031898,amu,"-4.13722911,-0.54481447,0.71788111"
93-
H2,1.007825031898,amu,"-2.98936044,-1.89643847,0.67525481"
94-
H3,1.007825031898,amu,"-3.82350396,-1.36897870,-0.79959895"
95-
C4,12.0,amu,"-2.29633137,-0.02340750,-0.20033798"
96-
N5,14.00307400425,amu,"-1.04367867,-0.33988530,0.22026959"
97-
H6,1.007825031898,amu,"-0.83565721,-1.23480242,0.63268716"
98-
O7,15.99491461926,amu,"-2.53843783,1.01723913,-0.80133635"
99-
C8,12.0,amu,"0.07799881,0.51193848,-0.08909869"
100-
H9,1.007825031898,amu,"-0.00852349,0.85610110,-1.12051350"
101-
C10,12.0,amu,"1.33003697,-0.32272735,0.04515648"
102-
O11,15.99491461926,amu,"1.37119608,-1.43642628,0.52536540"
103-
O12,15.99491461926,amu,"2.40157585,0.33960713,-0.40901359"
104-
C13,12.0,amu,"3.63784563,-0.37959411,-0.27153998"
105-
H14,1.007825031898,amu,"4.39947852,0.27618084,-0.67506237"
106-
H15,1.007825031898,amu,"3.83222787,-0.59851058,0.77457848"
107-
H16,1.007825031898,amu,"3.59594099,-1.31075114,-0.82929085"
108-
C17,12.0,amu,"0.14724729,1.73107180,0.83042409"
109-
H18,1.007825031898,amu,"-0.77570738,2.29505287,0.72647999"
110-
H19,1.007825031898,amu,"0.25602646,1.41105991,1.86589776"
111-
H20,1.007825031898,amu,"0.98830500,2.36567300,0.56117292"
89+
bIIIl,92.94310482862717,deg,CAM beta angle (IIIl representation)
90+
gIIIl,79.02358425686569,deg,CAM gamma angle (IIIl representation)
91+
C0,12.0,amu,"3.36632102,1.03556563,0.12894092"
92+
H1,1.007825031898,amu,"4.13722911,0.54481447,0.71788111"
93+
H2,1.007825031898,amu,"2.98936044,1.89643847,0.67525481"
94+
H3,1.007825031898,amu,"3.82350396,1.36897870,-0.79959895"
95+
C4,12.0,amu,"2.29633137,0.02340750,-0.20033798"
96+
N5,14.00307400425,amu,"1.04367867,0.33988530,0.22026959"
97+
H6,1.007825031898,amu,"0.83565721,1.23480242,0.63268716"
98+
O7,15.99491461926,amu,"2.53843783,-1.01723913,-0.80133635"
99+
C8,12.0,amu,"-0.07799881,-0.51193848,-0.08909869"
100+
H9,1.007825031898,amu,"0.00852349,-0.85610110,-1.12051350"
101+
C10,12.0,amu,"-1.33003697,0.32272735,0.04515648"
102+
O11,15.99491461926,amu,"-1.37119608,1.43642628,0.52536540"
103+
O12,15.99491461926,amu,"-2.40157585,-0.33960713,-0.40901359"
104+
C13,12.0,amu,"-3.63784563,0.37959411,-0.27153998"
105+
H14,1.007825031898,amu,"-4.39947852,-0.27618084,-0.67506237"
106+
H15,1.007825031898,amu,"-3.83222787,0.59851058,0.77457848"
107+
H16,1.007825031898,amu,"-3.59594099,1.31075114,-0.82929085"
108+
C17,12.0,amu,"-0.14724729,-1.73107180,0.83042409"
109+
H18,1.007825031898,amu,"0.77570738,-2.29505287,0.72647999"
110+
H19,1.007825031898,amu,"-0.25602646,-1.41105991,1.86589776"
111+
H20,1.007825031898,amu,"-0.98830500,-2.36567300,0.56117292"
112112
f_a,0.9262272280381801,,Fractional abundance of this isotopologue

‎examples/ac-ala-ome-3d/ac-ala-ome-r0123-output.txt

Lines changed: 48 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,5 @@
1+
Command: moments.py ac-ala-ome.xyz -r 0,1,2,3 -3d -o ac-ala-ome-r0123-moments.csv -p ac-ala-ome-r0123 > ac-ala-ome-r0123-output.txt
2+
13
Initial coordinates
24
Atom Mass X (A) Y (A) Z (A)
35
C 12.000000 -3.34552728 -1.10313280 0.10809435
@@ -24,27 +26,27 @@ H 1.007825 0.94878272 2.35782020 0.65464935
2426

2527
Principal Axis Coordinates
2628
Atom Mass a (A) b (A) c (A)
27-
C 12.000000 -3.36632102 -1.03556563 0.12894092
28-
H 1.007825 -4.13722911 -0.54481447 0.71788111
29-
H 1.007825 -2.98936044 -1.89643847 0.67525481
30-
H 1.007825 -3.82350396 -1.36897870 -0.79959895
31-
C 12.000000 -2.29633137 -0.02340750 -0.20033798
32-
N 14.003074 -1.04367867 -0.33988530 0.22026959
33-
H 1.007825 -0.83565721 -1.23480242 0.63268716
34-
O 15.994915 -2.53843783 1.01723913 -0.80133635
35-
C 12.000000 0.07799881 0.51193848 -0.08909869
36-
H 1.007825 -0.00852349 0.85610110 -1.12051350
37-
C 12.000000 1.33003697 -0.32272735 0.04515648
38-
O 15.994915 1.37119608 -1.43642628 0.52536540
39-
O 15.994915 2.40157585 0.33960713 -0.40901359
40-
C 12.000000 3.63784563 -0.37959411 -0.27153998
41-
H 1.007825 4.39947852 0.27618084 -0.67506237
42-
H 1.007825 3.83222787 -0.59851058 0.77457848
43-
H 1.007825 3.59594099 -1.31075114 -0.82929085
44-
C 12.000000 0.14724729 1.73107180 0.83042409
45-
H 1.007825 -0.77570738 2.29505287 0.72647999
46-
H 1.007825 0.25602646 1.41105991 1.86589776
47-
H 1.007825 0.98830500 2.36567300 0.56117292
29+
C 12.000000 3.36632102 1.03556563 0.12894092
30+
H 1.007825 4.13722911 0.54481447 0.71788111
31+
H 1.007825 2.98936044 1.89643847 0.67525481
32+
H 1.007825 3.82350396 1.36897870 -0.79959895
33+
C 12.000000 2.29633137 0.02340750 -0.20033798
34+
N 14.003074 1.04367867 0.33988530 0.22026959
35+
H 1.007825 0.83565721 1.23480242 0.63268716
36+
O 15.994915 2.53843783 -1.01723913 -0.80133635
37+
C 12.000000 -0.07799881 -0.51193848 -0.08909869
38+
H 1.007825 0.00852349 -0.85610110 -1.12051350
39+
C 12.000000 -1.33003697 0.32272735 0.04515648
40+
O 15.994915 -1.37119608 1.43642628 0.52536540
41+
O 15.994915 -2.40157585 -0.33960713 -0.40901359
42+
C 12.000000 -3.63784563 0.37959411 -0.27153998
43+
H 1.007825 -4.39947852 -0.27618084 -0.67506237
44+
H 1.007825 -3.83222787 0.59851058 0.77457848
45+
H 1.007825 -3.59594099 1.31075114 -0.82929085
46+
C 12.000000 -0.14724729 -1.73107180 0.83042409
47+
H 1.007825 0.77570738 -2.29505287 0.72647999
48+
H 1.007825 -0.25602646 -1.41105991 1.86589776
49+
H 1.007825 -0.98830500 -2.36567300 0.56117292
4850

4951
Interatomic Distance Matrix (A)
5052

@@ -150,19 +152,19 @@ I_alpha = 3.149934
150152
Rotor Axis
151153
lambda_a -0.7414280
152154
lambda_b -0.6419993
153-
lambda_c 0.1952472
155+
lambda_c -0.1952472
154156

155157
rho Axis
156158
rho_a -0.0139306
157159
rho_b -0.0027019
158-
rho_c 0.0007295
160+
rho_c -0.0007295
159161
|rho| 0.0142089
160162
r 0.9877945
161163

162164
PAM-RAM rotation matrix
163-
-0.980410784 0.190153777 -0.051344283
164-
-0.190153777 -0.845834931 0.498402257
165-
0.051344283 0.498402257 0.865424147
165+
-0.980410784 0.190153777 0.051344283
166+
-0.190153777 -0.845834931 -0.498402257
167+
-0.051344283 -0.498402257 0.865424147
166168

167169
Rho Axis System Parameters
168170
rho 0.014208898
@@ -171,37 +173,37 @@ A_ram 2955.4480 MHz
171173
B_ram 571.1263 MHz
172174
C_ram 518.8148 MHz
173175
D_ab -444.8225 MHz
174-
D_bc 635.3203 MHz
175-
D_ac 123.9968 MHz
176+
D_bc -635.3203 MHz
177+
D_ac -123.9968 MHz
176178
------------------------
177179
F 5.417868220 cm-1
178180
A_ram 0.098583134 cm-1
179181
B_ram 0.019050722 cm-1
180182
C_ram 0.017305799 cm-1
181183
D_ab -0.014837682 cm-1
182-
D_bc 0.021192003 cm-1
183-
D_ac 0.004136089 cm-1
184+
D_bc -0.021192003 cm-1
185+
D_ac -0.004136089 cm-1
184186

185187
Combined Axis System Parameters
186188
Ir IIr IIIr unit
187-
delta 2.4059922 2.2678994 1.3742868 rad
188-
epsilon 2.8463569 1.8282898 0.7136503 rad
189-
gamma 2.9433327 1.7621151 1.5194295 rad
190-
beta 2.8778673 1.6231187 0.1915746 rad
189+
delta 2.4059922 2.2678994 1.7673058 rad
190+
epsilon 0.2952357 1.3133028 0.7136503 rad
191+
beta 2.9433327 1.7621151 1.6221632 rad
192+
gamma 0.2637254 1.5184740 0.1915746 rad
191193
------------------------
192-
delta 137.85320 129.94106 78.74083 deg
193-
epsilon 163.08424 104.75329 40.88915 deg
194-
gamma 168.64054 100.96176 87.05690 deg
195-
beta 164.88965 92.99785 10.97642 deg
194+
delta 137.85320 129.94106 101.25917 deg
195+
epsilon 16.91576 75.24671 40.88915 deg
196+
beta 168.64054 100.96176 92.94310 deg
197+
gamma 15.11035 87.00215 10.97642 deg
196198

197199
Il IIl IIIl unit
198-
delta 2.4059922 2.2678994 1.3742868 rad
199-
epsilon 1.8660321 2.8840992 0.8571461 rad
200-
gamma 2.9433327 1.7621151 1.5194295 rad
201-
beta 1.8345217 3.0892703 1.3792217 rad
200+
delta 2.4059922 2.2678994 1.7673058 rad
201+
epsilon 1.2755606 0.2574935 0.8571461 rad
202+
beta 2.9433327 1.7621151 1.6221632 rad
203+
gamma 1.3070709 0.0523224 1.3792217 rad
202204
------------------------
203-
delta 137.85320 129.94106 78.74083 deg
204-
epsilon 106.91576 165.24671 49.11085 deg
205-
gamma 168.64054 100.96176 87.05690 deg
206-
beta 105.11035 177.00215 79.02358 deg
205+
delta 137.85320 129.94106 101.25917 deg
206+
epsilon 73.08424 14.75329 49.11085 deg
207+
beta 168.64054 100.96176 92.94310 deg
208+
gamma 74.88965 2.99785 79.02358 deg
207209

‎examples/ac-ala-ome-3d/ac-ala-ome-r13141516-ab.png

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‎examples/ac-ala-ome-3d/ac-ala-ome-r13141516-ac.png

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‎examples/ac-ala-ome-3d/ac-ala-ome-r13141516-bc.png

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