Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
RobertNachbar`ConsistentForceField`
$AllowSymbolicCFFEnergy  |
|
| | ||||
Details and Options
Examples
(1)
Basic Examples
(1)
Parameterize the molecule symbolically:
In[1]:=
mol=Molecule["C=C"];Block
=True,
[mol,"PrimaryParameters"{}]
 | $AllowSymbolicCFFEnergy |
 | CFFParameterize |
Out[1]=
Atoms{C,C,H,H,H,H},Stretch{{1,2},,},{1,3},,,{1,4},,,{2,5},,,{2,6},,,Bend{2,1,3},,,{2,1,4},,,{{3,1,4},,},{1,2,5},,,{1,2,6},,,{{5,2,6},,},Torsion{},Twist{{3,4},1,2,{6,5}},,OutOfPlane{{{1,2,3,4},},{{2,1,5,6},}},Nonbond{3,5},,,{3,6},,,{4,5},,,{4,6},,,StretchStretch{2,1,3},,,,{2,1,4},,,,{3,1,4},,,,{1,2,5},,,,{1,2,6},,,,{5,2,6},,,,StretchBend{1,2,5},,,,{1,2,6},,,,{2,1,3},,,,{2,1,4},,,,{3,1,2},,,,{3,1,4},,,,{4,1,2},,,,{4,1,3},,,,{5,2,1},,,,{5,2,6},,,,{6,2,1},,,,{6,2,5},,,,BendBend{1,2,5,6},,,,{2,1,3,4},,,,{3,1,2,4},,,,{4,1,2,3},,,,{5,2,1,6},,,,{6,2,1,5},,,,BendBendTwist{3,1,2,6},,,,{3,1,2,5},,,,{4,1,2,6},,,,{4,1,2,5},,,,OopOop{{{{3,4},1,2,{6,5}},}},Constraint{}
D
0,D
l
0,l
l
0,l
l
0,l
l
0,l
ℋ
ϕ
ϕ
0
ℋ
ϕ
ϕ
0
ℋ
η
η
0
ℋ
ϕ
ϕ
0
ℋ
ϕ
ϕ
0
ℋ
η
η
0
ℋ
ϕ,E
ℋ
χ
ℋ
χ
ϵ
H,H
*
H,H
ϵ
H,H
*
H,H
ϵ
H,H
*
H,H
ϵ
H,H
*
H,H
ℱ
D,l
0,D
0,l
ℱ
D,l
0,D
0,l
ℱ
l,l
0,l
0,l
ℱ
D,l
0,D
0,l
ℱ
D,l
0,D
0,l
ℱ
l,l
0,l
0,l
ℱ
D,ϕ
0,D
ϕ
0
ℱ
D,ϕ
0,D
ϕ
0
ℱ
D,ϕ
0,D
ϕ
0
ℱ
D,ϕ
0,D
ϕ
0
ℱ
l,ϕ
0,l
ϕ
0
ℱ
l,η
0,l
η
0
ℱ
l,ϕ
0,l
ϕ
0
ℱ
l,η
0,l
η
0
ℱ
l,ϕ
0,l
ϕ
0
ℱ
l,η
0,l
η
0
ℱ
l,ϕ
0,l
ϕ
0
ℱ
l,η
0,l
η
0
ℱ
ϕ,ϕ
ϕ
0
ϕ
0
ℱ
ϕ,ϕ
ϕ
0
ϕ
0
†
ℱ
ϕ,η
ϕ
0
η
0
†
ℱ
ϕ,η
ϕ
0
η
0
†
ℱ
ϕ,η
ϕ
0
η
0
†
ℱ
ϕ,η
ϕ
0
η
0
ϕ,ϕ
ϕ
0
ϕ
0
ϕ,ϕ
ϕ
0
ϕ
0
ϕ,ϕ
ϕ
0
ϕ
0
ϕ,ϕ
ϕ
0
ϕ
0
ℱ
χ,χ
Compute the symbolic energy:
In[2]:=
Block
=True,symbolicEnergy=
[mol,"PrimaryParameters"{}]
| $AllowSymbolicCFFEnergy |
| CFFEnergy |
Out[2]=
1
2
ℋ
η
2
(2.05773-)
η
0
1
2
ℋ
η
2
(2.05773-)
η
0
1
2
ℋ
ϕ
2
(2.11273-)
ϕ
0
1
2
ℋ
ϕ
2
(2.11273-)
ϕ
0
1
2
ℋ
ϕ
2
(2.11273-)
ϕ
0
1
2
ℋ
ϕ
2
(2.11273-)
ϕ
0
1
2
D
2
(1.33579-)
0,D
1
2
l
2
1.08549-
0,l
1
2
l
2
1.08549-
0,l
1
2
l
2
1.08549-
0,l
1
2
l
2
1.08549-
0,l
ϕ
0
ϕ
0
ϕ,ϕ
ϕ
0
ϕ
0
ϕ,ϕ
ϕ
0
ϕ
0
ϕ,ϕ
ϕ
0
ϕ
0
ϕ,ϕ
0,D
0,l
ℱ
D,l
0,D
0,l
ℱ
D,l
0,D
0,l
ℱ
D,l
0,D
0,l
ℱ
D,l
ϕ
0
0,D
ℱ
D,ϕ
ϕ
0
0,D
ℱ
D,ϕ
ϕ
0
0,D
ℱ
D,ϕ
ϕ
0
0,D
ℱ
D,ϕ
0,l
0,l
ℱ
l,l
0,l
0,l
ℱ
l,l
η
0
0,l
ℱ
l,η
η
0
0,l
ℱ
l,η
η
0
0,l
ℱ
l,η
η
0
0,l
ℱ
l,η
ϕ
0
0,l
ℱ
l,ϕ
ϕ
0
0,l
ℱ
l,ϕ
ϕ
0
0,l
ℱ
l,ϕ
ϕ
0
0,l
ℱ
l,ϕ
ϕ
0
ϕ
0
ℱ
ϕ,ϕ
ϕ
0
ϕ
0
ℱ
ϕ,ϕ
η
0
ϕ
0
†
ℱ
ϕ,η
η
0
ϕ
0
†
ℱ
ϕ,η
η
0
ϕ
0
†
ℱ
ϕ,η
η
0
ϕ
0
†
ℱ
ϕ,η
ϵ
H,H
6
()
*
H,H
9
()
*
H,H
ϵ
H,H
6
()
*
H,H
9
()
*
H,H
ϵ
H,H
6
()
*
H,H
9
()
*
H,H
ϵ
H,H
6
()
*
H,H
9
()
*
H,H
Convert the CFF parameters to raw form:
In[3]:=
rawParameters=
["Parameters"]/.q:Quantity[_,"AngularDegrees"]UnitConvert[q,"Radians"]/.q_QuantityQuantityMagnitude[q];
 | $CFFPublishedPatternsParameters |
Apply the raw parameters to the symbolic energy:
In[4]:=
symbolicEnergy//.rawParameters
Out[4]=
0.329258
Compare to the usual result:
In[5]:=
 | CFFEnergy |
Out[5]=
0.329258/mol
kcal
th
 |
|
""