Morse & Morse with Feynman-Hibbs corrections: Music implementation

1

To implement a new potential energy model into music, the following expressions are needed:
V(r
ij
) Expression for potential energy in kcal/Mol (dependant on r
ij
)
(dV/dr
ij
) x r
ij
- needed to use a potential during simulation
Below are all needed for pmap generation:
dV/dr
ij
x 1/r
ij

d( dV/dr
ij
x 1/r
ij
)/dr
ij
x 1/r
ij

d( d( dV/dr
ij
x 1/r
ij
)/dr
ij
x 1/r
i j
)/dr
ij
x 1/r
ij


Morse potential:

( ) exp 1 2exp 1
2
ij ij
M ij
eq eq
r r
V r D
r r

| | ( ( | | | |
| = ( ( | |
| |
|
( (
\ . \ . \ .
(1.1)
With V
M
(r
ij
) = Morse potential energy in kcal/Mol
D = Depth of potential energy well in kcal/Mol
r
eq

= equilibrium bond length in Armstrongs
= Force constant (sometimes referred to as in literature)
r
ij
= distance between two atoms in Armstrongs

exp 1 exp 1
2
ij ij
M
ij eq eq eq
r r
dV
D
dr r r r

| | ( ( | | | |
| = + ( ( | |
| |
|
( (
\ . \ . \ .
(1.2)

exp 1 exp 1
2
ij ij ij
M
ij
ij eq eq eq
r r r
dV
r D
dr r r r

| | ( ( | | | |
| = + ( ( | |
| |
|
( (
\ . \ . \ .
(1.3)
Eqn (1.3) used in morsepot.F90, function morse_multint

1
exp 1 exp 1
2
ij ij
M
ij ij ij eq eq eq
r r
dV
D
dr r r r r r

| | ( ( | | | |
| = + ( ( | |
| |
|
( (
\ . \ . \ .
(1.4)
Let:
( ) exp 1 exp 1
2
ij ij
ij
eq eq
r r
U r
r r

( ( | | | |
= + ( ( | |
| |
( (
\ . \ .

Thus:

( )
1
M
ij ij ij eq
dV
D U
dr r r r

=
(1.5)
Morse & Morse with Feynman-Hibbs corrections: Music implementation
2

Eqn (1.5) used morsepot.F90, function morse_snglintHOT
Using product rule:

( ) ( )
2
1
M
ij ij ij ij eq ij eq
dV d
D U D U
dr dr r r r r r

| |
' = +
|
|
\ .
(1.6)

1 1
M
ij ij ij ij eq ij
dV d
D U U
dr dr r r r r

| |

' = +
| `
|

\ . )
(1.7)

2
1 1 1
M
ij ij ij ij ij eq ij
dV d
D U U
dr dr r r r r r

| |

' = +
| `
|

\ . )
(1.8)
Eqn (1.8) used in morsepot.F90, function morse_snglintHOT
Using product rule:

3 2 2
1 1 1 1 1
2
M
ij ij ij ij ij ij eq ij ij eq ij ij
dV d d
D U U D U U U
dr dr dr r r r r r r r r r

| | | |

' ' '' = + + + | | ` `
| |

\ . ) ) \ .
(1.9)

3 2
1 1 1 2 1 1 1
M
ij ij ij ij ij ij ij eq ij ij ij ij
dV d d
D U U U U U
dr dr dr r r r r r r r r r

| | | | | |

' ' '' = + + + | | | ` `
| | |

\ . ) ) \ . \ .
(1.10)
Eqn (1.10) used in morsepot.F90, function morse_snglintHOT
With:

exp
( ) exp 1 1
4 2
ij ij
ij
eq eq eq
r r
U r
r r r

| | ( ( | | | |
| ' = ( ( | |
| |
|
( (
\ . \ . \ .

2
2
exp
( ) exp 1 1
8 2
ij ij
ij
eq eq eq
r r
U r
r r r

| | ( ( | | | |
| '' = + ( ( | |
| |
|
( (
\ . \ . \ .


Morse & Morse with Feynman-Hibbs corrections: Music implementation
3

Morse with Feynman-Hibbs correction:

2
2
( ) ( ) ( )
24
FH ij M ij M ij
B
h
V r V r V r
k T
| |
= + V
|
\ .
(2.1)
With:
V
FH
(r
ij
) = Feynman-Hibbs corrected potential energy in kcal/Mol
h = Plancks constant divided by 2,
= the reduced mass of H
2
molecule (mass/2 for fluid-fluid interactions, regular mass for
fluid-solid)
k
B
= Boltzmann constant
T = temperature in K
Let:
2
Fac24
24
B
h
k T
| |
=
|
\ .

2
2
( ) ( ) ( )
M ij M ij M ij
ij
V r V r V r
r
| |
'' ' V = +
|
|
\ .


2
( ) ( ) Fac24 ( )
FH ij M ij M ij
V r V r V r = + V
(2.2)

2
( ) ( ) Fac24 ( ) ( )
FH ij M ij M ij M ij
ij
V r V r V r V r
r
( | |
'' ' = + + ( |
|
(
\ .
(2.3)

2
2 2
( ) Fac24 ( ) ( ) ( )
FH
M ij M ij M ij M ij
ij ij ij
dV
V r V r V r V r
dr r r
| | | | | |
' ''' '' ' = + + | | |
| | |
\ . \ . \ .
(2.4)

2
2 2
( ) Fac24 ( ) ( ) ( )
FH
ij M ij M ij M ij M ij ij
ij ij ij
dV
r V r V r V r V r r
dr r r
( | | | | | |
' ''' '' ' ( = + + | | |
| | |
(
\ . \ . \ .
(2.5)

Eqn (2.5) used in morsefeynpot.F90, function morsefeyn_multint

2
1 1 2 2
( ) Fac24 ( ) ( ) ( )
FH
M ij M ij M ij M ij
ij ij ij ij ij
dV
V r V r V r V r
dr r r r r
| | | | | |

' ''' '' ' = + + | | | `
| | |
\ . \ . \ . )
(2.6)
Eqn (2.6) used in morsefeynpot.F90, function morsefeyn_snglintHOT
Morse & Morse with Feynman-Hibbs corrections: Music implementation
4

Let:
2
2 2
( ) ( ) Fac24 ( ) ( ) ( )
FH
ij M ij M ij M ij M ij
ij ij ij
dV
U r V r V r V r V r
r r dr
| | | | | |
' ''' '' ' = + + = | | |
| | |
\ . \ . \ .



1 1
( )
FH
ij
ij ij ij
dV
U r
dr r r
=
(2.7)

2
1 1 1
( ) ( )
FH
ij ij
ij ij ij ij ij
dV d
U r U r
dr dr r r r
| |
' =
|
|
\ .
(2.8)

2
1 1 1 1 1
( ) ( )
FH
ij ij
ij ij ij ij ij ij ij
dV d
U r U r
dr dr r r r r r
| | | |
' =
| |
| |
\ . \ .
(2.9)

2
1 1 1 1
( ) ( )
FH
ij ij
ij ij ij ij ij ij
dV d
U r U r
dr dr r r r r
| | | |
' =
| |
| |
\ . \ .
(2.10)
Eqn (2.10) used in morsefeynpot.F90, function morsefeyn_snglintHOT

2 2 3
1 1 1 1 1 1 1 2 1
( ) ( ) ( ) ( ) ( )
FH
ij ij ij ij ij
ij ij ij ij ij ij ij ij ij ij ij ij
dV d d
U r U r U r U r U r
dr dr dr r r r r r r r r r
| | ( | | | | | |
'' ' ' = + | ( | | |
| | | |
(
\ . \ . \ . \ .
(2.11)
Eqn used in morsefeynpot.F90, function morsefeyn_snglintHOT
With:
2 3
2 4 4
( ) ( ) Fac24 ( ) ( ) ( ) ( )
ij M ij M ij M ij M ij M ij
ij ij ij
U r V r V r V r V r V r
r r r
| | | | | | | |
' '' '''' ''' '' ' = + + + | | | |
| | | |
\ . \ . \ . \ .

2 2 3 3
4
2 2 4 8 4
( ) ( ) ( ) ( ) ( ) ( )
( ) ( ) Fac24
12
( )
M ij M ij M ij M ij M ij M ij
ij ij ij ij ij
ij M ij
M ij
ij
V r V r V r V r V r V r
r r r r r
U r V r
V r
r
| | | | | | | | | | | |
''''' '''' ''' ''' '' '' + + + | | | | | |
| | | | |
|
\ . \ . \ . \ . \ .
'' ''' = +
|
| |
|
'
|
|
|
\ . \ .

Morse & Morse with Feynman-Hibbs corrections: Music implementation
5

2 3 4
2 6 12 12
( ) ( ) Fac24 ( ) ( ) ( ) ( ) ( )
ij M ij M ij M ij M ij M ij M ij
ij ij ij ij
U r V r V r V r V r V r V r
r r r r
| | | | | | | | | |
'' ''' ''''' '''' ''' '' ' = + + + | | | | |
| | | | |
\ . \ . \ . \ . \ .

2
2
3
3
( ) exp 1 exp 1
2
exp
( ) exp 1 1
2 2
( ) exp 1
ij ij
M ij
eq eq eq
ij ij
M ij
eq eq eq
ij
M ij
eq eq
r r
V r D
r r r
r r
V r D
r r r
r
V r D
r r

| | ( ( | | | |
| ' = + ( ( | |
| |
|
( (
\ . \ . \ .
| | ( ( | | | |
| '' = ( ( | |
| |
|
( (
\ . \ . \ .
|
''' =

\
4
4
5
5
exp
1
4 2
exp
( ) exp 1 1
8 2
exp
( ) exp 1 1
16 2
ij
eq
ij ij
M ij
eq eq eq
ij ij
M ij
eq eq
r
r
r r
V r D
r r r
r r
V r D
r r

| | ( ( | | |
| + ( ( | |
| |
|
( (
. \ . \ .
| | ( ( | | | |
| '''' = ( ( | |
| |
|
( (
\ . \ . \ .
( | |
''''' = + ( |
|
(
\ .
eq
r
| | ( | |
|
( |
|
|
(
\ . \ .