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fdti.py
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Created
Wed, Oct 16, 17:08
Size
906 B
Mime Type
text/x-python
Expires
Fri, Oct 18, 17:08 (2 d)
Engine
blob
Format
Raw Data
Handle
21713930
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rLAMMPS lammps
fdti.py
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#!/usr/bin/env python
# fdti.py - integrate compute fep results using the trapezoidal rule
import
sys
,
math
if
len
(
sys
.
argv
)
<
3
:
print
"Finite Difference Thermodynamic Integration (Mezei 1987)"
print
"Trapezoidal integration of compute_fep results at equally-spaced points"
print
"usage: fdti.py temperature hderiv < fep.lmp"
sys
.
exit
()
rt
=
0.008314
/
4.184
*
float
(
sys
.
argv
[
1
])
hderiv
=
float
(
sys
.
argv
[
2
])
line
=
sys
.
stdin
.
readline
()
while
line
.
startswith
(
"#"
):
line
=
sys
.
stdin
.
readline
()
v
=
1.0
tok
=
line
.
split
()
if
len
(
tok
)
==
4
:
v
=
float
(
tok
[
3
])
lo
=
-
rt
*
math
.
log
(
float
(
tok
[
2
])
/
v
)
i
=
0
sum
=
0.0
for
line
in
sys
.
stdin
:
tok
=
line
.
split
()
if
len
(
tok
)
==
4
:
v
=
float
(
tok
[
3
])
hi
=
-
rt
*
math
.
log
(
float
(
tok
[
2
])
/
v
)
sum
+=
(
hi
+
lo
)
/
(
2
*
hderiv
)
lo
=
hi
i
+=
1
print
sum
/
i
# int_0^1: divide by i == multiply by delta
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