Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
tsoc
openmm
Commits
3bcd80b3
Commit
3bcd80b3
authored
Jul 07, 2010
by
Peter Eastman
Browse files
Reduced size of PME grid, since it was being made unnecessarily large for the requested accuracy.
parent
b41d77a9
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
9 additions
and
9 deletions
+9
-9
openmmapi/src/NonbondedForceImpl.cpp
openmmapi/src/NonbondedForceImpl.cpp
+3
-3
platforms/cuda/tests/TestCudaEwald.cpp
platforms/cuda/tests/TestCudaEwald.cpp
+2
-2
platforms/opencl/tests/TestOpenCLEwald.cpp
platforms/opencl/tests/TestOpenCLEwald.cpp
+2
-2
platforms/reference/tests/TestReferenceEwald.cpp
platforms/reference/tests/TestReferenceEwald.cpp
+2
-2
No files found.
openmmapi/src/NonbondedForceImpl.cpp
View file @
3bcd80b3
...
@@ -150,9 +150,9 @@ void NonbondedForceImpl::calcPMEParameters(const System& system, const Nonbonded
...
@@ -150,9 +150,9 @@ void NonbondedForceImpl::calcPMEParameters(const System& system, const Nonbonded
system
.
getDefaultPeriodicBoxVectors
(
boxVectors
[
0
],
boxVectors
[
1
],
boxVectors
[
2
]);
system
.
getDefaultPeriodicBoxVectors
(
boxVectors
[
0
],
boxVectors
[
1
],
boxVectors
[
2
]);
double
tol
=
force
.
getEwaldErrorTolerance
();
double
tol
=
force
.
getEwaldErrorTolerance
();
alpha
=
(
1.0
/
force
.
getCutoffDistance
())
*
std
::
sqrt
(
-
log
(
2.0
*
tol
));
alpha
=
(
1.0
/
force
.
getCutoffDistance
())
*
std
::
sqrt
(
-
log
(
2.0
*
tol
));
xsize
=
(
int
)
ceil
(
alpha
*
boxVectors
[
0
][
0
]
/
pow
(
0.5
*
tol
,
0.2
));
xsize
=
(
int
)
ceil
(
2
*
alpha
*
boxVectors
[
0
][
0
]
/
(
3
*
pow
(
tol
,
0.2
))
)
;
ysize
=
(
int
)
ceil
(
alpha
*
boxVectors
[
1
][
1
]
/
pow
(
0.5
*
tol
,
0.2
));
ysize
=
(
int
)
ceil
(
2
*
alpha
*
boxVectors
[
1
][
1
]
/
(
3
*
pow
(
tol
,
0.2
))
)
;
zsize
=
(
int
)
ceil
(
alpha
*
boxVectors
[
2
][
2
]
/
pow
(
0.5
*
tol
,
0.2
));
zsize
=
(
int
)
ceil
(
2
*
alpha
*
boxVectors
[
2
][
2
]
/
(
3
*
pow
(
tol
,
0.2
))
)
;
xsize
=
max
(
xsize
,
5
);
xsize
=
max
(
xsize
,
5
);
ysize
=
max
(
ysize
,
5
);
ysize
=
max
(
ysize
,
5
);
zsize
=
max
(
zsize
,
5
);
zsize
=
max
(
zsize
,
5
);
...
...
platforms/cuda/tests/TestCudaEwald.cpp
View file @
3bcd80b3
...
@@ -6,7 +6,7 @@
...
@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* *
* Portions copyright (c) 2008-200
9
Stanford University and the Authors. *
* Portions copyright (c) 2008-20
1
0 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Authors: Peter Eastman *
* Contributors: *
* Contributors: *
* *
* *
...
@@ -245,7 +245,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
...
@@ -245,7 +245,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
diff
+=
delta
.
dot
(
delta
);
diff
+=
delta
.
dot
(
delta
);
}
}
diff
=
sqrt
(
diff
)
/
norm
;
diff
=
sqrt
(
diff
)
/
norm
;
ASSERT
(
diff
<
5
*
tol
);
ASSERT
(
diff
<
2
*
tol
);
}
}
}
}
}
}
...
...
platforms/opencl/tests/TestOpenCLEwald.cpp
View file @
3bcd80b3
...
@@ -6,7 +6,7 @@
...
@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* *
* Portions copyright (c) 2008-200
9
Stanford University and the Authors. *
* Portions copyright (c) 2008-20
1
0 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Authors: Peter Eastman *
* Contributors: *
* Contributors: *
* *
* *
...
@@ -244,7 +244,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
...
@@ -244,7 +244,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
diff
+=
delta
.
dot
(
delta
);
diff
+=
delta
.
dot
(
delta
);
}
}
diff
=
sqrt
(
diff
)
/
norm
;
diff
=
sqrt
(
diff
)
/
norm
;
ASSERT
(
diff
<
5
*
tol
);
ASSERT
(
diff
<
2
*
tol
);
}
}
}
}
}
}
...
...
platforms/reference/tests/TestReferenceEwald.cpp
View file @
3bcd80b3
...
@@ -6,7 +6,7 @@
...
@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* *
* Portions copyright (c) 2008-200
9
Stanford University and the Authors. *
* Portions copyright (c) 2008-20
1
0 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Authors: Peter Eastman *
* Contributors: *
* Contributors: *
* *
* *
...
@@ -348,7 +348,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
...
@@ -348,7 +348,7 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
diff
+=
delta
.
dot
(
delta
);
diff
+=
delta
.
dot
(
delta
);
}
}
diff
=
sqrt
(
diff
)
/
norm
;
diff
=
sqrt
(
diff
)
/
norm
;
ASSERT
(
diff
<
5
*
tol
);
ASSERT
(
diff
<
2
*
tol
);
}
}
}
}
}
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment