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tsoc
openmm
Commits
b8f6d269
Commit
b8f6d269
authored
Jan 02, 2015
by
Jason Swails
Browse files
Changes to bring in line with SimTK style guide.
parent
ab82c962
Changes
33
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Showing
20 changed files
with
68 additions
and
27 deletions
+68
-27
openmmapi/include/openmm/AndersenThermostat.h
openmmapi/include/openmm/AndersenThermostat.h
+3
-1
openmmapi/include/openmm/CMAPTorsionForce.h
openmmapi/include/openmm/CMAPTorsionForce.h
+3
-1
openmmapi/include/openmm/CMMotionRemover.h
openmmapi/include/openmm/CMMotionRemover.h
+3
-1
openmmapi/include/openmm/CustomAngleForce.h
openmmapi/include/openmm/CustomAngleForce.h
+3
-1
openmmapi/include/openmm/CustomBondForce.h
openmmapi/include/openmm/CustomBondForce.h
+3
-1
openmmapi/include/openmm/CustomCompoundBondForce.h
openmmapi/include/openmm/CustomCompoundBondForce.h
+3
-1
openmmapi/include/openmm/CustomExternalForce.h
openmmapi/include/openmm/CustomExternalForce.h
+3
-1
openmmapi/include/openmm/CustomTorsionForce.h
openmmapi/include/openmm/CustomTorsionForce.h
+3
-1
openmmapi/include/openmm/HarmonicAngleForce.h
openmmapi/include/openmm/HarmonicAngleForce.h
+3
-1
openmmapi/include/openmm/HarmonicBondForce.h
openmmapi/include/openmm/HarmonicBondForce.h
+3
-1
openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h
openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h
+3
-1
openmmapi/include/openmm/MonteCarloBarostat.h
openmmapi/include/openmm/MonteCarloBarostat.h
+3
-1
openmmapi/include/openmm/MonteCarloMembraneBarostat.h
openmmapi/include/openmm/MonteCarloMembraneBarostat.h
+3
-1
openmmapi/include/openmm/PeriodicTorsionForce.h
openmmapi/include/openmm/PeriodicTorsionForce.h
+3
-1
openmmapi/include/openmm/RBTorsionForce.h
openmmapi/include/openmm/RBTorsionForce.h
+3
-1
openmmapi/include/openmm/System.h
openmmapi/include/openmm/System.h
+1
-1
openmmapi/src/System.cpp
openmmapi/src/System.cpp
+2
-1
platforms/reference/tests/TestReferenceCustomGBForce.cpp
platforms/reference/tests/TestReferenceCustomGBForce.cpp
+14
-7
platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp
.../reference/tests/TestReferenceCustomManyParticleForce.cpp
+2
-1
platforms/reference/tests/TestReferenceGBVIForce.cpp
platforms/reference/tests/TestReferenceGBVIForce.cpp
+4
-2
No files found.
openmmapi/include/openmm/AndersenThermostat.h
View file @
b8f6d269
...
...
@@ -123,7 +123,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/CMAPTorsionForce.h
View file @
b8f6d269
...
...
@@ -154,7 +154,9 @@ public:
*
* @returns false
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/CMMotionRemover.h
View file @
b8f6d269
...
...
@@ -67,7 +67,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/CustomAngleForce.h
View file @
b8f6d269
...
...
@@ -208,7 +208,9 @@ public:
*
* @returns false
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/CustomBondForce.h
View file @
b8f6d269
...
...
@@ -205,7 +205,9 @@ public:
*
* @returns false
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/CustomCompoundBondForce.h
View file @
b8f6d269
...
...
@@ -303,7 +303,9 @@ public:
*
* @returns false
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/CustomExternalForce.h
View file @
b8f6d269
...
...
@@ -205,7 +205,9 @@ public:
*
* @returns false
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/CustomTorsionForce.h
View file @
b8f6d269
...
...
@@ -211,7 +211,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/HarmonicAngleForce.h
View file @
b8f6d269
...
...
@@ -108,7 +108,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/HarmonicBondForce.h
View file @
b8f6d269
...
...
@@ -105,7 +105,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h
View file @
b8f6d269
...
...
@@ -177,7 +177,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
true
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
true
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/MonteCarloBarostat.h
View file @
b8f6d269
...
...
@@ -133,7 +133,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
true
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
true
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/MonteCarloMembraneBarostat.h
View file @
b8f6d269
...
...
@@ -230,7 +230,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
true
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
true
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/PeriodicTorsionForce.h
View file @
b8f6d269
...
...
@@ -114,7 +114,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/RBTorsionForce.h
View file @
b8f6d269
...
...
@@ -123,7 +123,9 @@ public:
*
* @returns true if force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;}
bool
usesPeriodicBoundaryConditions
()
const
{
return
false
;
}
protected:
ForceImpl
*
createImpl
()
const
;
private:
...
...
openmmapi/include/openmm/System.h
View file @
b8f6d269
...
...
@@ -230,7 +230,7 @@ public:
* If a force in this System does not implement usesPeriodicBoundaryConditions
* a OpenMM::OpenMMException is thrown
*
* @return true
o
f at least one force uses PBC and false otherwise
* @return true
i
f at least one force uses PBC and false otherwise
*/
bool
usesPeriodicBoundaryConditions
();
private:
...
...
openmmapi/src/System.cpp
View file @
b8f6d269
...
...
@@ -129,7 +129,8 @@ bool System::usesPeriodicBoundaryConditions() {
try
{
if
((
*
it
)
->
usesPeriodicBoundaryConditions
())
uses_pbc
=
true
;
}
catch
(
OpenMMException
&
e
)
{
}
catch
(
OpenMMException
&
e
)
{
all_forces_implement
=
false
;
}
}
...
...
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @
b8f6d269
...
...
@@ -140,7 +140,8 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
ASSERT
(
obc
->
usesPeriodicBoundaryConditions
());
ASSERT
(
standardSystem
.
usesPeriodicBoundaryConditions
());
ASSERT
(
customSystem
.
usesPeriodicBoundaryConditions
());
}
else
{
}
else
{
ASSERT
(
!
custom
->
usesPeriodicBoundaryConditions
());
ASSERT
(
!
obc
->
usesPeriodicBoundaryConditions
());
ASSERT
(
!
standardSystem
.
usesPeriodicBoundaryConditions
());
...
...
@@ -539,7 +540,8 @@ static void buildEthane( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
C_gamma
=
-
0.2863
;
H_radius
=
0.125
;
H_gamma
=
0.2437
;
}
else
{
}
else
{
C_radius
=
0.215
;
C_gamma
=
-
1.1087
;
H_radius
=
0.150
;
...
...
@@ -617,7 +619,8 @@ static void buildDimer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
C_gamma
=
-
0.2863
;
H_radius
=
0.125
;
H_gamma
=
0.2437
;
}
else
{
}
else
{
C_radius
=
0.215
;
C_gamma
=
-
1.1087
;
H_radius
=
0.150
;
...
...
@@ -744,7 +747,8 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
}
scaledRadiusJ
=
radiusJ
;
// errors++;
}
else
{
}
else
{
double
rJ2
=
radiusJ
*
radiusJ
;
...
...
@@ -774,7 +778,8 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
scaledRadiusJ
=
(
radiusJ
*
radiusJ
*
radiusJ
)
-
0.125
*
scaledRadiusJ
;
if
(
scaledRadiusJ
>
0.0
){
scaledRadiusJ
=
0.95
*
pow
(
scaledRadiusJ
,
(
1.0
/
3.0
)
);
}
else
{
}
else
{
scaledRadiusJ
=
0.0
;
}
}
...
...
@@ -849,9 +854,11 @@ void testGBVI(GBVIForce::NonbondedMethod gbviMethod, CustomGBForce::NonbondedMet
if
(
molecule
==
"Monomer"
){
buildMonomer
(
gbvi
,
positions
);
}
else
if
(
molecule
==
"Dimer"
){
}
else
if
(
molecule
==
"Dimer"
){
buildDimer
(
gbvi
,
positions
);
}
else
{
}
else
{
buildEthane
(
gbvi
,
positions
);
}
...
...
platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp
View file @
b8f6d269
...
...
@@ -66,7 +66,8 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
if
(
force
->
getNonbondedMethod
()
==
CustomManyParticleForce
::
CutoffPeriodic
)
{
ASSERT
(
force
->
usesPeriodicBoundaryConditions
());
ASSERT
(
system
.
usesPeriodicBoundaryConditions
());
}
else
{
}
else
{
ASSERT
(
!
force
->
usesPeriodicBoundaryConditions
());
ASSERT
(
!
system
.
usesPeriodicBoundaryConditions
());
}
...
...
platforms/reference/tests/TestReferenceGBVIForce.cpp
View file @
b8f6d269
...
...
@@ -128,7 +128,8 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
C_gamma
=
-
0.2863
;
H_radius
=
0.125
;
H_gamma
=
0.2437
;
}
else
{
}
else
{
C_radius
=
0.215
;
C_gamma
=
-
1.1087
;
H_radius
=
0.150
;
...
...
@@ -144,7 +145,8 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
GBVIForce
*
forceField
=
new
GBVIForce
();
if
(
applyBornRadiiScaling
){
forceField
->
setBornRadiusScalingMethod
(
GBVIForce
::
QuinticSpline
);
}
else
{
}
else
{
forceField
->
setBornRadiusScalingMethod
(
GBVIForce
::
NoScaling
);
}
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
){
...
...
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