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
f322abd1
Commit
f322abd1
authored
Mar 19, 2015
by
peastman
Browse files
Merge pull request #858 from peastman/reference
Simplification to reference platform tests
parents
476c1bab
f66c9b61
Changes
34
Show whitespace changes
Inline
Side-by-side
Showing
20 changed files
with
40 additions
and
90 deletions
+40
-90
platforms/reference/tests/TestReferenceAndersenThermostat.cpp
...forms/reference/tests/TestReferenceAndersenThermostat.cpp
+2
-3
platforms/reference/tests/TestReferenceBrownianIntegrator.cpp
...forms/reference/tests/TestReferenceBrownianIntegrator.cpp
+2
-5
platforms/reference/tests/TestReferenceCMMotionRemover.cpp
platforms/reference/tests/TestReferenceCMMotionRemover.cpp
+2
-1
platforms/reference/tests/TestReferenceCheckpoints.cpp
platforms/reference/tests/TestReferenceCheckpoints.cpp
+2
-2
platforms/reference/tests/TestReferenceCustomAngleForce.cpp
platforms/reference/tests/TestReferenceCustomAngleForce.cpp
+2
-2
platforms/reference/tests/TestReferenceCustomBondForce.cpp
platforms/reference/tests/TestReferenceCustomBondForce.cpp
+2
-1
platforms/reference/tests/TestReferenceCustomCompoundBondForce.cpp
.../reference/tests/TestReferenceCustomCompoundBondForce.cpp
+2
-6
platforms/reference/tests/TestReferenceCustomExternalForce.cpp
...orms/reference/tests/TestReferenceCustomExternalForce.cpp
+2
-1
platforms/reference/tests/TestReferenceCustomGBForce.cpp
platforms/reference/tests/TestReferenceCustomGBForce.cpp
+2
-7
platforms/reference/tests/TestReferenceCustomHbondForce.cpp
platforms/reference/tests/TestReferenceCustomHbondForce.cpp
+2
-5
platforms/reference/tests/TestReferenceCustomIntegrator.cpp
platforms/reference/tests/TestReferenceCustomIntegrator.cpp
+2
-12
platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp
.../reference/tests/TestReferenceCustomManyParticleForce.cpp
+2
-6
platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp
...rms/reference/tests/TestReferenceCustomNonbondedForce.cpp
+2
-18
platforms/reference/tests/TestReferenceCustomTorsionForce.cpp
...forms/reference/tests/TestReferenceCustomTorsionForce.cpp
+2
-3
platforms/reference/tests/TestReferenceEwald.cpp
platforms/reference/tests/TestReferenceEwald.cpp
+2
-8
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
+2
-4
platforms/reference/tests/TestReferenceGBVIForce.cpp
platforms/reference/tests/TestReferenceGBVIForce.cpp
+2
-3
platforms/reference/tests/TestReferenceHarmonicAngleForce.cpp
...forms/reference/tests/TestReferenceHarmonicAngleForce.cpp
+2
-1
platforms/reference/tests/TestReferenceHarmonicBondForce.cpp
platforms/reference/tests/TestReferenceHarmonicBondForce.cpp
+2
-1
platforms/reference/tests/TestReferenceKineticEnergy.cpp
platforms/reference/tests/TestReferenceKineticEnergy.cpp
+2
-1
No files found.
platforms/reference/tests/TestReferenceAndersenThermostat.cpp
View file @
f322abd1
...
...
@@ -48,12 +48,13 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
void
testTemperature
()
{
const
int
numParticles
=
8
;
const
double
temp
=
100.0
;
const
double
collisionFreq
=
10.0
;
const
int
numSteps
=
5000
;
ReferencePlatform
platform
;
System
system
;
VerletIntegrator
integrator
(
0.003
);
NonbondedForce
*
forceField
=
new
NonbondedForce
();
...
...
@@ -94,7 +95,6 @@ void testConstraints() {
const
double
temp
=
100.0
;
const
double
collisionFreq
=
10.0
;
const
int
numSteps
=
15000
;
ReferencePlatform
platform
;
System
system
;
VerletIntegrator
integrator
(
0.004
);
NonbondedForce
*
forceField
=
new
NonbondedForce
();
...
...
@@ -147,7 +147,6 @@ void testRandomSeed() {
const
int
numParticles
=
8
;
const
double
temp
=
100.0
;
const
double
collisionFreq
=
10.0
;
ReferencePlatform
platform
;
System
system
;
VerletIntegrator
integrator
(
0.01
);
NonbondedForce
*
forceField
=
new
NonbondedForce
();
...
...
platforms/reference/tests/TestReferenceBrownianIntegrator.cpp
View file @
f322abd1
...
...
@@ -48,10 +48,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testSingleBond
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
2.0
);
system
.
addParticle
(
2.0
);
...
...
@@ -88,7 +89,6 @@ void testTemperature() {
const
int
numParticles
=
8
;
const
int
numBonds
=
numParticles
-
1
;
const
double
temp
=
10.0
;
ReferencePlatform
platform
;
System
system
;
BrownianIntegrator
integrator
(
temp
,
2.0
,
0.01
);
HarmonicBondForce
*
forceField
=
new
HarmonicBondForce
();
...
...
@@ -125,7 +125,6 @@ void testTemperature() {
void
testConstraints
()
{
const
int
numParticles
=
8
;
const
double
temp
=
100.0
;
ReferencePlatform
platform
;
System
system
;
BrownianIntegrator
integrator
(
temp
,
2.0
,
0.001
);
integrator
.
setConstraintTolerance
(
1e-5
);
...
...
@@ -165,7 +164,6 @@ void testConstraints() {
}
void
testConstrainedMasslessParticles
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
0.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -200,7 +198,6 @@ void testRandomSeed() {
const
int
numParticles
=
8
;
const
double
temp
=
100.0
;
const
double
collisionFreq
=
10.0
;
ReferencePlatform
platform
;
System
system
;
BrownianIntegrator
integrator
(
temp
,
2.0
,
0.001
);
NonbondedForce
*
forceField
=
new
NonbondedForce
();
...
...
platforms/reference/tests/TestReferenceCMMotionRemover.cpp
View file @
f322abd1
...
...
@@ -49,6 +49,8 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
Vec3
calcCM
(
const
vector
<
Vec3
>&
values
,
System
&
system
)
{
Vec3
cm
;
for
(
int
j
=
0
;
j
<
system
.
getNumParticles
();
++
j
)
{
...
...
@@ -63,7 +65,6 @@ void testMotionRemoval() {
const
int
numParticles
=
8
;
const
double
temp
=
100.0
;
const
double
collisionFreq
=
10.0
;
ReferencePlatform
platform
;
System
system
;
VerletIntegrator
integrator
(
0.01
);
HarmonicBondForce
*
bonds
=
new
HarmonicBondForce
();
...
...
platforms/reference/tests/TestReferenceCheckpoints.cpp
View file @
f322abd1
...
...
@@ -48,6 +48,8 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
compareStates
(
State
&
s1
,
State
&
s2
)
{
...
...
@@ -71,7 +73,6 @@ void testCheckpoint() {
const
int
numParticles
=
10
;
const
double
boxSize
=
3.0
;
const
double
temperature
=
200.0
;
ReferencePlatform
platform
;
System
system
;
system
.
addForce
(
new
AndersenThermostat
(
0.0
,
100.0
));
NonbondedForce
*
nonbonded
=
new
NonbondedForce
();
...
...
@@ -125,7 +126,6 @@ void testSetState() {
const
int
numParticles
=
10
;
const
double
boxSize
=
3.0
;
const
double
temperature
=
200.0
;
ReferencePlatform
platform
;
System
system
;
system
.
addForce
(
new
AndersenThermostat
(
0.0
,
100.0
));
NonbondedForce
*
nonbonded
=
new
NonbondedForce
();
...
...
platforms/reference/tests/TestReferenceCustomAngleForce.cpp
View file @
f322abd1
...
...
@@ -47,11 +47,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testAngles
()
{
ReferencePlatform
platform
;
// Create a system using a CustomAngleForce.
System
customSystem
;
...
...
platforms/reference/tests/TestReferenceCustomBondForce.cpp
View file @
f322abd1
...
...
@@ -46,10 +46,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testBonds
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
platforms/reference/tests/TestReferenceCustomCompoundBondForce.cpp
View file @
f322abd1
...
...
@@ -52,11 +52,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testBond
()
{
ReferencePlatform
platform
;
// Create a system using a CustomCompoundBondForce.
System
customSystem
;
...
...
@@ -147,7 +147,6 @@ void testBond() {
}
void
testPositionDependence
()
{
ReferencePlatform
platform
;
System
customSystem
;
customSystem
.
addParticle
(
1.0
);
customSystem
.
addParticle
(
1.0
);
...
...
@@ -179,7 +178,6 @@ void testContinuous2DFunction() {
const
double
xmax
=
1.1
;
const
double
ymin
=
0.0
;
const
double
ymax
=
0.9
;
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
VerletIntegrator
integrator
(
0.01
);
...
...
@@ -227,7 +225,6 @@ void testContinuous3DFunction() {
const
double
ymax
=
0.9
;
const
double
zmin
=
0.2
;
const
double
zmax
=
1.3
;
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
VerletIntegrator
integrator
(
0.01
);
...
...
@@ -273,7 +270,6 @@ void testContinuous3DFunction() {
void
testMultipleBonds
()
{
// Two compound bonds using Urey-Bradley example from API doc
ReferencePlatform
platform
;
System
customSystem
;
customSystem
.
addParticle
(
1.0
);
customSystem
.
addParticle
(
1.0
);
...
...
platforms/reference/tests/TestReferenceCustomExternalForce.cpp
View file @
f322abd1
...
...
@@ -46,10 +46,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testForce
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @
f322abd1
...
...
@@ -51,6 +51,8 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testOBC
(
GBSAOBCForce
::
NonbondedMethod
obcMethod
,
CustomGBForce
::
NonbondedMethod
customMethod
)
{
...
...
@@ -58,7 +60,6 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
const
int
numParticles
=
numMolecules
*
2
;
const
double
boxSize
=
10.0
;
const
double
cutoff
=
2.0
;
ReferencePlatform
platform
;
// Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
...
...
@@ -190,7 +191,6 @@ void testMembrane() {
const
int
numMolecules
=
70
;
const
int
numParticles
=
numMolecules
*
2
;
const
double
boxSize
=
10.0
;
ReferencePlatform
platform
;
// Create a system with an implicit membrane.
...
...
@@ -280,7 +280,6 @@ void testMembrane() {
}
void
testTabulatedFunction
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -313,7 +312,6 @@ void testTabulatedFunction() {
}
void
testMultipleChainRules
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -341,7 +339,6 @@ void testMultipleChainRules() {
}
void
testPositionDependence
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -405,7 +402,6 @@ void testPositionDependence() {
}
void
testExclusions
()
{
ReferencePlatform
platform
;
for
(
int
i
=
3
;
i
<
4
;
i
++
)
{
System
system
;
system
.
addParticle
(
1.0
);
...
...
@@ -817,7 +813,6 @@ void testGBVI(GBVIForce::NonbondedMethod gbviMethod, CustomGBForce::NonbondedMet
const
int
numMolecules
=
1
;
const
double
boxSize
=
10.0
;
ReferencePlatform
platform
;
GBVIForce
*
gbvi
=
new
GBVIForce
();
std
::
vector
<
Vec3
>
positions
;
...
...
platforms/reference/tests/TestReferenceCustomHbondForce.cpp
View file @
f322abd1
...
...
@@ -49,11 +49,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testHbond
()
{
ReferencePlatform
platform
;
// Create a system using a CustomHbondForce.
System
customSystem
;
...
...
@@ -151,7 +151,6 @@ void testHbond() {
}
void
testExclusions
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -178,7 +177,6 @@ void testExclusions() {
}
void
testCutoff
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -206,7 +204,6 @@ void testCutoff() {
}
void
testCustomFunctions
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
platforms/reference/tests/TestReferenceCustomIntegrator.cpp
View file @
f322abd1
...
...
@@ -49,13 +49,14 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
/**
* Test a simple leapfrog integrator on a single bond.
*/
void
testSingleBond
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
2.0
);
system
.
addParticle
(
2.0
);
...
...
@@ -101,7 +102,6 @@ void testSingleBond() {
void
testConstraints
()
{
const
int
numParticles
=
8
;
const
double
temp
=
500.0
;
ReferencePlatform
platform
;
System
system
;
CustomIntegrator
integrator
(
0.002
);
integrator
.
addPerDofVariable
(
"oldx"
,
0
);
...
...
@@ -160,7 +160,6 @@ void testConstraints() {
*/
void
testVelocityConstraints
()
{
const
int
numParticles
=
10
;
ReferencePlatform
platform
;
System
system
;
CustomIntegrator
integrator
(
0.002
);
integrator
.
addPerDofVariable
(
"x1"
,
0
);
...
...
@@ -236,7 +235,6 @@ void testVelocityConstraints() {
}
void
testConstrainedMasslessParticles
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
0.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -282,7 +280,6 @@ void testWithThermostat() {
const
double
temp
=
100.0
;
const
double
collisionFreq
=
10.0
;
const
int
numSteps
=
5000
;
ReferencePlatform
platform
;
System
system
;
CustomIntegrator
integrator
(
0.003
);
integrator
.
addUpdateContextState
();
...
...
@@ -324,7 +321,6 @@ void testWithThermostat() {
* Test a Monte Carlo integrator that uses global variables and depends on energy.
*/
void
testMonteCarlo
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -379,7 +375,6 @@ void testMonteCarlo() {
void
testSum
()
{
const
int
numParticles
=
200
;
const
double
boxSize
=
10
;
ReferencePlatform
platform
;
System
system
;
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
boxSize
,
0
,
0
),
Vec3
(
0
,
boxSize
,
0
),
Vec3
(
0
,
0
,
boxSize
));
NonbondedForce
*
nb
=
new
NonbondedForce
();
...
...
@@ -422,7 +417,6 @@ void testSum() {
* Test an integrator that both uses and modifies a context parameter.
*/
void
testParameter
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
AndersenThermostat
*
thermostat
=
new
AndersenThermostat
(
0.1
,
0.1
);
...
...
@@ -448,7 +442,6 @@ void testRandomDistributions() {
const
int
numParticles
=
100
;
const
int
numBins
=
20
;
const
int
numSteps
=
100
;
ReferencePlatform
platform
;
System
system
;
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
system
.
addParticle
(
1.0
);
...
...
@@ -516,7 +509,6 @@ void testRandomDistributions() {
void
testPerDofVariables
()
{
const
int
numParticles
=
200
;
const
double
boxSize
=
10
;
ReferencePlatform
platform
;
System
system
;
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
boxSize
,
0
,
0
),
Vec3
(
0
,
boxSize
,
0
),
Vec3
(
0
,
0
,
boxSize
));
NonbondedForce
*
nb
=
new
NonbondedForce
();
...
...
@@ -571,7 +563,6 @@ void testPerDofVariables() {
* Test evaluating force groups separately.
*/
void
testForceGroups
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
2.0
);
system
.
addParticle
(
2.0
);
...
...
@@ -647,7 +638,6 @@ void testForceGroups() {
*/
void
testRespa
()
{
const
int
numParticles
=
8
;
ReferencePlatform
platform
;
System
system
;
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
4
,
0
,
0
),
Vec3
(
0
,
4
,
0
),
Vec3
(
0
,
0
,
4
));
CustomIntegrator
integrator
(
0.002
);
...
...
platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp
View file @
f322abd1
...
...
@@ -51,6 +51,8 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
Vec3
computeDelta
(
const
Vec3
&
pos1
,
const
Vec3
&
pos2
,
bool
periodic
,
const
Vec3
*
periodicBoxVectors
)
{
...
...
@@ -93,7 +95,6 @@ void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& p
ASSERT
(
!
system
.
usesPeriodicBoundaryConditions
());
}
VerletIntegrator
integrator
(
0.001
);
ReferencePlatform
platform
;
Context
context
(
system
,
integrator
,
platform
);
context
.
setPositions
(
positions
);
State
state1
=
context
.
getState
(
State
::
Forces
|
State
::
Energy
);
...
...
@@ -155,7 +156,6 @@ void validateStillingerWeber(CustomManyParticleForce* force, const vector<Vec3>&
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
boxSize
,
0
,
0
),
Vec3
(
0
,
boxSize
,
0
),
Vec3
(
0
,
0
,
boxSize
));
system
.
addForce
(
force
);
VerletIntegrator
integrator
(
0.001
);
ReferencePlatform
platform
;
Context
context
(
system
,
integrator
,
platform
);
context
.
setPositions
(
positions
);
State
state1
=
context
.
getState
(
State
::
Forces
|
State
::
Energy
);
...
...
@@ -340,7 +340,6 @@ void testExclusions() {
void
testAllTerms
()
{
int
numParticles
=
4
;
ReferencePlatform
platform
;
// Create a system with a CustomManyParticleForce.
...
...
@@ -424,7 +423,6 @@ void testParameters() {
}
system
.
addForce
(
force
);
VerletIntegrator
integrator
(
0.001
);
ReferencePlatform
platform
;
Context
context
(
system
,
integrator
,
platform
);
context
.
setPositions
(
positions
);
...
...
@@ -510,7 +508,6 @@ void testTabulatedFunctions() {
}
system
.
addForce
(
force
);
VerletIntegrator
integrator
(
0.001
);
ReferencePlatform
platform
;
Context
context
(
system
,
integrator
,
platform
);
context
.
setPositions
(
positions
);
...
...
@@ -562,7 +559,6 @@ void testTypeFilters() {
force
->
setTypeFilter
(
2
,
f2
);
system
.
addForce
(
force
);
VerletIntegrator
integrator
(
0.001
);
ReferencePlatform
platform
;
Context
context
(
system
,
integrator
,
platform
);
context
.
setPositions
(
positions
);
...
...
platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp
View file @
f322abd1
...
...
@@ -53,10 +53,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testSimpleExpression
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -79,7 +80,6 @@ void testSimpleExpression() {
}
void
testParameters
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -140,7 +140,6 @@ void testParameters() {
}
void
testExclusions
()
{
ReferencePlatform
platform
;
System
system
;
VerletIntegrator
integrator
(
0.01
);
CustomNonbondedForce
*
nonbonded
=
new
CustomNonbondedForce
(
"a*r; a=a1+a2"
);
...
...
@@ -171,7 +170,6 @@ void testExclusions() {
}
void
testCutoff
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -201,7 +199,6 @@ void testCutoff() {
}
void
testPeriodic
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -232,7 +229,6 @@ void testPeriodic() {
}
void
testTriclinic
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -292,7 +288,6 @@ void testTriclinic() {
}
void
testContinuous1DFunction
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -337,7 +332,6 @@ void testContinuous2DFunction() {
const
double
xmax
=
1.5
;
const
double
ymin
=
0.0
;
const
double
ymax
=
2.1
;
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -389,7 +383,6 @@ void testContinuous3DFunction() {
const
double
ymax
=
0.7
;
const
double
zmin
=
0.2
;
const
double
zmax
=
0.9
;
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -439,7 +432,6 @@ void testContinuous3DFunction() {
}
void
testDiscrete1DFunction
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -469,7 +461,6 @@ void testDiscrete1DFunction() {
void
testDiscrete2DFunction
()
{
const
int
xsize
=
10
;
const
int
ysize
=
5
;
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -503,7 +494,6 @@ void testDiscrete3DFunction() {
const
int
xsize
=
8
;
const
int
ysize
=
5
;
const
int
zsize
=
6
;
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -540,7 +530,6 @@ void testCoulombLennardJones() {
const
int
numMolecules
=
300
;
const
int
numParticles
=
numMolecules
*
2
;
const
double
boxSize
=
20.0
;
ReferencePlatform
platform
;
// Create two systems: one with a NonbondedForce, and one using a CustomNonbondedForce to implement the same interaction.
...
...
@@ -614,7 +603,6 @@ void testCoulombLennardJones() {
}
void
testSwitchingFunction
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -673,7 +661,6 @@ void testLongRangeCorrection() {
int
numParticles
=
gridSize
*
gridSize
*
gridSize
;
double
boxSize
=
gridSize
*
0.7
;
double
cutoff
=
boxSize
/
3
;
ReferencePlatform
platform
;
System
standardSystem
;
System
customSystem
;
VerletIntegrator
integrator1
(
0.01
);
...
...
@@ -748,7 +735,6 @@ void testLongRangeCorrection() {
void
testInteractionGroups
()
{
const
int
numParticles
=
6
;
ReferencePlatform
platform
;
System
system
;
VerletIntegrator
integrator
(
0.01
);
CustomNonbondedForce
*
nonbonded
=
new
CustomNonbondedForce
(
"v1+v2"
);
...
...
@@ -790,7 +776,6 @@ void testLargeInteractionGroup() {
// Create a large system.
ReferencePlatform
platform
;
System
system
;
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
boxSize
,
0
,
0
),
Vec3
(
0
,
boxSize
,
0
),
Vec3
(
0
,
0
,
boxSize
));
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
...
...
@@ -868,7 +853,6 @@ void testInteractionGroupLongRangeCorrection() {
const
int
numParticles
=
10
;
const
double
boxSize
=
10.0
;
const
double
cutoff
=
0.5
;
ReferencePlatform
platform
;
System
system
;
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
boxSize
,
0
,
0
),
Vec3
(
0
,
boxSize
,
0
),
Vec3
(
0
,
0
,
boxSize
));
CustomNonbondedForce
*
nonbonded
=
new
CustomNonbondedForce
(
"c1*c2*r^-4"
);
...
...
platforms/reference/tests/TestReferenceCustomTorsionForce.cpp
View file @
f322abd1
...
...
@@ -50,11 +50,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testTorsions
()
{
ReferencePlatform
platform
;
// Create a system using a CustomTorsionForce.
System
customSystem
;
...
...
@@ -141,7 +141,6 @@ void testTorsions() {
}
void
testRange
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
platforms/reference/tests/TestReferenceEwald.cpp
View file @
f322abd1
...
...
@@ -48,6 +48,8 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
EWALD_TOL
=
1e-5
;
const
double
PME_TOL
=
5e-5
;
...
...
@@ -59,9 +61,7 @@ void testEwaldExact() {
const
double
cutoff
=
1.0
;
const
double
boxSize
=
2.82
;
ReferencePlatform
platform
;
System
system
;
for
(
int
i
=
0
;
i
<
numParticles
/
2
;
i
++
)
system
.
addParticle
(
22.99
);
for
(
int
i
=
0
;
i
<
numParticles
/
2
;
i
++
)
...
...
@@ -112,7 +112,6 @@ void testEwaldPME() {
// Use amorphous NaCl system
// The particles are simple charges, no VdW interactions
ReferencePlatform
platform
;
System
system
;
for
(
int
i
=
0
;
i
<
numParticles
/
2
;
i
++
)
system
.
addParticle
(
22.99
);
...
...
@@ -217,7 +216,6 @@ void testEwaldPME() {
}
void
testEwald2Ions
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -244,7 +242,6 @@ void testEwald2Ions() {
}
void
testWaterSystem
()
{
ReferencePlatform
platform
;
System
system
;
static
int
numParticles
=
648
;
const
double
boxSize
=
1.86206
;
...
...
@@ -305,7 +302,6 @@ void testWaterSystem() {
void
testTriclinic
()
{
// Create a triclinic box containing eight particles.
ReferencePlatform
platform
;
System
system
;
system
.
setDefaultPeriodicBoxVectors
(
Vec3
(
2.5
,
0
,
0
),
Vec3
(
0.5
,
3.0
,
0
),
Vec3
(
0.7
,
0.9
,
3.5
));
for
(
int
i
=
0
;
i
<
8
;
i
++
)
...
...
@@ -373,7 +369,6 @@ void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
positions
[
i
]
=
Vec3
(
boxWidth
*
genrand_real2
(
sfmt
),
boxWidth
*
genrand_real2
(
sfmt
),
boxWidth
*
genrand_real2
(
sfmt
));
}
force
->
setNonbondedMethod
(
method
);
ReferencePlatform
platform
;
// For various values of the cutoff and error tolerance, see if the actual error is reasonable.
...
...
@@ -425,7 +420,6 @@ void testPMEParameters() {
positions
[
i
]
=
Vec3
(
boxWidth
*
genrand_real2
(
sfmt
),
boxWidth
*
genrand_real2
(
sfmt
),
boxWidth
*
genrand_real2
(
sfmt
));
}
force
->
setNonbondedMethod
(
NonbondedForce
::
PME
);
ReferencePlatform
platform
;
// Compute the energy with an error tolerance of 1e-3.
...
...
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
View file @
f322abd1
...
...
@@ -48,10 +48,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testSingleParticle
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
2.0
);
LangevinIntegrator
integrator
(
0
,
0.1
,
0.01
);
...
...
@@ -85,7 +86,6 @@ void testSingleParticle() {
}
void
testGlobalSettings
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
2.0
);
LangevinIntegrator
integrator
(
0
,
0.1
,
0.01
);
...
...
@@ -114,7 +114,6 @@ void testGlobalSettings() {
}
void
testCutoffAndPeriodic
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
@@ -183,7 +182,6 @@ void testCutoffAndPeriodic() {
}
void
testForce
()
{
ReferencePlatform
platform
;
const
int
numParticles
=
10
;
System
system
;
LangevinIntegrator
integrator
(
0
,
0.1
,
0.01
);
...
...
platforms/reference/tests/TestReferenceGBVIForce.cpp
View file @
f322abd1
...
...
@@ -50,10 +50,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testSingleParticle
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
2.0
);
LangevinIntegrator
integrator
(
0
,
0.1
,
0.01
);
...
...
@@ -89,8 +90,6 @@ void testSingleParticle() {
}
void
testEnergyEthane
(
int
applyBornRadiiScaling
)
{
ReferencePlatform
platform
;
const
int
numParticles
=
8
;
System
system
;
LangevinIntegrator
integrator
(
0
,
0.1
,
0.01
);
...
...
platforms/reference/tests/TestReferenceHarmonicAngleForce.cpp
View file @
f322abd1
...
...
@@ -46,10 +46,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testAngles
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
platforms/reference/tests/TestReferenceHarmonicBondForce.cpp
View file @
f322abd1
...
...
@@ -46,10 +46,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testBonds
()
{
ReferencePlatform
platform
;
System
system
;
system
.
addParticle
(
1.0
);
system
.
addParticle
(
1.0
);
...
...
platforms/reference/tests/TestReferenceKineticEnergy.cpp
View file @
f322abd1
...
...
@@ -44,10 +44,11 @@
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testCalcKE
()
{
ReferencePlatform
platform
;
System
system
;
for
(
int
i
=
0
;
i
<
4
;
++
i
)
system
.
addParticle
(
i
+
1
);
...
...
Prev
1
2
Next
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