Skip to content

GitLab

Commit 51828eaa authored by Peter Eastman's avatar Peter Eastman
Browse files

Merge branch 'master' into qc

parents cf8a03e8 5ed9dd65
Hide whitespace changes
Inline Side-by-side
Showing with 92 additions and 22 deletions
serialization/tests/TestSerializeCMAPTorsion.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CMAPTorsionForce force;
force.setForceGroup(3);
vector<double> map1(9);
for (int i = 0; i < 9; i++)
map1[i] = 0.1*i;
......@@ -64,6 +65,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CMAPTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumMaps(), force2.getNumMaps());
for (int i = 0; i < force.getNumMaps(); i++) {
int size1, size2;
......
serialization/tests/TestSerializeCMMotionRemover.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CMMotionRemover force(5);
force.setForceGroup(3);
// Serialize and then deserialize it.
......@@ -52,6 +53,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CMMotionRemover& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
}
......
serialization/tests/TestSerializeCustomAngleForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomAngleForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerAngleParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomAngleForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerAngleParameters(), force2.getNumPerAngleParameters());
for (int i = 0; i < force.getNumPerAngleParameters(); i++)
......
serialization/tests/TestSerializeCustomBondForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomBondForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerBondParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomBondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());
for (int i = 0; i < force.getNumPerBondParameters(); i++)
......
serialization/tests/TestSerializeCustomCompoundBondForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2012 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomCompoundBondForce force(3, "5*sin(distance(p1,p2))^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerBondParameter("z");
......@@ -76,6 +77,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomCompoundBondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumParticlesPerBond(), force2.getNumParticlesPerBond());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());
......
serialization/tests/TestSerializeCustomExternalForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomExternalForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerParticleParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomExternalForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
for (int i = 0; i < force.getNumPerParticleParameters(); i++)
......
serialization/tests/TestSerializeCustomGBForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomGBForce force;
force.setForceGroup(3);
force.setNonbondedMethod(CustomGBForce::CutoffPeriodic);
force.setCutoffDistance(2.1);
force.addGlobalParameter("x", 1.3);
......@@ -74,6 +75,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomGBForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
......
serialization/tests/TestSerializeCustomHbondForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomHbondForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.setNonbondedMethod(CustomHbondForce::CutoffPeriodic);
force.setCutoffDistance(2.1);
force.addGlobalParameter("x", 1.3);
......@@ -77,6 +78,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomHbondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
......
serialization/tests/TestSerializeCustomNonbondedForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,7 +42,11 @@ void testSerialization() {
// Create a Force.
CustomNonbondedForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
force.setUseSwitchingFunction(true);
force.setUseLongRangeCorrection(true);
force.setSwitchingDistance(2.0);
force.setCutoffDistance(2.1);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
......@@ -60,6 +64,11 @@ void testSerialization() {
for (int i = 0; i < 10; i++)
values[i] = sin((double) i);
force.addFunction("f", values, 0.5, 1.5);
std::set<int> set1, set2;
set1.insert(0);
set2.insert(1);
set2.insert(2);
force.addInteractionGroup(set1, set2);
// Serialize and then deserialize it.
......@@ -70,9 +79,13 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomNonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
ASSERT_EQUAL(force.getUseLongRangeCorrection(), force2.getUseLongRangeCorrection());
ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
for (int i = 0; i < force.getNumPerParticleParameters(); i++)
ASSERT_EQUAL(force.getPerParticleParameterName(i), force2.getPerParticleParameterName(i));
......@@ -111,6 +124,11 @@ void testSerialization() {
for (int j = 0; j < (int) val1.size(); j++)
ASSERT_EQUAL(val1[j], val2[j]);
}
ASSERT_EQUAL(force.getNumInteractionGroups(), force2.getNumInteractionGroups());
std::set<int> set1c, set2c;
force2.getInteractionGroupParameters(0, set1c, set2c);
ASSERT_EQUAL_CONTAINERS(set1, set1c);
ASSERT_EQUAL_CONTAINERS(set2, set2c);
}
int main() {
......
serialization/tests/TestSerializeCustomTorsionForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
CustomTorsionForce force("5*sin(x)^2+y*z");
force.setForceGroup(3);
force.addGlobalParameter("x", 1.3);
force.addGlobalParameter("y", 2.221);
force.addPerTorsionParameter("z");
......@@ -62,6 +63,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
CustomTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
ASSERT_EQUAL(force.getNumPerTorsionParameters(), force2.getNumPerTorsionParameters());
for (int i = 0; i < force.getNumPerTorsionParameters(); i++)
......
serialization/tests/TestSerializeGBSAOBCForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
GBSAOBCForce force;
force.setForceGroup(3);
force.setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
force.setCutoffDistance(2.0);
force.setSoluteDielectric(5.1);
......@@ -59,6 +60,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
GBSAOBCForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
......
serialization/tests/TestSerializeGBVIForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
GBVIForce force;
force.setForceGroup(3);
force.setNonbondedMethod(GBVIForce::CutoffPeriodic);
force.setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
force.setQuinticLowerLimitFactor(0.123);
......@@ -64,6 +65,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
GBVIForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
......
serialization/tests/TestSerializeHarmonicAngleForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
HarmonicAngleForce force;
force.setForceGroup(3);
force.addAngle(0, 1, 2, 1.0, 2.0);
force.addAngle(0, 2, 3, 2.0, 2.1);
force.addAngle(2, 3, 4, 3.0, 2.2);
......@@ -56,6 +57,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
HarmonicAngleForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
for (int i = 0; i < force.getNumAngles(); i++) {
int a1, a2, a3, b1, b2, b3;
......
serialization/tests/TestSerializeHarmonicBondForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
HarmonicBondForce force;
force.setForceGroup(3);
force.addBond(0, 1, 1.0, 2.0);
force.addBond(0, 2, 2.0, 2.1);
force.addBond(2, 3, 3.0, 2.2);
......@@ -56,6 +57,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
HarmonicBondForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
for (int i = 0; i < force.getNumBonds(); i++) {
int a1, a2, b1, b2;
......
serialization/tests/TestSerializeMonteCarloBarostat.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
MonteCarloBarostat force(25.5, 250.0, 14);
force.setForceGroup(3);
force.setRandomNumberSeed(3);
// Serialize and then deserialize it.
......@@ -53,6 +54,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
MonteCarloBarostat& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getDefaultPressure(), force2.getDefaultPressure());
ASSERT_EQUAL(force.getTemperature(), force2.getTemperature());
ASSERT_EQUAL(force.getFrequency(), force2.getFrequency());
......
serialization/tests/TestSerializeNonbondedForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,11 +42,17 @@ void testSerialization() {
// Create a Force.
NonbondedForce force;
force.setForceGroup(3);
force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
force.setSwitchingDistance(1.5);
force.setUseSwitchingFunction(true);
force.setCutoffDistance(2.0);
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
double alpha = 0.5;
int nx = 3, ny = 5, nz = 7;
force.setPMEParameters(alpha, nx, ny, nz);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
......@@ -62,12 +68,22 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
NonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
double alpha2;
int nx2, ny2, nz2;
force2.getPMEParameters(alpha2, nx2, ny2, nz2);
ASSERT_EQUAL(alpha, alpha2);
ASSERT_EQUAL(nx, nx2);
ASSERT_EQUAL(ny, ny2);
ASSERT_EQUAL(nz, nz2);
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
......
serialization/tests/TestSerializePeriodicTorsionForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
PeriodicTorsionForce force;
force.setForceGroup(3);
force.addTorsion(0, 1, 2, 3, 2, 1.0, 2.0);
force.addTorsion(0, 2, 3, 4, 2, 2.0, 2.1);
force.addTorsion(2, 3, 4, 7, 1, 3.0, 2.2);
......@@ -56,6 +57,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
PeriodicTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
for (int i = 0; i < force.getNumTorsions(); i++) {
int a1, a2, a3, a4, b1, b2, b3, b4, perioda, periodb;
......
serialization/tests/TestSerializeRBTorsionForce.cpp
View file @ 51828eaa
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -42,6 +42,7 @@ void testSerialization() {
// Create a Force.
RBTorsionForce force;
force.setForceGroup(3);
force.addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
force.addTorsion(0, 2, 3, 4, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7);
force.addTorsion(2, 3, 4, 7, -1, -2, -3, 1.1, 2.2, 3.3);
......@@ -55,6 +56,7 @@ void testSerialization() {
// Compare the two forces to see if they are identical.
RBTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
for (int i = 0; i < force.getNumTorsions(); i++) {
int a1, a2, a3, a4, b1, b2, b3, b4;
......
wrappers/generateWrappers.py
View file @ 51828eaa
......@@ -68,7 +68,7 @@ class WrapperGenerator:
def __init__(self, inputDirname, output):
self.skipClasses = ['OpenMM::Vec3', 'OpenMM::XmlSerializer', 'OpenMM::Kernel', 'OpenMM::KernelImpl', 'OpenMM::KernelFactory', 'OpenMM::ContextImpl', 'OpenMM::SerializationNode', 'OpenMM::SerializationProxy']
self.skipMethods = ['OpenMM::Context::getState', 'OpenMM::Platform::loadPluginsFromDirectory', 'OpenMM::Context::createCheckpoint', 'OpenMM::Context::loadCheckpoint']
self.skipMethods = ['OpenMM::Context::getState', 'OpenMM::Platform::loadPluginsFromDirectory', 'OpenMM::Context::createCheckpoint', 'OpenMM::Context::loadCheckpoint', 'OpenMM::Context::getMolecules']
self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
self.nodeByID={}
......
wrappers/python/CMakeLists.txt
View file @ 51828eaa
......@@ -57,6 +57,8 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
)
foreach(file ${STAGING_INPUT_FILES1})
set(STAGING_INPUT_FILES ${STAGING_INPUT_FILES} "${file}")
......@@ -106,7 +108,7 @@ mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
set(SWIG_OPENMM_DIR "${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen")
file(MAKE_DIRECTORY ${SWIG_OPENMM_DIR}/swig_lib/python)
### Create OpenMM_headers.xml ###
### Create OpenMMSwigHeaders.i ###
# Step 1 - Create Doxyfile to point to OpenMM headers
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/src/swig_doxygen/doxygen/Doxyfile.in
......@@ -130,7 +132,7 @@ set(SWIG_INPUT_FILES_REF
"${SWIG_OPENMM_DIR}/swig_lib/python/pythonprepend.i"
"${SWIG_OPENMM_DIR}/swig_lib/python/pythonappend.i"
"${SWIG_OPENMM_DIR}/OpenMM_docstring.i"
"${SWIG_OPENMM_DIR}/OpenMM_headers.i"
"${SWIG_OPENMM_DIR}/OpenMMSwigHeaders.i"
# "${SWIG_OPENMM_DIR}/OpenMM.i"
)
......@@ -153,7 +155,7 @@ add_custom_command(
-i "${CMAKE_CURRENT_BINARY_DIR}/src/swig_doxygen/doxygen/xml"
-c swigInputConfig.py
-d OpenMM_docstring.i
-o OpenMM_headers.i
-o OpenMMSwigHeaders.i
-a swig_lib/python/pythonprepend.i
-z swig_lib/python/pythonappend.i
WORKING_DIRECTORY "${SWIG_OPENMM_DIR}"
......@@ -164,6 +166,8 @@ add_custom_command(
COMMENT "Creating OpenMM Python swig input files..."
)
INSTALL_FILES(/include FILES "${SWIG_OPENMM_DIR}/OpenMMSwigHeaders.i")
#~ swig -python -c++ \
#~ -outdir $PYTHON_PACKAGE_DIR \
#~ -o OpenMMSwig.cxx \
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment