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Commit df2b723d authored by leeping's avatar leeping
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Merge branch 'master' of github.com:SimTk/openmm

parents a0f16cc0 7be6e8fb
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Showing with 137 additions and 124 deletions
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ df2b723d
......@@ -87,6 +87,7 @@ vector<string> RPMDIntegrator::getKernelNames() {
void RPMDIntegrator::setPositions(int copy, const vector<Vec3>& positions) {
kernel.getAs<IntegrateRPMDStepKernel>().setPositions(copy, positions);
forcesAreValid = false;
hasSetPosition = true;
}
......@@ -100,7 +101,7 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
// Call setPositions() on the Context so it doesn't think the user is trying to
// run a simulation without setting positions first. These positions will
// immediately get overwritten by the ones stored in this integrator.
vector<Vec3> p(context->getSystem().getNumParticles(), Vec3());
context->getOwner().setPositions(p);
isFirstStep = false;
......@@ -110,7 +111,7 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
if (enforcePeriodicBox && copy > 0 && (types&State::Positions) != 0) {
// Apply periodic boundary conditions based on copy 0. Otherwise, molecules might end
// up in different places for different copies.
kernel.getAs<IntegrateRPMDStepKernel>().copyToContext(0, *context);
State state2 = context->getOwner().getState(State::Positions, false, groups);
vector<Vec3> positions = state.getPositions();
......@@ -144,9 +145,9 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
pos[2] -= dz;
}
}
// Construct the new State.
State::StateBuilder builder(state.getTime());
builder.setPositions(positions);
builder.setPeriodicBoxVectors(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2]);
......@@ -168,16 +169,18 @@ double RPMDIntegrator::computeKineticEnergy() {
}
void RPMDIntegrator::step(int steps) {
if (context == NULL)
throw OpenMMException("This Integrator is not bound to a context!");
if (!hasSetPosition) {
// Initialize the positions from the context.
State s = context->getOwner().getState(State::Positions);
for (int i = 0; i < numCopies; i++)
setPositions(i, s.getPositions());
}
if (!hasSetVelocity) {
// Initialize the velocities from the context.
State s = context->getOwner().getState(State::Velocities);
for (int i = 0; i < numCopies; i++)
setVelocities(i, s.getVelocities());
......@@ -186,7 +189,7 @@ void RPMDIntegrator::step(int steps) {
// Call setPositions() on the Context so it doesn't think the user is trying to
// run a simulation without setting positions first. These positions will
// immediately get overwritten by the ones stored in this integrator.
vector<Vec3> p(context->getSystem().getNumParticles(), Vec3());
context->getOwner().setPositions(p);
isFirstStep = false;
......@@ -212,12 +215,12 @@ double RPMDIntegrator::getTotalEnergy() {
State prevState = getState(numCopies-1, State::Positions);
for (int i = 0; i < numCopies; i++) {
// Add the energy of this copy.
State state = getState(i, State::Positions | State::Energy);
energy += state.getKineticEnergy()+state.getPotentialEnergy();
// Add the energy from the springs connecting it to the previous copy.
for (int j = 0; j < numParticles; j++) {
Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
energy += 0.5*wn*wn*system.getParticleMass(j)*delta.dot(delta);
......
plugins/rpmd/platforms/cuda/src/kernels/rpmdContraction.cu
View file @ df2b723d
......@@ -23,13 +23,16 @@ extern "C" __global__ void contractPositions(mixed4* posq, mixed4* contracted) {
const int indexInBlock = threadIdx.x-blockStart;
__shared__ mixed3 q[2*THREAD_BLOCK_SIZE];
__shared__ mixed3 temp[2*THREAD_BLOCK_SIZE];
__shared__ mixed2 w[NUM_COPIES];
__shared__ mixed2 w1[NUM_COPIES];
__shared__ mixed2 w2[NUM_CONTRACTED_COPIES];
mixed3* qreal = &q[blockStart];
mixed3* qimag = &q[blockStart+blockDim.x];
mixed3* tempreal = &temp[blockStart];
mixed3* tempimag = &temp[blockStart+blockDim.x];
if (threadIdx.x < NUM_COPIES)
w[indexInBlock] = make_mixed2(cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
w1[indexInBlock] = make_mixed2(cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
if (threadIdx.x < NUM_CONTRACTED_COPIES)
w2[indexInBlock] = make_mixed2(cos(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES), sin(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES));
__syncthreads();
for (int particle = (blockIdx.x*blockDim.x+threadIdx.x)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
// Load the particle position.
......@@ -41,6 +44,7 @@ extern "C" __global__ void contractPositions(mixed4* posq, mixed4* contracted) {
// Forward FFT.
__syncthreads();
mixed2* w = w1;
FFT_Q_FORWARD
if (NUM_CONTRACTED_COPIES > 1) {
// Compress the data to remove high frequencies.
......@@ -54,6 +58,7 @@ extern "C" __global__ void contractPositions(mixed4* posq, mixed4* contracted) {
qimag[indexInBlock] = tempimag[indexInBlock < start ? indexInBlock : indexInBlock+(NUM_COPIES-NUM_CONTRACTED_COPIES)];
}
__syncthreads();
w = w2;
FFT_Q_BACKWARD
}
......@@ -74,13 +79,16 @@ extern "C" __global__ void contractForces(long long* force, long long* contracte
const mixed forceScale = 1/(mixed) 0x100000000;
__shared__ mixed3 f[2*THREAD_BLOCK_SIZE];
__shared__ mixed3 temp[2*THREAD_BLOCK_SIZE];
__shared__ mixed2 w[NUM_COPIES];
__shared__ mixed2 w1[NUM_COPIES];
__shared__ mixed2 w2[NUM_CONTRACTED_COPIES];
mixed3* freal = &f[blockStart];
mixed3* fimag = &f[blockStart+blockDim.x];
mixed3* tempreal = &temp[blockStart];
mixed3* tempimag = &temp[blockStart+blockDim.x];
if (threadIdx.x < NUM_COPIES)
w[indexInBlock] = make_mixed2(cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
w1[indexInBlock] = make_mixed2(cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
if (threadIdx.x < NUM_CONTRACTED_COPIES)
w2[indexInBlock] = make_mixed2(cos(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES), sin(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES));
__syncthreads();
for (int particle = (blockIdx.x*blockDim.x+threadIdx.x)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
// Load the force.
......@@ -94,6 +102,7 @@ extern "C" __global__ void contractForces(long long* force, long long* contracte
// Forward FFT.
mixed2* w = w2;
if (NUM_CONTRACTED_COPIES > 1) {
FFT_F_FORWARD
}
......@@ -110,6 +119,7 @@ extern "C" __global__ void contractForces(long long* force, long long* contracte
fimag[indexInBlock] = (indexInBlock < end ? make_mixed3(0) : tempimag[indexInBlock-(NUM_COPIES-NUM_CONTRACTED_COPIES)]);
}
__syncthreads();
w = w1;
FFT_F_BACKWARD
// Store results.
......
plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp
View file @ df2b723d
......@@ -271,7 +271,7 @@ void testCMMotionRemoval() {
pos += calcCM(state.getPositions(), system);
}
pos *= 1.0/numCopies;
ASSERT_EQUAL_VEC(Vec3(), pos, 0.5);
ASSERT_EQUAL_VEC(Vec3(0,0,0), pos, 0.5);
}
}
......
plugins/rpmd/platforms/opencl/src/kernels/rpmdContraction.cl
View file @ df2b723d
......@@ -23,13 +23,16 @@ __kernel void contractPositions(__global mixed4* posq, __global mixed4* contract
const int indexInBlock = get_local_id(0)-blockStart;
__local mixed4 q[2*THREAD_BLOCK_SIZE];
__local mixed4 temp[2*THREAD_BLOCK_SIZE];
__local mixed2 w[NUM_COPIES];
__local mixed2 w1[NUM_COPIES];
__local mixed2 w2[NUM_CONTRACTED_COPIES];
__local mixed4* qreal = &q[blockStart];
__local mixed4* qimag = &q[blockStart+get_local_size(0)];
__local mixed4* tempreal = &temp[blockStart];
__local mixed4* tempimag = &temp[blockStart+get_local_size(0)];
if (get_local_id(0) < NUM_COPIES)
w[indexInBlock] = (mixed2) (cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
w1[indexInBlock] = (mixed2) (cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
if (get_local_id(0) < NUM_CONTRACTED_COPIES)
w2[indexInBlock] = (mixed2) (cos(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES), sin(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES));
barrier(CLK_LOCAL_MEM_FENCE);
for (int particle = get_global_id(0)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
// Load the particle position.
......@@ -41,6 +44,7 @@ __kernel void contractPositions(__global mixed4* posq, __global mixed4* contract
// Forward FFT.
barrier(CLK_LOCAL_MEM_FENCE);
__local mixed2* w = w1;
FFT_Q_FORWARD
if (NUM_CONTRACTED_COPIES > 1) {
// Compress the data to remove high frequencies.
......@@ -54,6 +58,7 @@ __kernel void contractPositions(__global mixed4* posq, __global mixed4* contract
qimag[indexInBlock] = tempimag[indexInBlock < start ? indexInBlock : indexInBlock+(NUM_COPIES-NUM_CONTRACTED_COPIES)];
}
barrier(CLK_LOCAL_MEM_FENCE);
w = w2;
FFT_Q_BACKWARD
}
......@@ -73,13 +78,16 @@ __kernel void contractForces(__global real4* force, __global real4* contracted)
const int indexInBlock = get_local_id(0)-blockStart;
__local mixed4 f[2*THREAD_BLOCK_SIZE];
__local mixed4 temp[2*THREAD_BLOCK_SIZE];
__local mixed2 w[NUM_COPIES];
__local mixed2 w1[NUM_COPIES];
__local mixed2 w2[NUM_CONTRACTED_COPIES];
__local mixed4* freal = &f[blockStart];
__local mixed4* fimag = &f[blockStart+get_local_size(0)];
__local mixed4* tempreal = &temp[blockStart];
__local mixed4* tempimag = &temp[blockStart+get_local_size(0)];
if (get_local_id(0) < NUM_COPIES)
w[indexInBlock] = (mixed2) (cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
w1[indexInBlock] = (mixed2) (cos(-indexInBlock*2*M_PI/NUM_COPIES), sin(-indexInBlock*2*M_PI/NUM_COPIES));
if (get_local_id(0) < NUM_CONTRACTED_COPIES)
w2[indexInBlock] = (mixed2) (cos(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES), sin(-indexInBlock*2*M_PI/NUM_CONTRACTED_COPIES));
barrier(CLK_LOCAL_MEM_FENCE);
for (int particle = get_global_id(0)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
// Load the force.
......@@ -93,6 +101,7 @@ __kernel void contractForces(__global real4* force, __global real4* contracted)
// Forward FFT.
__local mixed2* w = w2;
if (NUM_CONTRACTED_COPIES > 1) {
FFT_F_FORWARD
}
......@@ -109,6 +118,7 @@ __kernel void contractForces(__global real4* force, __global real4* contracted)
fimag[indexInBlock] = (indexInBlock < end ? (mixed4) (0.0f, 0.0f, 0.0f, 0.0f) : tempimag[indexInBlock-(NUM_COPIES-NUM_CONTRACTED_COPIES)]);
}
barrier(CLK_LOCAL_MEM_FENCE);
w = w1;
FFT_F_BACKWARD
// Store results.
......
plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp
View file @ df2b723d
......@@ -272,7 +272,7 @@ void testCMMotionRemoval() {
pos += calcCM(state.getPositions(), system);
}
pos *= 1.0/numCopies;
ASSERT_EQUAL_VEC(Vec3(), pos, 0.5);
ASSERT_EQUAL_VEC(Vec3(0,0,0), pos, 0.5);
}
}
......
plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp
View file @ df2b723d
......@@ -155,7 +155,7 @@ void testCMMotionRemoval() {
pos += calcCM(state.getPositions(), system);
}
pos *= 1.0/numCopies;
ASSERT_EQUAL_VEC(Vec3(), pos, 0.5);
ASSERT_EQUAL_VEC(Vec3(0,0,0), pos, 0.5);
}
}
......
wrappers/generateWrappers.py
View file @ df2b723d
......@@ -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', 'OpenMM::Context::getMolecules']
self.skipMethods = ['OpenMM::Context::getState', 'OpenMM::Platform::loadPluginsFromDirectory', 'OpenMM::Platform::getPluginLoadFailures', 'OpenMM::Context::createCheckpoint', 'OpenMM::Context::loadCheckpoint', 'OpenMM::Context::getMolecules']
self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
self.nodeByID={}
......@@ -398,6 +398,7 @@ extern OPENMM_EXPORT void %(name)s_insert(%(name)s* set, %(type)s value);""" % v
Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox);
extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const char* directory);
extern OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_getPluginLoadFailures();
extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeSystem(const OpenMM_System* system);
extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeState(const OpenMM_State* state);
extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeIntegrator(const OpenMM_Integrator* integrator);
......@@ -804,6 +805,10 @@ OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_loadPluginsFromDirectory(const
vector<string> result = Platform::loadPluginsFromDirectory(string(directory));
return reinterpret_cast<OpenMM_StringArray*>(new vector<string>(result));
}
OPENMM_EXPORT OpenMM_StringArray* OpenMM_Platform_getPluginLoadFailures() {
vector<string> result = Platform::getPluginLoadFailures();
return reinterpret_cast<OpenMM_StringArray*>(new vector<string>(result));
}
static char* createStringFromStream(stringstream& stream) {
int length = stream.str().size();
char* result = (char*) malloc(length+1);
......@@ -1314,6 +1319,10 @@ MODULE OpenMM
character(*) directory
type(OpenMM_StringArray) result
end subroutine
subroutine OpenMM_Platform_getPluginLoadFailures(result)
use OpenMM_Types; implicit none
type(OpenMM_StringArray) result
end subroutine
subroutine OpenMM_XmlSerializer_serializeSystemToC(system, result, result_length)
use iso_c_binding; use OpenMM_Types; implicit none
type(OpenMM_System), intent(in) :: system
......@@ -1988,6 +1997,12 @@ OPENMM_EXPORT void openmm_platform_loadpluginsfromdirectory_(const char* directo
OPENMM_EXPORT void OPENMM_PLATFORM_LOADPLUGINSFROMDIRECTORY(const char* directory, OpenMM_StringArray*& result, int length) {
result = OpenMM_Platform_loadPluginsFromDirectory(makeString(directory, length).c_str());
}
OPENMM_EXPORT void openmm_platform_getpluginloadfailures_(OpenMM_StringArray*& result) {
result = OpenMM_Platform_getPluginLoadFailures();
}
OPENMM_EXPORT void OPENMM_PLATFORM_GETPLUGINLOADFAILURES(OpenMM_StringArray*& result) {
result = OpenMM_Platform_getPluginLoadFailures();
}
OPENMM_EXPORT void openmm_xmlserializer_serializesystemtoc_(OpenMM_System*& system, char*& result, int& result_length) {
convertStringToChars(OpenMM_XmlSerializer_serializeSystem(system), result, result_length);
}
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ df2b723d
......@@ -1341,7 +1341,6 @@ class GBVIGenerator:
for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]]
hit = 0
for i in range(len(hbGenerator.types1)):
types1 = hbGenerator.types1[i]
types2 = hbGenerator.types2[i]
......@@ -1945,23 +1944,17 @@ class AmoebaBondGenerator:
for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]]
hit = 0
for i in range(len(self.types1)):
types1 = self.types1[i]
types2 = self.types2[i]
if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
bond.length = self.length[i]
hit = 1
if bond.isConstrained:
sys.addConstraint(bond.atom1, bond.atom2, self.length[i])
elif self.k[i] != 0:
force.addBond(bond.atom1, bond.atom2, self.length[i], self.k[i])
break
if (hit == 0):
outputString = "AmoebaBondGenerator missing: types=[%5s %5s] atoms=[%6d %6d] " % (type1, type2, bond.atom1, bond.atom2)
raise ValueError(outputString)
parsers["AmoebaBondForce"] = AmoebaBondGenerator.parseElement
#=============================================================================================
......@@ -2093,13 +2086,11 @@ class AmoebaAngleGenerator:
type1 = data.atomType[data.atoms[angle[0]]]
type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]]
hit = 0
for i in range(len(self.types1)):
types1 = self.types1[i]
types2 = self.types2[i]
types3 = self.types3[i]
if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
hit = 1
if isConstrained and self.k[i] != 0.0:
angleDict['idealAngle'] = self.angle[i][0]
addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys)
......@@ -2127,13 +2118,6 @@ class AmoebaAngleGenerator:
angleDict['idealAngle'] = angleValue
force.addAngle(angle[0], angle[1], angle[2], angleValue, self.k[i])
break
if (hit == 0):
outputString = "AmoebaAngleGenerator missing types: [%s %s %s] for atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
outputString += " indices: [%6d %6d %6d]" % (angle[0], angle[1], angle[2])
raise ValueError(outputString)
#=============================================================================================
# createForcePostOpBendInPlaneAngle is called by AmoebaOutOfPlaneBendForce with the list of
......@@ -2169,7 +2153,6 @@ class AmoebaAngleGenerator:
type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]]
hit = 0
for i in range(len(self.types1)):
types1 = self.types1[i]
......@@ -2177,7 +2160,6 @@ class AmoebaAngleGenerator:
types3 = self.types3[i]
if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
hit = 1
angleDict['idealAngle'] = self.angle[i][0]
if (isConstrained and self.k[i] != 0.0):
addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys)
......@@ -2185,14 +2167,6 @@ class AmoebaAngleGenerator:
force.addAngle(angle[0], angle[1], angle[2], angle[3], self.angle[i][0], self.k[i])
break
if (hit == 0):
outputString = "AmoebaInPlaneAngleGenerator missing types: [%s %s %s] atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
outputString += " indices: [%6d %6d %6d]" % (angle[0], angle[1], angle[2])
raise ValueError(outputString)
parsers["AmoebaAngleForce"] = AmoebaAngleGenerator.parseElement
#=============================================================================================
......@@ -2562,7 +2536,6 @@ class AmoebaTorsionGenerator:
type3 = data.atomType[data.atoms[torsion[2]]]
type4 = data.atomType[data.atoms[torsion[3]]]
hit = 0
for i in range(len(self.types1)):
types1 = self.types1[i]
......@@ -2573,7 +2546,6 @@ class AmoebaTorsionGenerator:
# match types in forward or reverse direction
if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4) or (type4 in types1 and type3 in types2 and type2 in types3 and type1 in types4):
hit = 1
if self.t1[i][0] != 0:
force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 1, self.t1[i][1], self.t1[i][0])
if self.t2[i][0] != 0:
......@@ -2582,15 +2554,6 @@ class AmoebaTorsionGenerator:
force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 3, self.t3[i][1], self.t3[i][0])
break
if (hit == 0):
outputString = "AmoebaTorsionGenerator missing type: [%s %s %s %s] atoms: " % (type1, type2, type3, type4)
outputString += getAtomPrint( data, torsion[0] ) + ' '
outputString += getAtomPrint( data, torsion[1] ) + ' '
outputString += getAtomPrint( data, torsion[2] ) + ' '
outputString += getAtomPrint( data, torsion[3] )
outputString += " indices: [%6d %6d %6d %6d]" % (torsion[0], torsion[1], torsion[2], torsion[3])
raise ValueError(outputString)
parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement
#=============================================================================================
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ df2b723d
......@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2014 University of Virginia and the Authors.
Portions copyright (c) 2012-2015 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts
Contributors: Jason M. Swails, Peter Eastman
......@@ -31,7 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
from __future__ import division
from simtk.openmm import CustomGBForce, Discrete1DFunction
from simtk.openmm import CustomGBForce, Continuous2DFunction
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
......@@ -308,12 +308,11 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
custom.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
custom.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
......@@ -350,12 +349,11 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
custom.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
custom.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
......
wrappers/python/simtk/openmm/app/simulation.py
View file @ df2b723d
......@@ -135,7 +135,7 @@ class Simulation(object):
if endStep is None:
endStep = sys.maxint
nextReport = [None]*len(self.reporters)
while self.currentStep < endStep:
while self.currentStep < endStep and (endTime is None or datetime.now() < endTime):
nextSteps = endStep-self.currentStep
anyReport = False
for i, reporter in enumerate(self.reporters):
......
wrappers/python/simtk/openmm/app/statedatareporter.py
View file @ df2b723d
......@@ -55,7 +55,7 @@ class StateDataReporter(object):
"""
def __init__(self, file, reportInterval, step=False, time=False, potentialEnergy=False, kineticEnergy=False, totalEnergy=False, temperature=False, volume=False, density=False,
progress=False, remainingTime=False, speed=False, separator=',', systemMass=None, totalSteps=None):
progress=False, remainingTime=False, speed=False, elapsedTime=False, separator=',', systemMass=None, totalSteps=None):
"""Create a StateDataReporter.
Parameters:
......@@ -74,6 +74,7 @@ class StateDataReporter(object):
- remainingTime (boolean=False) Whether to write an estimate of the remaining clock time until
completion to the file. If this is True, you must also specify totalSteps.
- speed (bool=False) Whether to write an estimate of the simulation speed in ns/day to the file
- elapsedTime (bool=False) Whether to write the elapsed time of the simulation in seconds to the file.
- separator (string=',') The separator to use between columns in the file
- systemMass (mass=None) The total mass to use for the system when reporting density. If this is
None (the default), the system mass is computed by summing the masses of all particles. This
......@@ -113,6 +114,7 @@ class StateDataReporter(object):
self._progress = progress
self._remainingTime = remainingTime
self._speed = speed
self._elapsedTime = elapsedTime
self._separator = separator
self._totalMass = systemMass
self._totalSteps = totalSteps
......@@ -207,6 +209,8 @@ class StateDataReporter(object):
values.append('%.3g' % (elapsedNs/elapsedDays))
else:
values.append('--')
if self._elapsedTime:
values.append(time.time() - self._initialClockTime)
if self._remainingTime:
elapsedSeconds = clockTime-self._initialClockTime
elapsedSteps = simulation.currentStep-self._initialSteps
......@@ -284,6 +288,8 @@ class StateDataReporter(object):
headers.append('Density (g/mL)')
if self._speed:
headers.append('Speed (ns/day)')
if self._elapsedTime:
headers.append('Elapsed Time (s)')
if self._remainingTime:
headers.append('Time Remaining')
return headers
......
wrappers/python/simtk/openmm/app/topology.py
View file @ df2b723d
......@@ -59,6 +59,14 @@ class Topology(object):
self._bonds = []
self._periodicBoxVectors = None
def __repr__(self):
nchains = len(self._chains)
nres = sum(1 for r in self.residues())
natom = sum(1 for a in self.atoms())
nbond = len(self._bonds)
return '<%s; %d chains, %d residues, %d atoms, %d bonds>' % (
type(self).__name__, nchains, nres, natom, nbond)
def addChain(self, id=None):
"""Create a new Chain and add it to the Topology.
......@@ -291,6 +299,9 @@ class Chain(object):
for atom in residue._atoms:
yield atom
def __len__(self):
return len(self._residues)
class Residue(object):
"""A Residue object represents a residue within a Topology."""
def __init__(self, name, index, chain, id):
......@@ -309,6 +320,9 @@ class Residue(object):
"""Iterate over all Atoms in the Residue."""
return iter(self._atoms)
def __len__(self):
return len(self._atoms)
class Atom(object):
"""An Atom object represents a residue within a Topology."""
......
wrappers/python/simtk/testInstallation.py
View file @ df2b723d
......@@ -101,7 +101,7 @@ def run_tests():
d = f1-f2
error = sqrt((d[0]*d[0]+d[1]*d[1]+d[2]*d[2])/(f1[0]*f1[0]+f1[1]*f1[1]+f1[2]*f1[2]))
errors.append(error)
print("{} vs. {}: {:g}".format(Platform.getPlatform(j).getName(),
print("{0} vs. {1}: {2:g}".format(Platform.getPlatform(j).getName(),
Platform.getPlatform(i).getName(),
sorted(errors)[len(errors)//2]))
......
wrappers/python/simtk/unit/basedimension.py
View file @ df2b723d
#!/bin/env python
"""
Module simtk.unit.basedimension
......@@ -34,6 +32,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import print_function, division
__author__ = "Christopher M. Bruns"
__version__ = "0.6"
......
wrappers/python/simtk/unit/baseunit.py
View file @ df2b723d
......@@ -33,6 +33,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import print_function, division, absolute_import
__author__ = "Christopher M. Bruns"
__version__ = "0.6"
......@@ -44,6 +45,7 @@ class BaseUnit(object):
For example, meter_base_unit could be a BaseUnit for the length dimension.
The BaseUnit class is used internally in the more general Unit class.
'''
__array_priority__ = 100
def __init__(self, base_dim, name, symbol):
"""Creates a new BaseUnit.
......@@ -127,7 +129,7 @@ class BaseUnit(object):
self._conversion_factor_to_by_name[other.name] = factor
for (unit, cfac) in other._conversion_factor_to.items():
if unit is self: continue
if self._conversion_factor_to.has_key(unit): continue
if unit in self._conversion_factor_to: continue
self._conversion_factor_to[unit] = factor * cfac
unit._conversion_factor_to[self] = pow(factor * cfac, -1)
self._conversion_factor_to_by_name[unit.name] = factor * cfac
......@@ -138,7 +140,7 @@ class BaseUnit(object):
other._conversion_factor_to_by_name[self.name] = invFac
for (unit, cfac) in self._conversion_factor_to.items():
if unit is other: continue
if other._conversion_factor_to.has_key(unit): continue
if unit in other._conversion_factor_to: continue
other._conversion_factor_to[unit] = invFac * cfac
unit._conversion_factor_to[other] = pow(invFac * cfac, -1)
other._conversion_factor_to_by_name[unit.name] = invFac * cfac
......
wrappers/python/simtk/unit/constants.py
View file @ df2b723d
......@@ -29,13 +29,12 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from __future__ import print_function, division, absolute_import
__author__ = "Christopher M. Bruns"
__version__ = "0.5"
from unit_definitions import *
from .unit_definitions import *
#################
### CONSTANTS ###
......
wrappers/python/simtk/unit/mymatrix.py
View file @ df2b723d
......@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import print_function, division, absolute_import
import sys
......@@ -41,9 +42,9 @@ def eye(size):
[0, 0, 1]]
"""
result = []
for row in range(0, size):
for row in range(size):
r = []
for col in range(0, size):
for col in range(size):
if row == col:
r.append(1)
else:
......@@ -63,9 +64,9 @@ def zeros(m, n=None):
if n is None:
n = m
result = []
for row in range(0, m):
for row in range(m):
r = []
for col in range(0, n):
for col in range(n):
r.append(0)
result.append(r)
return MyMatrix(result)
......@@ -171,7 +172,7 @@ class MyMatrix(MyVector):
def __str__(self):
result = ""
start_char = "["
for m in range(0, self.numRows()):
for m in range(self.numRows()):
result += start_char
result += str(self[m])
if m < self.numRows() - 1:
......@@ -226,9 +227,9 @@ class MyMatrix(MyVector):
if self.numCols() != r:
raise ArithmeticError("Matrix multplication size mismatch (%d vs %d)" % (self.numCols(), r))
result = zeros(m, n)
for i in range(0, m):
for j in range(0, n):
for k in range(0, r):
for i in range(m):
for j in range(n):
for k in range(r):
result[i][j] += self[i][k]*rhs[k][j]
return result
......@@ -245,8 +246,8 @@ class MyMatrix(MyVector):
assert len(rhs) == m
assert len(rhs[0]) == n
result = zeros(m,n)
for i in range(0,m):
for j in range(0,n):
for i in range(m):
for j in range(n):
result[i][j] = self[i][j] + rhs[i][j]
return result
......@@ -263,8 +264,8 @@ class MyMatrix(MyVector):
assert len(rhs) == m
assert len(rhs[0]) == n
result = zeros(m,n)
for i in range(0,m):
for j in range(0,n):
for i in range(m):
for j in range(n):
result[i][j] = self[i][j] - rhs[i][j]
return result
......@@ -275,8 +276,8 @@ class MyMatrix(MyVector):
m = self.numRows()
n = self.numCols()
result = zeros(m, n)
for i in range(0,m):
for j in range(0,n):
for i in range(m):
for j in range(n):
result[i][j] = -self[i][j]
return result
......@@ -358,7 +359,7 @@ class MyMatrix(MyVector):
ipiv[icol] += 1
# We now have the pivot element, so we interchange rows...
if irow != icol:
for l in range(0,n):
for l in range(n):
temp = a[irow][l]
a[irow][l] = a[icol][l]
a[icol][l] = temp
......@@ -368,20 +369,20 @@ class MyMatrix(MyVector):
raise ArithmeticError("Cannot invert singular matrix")
pivinv = 1.0/a[icol][icol]
a[icol][icol] = 1.0
for l in range(0,n):
for l in range(n):
a[icol][l] *= pivinv
for ll in range(0,n): # next we reduce the rows
for ll in range(n): # next we reduce the rows
if ll == icol:
continue # except the pivot one, of course
dum = a[ll][icol]
a[ll][icol] = 0.0
for l in range(0,n):
for l in range(n):
a[ll][l] -= a[icol][l]*dum
# Unscramble the permuted columns
for l in range(n-1, -1, -1):
if indxr[l] == indxc[l]:
continue
for k in range(0,n):
for k in range(n):
temp = a[k][indxr[l]]
a[k][indxr[l]] = a[k][indxc[l]]
a[k][indxc[l]] = temp
......@@ -415,7 +416,7 @@ class MyMatrixTranspose(MyMatrix):
return MyVector(result)
def __setitem__(self, key, rhs):
for n in range(0, len(self.data)):
for n in range(len(self.data)):
self.data[n][key] = rhs[n]
def __str__(self):
......@@ -423,11 +424,11 @@ class MyMatrixTranspose(MyMatrix):
return "[[]]"
start_char = "["
result = ""
for m in range(0, len(self.data[0])):
for m in range(len(self.data[0])):
result += start_char
result += "["
sep_char = ""
for n in range(0, len(self.data)):
for n in range(len(self.data)):
result += sep_char
result += str(self.data[n][m])
sep_char = ", "
......@@ -443,11 +444,11 @@ class MyMatrixTranspose(MyMatrix):
return "MyMatrixTranspose([[]])"
start_char = "["
result = 'MyMatrixTranspose('
for m in range(0, len(self.data[0])):
for m in range(len(self.data[0])):
result += start_char
result += "["
sep_char = ""
for n in range(0, len(self.data)):
for n in range(len(self.data)):
result += sep_char
result += repr(self.data[n][m])
sep_char = ", "
......
wrappers/python/simtk/unit/prefix.py
View file @ df2b723d
......@@ -29,12 +29,13 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import print_function, division, absolute_import
__author__ = "Christopher M. Bruns"
__version__ = "0.6"
from baseunit import BaseUnit
from unit import Unit, ScaledUnit
from .baseunit import BaseUnit
from .unit import Unit, ScaledUnit
import sys
###################
......
wrappers/python/simtk/unit/quantity.py
View file @ df2b723d
......@@ -67,8 +67,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from __future__ import division, print_function, absolute_import
__author__ = "Christopher M. Bruns"
__version__ = "0.5"
......@@ -76,8 +75,8 @@ __version__ = "0.5"
import math
import copy
from standard_dimensions import *
from unit import Unit, is_unit, dimensionless
from .standard_dimensions import *
from .unit import Unit, is_unit, dimensionless
class Quantity(object):
"""Physical quantity, such as 1.3 meters per second.
......@@ -92,18 +91,8 @@ class Quantity(object):
Note - unit conversions will cause tuples to be converted to lists
4 - lists of tuples of numbers, lists of lists of ... etc. of numbers
5 - numpy.arrays
Create numpy.arrays with units using the Quantity constructor, not the
multiply operator. e.g.
Quantity(numpy.array([1,2,3]), centimeters) # correct
*NOT*
numpy.array([1,2,3]) * centimeters # won't work
because numpy.arrays already overload the multiply operator for EVERYTHING.
"""
__array_priority__ = 99
def __init__(self, value=None, unit=None):
"""
......@@ -136,7 +125,7 @@ class Quantity(object):
if len(value) < 1:
unit = dimensionless
else:
first_item = iter(value).next()
first_item = next(iter(value))
# Avoid infinite recursion for string, because a one-character
# string is its own first element
try:
......@@ -613,6 +602,9 @@ class Quantity(object):
"""
return bool(self._value)
def __bool__(self):
return bool(self._value)
def __complex__(self):
return Quantity(complex(self._value), self.unit)
def __float__(self):
......@@ -713,7 +705,7 @@ class Quantity(object):
else:
for i in range(len(value)):
value[i] = factor*value[i]
except TypeError as ex:
except TypeError:
if isinstance(value, tuple):
value = tuple([self._scale_sequence(x, factor, post_multiply) for x in value])
else:
......@@ -826,7 +818,6 @@ def _is_string(x):
except StopIteration:
return False
# run module directly for testing
if __name__=='__main__':
# Test the examples in the docstrings
......
wrappers/python/simtk/unit/standard_dimensions.py
View file @ df2b723d
......@@ -31,11 +31,12 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division, print_function, absolute_import
__author__ = "Christopher M. Bruns"
__version__ = "0.6"
from basedimension import BaseDimension
from .basedimension import BaseDimension
##################
### DIMENSIONS ###
......
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