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Commit 24608623 authored by leeping's avatar leeping
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Merge branch 'master' of github.com:SimTk/openmm

parents d71725d8 f915b68a
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examples/CMakeLists.txt
View file @ 24608623
...@@ -93,7 +93,7 @@ FOREACH(EX_ROOT ${F_EXAMPLES}) ...@@ -93,7 +93,7 @@ FOREACH(EX_ROOT ${F_EXAMPLES})
INSTALL(FILES ${EX_ROOT}.f90 DESTINATION examples) INSTALL(FILES ${EX_ROOT}.f90 DESTINATION examples)
ENDFOREACH(EX_ROOT ${F_EXAMPLES}) ENDFOREACH(EX_ROOT ${F_EXAMPLES})
INSTALL(FILES simulateAmber.py simulatePdb.py testInstallation.py argon-chemical-potential.py input.inpcrd input.prmtop input.pdb INSTALL(FILES simulateAmber.py simulatePdb.py simulateGromacs.py testInstallation.py argon-chemical-potential.py input.inpcrd input.prmtop input.pdb input.gro input.top
DESTINATION examples) DESTINATION examples)
INSTALL(FILES VisualStudio/HelloArgon.vcproj INSTALL(FILES VisualStudio/HelloArgon.vcproj
......
examples/argon-chemical-potential.py
View file @ 24608623
...@@ -15,6 +15,7 @@ ...@@ -15,6 +15,7 @@
# [1] Michael R. Shirts and John D. Chodera. Statistically optimal analysis of samples from multiple equilibrium states. # [1] Michael R. Shirts and John D. Chodera. Statistically optimal analysis of samples from multiple equilibrium states.
# J. Chem. Phys. 129:124105 (2008) http://dx.doi.org/10.1063/1.2978177 # J. Chem. Phys. 129:124105 (2008) http://dx.doi.org/10.1063/1.2978177
from __future__ import print_function
from simtk.openmm import * from simtk.openmm import *
from simtk.unit import * from simtk.unit import *
import numpy import numpy
...@@ -51,15 +52,15 @@ nlambda = len(lambda_values) ...@@ -51,15 +52,15 @@ nlambda = len(lambda_values)
volume = nparticles*(sigma**3)/reduced_density volume = nparticles*(sigma**3)/reduced_density
box_edge = volume**(1.0/3.0) box_edge = volume**(1.0/3.0)
cutoff = min(box_edge*0.49, 2.5*sigma) # Compute cutoff cutoff = min(box_edge*0.49, 2.5*sigma) # Compute cutoff
print "sigma = %s" % sigma print("sigma = %s" % sigma)
print "box_edge = %s" % box_edge print("box_edge = %s" % box_edge)
print "cutoff = %s" % cutoff print("cutoff = %s" % cutoff)
# ============================================================================= # =============================================================================
# Build systems at each alchemical lambda value. # Build systems at each alchemical lambda value.
# ============================================================================= # =============================================================================
print "Building alchemically-modified systems..." print("Building alchemically-modified systems...")
alchemical_systems = list() # alchemical_systems[i] is the alchemically-modified System object corresponding to lambda_values[i] alchemical_systems = list() # alchemical_systems[i] is the alchemically-modified System object corresponding to lambda_values[i]
for lambda_value in lambda_values: for lambda_value in lambda_values:
# Create argon system where first particle is alchemically modified by lambda_value. # Create argon system where first particle is alchemically modified by lambda_value.
...@@ -112,17 +113,17 @@ for (lambda_index, lambda_value) in enumerate(lambda_values): ...@@ -112,17 +113,17 @@ for (lambda_index, lambda_value) in enumerate(lambda_values):
context.setPositions(positions) context.setPositions(positions)
# Minimize energy from coordinates. # Minimize energy from coordinates.
print "Lambda %d/%d : minimizing..." % (lambda_index+1, nlambda) print("Lambda %d/%d : minimizing..." % (lambda_index+1, nlambda))
LocalEnergyMinimizer.minimize(context) LocalEnergyMinimizer.minimize(context)
# Equilibrate. # Equilibrate.
print "Lambda %d/%d : equilibrating..." % (lambda_index+1, nlambda) print("Lambda %d/%d : equilibrating..." % (lambda_index+1, nlambda))
integrator.step(nequil_steps) integrator.step(nequil_steps)
# Sample. # Sample.
position_history = list() # position_history[i] is the set of positions after iteration i position_history = list() # position_history[i] is the set of positions after iteration i
for iteration in range(nprod_iterations): for iteration in range(nprod_iterations):
print "Lambda %d/%d : production iteration %d/%d" % (lambda_index+1, nlambda, iteration+1, nprod_iterations) print("Lambda %d/%d : production iteration %d/%d" % (lambda_index+1, nlambda, iteration+1, nprod_iterations))
# Run dynamics. # Run dynamics.
integrator.step(nprod_steps) integrator.step(nprod_steps)
...@@ -138,7 +139,7 @@ for (lambda_index, lambda_value) in enumerate(lambda_values): ...@@ -138,7 +139,7 @@ for (lambda_index, lambda_value) in enumerate(lambda_values):
del context, integrator del context, integrator
# Compute reduced potentials of all snapshots at all alchemical states for MBAR. # Compute reduced potentials of all snapshots at all alchemical states for MBAR.
print "Lambda %d/%d : computing energies at all states..." % (lambda_index+1, nlambda) print("Lambda %d/%d : computing energies at all states..." % (lambda_index+1, nlambda))
beta = 1.0 / (BOLTZMANN_CONSTANT_kB * AVOGADRO_CONSTANT_NA * temperature) # inverse temperature beta = 1.0 / (BOLTZMANN_CONSTANT_kB * AVOGADRO_CONSTANT_NA * temperature) # inverse temperature
for l in range(nlambda): for l in range(nlambda):
# Set up Context just to evaluate energies. # Set up Context just to evaluate energies.
...@@ -159,13 +160,13 @@ try: ...@@ -159,13 +160,13 @@ try:
from timeseries import subsampleCorrelatedData from timeseries import subsampleCorrelatedData
from pymbar import MBAR from pymbar import MBAR
except: except:
raise "pymbar [https://simtk.org/home/pymbar] must be installed to complete analysis of free energies." raise ImportError("pymbar [https://simtk.org/home/pymbar] must be installed to complete analysis of free energies.")
# ============================================================================= # =============================================================================
# Subsample correlated samples to generate uncorrelated subsample. # Subsample correlated samples to generate uncorrelated subsample.
# ============================================================================= # =============================================================================
print "Subsampling data to remove correlation..." print("Subsampling data to remove correlation...")
K = nlambda # number of states K = nlambda # number of states
N_k = nprod_iterations*numpy.ones([K], numpy.int32) # N_k[k] is the number of uncorrelated samples at state k N_k = nprod_iterations*numpy.ones([K], numpy.int32) # N_k[k] is the number of uncorrelated samples at state k
u_kln_subsampled = numpy.zeros([K,K,nprod_iterations], numpy.float64) # subsampled data u_kln_subsampled = numpy.zeros([K,K,nprod_iterations], numpy.float64) # subsampled data
...@@ -176,24 +177,24 @@ for k in range(K): ...@@ -176,24 +177,24 @@ for k in range(K):
N_k[k] = len(indices) N_k[k] = len(indices)
for l in range(K): for l in range(K):
u_kln_subsampled[k,l,0:len(indices)] = u_kln[k,l,indices] u_kln_subsampled[k,l,0:len(indices)] = u_kln[k,l,indices]
print "Number of uncorrelated samples per state:" print("Number of uncorrelated samples per state:")
print N_k print(N_k)
# ============================================================================= # =============================================================================
# Analyze with MBAR to compute free energy differences and statistical errors. # Analyze with MBAR to compute free energy differences and statistical errors.
# ============================================================================= # =============================================================================
print "Analyzing with MBAR..." print("Analyzing with MBAR...")
mbar = MBAR(u_kln_subsampled, N_k) mbar = MBAR(u_kln_subsampled, N_k)
[Deltaf_ij, dDeltaf_ij] = mbar.getFreeEnergyDifferences() Deltaf_ij, dDeltaf_ij = mbar.getFreeEnergyDifferences()
print "Free energy differences (in kT)" print("Free energy differences (in kT)")
print Deltaf_ij print(Deltaf_ij)
print "Statistical errors (in kT)" print("Statistical errors (in kT)")
print dDeltaf_ij print(dDeltaf_ij)
# ============================================================================= # =============================================================================
# Report result. # Report result.
# ============================================================================= # =============================================================================
print "Free energy of inserting argon particle: %.3f +- %.3f kT" % (Deltaf_ij[0,K-1], dDeltaf_ij[0,K-1]) print("Free energy of inserting argon particle: %.3f +- %.3f kT" % (Deltaf_ij[0,K-1], dDeltaf_ij[0,K-1]))
examples/testInstallation.py
View file @ 24608623
from __future__ import print_function
# First make sure OpenMM is installed. # First make sure OpenMM is installed.
import sys import sys
try: try:
from simtk.openmm.app import * from simtk.openmm.app import *
from simtk.openmm import * from simtk.openmm import *
from simtk.unit import * from simtk.unit import *
except ImportError as err: except ImportError as err:
print "Failed to import OpenMM packages:", err.message print("Failed to import OpenMM packages:", err.message)
print "Make sure OpenMM is installed and the library path is set correctly." print("Make sure OpenMM is installed and the library path is set correctly.")
sys.exit() sys.exit()
# Create a System for the tests. # Create a System for the tests.
...@@ -19,28 +21,28 @@ system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCut ...@@ -19,28 +21,28 @@ system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCut
# List all installed platforms and compute forces with each one. # List all installed platforms and compute forces with each one.
numPlatforms = Platform.getNumPlatforms() numPlatforms = Platform.getNumPlatforms()
print "There are", numPlatforms, "Platforms available:" print("There are", numPlatforms, "Platforms available:")
print print()
forces = [None]*numPlatforms forces = [None]*numPlatforms
for i in range(numPlatforms): for i in range(numPlatforms):
platform = Platform.getPlatform(i) platform = Platform.getPlatform(i)
print i+1, platform.getName(), print(i+1, platform.getName(), end=" ")
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds) integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
try: try:
simulation = Simulation(pdb.topology, system, integrator, platform) simulation = Simulation(pdb.topology, system, integrator, platform)
simulation.context.setPositions(pdb.positions) simulation.context.setPositions(pdb.positions)
forces[i] = simulation.context.getState(getForces=True).getForces() forces[i] = simulation.context.getState(getForces=True).getForces()
del simulation del simulation
print "- Successfully computed forces" print("- Successfully computed forces")
except: except:
print "- Error computing forces with", platform.getName(), "platform" print("- Error computing forces with", platform.getName(), "platform")
# See how well the platforms agree. # See how well the platforms agree.
if numPlatforms > 1: if numPlatforms > 1:
print print()
print "Median difference in forces between platforms:" print("Median difference in forces between platforms:")
print print()
for i in range(numPlatforms): for i in range(numPlatforms):
for j in range(i): for j in range(i):
if forces[i] is not None and forces[j] is not None: if forces[i] is not None and forces[j] is not None:
...@@ -49,4 +51,6 @@ if numPlatforms > 1: ...@@ -49,4 +51,6 @@ if numPlatforms > 1:
d = f1-f2 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])) 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) errors.append(error)
print "%s vs. %s: %g" % (Platform.getPlatform(j).getName(), Platform.getPlatform(i).getName(), sorted(errors)[len(errors)/2]) print("{} vs. {}: {:g}".format(Platform.getPlatform(j).getName(),
Platform.getPlatform(i).getName(),
sorted(errors)[len(errors)//2]))
platforms/opencl/include/OpenCLContext.h
View file @ 24608623
...@@ -191,6 +191,12 @@ public: ...@@ -191,6 +191,12 @@ public:
int getDeviceIndex() { int getDeviceIndex() {
return deviceIndex; return deviceIndex;
} }
/**
* Get the index of the cl::Platform associated with this object.
*/
int getPlatformIndex() {
return platformIndex;
}
/** /**
* Get the PlatformData object this context is part of. * Get the PlatformData object this context is part of.
*/ */
...@@ -604,6 +610,7 @@ private: ...@@ -604,6 +610,7 @@ private:
double time; double time;
OpenCLPlatform::PlatformData& platformData; OpenCLPlatform::PlatformData& platformData;
int deviceIndex; int deviceIndex;
int platformIndex;
int contextIndex; int contextIndex;
int stepCount; int stepCount;
int computeForceCount; int computeForceCount;
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 24608623
...@@ -88,17 +88,25 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device ...@@ -88,17 +88,25 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
contextIndex = platformData.contexts.size(); contextIndex = platformData.contexts.size();
std::vector<cl::Platform> platforms; std::vector<cl::Platform> platforms;
cl::Platform::get(&platforms); cl::Platform::get(&platforms);
if (platformIndex < 0 || platformIndex >= (int) platforms.size())
throw OpenMMException("Illegal value for OpenCL platform index");
string platformVendor = platforms[platformIndex].getInfo<CL_PLATFORM_VENDOR>();
vector<cl::Device> devices;
platforms[platformIndex].getDevices(CL_DEVICE_TYPE_ALL, &devices);
const int minThreadBlockSize = 32; const int minThreadBlockSize = 32;
if (deviceIndex < 0 || deviceIndex >= (int) devices.size()) {
// Try to figure out which device is the fastest.
int bestSpeed = -1; int bestSpeed = -1;
int bestDevice = -1;
int bestPlatform = -1;
for (int j = 0; j < platforms.size(); j++) {
// if they supplied a valid platformIndex, we only look through that platform
if (j != platformIndex && platformIndex >= 0 && platformIndex < (int) platforms.size())
continue;
string platformVendor = platforms[j].getInfo<CL_PLATFORM_VENDOR>();
vector<cl::Device> devices;
platforms[j].getDevices(CL_DEVICE_TYPE_ALL, &devices);
for (int i = 0; i < (int) devices.size(); i++) { for (int i = 0; i < (int) devices.size(); i++) {
// if they supplied a valid deviceIndex, we only look through that one
if (i != deviceIndex && deviceIndex >= 0 && deviceIndex < (int) devices.size())
continue;
if (platformVendor == "Apple" && devices[i].getInfo<CL_DEVICE_VENDOR>() == "AMD") if (platformVendor == "Apple" && devices[i].getInfo<CL_DEVICE_VENDOR>() == "AMD")
continue; // Don't use AMD GPUs on OS X due to serious bugs. continue; // Don't use AMD GPUs on OS X due to serious bugs.
int maxSize = devices[i].getInfo<CL_DEVICE_MAX_WORK_ITEM_SIZES>()[0]; int maxSize = devices[i].getInfo<CL_DEVICE_MAX_WORK_ITEM_SIZES>()[0];
...@@ -137,15 +145,26 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device ...@@ -137,15 +145,26 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
} }
int speed = devices[i].getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>()*processingElementsPerComputeUnit*devices[i].getInfo<CL_DEVICE_MAX_CLOCK_FREQUENCY>(); int speed = devices[i].getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>()*processingElementsPerComputeUnit*devices[i].getInfo<CL_DEVICE_MAX_CLOCK_FREQUENCY>();
if (maxSize >= minThreadBlockSize && speed > bestSpeed) { if (maxSize >= minThreadBlockSize && speed > bestSpeed) {
deviceIndex = i; bestDevice = i;
bestSpeed = speed; bestSpeed = speed;
bestPlatform = j;
} }
} }
} }
if (deviceIndex == -1)
if (bestPlatform == -1)
throw OpenMMException("No compatible OpenCL platform is available");
if (bestDevice == -1)
throw OpenMMException("No compatible OpenCL device is available"); throw OpenMMException("No compatible OpenCL device is available");
device = devices[deviceIndex];
this->deviceIndex = deviceIndex; vector<cl::Device> devices;
platforms[bestPlatform].getDevices(CL_DEVICE_TYPE_ALL, &devices);
string platformVendor = platforms[bestPlatform].getInfo<CL_PLATFORM_VENDOR>();
device = devices[bestDevice];
this->deviceIndex = bestDevice;
this->platformIndex = bestPlatform;
if (device.getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>() < minThreadBlockSize) if (device.getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>() < minThreadBlockSize)
throw OpenMMException("The specified OpenCL device is not compatible with OpenMM"); throw OpenMMException("The specified OpenCL device is not compatible with OpenMM");
compilationDefines["WORK_GROUP_SIZE"] = intToString(ThreadBlockSize); compilationDefines["WORK_GROUP_SIZE"] = intToString(ThreadBlockSize);
...@@ -227,7 +246,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device ...@@ -227,7 +246,7 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
compilationDefines["SYNC_WARPS"] = "barrier(CLK_LOCAL_MEM_FENCE)"; compilationDefines["SYNC_WARPS"] = "barrier(CLK_LOCAL_MEM_FENCE)";
vector<cl::Device> contextDevices; vector<cl::Device> contextDevices;
contextDevices.push_back(device); contextDevices.push_back(device);
cl_context_properties cprops[] = {CL_CONTEXT_PLATFORM, (cl_context_properties) platforms[platformIndex](), 0}; cl_context_properties cprops[] = {CL_CONTEXT_PLATFORM, (cl_context_properties) platforms[bestPlatform](), 0};
context = cl::Context(contextDevices, cprops, errorCallback); context = cl::Context(contextDevices, cprops, errorCallback);
queue = cl::CommandQueue(context, device); queue = cl::CommandQueue(context, device);
numAtoms = system.getNumParticles(); numAtoms = system.getNumParticles();
......
platforms/opencl/src/OpenCLPlatform.cpp
View file @ 24608623
...@@ -133,7 +133,7 @@ void OpenCLPlatform::contextDestroyed(ContextImpl& context) const { ...@@ -133,7 +133,7 @@ void OpenCLPlatform::contextDestroyed(ContextImpl& context) const {
OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& platformPropValue, const string& deviceIndexProperty, OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& platformPropValue, const string& deviceIndexProperty,
const string& precisionProperty, const string& cpuPmeProperty) : removeCM(false), stepCount(0), computeForceCount(0), time(0.0) { const string& precisionProperty, const string& cpuPmeProperty) : removeCM(false), stepCount(0), computeForceCount(0), time(0.0) {
int platformIndex = 0; int platformIndex = -1;
if (platformPropValue.length() > 0) if (platformPropValue.length() > 0)
stringstream(platformPropValue) >> platformIndex; stringstream(platformPropValue) >> platformIndex;
vector<string> devices; vector<string> devices;
...@@ -161,6 +161,8 @@ OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& p ...@@ -161,6 +161,8 @@ OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& p
deviceIndex << contexts[i]->getDeviceIndex(); deviceIndex << contexts[i]->getDeviceIndex();
deviceName << contexts[i]->getDevice().getInfo<CL_DEVICE_NAME>(); deviceName << contexts[i]->getDevice().getInfo<CL_DEVICE_NAME>();
} }
platformIndex = contexts[0]->getPlatformIndex();
useCpuPme = (cpuPmeProperty == "true" && !contexts[0]->getUseDoublePrecision()); useCpuPme = (cpuPmeProperty == "true" && !contexts[0]->getUseDoublePrecision());
propertyValues[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex.str(); propertyValues[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex.str();
propertyValues[OpenCLPlatform::OpenCLDeviceName()] = deviceName.str(); propertyValues[OpenCLPlatform::OpenCLDeviceName()] = deviceName.str();
......
plugins/cpupme/src/CpuPmeKernels.cpp
View file @ 24608623
...@@ -95,6 +95,7 @@ static int getNumProcessors() { ...@@ -95,6 +95,7 @@ static int getNumProcessors() {
#define cpuid __cpuid #define cpuid __cpuid
#else #else
static void cpuid(int cpuInfo[4], int infoType){ static void cpuid(int cpuInfo[4], int infoType){
#ifdef __LP64__
__asm__ __volatile__ ( __asm__ __volatile__ (
"cpuid": "cpuid":
"=a" (cpuInfo[0]), "=a" (cpuInfo[0]),
...@@ -103,6 +104,19 @@ static void cpuid(int cpuInfo[4], int infoType){ ...@@ -103,6 +104,19 @@ static void cpuid(int cpuInfo[4], int infoType){
"=d" (cpuInfo[3]) : "=d" (cpuInfo[3]) :
"a" (infoType) "a" (infoType)
); );
#else
__asm__ __volatile__ (
"pushl %%ebx\n"
"cpuid\n"
"movl %%ebx, %1\n"
"popl %%ebx\n" :
"=a" (cpuInfo[0]),
"=r" (cpuInfo[1]),
"=c" (cpuInfo[2]),
"=d" (cpuInfo[3]) :
"a" (infoType)
);
#endif
} }
#endif #endif
......
plugins/rpmd/platforms/cuda/src/kernels/rpmdContraction.cu
View file @ 24608623
...@@ -114,8 +114,8 @@ extern "C" __global__ void contractForces(long long* force, long long* contracte ...@@ -114,8 +114,8 @@ extern "C" __global__ void contractForces(long long* force, long long* contracte
// Store results. // Store results.
force[forceIndex] = (long long) (FORCE_SCALE*freal[indexInBlock].x); force[forceIndex] += (long long) (FORCE_SCALE*freal[indexInBlock].x);
force[forceIndex+PADDED_NUM_ATOMS] = (long long) (FORCE_SCALE*freal[indexInBlock].y); force[forceIndex+PADDED_NUM_ATOMS] += (long long) (FORCE_SCALE*freal[indexInBlock].y);
force[forceIndex+PADDED_NUM_ATOMS*2] = (long long) (FORCE_SCALE*freal[indexInBlock].z); force[forceIndex+PADDED_NUM_ATOMS*2] += (long long) (FORCE_SCALE*freal[indexInBlock].z);
} }
} }
plugins/rpmd/platforms/opencl/src/kernels/rpmdContraction.cl
View file @ 24608623
...@@ -113,6 +113,6 @@ __kernel void contractForces(__global real4* force, __global real4* contracted) ...@@ -113,6 +113,6 @@ __kernel void contractForces(__global real4* force, __global real4* contracted)
// Store results. // Store results.
force[index] = convert_real4(FORCE_SCALE*freal[indexInBlock]); force[index] += convert_real4(FORCE_SCALE*freal[indexInBlock]);
} }
} }
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
View file @ 24608623
...@@ -336,7 +336,7 @@ void ReferenceIntegrateRPMDStepKernel::computeForces(ContextImpl& context, const ...@@ -336,7 +336,7 @@ void ReferenceIntegrateRPMDStepKernel::computeForces(ContextImpl& context, const
q[k] = t_complex(0, 0); q[k] = t_complex(0, 0);
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &q[0], &q[0]); fftpack_exec_1d(fft, FFTPACK_BACKWARD, &q[0], &q[0]);
for (int k = 0; k < totalCopies; k++) for (int k = 0; k < totalCopies; k++)
forces[k][particle][component] = scale2*q[k].re; forces[k][particle][component] += scale2*q[k].re;
} }
} }
} }
......
wrappers/python/CMakeLists.txt
View file @ 24608623
...@@ -13,6 +13,7 @@ mark_as_advanced(OPENMM_PYTHON_STAGING_DIR) ...@@ -13,6 +13,7 @@ mark_as_advanced(OPENMM_PYTHON_STAGING_DIR)
file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm) file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm)
file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/simtk/unit) file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/simtk/unit)
file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen/swig_lib/python) file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/src/swig_doxygen/swig_lib/python)
file(MAKE_DIRECTORY ${OPENMM_PYTHON_STAGING_DIR}/tests)
############################################################################## ##############################################################################
### Identify files that need to be copied from source area to staging area ### ### Identify files that need to be copied from source area to staging area ###
...@@ -46,7 +47,7 @@ file(WRITE "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/version.py" "git_revision ...@@ -46,7 +47,7 @@ file(WRITE "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/version.py" "git_revision
# set(temp2 "${temp2}\n${f}") # set(temp2 "${temp2}\n${f}")
# endforeach() # endforeach()
set(SUBDIRS src simtk) set(SUBDIRS src simtk tests)
foreach(SUBDIR ${SUBDIRS}) foreach(SUBDIR ${SUBDIRS})
file(GLOB_RECURSE STAGING_INPUT_FILES1 RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" file(GLOB_RECURSE STAGING_INPUT_FILES1 RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*README.txt" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*README.txt"
...@@ -55,6 +56,8 @@ foreach(SUBDIR ${SUBDIRS}) ...@@ -55,6 +56,8 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.sh" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.sh"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
) )
foreach(file ${STAGING_INPUT_FILES1}) foreach(file ${STAGING_INPUT_FILES1})
set(STAGING_INPUT_FILES ${STAGING_INPUT_FILES} "${file}") set(STAGING_INPUT_FILES ${STAGING_INPUT_FILES} "${file}")
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 24608623
...@@ -335,8 +335,8 @@ class PrmtopLoader(object): ...@@ -335,8 +335,8 @@ class PrmtopLoader(object):
% ((bondPointers[ii], % ((bondPointers[ii],
bondPointers[ii+1]),)) bondPointers[ii+1]),))
iType=int(bondPointers[ii+2])-1 iType=int(bondPointers[ii+2])-1
returnList.append((int(bondPointers[ii])/3, returnList.append((int(bondPointers[ii])//3,
int(bondPointers[ii+1])/3, int(bondPointers[ii+1])//3,
float(forceConstant[iType])*forceConstConversionFactor, float(forceConstant[iType])*forceConstConversionFactor,
float(bondEquil[iType])*lengthConversionFactor)) float(bondEquil[iType])*lengthConversionFactor))
return returnList return returnList
...@@ -383,9 +383,9 @@ class PrmtopLoader(object): ...@@ -383,9 +383,9 @@ class PrmtopLoader(object):
anglePointers[ii+1], anglePointers[ii+1],
anglePointers[ii+2]),)) anglePointers[ii+2]),))
iType=int(anglePointers[ii+3])-1 iType=int(anglePointers[ii+3])-1
self._angleList.append((int(anglePointers[ii])/3, self._angleList.append((int(anglePointers[ii])//3,
int(anglePointers[ii+1])/3, int(anglePointers[ii+1])//3,
int(anglePointers[ii+2])/3, int(anglePointers[ii+2])//3,
float(forceConstant[iType])*forceConstConversionFactor, float(forceConstant[iType])*forceConstConversionFactor,
float(angleEquil[iType]))) float(angleEquil[iType])))
return self._angleList return self._angleList
...@@ -411,10 +411,10 @@ class PrmtopLoader(object): ...@@ -411,10 +411,10 @@ class PrmtopLoader(object):
dihedralPointers[ii+2], dihedralPointers[ii+2],
dihedralPointers[ii+3]),)) dihedralPointers[ii+3]),))
iType=int(dihedralPointers[ii+4])-1 iType=int(dihedralPointers[ii+4])-1
self._dihedralList.append((int(dihedralPointers[ii])/3, self._dihedralList.append((int(dihedralPointers[ii])//3,
int(dihedralPointers[ii+1])/3, int(dihedralPointers[ii+1])//3,
abs(int(dihedralPointers[ii+2]))/3, abs(int(dihedralPointers[ii+2]))//3,
abs(int(dihedralPointers[ii+3]))/3, abs(int(dihedralPointers[ii+3]))//3,
float(forceConstant[iType])*forceConstConversionFactor, float(forceConstant[iType])*forceConstConversionFactor,
float(phase[iType]), float(phase[iType]),
int(0.5+float(periodicity[iType])))) int(0.5+float(periodicity[iType]))))
...@@ -429,8 +429,8 @@ class PrmtopLoader(object): ...@@ -429,8 +429,8 @@ class PrmtopLoader(object):
nonbondTerms = self.getNonbondTerms() nonbondTerms = self.getNonbondTerms()
for ii in range(0,len(dihedralPointers),5): for ii in range(0,len(dihedralPointers),5):
if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0: if int(dihedralPointers[ii+2])>0 and int(dihedralPointers[ii+3])>0:
iAtom = int(dihedralPointers[ii])/3 iAtom = int(dihedralPointers[ii])//3
lAtom = int(dihedralPointers[ii+3])/3 lAtom = int(dihedralPointers[ii+3])//3
chargeProd = charges[iAtom]*charges[lAtom] chargeProd = charges[iAtom]*charges[lAtom]
(rVdwI, epsilonI) = nonbondTerms[iAtom] (rVdwI, epsilonI) = nonbondTerms[iAtom]
(rVdwL, epsilonL) = nonbondTerms[lAtom] (rVdwL, epsilonL) = nonbondTerms[lAtom]
......
wrappers/python/simtk/openmm/app/modeller.py
View file @ 24608623
...@@ -769,6 +769,7 @@ class Modeller(object): ...@@ -769,6 +769,7 @@ class Modeller(object):
LocalEnergyMinimizer.minimize(context) LocalEnergyMinimizer.minimize(context)
self.topology = newTopology self.topology = newTopology
self.positions = context.getState(getPositions=True).getPositions() self.positions = context.getState(getPositions=True).getPositions()
del context
return actualVariants return actualVariants
def addExtraParticles(self, forcefield): def addExtraParticles(self, forcefield):
......
wrappers/python/src/swig_doxygen/swig_lib/python/extend.i
View file @ 24608623
...@@ -275,6 +275,7 @@ Parameters: ...@@ -275,6 +275,7 @@ Parameters:
} }
%feature(docstring, "This method exists only for backward compatibility. @deprecated Use deserialize() instead.") deserializeSystem; %feature(docstring, "This method exists only for backward compatibility. @deprecated Use deserialize() instead.") deserializeSystem;
%newobject deserializeSystem;
static OpenMM::System* deserializeSystem(const char* inputString) { static OpenMM::System* deserializeSystem(const char* inputString) {
std::stringstream ss; std::stringstream ss;
ss << inputString; ss << inputString;
...@@ -287,6 +288,7 @@ Parameters: ...@@ -287,6 +288,7 @@ Parameters:
return ss.str(); return ss.str();
} }
%newobject _deserializeForce;
static OpenMM::Force* _deserializeForce(const char* inputString) { static OpenMM::Force* _deserializeForce(const char* inputString) {
std::stringstream ss; std::stringstream ss;
ss << inputString; ss << inputString;
...@@ -299,6 +301,7 @@ Parameters: ...@@ -299,6 +301,7 @@ Parameters:
return ss.str(); return ss.str();
} }
%newobject _deserializeIntegrator;
static OpenMM::Integrator* _deserializeIntegrator(const char* inputString) { static OpenMM::Integrator* _deserializeIntegrator(const char* inputString) {
std::stringstream ss; std::stringstream ss;
ss << inputString; ss << inputString;
......
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