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Commit b18c82c8 authored by peastman's avatar peastman
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Merge pull request #115 from rmcgibbo/py3 

Small py3k fixes
parents 7dd882eb 6e89e067
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examples/argon-chemical-potential.py
View file @ b18c82c8
...@@ -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 @ b18c82c8
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]))
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ b18c82c8
...@@ -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]
......
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