def dialaSetup():
"""
This routine sets up the data structures needed for the following unit tests. This includes a copy of a LAMMPS walker with the alanine dipeptide and a 2D particle walker.
"""
import lammpsWalker
wlkr = lammpsWalker.lammpsWalker("input.diala", "log.diala.test")
ref_config = np.loadtxt("diala.structure").flatten()
ref_vel = np.loadtxt("vel.ref").flatten()
return wlkr, ref_config, ref_vel
def setImages(self, filename):
"""
Here we initialize an array of walker objects for the execution of the
string object.
"""
# start an array of walkers to store the string configuration.
self.images = []
for i in range(self.nimages):
wlkr = lammpsWalker.lammpsWalker(filename, index=i)
self.images.append(wlkr)
return 0
def main():
"""
definition of main scripting file for debugging purposes.
"""
# time the execution
starttime = time()
# in the serial version, lets just set rank=0
rank = 0
#---------------SET PARAMETERS -----------
if rank == 0: print "Setting up umbrella sampling parameters."
params = {}
# set the scratch directory for the calculation files
params['scratchdir'] = "/Users/jtempkin/enhanced_sampling_toolkit/neus/debug_US"
params['inputFilename'] = "/Users/jtempkin/enhanced_sampling_toolkit/neus/input.diala"
params['logFilename'] = params['scratchdir'] + "/log"
# here we will set the umbrella sampling parameters in the params dict
params['ncells'] = 144
params['cellWidth'] = 15
params['nwalkers'] = 1
params['walkerSteps'] = 50000
params['stepLength'] = 10
params['Ftype'] = 'transition'
# lets set the dynamics parameters that are needed to specify the walker
params['temperature'] = 310.0
params['timestep'] = 1.0
#--------------- INITIALIZATION--------
# only allow root rank to build files
if rank == 0:
print "Building scratch directory."
# construct the wkdir. This is where the intermediate dynamcs files will
# be written.
fileIO.makeWkdir(params['scratchdir'])
# construct the umbrella data structure
if rank == 0: print "Initializing the umbrella structure."
# create the partition object
system = partition.partition(params['ncells'])
# now we construct the umbrella windows
if rank == 0: print "Building the umbrellas."
# specify the list of boundaries, nboxes, 1/2 width of the windows
umbParams = {}
# right now, we will hardcode a 12x12 array using Erik's routine for gridding a space
umbParams['cvrange'] = np.array([map(float,entry.split(",")) for entry in "-180,180,12,15;-180,180,12,15".split(";")])
umbParams['wrapping'] = np.array(map(float, "1,1".split(',')))
system.umbrellas = fileIO.createUmbrellas(umbParams)
# build neighbor list
#system.buildNeighborList()
#----------------INITIALIZE THE ENTRY POINTS FROM FILE------------
# now we provide a data structure for entrypoints for each umbrella:
for i in range(len(system.umbrellas)):
system.umbrellas[i].entryPoints = []
# now load each entry point file from the data base and load as an array of
# ctypes pointers
for i in range(len(system.umbrellas)):
# load the numpy array
data = np.load("entryPoints/in_" + str(i) + "_w0.entryPoints.npy")
# now add each as a ctypes points to the entry points library
for j in range(data.shape[0]):
system.umbrellas[i].entryPoints.append(data[j].ctypes.data_as(ctypes.POINTER(ctypes.c_double)))
"""
#------------ GENERATE INITIAL ENTRY POINTS --------------
# sample umbrellas and construct F
if rank == 0: print "Seeding entry points from a conventional simulation."
# this
for i in range(len(system.umbrellas)):
print i
print "starting walker"
# lets instantiate a walker object to sample this window.
wlkr = lammpsWalker.lammpsWalker(params['inputFilename'])
print "minimize"
# minimize structure prior to dynamics
wlkr.minimize()
# set the dynamics to sample by langevin
wlkr.command("fix 1 all nve")
wlkr.command("fix 2 all langevin 310.0 310.0 30.0 20874")
print "setting colvars"
# set colvars for this walker (currently, alanine dipeptide dihedrals)
wlkr.colvars.append(['dihedral', 5, 7, 9, 15])
wlkr.colvars.append(['dihedral', 7, 9, 15, 17])
# set an array of starting/stoping restraints for equilibration
restraint = [[0.0, 100.0], [0.0, 100.0]]
# now specify colvars to dynamics routines
wlkr.setColvars()
# equilibrate the walker to the target point in CV space
wlkr.equilibrate(system.umbrellas[i].center, restraint, 100000)
# enter the sampling routine. This sampling routine will simply generate the initial
# entry point distribution
try:
system.sample(wlkr, params['walkerSteps'], i, 0, params, rank)
except errors.DynamicsError:
print "Rank", rank, "sampling error occured in umbrella", i, "."
continue
# now we are done populating the samples array, close the walker
wlkr.close()
# now we write out the entrypoints for each umbrella:
for i in range(len(system.umbrellas)):
np.save(params['scratchdir'] + "/in_" + str(i) + "_w0.entryPoints", system.umbrellas[i].entryPoints)
"""
#----------------MAIN LOOP----------------
if rank == 0: print "Sampling via NEUS."
# this
for i in range(len(system.umbrellas)):
print "Rank", rank, "sampling umbrella", i, "."
# lets instantiate a walker object to sample this window.
wlkr = lammpsWalker.lammpsWalker(params['inputFilename'], params['logFilename'], index=i)
wlkr.setTimestep(params['timestep'])
# set the dynamics to sample by langevin
wlkr.command("fix 1 all nve")
# the langevin fix here sets the temperature to 310K and the friction
# coefficient to 30 ps-1
wlkr.command("fix 2 all langevin " + " ".join([str(params['temperature']), str(params['temperature'])]) + " 30.0 20874")
# set colvars for this walker (currently, alanine dipeptide dihedrals)
wlkr.colvars.append(['dihedral', 5, 7, 9, 15])
wlkr.colvars.append(['dihedral', 7, 9, 15, 17])
# now specify colvars to dynamics routines
wlkr.setColvars()
# now we initialize the starting coordinates from the entry points library
temp_indx = random.randint(0, len(system.umbrellas[i].entryPoints)-1)
print system.umbrellas[i].entryPoints[temp_indx], temp_indx
print wlkr.lmp
wlkr.setConfig(system.umbrellas[i].entryPoints[temp_indx])
wlkr.command("run 0 post no")
print "drawing velocities"
# draw the velocities uniformly for now
wlkr.drawVel(distType = 'gaussian', temperature = params['temperature'])
# enter the sampling routine. This sampling routine will simply generate the initial
# entry point distribution
try:
system.sampleNeus(wlkr, params['walkerSteps'], i, 0, params, rank)
except errors.DynamicsError:
print "Rank", rank, "sampling error occurred in umbrella", i, "."
continue
# now we are done populating the samples array, close the walker
wlkr.close()
del wlkr
#gc.collect()
#----------------WRITE OUT DATA-------------
# now allow rank 0 to process data.
if rank == 0:
print system.F
fileIO.writeMat(system.F, params['scratchdir'] + "/F.out")
"""
print "Entering eigenvalue routine."
# solve eigenvalue problem for F
system.getZ()
fileIO.writeMat(system.z, params['scratchdir'] + "/z.out")
print "Computing the sensitivities."
bounds = system.getlogBound(system.F)
fileIO.writeMat(bounds, params['scratchdir'] + "/bounds.out")
"""
# now we will perform an analysis of the data and increase sampling of
# windows with high variance
if rank == 0:
print "Done!"
print "Total wallclock time was: " + str(time() - starttime) + " seconds."
return 0
def main():
"""
definition of main scripting file for debugging purposes.
"""
# time the execution
starttime = time()
# in the serial version, lets just set rank=0
rank = 0
#---------------SET PARAMETERS -----------
if rank == 0: print "Setting up umbrella sampling parameters."
params = {}
# set the scratch directory for the calculation files
params['scratchdir'] = "/Users/jtempkin/enhanced_sampling_toolkit/umbrella_sampling/debug_US"
params['inputFilename'] = "/Users/jtempkin/enhanced_sampling_toolkit/umbrella_sampling/input.diala"
# here we will set the umbrella sampling parameters in the params dict
params['ncells'] = 144
params['cellWidth'] = 60.0
params['nwalkers'] = 1
params['walkerSteps'] = 10000
params['stepLength'] = 10
params['Ftype'] = 'transition'
# lets set the dynamics parameters that are needed to specify the walker
params['temperature'] = 310.0
#--------------- INITIALIZATION--------
# only allow root rank to build files
if rank == 0:
print "Building scratch directory."
# construct the wkdir. This is where the intermediate dynamcs files will
# be written.
fileIO.makeWkdir(params['scratchdir'])
# construct the umbrella data structure
if rank == 0: print "Initializing the umbrella structure."
# create the partition object
system = partition.partition(params['ncells'])
# now we construct the umbrella windows
if rank == 0: print "Building the umbrellas."
# specify the list of boundaries, nboxes, 1/2 width of the windows
umbParams = {}
# right now, we will hardcore a 12x12 array using Erik's routine for gridding a space
umbParams['cvrange'] = np.array([map(float,entry.split(",")) for entry in "-180,180,12,30;-180,180,12,30".split(";")])
umbParams['wrapping'] = np.array(map(float, "1,1".split(',')))
system.umbrellas = fileIO.createUmbrellas(umbParams)
#------------ MAIN LOOP --------------
# sample umbrellas and construct F
if rank == 0: print "Entering main loop."
for i in range(len(system.umbrellas)):
print "Rank", rank, "sampling umbrella", i, "."
print "init walker"
# lets instantiate a walker object to sample this window.
wlkr = lammpsWalker.lammpsWalker(params['inputFilename'])
print "minimize"
# minimize structure prior to dynamics
wlkr.minimize()
# set the dynamics to sample by langevin
wlkr.command("fix 1 all nve")
wlkr.command("fix 2 all langevin 310.0 310.0 30.0 20874")
# set colvars for this walker (currently, alanine dipeptide dihedrals)
wlkr.colvars.append(['dihedral', 5, 7, 9, 15])
wlkr.colvars.append(['dihedral', 7, 9, 15, 17])
# set an array of starting/stoping restraints for equilibration
restraint = [[0.0, 100.0], [0.0, 100.0]]
print "setting colvars"
# now specify colvars to dynamics routines
wlkr.setColvars()
print "equilibrating"
# equilibrate the walker to the target point in CV space
wlkr.equilibrate(system.umbrellas[i].center, restraint, 100000)
# enter the sampling routine
try:
system.sample(wlkr, params['walkerSteps'], i, 0, params, rank)
except errors.DynamicsError:
print "Rank", rank, "sampling error occured in umbrella", i, "."
continue
# now we are done populating the samples array, close the walker
wlkr.close()
#----------------WRITE OUT DATA-------------
# now allow rank 0 to process data.
if rank == 0:
print system.F
fileIO.writeMat(system.F, params['wkdir'] + "/F.out")
print "Entering eigenvalue routine."
# solve eigenvalue problem for F
system.getZ()
fileIO.writeMat(system.z, params['wkdir'] + "/z.out")
print "Computing the sensitivities."
bounds = system.getlogBound(system.F)
fileIO.writeMat(bounds, params['wkdir'] + "/bounds.out")
# now we will perform an analysis of the data and increase sampling of
# windows with high variance
if rank == 0:
print "Done!"
print "Total wallclock time was: " + str(time() - starttime) + " seconds."
return 0
def main():
"""
definition of main scripting file for debugging purposes.
"""
# time the execution
starttime = time()
#--------------MPI INIT---------------------
# init communicator
comm = MPI.COMM_WORLD
# get proc rank
rank = comm.Get_rank()
nprocs = comm.Get_size()
#---------------SET PARAMETERS -----------
if rank == 0: print "Setting up umbrella sampling parameters."
params = {}
# set the scratch directory for the calculation files
params['scratchdir'] = "/Users/jeremytempkin/Documents/enhanced_sampling_toolkit/umbrella_sampling/debug_US"
params['inputFilename'] = "/Users/jtempkin/enhanced_sampling_toolkit/data/input.diala"
# here we will set the umbrella sampling parameters in the params dict
params['ncells'] = 3
params['cellWidth'] = 60.0
params['nwalkers'] = 1
params['walkerSteps'] = 1000
params['stepLength'] = 10
params['Ftype'] = 'transition'
# lets set the dynamics parameters that are needed to specify the walker
params['inputFilename'] = 'syn.in'
params['temperature'] = 310.0
#--------------- INITIALIZATION--------
# only allow root rank to build files
if rank == 0:
print "Building scratch directory."
# construct the wkdir. This is where the intermediate dynamcs files will
# be written.
fileIO.makeWkdir(params['scratchdir'])
# construct the umbrella data structure
if rank == 0: print "Initializing the umbrella structure."
# create the partition object
system = basisFunctions.partition(params['ncells'])
# now we construct the umbrella windows
if rank == 0: print "Building the umbrellas."
# specify the list of boundaries, nboxes, 1/2 width of the windows
umbParams = {}
# right now, we will hardcore a 12x12 array using Erik's routine for gridding a space
umbParams['cvrange'] = np.array([map(float,entry.split(",")) for entry in "-180,180,12,30;-180,180,12,30".split(";")])
umbParams['wrapping'] = np.array(map(float, "1,1".split(',')))
system.umbrellas = fileIO.createUmbrellas(umbParams)
#------------ MAIN LOOP --------------
# sample umbrellas and construct F
if rank == 0: print "Entering main loop."
for i in range(rank, len(system.umbrellas), nprocs):
print "Rank", rank, "sampling umbrella", i, "."
# lets instantiate a walker object to sample this window.
wlkr = lammpsWalker.lammpsWalker(params['inputFilename'])
# minimize structure prior to dynamics
wlkr.minimize()
# set colvars for this walker (currently, alanine dipeptide dihedrals)
wlkr.colvars.append(['dihedral', 5, 7, 9, 15])
wlkr.colvars.append(['dihedral', 7, 9, 15, 17])
# set an array of starting/stoping restraints for equilibration
restraint = [[0.0, 10.0], [0.0, 10.0]]
# now specify colvars to dynamics routines
wlkr.setColvars()
# equilibrate the walker to the target point in CV space
wlkr.equilibrate(system.umbrellas[i].center, restraint, 100000)
"""
# enter the sampling routine
try:
system.sample(wlkr, params['walkerSteps'], i, 0, params, rank)
except errors.DynamicsError:
print "Rank", rank, "sampling error occured in umbrella", i, "."
continue
"""
# now we are done populating the samples array, close the walker
wlkr.close()
#-----------------MPI COMMUNICATION------------
"""
Here we communicate the rows of F to each processor to set up and solve the
eigenvalue problem.
"""
# now reduce the F matrix at root, first making a send buffer,
system.Fbuff = copy.deepcopy(system.F)
comm.Reduce([system.Fbuff, MPI.DOUBLE], [system.F, MPI.DOUBLE], op=MPI.SUM, root=0)
# also share the F_error matrix
system.F_error_buff = copy.deepcopy(system.F_error)
comm.Reduce([system.F_error_buff, MPI.DOUBLE], [system.F_error, MPI.DOUBLE], op=MPI.SUM, root=0)
# issue a global MPI barrier to ensure data has been recieved.
comm.Barrier()
#----------------WRITE OUT DATA-------------
# now allow rank 0 to process data.
if rank == 0:
print system.F
fileIO.writeMat(system.F, params['wkdir'] + "/F.out")
print "Entering eigenvalue routine."
# solve eigenvalue problem for F
system.getZ()
fileIO.writeMat(system.z, params['wkdir'] + "/z.out")
print "Computing the sensitivities."
bounds = system.getlogBound(system.F)
fileIO.writeMat(bounds, params['wkdir'] + "/bounds.out")
# now we will perform an analysis of the data and increase sampling of
# windows with high variance
if rank == 0:
print "Done!"
print "Total wallclock time was: " + str(time() - starttime) + " seconds."
return 0
# -*- coding: utf-8 -*-
"""
A profiling run that tests the dynamics of calling propagate through the lammpsWalker API vs running dynamcis directly.
"""
import lammpsWalker
import dynamics
import os
nsteps = 1000000
stepLength = 5
temperature = 310.0
damping_coefficient = 30.0
scratchdir = os.path.abspath("data")
inputFilename = os.path.abspath("data/input.enk")
logFilename = scratchdir + "/log.lammps"
os.chdir(scratchdir)
# lets instantiate a walker object to sample this window.
wlkr = lammpsWalker.lammpsWalker(inputFilename, logFilename, index=0, debug=False)
# set langevin dynamics object and pass it to the walker.
dyn = dynamics.langevin(temperature, damping_coefficient, shake = True)
wlkr.setDynamics(dyn)
wlkr.setTimestep(1.0)
wlkr.drawVel()
for i in range(nsteps / stepLength):
wlkr.propagate(stepLength)
def main(debug=False):
"""
definition of main scripting file for debugging purposes.
"""
# time the execution
startTime = time()
if debug: print "WARNING: Debug passed as True. Will dump maximum set of internal values."
#---------------SET SIMULATION PARAMETERS -----------
params = {}
params = setParameters(params)
print "parameters initialized as: ", params
print "Building scratch directory."
# construct the wkdir. This is where the intermediate dynamics files will be written.
fileIO.makeWkdir(params['scratchdir'])
# make sure we've built the scratchdir since we'll assume it exists for the rest of the code
assert os.path.exists(params['scratchdir']), "The scratch directory was not created."
# we're going to move the wokring directory into the data directory
os.chdir(os.path.dirname(params['inputFilename']))
#--------------- INITIALIZATION OF PARTITION INSTANCE--------
# construct the umbrella data structure
# commented out below this block is the origional construction lines for the partition module.
# here we're simply loading this from a binary pickle written to file. This obviates the need to
# reconstruct the neighborlist every call
if os.path.exists(params['systemFile']):
with open(params['systemFile'], "r") as f_handle:
system = pickle.load(f_handle)
else:
system = partition_mod.partition(params['ncells'])
if debug: print system
# now we construct the umbrella windows
system.umbrellas = system.createUmbrellas(params['cvrange'], params['wrapping'], basisType=params['basisType'], neighborList=False)
with open(params['systemFile'], "w") as f_handle:
pickle.dump(system, f_handle, protocol=2)
# double check we've created as many windows as we said in ncells
assert len(system.umbrellas) == params['ncells'], "The number of cells specified does not equal the number of umbrellas created."
# debug prints
if debug:
for i in range(len(system.umbrellas)):
print "umbrella", i, system.umbrellas[i].center, system.umbrellas[i].width
# ------------------ SETTING THE DYNAMICS PARAMETERS FOR SAMPLING THE WINDOWS ----------------
# now set up partition with a list of associated ranks
system.rank_window_index = range(len(system.umbrellas))
# -------------- INITIALIZATION OF SYSTEM OBSERVABLES -------
# here we add a list of observables to compute
pmf_prototype = observables.pmf("pmf", np.zeros((180,180)))
system.addObservable(pmf_prototype)
"""
# now we check to make sure we've correctly set up the local observables
for window in system.umbrellas:
assert hasattr(window, "local_observables"), str(rank) + ": The local observables in window " + str(system.umbrellas.index(window)) + " was not created."
for window in system.umbrellas:
assert len(window.local_observables) == len(system.observables), str(rank) + ": The number of window observables does not match the number of partition observables."
"""
#----------------MAIN LOOP----------------
print "Sampling via equilibrium US."
for k in range(params['iterations']):
# ---------- RESET DATA USED FOR CURRENT ITERATION -------------
# reset the M matrix to zeros for this iteration of the algorithm
# this matrix will get populated from the inner loop
system.M = np.zeros((len(system.umbrellas), len(system.umbrellas)))
system.nsamples_M = np.zeros((len(system.umbrellas), len(system.umbrellas)))
# start a timer on root rank
st = time()
# this loop does one iteration of the update
for i in range(10):
print "sampling window", i
# lets instantiate a walker object to sample this window.
wlkr = lammpsWalker.lammpsWalker(params['inputFilename'], params['logFilename'], index=i, debug=debug)
# set langevin dynamics object and pass it to the walker.
dyn = dynamics.langevin(params['temperature'], params['damping_coefficient'], shake = True)
wlkr.setDynamics(dyn)
wlkr.setTimestep(1.0)
wlkr.drawVel()
# set colvars for this walker
wlkr.addColvars('c1', "dihedral", [9, 30, 37, 44])
wlkr.addColvars('c2','dihedral', [30, 37, 44, 64])
#wlkr.setOutput("traj.out", "dcd", params['scratchdir'] + "/" + str(i) + ".dcd", nSteps=1000)
#let's add an output for writing out the configurations in hdf5 format so we have an estimate for the local distribution
if os.path.exists(params['scratchdir'] + "/ep." + str(i) + ".h5py"):
f_handle = h5py.File(params['scratchdir'] + "/ep." + str(i) + ".h5py", "r")
config = random.choice(f_handle.keys())
wlkr.setConfig(f_handle[config][:])
wlkr.drawVel()
f_handle.close()
else:
try:
if os.path.exists(params['startingPoints'] + "/start." + str(i) + ".npy"):
config = np.load(params['startingPoints'] + "/start." + str(i) + ".npy")
wlkr.setConfig(config)
wlkr.drawVel()
else:
dragWalker(wlkr, system.umbrellas[i], nSteps=5)
assert system.umbrellas[i](wlkr.getColvars(), system.umbrellas) > 0.0, "The walker in " + str(i) + " did not initialize in the support of the window."
np.save(params['startingPoints'] + "/start." + str(i), wlkr.getConfig())
except AssertionError:
pass
# enter the sampling routine.
system.sample_US(wlkr, params['walkerSteps'], i, k, params, debug=True)
# now we are done populating the samples array, close the walker
wlkr.close()
del wlkr
if debug: print system.umbrellas[i].local_observables[0].data
# report time it too for root to move out of the barrier (ie all ranks have sampled)
print "Elapsed time in sampling routine on root rank after barrier: ", time() - st
# now let's time the communication section
st = time()
# ------------ EIGENVALUE PROBLEM --------------
"""
Step 2) solution of the eigenvalue problem at each rank
"""
# at rank, compute G and z
system.updateF('overlap')
system.k += 1
#system.computeZ()
if debug: print system.z
"""
Step 3) estimation of observables on each rank
"""
system.computeObservables()
"""
Step 4) all reduction of averaged observables to each processor
"""
if debug: print system.observables[0].data
"""
Step 5) writing local and global estimates of the observables on root rank only
"""
f_handle = h5py.File(params['scratchdir'] + "/F.out", "a")
f_handle.create_dataset("F." + str(k), data=system.F)
f_handle.close()
f_handle = h5py.File(params['scratchdir'] + "/z.out", "a")
f_handle.create_dataset("z." + str(k), data=system.z)
f_handle.close()
for obs in system.observables:
f_handle = h5py.File(params['scratchdir'] + "/" + obs.name, "a")
f_handle.create_dataset(obs.name + "." + str(k), data=obs.data)
f_handle.close()
print "Elapsed time in communication routine on root rank after barrier: ", time() - st
print "Done!"
print "Total wall clock time was: " + str(time() - startTime) + " seconds."
return 0