def test(self):
rho = 1e-3 # number density
nMol = 500 # number of particles
space = feasst.makeSpace(
feasst.args({
"dimen": "3",
"boxLength": str((float(nMol) / rho)**(1. / 3.))
}))
pair = feasst.makePairLJ(
space,
feasst.args({
"rCut": "3", # potential truncation at 3
"cutType": "lrc",
"molTypeInForcefield": "data.lj"
}))
criteria = feasst.makeCriteriaMetropolis(
feasst.args({"beta": str(1. / 0.9)}))
mc = feasst.MC(pair, criteria)
feasst.addTrialTransform(
mc,
feasst.args({
"transType": "translate",
"maxMoveParam": str(0.1)
}))
mc.nMolSeek(nMol)
mc.initLog("log", int(1e4))
mc.initMovie("movie", int(1e4))
mc.initRestart("tmp/rst", int(1e4))
mc.setNFreqTune(int(1e4))
mc.setNFreqCheckE(int(1e4), 1e-6)
mc.runNumTrials(int(1e7)) # run equilibration
# Run the production simulation and compute statistics on potential energy
mc.setNFreqTune(0) # do not tune during production
pe = feasst.Accumulator()
from itertools import islice, count
for itrial in islice(count(1), int(1e7) - 1):
mc.runNumTrials(1)
pe.accumulate(pair.peTot() / float(space.nMol()))
# Check average energy against the NIST SRSW
# https:#mmlapps.nist.gov/srs/LJ_PURE/mc.htm
# https:#www.nist.gov/programs-projects/nist-standard-reference-simulation-website
peAv = pe.average()
peStd = pe.blockStdev()
peSRSW = -9.9165E-03
peSRSWstd = 1.89E-05
self.assertAlmostEqual(peAv, peSRSW, delta=2.576 * (peSRSWstd + peStd))
def test(self):
feasst.ranInitByDate()
space = feasst.makeSpace(
feasst.args({
"dimen": "3",
"boxLength": "24.8586887"
}))
pair = feasst.makePairLJCoulEwald(
space,
feasst.args({
"rCut": str(space.minl() / 2.),
"molTypeInForcefield": "data.spce",
"alphaL": "5.6",
"k2max": "38"
}))
# acceptance criteria
temperature = 298 # Kelvin
beta = 1. / (temperature * feasst.idealGasConstant / 1e3) # mol/KJ
criteria = feasst.CriteriaMetropolis(beta, 1.)
mc = feasst.MC(space, pair, criteria)
feasst.transformTrial(mc, "translate", 0.1)
feasst.transformTrial(mc, "rotate", 0.1)
mc.initLog("log", int(1e4))
mc.initMovie("movie", int(1e4))
mc.initRestart("tmp/rst", int(1e4))
mc.setNFreqTune(int(1e4))
mc.setNFreqCheckE(int(1e4), 1e-6)
mc.nMolSeek(512)
mc.runNumTrials(int(1e6)) # run equilibration
# Run the production simulation
mc.initProduction()
mc.zeroStat()
mc.setNFreqTune(0)
mc.runNumTrials(int(1e6))
# Check average energy against Gerhard Hummer
# https:#doi.org/10.1063/1.476834
peAv = mc.peAccumulator().average() / float(space.nMol())
peStd = mc.peAccumulator().blockStdev() / float(space.nMol())
pePublish = -46.82 # published value
pePublishStd = 0.02
self.assertAlmostEqual(peAv,
pePublish,
delta=2.576 * (pePublishStd + peStd))
def test(self):
space = feasst.Space(3)
space.initBoxLength(24.8586887) # molecule-center based cut-off
pair = feasst.PairLJCoulEwald(space, space.minl() / 2.)
pair.initData(space.install_dir() + "/forcefield/data.spce")
pair.initKSpace(
5.6, # alpha*L
38) # k^2 < k2max cutoff
# Read the pre-equilibrated configuration of 512 water molecules
conf_file = feasst.make_ifstream(space.install_dir() + \
"/testcase/3_spce/2_nvt-mc/test.xyz")
pair.readxyz(conf_file)
pair.initEnergy()
# acceptance criteria
temperature = 298 # Kelvin
beta = 1. / (temperature * feasst.idealGasConstant / 1e3) # mol/KJ
criteria = feasst.CriteriaMetropolis(beta, 1.)
mc = feasst.MC(space, pair, criteria)
feasst.transformTrial(mc, "translate", 0.1)
mc.initLog("log", int(1e4))
mc.initMovie("movie", int(1e4))
mc.initRestart("tmp/rst", int(1e4))
mc.setNFreqTune(int(1e4))
mc.runNumTrials(int(1e6)) # run equilibration
# Run the production simulation
mc.zeroStat()
mc.runNumTrials(int(1e6))
# Check average energy against Gerhard Hummer
# https:#doi.org/10.1063/1.476834
peAv = mc.peAccumulator().average() / float(space.nMol())
peStd = mc.peAccumulator().blockStdev() / float(space.nMol())
pePublish = -46.
# pePublish = -46.82 # published value
pePublishStd = 0.02
self.assertAlmostEqual(peAv,
pePublish,
delta=2.576 * (pePublishStd + peStd))
def test(self):
space = feasst.Space(3)
rho = 1e-3 # number density
nMol = 500 # number of particles
space.initBoxLength(
(float(nMol) / rho)**(1. / 3.)) # set the cubic PBCs
pair = feasst.PairHardSphere(space)
pair.initData(space.install_dir() + "/forcefield/data.atom")
pair.initEnergy()
criteria = feasst.CriteriaMetropolis(1., 1.)
mc = feasst.MC(space, pair, criteria)
feasst.transformTrial(mc, "translate", 0.1)
mc.nMolSeek(nMol)
mc.initLog("log", int(1e4))
mc.initMovie("movie", int(1e4))
mc.initRestart("tmp/rst", int(1e4))
mc.setNFreqTune(int(1e4))
mc.runNumTrials(int(1e7)) # run equilibration
# Run the production simulation
mc.runNumTrials(int(1e7))
def test(self):
space = feasst.Space(3)
rho = 1e-3 # number density
nMol = 500 # number of particles
space.initBoxLength(
(float(nMol) / rho)**(1. / 3.)) # set the cubic PBCs
molNameSS = space.install_dir() + "/forcefield/data.lj"
space.addMolInit(molNameSS)
pair = feasst.PairLJ(space, 3) # potential truncation at 3
pair.initEnergy()
temperature = 0.9
criteria = feasst.CriteriaMetropolis(1. / temperature, 1.)
mc = feasst.MC(space, pair, criteria)
feasst.transformTrial(mc, "translate", 0.1)
mc.nMolSeek(nMol)
mc.initLog("log", int(1e4))
mc.initMovie("movie", int(1e4))
mc.initRestart("tmp/rst", int(1e4))
mc.setNFreqTune(int(1e4))
mc.runNumTrials(int(1e7)) # run equilibration
# Run the production simulation and compute statistics on potential energy
mc.setNFreqTune(0) # do not tune during production
pe = feasst.Accumulator()
from itertools import islice, count
for itrial in islice(count(1), int(1e7) - 1):
mc.runNumTrials(1)
pe.accumulate(pair.peTot() / float(space.nMol()))
# Check average energy against the NIST SRSW
# https:#mmlapps.nist.gov/srs/LJ_PURE/mc.htm
# https:#www.nist.gov/programs-projects/nist-standard-reference-simulation-website
peAv = pe.average()
peStd = pe.blockStdev()
peSRSW = -9.9165E-03
peSRSWstd = 1.89E-05
self.assertAlmostEqual(peAv, peSRSW, delta=2.576 * (peSRSWstd + peStd))
import feasst
space = feasst.makeSpace(feasst.args(
{"dimen" : "3", # 3D space
"boxLength" : "8"})) # cubic periodic boundaries
pair = feasst.makePairLJ(space, feasst.args(
{"rCut" : "3", # potential truncation
"cutType" : "lrc"})) # long range corrections
criteria = feasst.makeCriteriaMetropolis(feasst.args(
{"beta" : "1.2"})) # beta = 1/k_B/T
mc = feasst.MC(pair, criteria)
feasst.addTrialTransform(mc, feasst.args(
{"transType" : "translate", # attempt particle translations
"maxMoveParam" : "0.1"})) # maximum displacement for each dimension
mc.nMolSeek(50) # add particles
mc.initLog("log", int(1e4)) # output instantaneous values
mc.initMovie("movie", int(1e4)) # output xyz trajectory
mc.runNumTrials(int(1e6)) # perform MC trials
* Harold W. Hatch, [email protected] * * Permission to use this data/software is contingent upon your acceptance of * the terms of LICENSE.txt and upon your providing * appropriate acknowledgments of NIST's creation of the data/software. """ # # The following three lines are an alternative method to link _feasst.so # import os, sys # feasstdir = os.getenv("FEASST_INSTALL_DIR_") + "/build" # sys.path.append(feasstdir) import feasst feasst.ranInitByDate() space = feasst.makeSpace(3) space.initBoxLength(8) space.addMolInit("../forcefield/data.lj") pair = feasst.PairLJ(space, 3) # potential truncation at 3 pair.initEnergy() criteria = feasst.CriteriaMetropolis(1.2, 1.) # 1/kT = 1.2 mc = feasst.MC(space, pair, criteria) maxMoveParam = 0.1 feasst.transformTrial(mc, "translate", maxMoveParam) mc.nMolSeek(50) # add 50 particles mc.initLog("log", int(1e4)) mc.initMovie("movie", int(1e4)) mc.runNumTrials(int(1e6)) # mc.initWindows(1) # initialize parallel windows # mc.runNumSweeps(1, -1) # run until all windows sweep once
