def test(self):
space = feasst.Space(3)
space.initBoxLength(8)
pair = feasst.PairLJ(space, 3) # potential truncation at 3
molNameSS = space.install_dir() + "/forcefield/data.lj"
pair.initData(molNameSS) # initialize the sigma and epsilon
# create clones of Space and Pair to perform two separate tests
space2 = space.clone()
pair2 = pair.clone(space2)
# first, test the interaction between two particles
xAdd = feasst.DoubleVector(space.dimen()) # position to add is origin
pair.addMol(xAdd) # add first molecule
r = 1.2345
xAdd[0] = r # position of second particle
pair.addMol(xAdd) # add second particle
pair.initEnergy() # compute energy
peExact = 4 * (pow(r, -12) - pow(r, -6))
self.assertAlmostEqual(pair.peLJ(), peExact, 15)
peExactLRC = (8./3.)*feasst.PI*space.nMol()**2/space.vol() \
*((1./3.)*pair.rCut()**(-9) - pair.rCut()**(-3))
self.assertAlmostEqual(pair.peLRC(), peExactLRC, 15)
# second, compare with the reference configuration
config = space.install_dir() + \
"/testcase/1_lj/1_ref-config/lj_sample_config_periodic4.xyz"
conf_file = feasst.make_ifstream(config)
pair2.readxyz(conf_file) # read the xyz file
pair2.initEnergy() # compute energy
peLJ = -16.790321304625856
peLRC = -0.5451660014945704
self.assertAlmostEqual(pair2.peLRC(), peLRC, 15)
self.assertAlmostEqual(pair2.peLJ(), peLJ, 15)
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))
def test(self):
feasst.ranInitByDate() # initialize random number generator
space = feasst.Space(3, 0) # initialize simulation domain
space.initBoxLength(args.boxl)
addMolType = space.install_dir() + "/forcefield/" + args.molName
space.addMolInit(addMolType)
# initialize pair-wise interactions
pair = feasst.PairLJ(space, args.rCut)
pair.initEnergy()
# acceptance criteria
nMolMin = 0
import math
criteria = feasst.CriteriaWLTMMC(1. / args.temp, math.exp(args.lnz),
"nmol", nMolMin, args.nMolMax)
criteria.collectInit()
criteria.tmmcInit()
# initialize monte carlo
mc = feasst.WLTMMC(space, pair, criteria)
mc.weight = 3. / 4.
feasst.transformTrial(mc, "translate")
mc.weight = 1. / 8.
feasst.deleteTrial(mc)
mc.weight = 1. / 8.
feasst.addTrial(mc, addMolType)
# output log, lnpi and movie
mc.initLog("log", args.nfreq)
mc.initColMat("colMat", args.ncfreq)
mc.setNFreqCheckE(args.ncfreq, 1e-8)
mc.setNFreqTune(args.nfreq)
mc.initMovie("movie", args.nfreq)
#mc.initXTC("movie", args.nfreq)
mc.initRestart("tmp/rst", args.ncfreq)
# production tmmc simulation
if args.openMP:
mc.initWindows(
2., # exponent that determines size of windows
0) # extra macrostate overlap between processors
mc.runNumSweeps(
20, # number of "sweeps"
-1) # maximum number of trials. Infinite if "-1".
# test against SRSW values
self.assertAlmostEqual(criteria.pe(0).average(), 0, 13)
compareEnergyAndMacro(criteria, 1, self, -0.0006057402333333332,
6.709197666659334e-10,
-270.0061768 + 274.6763737666667,
0.037092307087640365)
compareEnergyAndMacro(criteria, 2, self, -0.030574223333333334,
9.649146611661053e-06,
-266.0191155333334 + 274.6763737666667,
0.03696447428346385)
compareEnergyAndMacro(criteria, 3, self, -0.089928316,
0.0001387472078025413,
-262.4277240666667 + 274.6763737666667,
0.037746391500313385)
compareEnergyAndMacro(criteria, 4, self, -0.1784570533333333,
3.3152449884326804e-05,
-259.11444086666665 + 274.6763737666667,
0.03809721387875822)
compareEnergyAndMacro(criteria, 5, self, -0.29619201333333334,
1.3487910636322294e-05,
-256.0144809 + 274.6763737666667,
0.03845757460933292)
* 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