def run(self,
orderMax=100,
orderMin=0,
temp=1.50,
mu1=0.0,
dmu2=0.0,
order=3,
steps=10000):
"""
Run a new simulation from scratch.
Parameters
----------
orderMax : int
Max number of particles to allow in this window (default=100)
orderMin : int
Min number of particles to allow in this window (default=0)
temp : double
Temperature (default = 1.5)
mu1 : double
Chemical potential of species 1
dmu2 : double
mu2 - mu1
order : int
Max order to record extensive moments up to
steps : int
Number of MC steps to perform
"""
s = feasst.Space(3, 0)
s.lset(15)
p = feasst.PairLJMulti(s, s.minl() / 4.0)
molA = os.path.dirname(os.path.realpath(__file__)) + "/data.lj"
molB = os.path.dirname(os.path.realpath(__file__)) + "/data.ljb"
s.addMolInit(molA)
p.initLMPData(molA)
s.addMolInit(molB)
p.initLMPData(molB)
p.rCutijset(0, 0, (p.sig(0) + p.sig(0)) / 2 * 3.0)
p.rCutijset(0, 1, (p.sig(0) + p.sig(1)) / 2 * 3.0)
p.rCutijset(1, 1, (p.sig(1) + p.sig(1)) / 2 * 3.0)
for i in range(2):
for j in range(2):
p.linearShiftijset(i, j, True)
s.updateCells(
p.rCutMaxAll()) # intermolecular potential needs max rcut
barrier = feasst.SpeciesBarriers(s.nParticleTypes())
radius = 4.0 # this goes to CENTER OF MASS, so pore radius actually = 4.5 with sigma/2 exclusion
eps_w = 3.0
width = 0.5
pt = [0.0, 0.0, 0.0]
barrier.addSqwCylinder(0, pt, radius, eps_w, width, 0)
barrier.addSqwCylinder(1, pt, radius - (p.sig(1) - p.sig(0)) / 2,
eps_w / 2.0, width, 0)
pairBarr = feasst.PairBarriers(s, barrier)
ipair = feasst.PairHybrid(s, max(p.rCutMaxAll(), width))
ipair.addPair(p)
ipair.addPair(pairBarr)
ipair.initEnergy()
assert (
barrier.safe(ipair)
) # check barrier doesn't violate any boundary conditions or allow periodic interactions
orderParam = "nmol"
beta = 1.0 / temp
cc = feasst.CriteriaWLTMMC(beta, math.exp(beta * mu1), orderParam,
orderMin - 0.5 * 1.0, orderMax + 0.5 * 1.0,
orderMax - orderMin + 1)
cc.addActivity(math.exp(beta * (mu1 + dmu2)))
mc = feasst.WLTMMC(s, ipair, cc)
em = feasst.AnalyzeExtensiveMoments(s, ipair)
em.setOrderParam(order, cc)
mc.weight = 0.6
feasst.deleteTrial(mc, molA)
mc.weight = 0.6
feasst.deleteTrial(mc, molB)
mc.weight = 0.6
feasst.addTrial(mc, molA)
mc.weight = 0.6
feasst.addTrial(mc, molB)
mc.weight = 0.2
feasst.xswapTrial(mc)
mc.weight = 0.4
feasst.transformTrial(mc, "translate", 0.4)
mc.nMolSeek(
orderMin, molA,
1000000) # mininum bound with pure A (smaller of the 2 species)
nfreq = 100000
mc.initLog("log", nfreq)
mc.initColMat("colMat", nfreq)
mc.setNFreqCheckE(nfreq, 1e-8)
mc.setNFreqTune(nfreq)
mc.initMovie("movie", nfreq * 1000)
mc.initRestart("tmp/rst", nfreq * 1000)
em.initFreq(5)
em.initPrintFreq(nfreq * 1000)
em.initFileName("extMom")
mc.initAnalyze(em)
cc.collectInit(4.0e-6) # start collecting TMMC matric at wlFlat == 18
cc.tmmcInit(5.0e-7) # switch to TMMC after 22
mc.wlFlatProduction(
22
) # after this # iterations, switch to "production" phase and measure
mc.runNumTrials(steps)
em.write()
def run (self, **kwargs):
"""
Run a new simulation from scratch.
Parameters
----------
orderMax : int
Max number of particles to allow in this window (default=100)
orderMin : int
Min number of particles to allow in this window (default=0)
temp : double
Temperature (default = 1.5)
mu1 : double
Chemical potential of species 1
dmu2 : double
mu2 - mu1
order : int
Max order to record extensive moments up to
steps : int
Number of MC steps to perform
lam11 : float
Value of lambda_11
lam22 : float
Value of lambda_22
molA : string
Filename for molA (1)
molB : string
Filename for molB (2)
"""
self.parse(kwargs)
s = feasst.Space(3,0)
s.lset(9.0)
p = feasst.PairLJMulti(s, s.minl()/2.0)
s.addMolInit(self.molA)
p.initLMPData(self.molA)
s.addMolInit(self.molB)
p.initLMPData(self.molB)
# Force-shift potential for each pair
p.rCutijset(0,0,(p.sig(0)+p.sig(0))/2*3.0)
p.rCutijset(0,1,(p.sig(0)+p.sig(1))/2*3.0)
p.rCutijset(1,1,(p.sig(1)+p.sig(1))/2*3.0)
p.setLambdaij(0,0, self.lam11)
p.setLambdaij(0,1, 0.5*(self.lamm11+self.lam22)) # LB mixing
p.setLambdaij(1,1, self.lam22)
p.lrcFlag = 0;
for i in range(2):
for j in range(2):
p.linearShiftijset(i,j,True)
s.updateCells(p.rCutMaxAll()) # intermolecular potential needs max rcut
ipair = feasst.PairHybrid (s, p.rCutMaxAll())
ipair.addPair(p)
ipair.initEnergy()
orderParam = "nmol"
beta = 1.0/self.temp
cc = feasst.CriteriaWLTMMC (beta, math.exp(beta*self.mu1), orderParam, self.orderMin-0.5*1.0, self.orderMax+0.5*1.0, self.orderMax-self.orderMin+1)
cc.addActivity(math.exp(beta*(self.mu1+self.dmu2)))
mc = feasst.WLTMMC (s, ipair, cc)
em = feasst.AnalyzeExtensiveMoments(s, ipair)
em.setOrderParam (self.order, cc)
mc.weight = 0.6
feasst.deleteTrial(mc, self.molA)
mc.weight = 0.6
feasst.deleteTrial(mc, self.molB)
mc.weight = 0.6
feasst.addTrial(mc, self.molA)
mc.weight = 0.6
feasst.addTrial(mc, self.molB)
mc.weight = 0.2
feasst.xswapTrial(mc)
mc.weight = 0.4
feasst.transformTrial(mc, "translate", 0.4)
mc.nMolSeek(self.orderMin, self.molA, 1000000) # mininum bound with pure A (smaller of the 2 species)
nfreq = 100000
mc.initLog("log", nfreq)
mc.initColMat("colMat", nfreq*1000)
mc.setNFreqCheckE(nfreq*1000, 1e-8)
mc.setNFreqTune(nfreq*1000)
mc.initMovie("movie", nfreq*1000)
mc.initRestart("tmp/rst", nfreq*1000)
em.initFreq(5) # from 1 -> 5 makes this as efficient as measuring 2nd vs 3rd order moments
em.initPrintFreq(nfreq*1000)
em.initFileName("extMom")
mc.initAnalyze(em)
cc.collectInit(4.0e-6) # start collecting TMMC matric at wlFlat == 18
cc.tmmcInit(5.0e-7) # switch to TMMC after 22
mc.wlFlatProduction(22) # after this number of iterations, switch to "production" phase and measure
mc.runNumTrials(self.steps)
em.write() # write at the end to ensure up-to-date
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)
type=str)
args = parser.parse_args()
print(args)
# if the lnz was set to some value, reweight to the given lnz
if (args.lnz != LNZDEFAULT):
criteria = feasst.CriteriaWLTMMC(args.inFile)
criteria.readCollectMat(args.inFile)
criteria.lnPIrw(math.exp(args.lnz))
criteria.printRWinit()
criteria.printCollectMat(args.outFile)
# otherwise, attempt to find saturation and reweight the lnzsat
else:
# if volume is not given or unphysical, attempt to find volume from restart
if (args.volume < 0):
assert (os.path.isfile(args.rstFile)) # provide either -v or -r flags
space = feasst.Space(args.rstFile)
else:
space = feasst.Space()
space.initBoxLength(1)
space.scaleDomain(args.volume)
pair = feasst.PairIdeal(space)
criteria = feasst.CriteriaWLTMMC(args.inFile)
wltmmc = feasst.WLTMMC(space, pair, criteria)
criteria.readCollectMat(args.inFile)
if (args.phaseBoundary != -1):
criteria.setPhaseBoundary(args.phaseBoundary)
wltmmc.printSat()
