tempData = state.dataManager.recordTemperature('all', 100)
state.activateFix(ljcut)
state.activateFix(bondHarm)
state.activateFix(angleHarm)
state.activateFix(dihedralOPLS)
state.activateFix(improperHarm)

unitEng = 0.066
unitLen = 3.5
unitMass = 12
writeconfig = WriteConfig(state, fn='poly_out', writeEvery=100, format='xyz', handle='writer')
writeconfig.unitLen = 1/unitLen
#temp = state.dataManager.recordEnergy('all', 50)
#reader = LAMMPS_Reader(state=state, unitLen = unitLen, unitMass = 12, unitEng = 0.066, bondFix = bondHarm, angleFix = angleHarm, nonbondFix = ljcut, dihedralFix = dihedralOPLS, improperFix=improperHarm, atomTypePrefix = 'PTB7_', setBounds=False)
reader = LAMMPS_Reader(state=state, unitLen = unitLen, unitMass = unitMass, unitEng = unitEng, nonbondFix = ljcut, atomTypePrefix = 'PTB7_', setBounds=False, bondFix = bondHarm,   angleFix = angleHarm, dihedralFix = dihedralOPLS,improperFix=improperHarm,)
reader.read(dataFn = 'poly_min.data')

#1 kelven = 1.38e-23 J/K  / (276/6.022e23) = .00301 temp units
#to tReal * conversion = LJ tempo
#pressure = pReal * unitLen^3/unitEng = 3.5^3/.066
#so to pressure / 649.62 = pReal
tUnit = 0.0301
pUnit = unitLen**3 / unitEng

'''
1 12
2 32.065
3 12
4 19
5 1
Exemplo n.º 2
0
state.activateFix(bondFENE)
state.activateFix(angleHarm)

#state.bounds = Bounds(state, Vector(-9, -10, -10), Vector(20, 24, 24))

writeconfig = WriteConfig(state,
                          fn='poly_out',
                          writeEvery=10,
                          format='xyz',
                          handle='writer')
temp = state.dataManager.recordEnergy('all', collectEvery=50)
reader = LAMMPS_Reader(state=state,
                       unitLen=1,
                       unitMass=1,
                       unitEng=1,
                       bondFix=bondFENE,
                       nonbondFix=ljcut,
                       angleFix=angleHarm,
                       atomTypePrefix='POLY_',
                       setBounds=True)

#state.bounds.lo = state.bounds.lo - Vector(0, 0, 3)
#state.bounds.hi = state.bounds.hi + Vector(0, 0, 3)

reader.read(dataFn='brush.data',
            inputFns=['brush.in', 'brush.init', 'brush.settings'])
print state.bounds.lo
print state.bounds.hi
InitializeAtoms.initTemp(state, 'all', 0.1)

state.atomParams.setValues('POLY_0', atomicNum=6)
Exemplo n.º 3
0
state.dt = 0.005

ljcut = FixLJCut(state, 'ljcut')
bondFENE = FixBondFENE(state, 'bondFENE')
angleHarm = FixAngleCosineDelta(state, 'angleHarm')
#tempData = state.dataManager.recordTemperature('all', 100)
state.activateFix(ljcut)
state.activateFix(bondFENE)
state.activateFix(angleHarm)

#state.bounds = Bounds(state, Vector(-9, -10, -10), Vector(20, 24, 24))

writeconfig = WriteConfig(state, fn='poly_out', writeEvery=10, format='xyz', handle='writer')
temp = state.dataManager.recordEnergy('all', collectEvery = 50)
reader = LAMMPS_Reader(state=state, unitLen = 1, unitMass = 1, unitEng = 1, bondFix = bondFENE, nonbondFix = ljcut, angleFix = angleHarm, atomTypePrefix = 'POLY_', setBounds=True)


#state.bounds.lo = state.bounds.lo - Vector(0, 0, 3)
#state.bounds.hi = state.bounds.hi + Vector(0, 0, 3)

reader.read(dataFn = 'brush.data', inputFns = ['brush.in', 'brush.init', 'brush.settings'])
print state.bounds.lo
print state.bounds.hi
InitializeAtoms.initTemp(state, 'all', 0.1)

state.atomParams.setValues('POLY_0', atomicNum=6)
state.atomParams.setValues('POLY_1', atomicNum=7)
state.atomParams.setValues('POLY_2', atomicNum=1)
state.activateWriteConfig(writeconfig)
Exemplo n.º 4
0
dihedralOPLS = FixDihedralOPLS(state, 'opls')
improperHarm = FixImproperHarmonic(state, 'imp')

tempData = state.dataManager.recordTemperature('all', 100)
state.activateFix(ljcut)
state.activateFix(bondHarm)
state.activateFix(angleHarm)
state.activateFix(dihedralOPLS)
state.activateFix(improperHarm)

unitLen = 3.5
writeconfig = WriteConfig(state, fn='poly_out', writeEvery=10, format='xyz', handle='writer')
writeconfig.unitLen = 1/unitLen
state.activateWriteConfig(writeconfig)

reader = LAMMPS_Reader(state=state, unitLen = unitLen, unitMass = 12, unitEng = 0.066, bondFix = bondHarm, angleFix = angleHarm, nonbondFix = ljcut, dihedralFix = dihedralOPLS, improperFix=improperHarm, atomTypePrefix = 'PTB7_', setBounds=False)
reader.read(dataFn = 'poly_min.data')

InitializeAtoms.initTemp(state, 'all', 0.1)

'''
1 12
2 32.065
3 12
4 19
5 1
6 12
7 16
8 16
9 12
10 1
Exemplo n.º 5
0
fixSpring.tetherFunc = springFuncEquiled
fixSpring.updateTethers() #tethering to the positions they fell into
fixSpring.k = 1000
fixSpring.multiplier = Vector(1, 1, 1) #now spring holds in both dimensions

#InitializeAtoms.initTemp(state, 'all', subTemp) #need to add keyword arguments
#okay, substrate is set up, going to do deposition
integrator = IntegratorVerlet(state)


#REMEMBER CHARGES
ewald = FixChargeEwald(state, "chargeFix", "all")
ewald.setParameters(64, 1.0, 3)
#state.activateFix(ewald)

reader = LAMMPS_Reader(state=state, unitLen = unitLen, unitMass = unitMass, unitEng = unitEng, bondFix = bondHarm, nonbondFix = ljcut,  angleFix = angleHarm, dihedralFix = dihedralOPLS, atomTypePrefix = 'EBZ_', setBounds=False)
reader.read(dataFn = 'ebz.data')

state.atomParams.setValues('substrate', atomicNum=1)
state.atomParams.setValues('EBZ_1', atomicNum=1)
state.atomParams.setValues('EBZ_2', atomicNum=1)
state.atomParams.setValues('EBZ_3', atomicNum=6)
state.atomParams.setValues('EBZ_4', atomicNum=6)

print("Average per particle energy: {}".format(integratorRelax.energyAverage()))

# Start deposition
toDeposit = [(7, 3), (6, 4)]
wallDist = 20
topWall = FixWallHarmonic(state, handle='wall', groupHandle='all', origin=Vector(0, 0, state.bounds.hi[2]), forceDir=Vector(0, 0, -1), dist=wallDist, k=10)
Exemplo n.º 6
0
dihedralOPLS = FixDihedralOPLS(state, 'opls')

tempData = state.dataManager.recordTemperature('all', 100)
state.activateFix(ljcut)
state.activateFix(bondHarm)
state.activateFix(angleHarm)
state.activateFix(dihedralOPLS)

unitLen = 3.55
writeconfig = WriteConfig(state, fn='dio_out', writeEvery=10, format='xyz', handle='writer')
writeconfig.unitLen = 1/unitLen
state.activateWriteConfig(writeconfig)

fixNVT = FixNVTRescale(state, 'temp', 'all', [0, 1], [0.1, 0.1], 1)
#state.activateFix(fixNVT)
reader = LAMMPS_Reader(state=state, unitLen = unitLen, unitMass = 12, unitEng = 0.07, bondFix = bondHarm, angleFix = angleHarm, nonbondFix = ljcut, dihedralFix = dihedralOPLS, atomTypePrefix = 'DIO_', setBounds=False)
reader.read(dataFn = 'DIO_VMD.data')

InitializeAtoms.initTemp(state, 'all', 0.1)
state.atomParams.setValues('DIO_0', atomicNum=6)
state.atomParams.setValues('DIO_1', atomicNum=1)
state.atomParams.setValues('DIO_2', atomicNum=53)

print state.atoms[0].pos.dist(state.atoms[1].pos)
integRelax = IntegraterRelax(state)
integRelax.run(100000, 1e-9)
InitializeAtoms.initTemp(state, 'all', 0.1)

integVerlet = IntegraterVerlet(state)
integVerlet.run(100000)
#print state.atoms[0].pos.dist(state.atoms[1].pos)
Exemplo n.º 7
0
unitLen = 3.55
writeconfig = WriteConfig(state,
                          fn='dio_out',
                          writeEvery=10,
                          format='xyz',
                          handle='writer')
writeconfig.unitLen = 1 / unitLen
state.activateWriteConfig(writeconfig)

fixNVT = FixNVTRescale(state, 'temp', 'all', [0, 1], [0.1, 0.1], 1)
#state.activateFix(fixNVT)
reader = LAMMPS_Reader(state=state,
                       unitLen=unitLen,
                       unitMass=12,
                       unitEng=0.07,
                       bondFix=bondHarm,
                       angleFix=angleHarm,
                       nonbondFix=ljcut,
                       dihedralFix=dihedralOPLS,
                       atomTypePrefix='DIO_',
                       setBounds=False)
reader.read(dataFn='DIO_VMD.data')

InitializeAtoms.initTemp(state, 'all', 0.1)
state.atomParams.setValues('DIO_0', atomicNum=6)
state.atomParams.setValues('DIO_1', atomicNum=1)
state.atomParams.setValues('DIO_2', atomicNum=53)

print state.atoms[0].pos.dist(state.atoms[1].pos)
integRelax = IntegratorRelax(state)
integRelax.run(100000, 1e-9)
InitializeAtoms.initTemp(state, 'all', 0.1)