def main():
# Create EAMPotential
eamPotentials = [EAMPotential("U", 92, 238.03, embed, density)]
pairPotentials = [Potential('U', 'U', pair_UU)]
cutoff = 8.0
#nrho = 962 # n points density
nrho = 5000 # n points density
#drho = 0.00103950 # distance points density
drho = 0.02 # distance points density
#nr = 1462 # n points embed & Vpair
nr = 5000 # n points embed & Vpair
dr = cutoff / nr # distance points embed & Vpair
from atsim.potentials import writeFuncFL
with open("U2.eam", 'wb') as outfile:
writeSetFL(nrho,
drho,
nr,
dr,
eamPotentials,
pairPotentials,
out=outfile,
comments=['Spline Uranium as U.eam', '', ''])
def testWriteSetFL(self):
"""Test creation of DYNAMO setfl formatted file for use with lammps pair_style eam/alloy"""
with open( os.path.join(_getResourceDirectory(), 'AlCu.eam.alloy'), 'r') as infile:
expectEAMTable = _parseSetFL(infile)
comments = [
'##Al-Cu EAM potentials from J. Cai and Y.Y. Ye##',
'##Phys. Rev. B 54, 8398-8410 (1996).############',
'################################################']
alEmbedFunc = TableReader(_openResource('setfl_AlEmbed.table'))
alElectronDensity = TableReader(_openResource('setfl_AlDensity.table'))
cuEmbedFunc = TableReader(_openResource('setfl_CuEmbed.table'))
cuElectronDensity = TableReader(_openResource('setfl_CuDensity.table'))
pairpot_Al_Al = TableReader(_openResource('setfl_AlAlPair.table'))
pairpot_Cu_Al = TableReader(_openResource('setfl_CuAlPair.table'))
pairpot_Cu_Cu = TableReader(_openResource('setfl_CuCuPair.table'))
eampots = [
potentials.EAMPotential('Al', 13, 26.982, alEmbedFunc, alElectronDensity, latticeConstant = 4.05, latticeType = 'FCC'),
potentials.EAMPotential('Cu', 29, 63.546, cuEmbedFunc, cuElectronDensity, latticeConstant = 3.615, latticeType = 'FCC')]
pairpots = [
Potential('Al', 'Al', pairpot_Al_Al),
Potential('Cu', 'Al', pairpot_Cu_Al),
Potential('Cu', 'Cu', pairpot_Cu_Cu) ]
nrho = 1000
drho = 1.0396723078e+00
nr = 3000
dr = 2.2282427476e-03
cutoff = 6.6825000000e+00
actualEAMTable = StringIO()
potentials.writeSetFL(
nrho, drho,
nr, dr,
eampots,
pairpots,
comments = comments,
out = actualEAMTable,
cutoff = cutoff)
actualEAMTable.seek(0)
actualEAMTable = _parseSetFL(actualEAMTable)
from . import testutil
testutil.compareCollection(self,expectEAMTable, actualEAMTable, places = 3)
def createPot(self):
eamPotentials = self.getEamPotentials()
pairPotentials = self.getPairPotentials()
with open(self.fileName, 'wb') as outfile:
writeSetFL(
self.nrho,
self.drho,
self.nr,
self.dr,
eamPotentials,
pairPotentials,
out=outfile,
comments=[
self.comment, "", ""
]) # <-- Note: title lines given as list of three strings
def main():
eamPotentials, pairPotentials = makePotentialObjects()
# Perform tabulation
# Make tabulation
nrho = 2000
drho = 0.05
nr = 2000
dr = 0.003
with open("Zhou_AlCu.eam.alloy", 'w') as outfile:
writeSetFL(
nrho, drho,
nr, dr,
eamPotentials,
pairPotentials,
out=outfile,
comments=['Zhou Al Cu', "", ""]) # <-- Note: title lines given as list of three strings
def main():
# Create EAMPotential
f_UU = buck(294.640000, 0.327022, 0.0)
eamPotentials = [EAMPotential("U", 92, 238.03, embed, density)]
pairPotentials = [Potential('U', 'U', f_UU)]
nrho = 50000
drho = 0.001
nr = 12000
dr = 0.001
from atsim.potentials import writeFuncFL
with open("U.eam", 'wb') as outfile:
writeSetFL(nrho,
drho,
nr,
dr,
eamPotentials,
pairPotentials,
out=outfile,
comments=['Buckingham Uranium as U.eam', '', ''])
def testWriteSetFLFromParameters(self):
"""Test that lammps.potentials.writeSetFL() can generate the Al_zhou.eam.alloy file from LAMMPS distribution"""
with open(os.path.join(_getResourceDirectory(), 'Al_zhou.eam.alloy'), 'r') as infile:
expectEAMTable = _parseSetFL(infile)
comments = [
'#-> LAMMPS Potential File in DYNAMO 86 setfl Format <-#',
'# Zhou Al Acta mater(2001)49:4005',
'# Implemented by G. Ziegenhain (2007) [email protected]']
#Density function
def densityFunction(r):
beta = 3.702623
r_e = 2.886166
lamb = 0.790264
f_e = 1.392302
num = f_e * math.exp( -beta * ( (r/r_e) - 1.0) )
den = 1.0 + (( (r/r_e) - lamb )**20)
return num/den
#Embedding function
def subembed(i, F_ni, rho_n, rho):
return F_ni * ((rho/rho_n) - 1.0)**float(i)
def embeddingFunction(rho):
rho_e = 20.226537
rho_n = 0.85 * rho_e
rho_o = 1.15 * rho_e
nu = 0.779208
if rho < rho_n:
return subembed(0, -2.806783, rho_n, rho) + \
subembed(1, -0.276173, rho_n, rho) + \
subembed(2, 0.893409, rho_n, rho) + \
subembed(3, -1.637201, rho_n, rho)
elif rho_n <= rho < rho_o:
return subembed(0, -2.806783, rho_e, rho) + \
subembed(1, -0.276173, rho_e, rho) + \
subembed(2, 0.893409, rho_e, rho) + \
subembed(3, -1.637201, rho_e, rho)
else:
return -2.829437 * ( 1.0 - math.log( (rho/rho_e)**nu)) * (rho/rho_e)**nu
#Pair potential
def ppotfunc(r):
A = 0.251519
alpha = 6.94219
r_e = 2.886166
kappa = 0.395132
B = 0.313394
beta = 3.702623
lamb = 0.790264
return ((A * math.exp( -alpha* ( (r/r_e) - 1.0) ))/ (1.0 + ( (r/r_e - kappa)**20))) - \
((B * math.exp( -beta * ( (r/r_e) - 1.0) ))/ (1.0 + ( (r/r_e - lamb)**20)))
alpp = potentials.Potential('Al', 'Al', ppotfunc)
nrho = 10001
drho = 0.00559521603477821424
nr = 10001
dr = 0.00101014898510148996
cutoff = 10.10250000000000092371
eampots = [
potentials.EAMPotential('Al', 1, 26.982, embeddingFunction, densityFunction, latticeConstant = 4.05, latticeType = 'FCC')]
pairpots = [ alpp ]
actualEAMTable = StringIO()
potentials.writeSetFL(
nrho, drho,
nr, dr,
eampots,
pairpots,
comments = comments,
out = actualEAMTable,
cutoff = cutoff )
actualEAMTable.seek(0)
actualEAMTable = _parseSetFL(actualEAMTable)
from . import testutil
testutil.compareCollection(self,expectEAMTable, actualEAMTable, places = 3, percenttolerance = 7.0)
def testExampleA_Density(self):
"""Test density functions correctly defined for EAM tabulation documentation example 2a"""
exampleModule = _loadModule(self.test_nameA)
shutil.copyfile(
os.path.join(_getLAMMPSResourceDirectory(),
"setfl_pair.lmpstruct"),
os.path.join(self.tempdir, "structure.lmpstruct"))
shutil.copyfile(
os.path.join(_getLAMMPSResourceDirectory(), "calc_energy.lmpin"),
os.path.join(self.tempdir, "calc_energy.lmpin"))
oldpwd = os.getcwd()
os.chdir(self.tempdir)
try:
def nullfunc(r):
return 0.0
eamPotentials, pairPotentials = exampleModule.makePotentialObjects(
)
pairPotentials = None
pairPotentials = [
Potential("Cu", "Cu", nullfunc),
Potential("Al", "Al", nullfunc),
Potential("Al", "Cu", nullfunc)
]
# Create EAMPotential
def embed(rho):
return rho
for epot in eamPotentials:
epot.embeddingFunction = embed
nrho = 50000
drho = 0.001
nr = 12000
dr = 0.001
from atsim.potentials import writeSetFL
with open("table.set", 'w') as outfile:
writeSetFL(nrho,
drho,
nr,
dr,
eamPotentials,
pairPotentials,
comments=['Zhou Al Cu', "", ""],
out=outfile)
inputExpect = [
(2.0 * 1.218017211, "Cu Cu"), # Cu Cu
(2.0 * 1.716990097, "Al Al"), # Al Al
(1.218017211 + 1.716990097, "Al Cu") # Al Cu
]
for expect, potmap in inputExpect:
with open("potentials.lmpinc", "w") as potfile:
potfile.write("pair_style eam/alloy\n")
potfile.write("pair_coeff * * table.set " + potmap + "\n")
runLAMMPS()
energy = extractLAMMPSEnergy()
self.assertAlmostEqual(expect, energy, msg=potmap)
# Now repeat for triplet of atoms
shutil.copyfile(
os.path.join(_getLAMMPSResourceDirectory(),
"setfl_triplet.lmpstruct"),
os.path.join(self.tempdir, "structure.lmpstruct"))
dens_Cu = [
p.electronDensityFunction for p in eamPotentials
if p.species == "Cu"
][0]
dens_Al = [
p.electronDensityFunction for p in eamPotentials
if p.species == "Al"
][0]
hyp = 3.818376618407357
inputExpect = [
(4 * dens_Cu(2.7) + 2 * dens_Cu(hyp), "Cu Cu"), # Cu Cu
(4 * dens_Al(2.7) + 2 * dens_Al(hyp), "Al Al"), # Al Al
(2 * dens_Cu(2.7) + 2 * dens_Cu(hyp) + \
2*dens_Al(2.7), "Al Cu"), # Al Cu
(2 * dens_Al(2.7) + 2 * dens_Al(hyp) + \
2*dens_Cu(2.7), "Cu Al") # Cu Al
]
for expect, potmap in inputExpect:
with open("potentials.lmpinc", "w") as potfile:
potfile.write("pair_style eam/alloy\n")
potfile.write("pair_coeff * * table.set " + potmap + "\n")
runLAMMPS()
energy = extractLAMMPSEnergy()
self.assertAlmostEqual(expect, energy, msg=potmap)
finally:
os.chdir(oldpwd)
def testExampleA_Pair(self):
"""Test pair-potentials correctly defined for EAM tabulation documentation example 2a"""
exampleModule = _loadModule(self.test_nameA)
shutil.copyfile(
os.path.join(_getLAMMPSResourceDirectory(),
"setfl_pair.lmpstruct"),
os.path.join(self.tempdir, "structure.lmpstruct"))
shutil.copyfile(
os.path.join(_getLAMMPSResourceDirectory(), "calc_energy.lmpin"),
os.path.join(self.tempdir, "calc_energy.lmpin"))
inputExpect = [
(1.24246478E-02, "Al Al"), # Al Al
(-0.121863537, "Al Cu"), # Al Cu
(-0.179150283, "Cu Cu") # Cu Cu
]
oldpwd = os.getcwd()
os.chdir(self.tempdir)
try:
_eampotentials, pairPotentials = exampleModule.makePotentialObjects(
)
eamPotentials = None
# Create EAMPotential
def density(r):
return 0.0
def embed(rho):
return 0.0
eamPotentials = [
EAMPotential("Cu", 29, 63.55, embed, density),
EAMPotential("Al", 13, 26.98, embed, density)
]
nrho = 50000
drho = 0.001
nr = 12000
dr = 0.001
from atsim.potentials import writeSetFL
with open("table.set", 'w') as outfile:
writeSetFL(nrho,
drho,
nr,
dr,
eamPotentials,
pairPotentials,
comments=['Zhou Al Cu', "", ""],
out=outfile)
for expect, potmap in inputExpect:
with open("potentials.lmpinc", "w") as potfile:
potfile.write("pair_style eam/alloy\n")
potfile.write("pair_coeff * * table.set " + potmap + "\n")
runLAMMPS()
energy = extractLAMMPSEnergy()
self.assertAlmostEqual(expect, energy, msg=potmap)
finally:
os.chdir(oldpwd)