def testLAMMPS():
"""Test potentials.writePotentials() for LAMMPS"""
pota = potentials.Potential("A", "B", lambda x: x)
potb = potentials.Potential("C", "D", lambda x: 6.0 - x)
expect = [
"A-B", "N 6 R 1.00000000 6.00000000", "",
"1 1.00000000 1.00000000 -1.00000000",
"2 2.00000000 2.00000000 -1.00000000",
"3 3.00000000 3.00000000 -1.00000000",
"4 4.00000000 4.00000000 -1.00000000",
"5 5.00000000 5.00000000 -1.00000000",
"6 6.00000000 6.00000000 -1.00000000", "", "C-D",
"N 6 R 1.00000000 6.00000000", "",
"1 1.00000000 5.00000000 1.00000000",
"2 2.00000000 4.00000000 1.00000000",
"3 3.00000000 3.00000000 1.00000000",
"4 4.00000000 2.00000000 1.00000000",
"5 5.00000000 1.00000000 1.00000000",
"6 6.00000000 0.00000000 1.00000000"
]
sbuild = StringIO()
potentials.writePotentials('LAMMPS', [pota, potb], 6.0, 6, sbuild)
sbuild.seek(0)
actual = sbuild.readlines()
msg = "%s != %s" % (expect, actual)
assert len(expect) == len(actual), msg
for e, a in zip(expect, actual):
a = a.decode()
assert os.linesep == a[-1]
a = a[:-1]
assert e == a
def potential_objects():
f_OO = potentials.potentialforms.buck(1633.00510, 0.327022, 3.948790)
f_UU = potentials.potentialforms.buck(294.640000, 0.327022, 0.0)
potential_objects = [
potentials.Potential('O', 'O', f_OO),
potentials.Potential('U', 'U', f_UU)
]
return potential_objects
def testWriteSinglePotential(self):
"""Test that atsim.potentials._lammps_writeTABLE._writeSinglePotential() works correctly"""
expect=["A-B",
"N 6 R 0.10000000 5.10000000",
"",
"1 0.10000000 4.90000000 1.00000000",
"2 1.10000000 3.90000000 1.00000000",
"3 2.10000000 2.90000000 1.00000000",
"4 3.10000000 1.90000000 1.00000000",
"5 4.10000000 0.90000000 1.00000000",
"6 5.10000000 -0.10000000 1.00000000"]
energyfunc = lambda x: 5.0-x
pot =potentials.Potential("A", "B", energyfunc)
sbuild = StringIO()
_lammps_writeTABLE._writeSinglePotential(pot, 0.1, 5.1, 6, sbuild)
sbuild.seek(0)
actual = sbuild.readlines()
msg = "%s != %s" % (expect, actual)
self.assertEqual(len(expect), len(actual), msg = msg)
for e,a in zip(expect, actual):
# a = a.decode()
self.assertEqual(os.linesep, a[-1])
a = a[:-1]
self.assertEqual(e,a)
def testForce():
"""Check that dlpoly.writeTABLE._calculateForce() wraps potentials.Potential.force to return -r dU/dr values needed by DL_POLY"""
potfunc = potentials.buck(1388.773, 2.76, 175)
pot = potentials.Potential("A", "B", potfunc)
expect = pytest.approx(-66990.0984477696)
actual = _dlpoly_writeTABLE._calculateForce(pot, 0.5)
assert expect == actual
def test_potclass_testForce_numderiv():
"""Check potentials.Potential.force() method"""
def energyfunc(r):
return 1388.773 * math.exp(-r / 0.362318841) - 175.0 / r**6
pot = potentials.Potential("A", "B", energyfunc, h=0.1e-5)
expect = 7.151
actual = pot.force(2.0)
assert pytest.approx(expect, abs=1e-3) == actual
def testWritePotentials(self):
"""Test _lammps_writeTABLE.writePotentials() function"""
pota =potentials.Potential("A", "B", lambda x: x)
potb =potentials.Potential("C", "D", lambda x: 5.0-x)
expect=[
"A-B",
"N 6 R 0.10000000 5.10000000",
"",
"1 0.10000000 0.10000000 -1.00000000",
"2 1.10000000 1.10000000 -1.00000000",
"3 2.10000000 2.10000000 -1.00000000",
"4 3.10000000 3.10000000 -1.00000000",
"5 4.10000000 4.10000000 -1.00000000",
"6 5.10000000 5.10000000 -1.00000000",
"",
"C-D",
"N 6 R 0.10000000 5.10000000",
"",
"1 0.10000000 4.90000000 1.00000000",
"2 1.10000000 3.90000000 1.00000000",
"3 2.10000000 2.90000000 1.00000000",
"4 3.10000000 1.90000000 1.00000000",
"5 4.10000000 0.90000000 1.00000000",
"6 5.10000000 -0.10000000 1.00000000"]
sbuild = StringIO()
_lammps_writeTABLE.writePotentials([pota,potb], 0.1, 5.1, 6, sbuild)
sbuild.seek(0)
actual = sbuild.readlines()
sbuild.seek(0)
msg = "%s != %s" % (expect, actual)
self.assertEqual(len(expect), len(actual), msg = msg)
for e,a in zip(expect, sbuild):
# a = a.decode()
self.assertEqual(os.linesep, a[-1])
a = a[:-1]
self.assertEqual(e,a)
def testWriteEAMFile(self):
"""Test _writeTABEAM.writeTABEAM() function"""
from io import StringIO
#Define potentials
ppbucku = potentials.Potential('U', 'U', _zerowrap(potentials.buck(668.546808, 0.408333, 0.0)))
ppbuckuc = potentials.Potential('U', 'C', _zerowrap(potentials.buck(30.885011, 0.814952, 0.0)))
ppswcc = potentials.Potential('C', 'C', _zerowrap(_stillingerWeber(1.1, 2.078, 1.368, 2.5257)))
densU = _densityFunction( 1.301894, 2.0, 0.668659, 1.862363, 2.0)
densC = _densityFunction(33.446287, 2.0, 1.318078, 1.512686, 2.0)
UEAMPot = potentials.EAMPotential('U', 92, 19.05, embeddingFunction, densU )
CEAMPot = potentials.EAMPotential('C', 6, 2.267,embeddingFunction, densC )
maxrho = 410.0
cutoff = 12.0
drho = dr = 0.01
nrho = int(maxrho // drho)
nr = int(cutoff // dr)
outfile = StringIO()
_dlpoly_writeTABEAM.writeTABEAM(
nrho, drho,
nr, dr,
[UEAMPot, CEAMPot],
[ppbucku, ppbuckuc, ppswcc],
outfile,
"Chartier/Van Brutzel Potentials")
outfile = StringIO(outfile.getvalue())
#Check structure of the file
self.assertEqual(2, self._countSections(outfile, 'embe'))
self.assertEqual(2, self._countSections(outfile, 'dens'))
self.assertEqual(3, self._countSections(outfile, 'pair'))
def test_potclass_testForceDeriv():
"""Check that analytical derivatives are used when available"""
# Create a callable that returns an analytical derivative which is very difficult to the (correct)
# numerical derivative - then look for this when the force() metho of the potential object is called.
deriv_force = 24.0
class AnalyticalDerivative(object):
def __call__(self, r):
return -3.0 * r + 5.0
def deriv(self, r):
return deriv_force
potfunc = AnalyticalDerivative()
pot = potentials.Potential("A", "B", potfunc)
expect = 2.0
actual = pot.energy(1.0)
assert pytest.approx(expect) == actual
# Now check the force.
assert pytest.approx(-deriv_force) == pot.force(1.0)
def testWriteSetFLFinnisSinclair_PairPotentialOrder(self):
"""Check that pair potentials are written in the correct order"""
nrho = 5
drho = 0.1
nr = 5
dr = 0.1
cutoff = 0.5
import collections
def defaultdens():
return lambda x: 0.0
defaultdict = collections.defaultdict(defaultdens)
eampot1 =potentials.EAMPotential('A', 1, 1.0, lambda x: 0.1, defaultdict)
eampot2 =potentials.EAMPotential('B', 2, 2.0, lambda x: 0.2, defaultdict)
eampot3 =potentials.EAMPotential('C', 3, 3.0, lambda x: 0.3, defaultdict)
pairpot_aa =potentials.Potential('A', 'A', lambda r: 1.0)
pairpot_bb =potentials.Potential('B', 'B', lambda r: 2.0)
pairpot_cc =potentials.Potential('C', 'C', lambda r: 3.0)
pairpot_ba =potentials.Potential('B', 'A', lambda r: 5.0)
pairpot_ac =potentials.Potential('A', 'C', lambda r: 6.0)
pairpot_bc =potentials.Potential('B', 'C', lambda r: 7.0)
# Define two species
sio = StringIO()
potentials.writeSetFLFinnisSinclair(
nrho, drho,
nr, dr,
[eampot2, eampot1],
[pairpot_bb, pairpot_aa, pairpot_ba],
comments = ['Comment1', 'Comment2', 'Comment3'],
out = sio,
cutoff = cutoff)
rvals = [0.0, 0.1, 0.2, 0.3, 0.4]
expect = [ r * pairpot_bb.energy(r) for r in rvals]
expect.extend([ r * pairpot_ba.energy(r) for r in rvals])
expect.extend([ r * pairpot_aa.energy(r) for r in rvals])
sio.seek(0)
actual = sio.readlines()
actual = actual[37:]
actual = [float(v) for v in actual]
from . import testutil
testutil.compareCollection(self,expect, actual)
# Try a ternary system
# Define two species
sio = StringIO()
potentials.writeSetFLFinnisSinclair(
nrho, drho,
nr, dr,
[eampot2, eampot1, eampot3],
[pairpot_bb, pairpot_aa, pairpot_ba, pairpot_cc, pairpot_ac, pairpot_bc],
sio,
['Comment1', 'Comment2', 'Comment3'],
cutoff)
rvals = [0.0, 0.1, 0.2, 0.3, 0.4]
expect = [ r * pairpot_bb.energy(r) for r in rvals]
expect.extend([ r * pairpot_ba.energy(r) for r in rvals])
expect.extend([ r * pairpot_aa.energy(r) for r in rvals])
expect.extend([ r * pairpot_bc.energy(r) for r in rvals])
expect.extend([ r * pairpot_ac.energy(r) for r in rvals])
expect.extend([ r * pairpot_cc.energy(r) for r in rvals])
sio.seek(0)
actual = sio.readlines()
actual = actual[68:]
actual = [float(v) for v in actual]
testutil.compareCollection(self,expect, actual)
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 testFluorite_NoPair(self):
"""Test EAM Tabulation using pair potentials for a fluorite structure"""
shutil.copyfile(
os.path.join(_getResourceDirectory(), 'calc_energy.lmpin'),
os.path.join(self.tempdir, 'calc_energy.lmpin'))
shutil.copyfile(
os.path.join(_getResourceDirectory(), 'CeO2-single_cell.lmpstruct'),
os.path.join(self.tempdir, 'structure.lmpstruct'))
oldpwd = os.getcwd()
os.chdir(self.tempdir)
try:
with open("potentials.lmpinc", "w") as potfile:
potfile.write("pair_style eam/fs\n")
potfile.write("pair_coeff * * eam.fs O Ce\n")
potfile.write("\n")
potfile.write("replicate 4 4 4\n")
# Now define potentials
def erf(x):
# save the sign of x
sign = 1 if x >= 0 else -1
x = abs(x)
# constants
a1 = 0.254829592
a2 = -0.284496736
a3 = 1.421413741
a4 = -1.453152027
a5 = 1.061405429
p = 0.3275911
# A&S formula 7.1.26
t = 1.0/(1.0 + p*x)
y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*math.exp(-x*x)
return sign*y # erf(-x) = -erf(x)
def morse(gamma, r_star, D):
def f(r):
return D*(math.exp(-2.0*gamma*(r-r_star)) - 2.0*math.exp(-gamma*(r-r_star)))
return f
def zw(origfunc):
def f(r):
if r == 0.0:
return 0.0
return origfunc(r)
return f
def zeropot(r):
return 0.0
def embedCe(d):
return -0.30766574471*(d**0.5)
def embedO(d):
return -0.690017059438*(d**0.5)
def densityCe(r):
m=8
a=1556.80263774 #tmpa #55,100//0.00002,0.0001
return (a/(r**m))*0.5*(1+erf(20*(r-1.5)))
def densityO(r):
m=8
a=106.855913747 #tmpa #55,100//0.00002,0.0001
return (a/(r**m))*0.5*(1+erf(20*(r-1.5)))
functionO_Ce = zw(potentials.plus(potentials.buck(351.341192796, 0.380516580733, 0.0), morse(1.86874578949, 2.35603812582, 0.719250701502)))
functionO_O = zw(potentials.buck(830.283447557, 0.352856254215, 3.88437209048))
functionCe_Ce = zw(potentials.buck(18600.0, 0.26644, 0.0))
potO_O = potentials.Potential('O', 'O', functionO_O)
potO_Ce = potentials.Potential('O', 'Ce', functionO_Ce)
potCe_Ce = potentials.Potential('Ce', 'Ce', functionCe_Ce)
eampotCe = potentials.EAMPotential('Ce', 92, 238, embedCe, {'Ce': zw(densityCe), 'O' : zw(densityO)})
eampotO = potentials.EAMPotential('O', 8, 16, embedO, {'Ce': zw(densityCe), 'O' : zw(densityO)})
eampots = [eampotCe, eampotO]
pairpots = [potO_O, potO_Ce, potCe_Ce]
drho = 0.001
nrho = int(100.0 // drho)
cutoff = 11.0
dr = 0.01
nr = int(cutoff // dr)
with open('eam.fs', 'w') as outfile:
potentials.writeSetFLFinnisSinclair(
nrho, drho,
nr, dr,
eampots,
[],
outfile,
["Yakub potential. Zero embed and density", "",""],
cutoff)
runLAMMPS()
energy = extractLAMMPSEnergy()
expect = -1001.27446044
self.assertAlmostEqual(expect, energy, places=5)
finally:
os.chdir(oldpwd)
def test_potclass_testEnergy():
"""Check potentials.Potential.energy"""
potfunc = potentials.buck(1388.773, 2.76, 175)
pot = potentials.Potential("A", "B", potfunc)
assert pytest.approx(-10041.34343169, abs=1e-5) == pot.energy(0.5)
def setUp(self):
super(DLPOLYWriteTABEAMTestCase_RunDLPoly, self).setUp()
shutil.copyfile(os.path.join(_getResourceDirectory(), 'CONTROL_CeO2'), os.path.join(self.tempdir, 'CONTROL'))
shutil.copyfile(os.path.join(_getResourceDirectory(), 'CONFIG_CeO2'), os.path.join(self.tempdir, 'CONFIG'))
shutil.copyfile(os.path.join(_getResourceDirectory(), 'FIELD_CeO2'), os.path.join(self.tempdir, 'FIELD'))
# Now define potentials
def erf(x):
# save the sign of x
sign = 1 if x >= 0 else -1
x = abs(x)
# constants
a1 = 0.254829592
a2 = -0.284496736
a3 = 1.421413741
a4 = -1.453152027
a5 = 1.061405429
p = 0.3275911
# A&S formula 7.1.26
t = 1.0/(1.0 + p*x)
y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*math.exp(-x*x)
return sign*y # erf(-x) = -erf(x)
def morse(gamma, r_star, D):
def f(r):
return D*(math.exp(-2.0*gamma*(r-r_star)) - 2.0*math.exp(-gamma*(r-r_star)))
return f
def zw(origfunc):
def f(r):
if r == 0.0:
return 0.0
return origfunc(r)
return f
def zeropot(r):
return 0.0
def embedCe(d):
return -0.30766574471*(d**0.5)
def embedO(d):
return -0.690017059438*(d**0.5)
def densityCe(r):
m=8
a=1556.80263774 #tmpa #55,100//0.00002,0.0001
return (a/(r**m))#*0.5*(1+erf(20*(r-1.5)))
def densityO(r):
m=8
a=106.855913747 #tmpa #55,100//0.00002,0.0001
return (a/(r**m))#*0.5*(1+erf(20*(r-1.5)))
functionO_Ce = zw(potentials.plus(potentials.buck(351.341192796, 0.380516580733, 0.0), morse(1.86874578949, 2.35603812582, 0.719250701502)))
functionO_O = zw(potentials.buck(830.283447557, 0.352856254215, 3.88437209048))
functionCe_Ce = zw(potentials.buck(18600.0, 0.26644, 0.0))
potO_O = potentials.Potential('O', 'O', functionO_O)
potO_Ce = potentials.Potential('O', 'Ce', functionO_Ce)
potCe_Ce = potentials.Potential('Ce', 'Ce', functionCe_Ce)
eampotCe = potentials.EAMPotential('Ce', 92, 238, embedCe, zw(densityCe))
eampotO = potentials.EAMPotential('O', 8, 16, embedO, zw(densityO))
self.eampots = [eampotCe, eampotO]
self.pairpots = [potO_O, potO_Ce, potCe_Ce]