def test_vararg_potentialform():
"""Check that a potential form that uses varargs works correctly"""
cfg_string = u"""[Pair]
O-O = as.polynomial 10.0 20.0 30.0
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
potfunc = tabulation.potentials[0].potentialFunction
assert pf.polynomial(1.6, 10.0, 20.0, 30.0) == potfunc(1.6)
# Now check its use in a custom potentialform
cfg_string = u"""[Pair]
O-O = mypoly 10.0 20.0 30.0
[Potential-Form]
mypoly(r, A, B, C) = as.polynomial(r, A,B,C) + 10.0"""
expect = pf.polynomial(1.6, 10.0, 20.0, 30.0) + 10.0
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
potfunc = tabulation.potentials[0].potentialFunction
assert pytest.approx(expect) == potfunc(1.6)
def test_add_zeroed_interactions():
with _get_resource_dir().join("setfl.aspot").open() as infile:
cfg = Configuration()
tab = cfg.read(infile)
# Check that eam potential exist
expect_embed = set(['Ga', 'In', 'O'])
actual_embed = set([ep.species for ep in tab.eam_potentials])
assert expect_embed == actual_embed
# Check that the defaulted embedding functions are instances of as.zero
zero_type = type(zero().func)
as_zero_func_species = set([
ep.species for ep in tab.eam_potentials
if hasattr(ep.embeddingFunction, "func")
and type(ep.embeddingFunction.func) == zero_type
])
# assert set(['O', 'Mg', 'Al']) == as_zero_func_species
assert set(['O']) == as_zero_func_species
# Check that null-density functions exist.
expect_density = expect_embed
actual_density = set()
for ep in tab.eam_potentials:
a = ep.species
actual_density.add(a)
assert expect_density == actual_density
# Check that tabulation can complete.
import io
outfile = io.StringIO()
tab.write(outfile)
def test_pair_configuration():
cfg_string = u"""[Pair]
O-O = as.buck 1000.0 0.3 32.0
U-O = as.buck 2000.0 0.2 0.0
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
assert tabulation.nr == 1001
assert tabulation.dr == 0.01
assert tabulation.cutoff == 10.0
assert tabulation.type == "Pair"
assert tabulation.target == "LAMMPS"
assert 2 == len(tabulation.potentials)
potlist = tabulation.potentials
expect = [("O", "O"), ("U", "O")]
actual = [(p.speciesA, p.speciesB) for p in potlist]
assert sorted(expect) == sorted(actual)
r = 1.3
buck_oo = pf.buck(r, 1000.0, 0.3, 32.0)
buck_uo = pf.buck(r, 2000.0, 0.2, 0.0)
expect = [(("O", "O"), pytest.approx(buck_oo)),
(("U", "O"), pytest.approx(buck_uo))]
actual = [((p.speciesA, p.speciesB), p.energy(r)) for p in potlist]
assert sorted(expect) == sorted(actual)
def test_lammps_setfl_crg_tabulate_UO2(lammps_run_fluorite_fixture):
tmpdir = lammps_run_fluorite_fixture
cfgobj = Configuration()
config_file = io.open(
_get_lammps_resource_dir().join("CRG_U_Th.aspot").strpath,
encoding="utf8")
tabulation = cfgobj.read(config_file)
with tmpdir.join("table.eam.alloy").open("w") as outfile:
tabulation.write(outfile)
with lammps_run_fluorite_fixture.join("potentials.lmpinc").open(
'w') as potfile:
potfile.write(u"""variable O equal 1
set type 1 charge -1.1104
set type 2 charge 2.2208
kspace_style pppm 1.0e-6
pair_style hybrid/overlay coul/long 10.0 eam/alloy
pair_coeff * * coul/long
pair_coeff * * eam/alloy table.eam.alloy O U
""")
runLAMMPS(cwd=tmpdir.strpath)
energy = extractLAMMPSEnergy(cwd=tmpdir.strpath)
expect = -163.072240194504
assert pytest.approx(expect) == energy
def test_custom_species_data():
cfg_file_path = _get_lammps_resource_dir().join("CRG_U_Th.aspot")
from atsim.potentials.config._config_parser import _RawConfigParser
inifile = _RawConfigParser()
inifile.read(u"{}".format(cfg_file_path.strpath))
inifile.add_section(u'Species')
inifile[u"Species"][u"U.atomic_mass"] = u"235"
inifile[u"Species"][u"U.lattice_constant"] = u"5.678"
inifile[u"Species"][u"Th.lattice_type"] = u"bcc"
modified = io.StringIO()
inifile.write(modified)
modified.seek(0)
cfgobj = Configuration()
tabulation = cfgobj.read(modified)
plist = tabulation.eam_potentials
upot = [p for p in plist if p.species == u"U"][0]
assert pytest.approx(235.0) == upot.mass
assert pytest.approx(5.678) == upot.latticeConstant
cepot = [p for p in plist if p.species == u"Th"][0]
assert cepot.latticeType == u'bcc'
def test_dlpoly_EAM_FS_tabulate_AlFe(tmpdir):
cfg_file_path = _get_lammps_resource_dir().join("AlFe_setfl_fs.aspot")
from atsim.potentials.config._config_parser import _RawConfigParser
inifile = _RawConfigParser()
inifile.read(u"{}".format(cfg_file_path.strpath))
inifile[u"Tabulation"][u'target'] = u"DL_POLY_EAM_fs"
modified = io.StringIO()
inifile.write(modified)
modified.seek(0)
cfgobj = Configuration()
tabulation = cfgobj.read(modified)
with tmpdir.join("TABEAM").open("w") as outfile:
tabulation.write(outfile)
_get_dlpoly_resource_dir().join("CONTROL_random_Al_Fe").copy(
tmpdir.join("CONTROL"))
_get_dlpoly_resource_dir().join("CONFIG_random_Al_Fe").copy(
tmpdir.join("CONFIG"))
_get_dlpoly_resource_dir().join("FIELD_random_Al_Fe").copy(
tmpdir.join("FIELD"))
runDLPoly(cwd=tmpdir.strpath)
actual = extractDLPOLYEnergy(cwd=tmpdir.strpath)
expect = -31.769632
assert pytest.approx(expect) == actual
def test_lammps_EAM_FS_tabulate_AlFe(lammps_run_fixture):
tmpdir = lammps_run_fixture
cfgobj = Configuration()
config_file = io.open(
_get_lammps_resource_dir().join("AlFe_setfl_fs.aspot").strpath,
encoding="utf8")
tabulation = cfgobj.read(config_file)
_get_lammps_resource_dir().join("random_Al_Fe.lmpstruct").copy(
tmpdir.join("structure.lmpstruct"))
_get_lammps_resource_dir().join("AlFe_mm.eam.fs").copy(
tmpdir.join("table.eam.fs"))
with tmpdir.join("potentials.lmpinc").open("w") as potfile:
potfile.write(u"pair_style eam/fs\n")
potfile.write(u"pair_coeff * * table.eam.fs Al Fe\n")
runLAMMPS(cwd=tmpdir.strpath)
expect = extractLAMMPSEnergy(cwd=tmpdir.strpath)
with tmpdir.join("table.eam.fs").open("w") as outfile:
tabulation.write(outfile)
runLAMMPS(cwd=tmpdir.strpath)
actual = extractLAMMPSEnergy(cwd=tmpdir.strpath)
assert pytest.approx(expect) == actual
def test_lammps_pair_configuration_tabulate(lammps_run_fixture):
tmpdir = lammps_run_fixture
cfg_string = u"""[Potential-Form]
buck(r, A, rho, C) : A*exp(-r/rho) - C/r^6
morse(r, gamma, r_star, D) : D*(exp(-2.0*gamma*(r-r_star)) - 2.0*exp(-gamma*(r-r_star)))
buck_morse(r, A, rho, C, gamma, r_star, D) : buck(r,A,rho,C) + morse(r, gamma, r_star, D)
[Pair]
O-U = buck_morse 1000.0 0.1 32.0 0.3 2.0 10.0
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
with tmpdir.join("table.lmptab").open("w") as outfile:
tabulation.write(outfile)
with lammps_run_fixture.join("potentials.lmpinc").open('w') as potfile:
potfile.write(
"pair_style hybrid/overlay zero {0} table linear {1}\n".format(
tabulation.cutoff, tabulation.nr))
potfile.write("pair_coeff * * zero\n")
potfile.write("pair_coeff 1 2 table table.lmptab O-U\n")
potfile.write("\n")
runLAMMPS(cwd=tmpdir.strpath)
energy = extractLAMMPSEnergy(cwd=tmpdir.strpath)
expect = pf.buck(2.0, 1000.0, 0.1, 32.0) + pf.morse(2.0, 0.3, 2.0, 10.0)
assert pytest.approx(expect) == energy
def main():
# Make a file like object from the potable input string given above.
potable_input_file = io.StringIO(potable_input)
# Create a Configuration() object and read input from the input file.
configuration = Configuration()
# ... Configuration is a factory class for PairTabulation and EAMTabulation
# objects. In the current case it will return a GULP_PairTabulation object.
tabulation = configuration.read(potable_input_file)
# The potable input defines a single pair potential.
# Potential objects are accessible from the tabulation object through
# its .potentials property.
potential_Si_O = tabulation.potentials[0]
# The potential-form for this interaction is now accessed.
multirange_potentialform = potential_Si_O.potentialFunction
# The potential-forms created from potable input are Multi_Range_Potential_Form
# objects. This is true even if only one range is defined, as is the case here.
#
# Let's get hold of the spline potential form through the Multi_Range_Potential_Form
# .range_defns property (which returns a list of MultiRangeDefinitionTuple)
#
spline_potentialform = multirange_potentialform.range_defns[
0].potential_form
# Now let's get hold of the spline coefficients
spline_coefficients = spline_potentialform.splineCoefficients
print("Spline coefficients are: {}".format(spline_coefficients))
def test_unknown_modifier_exception():
cfg_string = u"""[Pair]
U-O = unknown_modifier(as.buck 1000.0 0.3 32.0, as.constant 1.0)
"""
cfgobj = Configuration()
with pytest.raises(Unknown_Modifier_Exception):
tabulation = cfgobj.read(io.StringIO(cfg_string))
def test_trans_modifier():
cfg_string = u"""[Pair]
A-B = trans(pow(as.polynomial 3.0 2.0, as.constant 2), as.constant -2.0)
A-A = sum(as.buck 1000.0 0.1 0, trans(as.buck 1000.0 0.1 0, as.constant 1.0))
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
pots = tabulation.potentials
potdict = dict([((p.speciesA, p.speciesB), p) for p in pots])
ab = potdict[("A", "B")]
import sympy
r, A, B, C = sympy.symbols("r A B C")
ab_sympy = (A + B * (r - 2.0))**C
var_dict = dict(r=2.5, A=3.0, B=2.0, C=2.0)
expect = float(ab_sympy.subs(var_dict))
actual = ab.energy(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ab.potentialFunction, "deriv")
ab_deriv = sympy.diff(ab_sympy, r)
expect = float(ab_deriv.subs(var_dict))
actual = ab.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ab.potentialFunction, "deriv2")
ab_deriv2 = sympy.diff(ab_sympy, r, 2)
expect = float(ab_deriv2.subs(var_dict))
actual = ab.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
aa = potdict[("A", "A")]
r, A, B, C, D, E, F = sympy.symbols("r A B C D E F")
aa_sympy = (A * sympy.exp(-r / B) -
C / r**6) + (D * sympy.exp(-(r + 1) / E) - F / (r + 1)**6)
var_dict = dict(r=2.5, A=1000.0, B=0.1, C=0.0, D=1000.0, E=0.1, F=0.0)
expect = float(aa_sympy.subs(var_dict))
actual = aa.energy(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(aa.potentialFunction, "deriv")
aa_deriv = sympy.diff(aa_sympy, r)
expect = float(aa_deriv.subs(var_dict))
actual = aa.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(aa.potentialFunction, "deriv2")
aa_deriv2 = sympy.diff(aa_sympy, r, 2)
expect = float(aa_deriv2.subs(var_dict))
actual = aa.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
def test_dlpoly_pair_configuration_tabulate(tmpdir):
cfg_string = u"""[Tabulation]
target : DLPOLY
nr : 1000
cutoff : 6.5
[Potential-Form]
buck(r, A, rho, C) : A*exp(-r/rho) - C/r^6
morse(r, gamma, r_star, D) : D*(exp(-2.0*gamma*(r-r_star)) - 2.0*exp(-gamma*(r-r_star)))
buck_morse(r, A, rho, C, gamma, r_star, D) : buck(r,A,rho,C) + morse(r, gamma, r_star, D)
[Pair]
O-U = buck_morse 1000.0 0.1 32.0 0.3 2.0 10.0
"""
import py.path
this_dir = py.path.local(py.path.local(__file__).dirname)
dlpoly_resource_dir = py.path.local(
this_dir.dirname).join("dl_poly_resources")
templatevars = dict(speciesA="O",
speciesB="U",
Ax=0.0,
Ay=0.0,
Az=0.0,
Bx=2.0,
By=0.0,
Bz=0.0,
potDef="vdw 1\nO U tab\n")
# Write the config file
with dlpoly_resource_dir.join("CONFIG_pair.in").open() as config_template:
with tmpdir.join("CONFIG").open("w") as outfile:
outfile.write(config_template.read() % templatevars)
# Write the FIELD file
with dlpoly_resource_dir.join("FIELD_pair.in").open() as field_template:
with tmpdir.join("FIELD").open("w") as outfile:
outfile.write(field_template.read() % templatevars)
# Write the CONTROL file
dlpoly_resource_dir.join("CONTROL_pair").copy(tmpdir.join("CONTROL"))
# Finally write the TABLE file
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
with tmpdir.join("TABLE").open("w") as outfile:
tabulation.write(outfile)
runDLPoly(cwd=tmpdir.strpath)
energy = extractDLPOLYEnergy(cwd=tmpdir.strpath)
expect = pf.buck(2.0, 1000.0, 0.1, 32.0) + pf.morse(2.0, 0.3, 2.0, 10.0)
assert pytest.approx(expect) == energy
def test_pymath(potential_form, expected_output): cfg_string = base_template.format(potential_form) cfgfile = io.StringIO(cfg_string) cfgobj = Configuration() tabulation = cfgobj.read(cfgfile) pot = tabulation.potentials[0] actual = pot.energy(1.0) assert pytest.approx(expected_output) == actual
def test_pair_deriv():
"""Test that pair potentials defined in potentialfunctions expose their .deriv() functions"""
cfg_string = u"""[Pair]
O-O = as.buck 1000.0 0.3 32.0
"""
cfgobj = Configuration()
# import pdb; pdb.set_trace()
tabulation = cfgobj.read(io.StringIO(cfg_string))
potfunc = tabulation.potentials[0].potentialFunction
assert hasattr(potfunc, "deriv")
assert hasattr(potfunc, "deriv2")
assert pf.buck.deriv(1.6, 1000.0, 0.3, 32.0) == potfunc.deriv(1.6)
assert pf.buck.deriv2(1.6, 1000.0, 0.3, 32.0) == potfunc.deriv2(1.6)
# Test that cexprtk potentialform doesn't provide a .deriv function.
cfg_string = u"""[Pair]
O-O = my_buck 1000.0 0.3 32.0
[Potential-Form]
my_buck(r, A, rho, C) = A*exp(-r/rho) - C/r^6
"""
cfgobj = Configuration()
# import pdb; pdb.set_trace()
tabulation = cfgobj.read(io.StringIO(cfg_string))
potfunc = tabulation.potentials[0].potentialFunction
assert not hasattr(potfunc, "deriv")
assert not hasattr(potfunc, "deriv2")
def test_pair_model(tmpdir):
cfg = u"""[Tabulation]
target : excel
dr : 0.01
cutoff : 5
[Pair]
O-O : as.polynomial 0 1
Al-O : as.polynomial 0 2
"""
infile = io.StringIO(cfg)
configuration = Configuration()
tabulation = configuration.read(infile)
assert type(tabulation) is Excel_PairTabulation
out_path = tmpdir.join("pair.xlsx")
with tabulation.open_fp(out_path.strpath) as outfile:
tabulation.write(outfile)
wb = load_workbook(out_path.strpath)
assert ["Pair"] == wb.sheetnames
ws = wb["Pair"]
# Check column headings
assert ["r", "Al-O", "O-O"] == [c.value for c in next(ws.rows)]
# Check number of table rows
assert len(next(ws.columns)) == 502
# Check some values
assert ws["A2"].value == 0.0
assert ws["B2"].value == 0.0
assert ws["C2"].value == 0.0
assert ws["A3"].value == 0.01
assert ws["B3"].value == pytest.approx(2 * 0.01)
assert ws["C3"].value == pytest.approx(0.01)
assert ws["A502"].value == 5.0
assert ws["B502"].value == pytest.approx(2.0 * 5.0)
assert ws["C502"].value == pytest.approx(5.0)
def test_adp_in_lammps(tmpdir):
expect_dir = tmpdir.join("expect")
expect_dir.ensure(dir=True)
lmpin = _get_lammps_resource_dir().join("AlCu3.lmpstruct")
lmpin.copy(expect_dir.join("structure.lmpstruct"))
lmpin = _get_lammps_resource_dir().join("calc_energy.lmpin")
lmpin.copy(expect_dir.join("calc_energy.lmpin"))
# Copy existing table file
_get_lammps_resource_dir().join("AlCu.adp").copy(expect_dir.join("AlCu.adp"))
with expect_dir.join("potentials.lmpinc").open("w") as potentials:
potentials.write("pair_style adp\n")
potentials.write("pair_coeff * * AlCu.adp Al Cu\n")
runLAMMPS(cwd=expect_dir.strpath)
expect_energy = extractLAMMPSEnergy(cwd=expect_dir.strpath)
actual_dir = tmpdir.join("actual")
actual_dir.ensure(dir=True)
lmpin = _get_lammps_resource_dir().join("AlCu3.lmpstruct")
lmpin.copy(actual_dir.join("structure.lmpstruct"))
lmpin = _get_lammps_resource_dir().join("calc_energy.lmpin")
lmpin.copy(actual_dir.join("calc_energy.lmpin"))
with actual_dir.join("potentials.lmpinc").open("w") as potentials:
potentials.write("pair_style adp\n")
potentials.write("pair_coeff * * AlCu.adp Al Cu\n")
# Tabulate potential
cfg_file = _get_lammps_resource_dir().join("Al_Cu_adp.aspot")
configuration = Configuration()
tabulation = configuration.read(cfg_file.open('r'))
with actual_dir.join("AlCu.adp").open("w") as outfile:
tabulation.write(outfile)
runLAMMPS(cwd=actual_dir.strpath)
actual_energy = extractLAMMPSEnergy(cwd=actual_dir.strpath)
assert expect_energy == approx(actual_energy)
def test_sum_modifier_deriv():
"""Make sure the sum() modifier uses .deriv() methods correctly if they are available"""
cfg_string = u"""[Pair]
#no deriv
A-B = sum(born_mayer 1000.0 0.1, dispersion 32.0)
# both have deriv
B-C = sum(as.bornmayer 1000.0 0.1, as.buck 0 1.0 32.0)
#one_deriv
C-D = sum(as.bornmayer 1000.0 0.1, dispersion 32.0)
[Potential-Form]
born_mayer(r, A, rho) = A * exp(-r/rho)
dispersion(r, C) = - C/r^6
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
pots = tabulation.potentials
expect = [("A", "B"), ("B", "C"), ("C", "D")]
actual = [(p.speciesA, p.speciesB) for p in pots]
assert sorted(expect) == sorted(actual)
potdict = dict([((p.speciesA, p.speciesB), p) for p in pots])
assert not hasattr(potdict[('A', 'B')].potentialFunction, 'deriv')
assert hasattr(potdict[('B', 'C')].potentialFunction, 'deriv')
assert hasattr(potdict[('C', 'D')].potentialFunction, 'deriv')
expect_energy = pytest.approx(pf.buck(1.6, 1000, 0.1, 32.0))
expect_deriv = pytest.approx(pf.buck.deriv(1.6, 1000, 0.1, 32.0))
assert expect_energy == potdict[('A', 'B')].potentialFunction(1.6)
assert expect_energy == potdict[('B', 'C')].potentialFunction(1.6)
assert expect_deriv == potdict[('B', 'C')].potentialFunction.deriv(1.6)
assert expect_energy == potdict[('C', 'D')].potentialFunction(1.6)
assert expect_deriv == potdict[('C', 'D')].potentialFunction.deriv(1.6)
def test_adp_tabulation(tmpdir):
cfg_file = _get_lammps_resource_dir().join("Al_Cu_adp.aspot")
configuration = Configuration()
tabulation = configuration.read(cfg_file.open('r'))
assert type(tabulation) is ADP_EAMTabulation
# assert "eam_adp" == tabulation.tabulation_type
assert 10000 == tabulation.nrho
assert tabulation.drho == approx(2.2770502180000001e-03)
assert 10000 == tabulation.nr
assert tabulation.dr == approx(6.2872099999999995e-04)
assert 2 == len(tabulation.eam_potentials)
eam_dict = dict([(ep.species, ep) for ep in tabulation.eam_potentials])
assert ['Al', 'Cu'] == sorted(eam_dict.keys())
assert eam_dict['Al'].embeddingValue(0.1001902096E+01) == approx(-0.2418739157E+01)
assert eam_dict['Cu'].embeddingValue(0.1009492263E+01) == approx(-0.9390266026E+00)
assert eam_dict['Al'].electronDensity(0.1609791553E+01) == approx(0.7617792157E-01)
assert eam_dict['Cu'].electronDensity(0.1512859370E+01) == approx(0.1824604072E+00)
assert 3 == len(tabulation.potentials)
assert [('Al', 'Al'), ('Al','Cu'), ('Cu', 'Cu')] == sorted([tuple(sorted((p.speciesA, p.speciesB))) for p in tabulation.potentials])
pair_dict = dict([(tuple(sorted((p.speciesA, p.speciesB))), p) for p in tabulation.potentials])
assert pair_dict[('Al', 'Al')].energy(0.1123368233E+01) == approx(0.5178467078E+01)
assert pair_dict[('Al', 'Cu')].energy(0.1500522547E+01) == approx(0.2913519771E+01)
assert pair_dict[('Cu', 'Cu')].energy(0.1817755147E+01) == approx(0.2103976024E+01)
assert 1 == len(tabulation.dipole_potentials)
pair_dict = dict([(tuple(sorted((p.speciesA, p.speciesB))), p) for p in tabulation.dipole_potentials])
assert pair_dict[('Al', 'Cu')].energy(0.1634465200E+01) == approx(-0.5117209620E-01)
assert 1 == len(tabulation.quadrupole_potentials)
pair_dict = dict([(tuple(sorted((p.speciesA, p.speciesB))), p) for p in tabulation.quadrupole_potentials])
assert pair_dict[('Al', 'Cu')].energy(0.5044715650E+01) == approx(-0.4386367758E-02)
def test_sum_modifier():
cfg_string = u"""[Pair]
O-O = as.buck 1000.0 0.3 32.0
U-O = sum(as.buck 1000.0 0.3 32.0, as.constant 1.0)
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
potlist = tabulation.potentials
expect = [("O", "O"), ("U", "O")]
actual = [(p.speciesA, p.speciesB) for p in potlist]
assert sorted(expect) == sorted(actual)
r = 1.3
buck_oo = pf.buck(r, 1000.0, 0.3, 32.0)
expect = [(("O", "O"), pytest.approx(buck_oo)),
(("U", "O"), pytest.approx(buck_oo + 1.0))]
actual = [((p.speciesA, p.speciesB), p.energy(r)) for p in potlist]
assert sorted(expect) == sorted(actual)
def test_multirange_deriv():
"""Make sure that .deriv() methods are used where possible in MultiRangePotential"""
# Neither potentialform has deriv() - resultant doesn't have deriv()
cfg_string = u"""[Pair]
#no deriv
A-B = born_mayer 1000.0 0.1 >=3.0 dispersion 32.0
# both have deriv
B-C = as.bornmayer 1000.0 0.1 >=3.0 as.buck 0 1.0 32.0
#one_deriv
C-D = as.bornmayer 1000.0 0.1 >=3.0 dispersion 32.0
[Potential-Form]
born_mayer(r, A, rho) = A * exp(-r/rho)
dispersion(r, C) = - C/r^6
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
pots = tabulation.potentials
potdict = dict([((p.speciesA, p.speciesB), p) for p in pots])
assert not hasattr(potdict[('A', 'B')].potentialFunction, 'deriv')
assert hasattr(potdict[('B', 'C')].potentialFunction, 'deriv')
assert hasattr(potdict[('C', 'D')].potentialFunction, 'deriv')
assert pytest.approx(pf.bornmayer.deriv(
1.6, 1000.0, 0.1)) == potdict[('B', 'C')].potentialFunction.deriv(1.6)
assert pytest.approx(pf.buck.deriv(
3.2, 0, 1.0, 32.0)) == potdict[('B', 'C')].potentialFunction.deriv(3.2)
assert pytest.approx(pf.bornmayer.deriv(
1.6, 1000.0, 0.1)) == potdict[('C', 'D')].potentialFunction.deriv(1.6)
assert pytest.approx(pf.buck.deriv(
3.2, 0, 1.0, 32.0)) == potdict[('C', 'D')].potentialFunction.deriv(3.2)
def test_dlpoly_TABEAM_tabulate_CeO2(tmpdir):
# Copy files into the tmpdir.
rd = _get_dlpoly_resource_dir()
files = [("CONFIG_CeO2", "CONFIG"), ("CONTROL_CeO2", "CONTROL"),
("FIELD_CeO2", "FIELD")]
for src, dest in files:
src = rd.join(src)
dest = tmpdir.join(dest)
src.copy(dest)
# Tabulate the TABEAM potential
cfgobj = Configuration()
config_file = io.open(rd.join("CRG_Ce.aspot").strpath, encoding="utf8")
tabulation = cfgobj.read(config_file)
with tmpdir.join("TABEAM").open("w") as outfile:
tabulation.write(outfile)
runDLPoly(cwd=tmpdir.strpath)
actual = extractDLPOLYEnergy(cwd=tmpdir.strpath)
expect = -532.6778
assert pytest.approx(expect) == actual
def test_pair_eam(tmpdir):
cfg = u"""[Tabulation]
target : excel_eam
dr : 0.01
cutoff : 5
drho : 0.01
cutoff_rho : 5
[Pair]
O-O : as.polynomial 0 1
Al-O : as.polynomial 0 2
[EAM-Density]
O : as.polynomial 0 3
Al : as.polynomial 0 4
[EAM-Embed]
O : as.polynomial 0 5
Al : as.polynomial 0 6
"""
infile = io.StringIO(cfg)
configuration = Configuration()
tabulation = configuration.read(infile)
assert type(tabulation) is Excel_EAMTabulation
out_path = tmpdir.join("pair.xlsx")
with tabulation.open_fp(out_path.strpath) as outfile:
tabulation.write(outfile)
wb = load_workbook(out_path.strpath)
assert ["Pair", "EAM-Density", "EAM-Embed"] == wb.sheetnames
# Check [Pair] table
ws = wb["Pair"]
# Check column headings
assert ["r", "Al-O", "O-O"] == [c.value for c in next(ws.rows)]
# Check number of table rows
assert len(next(ws.columns)) == 502
# Check some values
assert ws["A2"].value == 0.0
assert ws["B2"].value == 0.0
assert ws["C2"].value == 0.0
assert ws["A3"].value == 0.01
assert ws["B3"].value == pytest.approx(2 * 0.01)
assert ws["C3"].value == pytest.approx(0.01)
assert ws["A502"].value == 5.0
assert ws["B502"].value == pytest.approx(2.0 * 5.0)
assert ws["C502"].value == pytest.approx(5.0)
# Check [EAM-Density] table
ws = wb["EAM-Density"]
# Check column headings
assert ["r", "Al", "O"] == [c.value for c in next(ws.rows)]
# Check number of table rows
assert len(next(ws.columns)) == 502
# Check some values
assert ws["A2"].value == 0.0
assert ws["B2"].value == 0.0
assert ws["C2"].value == 0.0
assert ws["A3"].value == 0.01
assert ws["B3"].value == pytest.approx(4 * 0.01)
assert ws["C3"].value == pytest.approx(3 * 0.01)
assert ws["A502"].value == 5.0
assert ws["B502"].value == pytest.approx(4.0 * 5.0)
assert ws["C502"].value == pytest.approx(3.0 * 5.0)
# Check [EAM-Embed] table
ws = wb["EAM-Embed"]
# Check column headings
assert ["rho", "Al", "O"] == [c.value for c in next(ws.rows)]
# Check number of table rows
assert len(next(ws.columns)) == 502
# Check some values
assert ws["A2"].value == 0.0
assert ws["B2"].value == 0.0
assert ws["C2"].value == 0.0
assert ws["A3"].value == 0.01
assert ws["B3"].value == pytest.approx(6 * 0.01)
assert ws["C3"].value == pytest.approx(5 * 0.01)
assert ws["A502"].value == 5.0
assert ws["B502"].value == pytest.approx(6.0 * 5.0)
assert ws["C502"].value == pytest.approx(5.0 * 5.0)
def test_product_modifier():
cfg_string = u"""[Pair]
A-B = product(as.buck 1000.0 0.2 32.0, as.polynomial 0.0 2.0, as.polynomial 1.0 -3.0 0.5)
A-C = sum(
product(
as.constant 2.0,
as.polynomial 1.0 2.0 1.5,
product(
as.polynomial 1.0 2.0 3.0,
as.polynomial 4.0 5.0 6.0
) ),
as.polynomial 0.0 -1.0)
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
pots = tabulation.potentials
potdict = dict([((p.speciesA, p.speciesB), p) for p in pots])
ab = potdict[("A", "B")]
import sympy
r, A, rho, C, p1_0, p1_1, p2_0, p2_1, p2_2 = sympy.symbols(
"r A rho C p1_0 p1_1 p2_0 p2_1 p2_2")
ab_sympy = (A * sympy.exp(-r / rho) -
C / r**6) * (p1_0 + p1_1 * r) * (p2_0 + p2_1 * r + p2_2 * r**2)
var_dict = dict(r=2.5,
A=1000.0,
rho=0.2,
C=32.0,
p1_0=0.0,
p1_1=2.0,
p2_0=1.0,
p2_1=-3.0,
p2_2=0.5)
expect = float(ab_sympy.subs(var_dict))
actual = ab.energy(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ab.potentialFunction, "deriv")
ab_deriv = sympy.diff(ab_sympy, r)
expect = float(ab_deriv.subs(var_dict))
actual = ab.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ab.potentialFunction, "deriv2")
ab_deriv2 = sympy.diff(ab_sympy, r, 2)
expect = float(ab_deriv2.subs(var_dict))
actual = ab.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
ac = potdict[("A", "C")]
r = sympy.symbols("r")
A = sympy.symbols("A")
p1_0, p1_1, p1_2 = sympy.symbols("p1_0 p1_1 p1_2")
p2_0, p2_1, p2_2 = sympy.symbols("p2_0 p2_1 p2_2")
p3_0, p3_1, p3_2 = sympy.symbols("p3_0 p3_1 p3_2")
p4_0, p4_1 = sympy.symbols("p4_0 p4_1")
ac_sympy = (A * (p1_0 + p1_1 * r + p1_2 * r**2) *
((p2_0 + p2_1 * r + p2_2 * r**2) *
(p3_0 + p3_1 * r + p3_2 * r**2))) + (p4_0 + p4_1 * r)
var_dict = dict(r=2.5,
A=2.0,
p1_0=1.0,
p1_1=2.0,
p1_2=1.5,
p2_0=1.0,
p2_1=2.0,
p2_2=3.0,
p3_0=4.0,
p3_1=5.0,
p3_2=6.0,
p4_0=0.0,
p4_1=-1.0)
expect = float(ac_sympy.subs(var_dict))
actual = ac.energy(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv")
ac_deriv = sympy.diff(ac_sympy, r)
expect = float(ac_deriv.subs(var_dict))
actual = ac.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv2")
ac_deriv2 = sympy.diff(ac_sympy, r, 2)
expect = float(ac_deriv2.subs(var_dict))
actual = ac.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
def test_throw_configuration_exception():
cfg = u"""[Tabulation]
target : eam_adp
drho : 2.2770502180000001e-03
nrho : 10000
nr : 10000
dr : 6.2872099999999995e-04
[EAM-Embed]
Al : as.zero
Cu : as.zero
[EAM-Density]
Al : as.zero
Cu : as.zero
[Pair]
Al-Al : as.zero
Cu-Al : as.zero
Cu-Cu : as.zero
"""
configuration = Configuration()
with raises(ConfigurationException):
configuration.read(io.StringIO(cfg))
cfg = u"""[Tabulation]
target : eam_adp
drho : 2.2770502180000001e-03
nrho : 10000
nr : 10000
dr : 6.2872099999999995e-04
[EAM-Embed]
Al : as.zero
Cu : as.zero
[EAM-Density]
Al : as.zero
Cu : as.zero
[Pair]
Al-Al : as.zero
Cu-Al : as.zero
Cu-Cu : as.zero
[EAM-ADP-Dipole]
Al-Al : as.zero
Al-Cu : as.zero
Cu-Cu : as.zero
"""
with raises(ConfigurationException):
configuration.read(io.StringIO(cfg))
cfg = u"""[Tabulation]
target : eam_adp
drho : 2.2770502180000001e-03
nrho : 10000
nr : 10000
dr : 6.2872099999999995e-04
[EAM-Embed]
Al : as.zero
Cu : as.zero
[EAM-Density]
Al : as.zero
Cu : as.zero
[Pair]
Al-Al : as.zero
Cu-Al : as.zero
Cu-Cu : as.zero
[EAM-ADP-Quadrupole]
Al-Al : as.zero
Al-Cu : as.zero
Cu-Cu : as.zero
"""
with raises(ConfigurationException):
configuration.read(io.StringIO(cfg))
def test_fs_AlFe():
cfg_file_path = _get_lammps_resource_dir().join("AlFe_setfl_fs.aspot")
with cfg_file_path.open() as config_file:
config_parser = ConfigParser(config_file)
assert config_parser.tabulation.target == "setfl_fs"
with cfg_file_path.open() as config_file:
cfgobj = Configuration()
tabulation = cfgobj.read(config_file)
# Now check that the EAM potentials are as they should be.
assert tabulation.target == "setfl_fs"
assert 2 == len(tabulation.eam_potentials)
epots = tabulation.eam_potentials
epot_dict = dict(zip([p.species for p in epots], epots))
assert ["Al", "Fe"] == sorted([p.species for p in epots])
# Check the embedding functions
alEmbedFunction_actual = epot_dict["Al"].embeddingFunction
for rho in range(1, 300):
expect = alEmbedFunction(rho)
actual = alEmbedFunction_actual(rho)
assert pytest.approx(expect) == actual
feEmbedFunction_actual = epot_dict["Fe"].embeddingFunction
for rho in range(1, 300):
expect = feEmbedFunction(rho)
actual = feEmbedFunction_actual(rho)
assert pytest.approx(expect) == actual
# print("{},{}".format(expect, actual))
# pytest.fail()
# Check the density functions
al_pot = epot_dict["Al"]
dens_dict = al_pot.electronDensityFunction
assert ["Al", "Fe"] == sorted(dens_dict.keys())
alAlDensFunction_actual = dens_dict["Al"]
alFeDensFunction_actual = dens_dict["Fe"]
for r in range(65):
r = r * 0.1
expect = alAlDensFunction(r)
actual = alAlDensFunction_actual(r)
assert pytest.approx(expect) == actual
expect = feAlDensFunction(r)
actual = alFeDensFunction_actual(r)
assert pytest.approx(expect) == actual
fe_pot = epot_dict["Fe"]
dens_dict = fe_pot.electronDensityFunction
assert ["Al", "Fe"] == sorted(dens_dict.keys())
feAlDensFunction_actual = dens_dict["Al"]
feFeDensFunction_actual = dens_dict["Fe"]
for r in range(65):
r = r * 0.1
expect = feAlDensFunction(r)
actual = feAlDensFunction_actual(r)
assert pytest.approx(expect) == actual
expect = feFeDensFunction(r)
actual = feFeDensFunction_actual(r)
assert pytest.approx(expect) == actual
# Check pair-potentials
ppots = tabulation.potentials
pairs = [(ppot.speciesA, ppot.speciesB) for ppot in ppots]
assert [("Al", "Al"), ("Al", "Fe"), ("Fe", "Fe")] == pairs
expect_dict = {
("Al", "Al"): ppfuncAlAl,
("Al", "Fe"): ppfuncAlFe,
("Fe", "Fe"): ppfuncFeFe
}
for actual_pp in ppots:
expect_pp = expect_dict[(actual_pp.speciesA, actual_pp.speciesB)]
for r in range(100):
r = r / 10.0
expect = expect_pp(r)
actual = actual_pp.energy(r)
assert pytest.approx(expect) == actual
def test_pow_modifier():
cfg_string = u"""[Pair]
A-B = pow(as.polynomial 3.0 2.0, as.constant 2)
A-A = pow(as.polynomial 3.0 2.0, pow(as.polynomial 0 2, as.constant 0.5))
A-C = pow(sum(as.buck 1000 0.3 0, as.polynomial 0 1 2), pow(sum(as.polynomial 0 0.1, as.polynomial 0 -0.05), as.constant 0.5))
A-D = pow(as.polynomial 1.0 2.0 3.0, as.polynomial 0 5 0.1, as.constant 0.01)
"""
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
pots = tabulation.potentials
potdict = dict([((p.speciesA, p.speciesB), p) for p in pots])
ab = potdict[("A", "B")]
import sympy
r, A, B, C = sympy.symbols("r A B C")
ab_sympy = (A + B * r)**C
var_dict = dict(r=2.5, A=3.0, B=2.0, C=2.0)
expect = float(ab_sympy.subs(var_dict))
actual = ab.energy(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ab.potentialFunction, "deriv")
ab_deriv = sympy.diff(ab_sympy, r)
expect = float(ab_deriv.subs(var_dict))
actual = ab.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ab.potentialFunction, "deriv2")
ab_deriv2 = sympy.diff(ab_sympy, r, 2)
expect = float(ab_deriv2.subs(var_dict))
actual = ab.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
ac = potdict[("A", "A")]
r = sympy.symbols("r")
# A-C = pow(sum(as.buck 100 0.2 0, as.polynomial 0 1 2), pow(sum(as.polynomial 0 0.1, as.polynomial 0 -0.05), as.constant 0.5))
# pow(as.polynomial 3.0 2.0, pow(as.constant 3, as.constant 2))
ac_sympy = (3.0 + 2.0 * r)**((2 * r)**0.5)
var_dict = dict(r=2.5)
actual = ac.energy(var_dict["r"])
expect = float(ac_sympy.subs(var_dict))
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv")
ac_deriv = sympy.diff(ac_sympy, r)
expect = float(ac_deriv.subs(var_dict))
actual = ac.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv2")
ac_deriv2 = sympy.diff(ac_sympy, r, 2)
expect = float(ac_deriv2.subs(var_dict))
actual = ac.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
ac = potdict[("A", "C")]
r = sympy.symbols("r")
A_buck, rho_buck, C_buck = sympy.symbols("A_buck rho_buck C_buck")
# A-C = pow(sum(as.buck 100 0.2 0, as.polynomial 0 1 2), pow(sum(as.polynomial 0 0.1, as.polynomial 0 -0.05), as.constant 0.5))
ac_sympy = ((A_buck * sympy.exp(-r / rho_buck)) +
(r + 2 * r**2))**((0.1 * r - 0.05 * r)**(0.5))
var_dict = dict(r=2.5, A_buck=1000, rho_buck=0.3)
actual = ac.energy(var_dict["r"])
expect = float(ac_sympy.subs(var_dict))
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv")
ac_deriv = sympy.diff(ac_sympy, r)
expect = float(ac_deriv.subs(var_dict))
actual = ac.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv2")
ac_deriv2 = sympy.diff(ac_sympy, r, 2)
expect = float(ac_deriv2.subs(var_dict))
actual = ac.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
ac = potdict[("A", "D")]
# A-D = pow(as.polynomial 1.0 2.0 3.0, as.polynomial 4 5 6, as.constant 3)
r = sympy.symbols("r")
p1, p2, p3, p4, p5, p6, p7 = sympy.symbols("p1 p2 p3 p4 p5 p6 p7")
ac_sympy = ((p1 + p2 * r + p3 * r**2)**(p4 + p5 * r + p6 * r**2))**p7
var_dict = dict(r=2.5,
p1=1,
p2=2,
p3=3,
p4=0,
p5=5,
p6=0.1,
p7=1.0 / 100.0)
expect = float(ac_sympy.subs(var_dict))
actual = ac.energy(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv")
ac_deriv = sympy.diff(ac_sympy, r)
expect = float(ac_deriv.subs(var_dict))
actual = ac.potentialFunction.deriv(var_dict["r"])
assert pytest.approx(expect) == actual
assert hasattr(ac.potentialFunction, "deriv2")
ac_deriv2 = sympy.diff(ac_sympy, r, 2)
expect = float(ac_deriv2.subs(var_dict))
actual = ac.potentialFunction.deriv2(var_dict["r"])
assert pytest.approx(expect) == actual
def test_gulp_pair_configuration_tabulate(tmpdir):
cfg_string = u"""[Tabulation]
target : GULP
dr: 0.01
cutoff : 15.0
[Pair]
O-U = as.bornmayer 1761.775 0.35642
O-O = as.buck 9547.96 0.2192 32.0
"""
gulp_input = u"""single
cell
5.468 5.468 5.468 90.0 90.0 90.0
frac
U 0 0 0
U 1/2 1/2 0
U 1/2 0 1/2
U 0 1/2 1/2
O 1/4 1/4 1/4
O 1/4 3/4 1/4
O 3/4 3/4 1/4
O 3/4 1/4 1/4
O 1/4 1/4 3/4
O 1/4 3/4 3/4
O 3/4 3/4 3/4
O 3/4 1/4 3/4
species
U 4.0
O -2.0
include potentials.lib
"""
# First calculate the expected energy using GULP's built-in analytical potentials
with tmpdir.join("potentials.lib").open("w") as potfile:
potfile.write("buck\n")
potfile.write("O O 9547.96 0.2192 32.0 15.0\n")
potfile.write("O U 1761.775 0.35642 0.0 15.0\n")
gulp_infile = io.StringIO(gulp_input)
gulp_infile.seek(0)
gulp_outfile = io.StringIO()
runGULP(gulp_infile, gulp_outfile, cwd=tmpdir.strpath)
gulp_outfile.seek(0)
expect = extractGULPEnergy(gulp_outfile)
tmpdir.join("potentials.lib").remove()
assert not tmpdir.join("potentials.lib").exists()
# Now build a potential model and tabulate it - then re-run the calculation and check the energies match.
cfgobj = Configuration()
tabulation = cfgobj.read(io.StringIO(cfg_string))
with tmpdir.join("potentials.lib").open("w") as potfile:
tabulation.write(potfile)
gulp_infile.seek(0)
gulp_outfile = io.StringIO()
runGULP(gulp_infile, gulp_outfile, cwd=tmpdir.strpath)
gulp_outfile.seek(0)
actual = extractGULPEnergy(gulp_outfile)
assert pytest.approx(expect, abs=1e-3) == actual