def myfcc(symbol, pbc):
"Make an fcc lattice with standard lattice constant"
if ismaster:
a = FaceCenteredCubic(symbol=symbol, size=(10,10,10), pbc=pbc)
dx = 0.01 * np.sin(0.1 * np.arange(len(a) * 3))
dx.shape = (len(a),3)
a.set_positions(a.get_positions() + dx)
a.set_momenta(np.zeros((len(a),3)))
#view(a)
else:
a = None
if isparallel:
a = MakeParallelAtoms(a, cpulayout)
return a
def MakeAtoms(elem1, elem2=None):
if elem2 is None:
elem2 = elem1
a1 = reference_states[elem1]['a']
a2 = reference_states[elem2]['a']
a0 = (0.5 * a1**3 + 0.5 * a2**3)**(1.0 / 3.0) * 1.03
if ismaster:
print "Z1 = %i, Z2 = %i, a0 = %.5f" % (elem1, elem2, a0)
# 50*50*50 would be big enough, but some vacancies are nice.
atoms = FaceCenteredCubic(symbol='Cu', size=(51, 51, 51))
nremove = len(atoms) - 500000
assert nremove > 0
remove = np.random.choice(len(atoms), nremove, replace=False)
del atoms[remove]
if elem1 != elem2:
z = atoms.get_atomic_numbers()
z[np.random.choice(len(atoms), len(atoms) / 2, replace=False)] = elem2
atoms.set_atomic_numbers(z)
if isparallel:
# Move this contribution into position
uc = atoms.get_cell()
x = mpi.world.rank % cpuLayout[0]
y = (mpi.world.rank // cpuLayout[0]) % cpuLayout[1]
z = mpi.world.rank // (cpuLayout[0] * cpuLayout[1])
assert (0 <= x < cpuLayout[0])
assert (0 <= y < cpuLayout[1])
assert (0 <= z < cpuLayout[2])
offset = x * uc[0] + y * uc[1] + z * uc[2]
new_uc = cpuLayout[0] * uc[0] + cpuLayout[1] * uc[1] + cpuLayout[
2] * uc[2]
atoms.set_cell(new_uc, scale_atoms=False)
atoms.set_positions(atoms.get_positions() + offset)
# Distribute atoms. Maybe they are all on the wrong cpu, but that will
# be taken care of.
atoms = MakeParallelAtoms(atoms, cpuLayout)
MaxwellBoltzmannDistribution(atoms, T * units.kB)
return atoms
def MakeAtoms(elem1, elem2=None):
if elem2 is None:
elem2 = elem1
a1 = reference_states[elem1]['a']
a2 = reference_states[elem2]['a']
a0 = (0.5 * a1**3 + 0.5 * a2**3)**(1.0/3.0) * 1.03
if ismaster:
print "Z1 = %i, Z2 = %i, a0 = %.5f" % (elem1, elem2, a0)
# 50*50*50 would be big enough, but some vacancies are nice.
atoms = FaceCenteredCubic(symbol='Cu', size=(51,51,51))
nremove = len(atoms) - 500000
assert nremove > 0
remove = np.random.choice(len(atoms), nremove, replace=False)
del atoms[remove]
if elem1 != elem2:
z = atoms.get_atomic_numbers()
z[np.random.choice(len(atoms), len(atoms)/2, replace=False)] = elem2
atoms.set_atomic_numbers(z)
if isparallel:
# Move this contribution into position
uc = atoms.get_cell()
x = mpi.world.rank % cpuLayout[0]
y = (mpi.world.rank // cpuLayout[0]) % cpuLayout[1]
z = mpi.world.rank // (cpuLayout[0] * cpuLayout[1])
assert(0 <= x < cpuLayout[0])
assert(0 <= y < cpuLayout[1])
assert(0 <= z < cpuLayout[2])
offset = x * uc[0] + y * uc[1] + z * uc[2]
new_uc = cpuLayout[0] * uc[0] + cpuLayout[1] * uc[1] + cpuLayout[2] * uc[2]
atoms.set_cell(new_uc, scale_atoms=False)
atoms.set_positions(atoms.get_positions() + offset)
# Distribute atoms. Maybe they are all on the wrong cpu, but that will
# be taken care of.
atoms = MakeParallelAtoms(atoms, cpuLayout)
MaxwellBoltzmannDistribution(atoms, T * units.kB)
return atoms
print " This is an s50 node on Niflheim."
fullhost = "niflheim-s50/%s" % (host.split(".")[0])
host = "niflheim-s50"
else:
fullhost = host
print "Current time is "+when
print ""
print "Preparing system"
initial = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size=(30, 30, 30),
symbol="Pt")
ReportTest("Number of atoms", len(initial), 108000, 0)
r = initial.get_positions()
r.flat[:] += 0.14 * sin(arange(3*len(initial)))
initial.set_positions(r)
print "Running self-test."
atoms = Atoms(initial)
atoms.set_calculator(EMT2013(PtY_parameters))
e = atoms.get_potential_energies()
f = atoms.get_forces()
if os.access(selfcheckfilename, os.F_OK):
olde, oldf = cPickle.load(open(selfcheckfilename))
de = max(fabs(e - olde))
df = max(fabs(f.flat[:] - oldf.flat[:]))
print "Maximal deviation: Energy", de, " Force", df
ReportTest("Max force error", df, 0.0, 1e-11)
ReportTest("Max energy error", de, 0.0, 1e-11)
del olde, oldf
else:
numbers = count.keys()
numbers.sort()
sum = 0
for i in numbers:
#print i, count[i]
sum += i*count[i]
ReportTest("Number of neighbors (EMT's NB list)", sum, 21*len(atoms), 0)
nblist = NeighborList(latconst * 0.5 * (1/sqrt(2) + 1), atoms, 0.0)
#nblist = NeighborCellLocator(latconst * 0.5 * (1/sqrt(2) + 1), atoms, 0.0)
fnb = FullNeighborList(latconst * 0.5 * (1/sqrt(2) + 1), Atoms(atoms))
TestLists(nblist, fnb, "nearest-neigbor lists (periodic)", 6)
ReportTest("Energy unperturbed 1", atoms.get_potential_energy(), epot, 1e-11)
atoms.set_positions(atoms.get_positions())
ReportTest("Energy unperturbed 2", atoms.get_potential_energy(), epot, 1e-11)
nblist = NeighborList(4.98409, atoms, 0.0)
fnb = FullNeighborList(4.98409, Atoms(atoms))
TestLists(nblist, fnb, "long neigbor lists (periodic)", 21)
ReportTest("Energy unperturbed 3", atoms.get_potential_energy(), epot, 1e-11)
atoms.set_positions(atoms.get_positions())
ReportTest("Energy unperturbed 4", atoms.get_potential_energy(), epot, 1e-11)
atoms = Atoms(atoms, pbc=(0,0,0))
nblist = NeighborList(latconst * 0.5 * (1/sqrt(2) + 1), atoms, 0.0)
fnb = FullNeighborList(latconst * 0.5 * (1/sqrt(2) + 1), Atoms(atoms))
TestLists(nblist, fnb, "nearest-neigbor lists (non-periodic)")
1, 0)
ReportTest("Forces required", pot.calculation_required(atoms, ["forces"]),
1, 0)
ReportTest("Stress required", pot.calculation_required(atoms, ["stress"]),
1, 0)
ReportTest("Magmom required", pot.calculation_required(atoms, ["magmoms"]),
1, 0)
e = atoms.get_potential_energy()
ReportTest("Energy not required",
pot.calculation_required(atoms, ["energy"]), 0, 0)
ReportTest("Forces required (II)",
pot.calculation_required(atoms, ["forces"]), 1, 0)
f = atoms.get_forces()
ReportTest("Energy not required (II)",
pot.calculation_required(atoms, ["energy"]), 0, 0)
ReportTest("Forces not required",
pot.calculation_required(atoms, ["forces"]), 0, 0)
ReportTest("Energy or forces not required",
pot.calculation_required(atoms, ["energy", "forces"]), 0, 0)
ReportTest("Energy or stress required",
pot.calculation_required(atoms, ["energy", "stress"]), 1, 0)
s = atoms.get_stress()
ReportTest("Stress not required",
pot.calculation_required(atoms, ["stress"]), 0, 0)
r = atoms.get_positions()
r[0, 0] += 0.1
atoms.set_positions(r)
ReportTest.Summary()
print " This is an s50 node on Niflheim."
fullhost = "niflheim-s50/%s" % (host.split(".")[0])
host = "niflheim-s50"
else:
fullhost = host
print "Current time is "+when
print ""
print "Preparing system"
initial = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
size=(30, 30, 30),
symbol="Cu")
ReportTest("Number of atoms", len(initial), 108000, 0)
r = initial.get_positions()
r.flat[:] += 0.14 * sin(arange(3*len(initial)))
initial.set_positions(r)
print "Running self-test."
atoms = Atoms(initial)
#atoms.set_calculator(EMT())
atoms.set_calculator(OpenKIMcalculator('EMT_Asap_Standard_AlAgAuCuNiPdPt__MO_118428466217_000'))
e = atoms.get_potential_energies()
f = atoms.get_forces()
if os.access(selfcheckfilename, os.F_OK):
olde, oldf = cPickle.load(open(selfcheckfilename))
de = max(fabs(e - olde))
df = max(fabs(f.flat[:] - oldf.flat[:]))
print "Maximal deviation: Energy", de, " Force", df
ReportTest("Max force error", df, 0.0, 1e-11)
ReportTest("Max energy error", de, 0.0, 1e-11)
print e[:20]
print sum(a), "near old position and", sum(b), "near new position."
print nr2, "atoms should be affected"
ReportTest("Number of affected atoms", nr, nr2, 0)
del np_atoms, np_nblist
if 1:
print
print "Testing perturbations of all the atoms"
magnarr = array((0.0, 0.01, 0.1, 1.0, 3.0, 10.0))
pick = argsort(random.random((len(magnarr), )))
for magn in take(magnarr, pick):
dx = magn * random.uniform(-1, 1, (len(atoms), 3))
print " Perturbation:", magn
atoms.set_positions(dx + atoms.get_positions())
nblist.check_and_update(atoms)
checklist(nblist, atoms, listcutoff)
print
print "Testing perturbations of single atoms"
magnarr = array((0.0, 0.01, 0.1, 1.0, 3.0, 10.0))
pick1 = argsort(random.random((len(magnarr), )))
for magn in take(magnarr, pick1):
numarr = array((1, 3, 10, len(atoms) / 2, -3))
pick2 = argsort(random.random((len(numarr), )))
for number in take(numarr, pick2):
# Pick number random atoms.
if number < 0:
# Find N neighboring atoms and perturb them
print sum(a), "near old position and", sum(b), "near new position."
print nr2, "atoms should be affected"
ReportTest("Number of affected atoms", nr, nr2, 0)
del np_atoms, np_nblist
if 1:
print
print "Testing perturbations of all the atoms"
magnarr = array((0.0, 0.01, 0.1, 1.0, 3.0, 10.0))
pick = argsort(random.random((len(magnarr),)))
for magn in take(magnarr, pick):
dx = magn * random.uniform(-1, 1, (len(atoms), 3))
print " Perturbation:", magn
atoms.set_positions(dx + atoms.get_positions())
nblist.check_and_update(atoms)
checklist(nblist, atoms, listcutoff)
print
print "Testing perturbations of single atoms"
magnarr = array((0.0, 0.01, 0.1, 1.0, 3.0, 10.0))
pick1 = argsort(random.random((len(magnarr),)))
for magn in take(magnarr, pick1):
numarr = array((1, 3, 10, len(atoms)/2, -3))
pick2 = argsort(random.random((len(numarr),)))
for number in take(numarr, pick2):
# Pick number random atoms.
boundaries = ((0, 0, 0), )
else:
boundaries = ((1, 1, 1), (0, 0, 0), (0, 0, 1))
for pbc in boundaries:
txt = nbltype + (" PBC=%1i%1i%1i " % pbc)
# Test that EMT reimported through OpenKIM gives the right results.
atoms_kim = FaceCenteredCubic(size=(10, 10, 10), symbol='Cu')
#atoms_kim = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
# size=(30, 30, 30),
# symbol="Cu")
natoms = len(atoms_kim)
atoms_kim.set_pbc(pbc)
r = atoms_kim.get_positions()
r.flat[:] += 0.1 * np.sin(np.arange(3 * natoms))
atoms_kim.set_positions(r)
atoms_emt = atoms_kim.copy()
kim = OpenKIMcalculator(openkimmodel, allowed=nbltype)
emt = EMT()
emt.set_subtractE0(False)
atoms_kim.set_calculator(kim)
atoms_emt.set_calculator(emt)
ek = atoms_kim.get_potential_energy()
ee = atoms_emt.get_potential_energy()
ReportTest(txt + "Total energy", ek, ee, 1e-8)
ek = atoms_kim.get_potential_energies()
ee = atoms_emt.get_potential_energies()
for i in range(0, natoms, step):
ReportTest(txt + "Energy of atom %i" % (i, ), ek[i], ee[i], 1e-8)
fk = atoms_kim.get_forces()
fe = atoms_emt.get_forces()
#print (y)
#print (len(y))
old_a = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol="Ar",
latticeconstant=5.256,
size=(1, 1, 1),
pbc=True)
a = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol="Ar",
latticeconstant=5.256,
size=(1, 1, 1),
pbc=True)
a.set_positions([[0, 0, 10], [2.628, 2.628, 0], [2.628, 0, 2.628],
[0, 2.628, 2.628]])
#a = run_md()
#msqdisp = properties.meansquaredisp(a, old_a)
#print(msqdisp)
atoms_old = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol="Ar",
latticeconstant=5.256,
size=(3, 3, 3),
pbc=True)
#final_atoms = run_md()
atoms = FaceCenteredCubic(size=(5,5,5), symbol="Cu")
pot = EMT()
atoms.set_calculator(pot)
for i in (1, 2):
print "*** Pass", i
ReportTest("Energy required", pot.calculation_required(atoms, ["energy"]), 1, 0)
ReportTest("Forces required", pot.calculation_required(atoms, ["forces"]), 1, 0)
ReportTest("Stress required", pot.calculation_required(atoms, ["stress"]), 1, 0)
ReportTest("Magmom required", pot.calculation_required(atoms, ["magmoms"]), 1, 0)
e = atoms.get_potential_energy()
ReportTest("Energy not required", pot.calculation_required(atoms, ["energy"]), 0, 0)
ReportTest("Forces required (II)", pot.calculation_required(atoms, ["forces"]), 1, 0)
f = atoms.get_forces()
ReportTest("Energy not required (II)", pot.calculation_required(atoms, ["energy"]), 0, 0)
ReportTest("Forces not required", pot.calculation_required(atoms, ["forces"]), 0, 0)
ReportTest("Energy or forces not required",
pot.calculation_required(atoms, ["energy", "forces"]), 0, 0)
ReportTest("Energy or stress required",
pot.calculation_required(atoms, ["energy", "stress"]), 1, 0)
s = atoms.get_stress()
ReportTest("Stress not required", pot.calculation_required(atoms, ["stress"]), 0, 0)
r = atoms.get_positions()
r[0,0] += 0.1
atoms.set_positions(r)
ReportTest.Summary()
boundaries = ((0,0,0),)
else:
boundaries = ((1,1,1), (0,0,0), (0,0,1))
for pbc in boundaries:
txt = nbltype + (" PBC=%1i%1i%1i " % pbc)
# Test that EMT reimported through OpenKIM gives the right results.
atoms_kim = FaceCenteredCubic(size=(10,10,10), symbol='Cu')
#atoms_kim = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]],
# size=(30, 30, 30),
# symbol="Cu")
natoms = len(atoms_kim)
atoms_kim.set_pbc(pbc)
r = atoms_kim.get_positions()
r.flat[:] += 0.1 * np.sin(np.arange(3*natoms))
atoms_kim.set_positions(r)
atoms_emt = atoms_kim.copy()
kim = OpenKIMcalculator(openkimmodel, allowed=nbltype)
emt = EMT()
emt.set_subtractE0(False)
atoms_kim.set_calculator(kim)
atoms_emt.set_calculator(emt)
ek = atoms_kim.get_potential_energy()
ee = atoms_emt.get_potential_energy()
ReportTest(txt+"Total energy", ek, ee, 1e-8)
ek = atoms_kim.get_potential_energies()
ee = atoms_emt.get_potential_energies()
for i in range(0, natoms, step):
ReportTest(txt+"Energy of atom %i" % (i,), ek[i], ee[i], 1e-8)
fk = atoms_kim.get_forces()
fe = atoms_emt.get_forces()
