def test_dense_forces(self):
orig_a = io.read('eam_crash2.poscar')
c = TabulatedAlloyEAM(fn='Cu_mishin1.eam.alloy')
for fac in [0.2, 0.3, 0.4, 0.5]:
a = orig_a.copy()
a.set_cell(fac * a.cell, scale_atoms=True)
a.set_calculator(c)
ffd, f0, maxdf = test_forces(a, dx=dx)
if maxdf > tol:
nfail += 1
print("forces .failed.")
print("max(df) = %f" % maxdf)
print("f - from potential")
for i, f in enumerate(f0):
print(i, f)
print("f - numerically")
for i, f in enumerate(ffd):
print(i, f)
print("difference between the above")
for i, f in enumerate(f0 - ffd):
print(i, f)
self.assertTrue(maxdf < tol)
def test_dense_forces(self):
orig_a = io.read('eam_crash2.poscar')
c = TabulatedAlloyEAM(fn='Cu_mishin1.eam.alloy')
for fac in [0.2, 0.3, 0.4, 0.5]:
a = orig_a.copy()
a.set_cell(fac*a.cell, scale_atoms=True)
a.set_calculator(c)
ffd, f0, maxdf = test_forces(a, dx=dx)
if maxdf > tol:
nfail += 1
print("forces .failed.")
print("max(df) = %f" % maxdf)
print("f - from potential")
for i, f in enumerate(f0):
print(i, f)
print("f - numerically")
for i, f in enumerate(ffd):
print(i, f)
print("difference between the above")
for i, f in enumerate(f0-ffd):
print(i, f)
self.assertTrue(maxdf < tol)
def run_forces_and_virial_test(test=None):
nok = 0
nfail = 0
for pot, par, mats in tests:
if len(sys.argv) > 1:
found = False
if par is not None:
for keyword in sys.argv[1:]:
if '__ref__' in par:
if par['__ref__'].lower().find(keyword.lower()) != -1:
found = True
try:
potname = pot.__name__
except:
potname = pot.__class__.__name__
for keyword in sys.argv[1:]:
if potname.lower().find(keyword.lower()) != -1:
found = True
if not found:
continue
try:
potname = pot.__name__
except:
potname = pot.__class__.__name__
if test is None:
print("--- %s ---" % potname)
if par is None:
c = pot()
else:
c = pot(**par)
if test is None and '__ref__' in par:
print(" %s" % par["__ref__"])
for imat in mats:
rattle = 0.5
mask = False
if isinstance(imat, tuple):
name, a = imat
else:
name = imat['name']
a = imat['struct']
if 'rattle' in imat:
rattle = imat['rattle']
if 'mask' in imat:
mask = imat['mask']
if test is None:
print("Material: ", name)
a.translate([0.1, 0.1, 0.1])
a.set_calculator(c)
masks = [None]
if mask:
masks += [
random_integers(0, len(a) - 1, size=len(a)) < len(a) / 2,
random_integers(0, len(a) - 1, size=len(a)) < len(a) / 4
]
for dummy in range(2):
if dummy == 0:
errmsg = 'potential: {0}; material: {1}; equilibrium' \
.format(potname, name)
if test is None:
print('=== equilibrium ===')
else:
errmsg = 'potential: {0}; material: {1}; distorted' \
.format(potname, name)
if test is None:
print('=== distorted ===')
for mask in masks:
if test is None and mask is not None:
print('--- using random mask ---')
c.set_mask(mask)
ffd, f0, maxdf = test_forces(a, dx=dx)
if test is None:
if abs(maxdf) < tol:
nok += 1
print("forces .ok.")
else:
nfail += 1
print("forces .failed.")
print("max(df) = %f" % maxdf)
print("f - from potential")
for i, f in enumerate(f0):
print(i, f)
print("f - numerically")
for i, f in enumerate(ffd):
print(i, f)
print("difference between the above")
for i, f in enumerate(f0 - ffd):
print(i, f)
else:
test.assertTrue(abs(maxdf) < tol,
msg=errmsg + '; forces')
sfd, s0, maxds = test_virial(a, de=dx)
if test is None:
if abs(maxds) < tol:
nok += 1
print("virial .ok.")
else:
nfail += 1
print("virial .failed.")
print("max(ds) = %f" % maxds)
print("s - from potential")
print(s0)
print("s - numerically")
print(sfd)
print("difference between the above")
print(s0 - sfd)
else:
test.assertTrue(abs(maxds) < tol,
msg=errmsg + '; virial')
pfd, p0, maxdp = test_potential(a, dq=dx)
if test is None:
if abs(maxdp) < tol:
nok += 1
print("potential .ok.")
else:
nfail += 1
print("potential .failed.")
print("max(dp) = %f" % maxdp)
print("p - from potential")
print(p0)
print("p - numerically")
print(pfd)
print("difference between the above")
print(p0 - pfd)
else:
test.assertTrue(abs(maxds) < tol,
msg=errmsg + '; virial')
a.rattle(rattle)
if test is None:
print('{0} tests passed, {1} tests failed.'.format(nok, nfail))
def run_forces_and_virial_test(test=None):
nok = 0
nfail = 0
for pot, par, mats in tests:
if len(sys.argv) > 1:
found = False
if par is not None:
for keyword in sys.argv[1:]:
if '__ref__' in par:
if par['__ref__'].lower().find(keyword.lower()) != -1:
found = True
try:
potname = pot.__name__
except:
potname = pot.__class__.__name__
for keyword in sys.argv[1:]:
if potname.lower().find(keyword.lower()) != -1:
found = True
if not found:
continue
try:
potname = pot.__name__
except:
potname = pot.__class__.__name__
if test is None:
print("--- %s ---" % potname)
if par is None:
c = pot()
else:
c = pot(**par)
if test is None and '__ref__' in par:
print(" %s" % par["__ref__"])
for imat in mats:
rattle = 0.5
mask = False
if isinstance(imat, tuple):
name, a = imat
else:
name = imat['name']
a = imat['struct']
if 'rattle' in imat:
rattle = imat['rattle']
if 'mask' in imat:
mask = imat['mask']
if test is None:
print("Material: ", name)
a.translate([0.1,0.1,0.1])
a.set_calculator(c)
masks = [None]
if mask:
masks += [random_integers(0, len(a)-1, size=len(a)) < len(a)/2,
random_integers(0, len(a)-1, size=len(a)) < len(a)/4]
for dummy in range(2):
if dummy == 0:
errmsg = 'potential: {0}; material: {1}; equilibrium' \
.format(potname, name)
if test is None:
print('=== equilibrium ===')
else:
errmsg = 'potential: {0}; material: {1}; distorted' \
.format(potname, name)
if test is None:
print('=== distorted ===')
for mask in masks:
if test is None and mask is not None:
print('--- using random mask ---')
c.set_mask(mask)
ffd, f0, maxdf = test_forces(a, dx=dx)
if test is None:
if abs(maxdf) < tol:
nok += 1
print("forces .ok.")
else:
nfail += 1
print("forces .failed.")
print("max(df) = %f" % maxdf)
print("f - from potential")
for i, f in enumerate(f0):
print(i, f)
print("f - numerically")
for i, f in enumerate(ffd):
print(i, f)
print("difference between the above")
for i, f in enumerate(f0-ffd):
print(i, f)
else:
test.assertTrue(abs(maxdf) < tol,
msg=errmsg+'; forces')
sfd, s0, maxds = test_virial(a, de=dx)
if test is None:
if abs(maxds) < tol:
nok += 1
print("virial .ok.")
else:
nfail += 1
print("virial .failed.")
print("max(ds) = %f" % maxds)
print("s - from potential")
print(s0)
print("s - numerically")
print(sfd)
print("difference between the above")
print(s0-sfd)
else:
test.assertTrue(abs(maxds) < tol,
msg=errmsg+'; virial')
pfd, p0, maxdp = test_potential(a, dq=dx)
if test is None:
if abs(maxdp) < tol:
nok += 1
print("potential .ok.")
else:
nfail += 1
print("potential .failed.")
print("max(dp) = %f" % maxdp)
print("p - from potential")
print(p0)
print("p - numerically")
print(pfd)
print("difference between the above")
print(p0-pfd)
else:
test.assertTrue(abs(maxds) < tol,
msg=errmsg+'; virial')
a.rattle(rattle)
if test is None:
print('{0} tests passed, {1} tests failed.'.format(nok, nfail))
def run_forces_and_virial_test(test=None):
for pot, par, mats in tests:
if len(sys.argv) > 1:
found = False
if par is not None:
for keyword in sys.argv[1:]:
if '__ref__' in par:
if par['__ref__'].lower().find(keyword.lower()) != -1:
found = True
try:
potname = pot.__name__
except:
potname = pot.__class__.__name__
for keyword in sys.argv[1:]:
if potname.lower().find(keyword.lower()) != -1:
found = True
if not found:
continue
try:
potname = pot.__name__
except:
potname = pot.__class__.__name__
if test is None:
print "--- %s ---" % potname
if par is None:
c = pot()
else:
c = pot(**par)
if test is None and '__ref__' in par:
print " %s" % par["__ref__"]
for imat in mats:
if isinstance(imat, tuple):
name, a = imat
else:
name = imat['name']
a = imat['struct']
if test is None:
print "Material: ", name
a.translate([0.1,0.1,0.1])
a.set_calculator(c)
for dummy in range(2):
if dummy == 0:
errmsg = 'potential: {0}; material: {1}; equilibrium' \
.format(potname, name)
if test is None:
print "...equilibrium..."
else:
errmsg = 'potential: {0}; material: {1}; distorted' \
.format(potname, name)
if test is None:
print "...distorted..."
ffd, f0, maxdf = test_forces(a, dx=dx)
if test is None:
if abs(maxdf) < tol:
print "forces .ok."
else:
print "forces .failed."
print "max(df) = %f" % maxdf
print "f - from potential"
print f0
print "f - numerically"
print ffd
else:
test.assertTrue(abs(maxdf) < tol,
msg=errmsg+'; forces')
sfd, s0, maxds = test_virial(a, de=dx)
if test is None:
if abs(maxds) < tol:
print "virial .ok."
else:
print "virial .failed."
print "max(ds) = %f" % maxds
print "s - from potential"
print s0
print "s - numerically"
print sfd
else:
test.assertTrue(abs(maxds) < tol,
msg=errmsg+'; virial')
pfd, p0, maxdp = test_potential(a, dq=dx)
if test is None:
if abs(maxdp) < tol:
print "potential .ok."
else:
print "potential .failed."
print "max(dp) = %f" % maxdp
print "p - from potential"
print p0
print "p - numerically"
print pfd
else:
test.assertTrue(abs(maxds) < tol,
msg=errmsg+'; virial')
a.rattle(0.5)